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Stream Maintenance Program Update 

Final Subsequent Environmental Impact Report 

Volume 1 



(i Horizon 


Santa Clara Valley Water District 

December 2011 


WATER and ENVIRONMENT 


Santa Clara Valley 
Water District A 

SI* " m 
















Final 

Subsequent Environmental Impact Report 

Santa Clara Valley Water District 
Stream Maintenance Program Update 

2012-2022 

Volume I of II 

Prepared for: 

Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95118-3686 
Contact: Kristen O’Kane 
408/265-2607, ext. 2692 

Prepared by: 

Horizon Water and Environment, LLC 
1330 Broadway, Suite 424 
Oakland, California 94612 
Contact: Michael Stevenson 

510/986-1852 


December 2011 



Horizon Water and Environment. 2011 (December). 
Stream Maintenance Program Update-2012-2022 
Final Subsequent Environmental Impact Report. 

HWE 10.005. Oakland, CA. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 




1. Introduction 


Contents 


1 Introduction.1-1 

1.1 FSEIR Context .1-1 

1.2 Comments on the DSEIR.1-2 

1.3 Organization and Contents of the FSEIR.1-3 

2 Summary of Public Participation.2-1 

2.1 Notice of Preparation and Public Scoping.2-1 

2.2 Notice of Availability of the DSEIR and Public Review.2-1 

2.3 Preparation of the FSEIR and Public Hearing.2-3 

3 Responses to Comments and DSEIR Revisions.3-1 

3.1 Comments Introduction.3-1 

3.2 List of Comment Letters Received.3-1 

3.3 Comments, Responses to Comments, and DSEIR Revisions.3-2 

3.4 Other Revisions to the DSEIR.3-101 


Volume I 

Appendix 

Appendix 

Appendix 

Appendix 

Appendix 


Appendices 

A Notice of Completion and Environmental Document Transmittal 
B DSEIR/NOA Distribution List 

C August 22, 2011 SCVWD Watershed Stewardship Division Letter to the San 
Francisco Regional Water Quality Control Board 

D Joint Aquatic Resource Permit Application 

E Inter-Agency Working Group Meeting Notes 


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Chapter 1 

Introduction 


1.1 FSEIR Context 

The Stream Maintenance Program (SMP) Update (SMP Update or Proposed Project) has 
been proposed by the Santa Clara Valley Water District (SCVWD). A Draft Subsequent 
Environmental Impact Report (DSEIR) for the SMP Update was prepared and distributed for 
public review on August 8, 2011, by SCVWD, as the lead agency under the California 
Environmental Quality Act (CEQA). This Final Subsequent Environmental Impact Report 
(FSEIR) addresses the potential environmental impacts of the proposed SMP Update and 
approvals necessary to continue carrying out its responsibilities in an environmentally 
responsible and cost effective manner, to act as the County of Santa Clara's (County) flood 
protection agency and the steward for its streams and creeks. 

The FSEIR is subsequent to the 2002 SCVWD Stream Maintenance program EIR. The 
Proposed Project would update the 2002 SMP, as necessary, to address new conditions and 
maintenance needs of SCVWD. The SMP Update (including the 2012 SMP Manual 
[Appendix A] and this CEQA document) is intended to support permitting for the next 10- 
year planning period beginning in 2012 and ending in 2022. However, the SMP is ongoing, 
and the time horizon for this FSEIR is indefinite. These SMP Update documents are intended 
to fully replace the original documents that guided the SMP from its inception through 
2012. The 2012 SMP Manual (included as Appendix A in Volume II of this FSEIR) and the 
contents of the FSEIR are meant to be read as companion documents. The FSEIR references 
or summarizes information (including figures and tables) presented in the 2012 SMP 
Manual frequently to avoid repeating information. The reader is encouraged to review the 
2012 SMP Manual while reviewing the FSEIR. 

The overall flood management goals of the SMP Update are to maintain the design flow or 
appropriate conveyance capacity of SCVWD facilities, and to maintain the structural and 
functional integrity of SCVWD facilities. To meet these goals, the SMP Update would 
prioritize and administer maintenance activities to achieve the following objectives: 

■ remove sediment to maintain the hydraulic, safety, and habitat functions of the 
creek systems; 

■ manage vegetation to maintain the hydraulic, safety, and habitat functions of the 
creek systems, and to allow for levee inspections and maintenance access; 

■ stabilize beds and banks of creeks and canals to protect existing infrastructure, 
maintain public safety, reduce sediment loading, protect water quality, and protect 
habitat values; and 

■ avoid, minimize, or mitigate impacts on the environment by incorporating stream 
stewardship measures into maintenance activities. 


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1. Introduction 


The SMP Update also seeks to obtain and maintain multi-year programmatic permits to 
regulate Proposed Project activities. 

See Chapter 2, Project Description, of the revised DSEIR (Volume II) for a complete 
description of the Proposed Project. 

This document has been prepared pursuant to the requirements of CEQA. Section 15132 of 
the State CEQA Guidelines state: 

The Final EIR shall consist of: 

The draft EIR or a revision of the draft [included as Volume II, the DSEIR as 
revised based on public comments and other necessary updates] 

A list of persons, organizations, and public agencies commenting on the 
DSEIR [included in Section 3.2 of this FSEIR] 

Comments and recommendations received on the DSEIR, either verbatim or 
in summary [included in Section 3.3 of this FSEIR] 

The responses of the Lead Agency [in this case, SCVWD] to significant 
environmental points raised in the review and consultation process 
[included in Section 3.3 of this FSEIR] 

Any other information added by the Lead Agency [in this case, SCVWD] 
[included in Section 3.4 of this FSEIR] 

The FSEIR provides the Santa Clara Valley Water District, public, responsible agencies, 
trustee agencies, and permitting agencies with information about the potential 
environmental effects associated with the adoption and implementation of the updated 
SMP. The FSEIR presents the comments received on the DSEIR and responses to these 
comments. The findings and a statement of overriding considerations are included in the 
public record but not in the FSEIR. 

1.2 Comments on the DSEIR 

The DSEIR was submitted to the State Clearinghouse for distribution to state agencies and 
was available to agencies and the public for review and comment for 45 days between 
August 8 and September 21, 2011. A public meeting was conducted on September 13, 2011 
to receive oral and written comments. One member of the public spoke at that meeting. 
Letters of comment were received from state agencies and commissions; regional/local 
agencies, municipalities, and districts; organizations; and individuals. 

1.3 Organization and Contents of the FSEIR 

The FSEIR, which consists of two volumes, will be the subject of a hearing to certify the 
SEIR. Volume I provides: 


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1. Introduction 


Chapter 1, Introduction, presents the FSEIR context and its objectives, summarizes 
the public review period for the DSEIR, and describes the organization and contents 
of the FSEIR. 

Chapter 2, Summary of Public Participation, summarizes the environmental and 
public review process, pursuant to CEQA. 

Chapter 3, Responses to Comments and DSEIR Revisions, lists and gives 
identifiers to agencies, organizations, and members of the public who commented 
on the DSEIR during the public review process, replicates in full the comment letters 
received, and gives responses to those comments. Comments within each letter are 
numbered sequentially. Excerpts of text from the DSEIR that have changed as a 
result of the comment/response are shown within the response, for ease of 
reference (in addition to being shown in Volume II). 

Appendix A presents the Notice of Completion and Environmental Document 
Transmittal for the DSEIR. 

Appendix B presents the DSEIR distribution list. 

Appendix C provides an August 22, 2011 letter from Ann Draper of the SCVWD 
Watershed Stewardship Division to Shin-Roei Lee of the San Francisco Regional 
Water Quality Control Board, which is referenced as an attachment in a response to 
Comment D-9. 

Appendix D provides the Joint Aquatic Resource Permit Application that was 
submitted with the original SMP permit applications to the San Francisco RWQCB, 
DFG, USACE, USEPA, USFWS, and NMFS in 2001, which is referenced as an 
attachment in a response to Comment N-21. 

Appendix E includes the Inter-Agency Working Group meeting notes from August 
26, 2010; October 20, 2010; and July 21, 2011, which are referenced as an 
attachment in a response to Comment N-21. 

Volume II is the DSEIR, as revised subsequent to its publication and public review. 
Revisions are shown with strik e through text for deletions and underlined text for additions. 


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Chapter 2 

Summary of Public Participation 


2.1 Notice of Preparation and Public Scoping 

Scoping refers to the public outreach process used under CEQA to determine the coverage 
and content of an SEIR. The scoping comment period offers an important early opportunity 
for public review and comment on the focus of the CEQA analysis. The scoping process for 
an SEIR is initiated by publication of the Notice of Preparation (NOP), as required by CEQA, 
which provides formal notice to the public and to interested agencies and organizations that 
a DSEIR is in preparation. During the scoping period, agencies and the public are invited to 
comment on the project, the approach to environmental analysis, and any issues of concern 
to be discussed in the DSEIR. Scoping also can assist the lead agency with identification of 
project alternatives and mitigation measures. CEQA does not require public meetings 
during the scoping phase. 

In accordance with State CEQA Guidelines (14 CCR 15082[a], 15103, 15375), SCVWD 
circulated an NOP for the Proposed Project on August 31, 2010 (Appendix B of the DSEIR, 
contained in Volume II of the FSEIR). The NOP, in which SCVWD was identified as lead 
agency for the Proposed Project, was circulated to the public; to local, state, and federal 
agencies; and to other interested parties. The purpose of the NOP was to inform responsible 
agencies and the public that the Proposed Project could have significant effects on the 
environment and to solicit their comments so that any concerns raised could be considered 
during the preparation of the DSEIR. In addition, SCVWD held a public scoping meeting on 
September 22, 2010, to provide the public with another opportunity to comment. 
Comments received in response to the NOP are included in Appendix B of the DSEIR 
(contained in Volume II of the FSEIR), and the preparers of the DSEIR considered these 
comments. No comments were received at the public scoping meeting. 

2.2 Notice of Availability of the DSEIR and Public Review 

After the DSEIR was completed, the District issued a notice of availability, providing 
agencies and the public with formal notification that the document was available for review. 
The notice was sent to the State CEQA Clearinghouse, all responsible and trustee agencies, 
persons and organizations requesting a copy, and the county clerk's office for posting. The 
notice also was published in the San Jose Mercury News, the Morgan Hill Times, and the 
Gilroy Dispatch. These actions triggered a 45-day public review period, during which the 
District received and collated public and agency comments on the project and the 
document. 

SCVWD hosted a public hearing after release of the document on September 13, 2011, at 
SCVWD's offices. The purpose of public circulation and the public hearings was to provide 


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2. Summary of Public Participation 


agencies and interested individuals with opportunities to comment on or express concerns 
regarding the contents of the DSEIR. 

For those interested, written comments or questions concerning the DSEIR could be 
submitted within the review period and directed to the name and address listed below. 
Submittal of written comments via e-mail (Microsoft Word format) was encouraged. 

Santa Clara Valley Water District 
Attention: Sunny Williams 
5750 Almaden Expressway 
San Jose, CA 95118-3686 

E-mail: smp_update@valleywater.org 
Subject Line: SMP Update EIR Comments 

During the review period for the DSEIR, all documents related to the Proposed Project were 
available for review on any SCVWD business day between the hours of 8:00 a.m. and 5:00 
p.m. Monday through Friday at SCVWD headquarters, located at the address shown above, 
and on SCVWD's Web site at www.valleywater.org under Quick Links, Public Review docs. 
The documents also were available at the libraries listed below during their normal 
operating hours. 

Dr. Martin Luther King, Jr. Library 
150 E. San Fernando Street 
San Jose, CA 95112 

Morgan Hill Public Library 
660 W. Main Avenue 
Morgan Hill, CA 95037 

Palo Alto Public Library 
1213 Newell Road 
Palo Alto, CA 94303 

Cupertino Public Library 
10800 Torre Avenue 
Cupertino, CA 95014-3207 

Milpitas Public Library 
160 N. Main Street 
Milpitas, CA 95035 

Alviso Library 
5050 N. 1st Street 
San Jose, CA 95134 


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2.3 Preparation of the FSEIR and Public Hearing 

CEQA requires the lead agency to prepare an FSEIR, addressing all substantive comments 
received on the DSEIR before approving a project. The FSEIR must include a list of all 
individuals, organizations, and agencies that provided comments on the DSEIR, and must 
contain copies of all comments received during the public review period along with the lead 
agency's responses. 

After review of the FSEIR, SCVWD staff will recommend to SCVWD's Board of Directors 
whether to approve or deny the Proposed Project. This governing body then will review the 
FSEIR, consider SCVWD staff recommendations and public testimony, and decide whether 
to certify the FSEIR and approve or deny the Proposed Project. 

If significant impacts are identified in the FSEIR that cannot be mitigated, a statement of 
overriding considerations must be included in the record of the Proposed Project approval 
and mentioned in the Notice of Determination, to be filed with the State Office of Planning 
and Research and at the office of the County Clerk (14 CCR 15093 [c]). 


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Chapter 3 

Responses to Comments and DSEIR Revisions 


3.1 Comments Introduction 

Comments provided on the DSEIR by agencies, organizations, and individuals during the 
public review period (August 8 through September 21, 2011) are documented in this 
chapter. A list of all commenters is provided in Section 3.2. SCVWD received 14 letters, 
containing a total of 177 comments. Comments could be submitted by letter, facsimile, 
email, voicemail, or verbally at public meetings; those received and responses to them are 
presented in Section 3.3. 

3.2 List of Comment Letters Received 

The comment letters received on the DSEIR were sorted by date, and then alphabetically by 
last name for those received on the same date. They were then assigned a letter designation 
on this basis. The commenters and identifiers are presented in order of receipt in Table 3-1. 
Table 3-2 presents the comment letters by commenter type. 

Table 3-1. Commenters on the DSEIR (numerical by alpha-letter number) 


Letter No. 

(# of Comments) 

Commenter 

Date of 

Comment 

A (1) 

Anthony Eulo, Program Administrator, City of Morgan Hill 

August 19,2011 

B (1) 

Libby Lucas, California Native Plant Society 

September 13,2011 

C (3) 

Libby Lucas, California Native Plant Society 

September 15,2011 

D (25) 

William Hurley, San Francisco RWQCB 

September 19,2011 

E (1) 

Cynthia Riordan 

September 20,2011 

F (3) 

Gary Arnold, District Branch Chief, CalTrans 

September 21,2011 

G (4) 

Libby Lucas, California Native Plant Society 

September 21,2011 

H (7) 

Libby Lucas, California Native Plant Society 

September 21,2011 

1(2) 

Libby Lucas, California Native Plant Society 

September 21,2011 

J (6) 

Cy Oggins, California State Lands Commission 

September 21,2011 

K (1) 

Libby Lucas, California Native Plant Society 

September 27,2011 

L (1) 

John Beall, 56 Centre St., Apt. 10, Mountain View, CA 94041 

September 28,2011 

M (9) 

Julie Gantenbein, Water and Power Law Group, PC; 
representing Guadalupe Coyote RCD 

September 28,2011 

N (113) 

Carl Wilcox, California Department of Fish and Game 

October 5,2011 


Table 3-2. Commenters on the DSEIR (by commenter type) 


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3. Responses to Comments and DSEIR Revisions 


Letter No. 

(# of Comments) 

Commenter 

Date of Comment 

State Agencies and Commissions 

F (3) 

Gary Arnold, District Branch Chief, CalTrans 

September 21,2011 

J (6) 

Cy Oggins, California State Lands Commission 

September 21,2011 

N (113) 

Carl Wilcox, California Department of Fish and Game 

October 5,2011 

Regional/Local Agencies, Municipalities, and Districts 

A (1) 

Anthony Eulo, Program Administrator, City of Morgan Hill 

August 19,2011 

D (25) 

William Hurley, RWQCB, San Francisco RWQCB 

September 19,2011 

Organizations 

B (1) 

Libby Lucas, California Native Plant Society 

September 13,2011 

C (3) 

Libby Lucas, California Native Plant Society 

September 15,2011 

G (4) 

Libby Lucas, California Native Plant Society 

September 21,2011 

H (7) 

Libby Lucas, California Native Plant Society 

September 21,2011 

1(2) 

Libby Lucas, California Native Plant Society 

September 21,2011 

K (1) 

Libby Lucas, California Native Plant Society 

September 27,2011 

M (9) 

Julie Gantenbein, Water and Power Law Group, PC; 
representing Guadalupe Coyote RCD 

September 28,2011 

Individuals 

E (1) 

Cynthia Riordan 

September 20,2011 

L (1) 

John Beall, 56 Centre St., Apt. 10, Mountain View, CA 94041 

September 28,2011 


3.3 Comments, Responses to Comments, and DSEIR Revisions 

This section presents a copy of each comment letter that was received on the DSEIR during 
the review period, bracketing the individual comments in alpha and numeric order. 
Responses to issues raised in each letter follow immediately after the letter, sequentially. 


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Letter A 


From: Anthony Eulo 

To: smp_update; 

Subject: SMP Comments 

Date: Friday, August 19, 2011 3:48:57 PM 

When conducting sediment and vegetation removal in the past, the District's activities have 
created low spots in the channel which become temporary or nearly-permanent ponds in the 
local creek. With landscape runoff feeding the ponds throughout the summer months, a 
mosquito breeding habitat is created in these low spots. Efforts should be made to maintain the 
flow in the creeks. 

Anthony Eulo 
Program Administrator 

City of Morgan Hill Please Think Before You Print 
100 Edes Court 
Morgan Hill, CA 95037 
408-310-4179 

City Environmental Programs on Facebook 



3. Responses to Comments and DSEIR Revisions 


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3. Responses to Comments and DSEIR Revisions 


Response to Comment A-l 

As indicated in Table 2-12 of the DSEIR, several Sediment Removal BMPs would be in place 
to avoid the creation of "low spots" in maintained reaches. BMP SED-2 would require the 
grading of channels to ensure that the transitions between areas upstream and downstream 
of the maintenance area would be smooth. In addition, BMP SED-3 stipulates that low-flow 
channels would undergo contouring to restore preconstruction conditions as closely as 
possible. In addition to these specific measures, the more general objectives of the SMP 
Update would provide consideration of pre- and post-project conditions of maintenance 
sites. Therefore, the creation of low spots or other adverse features that would degrade the 
physical or biological processes of the channels would be avoided to the extent possible. 

The District encourages County residents to contact the Santa Clara County Vector Control 
District if they are experiencing mosquito or other vector control issues. Residents may 
request services for mosquito abatement using the Vector Control District website 
(http://www.sccgov.org/portal/site/vector) or by calling 408-918-4770. 


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3. Responses to Comments and DSEIR Revisions 


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Letter B 


Santa Clara Valley 
Water District 


6 



REQUEST TO SPEAK 

FC 244 (06-13-11) 


► 

► 

► 


Meeting Date: ZZQfij 1 1 ^ 

Complete this form and return to Clerk. 

Comments may be limited to a specified time allotment. 

If you elect to distribute informational items to the Board/Committee, the Clerk is required to obtain a copy and keep it as part of the 
public record. Fifteen (15) copies of informational handout items should be supplied to Clerk for distribution to the 
Board/Committee, executive staff, and for the public record and public imormation copy. 


Personal Information: Except for your name and city of residence/fne information requested below is voluntary and used by staff 
to contact you if necessary. When you request to speak before tj?e legislative body, your name and city of residence are included in 
the Santa Clara Valley Water District’s official minutes. 


Name: 


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Address 




Phone: 


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Email: 


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Organization/Business Name (if applicable): 


QK Item LISTED on the Agenda (Item No. ) 


Subject: 


MA/m/ 


□ Item NOT LISTED on the Agenda (Public Comment) 


Subject. 


Note: The law does not permit Board/Committee action on or extended discussion of any item not on the agenda, except under 
special circumstances. If Board/Committee action is requested, the matter can be placed on a future agenda. 


□ 



ish to address the Board/Committee; however, I would like to have the following question(s) answered: 

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I I I do not wish to address the goard/Committee; however I would like to_haye the fc^winaslaten^Us^eatHrVQ thOfe6Q£d- — 

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Notice to Lobbyist: In compliance with the District’s Lobbyist Ordinance (Ord. 10-01) you must identify yourself as a lobbyist and 
the client(s) or business or organization on whose behalf your are representing. 

I am a O Registered Lobbyist and I represent: 

I am an Q Unregistered Lobbyist and I represent:__ 


Information about lobbying the Santa Clara Valley Water District may be found on the Internet by accessing the Board of Directors' 
website on the District's home page at http://www.valleywater.org. 


TIPS FOR ADDRESSING THE BOARD OR COMMITTEE 


Approach the public podium as soon as your name is called. 

Speak directly into the microphone. 

Clearly state your name for the record. 

If you are a lobbyist, identify yourself and your clients 

You are limited to the time allotted. Please watch the speaker clock on the podium. 

If you wish to speak to the Board/Committee on an item that is not on the agenda, there will be an opportunity under the 
section "Time Open for Public Comment on any item not on the Agenda.” Complete a Request to Speak form and provide it to 
the Clerk The Board/Committee Chair will call your name and indicate the allotted speaking time. 

If you wish to speak to the Board/Committee on an item on that is on the agenda, complete a Request to Speak form and 
provide it to the Clerk. When the specific item is considered, the Board/Committee Chair will call your name and indicate the 
allotted speaking time. 










































3. Responses to Comments and DSEIR Revisions 


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Response to Comment B-l 

Regarding the request for language on conservation protocols, this comment is not entirely 
clear regarding what is meant by conservation; this response assumes a concern about 
habitat conservation. 

Habitat conservation is discussed on a variety of points in Section 3.3, Biological Resources 
of the DSEIR. Habitat conservation plans are specifically discussed under Impact BIO-46: 
Conflicts with Adopted Habitat Conservation Plans or Natural Community Conservation 
Plans. This impact discusses potential effects of stream maintenance activities on the Santa 
Clara Valley Habitat Plan and the Three Creeks Habitat Conservation Plan. 

Regarding the request for language on pesticide protocols and seasonal constraints on the 
spraying impacts to critical habitat, the potential impacts of herbicide use have been 
thoroughly considered throughout the development of the SMP Update and related impact 
analysis, and herbicide use was determined to not have significant impacts because of 
multiple factors. Reference is made to Appendix J of the DSEIR, which discusses the 
District's proposed use of pesticides (including herbicides) in depth. Specific topics 
addressed by this appendix include: the process by which the District determines which 
herbicides to use; the herbicides used and their specific purposes; the species potentially at 
risk from those herbicides; the federal and state regulations related to herbicide use, 
including federal injunctions related to use in aquatic and upland habitats for endangered 
species; use limitations for various classes of herbicide; and additional herbicide use 
guidelines. 

All herbicide use is conducted by registered pesticide applicators (RPAs), in accordance 
with label instructions and a set of BMPs designed specifically for the SMP Update. 
Herbicide use directly within active waterbodies additionally must follow the requirements 
of the NPDES general permit for use of aquatic herbicides. All RPAs observe standard BMPs, 
such as use of personal protective equipment, observance of appropriate "dry times" (i.e., 
herbicides are applied far enough in advance of precipitation events such that runoff of the 
herbicide into water bodies is not of concern). The SMP Update-specific BMPs for herbicide 
use are summarized below (please see Table 2-12 in the DSEIR for the full text of each 
BMP): 


• BMP GEN-2: Instream Herbicide Application Work Window. This BMP restricts the 
season of use, to further reduce the potential for herbicide runoff beyond "dry time" 
requirements. This BMP also includes additional restrictions for streams known to 
support steelhead. 

• BMP GEN-8: Protection of Sensitive Fauna Species from Herbicide Use. This BMP 
contains special restrictions for herbicide use in habitat areas for particular species 
of concern, including steelhead, California red-legged frog, California tiger 
salamander, salt marsh harvest mouse, and Bay checkerspot butterfly. 

• BMP GEN-24: On-Site Hazardous Materials Management. This BMP contains a 
variety of measures to properly manage hazardous materials on-site, such as 


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secondary containment that would capture the herbicide if the primary container 
were to fail. 

• BMP GEN-26: Spill Prevention and Response. This BMP includes measures to reduce 
the potential for accidental releases and identifies the measures to be taken in the 
unlikely event of a release. This includes training of staff and having equipment on¬ 
site for containment and cleanup. 

• BMP HM-4: Posting and Notification for Pesticide Use. This BMP contains public 
notification requirements to reduce the risk to the public from herbicide use. 

All of these factors were considered in the impact analysis; as mentioned above, herbicide 
use was evaluated and found to be less than significant in the DSEIR, and the following 
impact discussions are of particular importance: 

• Impact BIO-3: Disturbance of Sensitive Plant Communities 

• Impact BIO-4: Impacts to Serpentine-Associated Special-Status Plant Species 

• Impact BIO-6: Impacts to Serpentine-Associated Special-Status Invertebrates 

• Impact BIO-8: Impacts on Steelhead 

• Impact BIO-9: Impacts on the Pacific Lamprey and Monterey Roach 

• Impact BIO-11: Impacts on the California Tiger Salamander 

• Impact BIO-12: Impacts on the California Red-Legged Frog 

• Impact BIO-22: Impacts on the San Francisco Common Yellowthroat 

• Impact BIO-23: Impacts on the Least Bell's Vireo 

• Impact HAZ-1: Use, Transport, or Accidental Release of Hazardous Materials such 
that a Significant Hazard to the Public or Environment Would Result 

• Impact HAZ-5: Create Safety Hazards or Releases of Hazardous Materials in 
Proximity to a School 

• Impact WQ-4: Water Quality Degradation Resulting in Violation of Water Quality 
Standards or Waste Discharge Requirements Caused by the Use of Pesticides, 
including Herbicides 

Regarding the request for language on pesticide protocols and seasonal constraints on the 
spraying impacts to recreation, potential temporary impacts on recreation because of 
vegetation management activities, including application of herbicides, are discussed under 
Impact REC-3: Temporary Disruption of the Use of, or Access to, Recreational Facilities. As 


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Final Subsequent Environmental Impact Report 


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3. Responses to Comments and DSEIR Revisions 


stated in this impact discussion, in-channel vegetation management activities may result in 
temporary disruption of recreational facilities. However, closures would be localized to a 
specific maintenance site, and alternative recreational opportunities would continue to be 
available along other streamside trails and recreational facilities in the overall Project Area 
(e.g., city and county parks). 

Additional discussion of potential human health impacts resulting from herbicide use is 
provided under the following impacts in the DSEIR: 

• Impact HAZ-1: Use, Transport, or Accidental Release of Hazardous Materials such 
that a Significant Hazard to the Public or Environment Would Result 

• Impact HAZ-5: Create Safety Hazards or Releases of Hazardous Materials in 
Proximity to a School 

• Impact WQ-4: Water Quality Degradation Resulting in Violation of Water Quality 
Standards or Waste Discharge Requirements Caused by the Use of Pesticides, 
including Herbicides 

The SMP Update-specific BMPs to protect against significant impacts to the public during 
herbicide use are summarized below (please see Table 2-12 in the DSEIR for the full text of 
each BMP): 

• BMP GEN-24: On-Site Hazardous Materials Management. This BMP contains a 
variety of measures to properly manage hazardous materials on-site, such as 
secondary containment that would capture the herbicide if the primary container 
were to fail. 

• BMP GEN-26: Spill Prevention and Response. This BMP includes measures to reduce 
the potential for accidental releases and identifies the measures to be taken in the 
unlikely event of a release. This includes training of staff and having equipment on¬ 
site for containment and cleanup. 

• BMP GEN-36: Public Outreach. This BMP describes the public outreach methods that 
are to be implemented before initiation of maintenance activities. Outreach includes 
newspaper notices, neighborhood work notices, Web site postings, and signs posted 
in advance of trail closures. 

• BMP GEN-37: Implement Public Safety Measures. This BMP states that if work is 
proposed adjacent to recreational trails, warning signs will be posted several feet 
beyond the limits of the work. 

• BMP HM-4: Posting and Notification for Pesticide Use. This BMP contains public 
notification requirements to reduce the risk to the public from herbicide use. 

The District agrees that global climate change and sea level rise have the potential to affect 
waterways and associated shoreline habitat. This may necessitate changes in the District's 
approach to maintenance and, perhaps more importantly, to flood management as a whole 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


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Project 10.005 




3. Responses to Comments and DSEIR Revisions 


in the lower portions of its maintenance reaches. However, the District is not aware at this 
time of any information to suggest that this may become an issue of concern for stream 
maintenance within the next 10 years of this program (the permit lifetime). As described in 
Chapter 2, Project Description of the DSEIR, the District would continue to conduct 
comprehensive reviews of its stream maintenance program at 5-year intervals, using the 
most current scientific information, and would adjust the program accordingly. This would 
include any appropriate changes related to the issues that the comment highlights. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


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December 2011 
Project 10.005 




Letter C 





From: J Lucasl099@aol.com [mailto:J Lucasl099@aol.com] 

Sent: Thursday, September 15, 2011 11:27 AM 
To: Raymond Fields 

Subject: Stream Maintenance Draft EIR 
Ray, 

As per my phone call, for some reason did not find a mention of the 3rd Addendum to Stream 
Maintenance DEIR in the Stream Maintenance DEIR that was in Palo Alto Library for review. Where 
should I be looking? 

Then, in thinking about protocols, was wondering what training you gave to staff for maintenance 
practices in regards critical habitat and special plant species...based on what biological review and 
consideration of what seasons especially to look for and to avoid impact to all such critical habitat and 
special plant species? 

Do regulatory agencies offer any such workshops to the District and to watershed open space districts? 

The extent of a ten year permit without particular protocols in place makes me nervous. What am I 
missing? 


Libby 



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Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


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Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Response to Comment C-l 

Information regarding the 3rd Addendum work activities has been incorporated into the 
SMP Update, in the discussion on page 2-21 in Section 2.2.4 and the associated analysis 
under each applicable section in Chapter 3, Environmental Setting and Impact Analysis, of 
the DSEIR. 

Response to Comment C-2 

Before initiation of SMP Update activities, one or more qualified SCVWD biologists would 
review the proposed maintenance activities to determine the biological resources that may 
occur in maintenance areas and the BMPs applicable to those resources. All SCVWD 
biologists are extremely well qualified; many have been with SCVWD for decades, and all 
are well trained in the biology of the plants and animals within the Project Area. SCVWD 
also employs specialists in certain areas, such as botany and fisheries, to address more 
technical, species-specific issues. Therefore, the BMPs listed in Table 2-12 of the DSEIR 
would be implemented, based on careful review of the applicability of these practices to any 
given program maintenance activity at hand. 

Furthermore, SCVWD maintenance staff members include biologists with years of 
experience in implementing these and similar BMPs. These biologists are very familiar with 
the biota of SCVWD facilities. When new maintenance staff members are employed, they are 
trained by experienced SCVWD biologists and maintenance staff members regarding 
appropriate procedures. In certain circumstances, such as when maintenance activities 
occur in habitat of fully protected species (such as the California clapper rail and salt marsh 
harvest mouse), qualified biological monitors are present to oversee that BMPs are applied 
effectively. 

Response to Comment C-3 

Specific protocols would be in place for the 10-year SMP Update permitted period. SCVWD 
field staff would be trained annually on listed species and habitat identification. Any 
sensitive areas within a work site would be identified by a qualified biologist before 
initiation of the work activity. BMPs would be implemented specific to the habitat and 
species in that area, including having a qualified biologist(s)/monitor section off areas 
where listed plant species or other methods may occur, to protect special-status species as 
described in BMPS GEN-6 through GEN-15.5 in Table 2-12 of the DSEIR. SCVWD notes that 
the SMP has been ongoing for a 10-year term over 2002-2012, with no substantial 
problems arising. 

Please also see response to Comment C-2. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


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December 2011 
Project 10.005 




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Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


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Matthew Rodriquez 

Secretary for 
Environmental Protection 


California Regional Water Quality Control Board 

San Francisco Bay Region 


1515 Clay Street, Suite 1400, Oakland, California 94612 
(510) 622-2300 • FAX (510) 622-2460 
http: / / www. waterboards. ca. gov/sanfr anciscobay 



Edmund G. Brown Jr. 


Governor 


Letter D 


September 19, 2011 

Site No. 02-43-C0652 

CIWQS Place ID No. 769408 (MB) 


Sent via electronic mail: No hardcopy to follow 

Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95118-3686 

Attn: Ms. Sunny Williams 

Email: smy iiydatefcvvallevvvater.ors 

Subject: Comments on the Draft Subsequent Environmental Impact Report for the 
Stream Maintenance Program, Santa Clara County, SCH No. 2000102055 

Dear Ms. Williams: 

The San Francisco Bay Regional Water Quality Control Board (Water Board) appreciates the 
opportunity to review the Draft Subsequent Environmental Impact Report for the Stream 
Maintenance Program in Santa Clara County (SDEIR). The SDEIR assesses anticipated 
environmental impacts resulting from routine stream maintenance activities within the creeks 
and canals under the 1,000 foot elevation contour that are in the jurisdiction of the Santa Clara 
Valley Water District (District). The District is in the process of applying for permit re-issuance 
for the Stream Maintenance Program (SMP) as the existing permit expires February 2012. The 
District has updated the SMP to reflect new conditions, maintenance needs, technology/methods, 
and regulatory policies. The proposed revisions of the SMP include updating the maintenance 
activities (sediment removal, vegetation management, bank stabilization and minor maintenance) 
with the addition of management of animal conflicts. 

The District has submitted the Application for 401 Certification/Waste Discharge Requirements 
for the SMP 2012-2022 Update (Application). The Application refers to the DSEIR for 
additional detailed information related to various sections of the Application including 
“Description of Activity and Environmental Impacts”, “Avoidance of Impacts”, and “Dredge & 
Fill Information”. Water Board staff has reviewed the DSEIR and provides the following 
comments. Full responses to these comments are necessary to facilitate the permitting process 
and developing the final EIR. 

Summary 

We have the following comments on the DSEIR as described in more detail further below. 

1. Project Description 


Preserving, enhancing , and restoring the San Francisco Bay Area’s waters for over 60 years 


Recycled Paper 






Stream Maintenance Program 
DSEIR 


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SF-RWQCB Comments 


a. Provide a distinction between maintenance to be conducted in each channel type. 

b. Provide more detail to the explanation on work windows and related rain events. 

c. Provide more detail to the description of maintenance work in waters of the State 
(outside of Corps jurisdiction). 

d. Provide an explanation regarding how the District will evaluate sediment source 
control for creeks that experience high sediment loads and therefore, increased 
maintenance needs. 

e. The CEQA assessment should provide a description of the types of activities 
which might warrant coverage under the State’s Aquatic Pesticide NPDES permit, 
or why coverage will not be necessary. 

2. Mitigation and Monitoring 

a. Provide more detail to the BMPs descriptions. 

b. Provide a rationale for applying mitigation credits to the SMP renewal. 

c. Provide more detail to the explanation regarding mitigation that would not be 
necessary for maintenance in canals. 

d. Provide more detail to the explanation regarding the requirement to implement the 
Water Quality Monitoring Plan and Sediment Characterization Plan. 

e. Provide more detail to the explanation regarding proposed mitigation for 
permanent impacts to waters of the State. 

3. Alternative Analysis - Provide more detail to the explanations regarding limiting 
maintenance work to avoid and minimize adverse impacts to waters of the State. 


Project Description - Specific Comments 

1. Maintenance Activities and Channel Types: The DSEIR should clearly explain the 

distinction between implementation of SMP maintenance activities in channels with high 
habitat values and functions (i.e. natural and unmodified channels) and channels with lower 
habitat values and functions (i.e. engineered and modified channels). The DSEIR states that 
all maintenance activities will occur in all of the District’s channels; however, it is not clear 
if the District will minimize maintenance activities to only when it is determined necessary 
and use alternative methods (i.e. different BMPs or less invasive techniques) of 
implementing maintenance activities that are less damaging in natural and unmodified 
channels to protect the habitat and associated beneficial uses. 


2. Work Windows: The District is proposing to conduct vegetation management activities 

(in/out-stream hand removal above ground and in/out-stream pruning) in “dry channels” year 
round or until December 31 st for work to be conducted in steelhead creeks; and sediment 
removal and bank repairs in dry channels until December 31 st . However, the maintenance 
activities will be terminated for the season if a rain event of 0.5 inches in 24-hours is 
forecasted. The DSEIR should include an explanation of the following: 

a. Define “dry channel”. 



b. Using a rainfall event of 0.5 inch in 24 hours as a trigger to stop maintenance in the 
channel may not be appropriate as rainfall has varying affects on in-channel flows 
depending on the creek and location in the watershed. For example, how will the 



Stream Maintenance Program 
DSEIR 


SF-RWQCB Comments 





District determine whether maintenance should be stopped or modified (i.e. 
additional BMPs) in the event of forecasted rain that is less than 0.5 inch in 24-hours 
for multiple consecutive days? Conducting maintenance in these types of conditions 
could potentially result in adverse impacts to water quality. Has the District 
considered using 10-percent of the channel forming flows as a trigger to stop 
maintenance as this would more channel-specific versus a general approach? 

c. The DSEIR should identify a specific plan that clearly explains the District’s 

procedures to be implemented for various rain event scenarios (i.e. 0.5 inch/24 hours, 
less than 0.5 inch/24 hours for multiple consecutive days, rain events exceeding what 
was originally forecasted) including, but not limited to, before-during-after storm 
event inspections, BMPs, corrective action, etc. 




3. Page 2-27: The DSEIR states “Upland vegetation activities and all other non-projected non¬ 
instream maintenance work may occur year-round, weather permitting. Upland vegetation 
activities would include work occurring above the bankfull hinge point (see figure 2-7) to the 
outer edge of SCVWD management area.” It should be noted that the area between the 
“bankfull hinge point” and “top of bank” as identified in Figure 2-7 of the DSEIR is within 
the bed and bank of the channel and therefore, considered Water Board jurisdiction. 
Therefore, the District will be required to adhere to permit requirements related to 
maintenance activities within the bed and bank, and riparian corridor. 

4. Figure 2-16: It appears the District plans to conduct sediment removal as “new work” along 
most of the Guadalupe Watershed. As considered in the 2002-2012 SMP, this again presents 
an opportunity to identify sediment sources that would benefit from stabilization to reduce 
maintenance needs. 




5. Appendix J - Pesticide Regulatory Information: This document should indicate that the 
District may need to obtain coverage under the Statewide General National Pollutant 
Discharge Elimination System Permit for the Discharge of Aquatic Pesticides for Aquatic 
Weed Control in Waters of the United States General Permit No. CAG990005 (Order No. 
2004-0009-DWQ). 

6. The DSEIR states that average maintenance time for bank stabilization project is 10 days. 
Therefore, it seems more appropriate to have a specific work window cut off date instead of 
“until completion”, which implies that the work can occur indefinitely. 


D7 

D8 

D9 


Mitigation and Monitoring 

1. Page 2-25: This section appears to imply that only sediment removal and ha nk repair 
activities will have field monitoring (inspections) of BMPs. The DSEIR should explain the 
process by which regular inspections of all BMPs will be conducted at all SMP maintenance 
sites. 

2. Page 2-26: This section should indicate that all maintenance sites will have adequate BMPs 
supplies on site and implemented in the event of rain. 

3. Page 2-36: Since the District has not satisfied all the mitigation requirements of the existing 
permit period (2002-2012), provide a rationale or justification for applying mitigation credits 
from the Stream and Watershed Protection component of the mitigation program for the 
2002-2012 period for impacts that will occur during the new permit term. 


4. Table 2-12: BMP Manual 



Stream Maintenance Program 
DSEIR 


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SF-RWQCB Comments 


DIO 


Dll 


D12 

D13 


D14 


D15 

D16 

D17 


a. GEN-3 (Avoid Exposing Soils with High Mercury Levels): The District has 
proposed that any sediment removal that will occur above the 2.33-year flow level 
that has a mercury concentration of 20 ppm or greater will require remediation. 
This mercury concentration far exceeds the Water Board’s sediment re-use 
guidelines for wetland surface (0.43 ppm) and for wetland foundation (0.70 ppm). 
Provide a rationale that shows sediments with mercury concentration up to 20 
ppm would not adversely impact water quality if exposed and subject to erosion. 

b. GEN-20 (Erosion and Sediment Control Measures): This BMP states that areas 
below the Ordinary High Water Mark (OHWM) are exempt from BMPs to 
control erosion and sedimentation. The District informed the Water Board during 
a meeting on August 12, 2011 that the Corps has defined OHWM as the top of 
bank specifically for the SMP renewal (2012-2022). Therefore, this BMP implies 
the entire bed and bank will be exempt from BMPs to control erosion and 
sedimentation. The DSEIR should also define OHWM as top of bank since the 
Corps has expanded their jurisdiction for the SMP renewal. The District needs to 
ensure that BMPs are implemented to avoid and minimize erosion and 
sedimentation of all exposed soil due to SMP activities during construction and 
post-construction. The DSEIR should clarify any distinction that may exist 
between BMPs to be implemented during construction activities and BMPs to be 
implemented after (post) construction activities are completed. 

c. GEN-28 (Fire Prevention): Appears to be missing some text. 

d. GEN-29 (Dust Management): This BMP should indicate that the water used to 
wash the various exposed surfaces (i.e. parking areas, staging areas, soil piles, 
graded areas, etc) will not be allowed to enter the water way. 

e. GEN-33 and GEN-34 (Dewatering for Non-Tidal Sites and Dewatering for Tidal 
Work Areas): 

i. These BMPs should indicate that cofferdams will not be constructed with 
earthen fill because water quality may be adversely impacted in the event of a 
cofferdam failure. 

ii. These BMPs should indicate that the District shall implement the Water 
Quality Monitoring Plan during dewatering activities in addition to adequate 
treatment. 

f. GEN-35 (Pump/Generator Operations and Maintenance): This BMP should 
include back-up measures in the event of a failure. 

g. SED-2 (Prevent Scour Downstream of Sediment Removal): This BMP should 
include monitoring of the transition zone and downstream for erosion for 
sediment removal activities. 

h. BANK-3 (Bank Stabilization Post-Construction Maintenance): Water Board staff 
recommends at least 48-hours notification of maintenance activities to be 
conducted at ha nk repair sites that are less than 2 years old. 


D18 




Canal Maintenance: The DSEIR states “no mitigation is necessary for impacts to non- 
jurisdictional “other waters”, which are limited to unvegetated areas or inoperable canals.” 
The DSEIR should explain what is meant by “unvegetated” and “inoperable canals” and why 
these areas would not be subject to State jurisdiction and why mitigation would not be 




Stream Maintenance Program 
DSEIR 


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SF-RWQCB Comments 


t 


D19 


necessary for impacts to waters of the State that may occur. Water Board staff will consult 
the Water Board legal department regarding regulatory requirements for such areas. 

Water Quality Monitoring Plan and Sediment Characterization Plan. The District will be 
required to conduct water quality monitoring and sediment characterization as specified in 
each approved plan. However, the DSEIR does not actually state that the District will 
actually implement the plans. 


a. 


b. 


On page 3.13-11, the DSEIR describes the Water Quality Monitoring Plan and 
Sediment Characterization Plan under the existing permit and associated testing 
results for the last few years. However, the DSEIR should explain that these 
plans are currently being revised for incorporation into the upcoming SMP, 
subject to Water Board approval. 

For each Water Quality Impact (WQ-1 through WQ-9), the DSEIR should 
indicate that the Water Quality Monitoring Plan and/or Sediment Characterization 
Plan shall be implemented where required as specified in each plan. 


7. Appendix C: 2012-2022 SMP Update Mitigation Approach Memorandum (Mitigation 
Memo) 


D20 


D21 


a. The District is proposing to apply “21+” acres of mitigation for tidal impacts 
incurred during the 2002-2012 SMP period as “mitigation credits” for the 2012- 
2022 SMP Update for impacts to tidal habitat. The District must provide 
documentation that shows impacts to tidal habitat during the 2002-2012 SMP 
period have been fully mitigated and the amount of excess mitigation available to 
use as mitigation credits for impacts to be incurred during the next permit period. 

b. In Sections 5.2 and 5.3, the District proposes mitigation that includes Invasive 
Plant Management Program and Riparian Restoration and Planting Program for 
impacts to wetlands and other waters, and woody riparian vegetation. These 
mitigation programs appear to be appropriate for woody riparian vegetation 
impacts, but not necessarily for wetland impacts as this type of mitigation would 
be considered out-of-kind and possibly off-site. That is, the Riparian Planting 
Program will be implemented along creek banks and floodplains and would 
consist of tree/shrub/low plant species and does not include aquatic vegetation 
species. The Invasive Plant Program would “address impacts by improving 
riparian habitat quality.” The Water Board understands and agrees that it is the 
intent of the District to design and implement a mitigation plan that will 
ultimately improve the habitat functions and values. Water Board policy is to 
first provide mitigation that is in-kind and on-site. However, it is understood that 
site conditions may not be suitable for in-kind mitigation and an alternative 
design that is considered out-of-kind but more suitable to improve the habitat 
functions and values may be more appropriate. The DSEIR should explain that 
the District will first consider mitigation that will provide the most appropriate 
habitat functions and values. 


c. Mitigation Ratios 


D22 



i. Riparian Planting Program and Invasive Plan Management. The District has 
proposed mitigation for impacts resulting from vegetation management and 
sediment removal activities, including impacts to wetlands (aquatic 
vegetation). The District has developed the Mitigation Feasibility Assessment 



Stream Maintenance Program 
DSEIR 


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SF-RWQCB Comments 



D22 


that provides a process to determine the most appropriate riparian planting 
plan for habitats of low, medium, and high quality. The District is proposing 
a flat 1.2:1 mitigation to impact ratio with variable success criteria that would 
depend on the existing site conditions and habitat value (high, medium, low) 
of the mitigation site. The District does not include in the DSEIR (mitigation 
memo) an important consideration, which is to determine the most appropriate 
mitigation credit for situations in which the functions and values of the 
mitigation site do not match the functions and values of the impact site. For 
example, a discrepancy may exists if impacts that would occur in an area with 
high habitat value and the only mitigation site available is in an area of lower 
habitat value with a lower success criteria due to the existing low habitat 
value of the mitigation site, resulting in a habitat of lower value than that of 
the original impact site. The scenario does not take into consideration that 
low quality habitat created to mitigate for impacts to a high-value habitat site 
and vice versa. That is, the mitigation ratio should be variable to 
accommodate the various habitat values. 


D23 


ii. In-stream Complexity: The proposed mitigation ratio of 0.5:1 for impacts to 
in-stream complexity is not acceptable. In addition, Water Board staff does 
not agree with the mitigation rationale/basis behind proposing that “erosion, 
deposition, tree-falls, and debris mobilization within a few years following the 
removal of instream complexity will naturally reintroduce some complexity to 
the stream,” because it is difficult to pre-determine the level of complexity 
that would establish naturally. Therefore, the District should re-evaluate the 
impacts to in-stream complexity and develop a more appropriate mitigation 
proposal for the loss of complexity. 


D24 


D25 


Alternative Analysis 

1. Limited Work in Unmodified Channels and Geomorphic Alternatives: Although neither of 
these alternatives was chosen as the environmentally superior alternative, Water Board staff 
recommends limiting channel maintenance to locations that are necessary in order to avoid 
and minimize adverse impacts to water quality and beneficial uses. In addition, Water Board 
recommends improving habitat functions and values via geomorphic 
restoration/enhancement where possible. 

2. The Alternative analysis did not include additional impacts that would occur during the 
removal of the dead vegetation after herbicide was applied. Therefore, it is possible that 
herbicide application with subsequent removal may result in more adverse impacts than if 
just hand removal was conducted. This would be considered an important distinction since 
vegetation management with herbicide is proposed along most of the locations in the 
District’s jurisdiction. 


Again, full responses to these comments are necessary to facilitate the permitting process and 
should also be useful in developing the final EIR. 

Please contact Margarete “Maggie” Beth at (510) 622-2338 or via e-mail at 
mabeth@waterboards.ca. gov if you have any questions. 







Stream Maintenance Program 

-7- 

SF-RWQCB Comments 

DSEIR 


Sincerely, 






William B. Hurley 

Senior Engineer 


cc: 

Bill Smith, SCVWD, BSmith@valleywater.org 

Kristen O’Kane, SCVWD, KOkane@valleywater.org 

Sunny Williams, SCVWD, sunnywilliams@valleywater.org 

Ken Schwarz, Horizon, ken@horizonh2o.com 

Michael Stevenson, Horizon, Michael@horizonh20.com 

Luisa Valiela, U.S. EPA, valiela.luisa@epamail.epa.gov 

Gary Stern, NMFS, Gary.Stern@noaa.gov 

Vincent Griego, USFWS, Vincent Griego@fws.gov 

Ryan Olah, USFWS, Ryan olah@fws.gov 

Greg Martinelli, CDFG, GMartinelli@dfe.ca.gov 

Tami Schane, CDFG, TSchane@dfe.ca.gov 

Cameron Johnson, US ACE, Cameron.l.iohnson@usace.army.mil 

Paula Gill, US ACE, Paula.C.Gill@usace.army.mil 

Ian Liffman, US ACE, Ian.Liffmann@usace.army.mil 

Jon Rohrbough, CC-RWQCB, irohrbough@waterboards.ca.gov 

















3. Responses to Comments and DSEIR Revisions 


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Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


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Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Response to Comment D-l 

In locations where SCVWD conducts channel maintenance, channels are categorized as 
either “modified" or “unmodified"; the classification “natural" does not exist for channels 
maintained under the SMP. Figure 5-1 in the DSEIR shows the locations of unmodified 
channels in the Project Area. At all its maintenance sites, regardless of channel type, SCVWD 
would evaluate on-site habitat functions and values before performing maintenance 
activities. For example, resource values of modified and unmodified channels are 
considered when planning and applying herbicide for vegetation management. In 
unmodified stream channels with higher resource values, SCVWD's preferred approach for 
instream herbicide application is to apply spot spray or cut stump treatments that are 
targeted directly to the invasive or non-native vegetation. When SCVWD is working 
modified channels, these same techniques may be used, but depending on the size of the 
channel, length of management, and species, broadcast spray or foliar application 
techniques also may be used. In general, the equipment does not change between channel 
types, but the application technique may differ, depending on resource sensitivity and 
practical management considerations. 

For all of its channel maintenance activities, SCVWD would use a series planning measures 
and BMPs to avoid and minimize potential impacts. To begin with, SCVWD would minimize 
its maintenance activities by focusing on those necessary to maintain channel conveyance 
capacity and fire safety to reduce flood risk and fire risk, respectively. In addition, the BMPs 
in the DSEIR (Table 2-12) describe the host of avoidance and minimization measures to 
specifically be taken for channels that involved particularly sensitive habitats. For example, 
BMPs GEN-4 through GEN-14 describe several avoidance and minimization measures to be 
taken to protect habitat for nesting birds, burrowing owls, bay checkerspot butterfly, salt 
marsh harvest mouse, clapper rail, bats, dusky-footed woodrat, and other sensitive plant, 
fish, and amphibian/reptile species. SCVWD always would minimize its maintenance 
activities, restricting them solely to the activities necessary to maintain channel conveyance, 
and thereby reduce flood risk. 

SCVWD does distinguish between the resource values of channel types in planning for and 
applying herbicide as a vegetation management technique. In unmodified stream channels 
with higher resource values, SCVWD's preferred approach for instream herbicide 
application would be to apply spot spray or cut stump treatments that are targeted directly 
to the invasive or non-native vegetation. In comparison, if SCVWD was working in modified 
channels, these same techniques may be used, but depending on size of the channel, length 
of management, and species, broadcast spray or foliar application techniques also may be 
used. In general, the equipment does not change between channel types, but the actual 
application technique may differ, depending on resource sensitivity and practical 
management considerations. The District implements these herbicide techniques in 
accordance with existing SMP permit authorizations and approved BMPs. 

Response to Comment D-2 

A “dry channel" is a channel where no flowing water is present in the channel. 


Santa Clara Valley Water District 
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Final Subsequent Environmental Impact Report 


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Project 10.005 




3. Responses to Comments and DSEIR Revisions 


To determine when to stop maintenance activities that occurred after October 15, SCVWD 
would rely on weather forecasts to prepare for situations when significant rains were 
anticipated. After October 15, 72-hour look-ahead weather forecasts from the National 
Weather Service (or local vendor such as the Western Weather Group) would be consulted. 
SCVWD would look for projected rainfall events with potentially more than 0.5 inches of 
rainfall anticipated within a 24-hour period (i.e., a significant rainfall event). If a significant 
rainfall was forecasted within the 72-hour forecast window, maintenance work that could 
result in sediment runoff to a stream would be stopped, to allow adequate time to install 
erosion control measures. This is a standard method of forecasting for significant rainfall 
events. Monitoring of channel-forming flows would not be appropriate because work could 
not be conducted in a channel if such flow was present. 

The specific details for when maintenance actions would occur after October 15 are 
provided in BMPs GEN-1 and GEN-2. Pre- and post-maintenance monitoring activities are 
described in the discussion of annual implementation of maintenance work, beginning on 
page 2-25 of the DSEIR. Maintenance activities would be monitored and reported in the 
annual Post-Construction Report (PCR), discussed in Section 2.3 of the DSEIR. 

Response to Comment D-3 

Thank for you for this information regarding the extent of RWQCB jurisdiction. 

Response to Comment D-4 

The comment is correct that much of the new sediment removal work during the 2012- 
2022 SMP Update period is anticipated to occur in the Guadalupe River watershed. SCVWD 
supports the idea that reducing watershed sediment loads is a good method to reduce 
maintenance needs as well as protect overall watershed health. 

Response to Comment D-5 

Coverage for aquatic pesticide application under the General NPDES permit for aquatic 
weed control is described in Section 3-13, on page 3.13-29 of the DSEIR. 

Response to Comment D-6 

As stated in BMP GEN-1, all ground-disturbing work conducted after October 15 would be 
maintained in a rapidly "winterizable” state, and winterization would be completed before 
the occurrence of a significant rainfall event. Only bank stabilization activities that were 
more than 50 percent complete would continue after October 15, and such activities would 
continue until complete or until a significant rainfall event was forecast. If a significant 
rainfall event was forecast and the work was not complete, the site would be winterized and 
no further work would be conducted until the next season. This approach is more 
responsive to the Regional Board's interests because it would allow SCVWD to complete 
necessary bank stabilization activities to reduce discharges of sediment to waterways. In 
other words, SCVWD's approach would reduce the potential for failed banks to remain 
unaddressed over a winter season, thereby reducing potential sediment discharges and 
supporting beneficial uses to the greatest extent possible. 


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In no event would work be conducted indefinitely—all activities would follow the criteria as 
described above. SCVWD would work diligently to complete bank stabilization activities as 
quickly as possible, especially when they occurred towards the end of the work season. 

Response to Comment D-7 

BMPs would continue to be applied for all SMP Update activities. As noted in Chapter 2, 
Project Description, for all covered activities, appropriate resource protection measures and 
BMPs would be identified and included in the work order. The District would continue to 
maintain its internal tracking system, requiring field crews to verify that BMPs are applied 
properly. In addition, SCVWD would continue to employ a field inspector to randomly visit 
sites and verify proper BMP implementation along with other compliance confirmations. 

Response to Comment D-8 

SCVWD agrees that BMPs should be implemented before a rain event. If a significant rainfall 
was forecasted in the next 72 hours (using the methods previously described in response to 
Comment D-2), necessary supplies would be brought to the site and made available for 
implementation. Current 72-hour forecasts are very reliable. It is exceedingly unlikely that 
an unexpected storm would occur in a time frame that would prevent SCVWD from bringing 
winterization materials to a site and installing them, before a storm's arrival. 

Furthermore, the cost to SCVWD associated with repairing insufficiently winterized sites 
would be substantial; it is in SCVWD's best interests to winterize active sites properly 
before a storm arrives. SCVWD's proposed approaches reflect its numerous years of 
experience in conducting similar activities and represent the best way to balance concerns 
relative to insufficient winterization with the need to complete necessary work to protect 
water quality during the winter season. In other words, SCVWD and the RWQCB share a 
common goal in having sites winterized in a timely manner, and seeing that necessary work 
is completed to prevent sediment discharges during the winter season. SCVWD's approach 
is designed to achieve that common goal. 

Response to Comment D-9 

The estimated impacts from the 2002 projected work amounts were the basis of the 
mitigation requirements for the existing permit period. The SMP is a continuing program 
for which all project impacts and mitigation have been examined in this SEIR. Thus, project 
activities and impacts since 2002 have been evaluated in conjunction with new activities 
and potential new impacts. Over the course of the first SMP period (2002-present), SCVWD 
has worked in fewer areas than originally projected in the 2002 EIR. SMP work activities 
through 2010, compared to the 2002 work projections, are summarized in Chapter 2, 
Project Description, and Tables 2-1, 2-2, and 2-3 of the DSEIR. Because SCVWD has not 
conducted all of the 2002 projected work, it has not incurred all of the impacts that were 
projected in 2002. SCVWD's Board recently approved purchase of a property (known as the 
"Castle & Cooke property") that will satisfy the remaining acquisition requirements in the 
first SMP mitigation period for California red-legged frog and a portion of the remaining 
freshwater wetland requirements. SCVWD is actively seeking additional properties to 
satisfy the remaining freshwater wetland requirements. Although SCVWD is completing all 


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existing SMP mitigation requirements, the original mitigation requirements were based on 
work estimates (projections). The estimated impacts in the 2002 FEIR projected work 
amounts are the basis for existing mitigation requirements. 


At the end of the 2010 work season (encompassing 2002-2009), SCVWD committed to 
provide additional mitigation in both the Santa Clara and Pajaro Basins, beyond the actual 
work impacts incurred. Table 3-3 provides a summary of SMP sediment removal impacts 
incurred and mitigation provided to date. Table 3-3 compares the actual work completed by 
SCVWD to its mitigation obligation. By completion of the 2010 maintenance season, SCVWD 
had provided additional mitigation of 21.35 acres of tidal wetland habitat in the Santa Clara 
Basin (draining to San Francisco Bay) and committed to provide 9.41 acres of freshwater 
wetland habitat, compared to the 2002 SMP FEIR required mitigation amounts. As of 2010, 
the District had provided an additional mitigation amount of 6.2 acres of freshwater 
wetland habitat in the Pajaro Basin (draining to Monterey Bay), compared to the actual 
work impacts incurred. 


Table 3-3. Comparison of Impact by Vegetation Type of Actual Sediment Removal (2002-2010) 
with 2002 SMP FEIR Projected Sediment Removal 


Watershed 

Vegetation Type 

Projected 
and Done 

Done 

(not projected) 

Projected 
(not done) 

Miles 

Impact 

Acres 

Miles 

Impact 

Acres 

Miles 

Impact 

Acres 

Lower 

Freshwater wetland 





1.06 

0.99 

Peninsula 

Tidal wetland 

0.50 



0.08 

0.06 

0.06 


Not wetland 

1.70 



0.00 

1.20 

0.00 

West Valley 

Freshwater wetland 


9.00 

0.81 

1.09 


2.80 


Tidal wetland 


4.80 

0.00 

0.00 


7.10 


Not wetland 

0.50 

0.00 

0.01 

0.00 

3.00 

0.00 

Guadalupe 

Freshwater wetland 


14.70 

3.08 

1.96 

1.70 

4.90 

River 

Tidal wetland 

0.00 

0.00 

0.00 

0.00 

1.45 

13.52 


Not wetland 

0.60 

0.00 

0.39 

0.00 

0.67 

0.00 

Coyote 

Freshwater wetland 


19.75 

1.55 

2.80 

4.70 


Creek 

Tidal wetland 


3.03 

0.08 

0.05 

0.22 

0.80 


Not wetland 


0.00 

0.03 

0.00 

2.50 

0.00 

SF Bay 

Freshwater wetland 

14.30 

45.85 

5.49 

5.88 

10.36 

15.29 

Basin 

Tidal wetland 


8.07 

0.15 

0.13 

5.23 

21.48 

total 

Not wetland 


0.00 

0.91 

0.00 

7.37 

0.00 

Pajaro 

Freshwater wetland 

7.31 

10.15 




7.70 

Basin total 

Not wetland 

0.45 

0.00 

0.31 

0.00 

2.70 

0.00 

Whole 

Freshwater wetland 

21.61 

56.00 

5.49 

7.38 

14.46 

22.99 

Program 

Tidal wetland 

3.30 

8.07 

0.15 

0.13 

5.23 

21.48 

total 

Not wetland 

4.65 

0.00 

1.22 

0.00 

10.43 

0.00 


Notes: 

Excess SF Bay Mitigation: Freshwater wetland, 9.41 acres 

Tidal wetland, 21.35 acres 


Excess Pajaro Mitigation: Freshwater wetland, 6.20 acres 

The excess mitigation is estimated by subtracting the "done not projected" impacts from the "projected not done" 
impacts. 

Source: Data compiled by Horizon Water and Environment in 2011 


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Ann Draper, Assistant Officer of SCVWD's Watershed Stewardship Division, sent a letter on 
August 22, 2011, to Shin-Roei Lee of the San Francisco RWQCB, describing the completion 
status of the SMP mitigation program to date. This letter is provided in Attachment C. As 
stated in that letter, SCVWD is committed to continue monitoring the original 2002 
mitigation program elements that have already been constructed. SCVWD also is strongly 
committed to completing its obligations for both the freshwater wetland creation and 
restoration, and the Stream and Watershed Protection programs. SCVWD will continue to 
work with the appropriate regulatory agencies to review and gain approval for potential 
mitigation sites, as opportunities for land acquisition become available. 

It is also noted that where projected work did not occur during the 2002-2012 SMP period, 
those "projected but not worked" channel areas would be removed from the pool of 
channels where mitigation is provided in perpetuity. Removing these channels from having 
"perpetual mitigation status" would be necessary for SCVWD to use past over-mitigation 
towards new channel areas. By removing the "projected but not worked" areas from the 
pool of work areas where perpetual mitigation is provided, SCVWD would be enabling other 
"new work areas" to be available to have mitigation credit applied. It is recognized that the 
terminology and process of how past and future mitigation would be applied may be 
somewhat confusing. Appendix C in the DSEIR is revised entirely in Volume II of this FSEIR 
to and provides clarifications on this process. 

Response to Comment D-10 

Mercury sampling and guidelines for soil reuse or disposal is conducted according to the 
sediment sampling plan approved by the San Francisco RWQCB. The State standard 
threshold for hazardous levels of mercury in soil is 20 parts per million (ppm). If soil 
exhibits this high concentration, it cannot be reused for wetland surface cover or foundation 
material. If soil exhibits mercury concentrations over 20 ppm, it must be disposed at a Class 
1 hazardous waste facility. 

For excavated soil to be reused as wetland surface cover or foundation material, the soil 
would have to meet the state's sediment reuse guidelines, as stated in the comment. Results 
of soil analysis would be presented to and discussed with the San Francisco RWQCB before 
initiating any activities being taken at a work site. If soils to be excavated as part of a bank 
stabilization activity, for example, exhibited mercury concentrations at the hazardous level, 
the site may be left alone (i.e., to avoid disturbance to contaminated soil), excavated and 
then capped to prevent future mobilization, or over-excavated to entirely remove the 
contaminated area. Any excavated soil that met the state's guidelines for sediment reuse 
could be used for wetland restoration. However, excavated soil that did not meet the state's 
reuse guidelines would be taken to an appropriate landfill, depending on the mercury 
concentrations. In all cases, guidance from the RWQCB would be sought before any activity 
began. 

Response to Comment D-ll 

Although USACE would take jurisdiction over all areas below top of bank, this does not 
mean that top of bank is equivalent to the Ordinary High Water Mark (OHWM) for the 
purposes of the Proposed Project and related environmental compliance. Therefore, the 


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BMP exempting erosion control measures below OHWM remains appropriate. Requiring 
such measures below OHWM would be infeasible because they would be subject to damage 
or dislocation during the subsequent rainy season, potentially creating greater problems 
than those that they are intended to address. 

Response to Comment D-12 

BMP GEN-28 on page 63 in Table 2-12 of the DSEIR is revised as follows: 

1. All earthmoving and portable equipment with internal combustion engines will 
be equipped with spark arrestors. 

2. During the high fire danger period (April 1-December 1), work crews will : a) H 
have appropriate fire suppression equipment available at the work site. 

Response to Comment D-13 

The text in BMP GEN-29 (under number 4 in Table 2-12 of the DSEIR) is revised as follows: 

The District will implement the Bay Area Air Quality Management District's 

(BAAQMD) required Dust Control Measures 

(http://www.baaqmd.gOv/~/media/Files/Planning%20and%20Research/CEQA/B 

AAQMD%20CEQA%20Guidelines%20May%202011.ashx?la=en). Current measures 

stipulated by the BAAQMD Guidelines include the following: 

1. All exposed surfaces (e.g., parking areas, staging areas, soil piles, graded areas, 
and unpaved access roads) shall be watered two times per day. 

2. All haul trucks transporting soil, sand, or other loose material off-site shall be 
covered. 

3. All visible mud or dirt track-out onto adjacent public roads shall be removed 
using wet power vacuum street sweepers at least once per day. The use of dry 
power sweeping is prohibited. 

4. Water used to wash the various exposed surfaces (i.e.. parking areas, staging 
areas, soil piles, graded areas, etc.) will not be allowed to enter the water wav. 

54. All vehicle speeds on unpaved roads shall be limited to 15 mph. 

66. All roadways, driveways, and sidewalks to be paved shall be completed as soon 
as possible. Building pads shall be laid as soon as possible after grading unless 
seeding or soil binders are used. 

76. Idling times shall be minimized either by shutting equipment off when not in use 
or reducing the maximum idling time to 5 minutes (as required by the California 
airborne toxics control measure Title 13, Section 2485 of California Code of 
Regulations [CCR]). Clear signage shall be provided for construction workers at 
all access points. 

87. All construction equipment shall be maintained and properly tuned in 
accordance with manufacturer's specifications. All equipment shall be checked by 
a certified visible emissions evaluator. 

98. Post a publicly visible sign with the telephone number and person to contact at 
the lead agency regarding dust complaints. This person shall respond and take 


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corrective action within 48 hours. The Air District's phone number shall also be 
visible to ensure compliance with applicable regulations. 

Response to Comment D-14 

SCVWD uses various materials for coffer darns, including earthen fill, sandbags, k-rails, and 
inflatable barriers. When earthen fill is used and presents a concern relative to sediment 
discharge, visqueen is placed over the coffer dam. Therefore, SCVWD does not believe that a 
substantial risk of sediment discharge exists from failure of earthen coffer dams, and no 
revisions to the BMP are warranted. 

Water quality monitoring of dewatering activities would be conducted according to the 
water quality monitoring plan presented to and approved by the San Francisco RWQCB. The 
water quality monitoring plan includes procedures for operational water quality 
monitoring. The results would be reported in the annual PCR, submitted to the RWQCB. 
Because water quality monitoring is a standard procedure required as a permit condition, 
further note of this action in the BMPs is unnecessary. 

Response to Comment D-15 

Staff would be on call during business hours, and security would be available at night and 
on weekends, to assist if a pump or generator failed. Pumps and generators would be 
regularly monitored for failure. As a standard operating procedure, if a pump or generator 
failed, then a new one would be brought to the work site. 

Response to Comment D-16 

SCVWD employs a field inspector to randomly visit work sites, to verify performance of 
BMPs and other aspects of maintenance activities. SCVWD is not aware of any past issues of 
downstream erosion from sediment removal activities. 

Response to Comment D-17 

It is important for SCVWD to be able to respond quickly and effectively to a damaged work 
site, to prevent the situation from worsening. The 24-hour notification of maintenance 
activities to be conducted at bank repair sites that are less than 2 years old is important to 
achieving that goal. For all other bank repairs, the permitting agencies would be given a 
greater period of time to review and comment, during the annual Notice of Proposed Work 
or via individual work orders, as discussed in Chapter 2, Project Description, of the DSEIR. 

Response to Comment D-18 

The following definitions have been added to the Glossary of Significant Terms. The 
definition of "unvegetated” has been added to page xxxii: 

Unvegetated _ Areas containing either no. or only ruderal. vegetation. 

Examples would be locations that are concrete, or that support primarily annual 
non-native grasses and forbs. These areas provide little to no habitat value and, as 


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such, maintenance activities in these locations would not have impacts requiring 
compensatory mitigation. 

The definition of “inoperable canals” has been added to page xxi: 

Inoperable Canals Canals that were historically, but are not currently, used to 
convey water for water supply purposes. Although inoperable, these canals typically 
convey storm and non-storm runoff entering from upslope locations. In general, 
these canals are unvegetated and do not support beneficial uses. However, pockets 
of wetland-associated or riparian vegetation exist in certain locations. Sediment 
removal, vegetation management, and bank stabilization activities in canals 
resulting in impacts to such vegetation fe.g., sediment removal that also results in 
removal of the associated vegetation) would require compensatory mitigation, 
consistent with the District's mitigation program. 

The definition of "non-jurisdictional" has been added to page xxiv: 

Non-Iurisdictional This term refers to USACE jurisdiction and was not intended 
to apply to RWOCB jurisdiction, under which “waters of the state” typically are 
construed to apply to a broader set of water bodies than “waters of the U.S.” The 
District looks to the RWOCETs input as to the extent and nature of jurisdiction 
regarding canals: regardless, the District believes that compensatory mitigation 
would only be necessary if maintenance activities had the potential to impact 
beneficial uses—specifically, in places where impacts to riparian or wetland 
vegetation would occur, but not in unvegetated areas. 

Response to Comment D-19 

The discussion of the SMP water quality monitoring and SMP sediment sampling (on page 

11 in Section 3.13 of the DSEIR) is revised as follows, to indicate that the plans are under 

revision: 

SMP Water Quality Monitoring 

As part of its implementation of the existing SMP, SCVWD removed sediment from 
approximately 37 creeks, rivers, canals, or channels in the Project Area from 2007 
through 2009, the most recent years for which data are available. SCVWD has been 
conducting water quality monitoring as required by permits (Order R2-2002-0028 
and Order R3-2002-0008) issued by the San Francisco Bay and Central Coast 
Regional Water Quality Boards for the multi-year sediment removal program. As 
part of the SMP Update, these permits are in the process of being revised along with 
the associated Water Quality Monitoring Plans. Once updated and approved, these 
Water Quality Monitoring Plans will be incorporated into the final 2012-2022 SMP 
Update. In general, turbidity, water temperature, dissolved oxygen, and pH were 
monitored upstream and downstream of any in-channel water diversions before, 
during, and following sediment removal activities in creeks. During 2007, the 
removal of approximately 33,523 cubic yards of sediment from 17 project sites on 
15 creeks did not result in any water quality exceedances, unplanned releases, or 


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episodes of noncompliance with permits (SCVWD 2008). The 2008 sediment 
removal activities removed 8,845 cubic yards of sediment from 14 project sites on 
13 water bodies and did not result in any water quality exceedances, unplanned 
releases, or episodes of non-compliance (SCVWD 2009). 

SMP Sediment Sampling 

In addition to its water quality monitoring, SCVWD has sampled the sediments 
removed as part of its SMP implementation. Similar to the Water Quality Monitoring 
Plans discussed above, the existing Sediment Characterization Plans associated with 
the RWOCB permits are being revised, and once approved, will be incorporated into 
the final 2012-2022 SMP Update. Sediment sampling is undertaken to: comply with 
SCVWD's current WDRs; characterize the sediments to establish if they are suitable 
for reuse as a construction material ("foundation limit"), a topsoil or soil 
amendment ("surface limit"); and determine what type of disposal may be required 
(e.g. reuse, landfill, hazardous waste collection site). An exceedance of a "hazardous 
limit" indicates that the soil should be considered hazardous waste. 

In addition, each pertinent Water Quality Impact, Impact WQ-1 through Impact WQ-7, is 
revised as follows, to indicate that the appropriate plan will be implemented as specified: 

Impact WQ-1: Water Quality Degradation Resulting in Violation of Water 
Quality Standards or Waste Discharge Requirements Caused by Ground- 
Disturbing Activities (Significance Criterion A; Less than Significant) 

Disturbing soil on the banks and within the beds of surface water bodies could cause 
sediment to be eroded and transported downstream. Adverse effects of accidental 
sediment releases could include increased turbidity, which could cause an increase 
in water temperature and a corresponding decrease in dissolved oxygen levels. 
Increased turbidity and water temperatures, and lower dissolved oxygen levels 
could potentially exceed water quality standards and impair beneficial uses. Where 
required, the applicable Water Quality Monitoring and/or Sediment 

Characterization plans will be implemented as specified by the RWOCB permits. 

Impact WQ-2: Water Quality Degradation Resulting in Violation of Water 
Quality Standards or Waste Discharge Requirements Caused by Instream 
Maintenance Activities (Significance Criterion A; Less than Significant) 

The Proposed Project activities may be located in waters subject to tidal flows or 
water bodies with flowing water. As a result, SCVWD may need to prevent 

inundation by tidal flows and divert flowing water around the proposed 

maintenance activities by placement of dewatering systems and cofferdams. Where 
required, the applicable Water Quality Monitoring and/or Sediment 

Characterization plans will be implemented as specified by the RWOCB permits. The 
use and potential effects of these systems for each of the Proposed Project's 
maintenance activities are described below. 


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Impact WQ-3: Water Quality Degradation Resulting in Violation of Water 
Quality Standards or Waste Discharge Requirements Caused by the Accidental 
Release of Hazardous Materials (Significance Criterion A; Less than 
Significant) 

The Proposed Project includes activities that would require the use of heavy 
equipment, which could result in accidental releases of hazardous materials and 
subsequent effects on stream water quality as described below. Where required, the 
applicable Water Quality Monitoring and/or Sediment Characterization plans will 
be implemented as specified by the RWOCB permits. 

Impact WQ-4: Water Quality Degradation Resulting in Violation of Water 
Quality Standards or Waste Discharge Requirements Caused by the Use of 
Pesticides, including Herbicides (Significance Criterion A; Less than 
Significant) 

The use of pesticides, including herbicides, by the Proposed Project could result in 
potential violations of water quality standards or waste discharge requirements, if 
the pesticides were improperly applied, spilled into local water bodies, or 
transported to groundwater. Where required, the applicable Water Quality 
Monitoring and/or Sediment Characterization plans will be implemented as 
specified by the RWOCB permits. 

Impact WQ-5: Water Quality Degradation Resulting in Violation of Water 
Quality Standards or Waste Discharge Requirements Caused by the 
Disturbance of Existing Contamination (Significance Criterion A; Less than 
Significant) 

SCVWD-maintained channels (and to a lesser extent, canals) would receive and 
convey stormwater runoff from surrounding developed areas. Contaminants from 
stormwater runoff, such as metals and petroleum residues, could adhere to fine 
sediments that settled and accumulated in the stream or canal bottom. Large 
quantities of organic matter mingled with fine sediments would encourage sorption 
of urban contaminants. Sediments near storm drain outfalls may contain high 
concentrations of urban contaminants. The transport of contaminated soils 
downstream could result in a violation of water quality standards or waste 
discharge requirements. Where required, the applicable Water Quality Monitoring 
and/or Sediment Characterization plans will be implemented as specified by the 
RWOCB permits. 

Impact WQ-6: Compliance with CWA Section 303(d) Total Maximum Daily 
Loads (Significance Criterion A; Less than Significant) 

Table 3.13-2 lists impaired water bodies and the corresponding TMDLs for each one 
as identified by the RWQCBs and USEPA. Only TMDLs approved by USEPA are 
enforceable. No additional contributions of 303(d) listed constituents are allowed 
until a TMDL has been approved. Currently, TMDLs established to control and 
reduce mercury and PCB contamination within the Project Area would apply to the 


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SMP Update. As part of the TMDL enforcement procedure, the RWQCBs could add 
TMDL conditions to municipal permits and WDRs. Where required, the applicable 
Water Quality Monitoring and/or Sediment Characterization plans will be 
implemented as specified by the RWOCB permits. 

Impact WQ-7: Water Quality Degradation Resulting in Violation of Water 
Quality Standards or Waste Discharge Requirements Caused by Sediment 
Handling and Disposal (Significance Criterion A; Less than Significant) 

Sediment removed from stream channels during stream maintenance could contain 
contaminants. Improper handling and disposal of contaminated sediment could 
impact the beneficial uses of a stream. Also, sediment transport and disposal 
activities could result in sediment spills, which could impact water quality if 
sediments were spilled into the storm drain network or directly into water bodies. 
Where required, the applicable Water Quality Monitoring and/or Sediment 
Characterization plans will be implemented as specified by the RWOCB permits. The 
potential of the Proposed Project's activities to involve sediment handling and 
disposal is further described below. 

Response to Comment D-20 

By the end of the 2010 work season, the District had provided more mitigation in both the 
Santa Clara and Pajaro Basins than what was required, considering the work that was 
conducted and the impacts incurred. Volume II, Appendix C, Table 1 provides a summary of 
sediment removal impacts incurred between 2002-2010 and mitigation provided to date. 
This table compares impacts to mitigation requirements by accounting for three 
workprojection situations: (1) where work was projected and done; (2) where work was 
not projected and done; and (3) where work was projected and not done. As shown in the 
table, mitigation was accrued when the amount of work "projected and not done" was 
greater than the amount of work "done but not projected." In other words, when the District 
overall did less work then they projected, but provided mitigation for the entire projected 
amount, then mitigation was provided without associated impacts as shown below the 
table. As of the conclusion of the 2010 maintenance season, the District had provided an 
additional 9.41 acres of freshwater wetland habitat and 21.35 acres of additional tidal 
wetland habitat in the Santa Clara Basin, and provided additional mitigation of 6.2 acres of 
freshwater wetland habitat in the Pajaro Basin. These additional mitigation acres that were 
provided are considered additional to the mitigation that was necessary, based on the 
actual impacts from work activities that were performed. 

Response to Comment D-21 

The comment reviews and describes the role that the Invasive Plant Management Program 
and Riparian Restoration and Planting Program elements of the 2012-2022 mitigation 
approach (Appendix C of the DSEIR) address potential impacts to woody riparian 
vegetation. The comment suggests less certainty exists regarding how these mitigation 
approaches may help address mitigating impacts to wetlands. The comment requests that 
SCVWD first consider using mitigation approaches that will provide the most appropriate 
habitat functions and values. The invasive plant management and riparian restoration 


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mitigation elements would improve multiple functions and values for on-site channel 
habitat for birds, amphibians, and other wildlife by providing shading, sources of organic 
matter, and coarse woody debris; improving overall channel corridor vegetation and bank 
structure; and providing other water quality benefits to aquatic species. 

District studies on wetland vegetation growth suggest that the loss of instream wetland 
vegetation caused by SMP maintenance activities of sediment removal and vegetation 
management self-recovers on average within 1-2 years following maintenance activities. 1 
Because of this and the difficulty in restoring instream wetland vegetation resulting from 
the loss and relocation of juvenile plantings during high flow events, SCVWD's overall 
approach for on-site mitigation activities emphasizes ways to improve and enhance 
functions and values on-site (including those functions listed above), which together create 
an improved channel setting that also results in an improved aquatic habitat, likely to foster 
regrowth and the return of aquatic wetland plants. SCVWD agrees with the suggestion in 
Comment D-21 that SCVWD should prioritize mitigation approaches that are appropriate in 
terms of their replacement of impacts functions and values and, where possible, the 
replacement of in-kind functions and values on-site with similar in-kind functions and 
values as the top priority. 

Response to Comment D-22 

The comment indicates a possible misunderstanding about how the MFA assessment 
process would be used to evaluate conditions at bank stabilization sites versus its use in 
mitigating impacts caused by vegetation management and sediment removal activities. 
Unlike bank stabilization activities that typically are fairly limited in their length, vegetation 
management and sediment removal maintenance activities may occur at varying lengths 
across a reach of a flood protection channel. SCVWD would evaluate reaches 
comprehensively for their vegetation management and sediment removal needs. Based on 
an evaluation of the on-site reach areas to be impacted and the functions and values 
occurring at the maintenance reach, SCVWD would develop a reach-specific mitigation 
approach. The reach-specific mitigation approach may include several components of 
invasive plant management, riparian planting, and instream complexity development. For 
aspects involving riparian planting/restoration, the MFA process would be applied to 
determine performance standards. 

As described in response to Comment D-21, SCVWD's overall mitigation approach for reach- 
based vegetation management and sediment removal would be to prioritize and emphasize 
on-site mitigation steps to improve and enhance on-site functions and values. SCVWD 
agrees with the suggestions proposed in Comments D-21 and D-22, that SCVWD should 
prioritize mitigation approaches that are appropriate in terms of their replacement of 
impacts functions and values and, where possible, in-kind functions and values should be 
replaced on-site with similar in-kind functions and values. 


1 Santa Clara Valley Water District. 2002 (July). Instream Wetland Vegetation Regrowth Study Fourth Annual 
Report: Results for 2001. Prepared in accordance with the California Regional Water Quality Control Board, 
San Francisco Bay Region, Order 98-088. Prepared by G. Rankin and J. Hillman. San Jose, California. 


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3. Responses to Comments and DSEIR Revisions 


Furthermore, as described in the response to Comment D-21, the invasive plant 
management and riparian restoration mitigation elements would improve multiple on-site 
functions and values for channel habitat, for birds, amphibians, and other wildlife, by 
providing shading, sources of organic matter, and coarse woody debris; improving overall 
channel corridor vegetation and bank structure; and providing other water quality benefits 
to aquatic species. Because habitat impacts caused by vegetation management and 
sediment removal activities are temporary in nature, the invasive plant management and 
riparian restoration mitigation elements would be applied at a 1.2:1 ratio. The additional 20 
percent mitigation, beyond replacement mitigation, would be provided to address the 
temporal gap between the time when the maintenance impacts occurred and the time when 
the flood protection channel typically could be expected to "self-recover” in terms of 
regrowth of aquatic wetland and riparian vegetation. 

Response to Comment D-23 

The comment states that the proposed mitigation ratio of 0.5:1 for maintenance impacts to 
instream complexity features is not acceptable, and requests that SCVWD re-evaluate the 
mitigation proposal for the loss of instream complexity. Based on further review, SCVWD 
has revised the mitigation ratio for instream complexity mitigation to 1:1 (impact-to- 
mitigation). The discussion in the second paragraph under Mitigation Measure BIO-9 and 
Appendix L of the DSEIR is revised as follows, to reflect this modification: 

If such high-quality features must be removed during Proposed Project activities, 
compensatory mitigation will be provided by the installation of instream complexity 
features on a ©rSl:l f impact: mitigation :impact) basis, on the basis of either the 
number of complexity features or the area that is affected hydraulically by the 
features that are removed; the fisheries ecologist will determine which of these two 
metrics is appropriate based on the values to fish provided by the impacted 
features. Thus, one instream complexity feature will be installed for every twe one 
that are is removed, or an instream complexity feature hydraulically affecting 
roughly half the same area of the feature(s) removed will be installed. This ratio is 
l e ss than 1:1 und e r th e und e rstanding that e rosion, d e position, tr ee- falls, and d e bris 
mobilization within a f e w y e ars following th e r e moval of instr e am compl e xity wi fi 
naturally r e introduc e som e compl e xity to th e str e am. 

Response to Comment D-24 

The District appreciates the comment and concurs with these recommendations. 

Response to Comment D-25 

SCVWD removes dead vegetation if it poses a fire or flooding hazard (i.e., accumulated fuel 
potential or bulk near bridges), or if specifically directed to do so by another agency or 
party. However, in cases where the dead vegetation posed no danger, it would be allowed to 
compost naturally on-site. In either case, vegetation management conducted using 
herbicides still would have less of an overall impact on the Project Area compared with 
hand removal because of the less frequent need to conduct follow-up removal. Herbicide 
application would require 1-2 trips to apply and remove (as needed) at a worksite, but 


Santa Clara Valley Water District 

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3-23 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


several trips per year would be needed to address regrowth using only hand removal 
techniques. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-24 


December 2011 
Project 10.005 




Letter E 


I'm here to talk about the Permanente Creek Flood Protection 
Project and the 2 alternatives to the hydrology and hydraulic 
analysis. 

The first alternative would put flood detention basins in Rancho 
San Antonio County Park and McKelvey Park only and a flood 
catchment pipe along Cuesta Drive. No catchment basin would 
be dug in Cuesta Annex. 

The 2nd alternative calls for detention basins in all 3 locations. 
Construction projects should be as noninvasive to the environment 
as possible and if your project can be successfully completed 
without destroying the Cuesta Annex, a 12 acre parcel in its 
natural state which is enjoyed by many residents and others and 
home to heritage fruit trees, oaks and many species of birds, why 
are you even offering a 2nd more destructive, $7 million more 
costly alternative to the MVCC? Alternative 1 is more true to the 
language in your ballot measure Clean, Safe Creeks and the need 
to protect and preserve our natural environment. The impact on 
residents in terms of noise and air pollution and traffic congestion 
would be much less with alternative #1. Alternative #2 will bring 
mercury and other pollutants from the Lehigh Cement Plant into 
the Cuesta Annex. 


v When our State is $25 billion in debt it is incumbent upon you to 



show fiscal responsibility. If your board truly wanted to be the 
benchmark for using taxpayer dollars wisely, you would take the 
$40 million which has been allocated to contain a flood which has 
a 1 % chance of occurring in 100 years and redirect the money to 
repairing our reservoirs, many of which cannot be filled to 
capacity because, in the event of an earthquake, they would be 
damaged and flood communities in the area. The likelihood of 
that happening is significantly higher than 1%. 

In the numerous meetings I have attended over the past year 
dealing with your Permanente Creek Project, I haven't heard one 
individual express concern that flood waters would reach his 
home. There is no history of flooding and this is a colossal waste 
of money. 


Cynthia Riordan 



3. Responses to Comments and DSEIR Revisions 


Response to Comment E-l 

This comment is not applicable to the Stream Maintenance Program and has been 
forwarded to SCVWD staff working on the Permanente Creek project. 


Santa Clara Valley Water District 

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3. Responses to Comments and DSEIR Revisions 


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Santa Clara Valley Water District 

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Sent By: CALTRANS TRANSPORTATIO PLANNING; 510 286 5560; 


Sep-21-11 2:42PM; 


Page 1/2 




EDMUND BROWN', JR.Dmwnpr 


DEPARTMENT OF TRANSPORTATION 

P.O. BOX 23660 

OAKLAND, CA 94623-0660 

PHONE (510)286-5541 

PAX (510) 286-5559 

TTY 711 


Letter F 



Ftexycur power! 
Be energy* efficient! 


September 21,2011 


Ms, Sunny Williams 
Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95118-3614 


SCL-GEN 
SCL000119 
SCH# 2000102055 


Dear Ms. Williams: 

Stream Maintenance Program Update - Draft Subsequent Environmental Impact Report 
(DSEIR) 

Thank you for continuing to include the California Department of Transportation (Department) in 
the environmental review process for the above-referenced proposed project. We have reviewed 
the DSEIR and have the following comments to offer. 



Hydrology 

The Department will need to engage project level documents, to ascertain runoff or changes to 
flow patterns and streambed alterations, which could lead to scour conditions for bridges or 
culverts downstream of such activities. Project level hydrological studies may need to be 
conducted, as specific projects under the stream maintenance program progress. 



Transportation Permit 

Project work that requires movement of oversized or excessive load vehicles on State roadways, 
such as the State roadways listed in Section 3.12.3 of the DSEIR, requires a transportation permit 
issued by the Department. To apply, a completed transportation permit application with the 
determined specific route(s) for the shipper to follow from origin to destination must be submitted 
to the address below. 


Office of Transportation Permits . 

California DOT Headquarters 
P.O. Box 942874 
Sacramento, CA 94274-0001 . 

Further information is available on the following website: 
http://www.dot.ca.gov/hq/traffops/developserv/permits/applicatiohs/index.html. 


F3 


Encroachment Permit 

Work that encroaches onto the State right-of-way (ROW) requires an encroachment permit that is 
issued by the Department. To apply, a completed encroachment permit application, environmental 
X documentation, and five (5) sets of'plans clearly indicating State ROW must be submitted to the 


H Caltrane improves mobility ncwse Californm* 


Sent By: CALTRANS TRANSPORTATIO PLANNING; 510 286 5560; Sep-21-11 2:42PM; Page 2/2 


Ms, Sunny Williams/Santa Clara Valley Water District 
September 21,2011 
Page 2 



address below. Traffic-related mitigation measures should be incorporated into the construction 
plans during the encroachment permit process. 

Office of Permits 
California DOT, District 4 
P.O. Box 23660 
Oakland, CA 94623-0660 

Further information is available on the following website: 
http://www.dot.ca.gov/hq/traffopVdevdopserv/permits. 

Please feel free to contact Brian Brandert at (510) 286-5505, if you have any questions regarding 
this letter. 



Local Development-Intergovernmental Review 
c: Scott Morgan (State Clearinghouse) 


"Callramt improves mobility across California ” 



3. Responses to Comments and DSEIR Revisions 


Response to Comment F-l 

SCVWD is committed to avoiding impacts to infrastructure that result from its maintenance 
activities. The District is not aware of any situations during the first 10 years of the SMP 
when maintenance activities have led to scour conditions for bridges or culverts 
downstream. If information should become available in the future that suggested the 
potential for such problems, the District would investigate further, conduct any necessary 
studies, and adjust its maintenance activities accordingly. 

Response to Comment F-2 

SCVWD appreciates Caltrans' provision of information regarding the need for a 
transportation permit when moving oversized or excessive load vehicles on state roadways. 

Response to Comment F-3 

SCVWD appreciates Caltrans' provision of information regarding the need for an 
encroachment permit for work that encroaches onto the state's right-of-way. 


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Letter G 


From: 

To: 

Subject: 

Date: 


JLucas1099@aol.com 

smp update; 

Stream Maintenance Program Update 2012-2022 DEIR 
Monday, September 19,2011 3:38:31 PM 


Santa Clara Valley Water District September 19, 

2011 

Attention: Sunny Williams, SMP Update Comments 
5750 Almaden Expressway, San Jose, CA 95118 

Dear Santa Clara Valley Water District Board and Staff, 

In regards the Draft Environmental Impact Report for the District's Stream Maintenance Program 
Update 2012-2022 there are a sufficient number of concerns in this long term permit that lead me 
to encourage you to include a five-year review and amendment window. 

~ In particular the issue of climate change may result in more frequent and intense storm events 
that may re-contour stream channels, and alter wetlands and marsh inundation regimen. Might 
it increase temperatures in watersheds sufficiently to place critical habitat for species in jeopardy or 
result in new listings on the Special Status Plant List? Should an alternatiive management plan 
be included in DEIR to accomodate this? 


I would like to forward to you the Midpeninsula Regional Open Space District's rare plant protection 
protocols in separate submittal which I requested from their Senior Resource Management 
Specialist, Cindy Roessler. 

~ The width of a riparian corridor and the depth of shade afforded by a stream's canopy are a 
critical factor in filtering out pollutants, controlling erosion and in avoidance of algae blooms. 

The Soil Conservation Service used to recommend a 50 to 75 foot riparian setback to accomplish 
basic water quality and stream stability. Can such buffers be mandated? In particular, I was unable 
to find criteria for maintaining a sustainable level of SRA, shaded riverine aquatic habitat, in 
streams that support coldwater and anadromous fish runs. Once the Carmel River developed lethal 
algae blooms that killed dogs. Will global warming make this more likely? Please monitor stream 
temperatures and retain as much vegetative shade cover on west banks as possible. 



~ In regards the use of chemical sprays, I did not find mention of the window of applicability that is 
mandated for certain species such as California Clapper Rail. As an example in Palo Alto Baylands 
Imazapyr use was timed to avoid Clapper Rail nesting season (a window in early weeks of 
September) in spraying phragmites. As explained by Bayland Ranger .."(It should be noted that 
rails do not utilize the flood basin. The extremely muted tidal action is not to their liking.) We 
created pre-determined crossing areas in non-pickleweed areas for the contractor to enter the 
phragmites treament areas to minimize impact on salt marsh harvest mice A good deal of the 
treatment was done with people on foot with back pack sprayers. The contractor also used a 
vehicle called an aqua smog that allowed them to treat large stands of the weed effectively. We 


















also had staff present to do wildlife inspections. Signs were posted all around the treatment area in 
advance of the spraying, (re interface with adjacent recreation trail use) The four years of herbicide 
applications had limited success. We have tried other techniques such as black tarping and salt 
applications. We are still monitoring the success of these techniques. I believe we will need to use 
a multitude of techniques to control the phragmites inthe basin." (Please note Palo Alto Flood Basin 
is listed as Clapper Rail habitat on DEIR map). 


~ Do not remember the DEIR best management practices in regards the use of grazing, fire 
control or forest management measures in the watersheds. Will return to Palo Alto Library 
tomorrow for further review, 

however, would like to send these comments at this time. 


Also would like to submit more detailed analysis of DEIR habitat maps along with historic maps of 
baylands marsh habitat that perhaps are more precise in certain areas. 

Thank you for the opportunity to review this extensive Stream Maintenance Program 2012-2022 
DEIR. 


Libby Lucas, Conservation, CNPS 

174 Yerba Santa Ave., Los Altos, CA 94022 



From: 

To: 

Subject: 

Date: 


Cindy Roessler 
ilucasl099@aol.com; 

Rare plant protection at MROSD 
Thursday, September 15, 2011 4:30:34 PM 


Perhaps the best place to see what our policy is to protecting rare plants is in our 
draft Resource M anagement Policies which are posted on our website here: 

http://www.openspace.org/plans proiects/downloads/2011.02. 

RM PoliciesPrpsdUpdate.pdf 

The best management practices we implement with our vegetation management 
contractor (including protection of rare plants): 

• A District biologist will preview all work sites in the field prior to work by 
the contractor to determine site conditions and develop site-specific avoidance 
measures. 

• Spraying of glyphosate in a Roundup Pro®formulation at terrestrial 
locations by spot spray method will be at 1.0 to 2.0% concentration. 

• Application of glyphosate in a Roundup Pro®formulation at terrestrial 
locations by stump treatment method will be at 50 tol00% concentrate and 
placed on woody stump surfaces immediately after cutting. 

• Spraying of aminopyralid in a M ilestone VM ©formulation will be applied 
by spot spray method with backpack sprayers only and at a rate of 7 fluid 
ounces per acre per year. 

• No other herbicides, formulations or methods than specifically listed above 
are permitted under this contract. Surfactants and other adjuvants will be 
consistent with the Pest Control Recommendations, [note to Abhors - thus, 
Garlon and AquaMaster have been removed from services that we will 
request from contractor], 

• No herbicide treatment will occur within 15 feet of aquatic features. For 
purposes of this work, aquatic features are defined as any natural or manmade 
lake, pond, river, creek, drainageway, ditch, spring or similar feature that holds 
water at the time of treatment or typically become inundated during winter 
rains. 

• Between 15 and 100 feet of aquatic features, herbicide use is restricted to 
spraying of glyphosate by backpack sprayer. Other herbicides, broadcast 
spraying (such as by boom sprayer) or tank spraying with hoses and wands are 
not allowed in this zone. 

• No work will be conducted within 50 feet of rare plants. District biological 
staff will refer to maps of rare plants and conduct site assessment to determine 
the presence of rare species or potential habitat prior to work being conducted 








by the contractor. 

• District staff will work with Contractor to design site-specific mowing and 
brush cutting techniques to avoid nesting birds, such as but not limited to 
detection of wildlife in the project area, equipment modifications, mowing 
patterns and buffer strips. 

• Contractor will have a Pest Control Business License and Qualified 
Applicator License. 

• Contractor will implement all public and employee safety standards 
regarding the storage, mixing, transportation, disposal and application of 
herbicides 

• Contractor will follow all herbicide label requirements, and to protect the 
environment, including but not limited to not spraying in sensitive areas, 
avoiding weather conditions that might result in drift, and avoiding native plant 
species. 

• Contractor will conduct herbicide work in a manner consistent with Pest 
Control Recommendations provided by the District. 

• Application of herbicides will be in accordance with the California Red- 
Legged Frog Injunction ("Court Issues Stipulated Injunction Regarding Pesticides 
and the California Red-Legged Frog", http://www.epa.gov/espp/litstatus/redleq- 

froq/rlf.htm , retrieved on 1/23/2009). 


P? 


OPEN 

SPACE 


Cindy Roessler 

Senior Resource Management Specialist 
croessler(a)openspace.org 

Midpeninsula Regional Open Space District 
330 Distel Circle, Los Altos, CA 94022 
P: (650) 691-1200 - F: (650) 691-0485 
www.openspace.org | twitter: (g)mrosd 













3. Responses to Comments and DSEIR Revisions 


Response to Comment G-l 

SCVWD does not believe that the effects of global climate change on the frequency or 
intensity of storm events, or on sea levels, will be so much greater during the 10-year period 
2012-2022, as compared to the 5-year period 2012-2016, to warrant restriction of the SMP 
Update to a 5-year period instead of 10 years. Any relevant impacts of global climate change 
on the effects of SMP Update activities during the period 2012-2022 were taken into 
consideration in the DSEIR. 

Response to Comment G-2 

SCVWD appreciates being provided the list of BMPs implemented by the Midpeninsula 
Regional Open Space District (MROSD) to protect rare plants. Please refer to the response to 
Comment H-2 with regard to this list (the list is provided in an e-mail from Cindy Roessler 
to Libby Lucas that is included as an attachment to Comment Letter G). 

Response to Comment G-3 

SCVWD does not have the authority to mandate the width of vegetated riparian buffers. 
Also, the need for adequate flood protection would preclude SCVWD's ability to maintain a 
50- to 75-foot vegetated buffer along all SCVWD-maintained streams. Under the updated 
program, SCVWD would continue to implement BMPs to minimize impacts to riparian 
vegetation (as described in Table 2-12 of the DSEIR) and would not remove riparian 
vegetation during maintenance activities unless necessary to meet flood protection needs or 
to conduct levee inspections. 

SCVWD agrees that Shaded Riverine Aquatic habitat is important to limit maximum 
temperatures in certain reaches of stream, although as discussed under Impact BIO-8, 
canopy openings that provide more light also increase productivity, which directly benefits 
steelhead. 1 As a result, no standard "sustainable level" of Shaded Riverine Aquatic habitat is 
targeted by the SMP Update. Although global warming may increase stream temperatures 
somewhat, potentially increasing the likelihood of algae blooms, SCVWD does not believe 
that the effects of global climate change on stream temperatures will be substantial over the 
10-year period of this SMP Update. The comment's request for monitoring of stream 
temperatures and retaining vegetative shade cover on west banks of creeks is noted. 

Response to Comment G-4 

Per BMP GEN-6, which was included in the DSEIR, no maintenance work (including 
herbicide spraying) will be conducted in or immediately adjacent to suitable California 
clapper rail habitat prior to September 1 in any given year to avoid nesting rails. 


1 Casagrande, J. M. 2010. Distribution, abundance, growth, and habitat use of steelhead in Uvas Creek, 
California. Master's thesis. San Jose State University, San Jose, California. 


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Letter H 


From: 

To: 

Subject: 

Date: 


JLucas1099@aol.com 

smp update; 

Stream Maintenance Program Update 2012-2022 DEIR Comments continued 
Wednesday, September 21,2011 11:35:09 AM 


Santa Clara Valley Water District September 21,2011 

5750 Almaden Expressway, San Jose, CA 95118 

Attention: Sunny Williams, SMP Update Comments (cont.) 

Dear Santa Clara Valley Water District Board and Staff, 

In further review of the Draft Environmental Impact Report for the District's Stream Maintenance 
Program Update 2012-2022,1 would like to draw your attention to certain deficiencies in elements 
of this DEIR. 



~ In maps denoting habitat for species of tiger salamander Figure 3.3-10), red-legged frog 
(Figure3.3-13), western pond turtle and San Francisco dusky-footed wood rat there is none shown 
north of Calero Reservoir. Please explain omission in designating viable vegetative 
stream habitat in North County watersheds? 



~ In regards best management practices for implementing spraying and vegetative controls in this 
foothills' watershed, based on appropriate mapping of biological indicators and rare plants, I would 
like to submit, as an attachment, the rare plant protection protocols of the Midpeninsula Regional 
Open Space District. Please note the eighth bullet which says "No work will be conducted within 50 
feet of rare plants. District biological staff will refer to maps of rare plants and conduct site 
assessment to determine the presence of rare species or potential habitat prior to work being 
conducted by the contractor". Should SCVWD staff consider reference to Midpeninsula's biological 
staff and rare plant maps when conducting maintenance in Sierra Azul foothills watersheds of 
North County, for which this DEIR provides inadequate protocols for maintenance? 


~ Also, please incorporate the last bullet in this policy which notes that "Applictions of herbicides 
will be in accordance with the California Red-Legged Frog Injunction ("Court Issues Stipulated 
Injunction Regarding Pesticides and the California Red-Legged Frog", http://www.epa.gov/litstatus/ 

redleq-froq/rlf.htm , retreived of 1/23/2009). The East Fork of Permanente Creek was found to 

have a red-legged frog colony at upper edge of Rancho San Antonio and further up creek on 
Monte Bello Ridge. Is prime Red-Legged Frog habitat likely to be found at similar elevations of 
Guadalupe, Los Gatos, Saratoga, Wildcat and San Francisquito Creeks? Please 
reference SCVWD's half a century of records of species observed in these upper stream 
watersheds. 


H4 


~ Mention is made in the DEIR of there being only two Habitat Conservation Plans approved for 
Santa Clara County at this time, a Zanker Road Resource Management HCP covering salt marsh 
\J/ harvest mouse habitat in Alviso, and a Metcalf HCP for the Bay Checker Spot Butterfly at Santa 













A Teresa Hills. The mention includes the names of PG&E, Hicks Road and Vasona in association 
with the Metcalf HCP which appears confused. Also, does the Zanker Road Resource 
Management HCP accomodate SCVWD's Salt Marsh Harvest Mouse mitigation acreage in lower 
Coyote Creek? On page L-9 it states that "mitigation areas will be preserved and managed in 
H4 perpetuity by SCVWD. Mitigation could occur on lands acquired or owned by SCVWD, or on 

permanently protected lands not owned by SCVWD but by another entity." Shouldn't it be important 
to clarify such mitigation lands on a map in order to coordinate the best conservative maintenance 
practices possible? 

Lower Coyote Creek mitigation wetlands and critical habitat deserve more careful delineation in 
BMP's. 

~ In Figures 3.3-18 and 3.3-20 does there need to be more precise mapping on location of critical 
habitat of endangered species and species of special concern? I will submit maps of regulatory 
agency sitings that do not entirely agree with marsh/wetlands critical habitat data represented on 
H5 these figures. The continuity of habitat for the Salt Marsh Harvest Mouse seems to 

be compromised at confluence of Lower Penintencia and Coyote Creeks at Dixon Landing Road. 
Saratoga Creek should be changed to San Tomas Aquino Creek. The California Clapper Rail and 
Western Pond Turtle colony on Moffett Channel, bayward of Lockheed and Moffett Field need to be 
noted for seasonal considerations and conservative spray regimens. Sunnyvale East Channel 
overflow wetlands and Sunnyvale West Channel can use benign protocol. Where is Moffett Slough? 

~ As mentioned at the September 13 Board Meeting's public hearing, I would urge the District to 
incorporate more stringent safety measures for chemical applications in relation to recreational use 
and wildlife corridors. Sensitive receptors have a wide range in severity of exposure for momentary 
as well as cumulative impacts from vegetative sprays. Cats have been known to pass through 
H6 sprayed grass along a road and lick their fur with lethal results. Seasonal susceptability criteria for 
steelhead and snowy plovers are of equal concern. Also please adjust the steelhead streams 
(Figure 3.3-8) to include Guadalupe Creek, and Los Gatos Creek, and Alamitos and Calero Creeks 
to sustain runs of brown trout. Shaded Riverine Aquatic habitat criteria is an important 
consideration in tree removal or vegetation management on these streams. Stream temperatures 
need to stay cool to sustain a cold water fishery which, with global warming, is becoming a critical 
concern. 

~ Am still unable to find the best management protocols in this DEIR in regards grazing but hope 
you will include language that has already been prepared for the Santa Clara County HCP. This 
™ DEIR needs to find a means to include appropriate reference to scientific data and methodology of 
habitat conservation that has been achieved in the County's HCP, and which will be implemented 
within this permit's ten year time frame. 

Thank you for the opportunity to comment further on this Stream Maintenance Program Update. 
Sinverely, 


Libby Lucas, Conservation, CNPS 



174 Yerba Santa Ave., Los Altos, CA 94022 



3. Responses to Comments and DSEIR Revisions 


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3. Responses to Comments and DSEIR Revisions 


Response to Comment H-l 

The maps cited in the comment do in fact show habitat for these species north of Calero 
Reservoir. For example, the figures showing the areas where the California tiger salamander 
(Figure 3.3-10) and California red-legged frog (Figure 3.3-13) are extant indicate that these 
species likely are extant immediately north of Calero Reservoir. Areas farther north, where 
these species are indicated as having been extirpated, are heavily urbanized, have no recent 
records of the species, and lack suitable habitat for them. Figure 3.3-19 depicts locations of 
western pond turtle records but not western pond turtle habitat; all known locations of 
western pond turtle occurrence are shown in this figure. The DSEIR does not include a map 
showing locations of San Francisco dusky-footed woodrats. 

Response to Comment H-2 

SCVWD appreciates being provided the list of BMPs implemented by the MROSD to protect 
rare plants. However, SCVWD disagrees that the DSEIR provides inadequate protocols for 
protecting rare plants during maintenance activities. BMP GEN-9 provides for a qualified 
botanist to identify any work areas where special-status plants may occur, conduct a survey 
of those areas at a level of effort necessary to determine the locations of any such plants, 
and implement a number of measures to avoid and minimize, to the extent feasible, impacts 
to those plants. Such measures would include flagging or otherwise delineating in the field 
the locations of special-status plants and the identification, by the botanist, of buffers 
adequate to avoid impacts. In the event that impacts could not be avoided, the DSEIR 
provides compensatory mitigation for impacts to species that may be significantly impacted 
(Mitigation Measures BIO-4 and BIO-5). 

SCVWD's BMP to protect special-status plants is analogous to the measures implemented by 
the MROSD, but the need for and objectives of the SMP Update differ from those of the 
MROSD, and thus complete consistency between the measures of the MROSD and SCVWD 
would be impractical. 

Response to Comment H-3 

The California red-legged frog injunction referred to in the comment applies to projects that 
do not have a Biological Opinion from the USFWS, covering impacts of pesticide use on the 
red-legged frog. SCVWD is in consultation with the USFWS regarding potential take of the 
red-legged frog as a result of SMP Update activities, including pesticide use. Thus, with 
issuance of a Biological Opinion by the USFWS for the SMP Update, the maintenance 
activities would not have to comply with the injunction. Nevertheless, many of the measures 
required by the injunction to avoid impacts to red-legged frogs are included in SCVWD's 
BMPs. 

Please refer to Figure 3.3-13 regarding the expected distribution of the California red- 
legged frog. This figure also depicts the locations of all known records (including SCVWD's 
records) of the species within the Project Area. As indicated in this figure, the red-legged 
frog is expected to be extant in the upper reaches of the Guadalupe River watershed and the 
Los Gatos, Saratoga, Wildcat, and San Francisquito creek watersheds. 


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3. Responses to Comments and DSEIR Revisions 


Response to Comment H-4 

The comment indicates that the mention of PG&E, Hicks Road, and Vasona in association 
with the Metcalf HCP in the DSEIR "appears confused." The name of PG&E's HCP as 
referenced on page 3.3-189 of the DSEIR is the "Metcalf-El Patio, Metcalf-Hicks/Vasona 
HCP." 

What the comment means by the question, "... does the Zanker Road Resource Management 
HCP accommodate SCVWD's Salt Marsh Harvest Mouse mitigation acreage in lower Coyote 
Creek?" is unclear. SCVWD's salt marsh harvest mouse preserve in the Coyote Creek bypass 
is not included within or associated with the Zanker Road Resource Management HCP, 
which covers activities only within a confined area on the Zanker Road Resource 
Management site. 

Illustrating the prime locations for mitigating SMP Update impacts on a map is not possible 
because of the large number of potential mitigation locations for any given impact and the 
number of types of mitigation that may be required. For example, numerous areas exist 
throughout the Project Area in which wetland or riparian habitat mitigation could occur, 
invasive plant removal could take place, or California tiger salamander mitigation could be 
achieved. SCVWD would assess mitigation needs as potential impacts occurred and would 
identify mitigation areas as described in the mitigation program. 

SCVWD disagrees with the comment that "Lower Coyote Creek mitigation wetlands and 
critical habitat deserve more careful delineation in BMP's." BMPs apply equally to their focal 
resources (i.e., the resources being protected by the BMPs) wherever they occur, and they 
are not intended to be more or less stringent depending on the locations of those resources. 
The BMPs and mitigation measures included in the DSEIR are adequate to mitigate all 
impacts to biological resources to a level of less than significant (with the exception of 
habitat fragmentation impacts). 

Response to Comment H-5 

SCVWD believes that the mapping of Foothill yellow-legged frog habitat in Figure 3.3-18 
and the mapping of habitat for the western snowy plover, California clapper rail, and 
Alameda song sparrow in Figure 3.3-20 are sufficiently precise for the purposes of 
environmental review by the DSEIR. Figure 3.3-18 depicts all known locations of foothill 
yellow-legged frogs and illustrates all areas where the species is thought likely to be extant. 
With regard to the mapping of "critical habitat", the only critical habitat proposed or 
designated by resource agencies under the FESA for these species is proposed critical 
habitat for the western snowy plover, which is shown in Figure 3.3-20. 

SCVWD understands that continuity of habitat along Lower Penitencia Creek and Coyote 
Creek is affected by the road crossings in the Dixon Landing Road/Interstate 880 area, but 
the effects of these road crossings on habitat continuity are outside the control of SCVWD 
and would be unrelated to SMP Update activities in these areas. 

Figures 3.3-20 and 3.3-22 are revised to correctly label San Tomas Aquino Creek. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-32 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Figure 3.3-12 is revised to show the location of the western pond turtle occurrence north of 
Moffett Field. However, the BMPs in the DSEIR would be adequate to protect California 
clapper rails and western pond turtles wherever they may occur, and therefore no special 
considerations are needed for this particular area. 

The question, "Where is Moffett Slough?" is confusing; Moffett Channel is located west of 
Pond A4 but is not explicitly labeled in any figures. SCVWD is unaware of a waterbody 
named "Moffett Slough." 

Response to Comment H-6 

The BMPs and other procedures related to the application of pesticides that are described in 
Chapter 2, Project Description, and Appendix J of the DSEIR would be adequate to reduce 
impacts of pesticides on biological resources to the extent feasible, and the compensatory 
mitigation that would be provided would reduce impacts to wetlands, riparian habitats, 
steelhead, and other biological resources, resulting from pesticide application, to less-than- 
significant levels. Restrictions on timing, method, and location of pesticide application, as 
well as the relatively benign nature (from the perspective of toxicity) of the herbicides used 
by SCVWD, would minimize adverse effects of herbicides on biological resources other than 
the plants targeted by these herbicides. 

The statement, "please adjust the steelhead streams (Figure 3.3-8) to include Guadalupe 
Creek, and Los Gatos Creek, and Alamitos and Calero Creeks to sustain runs of brown trout" 
is unclear. The brown trout is not native to County streams, and although it has been 
stocked in county streams in the past, such as in Coyote Reservoir in 1938 1 , it is not known 
to be naturalized within Project Area streams. If the comment is suggesting that flows 
within those creeks should be adjusted to support this non-native fish, such an adjustment 
would adversely affect flows for steelhead and potentially increase competition for food or 
space between steelhead and non-native brown trout, which would be undesirable. 

SCVWD agrees that Shaded Riverine Aquatic habitat is important, to limit maximum 
temperatures in certain reaches of stream, although as discussed under Impact BIO-8, 
canopy openings that would provide more light also would increase productivity, which 
would directly benefit steelhead. 2 

Response to Comment H-7 

The comments regarding appropriate grazing protocols and incorporation of information 
collected for the HCP are noted. Please also refer to the response to Comment N-3 with 
respect to grazing. SCVWD used the best available scientific and professional data in 
preparing the DSEIR, including the draft Valley Habitat Plan and the resources that were 
used to prepare that plan. 


1 Leidy, R.A., G.S. Becker, and B.N. Harvey. 2005. Historical distribution and current status of 
steelhead/rainbow trout (Oncorhynchus mykiss) in streams of the San Francisco Estuary, California. Center for 
Ecosystem Management and Restoration, Oakland, CA. 

2 Casagrande, op. cit. 


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Final Subsequent Environmental Impact Report 


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3. Responses to Comments and DSEIR Revisions 


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Santa Clara Valley Water District 

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Letter I 


From: 

To: 

Subject: 

Date: 


JLucas1099@aol.com 

smp update; 

Stream Maintenance Program Update 2012-2022 DEIR Comment #3 
Wednesday, September 21,2011 4:25:23 PM 


Santa Clara Valley Water District 


September 21,2011 


5750 Almaden Expressway, San Jose, CA 95118 
Attention: Sunny Williams SMP Update Comments (cont.) 

Sunny, 

Couple more comments, as a postscript, 

~ Appendix G Special Status and Locally Significant Plant Species Considered but Rejected for 
Occurance, A brief consensus of our California Native Plant Society Santa Clara Valley Chapter 
requests that this list be retained as viable species for review, in that these species could feasibly 
occur. In consideration of the extensive acreage of Santa Clara County land that, due to remote 
location and/or private ownership, has not been reviewed, it seems a responsible conservative 
program to retain all aspects of this Special Status and Locally Significant Plant Species listing. 

~ In regards retaining viability of mitigation habitat, to which the SCVWD is committed, might it be 
feasible to illustrate on a DEIR Figure map the prime habitat mitigation locations? For 
instance, the SRA mitigation for riparian losses on Guadalupe River that were to be achieved on a 
stretch of Guadalupe Creek from Almaden Expressway to Masson Dam, could be assessed as to 
extent of shaded riparian canopy and the successful return of a coldwater steelhead/salmon 
fishery. Do summer stream temperatures stay below 20.0 deg. C? 

~ As seem to have run out of time today to deliver marsh habitat maps to your District offices could 
I please have a continuance on this aspect of data support submittal until next Tuesday, at the 
latest. 

Thank you again for any and all considerations of these comments. 


Libby Lucas, Conservation 

Santa Clara Valley Chapter, CNPS 

174 Yerba Santa Ave., Los Altos, CA 94022 











3. Responses to Comments and DSEIR Revisions 


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3. Responses to Comments and DSEIR Revisions 


Response to Comment 1-1 

SCVWD disagrees with the comment that the special-status plants listed in Appendix G 
should be retained as species that reasonably could be expected to be significantly impacted 
by SMP Update activities. SCVWD and H. T. Harvey & Associates botanists carefully 
considered the distribution, habitat affinities, and elevation range of these species when 
determining which species may or may not occur within the Project Area, and considered 
the distribution, abundance, and level of endangerment of California Native Plant Society 
(CNPS) List 3 and 4 species when determining which of those species could be significantly 
impacted by SMP Update activities. All of the species on the list in Appendix G either are not 
expected to occur in the Project Area, or would not be impacted significantly by the 
Proposed Project. For the latter group, the number of individuals of these species that could 
potentially be impacted by SMP Update activities would be so low, relative to the species' 
regional populations and distribution, that SMP Update activities would not substantially 
impact these species' populations. 

Response to Comment 1-2 

Illustrating the prime locations for mitigating SMP Update impacts on a map is not possible 
because of the large number of potential mitigation locations for any given impact and the 
number of types of mitigation that may be required. For example, numerous areas exist 
throughout the Project Area in which wetland or riparian habitat mitigation could occur, 
invasive plant removal could take place, or California tiger salamander mitigation could be 
achieved. SCVWD would assess mitigation needs potential impacts occurred and would 
identify mitigation areas as described in the mitigation program. 

In response to the question regarding the reach of Guadalupe Creek between Almaden 
Expressway and Masson Dam, based on measurements conducted by SCVWD over the last 
2 years, average summer time temperatures in this reach are below 20°C. 1 


1 SCVWD. 2011 [August]. Final Water Year 2010 Mitigation Monitoring Report for the Downtown and Lower 
Guadalupe River Projects. San Jose, CA. 


Santa Clara Valley Water District 

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Final Subsequent Environmental Impact Report 


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STATE OF CALIFORNIA 


Letter J 


IDMUND G. BROWN JR., Governor 


CALIFORNIA STATE LANDS COMMISSION 

100 Howe Avenue, Suite 100-South 
Sacramento, CA 95825-8202 


CURTIS L. FOSSUM, Executive Officer 
(916)574-1800 FAX (916) 574-1810 

California Relay Service From TDD Phone 1 - 800 - 735-2929 

from Voice Phone 1 - 800 - 735-2922 


Contact Phone: (916)574-1890 
Contact FAX: (916)574-1885 



September 21, 2011 


File Ref: SCH# 2000102055 


Sunny Williams 

Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95118 


Subject: Supplemental Environmental Impact Report (SEIR) for the Santa Clara 
Valley Water District Steam Maintenance Program, Santa Clara County 

Dear Ms. Williams: 

Staff of the California State Lands Commission (CSLC) has reviewed the subject SEIR 
for the Steam Maintenance Program (SMP) Update (Update or Project), which is being 
prepared by the Santa Clara Valley Water District (SCVWD) as the lead agency under 
the California Environmental Quality Act (CEQA) (Pub. Resources Code § 21000 et 
seq.). The CSLC has prepared these comments as a trustee and/or responsible 
agency because of its trust responsibility for projects that could directly or indirectly 
affect sovereign lands, their accompanying Public Trust resources or uses, and the 
public easement in navigable waters. 

CSLC Jurisdiction 


The CSLC has jurisdiction and management authority over all ungranted tidelands, 
submerged lands, and the beds of navigable lakes and waterways. The CSLC also has 
certain residual and review authority for tidelands and submerged lands legislatively 
granted in trust to local jurisdictions (Pub. Resources Code §6301 and §6306). All 
tidelands and submerged lands, granted or ungranted, as well as navigable lakes and 
waterways, are subject to the protections of the Common Law Public Trust. 

As genera! background, the State of California acquired sovereign ownership of all 
tidelands and submerged lands and beds of navigable lakes and waterways upon its 
admission to the United States in 1850. The State holds these lands for the benefit of 
all people of the State for statewide Public Trust purposes, which include but are not 
limited to waterborne commerce, navigation, fisheries, water-related recreation, habitat 
preservation, and open space. On tidal waterways, the State's sovereign fee ownership 
extends landward to the mean high tide line, except for areas of fill or artificial accretion 
or where the boundary has been fixed by agreement or a court. 






Page 2 


September 21, 2011 


Sunny Williams 


On navigable non-tidal waterways, including lakes, the State holds fee ownership of the 
bed of the waterway landward to the ordinary low watermark and a Public Trust 
easement landward to the ordinary high water mark, except where the boundary has 
been fixed by agreement or a court. Such boundaries may not be readily apparent from 
present day site inspections. 

Based on a review of the information contained in the draft SEIR, CSLC staff has 
determined that the proposed Project may include portions of the Lower Guadalupe 
River and Coyote Creek. Both of these waterways include State-owned sovereign land. 
If any portion of the proposed Project extends into the beds of these waterways, a lease 
for the use of sovereign land will be required from the CSLC for the portion of the 
Project encroaching on State-owned lands. Prior to initiating activities in areas that may 
implicate the CSLC’s leasing jurisdiction, please provide the CSLC Land Management 
Division staff listed at the end of this letter with additional information (e.g., detailed 
maps) to enable CLSC staff to determine which components of the Project will require a 
lease or amended lease. 

Project Location and Description 

The SCVWD is responsible for water supply, flood protection, and stream stewardship 
in Santa Clara County. The Project area includes streams within the Santa Clara and 
Pajaro basins. SCVWD flood protection facilities require maintenance to maintain the 
desired function of each facility. SCVWD approved the initial SMP in 2002 for a 10-year 
period, received authorizations from all permitting agencies with jurisdiction over the 
program and began work the same year. SCVWD seeks approval of the SMP Update 
and Program Manual for the next 10 years (2012-2022). 

i 

The SMP Update would be a continuation of past routine creek and canal maintenance 
activities in most of the same areas using many of the same techniques, but would 
incorporate a more comprehensive approach to managing and tracking the 
maintenance work and costs, monitoring environmental conditions, and providing 
program mitigation. The SMP Update would involve five categories of work activities: 

• Bank stabilization; 

• Sediment removal; 

• Vegetation management; 

• Management of animal conflicts; and 

• Minor maintenance. 

Bank stabilization treatment includes soft and hardscape elements. While SCVWD 
favors soft bank stabilization approaches in place of methods that create more 
hardened banks, hardscape elements may potentially include use of rock blankets, 
boulder revetments, concrete blocks, gunite slope protection, etc. Sediment removal 
activities may occur on approximately 43 miles of creeks and canals in the Project area, 
including approximately 19 miles of new channel areas not included in the original 





Sunny Williams 


Page 3 


September 21, 2011 


program. New sediment removal activities are proposed to include portions of the 
Guadalupe River and Coyote Creek. 

Environmental Review 


Permits and Approvals 

1. Section 2.5 lists state and federal agencies granting permits and approvals to 
SCVWD to implement the SMP. Based on the jurisdictional determination for the 
Lower Guadalupe River and Coyote Creek, the CSLC may be a CEQA 
responsible and/or trustee agency and should be added to Table 2-10 (Agency 
Approvals). 

Bank Stabilization 


2. Table 2-4 identifies bank stabilization treatments and notes whether the 
technique requires review by regulatory agencies. Please note that any bank 
stabilization treatment proposed on State-owned sovereign land would require 
CSLC review and approval. 

Sediment Removal 


3. Table 2-5 provides the volume of sediment removed in cubic yards (cu yds) 
during the 2002-2009 time span of the original program (approximately 371,000 
cu yds). Table 2-6 projects the amount of sediment removal work for the 10-year 
period between 2012 and 2022 in miles, but does not provide the volume 
projected to be removed in cu yds. Please provide the projected volume of 
sediment to be removed, generally during the 2012-2022 SMP, and specifically 
for the Guadalupe River and Coyote Creek areas. Any sediment removal 
proposed on State-owned sovereign lands would require CSLC review and 
approval. 

4. The SEIR states (page 3.6-20) that sediment removal activities could potentially 
disturb known existing contaminated sites. Portions of the Guadalupe River 
watershed within the Project area are affected by historic mercury mining 
activities. Soil and groundwater in some areas of this watershed contain 
hazardous levels of mercury contamination. Proposed maintenance activities 
involving ground disturbance, such as sediment removal and bank stabilization, 
may expose and potentially release mercury or methylmercury into the 
environment. 

The SEIR relies on Best Management Practice (BMP) GEN-3 to avoid exposing 
soils with high mercury levels. BMP GEN-3 requires testing and remediation 
practices including excavation and removal of contaminated soils. The SEIR 
reaches the following conclusion: 



Page 4 


September 21, 2011 


Sunny Williams 



“Implementation of BMPs to properly handle and remediate contaminated 
soils from Proposed Project maintenance activities, would prevent any 
planned maintenance activities (including sediment disposal or reuse) from 
disturbing known active contamination or remediation efforts. Through 
implementation of BMP GEN-3, activities in the Guadalupe River watershed 
would also avoid or minimize the potential for disturbance to existing mercury 
contamination. Therefore, this impact would be less than significant and no 
mitigation would be required. ” 

While the CSLC supports efforts to avoid or minimize disturbance to existing 
mercury contamination and testing/remediation through implementation of BMP 
GEN-3, CSLC staff disagrees with the conclusion that the impact would be less 
than significant and no further mitigation would be required. Sediment removal 
activities from the proposed Project may still result in the potentially significant 
impact of exposing mercury and releasing mercury or methylmercury 
downstream onto CSLC-managed riverbeds and bays. Such an impact may 
constrain future CSLC actions in the interest of the State. These contaminants 
could become a liability or responsibility for projects that may be implemented by 
the CSLC or others on sovereign land. Future efforts to enhance and support 
Public Trust uses, including but not limited to navigation, recreation, access, 
habitat restoration and invasive species management, would potentially have to 
mitigate for disturbance of mercury and other metallic particles originating from 
upstream ground disturbance. Such impacts and mitigation could add substantial 
costs or controversy to future projects that benefit Californians, their enjoyment of 
public lands and waterways, and the habitat values of these areas. 

CSLC staff requests that the SCVWD consider additional measures to mitigate 
'this potentially significant impact (e.g., specification of treatments to 
contaminated soils excavated so as to eliminate, to the extent feasible, the 
potential for erosion or methylation of mercury into downstream waters, 
establishing work windows when water levels are at their lowest, etc.). 


Cultural Resources 


5. Section 3.4 states that ground-disturbing maintenance activities conducted under 
the proposed Project would have the potential to disturb known or previously 
undiscovered cultural resources within the Project area. 



The SEIR should state that title to all abandoned shipwrecks and all 
archaeological sites and historic or cultural resources on or in the tide and 
submerged lands of California is vested in the state and under the jurisdiction of 
the CSLC. Any submerged archaeological site or submerged historic resource 
remaining in state waters for more than 50 years is presumed to be significant. 
The recovery of objects from any submerged archaeological site or shipwreck 
may require a salvage permit under Public Resources Code section 6309. CSLC 
staff requests that the SCVWD consult with CSLC staff, in conformance with 



Page 5 


Sunny Williams 


September 21,2011 



BMP GEN-40, should any cultural resources be discovered on the State’s tide 
and submerged lands during the Project’s ground-disturbing maintenance 
activities. 


Thank you for the opportunity to comment on the SEIR for the Project. As a responsible 
agency, the CSLC may need to rely on the final SEIR for the issuance of a lease and, 

therefore, we request that you consider our comments prior to adoption of the SEIR. 

■ 

Please send copies of future Project-related documents or refer questions concerning 
environmental review to Joan Walter, Environmental Scientist, at (916) 574-1310 or via 
e-mail at ioan.walter@slc.ca.gov . For questions concerning archaeological or historic 
resources under CSLC jurisdiction, please contact Senior Staff Counsel Pam Griggs at 
(916) 574-1854 or via email at pamela.qriqqs@slc.ca.gov . For questions concerning 
CSLC leasing jurisdiction, please contact Mary Flays, Public Land Manager, at (916) 
574-1812, or via email at marv.hays@sic.ca.qov . 


Sincerely, 



Division of Environmental Planning 
and Management 


cc: Office of Planning and Research 
M. Hays, LMD, CSLC 
J. Walter, DEPM, CSLC 
P. Griggs, LEGAL, CSLC 



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3. Responses to Comments and DSEIR Revisions 


Response to Comment J-l 

The District would coordinate with the California State Lands Commission (CSLC) regarding 
any maintenance activities to be conducted within the CSLC's jurisdiction. 

Response to Comment J-2 

Table 2-10 on page 28 of the DSEIR is revised as follows, adding the California State Lands 
Commission to the list of agencies: 


Table 2-10. Agency Approvals 


Agency 

Applicable 
Law/Regulations 
Guiding Jurisdiction 

Current or Prior Permits or Approvals for Maintenance 

Description 

Original Date of 
Issuance 

Date of 
Expiration 

California 
Department of 
Fish and Game 
(DFG) 

Fish and Game Code 
Section 1602 

Lake and Streambed 
Alteration 

Agreement, 
Notification No. R3- 
200-0119 

July 8, 2002 

Dec 31, 2014 

Fish and Game Code 
Section 2081 
(California 

Endangered Species 
Act) 

N/A 

N/A 

N/A 

California State 
Lands 

Commission 

State Lands Act 

Lease of State Lands 

Various 

Various 


Response to Comment J-3 

Please see response to Comment J-l. SCVWD would coordinate as necessary with CSLC 
regarding the techniques to be used for any bank stabilization activities within CSLC's 
jurisdiction. 

Response to Comment J-4 

When developing projections, SCVWD identifies the locations for sediment removal, but 
does not project the associated sediment volumes. The volumes of sediment to be removed 
are determined on an annual basis through an assessment of that year's project sites. 

Response to Comment J-5 

Please see the discussion in Section 3.13 of the DSEIR regarding water quality. Regulation of 
water and sediment quality is primarily under the jurisdiction of the State Water Resources 
Control Board and its Regional Water Quality Control Boards, per the federal Clean Water 


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3. Responses to Comments and DSEIR Revisions 


Act and California Porter-Cologne Water Quality Control Act. Therefore, potential impacts of 
ground-disturbing activities, such as sediment removal and bank stabilization on water and 
sediment quality, are discussed in detail in Section 3.13. 

Specifically, these potential impacts discuss SCVWD's evaluation related to existing mercury 
contamination for the Project Area, including lands that could be managed by the CSLC: 

• Impact WQ-5: Water Quality Degradation Resulting in Violation of Water Quality 
Standards or Waste Discharge Requirements Caused by the Disturbance of Existing 
Contamination 

• Impact WQ-6: Compliance with CWA Section 303(d) Total Maximum Daily Loads 

• Impact WQ-7: Water Quality Degradation Resulting in Violation of Water Quality 
Standards or Waste Discharge Requirements Caused by Sediment Handling and 
Disposal 

The potential to disturb, distribute, and dispose existing mercury contamination in the 
Project Area is included in these impact discussions. Additionally, mercury and methylation 
were thoroughly discussed in the water quality section of the 2002 SMP FEIR. 

In support of and in compliance with the Guadalupe River Mercury TMDL, issued by the San 
Francisco RWQCB in 2010, SCVWD conducts an extensive water and sediment quality 
monitoring program and has undertaken many projects in the Guadalupe River watershed 
to reduce mercury loading to San Francisco Bay. Most of this work has been performed in 
the upper Guadalupe River watershed and includes: removal of all visible calcine on 
SCVWD-owned land along Alamitos Creek; removal of 12,000 cubic yards of calcine material 
from Jacques Gulch; and installation of water circulation devices in the Almaden, Calero, 
Guadalupe reservoirs and Almaden Lake to reduce mercury methylation. These efforts have 
reduced the concentration of mercury moving downstream through the Guadalupe River 
watershed by over 80 percent, as reflected in data from SCVWD's mercury mass load 
monitoring efforts over the past 2 years. This mercury monitoring data and SCVWD's 
mercury reduction efforts are reported to the RWQCB and other federal and state agencies 
as part of specific regulatory requirements, including Clean Water Act Section 402 (NPDES), 
CWA Section 303 (TMDL), and Waste Discharge Requirements issued by the San Francisco 
RWQCB. Furthermore, ongoing SMP maintenance activities are regulated by the San 
Francisco RWQCB under CWA Section 401. 

The SMP Update would further contribute to mercury load reduction by removing fine 
sediment containing mercury from the system, countywide. Removed sediment from 
maintenance channels would be tested and handled properly, to ensure contaminated 
sediment was not re-released to the creek system. BMPs, including work windows, would 
be implemented for all ground-disturbing activities. The applicable BMPs for ground- 
disturbing activities and potential impacts on mercury distribution are described in 
Table 2-12 of the DSEIR and identified in the water quality impacts referenced above. With 
implementation of the SMP Update BMPs, and in compliance with existing regulations over 
water and sediment quality (particularly within the Guadalupe River watershed), SCVWD 
would avoid, reduce, and minimize potential impacts on existing mercury contamination in 


Santa Clara Valley Water District 

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Final Subsequent Environmental Impact Report 


3-38 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


the County and, therefore, would prevent future impacts on CSLC management actions and 
Public Trust uses. As such, no significant impacts would be anticipated, and the two 
mitigation measures suggested by CSLC are unnecessary. 

Response to Comment J-6 

Please see response to Comment J-l. The District will coordinate as necessary with CSLC 
regarding impacts to any significant cultural resources under CSLC's jurisdiction that 
resulted from program maintenance activities. 


Santa Clara Valley Water District 

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Final Subsequent Environmental Impact Report 


3-39 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


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Santa Clara Valley Water District 

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Letter K 


Page 1 of 1 


K1 


Subj: 

Date: 

From: 

To: 


Sunny 

Within the hour the maps that I wili deliver to reception are: 

~ A - South Bay Salt Pond Restoration Project Figure 3.6-7 Salt Marsh Harvest Mouse Habitat & Locations 

~ B - 1978 EIR map of Endangered Species in Bayiands locations of California Clapper Rail and Least Tern 
- it should be noted that as bay waters rise these species are retreating to uplands and up sloughs inland to 
lower reaches of San Tomas Aquino, Sunnyvale East, Sunnyvale West, Stevens Creek and Matadero Creek 

~ C - Coyote Creek Salt Marsh Harvest Mouse mitigation of 55 acre marsh to replace prime habitat lost in 
flood control project removal of oxbow and to assure continuity of corridor around end of Bay/Newby Island 
and mitigation to monitor Salt Marsh Yellow Throat populations - also creation of 14.5 acre water bird pond 
- there are further wetland mitigation sites in Reach 2 and Reach 3 of Coyote Creek project to consider. 

~ D - Guadalupe Creek SRA mitigation for loss to Downtown Guadalupe River Flood Project riparian corridor 
and degradation of coldwater fisheries habitat - from Almaden Expressway to Masson Dam - so Guadalupe 
Creek and Los Gatos Creek need conservative maintenance protocols suited to coldwater fishery streams 

~ E - Please note if San Francisquito Creek future flood control project and present maintenance may impact 
old successful! mitigation marsh of Faber Tract, and riparian mitigation for Matadero Creek. 

Hope this is somewhat clear as to my concerns with the Bayiands maps in this Stream Maintenance DEIR that 
had wide red lines for routine stream and marsh maintenance in these sensitive mitigation habitat areas. 

LibbvXucas, Conservation 

174 verba Santa Ave., Los Altos, CA 94022 


Stream Maintenance Program Update 2012-2022 - map submittal 

9/27/2011 10:43:16 AM Pacific Daylight Time 

JLucasI 099@aol.com 
sunnywiliiam s@v all ev water.org 


Tuesday, September 27, 2011 America Online: JLucasI099 










































































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California clapper rail secondary nesting areas 

(JUNE-JULY) 

CALIFORNIA LEAST TERN NESTING AREA 
(LATE APR!t.- JULY) 


ES&ga&si 


ESTUARINE FLATS 


SALT MARSHES AND SLOUGH "EYEBROWS" 


<7 A « 

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Figure 4-8 

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IN THE BAVLANOS 



Tl.T MARSH HARVEST MOUSE - PRESENT IN LOW NUMBERS THROUGHOUT 
ME BAY LANDS - ALL BAY LANDS MARSH IS POTENTIAL HABITAT. 


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Wetland Mitigation Site. 



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San Francisco Bay Bird Observatory 


COYOTE CREEK FLOOD CONTROL PROJECT 


REACH 1A WATERBIRD POND MONITORING PROGRAM 

ANNUAL REPORT 
JUNE 1999 THROUGH JUNE 2000 


2 March 2001 


Prepared By: 

\ 


Cheryl Millett 
Biologist 

San Francisco Bay Bird Observatory 

P.O. Box 247 
Alviso, CA 
95002-0247 


Prepared For: 


Louisa Squires 

Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 
95118 












1. EXECUTIVE SUMMARY 


The San Francisco Bay Bird Observatory monitored bird use and managed pond 
water depth at the Coyote Creek Reach 1A waterbird pond. Work was done from June 
1999 through June 2000 as part of ongoing monitoring since October 1993. The 
monitoring included surveys of waterbird use of the pond and measurements of water 
depth and salinity. Pond management included intake of water from Coyote Creek and 
outlet of water to Salt Marsh Harvest Mouse Marsh Management Area to maintain a pond 
water level that encouraged maximum waterbird use. 

The waterbird pond continued to be used extensively by a large number of birds 
(35,276) of 48 different species as wintering habitat, spring and autumn migratory' 
stopover habitat, and less so as breeding habitat. Overall bird use has continued to decline 
since the second year of the study (from a mean of 1333 in 1994-1995 to a mean of 739.7 

in 1999-2000), with a continued decrease in shorebirds in particular. Generally, 

/ 

shorebirds were most abundant during spring and autumn migration, while waterfowl 
numbers were highest during fall migration and gulls were most numerous in winter. 

Since the 1995 floods deposited sediments in the pond, it has been necessary' to 
adjust the water management to maintain water depths at the target elevations (from 2.6 
NGVD in 1993-1994 to 2.95 in 1999-2000). This increased target water level has been 
difficult to maintain during times of hot, dry weather, as seen in the low pond water 
depths in September 1999 and May 2000. It may be necessary to remove sediment if it 
becomes increasingly difficult to maintain target water levels in the pond. Removal 
activities should be planned to reduce impacts on pond inhabitants by avoiding the 
breeding season and fall and spring migratory seasons. 





2. INTRODUCTION 

The Santa Clara Valley Water District Waterbird Pond is located along Reach l A 
of lower Coyote Creek. It was constructed as part of the Lower Coyote Creek Flood 
Control Project to mitigate for impacts of the project on bird use of an adjacent salt pond 
(Duke et. al 1996). Bird use of the waterbird pond has been monitored since 1993 (Otahal 
and Jaramiflo 1998a). The purpose of this monitoring program is to determine the extent 
of use of the pond as stopover and winter habitat by migratory waterbirds, especially 
waterfowl and shorebirds (H.T. Harvey and Associates 1992). Salinity and water levels 
were monitored to maintain characteristics favorable for migratory waterbirds. 

This report documents three monitoring tasks: I) weekly surveys of birds present 
on the pond, 2) bi-monthly pond level measurements in feet (ft) NGVD (National 
Geodetic Vertical Datum) and 3) weekly pond salinity measurements. This report 
summarizes the findings of the June 1999 through June 2000 survey period. 

3. METHODS 

3.1 Bird Census 

Avian use of the pond was monitored using total area counts, counting all 

Sc 

individual waterbirds using the pond at one time. Non-waterbirds using the pond, for 
example swallows and raptors, were not included in surveys. Each survey took 
approximately one hour and was conducted in the morning hours irrespective of tide 
level. The observer traveled around the circumference of the pond and observed from 
three set points, enabling complete visual coverage of the pond. Surveys were conducted 
using binoculars and a spotting scope. 


2 



TABLE 1, Species, totals and mean number per survey observed during the June 1999 - June 2000 study period, 

7 . i r" ” * t ,u ’ * » r~ 


separated by group. 

..j 



-j j 1 


4 



1 

r 

: | 

SHOREBtRDS: 




WATERFOWL: j 


SPECIES 

TOTAL 

MEAN 

PER 

CENSUS 


SPECIES TOTAL 

MEAN 

PER 

CENSUS 

UNIDENTIFIED DOWITCHER 

7695 

153.90 


NORTHERN SHOVELER ,7187 

143.74 

AMERICAN AVOCET 

4519 

90.38 


GADWALL 1 1172 

23 44 

WESTERN SANDPIPER 

2708 

54.16 


MALLARD 

612 

12.24 

BUCK-NECKED STILT 

1139 

22.78 


RUDDY DUCK 

! 395 

7.90 

LEAST SANDPIPER 

332 

6.64 


GREEN-WINGED TEAL 

_201_ 

4,02 

WILLET 

121 

2.42 


CINNAMON TEAL 

187 

3.74 

KILLDEER 

98 

1,96 


NORTHERN PINTAIL 

147 

2.94 

WILSONS PHAUROPE 

79 

1.58 


CANADA GOOSE 

62 

1.24 

MARBLED GODWIT 

61 

1.22 


GREATER SCAUP 

19 

0.38 

GREATER YELLOWLEGS 

48 

0.96 


REDHEAD- 

6 

0.12 

DUNUN 

24 

0.48 


BLUE-WINGED TEAL 

4 

0.08 

SEMIPALMATED PLOVER 

5 

0.10 


BUFFLEHEAD 

3 

0.06 

LESSER YELLOWLEGS 

4 

0.08 


CANVASBACK 

3 

0.06 

RED-NECKED PHALAROPE 

2 

0.04j 

AMERICAN WIG EON 

1 

0.02 

LONG-BILLED CURLEW 

1 

0.021 

COMMON GOLDENEYE 

1 

0.02 

PECTORAL SANDPIPER 

V 

0.02 

i 

TOTAL 

10,000 

200.00 

TOTAL j 16,837 

336.74 


PROP. OF GRAND TOTAL 

28.3 


PROP. OF GRAND TOTAL 1 47J, 

. „ 


MAXIMUM PER SURVEY 

1,007 


MAXIMUM PER SURVEY 

1,465 



MINIMUM PER SURVEY 

2 


MINIMUM PER SURVEY 

0 



NUMBER OF SPECIES 

15 


NUMBER OF SPECIES 1 

17 








. 


























GULLS: 

. 



OTHER WATERBIRDS: 



SPECIES 

TOTAL 

MEAN 

PER 

CENSUS 


SPECIES 

TOTAL 

MEAN 

PER 

CENSUS 

-- 

CALIFORNIA GULL 

4964 

99.28 


AMERICAN COOT 

790 

15 80 

HERRING GULL 

1983 

39.66 

. 


COMMON MOORHEN 

21 

0.42 

RING-BILLED GULL 

441 

8.82 


SNOWY EGRET 

20 

0.40 

THAYER’S GULL 

166 

3.32 


GREAT BLUE HERON 

12 

0.24 

GLAUCOUS-WINGED GULL 

12 

0.24 


GREAT EGRET 

9 

0.18 

WESTERN GULL 

8 

0.16 


PIED-BILLED GREBE 1 

2 

0.04 

FORSTER'S TERN 

7 

0.14 

. 

TOTAL 

854 

17.08 

MEW GULL 

3 

0.06 


PROP. OF GRAND TOTAL 

2.4 


BONAPARTE’S GULL 

2 

004 


MAXIMUM PER SURVEY 

94 

u—. 


GUUCOUS GULL 

1 

0.02 


MINIMUM PER SURVEY 

0 


TOTAL 

7,587 

151.74 


NUMBER OF SPECIES 

6 


PROP. OF GRAND TOTAL 

21.5 






MAXIMUM PER SURVEY 

1,526 




. ■ 


MINIMUM PER SURVEY 

0 

: 





NUMBER OF SPECIES 

10 

} 








— 




OVERALL TOTAL 

35,278 

| 705.56 





MAXIMUM BIRDS PER SURVEY 

‘ 1,844 

: 





MINIMUM BIRDS PER SURVEY 

78 

j 





TOTAL NUMBER OF SPECIES 1 

48 

1 







1 


. 

. . ........ 




'NOTE THAT THE TWO DOWITCHER SPECIES (S HORT-BILLED DOWITCHER AND LONG-BILLED DOWITCHER) 
ARE LUMPED UNDER UNIDENTIFIED DOWITCHER HERE AND THEREFORE CONSTITUTE TWO SPECIES. 








*1 




SHO REBIRDS: 


SPECIES 


UNIDENTIFIED DOW HCHER 
AMER ICAN AVOCET 


WESTERN SANDPIPER 


BLACK- NECKED STILT 


L EAST SAN DPIPER 
WILLET 

kFlldeer _ 

WILSONS P HALAROPF~ 

. mar BLEP GO DWiT 
GREATER YELLOWLEGsT 
D UNLIN 

SEMIPALMATE D plovefT 
LESSER YELLQWLEGS 
L ONG-BI LLED CURLEW^ 


PECTORAL SANDP IPER 

red- neck ed phalarope 

[TOTAL ~ 

PROP! OF GRAND TOTAL 

maximum p er survey 

MIN IMUM PER SURVEY^ 

numb er OFspiciis' 


MEAN 
PER 

T OTAL CENS US 
76931 167.241 


3926 85 .35| 

2707T 58.86 


1124 


332 


121 


92 


24.43 


7.22 


2.63 


79 


2.00 


61 


48 

24 


1.72 


1.33 


1.04 

0.52 


0.11 


0.09 


1 


0.02 


1 


0.02 

^ 0 . 02 ] 

162 19] 352.59 

47.7 
1,465 


WATERFOWL: 


[SPECIES 


NORTH ERN S HOVELER 


[GAD W ALL 

r ft a a. 4 * + _ 


MALLARD 


RUDDY DUCK 


GREEN-W INGED TEAL 


CINNAM ON TEAL 


NORTHERN^ PINT AIL 
CANA DA GOOSE ~~ 
GREATER SCA Up" 
REDHEAD 


B LUE-W INGED TEAL 


BUFFLEHEAD 


C ANVASBAC K 
AMER ICAN WIGEON 
COMMON GOLDENFYF 


T O TAL_ 

PROP. OF GRA ND TOTaT 

maximum per Purvey” 

MINIM UM P ER SURVEY 

[number of species 


t ota l 

7187] 


_369; 

201 


1Q7_ 

62 


31 


1,007 


15 


3.48 

2.33 


0.07 
0.02 
0.02 

93721 203.74] 

27.5 


GULLS: 


SPECIES 
CALIFORNIA GULL 
HERRING GULL 
RING-BILLED gull 
THAYER'S GULL 
G LAUCOU SAVING EDGULL 
WESTER N GULL 
FORSTER'S T ERN 
MEW GULL 
[BONAPAOTESGULL 
GLAUCOUS GULL 
TOTAL 
PROP. OF GRAND TOTA L 
MAXIM UM PER SURVEY 
MINIMUM^ ER SURVEY 
[NUMBE R OF SPECIES 


OVERALL TOTA L 
TOTAL NUM BER OF SPECIES 1 


TOTAL 


1983 


441 


166 


12 


8 


1,526 


MEAN 
PER 
CENSUS 


4964 107.91 


43.11 


9.59 


3.61 


0.26, 

0.17 


0.151 


0.07 

0.04 


0.021 


7567 1 164.93 

22.3 


34,0261 739.70 


\ 0TH E R~W A T ERbIRDS: 


SPE CIES_ 

- AMERICAN COOT 
TsNOWY EGRE T 

[common mo orhen" 

G REAf BLUE H ERON^ 
GREAT EG RET 
[PI ED-BIL LED GREBE 
[ TOTAL - _ 

PROP. OF GRAND TOTAI~ 
[MAXIMUM PE R SURVEY 
MINIM UM PER SURVEY” 
[NUMB ER OF SPECIES 




total 


16 


11 


0.24 


18.43 


94 







Table 6 


era Endangered, or Lenalljr-Unique -Bird s in the Project Area 


>ecies 


1 


tlifornia Brown Pelican (FE, CE, CP) 
)U t 3 i e -crested Cormorant (SC-2) 
ilifrnia Gull (SC-3) 
orthern Harrier (SC-2) 
harp -shinned Hawk (SC-2) 
ooper's Hawk (SC—2) 

>lack-shouldered Kite (CP) 

Jolden Eagle (CP, SC-3) 

California Clapper Rail (FE, CE, CP) 

*}'• 

lestera Bluebird (CSE) 

I 

j§llow Warbler (SC-2) 

,alt Harsh Yellow throat (CSE) 


1 


X 


X 


X 


X 


X 


Reach 

IB 2 2 


X 


X 


X 

X 

X 

X 

X 

X 


X 


X 


3 


X 


X 


X 


Sderal Endangered (FE), California Endangered (CE) California Fully 

Itected (CP), California Special Concern (SC-1, SC-2, 3), 

lidard Exception List (CSE) 

CH 1A is the stretch of Coyote Creek north of Newby Island and downstream 
iOH 1A is tne strewn ui are no t proposed here. 

|>wer Pentencia Creek; flood-contro feasible, structural 

ft IB is Coyote Slough and included in the tnree leas 

K\ • 

irnatives. 




Table 7 


Rare, Endanger ed, or Locally Unique 
in Vicinity of Project Area 


ppecies 


1 


I White Pelican (SC-1) 

Peregrine Falcon (FE, CE, CP) 
California Black Rail (CR, CP) 
Snowy Plover (SC-2) 

California Least Tern (FE, CE, CP) 
Burrowing Owl (SC-2) 

Short-eared Owl (SC-2) 


^Federal Endangered (FE), California Endangered (CE), 
Protected (CP), California Special Concern (SC-1, SC-2 
Standard Exception List (CSE). 






./V'MVVVVIWWII 


Birds 


California Fully 
, SC-3), and California 




















































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■ State agency tentatively grants $8M 
for first of several projects to keep 
San Francisquito Creek in its banks 


BY JASON GREEN 

Daily News Staff Writer 


A funding!drought for a plan to prevent San Francisquito 
Creek from overtopping its banks could be over. 

The California Department of Water Resources on Wednes¬ 
day recommended awarding $8 million to the San Francisquito 
Creek Joint Powers Authority for construction of the first in a 
series of projects to stave off a 100-year flood. 

Scheduled to be built in two phases, the San Francisco Bay to 
Highway 101 project will ramp up flood protection for East Palo 
Alto and Palo Alto by widening 
the mouth of the creek, relocat- ON THE WEB 


ing levees and excavating the 
channel, said Len Materman, the 
authority’s executive director. 

“We’re pretty excited about 
this*” Materman said of the $8 


For more information about 
the San Francisquito Creek 
Joint Powers Authority, visit 
www.sfcjpa.org 


million award. “It represents a 

huge infusion of cash to start construction.” 


The funding, however, isn’t, locked in quite yet. The Depart¬ 
ment of Water Resources will take public comment on its award 
recommendations over the next two weeks. Of the 41 agencies 
that applied for funding in April, 23 didn’t make the cut, and Ma¬ 
ter man expects them to ask the state agency for a change of heart. 

Looking to retain its award, the authority’s board of directors 
approved a letter Thursday thanking the state agency and under¬ 
scoring the importance of the Bay-101 project. 

This vital funding will allow us to begin to solve the flood¬ 
ing risk since a storm damaged approximately 1,700 properties 
in our watershed 13 years ago. The project recommended for 
funding will protect residents living below sea level in homes 
with roof lines below an uncertified levee, and protect major lo¬ 
cal, state, and federal infrastructure,” the letter states. 

The award won’t cover the full cost of the Bay-101 proj¬ 
ect, which could total $24 million, but it represents a major 


CREEK, page 44 



From page At 


step forward for a flood-control plan that 
has historically struggled for funding, said 
Palo Alto Council Member Pat Burt, who 
sits on the authority’s board of directors. 

“It’s probably the single-largest outside 
funding we’ve received,” Burt said. 

The authority also hopes to apply $10 
million in Measure B funds toward the 
project, Burt said. The remaining gap 
could be plugged with matching funds or 
potentially through an assessment district, 
he added. 

Formed .shortly after the creek flooded 
in 1998, the authority changed course with 
the hiring of Materman in 2008, Burt said. 
Instead of focusing on an all-encompassing 
plan backed by congressional dollars, the 
authority has developed a series of flood- 
control projects and pursued alternate 
sources of funding from agencies such as 
the Department of Water Resources. 

So far, the strategy appears to be work¬ 
ing, Burt said. Palo Alto has secured a 
grant to replace the Newell Road bridge 
and Menlo Park is working on a similar 
effort with the Middlefield Road bridge. 
Both bridges are among four that will need 
to be replaced to increase the creek’s ca¬ 
pacity to handle a 100-year flood. 

Meanwhile, Caltrans is steaming for¬ 
ward with a plan to add a second culvert 
where the creek passes under Highway 
101 . 

“We’ve been able to cobble together 
some pieces that didn’t seem possible ... 
when this change in strategy occurred,” 
Burt said. 

The Bay-101 project is the most impor¬ 
tant piece of the puzzle, Materman said. 
Without it, upstream improvements, such 
as the removal of bottlenecks, won’t be 
effective. With the funding secured, con¬ 
struction could start sometime next year. 

“We’re getting much closer to turning 
shovels on a project that: will make the area 
safer,” said Materman, noting that the ulti¬ 
mate goal is to nullify the flood insurance 
requirement for 5,300 properties in Palo 
Alto, Menlo Park and East Palo Alto. 

Palo Alto resident Lorraine Brown wel¬ 
comed news of the progress Friday. Her 
house was among those damaged when 
the creek spilled out of its banks in 1998. 
She recalled passing her young children 
through a window to a firefighter as a com¬ 
bination of creek and storm drain waters 
flooded her Walter Hays Drive residence, 

“I will be the happiest person in the 
world,” she said, “if my house never floods 
again.” 

Email Jason Green at 
jgreen© daily news.group, com . 

image courtesy of the San Francisquito Creek 

Joint Ppwers Authority 








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3. Responses to Comments and DSEIR Revisions 


Response to Comment K-l 

SCVWD appreciates the maps and information that were provided with this comment. 
Because these maps are associated with Comment H-5, please also refer to the response to 
Comment H-5. 

The salt marsh harvest mouse map from the South Bay Salt Ponds Restoration Project 
(provided with the comment) was used to help prepare Figure 3.3-22 of the DSEIR. 

The DSEIR also reflects any relevant information regarding the California clapper rail and 
California least tern that are provided on the 1978 map. With respect to the comment that 
"as bay waters rise these species are retreating to uplands and up sloughs inland to lower 
reaches of San Tomas Aquino, Sunnyvale East, Sunnyvale West, Stevens Creek, and 
Matadero Creek," SCVWD is not aware of any records of these species, nor any observations 
reported by birders or others, to suggest that these species are occurring farther up these 
creeks now than they did historically. 

The information provided regarding SCVWD's salt marsh harvest mouse, San Francisco 
common yellowthroat, and wetland mitigation areas, as well as bird use of the Coyote Creek 
Reach 1A waterbird pond, is noted. These areas, and the species that use them, were all 
considered in the DSEIR analysis. 

The comment suggests that maintenance in the reach of Guadalupe Creek (between 
Almaden Expressway and Masson Dam) and in Los Gatos Creek need to be conservative to 
protect coldwater fisheries (e.g., from the loss of Shaded Riverine Aquatic habitat). SCVWD 
agrees that Shaded Riverine Aquatic habitat is important to limit maximum temperatures in 
certain reaches of stream, although as discussed under Impact BIO-8, canopy openings that 
would provide more light also would increase productivity, which would directly benefit 
steelhead. 1 

The comment asks whether the future San Francisquito Creek flood protection project, and 
the current maintenance of that creek, may impact mitigation habitat within the Faber 
Tract. The San Francisquito Creek project's CEQA document would analyze the effects of the 
project on the Faber Tract and on existing riparian mitigation associated with the 
Matadero/Barron Creeks Long-Term Remediation Project. The San Francisquito Creek Joint 
Powers Authority is the lead agency for that project. San Francisquito Creek is not 
connected to the Faber Tract, so present maintenance activities would not impact the Faber 
Tract. 

This comment lists several mitigation areas that would be affected by SMP Update activities. 
In some cases, such as Lepidium management in the salt marsh harvest mouse mitigation 
habitat in the Coyote Creek bypass, SMP Update activities would help to maintain the 
functions and values of the mitigation site. Similarly, vegetation management activities 
along stream reaches that were so heavily shaded as to adversely affect stream productivity 
may create canopy openings that would increase productivity and benefit steelhead. 2 

1 Casagrande, op. cit. 

2 Ibid. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-41 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Although the comment briefly references mitigation sites, the comment does not pose a 
question or identify any deficiency in the DSEIR, and thus a response is not possible. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-42 


December 2011 
Project 10.005 




Letter L 


Michael Stevenson 


From: 

Sent: 

To: 

Subject: 

Attachments: 


John Beall [jhnbeall@yahoo.com] 
Wednesday, September 28, 2011 1:58 PM 
smp_update 

Comments for Stream Maint. Program DSEIR 
TUC BMP Statements 110825.xls 


Sunny, 

My comments include the attached excel file with Draft BMP's for invasive plants in right of ways. It is being 
developed by a committee of the California Invasive Plant Pest Council. The SCVWD has turned its levees and 
our streams into a highway for invasive plants. Yet the Stream Maint Program DSEIR does not mention how 
they will work to avoid encouraging invasive plants from propagating while doing stream maint.work. 
Constantly sprayed, cut, and disturbed streams and levees are a magnet and a highway for new weeds to infest 
our county. 

The SCVWD has done extensive surveys of plants along creeks over the last 75 years. These plant lists should 
be checked for "rare" noxious weeds (CDFA and USDA lists). If listed weeds have been found at some point in 
time the SCVWD should revisit the sites to see if they still exist at the sites (or if the weeds have spread or no 
longer exist at the sites). 

Thanks, 

John Beall 
56 Centre st. apt 10 
Mountain View Ca 94041 


John Beall 


Planning Statements 


BMP# BMP Statement Reviewer's Comments 


PL1 

Plan to integrate cleaning routines in all land 
management activities. 

PL2 

Survey for invasive plant infestations before 
implementing activities. 

PL3 

Plan to minimize the movement of viable 
invasive plant material during activities. 

PL4 

Schedule activities to maximize the 

effectiveness of control efforts and minimize 
potential for introduction and spread of 
invasive plants. 

PL5 

Plan to minimize disturbance during activities. 

PL6 

Monitor sites, transport routes and right-of- 
ways during day-to-day activities and post¬ 
management activities; determine necessary 
treatments based on the presence of invasive 
species. 

PL7 

Inform and educate the general users in the 
area about common invasive plants, their 
impacts, and ways to prevent their 
introduction and spread. 

PL8 

Prevention for inter-agency communication, 
design, planners 

TEV1 

Integrate cleaning routines of tools, 
equipment, vehicles and pack animals into all 
activities. 

TEV2 

Before starting field work, identify areas 
where tools, equipment and vehicles can be 
cleaned. 

TEV3/4 

Inspect and clean tools, equipment, vehicles 
and pack animals before and after each 
activity for soil and plant material. 

CB1 

Wear clothing, gear, and footwear that 
prevents the spread of soil and plant material. 


Source BMP Statements Source 




Prior to implementing land management 
activities scout for, locate and document 
invasive plant infestations. 

Wl DNR Roadside Invasives, BMP #SD1; p. 11 



Plan activities to limit the potential for 
introduction and spread of invasive species, 
prior to construction. 

Wl DNR Roadside Invasives, BMP #SD3; p. 13 



Monitor and evaluate the success of 
revegetation in relation to project plans and 
specifications. 

National Park Service Pacific West Region Weed 

Prevention in Parks Best Management Practices for 
Maintenance & Construction Activities, p. 11, Post-work 
Revegetation, Monitoring 







Identify sites where heavy equipment and 
vehicles can be cleaned. 

National Park Service Pacific West Region Weed 

Prevention in Parks Best Management Practices for 
Maintenance & Construction Activities, p. 4 






































CB2 

Carry appropriate cleaning equipment to 
remove soils, seeds, and plant material. 

CB3 

Clean clothing and footwear in areas that are 
already infested with invasive plants, and 
easily accessible for monitoring for new 
infestations. 

CB4 

Clean clothing, gear, and footwear before 
leaving an area infested with invasive plants. 

WD1 

Designate waste disposal areas for invasive 
plant materials. 


Carry appropriate equipment (i.e. wire 
brush, small screwdriver, boot brush) to help 
remove soils, seeds, plant parts, seeds and 
invertebrates. 

Wl DNR Roadside Invasives, BMP #VM6c; p. 20 

Clean clothing and all equipment in areas 
that are easily accessible for monitoring and 
control if necessary. 

Wl DNR Roadside Invasives, BMP #VM5c; p. 20 

Plan for appropriate cleaning of clothing, 
footwear, and gear and inform workers 
about possible seeds carried on their 
clothing, footwear and gear. 

Wl DNR Roadside Invasives, BMP ffVM6b; p. 20 

Designate an area for dumping woody 
material if it is infested with invasive species. 

Wl DNR Roadside Invasives, BMP #TM9a; p. 26 














3. Responses to Comments and DSEIR Revisions 


Intentional blank page 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Response to Comment L-l 

The current extent of invasive plants in the Project Area is discussed throughout Section 3.3, 
Biological Resources of the DEIR. In particular, starting on page 3.3-32, a discussion of 
various invasive species currently present in the Project Area is presented. Impact BIO-1 
includes a discussion of the potential to increase invasive species cover (see the second 
paragraph on page 3.3-69). Impact BIO-44 specifically discusses invasive species. Reviewers 
are directed to review this impact discussion and Mitigation Measure BIO-16 in particular, 
which provides a detailed, two-pronged approach to addressing invasive plants in the 
county. This measure incorporates the California Invasive Pest Council's guidance. 

See also the discussion on the riparian planting component of the SMP Update mitigation 
program (revised Appendix C of the FSEIR, Volume II). This component would involve 
increasing the quality and quantity of native-dominated riparian plants throughout the 
county. This program has been developed to inhibit re-colonization by invasive plant 
species. 

In addition, several BMPs address invasive species. BMP VEG-2 describes proper disposal of 
removed invasive species to prevent further propagation. BMP REVEG-2 states that 
revegetation and replacement plantings would consist of locally collected native species. 

SCVWD staff, trained to recognize invasive and noxious weeds, would conduct annual 
surveys of creeks maintained under the SMP Update. As discussed in the DSEIR, SMP Update 
Manual, and the compensatory mitigation program (including the Invasive Plant 
Management Program and the Riparian Planting Program), the SMP Update would 
incorporate appropriate measures to survey, monitor, and reduce the extent of invasive 
plants throughout the county while elevating the quality and quantity of native riparian 
plants. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-43 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Intentional blank page 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-44 


December 2011 
Project 10.005 




Letter M 


Water and Power Law Group PC 

2140 Shattuck Avenue, Ste. 801 
Berkeley, CA 94704-1229 
(510) 296-5588 
(866) 407-8073 (efax) 
igantenbein(5>waterpowerlaw.com 

www.waterpowerlaw.com 


September 28, 2011 


Sunny Williams 

Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95118-3686 
E-mail: smp_update@valleywater.org 

Re: SMP Update EIR Comments 

Dear Ms. Williams, 

Please find attached the Guadalupe Coyote Resource Conservation District’s comments 
on the Santa Clara Valley Water District’s “Stream Maintenance Program Update 2012-2022 
Draft Subsequent Environmental Impact Report.” Thank you for the opportunity to comment, 
and for extending the deadline for comment. 

Please contact Nancy Bernardi ( gcrcd@pacbell.net) with any questions regarding these 
comments. 


Sincerely, 



Julie Gantenbein 

Water and Power Law Group PC 

2140 Shattuck Ave., Suite 801 
Berkeley, CA 94704 
(510) 296-5590 

j gantenbein @ waterpowerlaw.com 


Attorney for the Guadalupe Coyote 
Resource Conservation District 










Comments on Stream Maintenance Program Update 2012-2022 Draft Subsequent 

Environmental Impact Report 


Carson Cox 

Consultant, Guadalupe-Coyote Resource Conservation District 

September 28,2011 

The Guadalupe Coyote Resource Conservation District provides these comments on the 
Santa Clara Valley Water District’s (SCVWD) Stream Maintenance Program Update 2012-2022 
Draft Subsequent Environmental Impact Report (2012 SMP DSEIR). 

The GCRCD works to promote preservation of species diversity and management of 
riparian corridors for protection of wildlife, aquatic resources and water quality. We have 
become involved in the flood control projects on the Guadalupe River in furtherance of this 
work. 


We have significant concerns regarding the environmental impacts of SCVWD and U.S. 
Army Corps of Engineer’s construction, operation and maintenance of the flood control projects 
on the Guadalupe River. While we recognize the importance of flood protection, we disagree 
with the manner in which it has been carried out on the Guadalupe River to date. We believe 
that the geomorphological function of the river has been severely compromised, with corollary 
impacts to fisheries, fishery habitat and recreation. We believe a better strategy for flood 
protection would be to remove infrastructure from the floodplain, and restore geomorphological 
function to the river. We will continue to advocate for this strategy, but we recognize there are 
limitations on its implementation that should be addressed collaboratively. So, we remain 
committed to working with the SCVWD and other jurisdictional agencies to help adaptively 
manage the flood control projects while we continue to look for opportunities to restore and 
enhance the geomorphological function of the river for the benefit of flood protection, fisheries 
and recreation. In the interest of ongoing collaboration, we offer comments and 
recommendations on the 2012 SMP DSEIR to help assure the 2012-2022 Stream Maintenance 
Program (2012 SMP) balances environmental protection with the SCVWD’s obligations to 
provide flood protection. 

Given the length and complexity of the document, we organize our comments topically. 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


1 



Process 


Annual Work Sequence 

The GCRCD is concerned that the process for design and implementation of SMP 
activities does not include pre-implementation consultation with appropriate resource agencies to 
ensure that Best Management Practices (BMPs) are incorporated and potential environmental 
impacts are avoided or minimized. We request that the 2012 SMP process be revised to include 
an annual pre-implementation review of proposed work with resource agencies to discuss site- 
specific requirements, environmental constraints, and BMPs. 

The 2012 SMP provides a three-phase process for work planning, implementation and 

review: 

1. Work Plan Development 

• Initial survey and identification of work needs 

• Site assessment and project designs for proposed projects 

• Annual Work Plan submitted to agencies, with additional Notices of 
Proposed Work (as needed) 

2. Implementation 

• Pre-maintenance planning, logistics, site-specific requirements, 
constraints, and BMPs 

• Work implemented during the summer season, or as described in the 
work order 

3. Annual Reporting 

• Post-Construction Report (PCR) summarizing work conducted and 
mitigation monitoring 

• End-of-year meeting with SCVWD staff to review prior year’s work 


DSEIR, § 2.3.1, pp. 2-25 - 2-30, Fig. 2-41. 

The proposed 2012 SMP process includes an end-of-year “lessons learned meeting” 
between resource agency and SCVWD staff to review the Post-Construction Report and to 
“evaluate the effectiveness of both resource protection and maintenance methods used in the 
preceding construction season.” Id., p. 2-30. While we agree there is value in a post-action 
review, we submit that there is equal or greater value in pre-action coordination designed to 
proactively avoid impacts. The preference should be for avoidance rather than mitigation of 
impacts. 

We believe that a step for early resource agency review could be incorporated into the 
SMP process without causing undue delays. Phase 1 of the 2012 SMP Annual Work Sequence 
already proposes that “[p]re-work meetings would be held with appropriate SCVWD staff to 
discuss site-specific requirements, environmental constraints, and BMPs.” Id., § 2.3.1, p. 2-25. 

Y Agency consultation could be incorporated into this step. 

GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 

2 




Agency consultation is necessary to assure the SCVWD properly exercises its broad 
discretion under the program. For example, BMP VEG-3: Use Appropriate Equipment for 
Instream Removal states: “[w]hen using heavy equipment to cut or remove instream vegetation, 
low ground pressure equipment, such as tracked wheels will be utilized to reduce impacts to the 
streambed.” Id ., Table 2-12, p. 2-70. The BMP does not specify when the use of heavy 
equipment may or may not be appropriate, or what type of wheel to use under different 
conditions. We understand that BMPs must be broad enough to permit general 
application. However, the potential environmental impacts from the use of heavy machinery in a 
stream will be significant under many circumstances and potential impacts should be discussed 
with regulatory agency staff prior to implementation. 

Over the last decade the GCRCD has commented on a number of SMP actions which we 
believe have resulted in unintended, but significant, impacts to the stream. A simple review 
process with regulatory agency staff could ensure that all relevant information, including actions 
necessary to maintain project features and avoid or mitigate potential impacts to natural 
resources, are fully considered prior to the action. 


Public Outreach 

The Public Outreach BMP states, “[ljocal governments (cities and County) will be 
notified of scheduled maintenance work. The annual work plan will be submitted to the public 
works departments, local fire districts, and the District’s Zone Advisory Committee.” Id., Table 
M2 2-12, p. 2-65. The GCRCD is a public agency constituted pursuant to the Public Resources Code 
§§ 9151 et seq. We respectfully request that notification of scheduled maintenance work and a 
copy of the annual work plan be provided to the GCRCD as an interested government agency. 

Notification 



The Bank Stabilization Post-Construction Maintenance BMP (BMP BANK-3) states, 
“[t]he District may maintain or repair bank stabilization projects that are less than 2 years old 
that are damaged by winter flows. The District will notify the regulatory agencies 24 hours prior 
to beginning the work and the work will be reported as part of the Post-Construction Report 
submitted by January 15 of each year or if necessary, the subsequent year.” Id., Table 2-12, p. 2- 
71. The above referenced 24-hour notice period will not permit meaningful review of the 
proposed action or alternatives. 

The GCRCD is concerned that without a meaningful review by regulatory agencies there 
will be a tendency to repeat the initial maintenance treatment regardless of its effectiveness. We 
therefore request that the BMP be revised to include a reasonable review period (generally 30 
days or more) for repair of maintenance sites within the first two years of project completion, 
and include an assessment of causal factors of damage and consideration of alternate design 
approaches. Resource agency review and consideration of both root causes of project damage 
and alternate design approaches for avoidance of future damage will help insure that design 
limitations are identified and corrected. Although we recognize that this recommendation will 
require additional planning and coordination by SCVWD staff, taking the time to properly 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


3 




identify the cause of damage will help make the program more efficient, economical and 
environmentally effective long-term. 


Impact Assessment and Mitigation Measures 


The 2012 SMP DSEIR discusses a number of potentially significant direct and 
cumulative project impacts, as well as the mitigation measures and BMPs designed to reduce or 
avoid these impacts. However, the GCRCD is concerned that several potentially significant 
impacts, particularly on salmonid habitat, are not adequately addressed. Specifically, we believe 
that the following issues need to be more thoroughly addressed in the Final SEIR document: 

1. Impacts to Chinook salmon and necessary mitigation; 

2. Direct disturbance of steelhead and Chinook habitat from heavy equipment in the 
stream channel; 

3. Direct and cumulative impacts from sediment removal activities; and 

4. Direct and cumulative impacts from bank stabilization activities. 

We describe each of these potential impacts below. 


Impacts to Chinook salmon and necessary mitigation 


M4 


The 2012 SMP DSEIR contains conflicting and inadequately-supported statements 
regarding the status and occurrence of Chinook salmon in the SMP project area, and does not 
adequately assess and mitigate for potentially significant impacts to this species from the 
program. 


The DSEIR correctly identifies Chinook salmon as a native species utilizing habitat in the 
project area for migration, spawning, and rearing. See DSEIR, p. 3.3 169-170. The DSEIR also 
recognizes that a portion of the project area is designated as Essential Fish Habitat (EFH) by the 
Pacific Fishery Management Council’s Salmon Fishery Management Plan under authority of the 
Magnuson-Stevens Fishery Conservation and Management Act (id., p. 3.3 171-173). Further, 
the DSEIR recognizes that Chinook salmon, though rare, would be impacted by proposed project 
activities. Id., p. 3.3-169. These findings indicate that impacts to Chinook habitat from project 
activities would meet the threshold of significance under state CEQA guidelines as described in 
Section 3.3.2 Regulatory Setting. 



However, the DSEIR also contains statements regarding the status of Chinook in the 
project area that directly conflict with the above findings. For example, in Section 3.3.4: Impact 
BIO-14: Impacts on Non-Special-Status Fish and Amphibians the DSEIR states, “genetic 
analysis has confirmed that Chinook in South Bay streams are all derived from hatchery stock.” 
Id., p. 3.3-169. However, in the subsequent Section 3.3.4: Impact BIO-15: Impacts on Essential 
Fish Habitat the DSEIR states, “although spawning has been documented in SCVWD- 
maintained creeks, whether up-migrating adults have hatched on these creeks or if the adults that 
were observed were direct strays from other areas is unknown.” Id., 3.3-171. The second 
statement, that the natal origin of spawning Chinook is “unknown” directly conflicts with the 
previous statement that “genetic analysis has confirmed that Chinook in South Bay streams are 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


4 



all derived from hatchery stock.” Id., p. 3.3-169 (emphasis added). The DSEIR does not cite 
adequate data to establish this latter assertion. The modem scientific method demands a certain 
degree of precision and objectivity when analyzing data, and care should be taken to ensure the 
accuracy of statements made. It does not appear that the impact analysis for Chinook salmon 
presented in the DSEIR meets standard scientific practices for consistency and objectivity. 


M4 


The DSEIR’s finding (that no evidence exists that Chinook salmon are native or 
naturalized in the project area and thus no significant impacts can be expected from project 
activities) is wrong. The GCRCD has entered evidence into the administrative record 
establishing the historical presence of self-sustaining Chinook salmon runs in the project area. 
See e.g., letter from U.S. Fish and Wildlife Service to U.S. Army Corps of Engineers (June 23, 
1995) (Attachment 1); John E. Skinner, A Historical Review of the Fish and Wildlife Resources 
of the SF Bay Area (prepared on behalf of California Department of Fish and Game) (June 1962) 
(Attachment 2)). We acknowledge that historical presence of Chinook in the system does not 
conclusively establish that the current Chinook run is native and self-sustaining. However, 
historical presence, in addition to designation of EFH and regular and ongoing use of the project 
area by Chinook for migration, spawning and rearing, does support our argument that the river 
can support salmon, and the SCVWD’s actions in operating and maintaining its water supply and 
flood control projects impact the salmon that are presently in the system. The SCVWD’s 
participation in the Fish and Aquatic Habitat Collaborative Effort, which commits the SCVWD 
to spend $ 42 million to contribute to the restoration of salmon and steelhead in the Guadalupe 
River and Coyote and Stevens Creek, would also seem to support this argument. 

We request that SCVWD revise its CEQA analysis to quantify and evaluate potential 
impacts to Chinook populations and habitat from project activities, identify available best 
management practices to avoid these impacts, and develop mitigation measures for unavoidable 
impacts. We further request that statements in the 2012 SMP DSEIR regarding status and origin 
on Chinook salmon in the project area be corrected to reflect standards of scientific objectivity. 


If the natal origin of spawning Chinook is unknown, or if conflicting evidence is on 
record, the conservative approach under CEQA would be to proceed on the assumption that the 
population is native or naturalized. See, e.g., 14 CCR § 15064(g) (“[i]f there is disagreement 
among expert opinion supported by facts over the significance of an effect on the environment, 
the Lead Agency shall treat the effect as significant...”). The fact that a significant portion of the 
project area is currently designated by the Pacific Fishery Management Council’s Salmon 
Fishery Management Plan as Essential Fish Habitat only reinforces this approach. The DSEIR 
however, takes the opposite approach. The document states that Chinook are successfully 
spawning and rearing in the project area, but finds “[bjecause no evidence exists that Chinook 
salmon have naturalized in SCVWD-maintained creeks, Proposed Project activities are not 
expected to affect adversely the viability of this species’ populations in the Project Area. As a 
result.. .impacts on this species would be less than significant.” Id., p. 3.3-173. 


Eauinment in the Stream Channel 



Although the 2012 SMP includes BMPs to reduce impacts from heavy machinery in the 
stream channel (e.g. VEG-3 and GEN-23), the DSEIR impact assessment does not present an 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


5 



t evaluation of such impacts, nor are impacts to fish habitat from heavy equipment addressed as 
part of the SMP project’s mitigation requirements. 


Disturbance from heavy equipment in streams can have significant impacts on fish and 
benthic macroinvertebrate populations. Salmonids such as steelhead and Chinook are 
particularly susceptible to such disturbance as these species rely on interstitial spaces in gravels 
and cobbles for egg and fry development. Salmonid juvenile and adults also depend on 
macroinvertebrates produced from the same interstitial spaces in gravel habitat as a major food 
source. Disturbance to these habitat elements by heavy machinery during stream maintenance 
activities (e.g., bank stabilization, vegetation management, and sediment removal) from direct 
crushing or filling of interstitial spaces with fine sediment can therefore be reasonably expected 
to result in significant impacts to steelhead, Chinook salmon and other native fishes. 

The GCRCD requests that the 2012 SMP SEIR be revised to include a specific analysis 
on impacts to fish habitat from heavy machinery use in the active channel. This assessment 
should include an assessment of impacts to fish habitat in general, as well as specific impacts to 
Chinook and steelhead spawning and rearing habitat quality and quantity. This assessment 
should be used to estimate potential impacts from the use of heavy machinery in the active 
stream channel as part of proposed 2012 SMP activities, assess the adequacy of existing BMPs 
and propose additional BMPs as appropriate, and evaluate the need for specific mitigation 
measures to address significant impacts to Chinook and steelhead spawning and rearing habitat 
quality and quantity. 

Sediment Removal Activities 


The GCRCD is concerned that the impact assessment mitigation strategy presented in the 
2012 SMP DSEIR does not fully address direct and cumulative impacts from sediment removal 
activities. In addition, the impact assessment and mitigation should include Chinook salmon. 

Direct Impacts . The 2012 SMP DSEIR identifies direct impacts from sediment removal 
activities, including those on salmonid spawning and rearing habitats. To mitigate for these 
impacts the SCVWD will implement gravel augmentation, described as follows: “[i]f more than 
500 square feet of high-quality gravel will be removed along steelhead streams, compensatory 
mitigation will be provided by the installation of suitable spawning gravel along the affected 
creek at a 1:1 (mitigation:impact) ratio on a square footage or acreage basis.” DSEIR, Mitigation 
Measure BIOS: Augmentation of Spawning Gravel, p. 3.3-123-124. 



The GCRCD fully supports mitigation for impacts to high-quality gravel. We have long 
maintained that gravel habitat for Chinook and steelhead in the project area is negatively 
impacted by ongoing construction, operation and maintenance of SCVWD facilities, thus we 
welcome the proposal to mitigate for sediment removal activities. However, we are concerned 
that the DSEIR does not explain how the “500 square feet of high-quality gravel” threshold was 
established and are concerned that it will not address many, if not most, impacts to Chinook and 
steelhead habitat from sediment removal activities. 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


6 


'' Mitigation Measure Bio-8 presents a number of criteria to determine whether gravel 

impacted by SMP sediment removal activities is “high-quality” including the criterion 
“Minimum patch size greater than 1.1 m2 (Trush 1991).” Id., p. 3.3-124. However, the DSEIR 
does not state a scientific basis for finding that mitigation is necessary only when impacts to high 
quality habitat are in excess of 500 square-feet. The GCRCD questions why mitigation is 
required only after the 500 square-feet threshold, when Trush 1991 as referenced in the criteria 
appears to establish that impacts to otherwise high quality gravel over a patch size of 1.1 square- 
meter, or 11.8 square-feet, is biologically significant. The GCRCD requests that the basis for the 
500 square-feet mitigation threshold be assessed and explained, and/or the mitigation threshold 
for sediment removal activities be refined to conform to the biological patch size significance 
level established by Trush 1991. Lastly, the GCRCD requests that the impact assessment and 
mitigation strategy for sediment removal activities be expanded to include Chinook salmon in 
applicable stream reaches the throughout the project area. 

Cumulative Impacts. The GCRCD is concerned that the impacts assessment and 
M6 mitigation strategy do not adequately address cumulative impacts from sediment removal 
activities on Chinook and steelhead habitats. The 2012 SMP DSEIR does not present an 
assessment of the impacts of proposed sediment removal activities when added to sediment- 
related impacts from closely related past, present, and planned flood control and water supply 
activities. This assessment is necessary in order to identify the full scale of potential impacts, 
especially to Chinook and steelhead spawning and rearing habitats, and to identify necessary 
impact avoidance and mitigation strategies. 

As a specific example, assessment of cumulative impacts is necessary to be able to 
calculate the adequacy of the 500 square-foot mitigation trigger for gravel augmentation in 
mitigation measure Bio-8 discussed above. It is impossible to establish a mitigation threshold 
for impacts to high-quality steelhead habitat from individual sediment removal actions unless 
one also understands how gravel/salmonid habitat has been, is being, and likely will be impacted 
by the operation of water supply and flood control facilities. Past, current and future project 
impacts to gravel supply throughout the project area dictate the environmental significance of 
individual sediment removal actions, and thus must be included as a factor in determining 
appropriate impact avoidance and mitigation strategies. 

We request that an assessment of cumulative impacts from related past, present and 
future flood control and water supply activities be presented, and that impact and mitigation 
thresholds be designed to address both site-specific and cumulative impacts. 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


7 



Direct and cumulative impacts from bank stabilization activities 


Direct Impacts . The GCRCD is concerned that the DSEIR does not adequately assess 
potential impacts from bank stabilization activities on fish present in the project area, particularly 
salmonids. With respect to impacts to steelhead, the DSEIR describes impacts from bank 
stabilization activities as “difficult to quantify, because stabilization activities cannot be 
projected and because the magnitude of the impact of stabilization would depend on the type of 
repair method used and the location of the repair.” DSEIR, p. 3.3-106. Although the DSEIR 
estimates that approximately 1 mile of bank stabilization work per year will be done throughout 
the project area, the DSEIR concludes that “little long-term adverse impact to steelhead habitat is 
expected to occur as a result of 2012-2022 bank stabilization activities.” Id., p. 3.3-106. 

Although the GCRCD understands the difficulty in quantifying impacts from 
maintenance activities that cannot be specifically predicted, there does appear to be an approach 
available for cumulative assessment of potential impacts from bank stabilization activities. The 
DSEIR states that the SCVWD “has made a commitment that no more than half of the bank 
repairs will consist of impervious hardscape bank stabilization work (all watersheds combined) 
each year.” DSEIR, Appendix A: 2012 Stream Maintenance Program Manual, p. 6. Given the 
estimate of 1 mile of bank stabilization work based on 2002 to 2012 SMP program activities, this 
could result in up to Vi mile per year of hardscape being installed in the project area from 2012- 
2022. The DSEIR should use this as a conservative estimate of type and extent of impact to 
carry out a quantified analysis of proposed bank stabilization activities. 

As part of this assessment, mitigation implementation thresholds and rates should be 
evaluated. For example, Mitigation Measure BIO-9: Augmentation of Instream Complexity for 
Non-Tidal Stream Fish mitigates for the loss of high value habitat features from maintenance 
activities, including bank stabilization, on a 0.5:1 (mitigation:impact) basis (DSEIR, p.3.3-124- 
125). No analysis is presented regarding how this basis was developed. The DSEIR should 
contain an evaluation of whether the 0.5:1 (mitigation:impact) compensatory mitigation basis is 
sufficient given the scale of potential impacts (i.e. Vi mile of new hardscape per year, or 5 miles 
of new hardscape over the full project period). 

Cumulative Impacts . The above quantified impact assessment approach should be used 
to evaluate cumulative impacts of bank stabilization activities in conjunction with recent, 
ongoing and planned flood control and water supply actions. A significant amount of the stream 
banks in the project area have been armored or otherwise hardened for flood control and water 
supply purposes in recent years. The 2012 SMP project proposes to harden up to an additional 
five miles of stream bank between 2012 and 2022 (/ DSEIR, Appendix A, p. 6) which can 
reasonably be expected to have a significant impact on salmonid habitat, riparian cover, and 
ecosystem functions. The GCRCD requests that the 2012 SMP SEIR present an evaluation of 
proposed bank stabilization impacts in the context of these recent, ongoing, and expected stream 
bank hardening actions. 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


8 



Best Management Practices 


For the 2012 SMP, the SCVWD Board of Directors has established a Water Resources 
Stewardship Ends Policy stating, “[pjrogram elements are designed to avoid, minimize or 
mitigate potential impacts in balance with the need to conduct work in streams to carry out the 
District’s mission.” DSEIR, Ends Policies - Board of Directors Established, E-4 Water 
Resources Stewardship, Appendix A, p. 3. The GCRCD supports this policy and its expression in 
the development of BMPs for proposed project activities. However, additional BMPs are 
necessary to prioritize low- environmental- impact maintenance activities, and request that BMPs 
be reviewed and augmented as appropriate to ensure that the Water Resources Stewardship Ends 
Policy is achieved. 

In addition, the GCRCD has the following specific comments: 

Bank Stabilization BMPs . The DSEIR contains only three BMPs for bank stabilization: 

1) Bank Stabilization Design to Prevent Erosion Downstream 

2) Concrete Use Near Waterways 

3) Bank Stabilization Post-Construction Maintenance 

Id., p. 2-71. 

Given the potentially significant impact of bank stabilization activities (both on an 
individual activity and cumulative basis) the GCRCD requests that the BMP list be expanded to 
include specific practices for prioritization of soft bank stabilization approaches that minimize 
impacts to stream habitats. The DSEIR does contain introductory statements indicating that the 
SCVWD is in favor of such approaches: “SCVWD favors the use of soft bank stabilization 
approaches that use bio-technological approaches in place of methods that create more hardened 
banks.” DSEIR, p. 2-15. However, specific BMPs are necessary to insure that soft bank 
stabilization practices receive priority during the planning of individual maintenance activities 

Management of Animal Damage BMPs . The GCRCD requests that the BMP Avoid 
Redistribution of Rodenticides (DSEIR, ANI-1, p. 2-72) be revised to reflect the increased 
secondary toxicity of new anticoagulant rodenticides. New anticoagulant rodenticides developed 
in the past four to five years are significantly more toxic than previous generations and pose an 
increased risk of secondary, non-target species poisoning. Of particular concern is secondary 
mortality to owls, hawks and other wildlife that may feed on dead or dying rodents containing 
toxic levels of anticoagulants. The GCRCD requests that the ANI-1 BMP be reviewed and 
revised as appropriate to reflect the latest BMPs, including restrictions on use, frequency of 
carcass retrieval interval, and other methods of reducing and avoiding secondary mortality. 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


9 



Conclusion 


Please contact Nancy Bernardi ( gcrcd@pacbell.net) with any questions regarding these 
comments. 


Sincerely, 



Carson Cox 

Consultant to the Guadalupe 
Resource Conservation District 


GCRCD’s Comments re 2012 SMP DSEIR 
September 28, 2011 


10 









07/25/95 JL3: CO 

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FISH & WILDLIFE 

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. § 

/Mfa (J*fKg it / jj_ 



IN TQr 


United States Department of the Interior 


FISH AND WII.DLLFE SERVICE 
Ecological Services 
Sacramento field Office 
2800 Cottage Way, RoomE-1853 
Sacramerito, California 95825-1844 


In Reply Rafar To 
PN 21227S92 


Juno 23, 1995 


District Engineer 

Corps of Engineers, Saxy Francisco District 

Attention: Regulatory Functions Branch (Holly Haxtindaia) 

211 Hain Street 

San Francisco, California. 941G5-19G5 

m 

Subject: Buhlic Notice )Xo. 2122759? 4 Santa Clara Vallay latar Dislzrict, 

Ground Vanar Recharge Project Located on Tan Creaks in Santa Clara 
VaHay, Santa Clara Country > San Jose, California 

Dear Sir: ' . 

The' U.S. Fish and Wildlife Service (Sei-rics) has reviewed Public Notice 
21227592, dated. Hay 15, 1995. The proposed project if permitted by the 0.3. 
Ait/ Corps ox Engineers (Corps) would a<mu3.11y permit the cons truer ion and 
removal cf 39 gravel darts . and permit the i—jsta 11acion of a concrete foundation 
for a wooden fla-shboard dam. The proposed dans wauld be cons ittlic ted cu 10 
lenazats creeks entering the Santa Clara '/alley. The proposed permit wxruld be 
irrued for a 5-year period- The following commend; have been prepared under 
the authority, 2 nd in. accordance with provisions, of the Fish.’and Wildlife 
Coordination Act. 


Project Description. 

■ 

Tha Santa Clara Valley Water District (SCVWD) proposes to place and remove up 
tc 23,854 cubic yards (GY) of gravel annually for the construction of 39 
gravel dam s These dam s at a constructed on an annual basis ho impound water 

ter percolation into the gxoundvatai table of Santa Clara Vail ay. 

■ v 

. ' 

Gravel dams would be constructed on the following creeks: Coyote Creek (5 

dams), Stevens Creek (3 dams) , East little Llagas Greek (3 dams) , Teimant 

Creek. (2 dams), tfadtorte Channel (7 dams), Llagas Creek (3 dams), Los Gatos 

Creek (4 dams), Saratoga Creek (4 dams), Guadalupe Creek (4 dams) , and 

Guadalupe River (3 dams) . Dams constructed on Madrone Channel and lower 

Coyote Creek would be in place throughout the year unless removed to prevent 

possible flooding during high, water events. 

Service Hicigation Policy , 

p 

Because wetlands in California' are relatively scarce due to past and. current 
losses, the riparian, emergent wetlands, and iristxeam habitats within Coyote 
Creek, Stevens Creek, East Little Llaga:> Creek, Tennant Creek,, Llagas Creek, 
Los Gatos Creek, Saratoga Creek, Guadalupe Creek, and Guadalupe River, have 
been identified by tha Service, as Resoucee Category 2, These wetlands .and 
instrearn habitats are of high value co :nigratory birds, amphibians, and fish. 
The Service's mitigation goal for this issource category is no net loss of in- 
kind habitat value, which means that foe any habitat value losses due to the 
project, in-kind habitat/value would be sought. "In-kind replacement" means 
to provide or manage substitute resources to replace the habitat value of lost 
resources, where such substitute resources are physically and biologically the 


















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FISH & WILDLIFE 



jama or closely approximate to those Lust. 


1 


Caclarvd and in^tream habitats within Midrone Channel have bean identified as 
Resource Cace^ory 3. The Service's mit igat;ion goal for resource category 3 is 
no net loss ot habitat value while Eainuniting loss of in-kind Values, If 
losses are likely to occur, then the Service recommends ways to Immediately 
rectify them or reduce or eliminate th^m over time. 


In is the Regional policy of the Service to ansura no net loss of we tla nd 
acreage or 'Value, 'which ever is greata:;. To offset unavoidable resource 
losses from acceptable projects, the Service recommends char aDorooriara 
mitigati.cn be provided. Tile Council an Environmental Quality regulations for 
imp lamenting the National Environmental Policy Act (NI?A) define mitigation to 
include:. 1) avoiding the Impact; 2) minimizing die impact; 3) rectifying the 
inpact; 4} reducing or alirainating the impact ov^r time; arid 5) compensating 
for impacts. The Service suopotts and adapts this definition a£ mitigation 
and considers the specific elements to represent the desirable sequence of 
steps in. the mitigation process. 


f* 

ihcuial Hasourtac 



Historically, the Guadalupe River and uther yatsr.iays in the SaiYta Clara 
v"alley probably supported sail -sustaining runs of both salmon and steelhaad 
“cue,. However, modifications to th3se. k . vazervays through urban encroachment 
Ar.d flood control projects have resulted in the loss of riparian and in stream 
habitats. Furthermore, secondary impacts of cavsiopmant har resulted in 
changes to the annual hydrology. md vutar quality within. chase. drainages. 


Currar.tlv. smao.1 cut 
Frcut ^_er r i 

-i ■ ■ 1 " 


l-cuz an d 
Ciouar ?eru. 



saLnon and s tea lhead "1“ 

EaTeiliaa d S 


Coyote an c 
ava been. 


TToserved in tns (jiiacalupa Rivar (Instream Recharge Program Draft IrrnLronoaiitial 
Inpact Report, 1995) . Staelhead trout: migrate irxco freshwater coastal screams 
fron ocean, vatets co spawn, generally cluring January, February, and March each, 
year. After spawning, the adults return to the ocean. Young staelhead 
usually spend 2 years in the stream system before migrating to the ocean. The. 
bulk of the cLawistrrearn migration ox stf-elhaad smoLts typically occurs from 
March through May, aithough soma moro'sme rvc may cccur all year. 


*1 


£ 




Saloon have been reported to enter the Guadalupe River as early as August, but 
would be ei-Lpectad to bo praeent in the rivar from 'Tovamber through January. 
After 3paLw*r.ing adult chinook saloon die. The downstream migration of yearling 
china ok: salmon typically cakas place during the months of March, April, and 
May. 

Anadromous fish face numerous obstacles in fbair attempts to establish, and 
maintain s&lf-sujcaiding populations vithir. the project area. Upstream and 
downstream fish passage problems (e..g. lack of attractive flows, blocked fish 
ladders, arid drop structures without fish , sporadic base flo^s, high 

water temperatures , inuoadatian/dewatering of redds through dam construction, 
and insufficient spawning and rearing habitats are all factors which prevent 
the racovecy of aoudromous fish populations in the Santa Clara Valley. 

Several streams within the project araa also provide habitac for resident 
papulations of rainbow trout. Ocher fish species present within, the streams 
of Santa Clara Valley include, Sacramento blackfish, Sacramento squawfish, 
Sacraments sucker, channel catfish, threespine stickleback, bluegi.ll, 
largemouth bass- and- mosquitaEish * 
























uV/iS-r 95 


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FISH k WtLDLIFE 


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I" addicion Co providing habitat for fisheries resources, these scream 
corridors provide rare open space within che urban setting of San Jose, The 
diverse habita.cs along these corridors provide cover, water, food, and nesting 
araas for a large and diverse number of bird species. A draft EIR/EIS 
prepared for che Upper Guadalupe River Flood Control Project retorted a tonal 
of 121 species of birds within the Riv?r corridor. Numerous small mammals and 
he rpa to fauna. are known to usa the near-scream habitats as well. Species of 
nota include rad-legged frog 3 , western spadefaot toad, and western pond 
truxcle- 



S.d5ource Impacts 


■ice is particularly ccncsmed with the project's historic and current 
on che Guadalupe River, Stevens, and Coyote Creek:, a s these str eams 


The Sarvi 
Impacts 

and chair tributaries s.upport significant: runs of steelhead trout and chinook. 
salmon and resident populations of rainbow trout. Specific tonesrns and 
irapacts include: 1 ) sediiaaac release uKeto dams are rsmovsd or are washed out 
during linear storms 1 * Fine sediments and the high organic content of washed 
out ponded areas adversely impact spawning gravels and smother eggs and 
juvenile fish;"- 2 ) dewatering of the stream Jo wins cream oi- r the dam site during 
eons "true niem activities. Construction of dams may strand fish; 3 ) dams 
remain Leg in place year-round prevent upstream migration of ajiadromous fish 
unless adeqriace fish passage is provided; 4 ) ponds created behind dam sites 
create poor habitat for spa-vrnir.g and juvenile, salmon ids arid contribute to 
increased water tampercruras affecting cish papulations within che pool and 



to 

-y ror XLsn ana other 
wildlife' species; and s) increased sedisancacion within ponded areas 
contributes to changes in the stream geomorobology, further contributing to 
stream instability : increased erosion, increased sedimentation. sad highsr 
water tamperaturas. 


Sansisiva, Soaulas 

Iha project site. contains suitable babiiac for tha California, rad-leg^ed frog, 
-eacsm spdderoot Co ad, and western pond turtle- The California ■ rad 'Tagged 
frog was proposed endangered on February 2,. 1594 (59 FR. 4333), and the. western 
spade foot toad, and che western pond turtle are Category 2 candidate species 
(59 F?_ 53996) . Habitat destruction, alteration, and the introduction of ooti- 
native fish and amphibian 3pecies [such as largemouth bass (Nicropteras - 
s^-laaides) and bull frogs (ilana aacgsbeLinz) ) have been referenced as reasons 
far che decline of these specie. This pr-n j^-r contribute to th e. 

continued decline of these species within Santa Clara Valley. ^ 

c 3mm find a. tiotl S 


The Service recognizes th®. progress "ha: SCWD Lis made in developing a more 
environroentally sensitive project. SCVWD's recant addition of a fisheries 
biologist to their scoff should help District's ability to assess impacts 

to fisheries resources and develop effective measures to remediate ongoing 
impacts. However, ic remains tha Ser/i-ic's position that this project will 
result in continued substantial impacts to significant aquatic resources. 

Tha current practice of breaching the d:uii and construct ing a low flow chann el 
far a maximum of 50 feet above tha dara ice, rnay fesuLC in a wide brard^d 
chann el upscraara of the dam which cannot be by fish and may ■ 

contribute to elevated water temperatures. SCVWH should consider consulting 
with an expert in fluvial gaomorphology za develop sc true tural features which 
would restore or establish a low flow channel once a dam has been removed. 

























BSltJ 979 2123 


FISH & WILDLIFE 


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SCWD has identified potential impact;; due to flooding Co the riparian, 
habitats adjacent to the proposed dam Locations. Approximately 0.6 acre o£ 
riparian habitat and 1,400 linear feet: of shaded aquatic habitat would- 
potentially bo lost due co this projer-t. SCVX7D has proposed to mitigate for 
the 0.5 acre loss on cva mitigation sites by creating approximately 1.5 acraa 
of riparian habitat and 1.SQ4 linear tean of shaded aquatic habitat. 

Mitigation ratios developed for this project are based on c an opy tyoe^ with 
non-native, habitat replaced at a ratio or 1:1 and native canopy with riantve 
undarstory replaced at a ratio of 3:1. The Service recommends that all 
riparian communities bo replaced at: the higher 3:1 ratio, utilising native 
vegetation. To mlcigacB for the loss of shaded aquatic and scream habitats 
due to ponding the Service recoramerjds the adoption of the special conditions 
identified below« 

As gravel dams only contribute approx:* nacaly 15 percent (22,000 AF/yr) o£ 
SGWD's total recharge capabilities, tha District should continue to explore 
alternatives tc the summer dam program. Specifically, SCVTO-^hould make ' 
further use of off-stream recharge ponds and Injeocion wells. Both o£ these 
> methods axa proven technologies and are currently being, used by ch<a District. 

' ' 

Year-round standing water has the potential to severely irrpact California, red- 
lagged frog populations by allowing predator populations co increase over-time 
in tts habitat and by allowing bullfrogs greater dispersal ability into 
refugia for the red-legged frog. ' 'Jacee. rslsa^es from impounded areas have t h e 
potential to flush California rad-lagged frog ej|gs and larvae into unsuitable 
habitat and may cause a same-yeax reproductive fcaiLuxa for that segment: of the 
population- Due Co che presence of a proposed species we recom m e n d that: the' 
Corps conference an the effaces of the proposed action cm cha California rad- 
lagged frog. Should the California red-legged frog, become listed during the 
neioc five years, t'na Carps would be required cc initiate consultation on the 
species pursuanc to tha EndajQ^ered Specie Act of 1973, as amended. 


Conclusions 

In our previous responses co the Corps an this project, the Service has 
recommended permit denial. Tha Service continues to object to the issuance, of 
chis pernio. Should the Corps continue co permit this activity, the following 
special conditions should be included ls part cf this project. 

1. Summer dam construction will not begin until after Mhv■ 15 of each 
year. All dams will be removed prior to October L o£ each year. 

i 

2. Prior CO che issuance o£ -any ifu.cux^ permit for this activity, JSCVWB 

sh all a charier management Dlan and »>1 

ba rriers to anadromeus fish a~'^rataon along toe kuibaLiipa River, 
"Coyata Creek, and Stevens CrsukI This measure is designed to provide 
direct replacement'of lost habitat due to the historic and continuing 
activities of SGVHD . 

3. CThen. Fish passage problems arc resolved for a particular reach. o£ 
stream or river, the permittee- will install fish passage* structures 
at all summer and permanent dnms along chat reach within 6 months. 

Any fish passage structure constructed will be acceptable to the 
Service, the National Marine Fisheries Service, and California 
Department of Fish and Game. 

4. .\s summer dams are removed each year, a low flow channel will be 
constructed to connect the low flow channels above and belcr-/ che dam 
sits. 

■ 

All summer dams cons true, ced on Stevens Creefe will have fish passage 

structures acceotable co the Service, the National Karine Fisheries 

<■ * _ 

Service, and California Dep^rt/nenc of Fish and Gama. 


5 . 


















oxa 37y ZL'-O 


FISH & WILDLIFE 


®008/008 


( 




5 


If you have any questions about; these coinmenrs, please contact Mark 

LiUHLeflaid (Wetlands Branch) at (916) 979-2113, or Alison Willy (Endangered 

Species) at (916) 979-2752. 


Sincerely yours. 



Field Supervisor 
Dapartment; of the interior 
Coordinator 


cc: Reg. Dir- (AFWE) , FWS, Porrltmd* OR 

Dir., CDFG, Sacramento,. CA 
Reg. Mgr., CDFG, Reg. Ill, Yountvillc * 
ERA, San Francisco 
NMFS , Sane a Rasa 
ao'olicant 


Rafaraaces 

Draft Environmental -Impact Report' Instream Racharra Fro^rsit . (March 1995) , 
Santa Glara Valiev Water District. Prepared by FLT. Harv&v and Associates. and 
David, J. 5owars end i35aciat23 : Inc, 











CALXU'. uurj..* 


■ i ' 


, i 

■ i ■* 

THE RESOURCES AGENCY OF CALIFORNIA 

department of fish and 'game 

WATER PROJECTS BRANCH 

• c 

dl o- 

CL. I 

An Historical Review of the R4X534 


FiSH AND WILDLIFE RESOURCES 

OF THE 

SAN FRANCISCO BAY AREA 


By 

JOHN E. SKINNER 


WATER PROJECTS BRANCH REPORT No. 1 

EDMUND G. BROWN 
Governor 


WILLIAM E. WARNE, Administrator 
The Resources Agency 


June, 1962 


WALTER T. SHANNON. Director 
Department of Fish and Gama 


I 


■ > 


AUe 16 1963 









48 


Department of Fish and Game 


in 

a 


o 

CL 


o 


in 

z: 

o 


20 


ia 


16 


14 


12 


10 


8 


6 


4 


2 



COMPARATIVE LANDINGS OF SALMON 
FOR THE STATE AND SAN FRANCISCO 
SAY AREA 1916 - 1958 


FIG. 24 

STIPPLED - STATE 


BLACK-8AY AREA 


was made in 1917. The average was between one and 
two million pounds a year, bur rhe fishery could have 
sustained perhaps cwo to three times that much. Legis¬ 
lative action banning the use of gill nets in what was 
the principal shad fishing area all but eliminated the 
commercial fisheryafcer 1957. 

Striped Bass. Striped Bass were introduced into 
Carquincz Strait in 1879 from New Jersey. By 1890 
a few were being taken commercially and the species 
was highly favored in the San Francisco market. They 
commanded a good price and supported a fair fishery 
until legislative action in 1935 prohibited the commer¬ 
cial take. Like shad, almost all were taken and landed 
in San Francisco, Pittsburg and other ports in the 
Bay Area, 

Berween 191 <5 and 1955 the landings averaged 600 to 
700 thousand pounds a year and twice exceeded a 


million pounds. The peak commercial catch, reported 
at 1,776,000 pounds, occurred in 1908. 

Striped bass have been popular with sportsmen 
since their introduction. The total take by anglers 
each year is in the neighborhood of 600,000 to 1 , 200 ,- 
000 fish, or two to four million pounds. 

he combined landings of rhese three species at San 
Francisco have varied considerably with salmon, of 
course, being the most influential. Since 1916 the least 
amount recorded was 1,3 33,641 pounds in 1941, and 
the highest better than 12 million pounds in 1918 . 
The average is just under 6 million pounds a year. 

The annual state-wide landings have fluctuated with 
the Bay Area catch, the low of just under 4 million 
pounds coming in 1941, and the high of over 17 mil¬ 
lion occurring in 1917, The state-wide average is 
rween seven and nine million pounds. The percentage 














































































































































































































































































































































































































ANADROMOUS FISHERIES 


INTRODUCTION 

The anadromous fishes of the Bay Area include such 
favored species as king and silver salmon, steelhead 
trout, sturgeon, striped bass and American shad. With 
the exception of shad and striped bass, all are native 
species. Several other anadromous species are found in 
the Bay (Appendix C-l), although they are rare or of 
minor importance co.the sport or commercial fisheries. 

The general distribution of steelhead trout (Salmo 
gairdnerii ), commonly called steelhead, is in the coastal 
streams of the Pacific Coast of North America, from 
the United States-Mexico boundary or possibly even 
Baja California northward to and including Alaska, 
according to Shapovalov and Taft (1954). The general 
distribution of stiver salmon (Oncorhymchus kimteh) 
is from some of the streams entering Monterey Bay, 
California, to the Amur River in Asia, according to 
Shapovalov and Taft. In California both species be¬ 
come increasingly common from south to north. 

Sreelhead are common to both the Sacramento and 
Klamath River systems. Silver salmon are native to the 
Klamath River but not the Sacramento River. 

Silver salmon enter the commercial catch through 
the offshore troll fleet, but in the San Francisco Area 
are a minor constituent of the salmon fishery. 

The king or chinook salmon (Oncorhynchus tsha- 
-'i wytscha) fishery in California has always been cen¬ 
tered in the Bay Area. Originally most of the State's 
catch was made inside the Golden Gate, principally 
by the gill net fishery. A/ter 1900, the ocean troll 
catch increased rapidly and by 1915 surpassed the 
river gill net catch. 

Within the Bay, the principal method of taking king 
salmon was, from the earliest days, by means of gill or 
trammel nets. 

The fishing area was modified greatly by legis¬ 
lative action, and finally in 1957, was closed altogether 

most types of commercial fishing. Since then, the 
entire commercial salmon catch has come from the 
ocean. 

The striped bass (Roccvs saxatiiis) fishery is almost 
exclusively confined to the Bay Area. Prior to the re¬ 
moval of this fish from the roster of commercial 
species in 193 5, the same men, using essentially the 
Slme boats and gear employed in the salmon fishery, 
jiso fished for striped bass. The fishing area and legis¬ 
lative restrictions of this fishery closely parallel those 
°f the salmon fishery. 

As in the case of the striped bass, almost 100 percent 
J the shad {Alosa sapidissirna) catch was made in the 
Area, The fishery was pretty much restricted to 


the river between Carquinez Strait and Rio Vista, until 
1^51 when the upstream limit for commercial fishing 
was moved down-river to Stake Point near Pittsburg. 
The same fleet and essentially the same methods as de¬ 
scribed for salmon and striped bass was employed for 
shad. Legislation in this fishery* closely paralleled chat 
for the striped bass and salmon fisheries. 

KING SALMON 

The Commercial Fishery 

Early History. Indians along the river apparently 
were actively engaged in fishing for king salmon when 
Juan Batiste de Anza first sighted Carquinez Strait in 
177<5. The Indians are said to have used nets and fished 
for them from rafts. The interior Indians-were also 
known to rely heavily upon them for food. Crude 
weirs, spears and frequently clubs or bare hands were 
used to capture them. 

Later on (1850), Italian immigrants began to fish 
for them in the Sacramento and San Joaquin Rivers 
and San Pablo Bay. During the gold rush and the rail¬ 
road building era they were an important item of food 
wherever they were found. Eventually commercial 
salmon fishing extended for a considerable distance 
up the Sacramento River and into many of its tribu¬ 
taries. 

Early accounts by Livingston Stone, the famous fish 
culrurist of the U. S. Fish Commission, testify to the 
great abundance of king salmon in the upper reaches 
of the Sacramento in the early years. For many years 
he operated Baird Hatchery on the McCloud River, 
taking eggs for the purpose of introducing Icing salmon 
elsewhere in the United Scares. 

During the 1850's salmon fishing and processing be¬ 
came a lucrative business. Quick to grasp the great 
potential of the salmon resource three men, George W. 
and William Hume and A. S. Hapgood initiated one 
of the mosr profitable enterprises on the West Coast. 
William Hume had arrived in Sacramento in 1850 
from the East Coast and talked his brother, George, 
into coming West in 1855. On a return trip to the East 
Coast in 1863 George induced his boyhood friend and 
schoolmate, A. S. Hapgood, a tinner, to come to 
Sacramento. 

Hapgood arrived in Sacramento on March 24 % 1864 
and he and the Hume brothers immediately set abour 
their task. By late summer or early fall a crude but 
nonetheless functional canning operation under the 
name of Hapgood, Hume and Company was estab¬ 
lished. This was the first cannery on rhe West Coast 
and the first salmon cannery in the world. Their can- 


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58 


Department of 


nery was built on a floating scow in the town of 
Washington (Broderick) on the Sacramento River 
across from the cicy of Sacramento. 

The first season’s operation was not entirely suc¬ 
cessful since only half of the 4,000 cases canned were 
merchantable. Each case contained four dozen one- 
pound cans. The young industry also received a tem¬ 
porary set-back when skeptical Americans would have 
nothing to do with the produce After considerable 
searching they found a ready market for canned 
salmon in Australia and later South America. Poor 
salmon runs in 1864, 1865 and 1866 forced them to 
look elsewhere to enlarge their business. As a result 
they established the first cannery on the Columbia 
River near Eagle Cliff in 1866. But by 1881 there 
were 21 canneries in California, most of them in the 
Bay Area. 

Our first quantitive records concerning saLmon 
catches in those early years are largely from cannery 
records. 

Shortly after the gold rush many rivers became 
badly silted, which all but destroyed their use for 
salmon. Railroad construction crews did similar dam¬ 
age by dynamiting along the Sacramento River and 
its important spawning tributaries. Often, streams 
were made impassable to salmon as a result of the 
rocks and debris permirted co enter them. Lumbering 
was also responsible for silting and blocking many of 
the smaller spawning tributaries. 

The salmon runs of the Sacramento and San Joa¬ 
quin river system have fluctuated a great deal since 
records were first kept. Peak runs have occurred at 
intervals of 8 co 30 years followed by poor catches 
midway berween the peaks. 

Water development projects have made serious in¬ 
roads on the salmon populations of California, par¬ 
ticularly in the Central Valley. Dams were built on 
streams tributary to the San Joaquin River prior to 
1900. In the last 25 years a large number of public and 
private projects and the gigantic Central VaJley Proj¬ 
ect have been built on the major rivers in the Central 
Valley. These projects have unquestionably had a 
great influence on king salmon and other anadromous 
species by preventing access to spawning areas above 
the dams, and by reducing the flow of water below 
the dams or changing the general regime of the 
streams. 

In the early years silver salmon and stcelhead runs, 
also, were adversely affected by saw mills, flour mills 
and water supply reservoirs on the coastal streams. 

It is beyond the scope of this report to provide but 
a small portion of the available information on the 
king salmon of the Sacramemo-San Joaquin system. 
Several excellent publications are Listed in the refer¬ 
ences which describe the life history and fishery for 
this species. 

Although the fishery for king salmon is centered in 
the Bay Area, few kings actually spawn in any of 


FrsH and Game 


the local streams. They generally enter the larger riWV 
ers along the coast north of San Francisco. By f^ r ’ 
greatest proportion however, has always passed' 
through the Golden Gate co ascend the Sacrament ? 
and San Joaquin rivers on the way to ancestral spa v^J 
mg grounds in these rivers and their tributaries. 



There were three principal methods employed ^ L 10 . 
commercially fishing saLmon before 1870. The most" 
profitable, drift gill netting, was introduced short! m 
after 1850 by the Italians. Fyke net Ashing was ertwi 
ployed also at this rime and according to Jordan andli 
Gilbert ( 1887) in 1852'and 1853, fishermen co 
monly caught 700 to 800 pounds a day in their fyke^ 
nets at Rio Vista. Sweep seines were used but no menT 
rion is made of the success encountered. vf 

he gold rush and inflationary conditions led to a vi i 
rapid expansion of the fishery. Jordan states that be*;., 
tween 1850 and i860 salmon frequently brought a do)-v 
lar a pound and that five dollars was a small price for r 
a whole salmon. Complete data are lacking on the 
amount of salmon caught and canned before 1870 but 
during 1864 and 1865 two thousand cases (48 one- ’ 
pound cans each) were canned each year. Lirtle else 
about the fishery is available until 1872. 


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1870 to 1915. By 1870 the king salmon runs began 
to decline and the newly formed ( 1870) State Board 
of Fish Commissioners expressed concern for the fish¬ 
ery. Hydraulic gold mining activities had all but de : 
stroyed the American, Feather, and Yuba Rivers, ac¬ 
cording to their reports. Even so, the catch about 
1874-1875 was 4 to 5 million pounds, worth 8500,000 
a year. 

The U. S- Fish Commission sent Mr, Livingston 
Stone to California in 1872 to procure salmon eggs 
for the East Coast. He arrived in August of that year 
and immediately sec up operations on the McCloud 
River. Thus began salmon fish cultural operations in 
California. It is from Stone’s annual reports that much 
of our early knowledge of Sacramento king salmon 
was obtained. 


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Because of the decline in the fishery the California 
Commission contracted with the U. S. Commission 
to supply eggs for propagation purposes to stock 
the Sacramento River. Shortly thereafter, the commer¬ 
cial salmon catch began to increase and by 1880 had 
reached almost 11 million pounds. At the time, the in¬ 
crease was attributed chiefly to fish cultural operations 
by the early pioneers, thus lending great impetus to 
this phase of fishery management. Since 1872 many 
millions of fry have been released into the river and 
this activity still continues today. Shebley ( 1922) 
summarized fish distribution activities in California 
through 1921. His article also gives an account of the 
history of fish cultural operations in this State. 

Jordan and Gilbert (1887) provide an idea of the 
fishery of their time in the following paragraph: 

“Since 1866 salmon fishing has fallen off very fast 
at Collinsville and Blade Diamond (Pittsburgh In the 


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65 


Fish and Wildlife Resources, San Francisco Bay Area 


cfifi items in Table 12 to be the principal constituents 
in the diet of king salmon. 


TABLE 1 2 

FOOD OF ADULT KING SALMON- 


hem 

^Jorrhem Anchovy 

Rockfishes —<_ 

Euphausiids J-- 

Pacific herring'- 

Squid-- 

Or her Fishes -- 

Crab Megilops ..__ 


Percentage of 
Total Volunre 

_ 29.1 

_ 22.5 

_ 14.9 

_ 12J 

— 9.3 

_ 73 

_ 4.0 


From August to November (season closed to fishing 
November 15 to ebruary 11) anchovies were the 
major item. I hey probably continue to be the most 
important item until herring arrive in November or 
December. Herring are the principal item from at 
least February to April when euphausiids, squid and 
crab megalops predominate. Rockfishes become im¬ 
portant in May and are the most frequent item in June 
and July when anchovies again begin to occur. 

Within San Francisco Bay northern anchovies were 
the most common item observed; however, as a rule 
salmon taken in the Bay axe maturing and Merkel 
found that most salmon had ceased feeding. 

Ocean Life. After the juvenile salmon enter the 
ocean, their movements axe not well known, but 
marked Sacramento River fish have been taken south 
of Monterey and north to British Columbia. One 
marking experiment, for example, indicated a majority 
oi those released in the Sacramento River were later 
caught off Washington and Oregon. 

King salmon are voracious feeders and grow exceed¬ 
ingly fast while in the ocean. By the time they mature 
three to seven years later, they may weigh in excess 
of 70 pounds. The average weight upon returning is 
£ 0 pounds, although 50 pound fish are not uncommon. 
Kings are the largest of all salmon, with indviduals 
of over 100 pounds having been caught. 

Most king salmon mature at three or four years: 
mveyer, grilse, that is, fish which mature after one 
g owing season in the ocean, axe not uncommon. After 
■Tiacuring in the ocean salmon return to their native 
streams to spawn and die. The amount of straying is 

remarkably low, 

Sources of Mortality. While in the ocean king sal- 

mon themselves axe prey for ocher species of fish. 

ihey are also subjected to an intense troll fishery by 

both sport and commercial fishermen. Upon entering ■ 

Sacramenco-San Joaquin System, they formerly 

subjected to the highly efficient gill net fishery . 

^ .Carquinez Strait and Suisun Bay. Legislation eh- 

acted in the spring of 1957 and effective September 

^ of chat yeax. eliminated the latter source of exploi¬ 
tation. 


The young fish before entering the ocean must also 
cope with numerous hazards. In the first place the 
alevins and fry are prey for many other species of fish. 
Secondly, they are vulnerable to a great many water 
diversions all along the Sacramento and San Joaquin 
Rivers and the Bay until they finally pass out of the 
Golden Gate. 

Pollution is still another hazard and adults as well 
as the young are susceptible. Warren (1949) reported 
the kill of a considerable number of adult salmon from 
sewage po lution while the fish were on their spawn- 
ing migration in the I uolumne and San Joaquin rivers. 

i he young may find themselves in a particularly 
precarious postion with respect to pollution in the 
Bay Area because of the tidal prism; they may be 
flushed back and forth tbxough several tidal cycles 
before escaping from contaminated areas. 


SILVER SALMON AND STEELHEAD TROUT 

In the Bay Area both silver salmon and sceelhead 
are important primarily for their contribution to the 
sport fishery. Sceelhead are, or were, found in a num¬ 
ber of tributaries to San Francisco Bay including the 
Sacramento River system, and In the principal tribu¬ 
taries of I omales Bay as well as most coastal streams. 
With a few exceptions silver salmon were restricted to 
coastal streams in the Bay Area. They are nor native 
to the Sacramento River but were introduced there 
in 1956. 

Since 1927 it has not been permissible to take steel- 
head commercially. Silver salmon have formed a very 
minor part of the ocean salmon catch in the Bay Area 
and were unknown to the Sacramenco-San Joaquin 
gill ner fishery until 1957 when returns of che 1956 
experimental stocking by the California Department 
of Fish and Game contributed substantially to an 
otherwise poor salmon catch. 

When Captain Wakeman, under hire of the State 
Board of Fish Commissioners, in 1870 surveyed che 
fisheries of the Bay Area, his survey included the 
coastal srtreams from Spanishtown on Pibrcitos Creek 
to Pescadero. He described the wretched conditions 
of the streams due to the logging, saw mills and flour 
mills located on them. The inference from his descrip¬ 
tion is that the streams had once been very productive 
of silver salmon and sceelhead trout but at the time of 
his survey were greatly degraded. The fish taken were 
sold locally rather than being shipped to San From 
cisco. 

Wakeman points out that trout and salmon from 
these streams brought 75 cents per pound in 1870. 
He claims that a wagon load of these “beautiful 1 * fish 
weighing 2 to 30 pounds each were taken daily from 
Pescadero Creek between October and March. Ap¬ 
parently San Gregorio Creek also produced fish in 
commercial quantities at that time. 


















66 


Department of Fish and Game 


SILVER SALMON 

Silver Salmon Spori Fishery 

Silver salmon ascend mosc coastal screams and sup¬ 
port a seasonal fishery In the winter. They axe taken 
by anglers both in che streams and in the lagoons at 
the stream mouths. Pescadero and Papermill Creeks 
are probably the most notable streams in the area. 
Actual data on the number of anglers who engage 
in silver salmon fishing, or on their catch, are not 
available. 

he spore troll fishery in the ocean takes a fair 
number of silvers, but che proportion is quite small 
as compared co king salmon. The year 1957 was an 
exception in char king salmon catches were poor 
while silver salmon were much more abundant than 
usual. 

Veteran anglers feel the silver is a gamer fish than 
the king when taken on rod and reeL 

Introduction of Silver Salmon into the Sacramento 
River System. Preliminary results of che experi¬ 
mental introduction of silver salmon into the Sacra¬ 
mento Valley have been impressive. The initial stock¬ 
ing took place in A4arch of 1956 when 43,025 yearling 
silvers were released in Mill Creek, Tehama Counuy, 
by the California Department of Fish and Game. The 
time and location of these and subsequent releases are 
show in Table 13: 


TABLE 13 

TIME AND LOCATION OF SILVER SALMON 
INTRODUCTIONS TO SACRAMENTO 
RIVER SYSTEM, 1 956A 958 


Date 

Location 

dumber of 
Finger ling? 

March 19, 21, 22, 1956 

Mill Creek at 



Child's Meadow 

24,150 (coral) 

March 20, 1956 

Mill Creek ac 



Ward Dam 

6,300 

March 23, 1956 

Mill Creek ac 



Clough Dam 

12,757 

February 14-19, 1957 

Mil! Creek ac 



Child's Meadow 

28,340 (total) 

March 20-21, 1957 

Mill Creek ac 



Clough Dam 

12,575 

April 13-29, 1958 

Mill Creek ac 



Ward Dam 

18,003 (coral) 

April 15, 1958 

Mill Creek ar 

- 


Child's Meadow 

10,797 

December IS, 17, 1958 1 

Sacramento River 



at Ball’s Ferry 

21,418 (total) 

December 16, 1958 1 

Chico Creek 



Ponderosa Way 

4,624 

December 17, 1958 1 

Deer Creek ac 



Highway 99E 

9,489 

1 Thcv: vrei$ Gth raised at 

Coleman National Fish Ha 

ichery of Lbe U.S. 


Fisb QDd Wildlife Service from egg s lukeD from returning aduh 
silver film on of the 1956 and 1957 plants. 


The first recorded adult fish to be taken by angling' 
was in August L956. In 1957 silvers were caught by 
commercial fishermen in the Delta. The first naturally 
spawned silvers were observed by Departmental per¬ 
sonnel in Mill Creek in che winter and spring of 1958 


when 49 fish averaging one co four inches were taken 
in traps. 

In December of 1956 three of the fish stocked the 
previous March strayed into the American River o t 
their return from the ocean and were taken ac Nimbus 

atchery. Silver salmon have since appeared in the 
Feather and Mokelumne rivers also. 

1 he following gives an indication of che early suc¬ 
cess of the introduction (Data from Quarterly Reports 
of F7R Sacramento-San Joaquin Salmon and Steclhead 
Study). 

For the 1957-58 season (July 1, 1957-June 30, 1958) 
fishery personnel actually counted 1,523 returning 
adult silver salmon in the upper Sacramento River 
Through tagging operations it was estimated that the 
total run consisted of approximately 4,180 two-year- 
old fish of the 1957 plants and 2,240 three-year-old 
fish from che original 1956 release. The estimated 
catch by anglers, extended on a basis of 41 tag re¬ 
rums, was 312 fish. 

During che 1958-59 season the run was estimated at 
5,600 three-year-old fish and 6,000 cwo-year-old fish 

Table 14 gives the numbers of each species passing 
the Clough Dam counting station on Mill Creek, 
Tehama County, during the period September 28- 
October 31, 1957. 

table u 

SALMON AND STEELHEAD PASSING THE CLOUGH 

DAM COUNTING STATION, MILL CREEK, TEHAMA 
COUNTY (SEPTEMBER 28-OCTOBER 31, 1957) 


Tii 

strear 

the b 
Nove 

Th 

have 
the h 
sa ImO 
in th* 
the e: 

Th 

dune. 
of th 
will ; 
but c 

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and t 
descri 
and □ 
of a 
insure 
male 
larger 
males 
come* 
posits 
fcrrili: 
proce; 
eggs 


Species 

Number 

Percentage < 

King Salmon 

465 

16.6 

Silver Salmon 

1,506 

53.7 

Steelhead Trout 

833 

29.7 


2,804 

100.0 


.Silver Salmon Life History Notes 

In the Bay Area, silver salmon occur in mosc of tb* 
creelcs directly tributary to the Pacific Ocean and ai 
least a few screams tributary to San Francisco 
Perhaps che most notable streams in this region io 
which silver salmon now occur are Pescadero, San 
Gregorio, Gazos, and Papermill creeks. 

Silver salmon have been the subject of a number 
of investigations in California, bur have been over¬ 
looked to some extent in favor of the larger and more 
valuable king salmon. 


f 


more, 
perce i 
prope 

Th i 
result 
rigors 

Era 

38 da; 
days a 
from 
the in 

As i 
effect 
silt is 

of sil- 
gravel 
to 85 


Shapovalov and Taft (1954) made an exhaustive 
suudy of the life history of this species, and their work 
includes the findings of other investigators as well 
Most of the ensuing irtformarion on this species ^ 
based upon their work. Their scudies were conduct^ 
from 1932 to 1942, principally on Waddell - Creek* 
Santa Cruz County. This is a typical coastal srreaflJ 
just south of Pescadero, except that ac the rime of the 
srudy it had been relatively untouched by logging of 
other human activities for many years. It was al^ 
closed to fishing. ' I 


Stn 
able, i 

the so 

feed z 
move 

A r 
salrnoi 
This, 
chief). 
tOUch; 














I 


Department of Fish and Game 


88 

Lehman (}95 3 ) studied the fecundity of this species 
and found that egg production is correlated with age, 
length and weight. He found thac production of Hud- 
son River shad varied from 116,000 to 4,680,000 eggs 
per fish. This is much greater than has been previously 
reported by other investigators. 

Embryology. The incubation rate has been estab¬ 
lished for this species under experimental conditions 
and found to vary from 6 days at 57° F. to 3 days 
at 74° F. Under natural conditions in California rivers, 
hatching probably occurs in 4 ro 6 days. 

Stream Life. The young fish gradually move 
downstream after hatching, but may remain in cer¬ 
tain freshwater localities for extended periods of time. 
They are abundant in the lower Sacramento and San 
Joaquin Rivers (near Rio Vista and Antioch, respec¬ 
tively) during the Late summer and fall, and are preva¬ 
lent throughout the entire Delta as late as the month 
of October. Most of the young fish move into brack¬ 
ish water the fall and winter following hatching, but 
a few appear to remain until the following year. 

Bi-weekly sdne samples taken over a period of a 
year near Antioch on the San Joaquin River indicate 
the young reach an average length of about 3 to 4 
inches by October. Seine samples throughout the 
Delta in two consecutive years (1956 and 1957) indi¬ 
cate some variation in the average length of fish at 
different locations but most were between the values 
given. Mansuerti and Kolb state that they may attain 
a length of 6 or 7 inches in 7 months under favorable 
conditions on the East Coast. 

Their food habits on our coast have not been studied 
In detail although several shad examined at the Cali¬ 
fornia State Fisheries Laboratory contained anchovies 
and euphausiids. he diet is probably similar to that 
of Atlantic Coast shad in consisting principally of 
small shrimp, copepods and aquatic worms. Insects 
may be important to the juvenile fish in freshwater. 

Ocean Life. Virtually nothing is known about shad 
once they reach San Pablo Bay, A few fish have been 
taken incidentally by commercial fishermen near Mon¬ 
terey, but they do not appear regularly in any type 
of gear or at any location. Well defined north-south 
ocean migrations occur on the Atlantic Coast but such 
has not been observed here. 

By the time they reruxn to spawn, the males aver¬ 
age three pounds and the females almost four pounds. 
Six to eight pound fish are quite rare. 

Sources of Mortality. Young fish are subjected to 
the same hazards as downstream migrant salmon "and 
stcelhead in the Sacramento system. These hazards in¬ 
clude diversions, predators, irrigation pumps and pol¬ 
lution. The larvae particularly, may suffer exceptional 
morality since they are pelagic and vulnerable to the 
many plankton feeding fishes in these river systems. 

Shad are most abundant in the Bay Area during lace 
fall and winter. The young probably prefer the shore¬ 


line as they move downstream and hence would be 
vulnerable to diversions and polluted areas along the 
river banks. 

The Tracy Pumping Plant and the Pacific Gas and 
Electric Company's Contra Costa Steam Plant have 
been particularly troublesome diversions in the past. 

Shad are an extremely delicate fish and the slightest 
physical injury usually results in death. The effects 
ot various pollutants on shad are not known, but it 
may be inferred that this species is more susceptible 
to toxic or deleterious substances than many other 
species. 


MISCELLANEOUS ANADROMOUS FISHES 

In addition to the anadromous species already dis¬ 
cussed there are a few others which either pass 
through the Bay Axea to spawn in the freshwater 
tributaries or spend most of their life in the Bay except 
to spawn in freshwater. 

The Pacific lamprey (Entospbenus tridentatus) can 
be observed each spring, mostly during the period 
April to June, as they attempt to pass' over the dams 
of Central Valley streams. They spawn in the smaller 
tributaries of the rivers they ascend. Like salmon, the 
adults die after spawning. 

Just what role this parasite plays in the overall pic¬ 
ture of our fishery resources has not been determined. 
It is not caught commercially and is generally dis¬ 
dained by all who come in contact with it. Lampreys 
are eaten by several species of fish, but so far as is 
known they are not an important forage species. It 
might be mentioned here, however, that lampreys are 
used as bait in the commercial sturgeon fishery on 
the Columbia River. 

These parasites attach themselves to the host fish 
by means of their mouth, which is so modified as 
to form a very effective suction disk. Once attached 
they rasp through the skin and flesh of the victim 
and suck out the body fluids. 

Lampreys are used as food to some extent, par¬ 
ticularly by the Indians of several coastal streams. 

Freshwater smelt (Hypomesus olidm) and Sacra¬ 
mento smelt {Spirinchus thaieiebthys) are common in 
the Delta from late winter to early summer. They 
spawn in many of the same areas as striped, bass and 
shad but do not ascend the rivers much above tide¬ 
water. Theix most important contribution is as forage 
for food and game fishes, particularly striped bass. 

hey seldom exceed 5 inches in length and are ex¬ 
tremely delicate. They travel in large schools which 
are followed and preyed upon by larger carnivorous 
fish. 

Other anadromous fish which are rare or occasion¬ 
ally stray into the Bay are the pink chum and red 
salmon. 







89 


Fish and Wildlife Resources, San Francisco Bay Ajlea 


COMMENTS ON THE FUTURE OF THE 
ANADROMOUS FISHES 

The continued maintenance of our anadromous fish 
resources is one of che gravest problems facing fishery 
managers. Dams and ocher barriers reduce stream 
flop's* destroy and block spawning grounds and pre¬ 
vent the upstream passage of fish. They may" also 
hinder che downstream migrants even where successful 
methods have been employed to pass the adults up- 
scream over the dam. Industrial and agricultural diver¬ 
sions are responsible for che loss of enormous numbers 
of che small downstream migrants. Poor logging and 
mining practices destroy spawning areas or form bar¬ 
riers to the ascent of fish. In some instances poor log¬ 
ging practices have destroyed entire small watersheds 
through erosion and destruction of che stream bottoms 
and che upsetting of rhe temperature regimes to such 
an extent as to cause severe reductions in fish popula¬ 
tions and fish food organisms. 

fn California, generally, dams appear to be the mosc 
serious factor in diminishing salmon runs. Untold miles 
of spawning tributaries have either been inundated or 
cue off by impassable barriers. Shasta Dam alone on che 
Sacramento River eliminated approximately 50 percent 
of che available spawning area of this river system. For¬ 
tunately, the flow and temperature regime below the 
dam is favorable co salmon. Prianc dam eliminated 
about 36 percent of che spawning area of the Upper 
San Joaquin River. Folsom Dam on che American 
River also eliminated valuable spawning areas. The 
latter Joss was at least partially compensated for by 
Ximbus Hatchery with its capacity of 30 million eggs 
annually (Equivalent co d,000 female spawners). 
Similarly, Coleman Fisheries Station on Battle Creek 
near Redding has made up in pare for the loss of 
spawning areas above Shasta Dam. No such provision 
was made at Frianr Dam. 

Ar the present rime the principal spawning areas on 
the Feather River are still accessible. A ladder on 
Sucter-Butte Dam enables fish to negotiate this obstruc- 
tton. The gigantic dam being constructed by che State 
above Oroville, however, will eliminate more spawning 
area and result in controlled flows below the dam. State 
agencies are cooperating to bring' abouc the greatest 
protection of the river’s salmon resource. 

As rhe California Water Plan progresses, even 
greater curtailments in spawning areas are inevitable. 
On che Sacramento River che proposed Iron Canyon 

pm, if built, will cut off an area used by 94 percenr 
°f the present salmon runs in this river system. This 
estimate is based on annual counts of salmon spawners 
(Hallock 1957). 

Perhaps the greatest potential blow to all anadro- 
m ° u s species, and a number of orher species as well, 
are he salt water barriers being considered for the Bay 
A ea. A number of plans for such barriers have been 

Sgcsted, all of which would have major repercussions 


on che anadromous fisheries resources of the Sacra- 
mento-San Joaquin River systems. 

At the present rime the only one under serious con¬ 
sideration is the modified Biemond Plan which, in¬ 
cidentally, is also che most favorable from a fisheries 
point of view. Fisheries personnel under contract to 
the Department of Water Resources are now evaluat¬ 
ing the effect of this plan on the fisheries resources. In¬ 
formation already has been published for other-salt 
water barrier plans including, that of the unction Point 
Barrier, which it is believed would affect the resources 
on about the same order of magnitude as the Biemond 
Plan, Fisk (1957) has estimated the effects of the Bie¬ 
mond Salinity Control Barrier Plan on fish life. (Table 

31) 

These reductions are expected co occur-even chough 
several types of fish salvage facilities will be employed/ 

The “California Water Plan 11 embodies over 200 
major dams throughout the State, many of which 
would affect anadromous fish. The Delta area, as one 
of the focal points in the plan) would see the construc¬ 
tion of more and greater diversions and pumping facili¬ 
ties. 

All of these facts impressively point out that many 
adverse developments from water manipulation proj¬ 
ects, as far as anadromous fish are concerned, can be 
expected for some rime to come. 

Projects such as those outlined are not che only 
source of concern. More urban and industrial develop¬ 
ment, particularly in the Bay Area and aJong che Sacra¬ 
mento and San Joaquin rivers, muse also be anticipated. 
This will result in a greater volume of waste which 
must be adequately treated if pollution problems are 
nor to be intensified. 

Fortunately, significant advances have been made in 
abating domestic sewage polludon in and around che 

TABLE 31 

ANTICIPATED EFFECT OF THE PROPOSED BIEMOND 
SALINITY CONTROL BARRIER ON FISH 
LIFE UNDER TWO PROPOSALS 

Anticipated 
Population Lois or 
Criiu in Percentage 

Single Three 

Species Rivet System Screen 1 Screen 3 

King SalrYiOn —__Sacrarnenca _ _ —12.0 —3 .4 

KJng Salmon._—San Joaquin.._—18.0 —4J 

King Salmon __Mokelumne _“24.0 —24.0 

Silver Salmon__ Sacramento - _ __ —14.0 —3.4 

Srcrihead Trout_Sacramento__—9.0 —1,2 

Striped Bass___.Sacramenco-San Joaquin _ —15.0 —15.0 

Shad----„._Sacramenro-San Joaquin^ —25.0 —25.0 

White Sturgeon __$acramenco-San Joaquin _ —5.0 —5.0 

Catfish-----Saeramento-nSan Joaquin— —25.0 —25.0 

Pan fish (Black bass, 

Sunfish, ecc.)---Sacramenco-San Joaquin—-|-25.0 +25.0 

1 Under this plan there would be a single large fish screen at the DeJtn 
Pumping PInnt, 

* In addition io the Bjh screen nt the pumping plan!, so cans arc proposed 
at Walnut Crovp oo the Sacramento River and Parodlse Cut on the 
San Jo^Quin River. 


























1 


THE FRESHWATER FISH AND FISHERIES OF 
THE SAN FRANCISCO BAY AREA 


l. 


HISTORICAL REVIEW 

The freshwater fish fauna of the San Francisco Bay 
Area is quite varied and supports a large angling popu¬ 
lation. This was not always so v however; the area orig¬ 
inally was deficient in natural lakes and warmwater 
streams and the many varieties of so-called warmwater 
or spiny-rayed gamefish. The only native warmwa- 
ter gamefish found here was the Sacramento perch 
(Arcboplites imemiptus). 

Salmonids on the other hand inhabited virtually 
every stream. Native populations of rainbow trout 
(Salmo gabrdneri) were found in most streams with 
a year-around supply of cool water. Silver salmon and 
steelhead also favored the cooler waters and utilized 
many of the intermittent streams for spawning. 

Salmonids as a group have always been particularly 
favored both for food and sport and even in the early 
days of San Francisco were heavily exploited by an¬ 
glers. Besides angling they were taken by spears, traps, 
weirs, explosives and any other available means. 

As the population of the Bay Area increased be¬ 
tween 1850 and 1890, the local redwood forests were 
timbered off and public water supplies were devel¬ 
oped. Coastal streams suffered from pollution by saw¬ 
dust, grist, and siltation. The.streams were obstructed 
by log jams and were (jammed to form water supply 
- reservoirs and to harness their energy for the operation 
of sawmills and flour mills. Records of the Fish and 
Game Commission relating to this early period indi¬ 
cate the local salmonid fisheries suffered a severe 
setback. 

It is of passing interest to note that the first hatchery 
and fish cultural station in California was established 
'On the grounds of the University of California at 

■ Berkeley in 1869. The station, operated by “The Cali- 
forma Acclimatization Society”, and operated under 

T the supervision of Mr. J. G. Woodbury, sold the fish 
jr to the State Fish Commission. 

Immediately after the legislature established che 
J State Board of Fish Commissioners ( L 870) this body 
v. set about to import prominent gamefish species of the 
East'and Midwest. The black basses, panfishes (green 

■ sunfish, bluegills, etc.) catfishes, perches, and eastern 
brook and brown trout were among the freshwater 
varieties introduced. Most of them did extremely well 

T ki their new environment. As a matter of fact, the 
Produced species now sustain virtually all warm- 


water angling in che Bay Area. The more common 
freshwater fish species are listed in Appendix F-l. Ini¬ 
tial introductions of selected species now occurring in 
.the Bay Area are given in Appendix F-2. 

Abouc 1884 the Stater Board of Fish Commissioners 
was concerned about the vanishing Sacramento perch. 
The species was disappearing at an alarming rate, pre¬ 
sumably because of overfishing and reclamation. More 
recently, the introduction of alien species also has been 
blamed for the perch scarcity. 

Sacramento perch and several non-game varieties 
found their way into the San Francisco commercial 
trade to some extent before 1870. They were obtained 
by seining in the Delta, in the lower reaches of the 
rivers tributary to the Delta, and in Clear Lake, Lake 
County^ 

he latgemouth and smaUmouth basses ( Microp - 
terns salmotdes and Micropterus dolcmieui) respec¬ 
tively, both highly esteemed as food and gamefish in 
the East and Midwest, were among the first varieties 
brought to California. They were brought out by 
Livingston Stone in 1874 and stocked in Alameda 
Creek and che Napa River. By 1890, most of the suit¬ 
able lakes and streams in the Bay Area were well 
stocked with them. 

The white catfish (Ictalunts cams) and brown 
bullhead (Ictahints nekniloms) were introduced by 
Stone in 1874. Panfish and crappies were first intro¬ 
duced between 1890 and 1891 into Southern California 
and made their way to Bay Area waters through later 
transplantations. 

White catfish and brown bullheads increased at such 
a prolific race that they supported a substantial com¬ 
mercial fishery from the rum of the century until 
1953 when che fishery was abolished by the legisla¬ 
ture. Most of the catch, though landed at Pittsburg, 
was made in the Delta. Special fyke nets were em¬ 
ployed. 

Other freshwater species entering the commercial 
catch included carp (Cyprinus carpio)^ which were 
first introduced from Europe in 1872, and the native 
hardhead (Mylopharodon conocephalvs) x squawfish 
('Ptchocheikts grandis ), splittail (Pogomcbthys macro- 
lepidotus ), and Sacramento blackfish, (Ortbodcm mi- 
crolepidotus ). For the mosc part the latter species were 
taken incidental to shad and salmon by the Pittsburg 
fleet and landed at either Pittsburg or San Francisco. 
The Department of Fish and Game issues special per- - 
mits to commercial operators to fish for some of these 



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Fish and Wildlife Resources, San Francisco Bay Area 


169 


■ ■ ANADROMOUS FISHERIES 

Any detailed analysis of the factors affecting the 
abundance and landings in this group of fishes would 
be exceedingly difficult. Environmental conditions 
have been so greatly modified by man’s activities that 
it is virtually impossible to ascertain the relative effect 
of anv one factor on these resources. 


King Salmon 

The commercial fishery formerly consisted of the 
gill net fleet, which always operated inside the Golden 
G-ate, and the ocean troll fleet* The former was abol¬ 
ished by the legislature in 1957. 

The gill net fishery landings exhibited tremendous 
fluctuations from year to year throughout the re¬ 
corded history of the fishery. However, the trend over 
che ninety-year period for which catch figures are 
available was downward. The 1957 catch was the 
smallest ever recorded. 

There axe several explanations which could account 
for the decrease. One cause can be ascribed to water 
development projects in California. Virtually every 
permanent stream the full length of che Central Valley 
has one or more dams constructed across it. These 
have eliminated spawning areas and adversely affecced 
temperature and flow regimes. Unscreened water di¬ 
versions also take a heavy toll of small fish. 

Since both the gill net fishery and the ocean troll 
fishery operated on the same salmon stocks the latter 
certainly contributed substantially to the reduction in 
the gill net landings, here has been a large increase 
in the size of the ocean troll fleet and its catch over 
former years as well as a spectacular increase in the 
ocean spon: fishery in the last 15 years. 

Although the salmon resources cercainly have been 
overfished at various periods throughout the last 50 
. or 60 y^ars, it is quite unlikely that overfishing alone 
has been responsible for the long-term decline. 

Pollution has also been involved in che salmon de- 
feline. However, it is impossible to demonstrate che 
■ relative effects of pollution on che resource. Mining 
;_and logging pollution and silt have been prevalent in 
v some streams, domestic sewage and dairy pollution in 
■/.others, and cannery and winery wastes in still others. 

. 'Along the Bay proper, the numerous industrial waste 
: outfalls threaten the small downstream migrants which 
xare inadvertently swept into the vicinity of them. 
^Uncreated or inadequately treated domestic sewage 
;discharges both in the Bay and in upstream tributaries 
Tcreace similar problems. 


' r §lripad Bass 

Generally speaking, this fishery has remained rela- 
lively stable. The species was completely removed 
■/from the commercial category in 1935 and since then 


a " r 

has been subjected to hook-andTine fishing only, ex¬ 
cept for fish which were taken incidentally with shad 
and salmon by the gill net fishery. The sport fishery 
is so intense it is believed that up to 25 percent of all 
legal-sized fish are removed from the fishery each year. 

A review of the catch records and other pertinent 
data revealed a decline in the fishery from T944 

. * i 

through 1955. As a consequence, further restrictions 
in size and bag limits were put into effect to bring 
the fishery into balance. This appears'to have been 
accomplished. 

Under present conditions, it appears chat the sport 
fishery is now exerting sufficient pressure to have a 
definite influence on striped bass stocks. The govern¬ 
ing factor, however, lies in the change in environ¬ 
mental conditions. These have been modified so 
greatly over the past fifty years that there has been 
an appreciable loss in che total habitat available to 
striped bass. 

Ac least three adverse factors, excluding angling, are 
affecting che striped bass population: reclamation, 
water development projects, and pollution. It would 
be next to impossible to evaluate the relative impor¬ 
tance of each..Reclamation, many years ago, resulted 
in extensive habitat changes which removed rich nurs¬ 
ery grounds. Water development projects have modi¬ 
fied temperature, flow, and salinity patterns in the 
Delta and in spawning areas, and numerous diversions 
take a heavy toll of fish. Pollution has resulted in an 
extensive loss of habitat, destruction of forage organ¬ 
isms, and, frequently, in the outright killing of the fish 
themselves. 

The absence of striped bass in many areas of the 
Bay may be taken as rather clear evidence of pollution. 
South San Francisco Bay in particular can be cited, 
and there are other once-favorable localities which are 
now similarly devoid of striped.bass. 

Shad 

Shad landings, in the past, have been influenced 
strongly by economic conditions. Generally the catch 
was considerably less than the fishery could have sup¬ 
plied. Nevertheless, there appears to have been a defi¬ 
nite decline in rhe fishery, unrelated to economic con¬ 
ditions, and presumably caused by the same factors 
which have influenced salmon and striped bass popu¬ 
lations. The. most significant recent development with 
respect co the shad resource is the evolution of the 
sport fishery in the past few years. 


WATERFOWL 

There has been a decided reduction in the water- 
fowl of the Bay Area, both in resident and wintering 
populations. Reclamation of che marshlands and tidal 
fiats has unquestionably been the major causative fac¬ 
tor in the decrease. Most of the breeding areas around 


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3. Responses to Comments and DSEIR Revisions 


Intentional blank page 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Response to Comment M-l 

This SMP Update is a continuation of a program that has been ongoing since 2002. Since the 
initiation of the SMP, the District has provided advanced notification of proposed work, 
either as part of the Notice of Proposed Work (first phase of the annual work sequence) or 
as an individual work order (for projects occurring after Phase 1 of the work sequence). In 
either case, regulatory agencies have been able to provide comments or request additional 
information from the District regarding proposed work during this notification period. This 
opportunity for comment/questions before implementation of work would continue under 
the 2012-2022 SMP Update. 

In addition, the regulatory agencies participate annually in a “lessons learned" meeting that 
provides an opportunity to identify appropriate refinements to the program. Although other 
refinements to the notification and review process have been discussed, to date, the 
concerns identified by the commenter have not been raised by the regulators. 

Response to Comment M-2 

The Notice of Proposed Work (NPW) for the Stream Maintenance Program is sent to city 
public works departments that may have approval authority over SCVWD's maintenance 
activities. The District's Zone Advisory Committee, now the Flood Protection and Watershed 
Advisory Committees) assist SCVWD's Board of Directors with policies and issues 
pertaining to flood protection and stream stewardship. The Advisory Committee includes 
representatives of the cities and the County as well as at-large members who represent the 
community. The local fire districts receive the NPW to ensure access for emergency 
response vehicles. Guadalupe Coyote RCD (GCRCD) may obtain a copy of the NPW by 
submitting a Public Information Request through Access Valley Water at 
www.valleywater.org. 

BMP GEN-36 in Table 2-12 of the DSEIR is revised as follows: 

The annual work plan NPW will be submitted to public works departments, local 
fire districts, and the District's Zon e Advisory Committ ee Flood Protection and 
Watershed Advisory Committees . 

Response to Comment M-3 

SCVWD appreciates the concern expressed in the comment. As noted in response to 
Comment D-17, the 24-hour notification time frame for follow-up maintenance activities 
conducted at bank repair sites that are less than 2 years old would be important to prevent 
a situation from worsening. This time frame would allow SCVWD to be able to respond 
quickly and effectively to a damaged work site. For all other bank repairs, the permitting 
agencies would be given a greater period of time to review and comment, when notified as 
part of the annual Notice of Proposed Work or via individual work orders, as discussed in 
Chapter 2, Project Description, of the DSEIR. 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-45 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


Response to Comment M-4 

The comment makes the following statement, which is not supported by the DSEIR: “The 
DSEIR (correctly) identifies Chinook salmon as a native species utilizing habitat in the 
project area for migration, spawning and rearing.” In fact, the discussion on page 136, in 
Section 3.3 of the DSEIR, identifies Chinook as not native, stating “that the rivers and creeks 
of Santa Clara County are home to 12 native species of fish,” and, “The non-special-status 
fish and amphibians that would be impacted by the Proposed Project are relatively 
abundant and widespread, with the exception of the Chinook salmon, which is not native 
[emphasis added] to South Bay streams.” The comment is correct to note that, although the 
Chinook salmon in the Project Area are recognized as strays from hatchery releases, the 
National Marine Fisheries Service (NMFS) still considers habitat used by Chinook salmon in 
the South Bay as essential fish habitat (EFH). However, to meet the threshold for 
significance under CEQA and the State CEQA Guidelines, the species itself would have to be 
rare; the term rare, as defined by Section 15380 is as follows: “a) Although not presently 
threatened with extinction, the species is existing in such small numbers throughout all or a 
significant portion of its range that it may become endangered if its environment worsens; 
or b) The species is likely to become endangered within the foreseeable future throughout 
all or a significant portion of its range and may be considered 'threatened' as that term is 
used in the Federal Endangered Species Act.” 

The Central Valley fall-run Chinook salmon in the South San Francisco Bay do not warrant a 
“rare” designation. The NMFS completed a comprehensive, scientific review in 2008 and 
found that Central Valley fall-run Chinook salmon populations, whose range includes the 
Sacramento and San Joaquin Rivers and tributaries, were more robust than previously 
thought. Subsequently, this Distinct Population Segment did not warrant a “threatened” 
status under the Endangered Species Act, and long-term trends show the population to be 
stable. Additionally, the fish found in the South Bay are genetically consistent with hatchery 
fish (i.e., Feather River stock), and the hydrology and temperature of South Bay streams do 
not, and historically have not, supported a fall-run fish that can ascend larger rivers as early 
as July. The comment may be confusing the term “naturalization” with “natal,” in which a 
non-native species is said to be naturalized “when its reproduction is sufficient to support 
it." Whether the fish have naturalized in Santa Clara Valley is not known, or to cite the 
language in the DSEIR (in the third paragraph under Impact BIO-15), “Although spawning 
has been documented in SCVWD-maintained creeks, whether up-migrating adults have 
hatched on these creeks or if the adults that were observed were direct strays from other 
areas is unknown." 

SCVWD appreciates that the GCRCD has entered information into the administrative record. 
However, these documents do not establish the historic presence of a self-sustaining 
Chinook salmon run, and no disagreement exists among expert opinion regarding the facts 
about the significance of an effect on the environment (see previous paragraph regarding 
NMFS findings). The USFWS document was written before much data collection effort had 
begun to determine the origin of the Chinook salmon in the County, and the record simply 
states that Chinook salmon were observed in the Guadalupe River. When reading and 
interpreting Skinner (1962), as in the comment, the entire document should be cited and 
coupled with an understanding of the life history of salmon and steelhead. This is 
particularly important when used to discuss the occurrence of Chinook salmon in County 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-46 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


streams. The content of the Skinner document relies heavily on commercial catch records 
and not on specific stream survey data, especially in regard to the County. Rather, some 
vague correlation is presented that salmon may make use of South Bay streams, although 
language is used in the document that strongly suggests just the opposite. Please refer to 
page 58, regarding Chinook salmon: “Although the fishery for king salmon is centered in the 
Bay Area, few kings actually spawn in any of the local streams. They generally enter the 
larger rivers along the coast north of San Francisco Bay. By far the greatest proportion 
however, has always passed through the Golden Gate to ascend the Sacramento and San 
Joaquin rivers are the way to ancestral spawning grounds in these rivers and tributaries." 
The non-site-specific reference to “few kings actually spawning in any local streams" in the 
Bay Area is indicative that some Chinook salmon may have strayed from their “ancestral" 
course and the fact that streams within San Francisco Bay, particularly South Bay streams, 
flowed to the Bay intermittently. 

SCVWD has committed considerable resources to determine the origin of Chinook salmon in 
Santa Clara Valley. Chinook and steelhead populations' genetics, radio telemetry and 
trapping of adult Chinook, and historical ecology assessments are a few of the efforts 
SCVWD has funded and shared with the GCRCD. The most current, scientific information has 
been utilized in this DSEIR analysis as well as in other documents SCVWD has produced. 
Therefore, SCVWD believes that its analysis of Chinook salmon in the DSEIR is correct and 
revisions for this species are not required. Mitigation measures (i.e., gravel augmentation, 
instream complexity) and BMPs (GEN-1, -2, -4, -8, -20, -23, -26, -30, -32, and -33) in the SMP 
Update would provide ancillary protection for Chinook salmon while still focusing on native 
fish that are imperiled (i.e., steelhead). If more current, creditable, scientifically defensible 
information is available in the future, SCVWD will utilize that new information. 

Response to Comment M-5 

The comment suggests that heavy equipment in stream channels will have a substantial 
effect on fish habitat and benthic macroinvertebrate populations, and that the effects of 
heavy equipment in streams are not adequately described in the DSEIR. SCVWD 
acknowledges the effects of heavy equipment, but disagrees that such impacts were 
inadequately addressed in the DSEIR. Heavy equipment only would be operating within 
stream channels during sediment removal and bank stabilization projects. During such 
projects, the physical alteration of the substrate (e.g., removal in the case of sediment 
removal, and removal or replacement of at least a portion of the channel bed with more 
stable materials in the case of bank stabilization) would have a much greater effect on fish 
habitat and benthic macroinvertebrates than simply the operation of heavy equipment. 
Because the use of heavy equipment would occur in areas where even greater impacts from 
sediment removal and substrate alteration would happen, as discussed in the DSEIR, a 
lengthy discussion of the additional effects of using equipment to perform these activities is 
unnecessary. In addition, crushing of invertebrates by heavy equipment was discussed in 
the DSEIR (e.g., the second paragraph on page 3.3-52). 

Nevertheless, the DSEIR is revised as follows to include explicit discussion of the effects of 
heavy equipment on the stream substrate and on macroinvertebrate populations: 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


3-47 


December 2011 
Project 10.005 




3. Responses to Comments and DSEIR Revisions 


The ninth paragraph in Bank Stabilization, Fish, under Determination of Impacts to Wildlife 
and Fisheries has been added (on page 3.3-50 of the DSEIR): 

Bank stabilization activities often necessitate the operation of heavy equipment 
within the stream bed (after dewateringl. Movement of heavy equipment may 
compact the substrate, potentially killing benthic invertebrates (which may serve as 
prey for fish), embedding gravel within finer sediments, and otherwise altering 
habitat for fish and their prey. 

The fourth paragraph on Invertebrates, under Determination of Impacts to Wildlife and 
Fisheries (on page 3.3-52 of the DSEIR): 

Invertebrates. Invertebrates occur in and adjacent to channels where bank 
stabilization activities are planned. In these areas, invertebrates could be either 
killed directly (e.g., by crushing) or adversely affected by the loss of host plants or 
disturbance of refugia. For species such as moths and butterflies, host plants may be 
damaged or killed as a result of work site clearing (e.g., before the installation of 
bank armoring or during the creation of access roads or staging areas), crushing by 
equipment, trampling by personnel, and soil compaction by heavy equipment. In 
addition, these species may be adversely affected by habitat conversion, which could 
result from the unintentional introduction of non-native grasses and forbs to work 
sites. Bank stabilization activities often necessitate the operation of heavy 
equipment within the stream bed (after dewatering). Movement of heavy 
equipment may compact the substrate, potentially killing benthic invertebrates, 
embedding gravel within finer sediments, and otherwise altering habitat conditions. 

Following the sixth paragraph under Impact BIO-8 (starting on page 3.3-99 of the DSEIR): 

Bank stabilization and sediment removal activities often necessitate the operation of 
heavy equipment within the stream bed (after dewatering). Movement of heavy 
equipment may compact the substrate, potentially killing benthic invertebrates 
(which may serve as prey for steelhead). embedding gravel within finer sediments, 
and otherwise altering habitat for fish and their prey. 

The second paragraph under Impact BIO-9 (on page 3.3-109 of the DSEIR): 

As described under Determination of Impacts to Wildlife and Fisheries, proposed 
maintenance activities may result in adverse effects to habitat used by both of these 
fish through dewatering, fish relocation, increased turbidity, changes in habitat 
structure, effects of heavy equipment use on these species, their prey, and their 
habitat, and other impact pathways. Permanent habitat impacts to these species' 
habitats are expected to be very limited but could potentially occur if bank 
stabilization activities replaced their habitat with hardscape. Electrofishing for fish 
relocation, stranding, herbicide and surfactant use, and increased turbidity may 
result in the direct injury or mortality of individual fish. 

SCVWD agrees with the comment that disturbance of stream sediments can result in 
adverse effects on fish habitat, including salmonid spawning habitat, and the DSEIR includes 


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compensatory mitigation measures (Mitigation Measures BIO-8 and BIO-9 addressing 
gravel augmentation and replacement of instream habitat complexity) and a number of 
BMPs (e.g., GEN-4, -20, -26, and others) to minimize the effects of SMP Update activities on 
fish habitat. 

Response to Comment M-6 

SCVWD is pleased that the GCRCD supports gravel augmentation as a mitigation measure. 
After discussions with the NMFS, SCVWD has revised the mitigation strategy for gravel 
augmentation, reducing the threshold for evaluation of gravel for suitability as spawning 
habitat, and for mitigation, to 100 square feet of “high quality” gravel impacted instead of 
500 square feet that was outlined in the DSEIR. SCVWD has analyzed the last 10 years of 
sediment removal data to understand what the magnitude for replacement may look like for 
mitigation. SCVWD believes, and NMFS supports, the 100-square foot threshold as a fair 
compromise to minimize impacts to steelhead while still providing benefit to the species. 
The objective for sediment removal in this program includes removing sediment for 
channel capacity to alleviate or reduce flooding, remove mercury laden or other 
contaminated soils, ensure proper function of instream structures (i.e., stream gauge, fish 
ladder, outfalls, tide gates), and provide for anadromous fish passage. All of these objectives 
would provide benefits to the community while some would provide direct benefits to the 
natural resources. As previously stated, although directed at steelhead, this mitigation 
measure would provide benefit to Chinook salmon. 

Therefore, the discussion under Mitigation Measure BIO-8 of the DSEIR is revised as 
follows: 

[in the second sentence of the first paragraph] 

SCVWD will implement gravel augmentation as mitigation for SMP impacts to CCC 
and SCCC steelhead spawning habitat. If more than 500 100 square feet of sediment 
removal is proposed along steelhead streams, an SCVWD fisheries ecologist will 
assess the sediment removal site for spawning and rearing habitat quality before 
the initiation of work. 

[in the first sentence of the last paragraph] 

If more than 500 100 square feet of high-quality gravel will be removed along 
steelhead streams, compensatory mitigation will be provided by the installation of 
suitable spawning gravel along the affected creek at a 1:1 (mitigatiomimpact) ratio 
on a square footage or acreage basis. 

Furthermore, the identical sentences in the Mitigation Monitoring and Reporting Plan 
Matrix in Appendix L of the DSEIR are likewise revised. 

Appendix C in the DSEIR is revised entirely in Volume II of this FSEIR. 

SCVWD concludes that with this mitigation, the Proposed Project would not make a 
considerable contribution to any significant cumulative impacts relative to spawning gravel. 


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Therefore, no further assessment of cumulative impacts beyond that already conducted in 
the DSEIR is necessary to evaluate the size threshold for mitigation, or for any other reason. 

Response to Comment M-7 

Per the comment, third paragraph under Impact BIO-8 (on page 3.3-99 of the DSEIR) is 
revised as follows so that the discussion of bank stabilization impacts to steelhead includes 
more quantification of the potential impacts to habitat used by these fish. These revisions 
include the assumption that no more than half of bank repairs would consist of impervious 
hardscape bank stabilization work, as well as information on the extent of modified and 
unmodified channels that were impacted by bank stabilization projects in the Santa Clara 
and Pajaro Basins during the period 2002-2010 (this information provides a crude estimate 
of the potential annual bank stabilization needs during the 2012-2022 period): 

The extent of potential impacts to steelhead and their habitat resulting from bank 
stabilization activities is difficult to quantify, because stabilization activities cannot 
be projected and because the magnitude of the impact of stabilization would depend 
on the type of repair method used and the location of the repair project. However, 
the extent of bank stabilization work that is expected to occur in steelhead habitat 
would be relatively low, based on SMP activities conducted since 2002 . Between 
2002 and 2010. (approximat e ly less than 1 mile of bank stabilization work per year 
has occurred throughout the Project Area, including non-steelhead streams)-. 
SCVWD's records indicate that less than 20 percent of this bank stabilization work 
occurred in unmodified channels, which likely provide the highest-qualitv habitat 
for steelhead. Furthermore. SCVWD expects that no more than half of the bank 
repairs during the period 2012-2022 to consist of impervious hardscape bank 
stabilization work. As a result, and because of the potential long-term benefits of 
bank stabilization to steelhead habitat described above, little long-term adverse 
impact to steelhead habitat is expected to occur as a result of 2012-2022 bank 
stabilization activities. 

Please see response to Comment D-23 regarding revisions to Mitigation Measure BIO-9. 

Cumulative impacts of the SMP Update on biological resources are described in Section 4.5 
of the DSEIR. The cumulative impacts analysis considered the effects of proposed SMP 
Update activities in combination with effects of other projects, including SCVWD's capital 
projects and other activities that could affect biological resources such as streams, 
streambanks, riparian habitat, and fish. That impacts analysis determined that, with the 
implementation of mitigation measures not only by the SMP Update, but also by SCVWD's 
capital projects and other projects that could affect these resources, cumulative impacts to 
these resources (aside from habitat fragmentation impacts) would be less than significant. 
The SMP Update would mitigate its impacts on steelhead and their habitat, including both 
instream habitat and riparian habitat, adequately; SCVWD is in consultation with NMFS to 
obtain approval to impact steelhead and its habitats. 

Response to Comment M-8 


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3. Responses to Comments and DSEIR Revisions 


As shown in Table 2-4 of the DSEIR, the majority of bank stabilization methods would use 
biotechnical or "soft" features. SCVWD is committed to prioritizing softscape approaches for 
bank stabilization. However, site conditions would vary and flood protection would be the 
first goal for stream management activities. As stated on page 2-17 of the DSEIR, "sites with 
eroding or destabilized banks are evaluated for their local on-site soil conditions, slope 
stability, channel position, and geomorphic processes. An overall assessment is performed 
to determine the most appropriate treatment to stabilize the bank, with consideration of 
habitat, species use, and other site beneficial uses. Based on the condition assessment, the 
SCVWD design engineer will develop a treatment approach that stabilizes the streambank 
while trying to minimize the use of hardscape. Depending on work site conditions and 
hydraulic forces, the design engineer may favor the use of hardscape elements over 
softscape treatments if there is an increased risk for potential failure of the softscape 
treatments over the longer-term." 

Evaluation of all potential impacts resulting from bank stabilization activities using both 
biostabilization and hardscape techniques were conducted in each resource section in 
Chapter 3, Environmental Setting and Impact Analysis, of the DSEIR. Please refer to the 
specific "bank stabilization" subheadings under each impact. BMPs necessary to reduce the 
level of potentially significant impacts resulting from bank stabilization efforts are 
identified under each impact. 

More BMPs than just the three bank stabilization-specific BMPs (BANK-1 through BANK-3, 
detailed in Table 2-12 of the DSEIR) would apply to bank stabilization efforts. For example, 
construction-related impacts of bank stabilization installation for soft or hardscape designs 
would be similar, and appropriate BMPs such as GEN-1, -20, -26, and -33 (identified by 
resource topic in Chapter 3 of the DSEIR) would be applied for construction of each work 
site, whether the design included hardscape or not. Impacts of softscape and hardscape 
bank stabilization approaches would be mitigated through the Mitigation Feasibility 
Assessment and implementation of on-site and/or off-site mitigation. 

The SMP Update and relevant BMPs are designed to meet the Water Resources Stewardship 
Ends Policy; one of the governance policies of SCVWD's Board of Directors, adopted in April 
2004 and revised in July 2011. Preference for use of soft bank stabilization approaches 
would be incorporated directly into the SMP Update. No further mitigation measures or 
BMPs would be necessary to reduce impacts of bank stabilization activities. 

Response to Comment M-9 

This comment requests that BMP ANI-1 be revised to reflect the increased secondary 
toxicity (i.e., poisoning of raptors or scavengers that eat poisoned rodents) of new 
anticoagulant rodenticides. However, SCVWD uses older, "first-generation" formulations of 
anticoagulants rather than these newer, more toxic formulations. SCVWD proposes to use 
two anticoagulants, diphacinone and chlorophacinone, both of which are considered first- 
generation chemical compounds by USEPA 1 . First-generation anticoagulants are chronic in 
their action, requiring multiple feedings over several days to a week or more to produce 


1 U.S. Environmental Protection Agency. 2011. Final risk mitigation decision for ten rodenticides. Available at: 
http://www.epa.gov/pesticides/reregistration/rodenticides/finalriskdecision.htm . 


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death, whereas second-generation anticoagulants (e.g., bromadiolone and brodifacoum) are 
more potent and can produce death after one feeding. Non-target species such as raptors or 
scavengers would have to eat multiple poisoned rodents for mortality to occur from the 
first-generation pesticides used by SCVWD. 1 A study published by Eason et al. in 2002 2 
stated that the risk to avian predators from secondary poisoning from first-generation 
anticoagulants appeared to be an order of magnitude lower than that of second-generation 
anticoagulants. As a result, SCVWD is using anticoagulants that have the lowest risk of 
secondary poisoning but will still be effective for SCVWD's needs, rather than using the 
newer pesticides about which the comment expresses concern. 

Comparing the two anticoagulants used by SCVWD, diphacinone has a higher risk of 
secondary toxicity than chlorophacinone. Therefore, SCVWD uses diphacinone only when 
chlorophacinone is not adequately effective. For example, SCVWD did not use diphacinone 
at all in 2010 because it was not determined to be necessary. In cases where diphacinone is 
required, it typically is inserted belowground for gopher control. Any gophers killed by 
diphacinone are expected to die underground, where a very low potential exists for raptors 
or scavengers to detect and eat them. Nevertheless, BMP ANI-1 will be revised to further 
minimize the risk of secondary poisoning, as follows: 

Carcass surveys will be conducted periodically when acute poisons and first 
generation anticoagulants are used. The frequency of the carcass surveys will be 
specific to the type of rodenticide used In ar e as wh e r e rod e nticid e s ar e us e d, carcass 
r e tri e val surveys will b e conduct e d as follows to minimize secondary poisoning 
impactS v 

• Acute toxins- Daily , carcass surveys, beginning the first day after application 
until the end of the baiting period for acute toxins used above-ground . 

• Anticoagulants- W ee klv for anticoagulants Within 7 days of installation of first 
generation anticoagulant bait, and weekly thereafter. Anytime a carcass is 
found, daily carcass surveys will begin for as long as carcasses are found until 
no carcasses are found during a daily survey. Once no carcasses are found, 
carcass surveys will return to the weekly carcass survey timeline maximum 
from the date of initial installation of an anticoagulant bait station. 

In addition, twic e p e r y e ar District biologists will conduct daily carcass surv e ys for a 
full cycl e of a baiting trap, to minimiz e s e condary poisoning impacts. To verify that 
the frequency of carcass surveys is adequate, a biologist will conduct daily carcass 
surveys 2 times per year over one baiting cycle. Based on the results of these surveys, 
the timing of carcass surveys will be adjusted if necessary. 

Any spilled bait will be cleaned up immediately. 

Thus, carcass surveys for anticoagulant use will commence one week after application 
(because these anticoagulants can take up to a week to kill rodents) and will continue daily 
thereafter, as long as carcasses continue to be found during each visit. 


1 U.S. Environmental Protection Agency. 1998. R.E.D. Facts. Rodenticide cluster. Prevention, Pesticides and 
Toxic Substances (7508W). EPA-738-F-98-004. 

2 Eason, C. T., Murphy, E. C., Wright, G. R. G., Spurr, E. B. 2002. Assessment of risks of brodifacoum to non¬ 
target birds and mammals in New Zealand. Exotoxicology 11:35-48. 


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CALIFORNIA 

R5H : :GAV£ 


State of California - The Natural Resources Agency 

DEPARTMENT OF FISH AND GAME 

Bay Delta Region 

7329 Silverado Trail 

Napa, CA 94558 

(707) 944-5500 

www.dfa.ca.gov 


EDMUND G, BROWN JR Governor 

CHARLTON H. BONHAM, Director 

Letter N 



October 5, 2011 


Ms. Sunny Williams, Environmental Planner 
Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95118 

sunnvwilliams@vallevwater.org 

Dear Ms. Williams: 

Subject: Stream Maintenance Program Update 2012-2022, Draft Subsequent 

Environmental Impact Report, SCH #2000102055, Santa Clara County 

The Department of Fish and Game (DFG) has reviewed the Santa Clara Valley Water 
District’s (District) document provided for the subject program, and we have the following 
comments. 

General Comments: 

Due to the widespread implementation of burrowing rodent control activities, 
including the use of rodenticides, DFG advises the District to prepare a 
Pesticide/Pest Management Plan for appropriate wildlife agency review and 
approval. 

Due to the planned widespread use of herbicides for vegetation management, DFG 
advises the District to prepare an Herbicide Use Plan for appropriate wildlife agency 
review and approval. 

DFG advises the District to prepare a Grazing Management Plan for appropriate 
wildlife agency review and approval. 

DFG acknowledges there are both ecological services-based and land acquisition- 
based components to the mitigation program for the Stream Maintenance Program 
Update (SMP). While some ecological services-based mitigation is acceptable, DFG 
emphasizes the need for land acquisition-based mitigation. It is a requirement for 
impacts to state-listed species. DFG requests that text be added to the draft 
Subsequent Environmental Impact Report (SEIR) stating “The District shall provide 
for compensatory mitigation by acquiring or protecting appropriate mitigation lands 
and populations of special status species with a conservation easement that is made 
out in favor to the appropriate wildlife agencies. Any mitigation lands with a 
conservation easement shall include an endowment and long-term management 
plan.” 















Ms. Sunny Williams 
October 5, 2011 
Page 2 


4. The document makes numerous references to “work area percentage” for sediment 
removal and vegetation management activities. There are several references to 
Chapter 2 to find discussion on this. However, “work area percentage” is not 
mentioned in Chapter 2. Please provide a thorough description of how “work area 
percentage” will be calculated for these activities. 

5. The document describes the development of several Habitat Mitigation and 
Management Plans for special-status species. DFG requests that these plans be 
submitted to DFG for review and approval prior to being finalized. 

7. DFG recommends the District revise and clarify different types of temporal biological 
impacts in the Final EIR. Types of temporal impacts may include one-time 
temporary habitat impacts that can be restored, short-term habitat impacts that can 
be restored, permanent impacts where habitat is permanently removed, and 
repeated impacts where habitat is either permanently removed or habitat begins to 
re-establish and is repeatedly removed. This last type of impact generally is the 
greatest and the final EIR should identify additional incremental mitigation for these 
types of impacts. 

Species presence in the habitat types during the various types of impacts should 
also be evaluated and impacts to listed and sensitive species should be mitigated. 
For listed species, take could occur with temporary impacts, short-term impacts, 
permanent impacts and repeated impacts. DFG recommends the District analyze 
repeated impacts to see if any listed or sensitive species would be affected by these 
impacts and if habitat and species re-establish in between impact events, then 
additional mitigation beyond one-time compensation should be identified in the Final 
EIR. 

DFG generally recognizes temporary impacts as those where the impacted site 
supports an herbaceous vegetation habitat that can grow to maturity in a single 
growing season, the impacted site is recontoured and seeded by October 31 of the 
year of the temporary impact; and the impact site achieves vegetation success as 
described in a Vegetation Restoration Plan approved by DFG. 

DFG recommends short-term habitat impacts be described as single year impacts to 
sites supporting woody vegetation, such as chaparral or riparian areas, where the 
impacted site is re-planted with appropriate, naturally occurring 
vegetation prior to November 30 within the year of impact and the site is managed 
and monitored for a multi-year period to achieve revegetation success as described 
in a Vegetation Restoration Plan approved by DFG. 

DFG recommends permanent impacts be any impacts that permanently remove 
habitat or remove the habitat for more than two growing seasons. DFG 
▼ recommends that all permanently impacted habitat types be mitigated by 



Ms. Sunny Williams 
October 5, 2011 
Page 3 


N7 



conservation and enhancement of similar habitat on at least a 1:1 ratio. If the habitat 
is sensitive or support sensitive or listed species, DFG recommends additional 
mitigation. 


DFG recommends the repeated or recurring impacts be carefully evaluated to 
determine whether the activities will permanently remove habitat or whether habitat 
is expected to temporarily re-establish in between impacting events. Also, repeated 
impacts should be analyzed to identify whether sensitive or listed species will be 
impacted by the action and whether sensitive or listed species could re-establish in 
the area in between impacting events. Any impacts to sensitive or listed species 
should be mitigated by the permanent conservation enhancement, management and 
funding of occupied habitat sufficient to offset the impacts. Recurring impacts that 
repeatedly take listed species should be mitigated through additional incremental 
habitat conservation or sufficient habitat should be conserved and managed to 
conserve the species. 

DFG will consider the analysis of impacts and the mitigation measures in the Final 
EIR related to these topics when developing permits and approvals as a responsible 
agency. The District should obtain a California Endangered Species Act (CESA) 
Incidental Take Permit (ITP) for any take of state listed species. DFG is available to 
work with SCVWD to develop a 10-year ITP to provide take authorization for state 
listed species impacts during the next 10-year SMP implementation period. 
Additionally, approval and implementation of the draft Santa Clara Valley Habitat 
Plan, if finalized as a Natural Community Conservation Plan with an associated 
permit, may also be able to contribute to overall species conservation and may mesh 
with certain mitigation needs of the SMP. 


Executive Summary 

Pages ES-6 and 2-17 (Chapter 2) - Sediment disposal sites: The draft SEIR identifies 
several sediment reuse locations but states that the District may add other upland or 
aquatic sites to its disposal options. Additional disposal sites should be identified in the 
Final SEIR. Any additional new sediment reuse location sites would require additional 
California Environmental Quality Act (CEQA) review. 

Pages ES-7and 2-20 (Chapter 2) - Tree removal: The draft SEIR states that the removal of 
trees and shrubs less than or equal to 12 inches diameter at breast height (dbh) is 
permissible only if they are required for bank stabilization projects, ecological 
health/stewardship purposes, or to maintain flow conveyance. What is the rationale for 
increasing the maximum diameter of tree removal from 6 inches dbh under the 
2002-2012 SMP to 12 inches dbh under the SMP Update (2012-2022)7 In addition, 
describe how the District will determine when it is appropriate to remove a tree for health 
and/or stewardship purposes. 



Ms. Sunny Williams 
October 5, 2011 
Page 4 


N10 

Nil 

N12 


N13 


Page ES-8- Grading: Among the items listed under Minor Maintenance Activities 
proposed under the SMP Update, the District proposes to grade small areas without 
vegetation above stream banks to improve drainage and reduce erosion. Please disclose 
the estimated area that would be graded for this purpose. 

Page ES-8 - Canals: The draft SEIR states that the SMP Update would include routine and 
periodic maintenance on canals. Please clarify whether sediment removal activities are 
anticipated to occur when canals are dry or whether dewatering will be required. 

Pages ES-10 and 2-26 (Chapter 2) - Work windows: The draft SEIR describes a work 
window for sediment removal, in-stream vegetation and herbicide application, and bank 
stabilization, which would generally occur between June 15 and October 15. The document 
then states that if the fall season remains dry, work could continue until the first significant 
rainfall event occurred (defined as local rainfall of 0.5 inches or greater within the watershed 
over a 24-hour period), and that no instream work (excluding hand pruning and hand 
removal in non-steelhead streams) would continue later than December 31. 

DFG advises the District to retain the same type of work window that has been utilized 
under the existing SMP, which allows work to continue beyond October 15 until 
October 30 if more than 50 percent of a project is complete. Certain activities (such as 
small sediment removal projects or vegetation management) that may be stopped quickly 
and the site winterized effectively may be appropriate to continue into the fall season, 
pending a dry weather pattern. However, activities such as bank stabilization, large 
sediment removal projects, or any projects involving dewatering should be restricted to the 
June 15 through October 15 work window (with the extension to October 30 for projects that 
are more than 50 percent complete) due to the fact that these types of projects are not 
easily completed and the site winterized appropriately on short notice. Significant rainfall 
has begun in October during the past two fall seasons. These work windows are 
established to minimize impacts and appropriately protect the existing aquatic resources 
and should be adhered to. 

Pg ES-11 - Impervious hardscape: The draft SEIR states that the District has committed 
that no more than half of non-in-kind bank repairs will consist of impervious hardscape each 
year. DFG commends the District for striving to reduce the amount of hardscape used in 
District streams. However, much of the existing hardscape in District streams has been 
inappropriately placed in past years (much of it prior to the existence of the SMP). DFG 
advises the District to replace hardscape with natural materials, including plantings, in as 
much of the District SMP projects as practicable, rather than using “no more than half of 
non-in-kind repairs” as a benchmark for determining the use of hardscape versus more 
natural materials in bank repair projects. 


Chapters 2 and 3 

N14 v , Page 2-5- Table 2-2: Footnote 1 below the table refers to sediment removal. Please 

▼ correct the footnote to say “Certain locations may have been the subject of channel hand 



Ms. Sunny Williams 
October 5, 2011 
Page 5 


N14 t 
N15 

N16 

N17 


removal more than once during the 2002-2009 period, but their length are only counted 
once in this column.” 

Page 2-6 - Table 2-3: The table shows one-foot of in-kind repair for the Santa Clara Basin, 
and 6,403 feet of in-kind repair for the Pajaro Basin. Please clarify what is meant by this (is 
this in reference to hardscape or softscape?). 

Page 2-6 - Dam outlet structures: The draft SEIR states that the SMP includes channel 
maintenance at dam outlet structures immediately downstream of reservoirs. Please clarify 
whether this activity is included under the District’s Dam Maintenance Program, and if so, 
why it is covered under the SMP, and how impacts resulting from this activity would be 
properly tracked and mitigated under the two programs. 

Pages 2-15 and 2-16 - Table 2-4: Table 2-4 presents proposed mitigation ratios for various 
bank stabilization methods. While many of the proposed mitigation ratios that incorporate 
planting appear to be appropriate for the given bank stabilization method, several of these 
were mitigated at higher ratios under the original SMP. There is no rationale provided for 
the District’s decision to lower these mitigation ratios. 

For example, 2A (live construction with boulder toe) is mitigated at 1:1 if the boulder toe is 
vegetated or 1.5:1 if the boulder toe is not vegetated. The mitigation ratio for this method 
where the boulder toe is not vegetated was 3:1 under the original SMP. Several other 
examples with a similar issue regarding an unvegetated boulder toe are 3A (contour 
wattling with boulder toe), 4A [brush mattress (brush layering) with boulder toe], and 5A 
[surface matting (erosion mats) with boulder toe]. In all of these instances, the original SMP 
incorporated a 3:1 mitigation ratio for an unvegetated boulder toe. Please incorporate the 
original agreed upon 3:1 mitigation ratio. 

Other examples include 7 (cellular confinement), 8 (rock blanket), 8A (boulder revetment, 
which was named boulder rip-rap under the original SMP), and 9A (articulated concrete 
blocks with planted areas), which are proposed at a mitigation ratio of 2:1, while under the 
original SMP, those methods were mitigated at a ratio of 3:1. Again, the document does not 
explain the rationale for lowering the mitigation ratios for these methods under the SMP 
Update. DFG advises the District to increase the proposed mitigation ratios for these 
methods (with the exception of 9A; see discussion in next paragraph) to the levels provided 
under the original SMP unless the District can provide an adequate rationale for reducing 
them. 

In addition, DFG advises the District to eliminate certain bank stabilization methods, 
including 9 (articulated concrete blocks), 9A (articulated concrete blocks with planted 
areas), 10 (concrete crib walls), and 12 (gunite slope protection), due to the fact that the 
District has had little to no need for installing these methods under the original SMP, they 
are prone to failure when installed, their lack of habitat value, and the fact that other natural 
methods are available and have been demonstrated to be equally or more effective. 


Ms. Sunny Williams 
October 5, 2011 
Page 6 


N18 


N19 


N20 


N21 


Page 2-24 - Emergency repairs: The draft SEIR lists activities that are not included in the 
SMP Update, including emergency repair work. Please note that it is not necessary to 
notify DFG before beginning emergency (as defined in Section 21060.3 of the Public 
Resources Code) repair work necessary to protect life or property. DFG must be notified 
within 14 days after beginning emergency repair work. Information regarding emergency 
repair work can be accessed at http://www.dfq.ca.qov/habcon/1600/forms.html . 

Page 2-21 - Gabions: The bottom paragraph mentions the use of “hard structures” 
including sacked concrete and gabions. DFG advises the District to eliminate the use of 
sacked concrete as a type of bank stabilization method (see discussion above). Gabions 
are not included in Table 2-4 and should be eliminated from the text in this section. 

Page 2-27 - Hybrid bank stabilization: The term “hybrid" used in Table 2-4 should be 
defined in the text on this page where the terms “hardscape” and “softscape” are defined. 
Please clarify how the use of hybrid bank stabilization methods fit into the District’s 
commitment that no more than half of non-in-kind bank repairs will consist of impervious 
hardscape each year. Does the “no more than half include hardscape such as rock toe 
that is a component of the hybrid methods? If not, would it be accurate to say that the 
District can achieve this commitment? 


Pages 2-35, 3.3-42, 3.3-43, 3.3-72, 3.3-73, 3.3-79, 3.3-87, 3.3-99, 3.3-144, and 3.3-163- 
Mitigation in perpetuity: The draft SEIR discusses the original mitigation program 
developed to address compensatory mitigation for the SMP 2002-2012, and the fact that the 
mitigation provided for the stream reaches in that original program continues in perpetuity. 
The document states that the compensatory mitigation program proposed for the SMP 
2012-2022 addresses potential impacts anticipated for new work sites that were not 
included in the original SMP 2002-2012 work projections and not accounted for in the initial 
mitigation package, and that additional mitigation would be required for the new work sites 
only. This implies that the intent of the original SMP 2002-2012 is to mitigate for impacts to 
stream reaches that would undergo repeated maintenance in perpetuity. 

DFG needs clarification on this proposition. Margaret Paul (Environmental Scientist, DFG) 
stated that the CEQA and Lake and Streambed Alteration Agreement (LSAA) negotiations, 
which she participated in, of the SMP 2002-2012 was to mitigate in perpetuity for impacts 
that occurred (some repeatedly) within the term of the original SMP 2002-2012. The 
original SMP was not developed such that there could be repeated impacts in perpetuity 
without additional CEQA review, permitting, and mitigation after the original SMP 2002-2012 
term. 

Under CEQA, the SMP 2012-2022 is a project. The District has identified the term of this 
project as ten years. It is assumed that there may be repeated disturbances to certain 
areas during the ten-year term of the SMP program. DFG permits and approvals will cover 
impacts to those areas for the ten-year term. If, after the ten-year term, the District wishes 
to continue to implement the SMP, this would be considered a new project under CEQA, 
which would require new CEQA review, permitting, and mitigation. 







Ms. Sunny Williams 
October 5, 2011 
Page 7 


N22 


N23 


N24 


N25 


Pages 2-36, 3.3-73, and 3.3-79 - Programmatic mitigation program: The draft SEIR 
describes the District’s mitigation approach under the new SMP 2012-2022, which includes 
a new component where ecological services are provided annually on an as-needed basis. 
Please describe what is meant by bullet number 3 (New Programmatic Mitigation) on page 
2-36, and how the instream complexity and gravel augmentation mitigation programs differ 
from ecological services-type mitigation. 

The draft SEIR states that the District proposes to choose between long-term land 
acquisition projects or ecological services-based annual mitigation projects for its 
maintenance impacts. A portion of the mitigation identified for state listed species in the 
draft SEIR relies on the implementation of Mitigation Measure BIO-1 and Mitigation 
Measure BIO-2, which may include, but do not require, in-perpetuity mitigation. Fish and 
Game Code Section 2081 requires impacts to any state listed species be fully mitigated and 
fully funded. A component to an ITP requires conservation of lands that have these species 
present. DFG will consider, for an ITP, a dual component strategy of conservation of the 
species on occupied land that will be both 1) land that will be conserved as part of the 
mitigation into perpetuity and 2) land that would need wildlife habitat enhancement. 

Page 2-37 - Table 2-9: Table 2-9 presents the proposed mitigation ratios for sediment 
removal and vegetation management activities under different types of mitigation 
components. It is unclear how some of these mitigation ratios were developed. Please 
clarify how each of these ratios was derived. DFG would review this on a case by case 
basis. 

However, DFG finds several of the ratios provided in Table 2-9 to be inadequate to 
compensate for the impacts. For example, how did the District determine a mitigation ratio 
of 1.2:1 for the invasive plant management program and the riparian restoration and 
planting program? Planting or restoration of 1.2 acres for every acre of riparian habitat 
impacted does not appear to adequately compensate for the temporal loss that would occur 
while the newly planted or restored riparian habitat grows to attain the equivalent functions 
and values of the impacted riparian habitat. 

Another example is the mitigation ratio of 0.5:1 for instream habitat complexity features. 

DFG does not agree that placing 0.5 acres of instream habitat complexity for every acre of 
impacted stream adequately compensates for the impact to instream habitat complexity. 
DFG advises the District to reevaluate the mitigation ratios provided in this table and adjust 
them to adequately compensate for the incurred impacts, along with a justification for each 
ratio. 

Page 2-38 - Permits and approvals: Table 2-10 lists the agency permits and approvals 
issued for the SMP, including their original dates of issuance and dates of expiration. 

Please revise the table to accurately portray the 1602 LSAA issued by DFG: 

• R3-2001-0119 issued on July 8, 2002; expiration date of December 31, 2006 

• Extension issued December 1, 2006; expiration date of December 31, 2007 



Ms. Sunny Williams 
October 5, 2011 
Page 8 



N25 


Extension issued December 3, 2007; expiration date of December 31,2008 
Extension issued December 17, 2008; expiration date of December 31,2009 
Extension issued January 7, 2010; expiration date of December 31,2010 
1600-2009-0361-R3 issued January 12, 2011; expiration date of December 31,2014 


N26 


N27 


Page 2-40 - Work windows: Table 2-11 shows a comparison of key differences between 
the 2002 SMP and 2012 SMP Update. There are a couple inconsistencies in the table and 
other parts of the document. The last column on page 2-40 shows a work window of July 1 
to October 15 for bank stabilization, whereas there are several references to June 15 
(including pages ES-10 and 2-26 and BMP GEN-1) as the beginning of the instream work 
window for activities including sediment removal, herbicide application, and bank 
stabilization. Please correct the table to accurately reflect a consistent work window. 

The last column in Table 2-11 states that work may continue until completion, or until the 
first 5-day forecast that includes significant rainfall. There are numerous references in other 
parts of the document (including but not limited to pages 8 and 41 in the SMP Manual, page 
2-26, and page 3.3-161) to a 48-hour, 3-day, or 72-hour forecast. Please modify the table 
and text to reflect a consistent forecast (5-day) on which to base a decision to continue 
work. Please note that other comments in this letter address the District’s proposal to 
continue work instream after October 15. 

Page 2-41 - Rodenticides: The last row in Table 2-11 under Management of Animal 
Conflicts describes a change from the 2002 SMP pertaining to rodenticides and fumigants. 
Under the original 2002 SMP, no rodenticides or fumigants were to be used near salt marsh 
harvest mouse ( Reithrodontomys raviventris) range, one-half mile of burrowing owl ( Athene 
cunicularia) locations, or potential range of sensitive amphibians. Under the 2012 SMP 
Update, the requirements change, where no rodenticides or fumigants will be used within 
the current mapped potential range of sensitive amphibians, and specifically designed bait 
stations will be used to prevent entry of California tiger salamander ( Ambystoma 
califbrniense), California red-legged frog ( Rana aurora draytonii ), foothill yellow-legged frog 
(Rana boylii), or salt marsh harvest mouse. 

Does the District propose to use the designed bait stations to prevent entry of amphibians 
as a precautionary measure since there is to be no use of rodenticides within the current 
mapped potential range of sensitive amphibians, or does the second measure conflict with 
the first? How does the specifically designed bait stations effectively exclude a species 
such as salt marsh harvest mouse, while allowing other access to target species of 
rodents? BMP ANI-3 on page 2-73 indicates that the District intends to implement a 
656-yard buffer around known locations of burrowing owl where no rodenticides or 
fumigants will be used. Table 2-11 does not appear to reflect this measure. 



N28 


Page 2-44 - Snags: Table 2-11 states that hand removal of woody vegetation may be done 
for ecological health/stewardship, including snag removal. DFG considers snags to be an 
important wildlife habitat component which acts as a natural source of woody debris, as well 


Ms. Sunny Williams 
October 5, 2011 
Page 9 


N28 

N29 

N30 

N31 

N32 


as, for food, shelter, and nesting habitat for a wide variety of wildlife, including bats and 
cavity-nesting birds. Please disclose criteria the District would use to determine the 
necessity to remove snags. 

Page 2-44 - Stump treatment: Table 2-11 lists stump treatment under hand removal 
activities, rather than categorizing it under herbicide use. What is the District’s rationale for 
this and how will this affect the District’s quantification of herbicide use in the SMP 
program? 

Pages 2-46 and 3.3-161 - Instream herbicide use: Table 2-11 shows instream herbicide 
use between June 15 and October 15. Please modify this work window to end August 15 in 
the Guadalupe and Coyote watersheds to minimize impacts to upmigrating Chinook salmon 
and ensure that the text on page 3.3-161 is consistent with this. 

Page 2-48 - BMP GEN-2: BMP GEN-2 Instream Herbicide Application Work Window 
states that any modifications to the use of herbicides and surfactants instream will require 
review and approval by the National Marine Fisheries Service (NMFS). Please revise to 
include review and approval by DFG for modifications to the use of these materials 
anywhere in the SMP (instream or upland). 

Page 2-49 - BMP GEN-6: The first bullet in BMP GEN-6 Minimize Impacts to Nesting Birds 
via Site Assessments and Avoidance Measures states project areas will be checked for 
nesting birds within two weeks prior to starting work, and if a lapse of two weeks or longer 
occurs, another focused survey will be initiated. Please revise to checking for nesting birds 
within one week prior to starting work, and if a lapse of one week or longer occurs, another 
focused survey will be initated. The second bullet refers to a buffer of 25 feet for ground¬ 
nesting non-raptors. Please revise to a buffer of 50 feet for ground-nesting non-raptors. 


Pages 2-50, 3.3-197, and 3.3-198 - BMP GEN-7 and Mitigation Measure BIO-13: 

Implement Compensatory Mitigation for the Burrowing Owl: BMP GEN-7 and Mitigation 
Measure BIO-13 refer to burrowing owl eviction, relocation, burrow destruction, and artificial 
burrows. Due to the historical and continual loss of habitat and the rarity of the burrowing 
owl in the state, particularly in Santa Clara County, DFG, as a trustee agency, will neither 
recommend nor approve burrowing owl eviction or relocation, passive or otherwise. These 
N33 activities can lead to mortality in a significant number of owls. DFG Fish and Game Code 

Section 3503 says “It is unlawful to take, possess, or needlessly destroy the nest or eggs of 
any bird, except as otherwise provided by this code or any regulation made pursuant 
thereto.” Section 3503.5 says “It is unlawful to take, possess, or destroy any birds in the 
orders Falconiformes or Strigiformes (birds of prey), or to take, possess, or destroy the nest 
or eggs of any such bird except as otherwise provided by this code or any regulation made 
pursuant thereto.” 

DFG cannot approve the use of artificial burrows. Historically, what applicants have done to 
address burrowing owl issues is to avoid, minimize, and mitigate for their impacts. This can 
V be done by avoiding activities during the nesting period, and putting into conservation, via 



Ms. Sunny Williams 
October 5, 2011 
Page 10 



fee title or a conservation easement, land that contains nesting burrowing owls. Another 
alternative is to purchase credits from an approved burrowing owl conservation bank. DFG 
is available to consult with the District on a case-by-case basis for projects involving 
burrowing owls. 


Page 2-51 - BMP GEN-9: The third item under BMP GEN-9 refers to special-status plant 
surveys being conducted at appropriate times of year to identify plants. Please revise the 
text to state “' he District will conduct updated focused-species rare plant blooming-period 
surveys according to the Protocols for Surveying and Evaluating Impacts to Special-Status 
Native Plant Populations and Natural Communities (CDFG 2009).” The survey protocol can 
be accessed at http://www.dfq.ca.qov/bioqeodata/cnddb/pdfs/Protocols for Surveying 
and Evaluating lmpacts.pdf. 


Page 2-53 - BMP GEN-12: BMP GEN-12 refers to a 25-foot buffer that will be established 
around any active western pond turtle nests. DFG advises the District to increase this 
buffer to 50 feet. Include the presence of a full-time biological monitor when maintenance 
activities are conducted in the vicinity of the active nest. 

Pages 2-56 and 3.3-222 - San Joaquin kit fox: Impact BIO-40: Impacts on the San Joaquin 
Kit Fox describes the San Joaquin kit fox (Vulpes macrotis mutica) as federally endangered. 
Please revise to include the status of this species as state threatened. BMP GEN-5.5 
Avoidance of Impacts on the San Joaquin Kit Fox states that if a natal/pupping den is 
discovered within the project area or within 200 feet of the project boundary, the U.S. Fish 
and Wildlife Service (USFWS) will be immediately notified and that destruction of any 
known or natal/pupping kit fox den would require take authorization from USFWS. Please 
revise this BMP to include the requirement of take authorization from D r G if take (defined 
by Fish and Game Code 86 as to hunt, pursue, catch, capture, or kill, or attempt to hunt, 
pursue, catch, capture, or kill) will occur. 

Page 3.3-10 - Incidental Take of state-listed species: The draft SEIR refers to the need for 
a CESA take permit or other approval for several state listed species, including but not 
limited to California clapper rail ( Rallus longirostris obsoletus ), California black rail 
(Laterallus jamaicensis coturniculus), California condor ( Gymnogyps californianus), bald 
eagle ( Haliaeetus leucocephalus), and salt marsh harvest mouse. These five species are 
fully protected species for which there is not a permitting process for their take (Fish and 
Game Code sections 3511 and 4700). Take, as defined by Fish and Game Code Section 
86, means to hunt, pursue, catch, capture, or kill, or attempt to hunt, pursue, catch, capture, 
or kill. Therefore, any activities that result in take of these species, including being captured 
in a trap or poisoning from herbicide or rodenticide (either by direct consumption or by 
secondary poisoning) must be completely avoided for these species. 

Page 3.3-41 - Herbicide: In the fourth paragraph there is a sentence that states that in 
general, herbicide has less impact than hand removal because hand removal is targeted to 
specific plants. Please clarify the intent of this statement. 










Ms. Sunny Williams 
October 5, 2011 
Page 11 


Page 3.3-42, 3.3-72, 3.3-79, 3.3-142, 3.3-162, and 3.3-163 - Quantification of impacts: The 
draft SEIR discusses the District’s intent to refine the quantification of impacts during 
implementation of project activities and tallying those impacts up at the of the end of a given 
year such that they would be used as the basis for determining mitigation, which would then 
be implemented at either that year’s end or the following year. How would this method 
account for temporal loss of habitat? Also, DFG does not find this method appropriate for 
state listed species, because CESA ITPs are issued with impacts identified and quantified 
and the mitigation is described in the Permit. 

Pages 3.3-60-3.3-62: Pyramat and chain link fencing: The draft SEIR identifies several 
materials in the Management of Animal Conflicts portion of the SMP to prevent burrowing 
animals from establishing new burrows. Materials proposed include surface application of 
erosion control blankets, pyramat, and chain link fencing. DFG does not approve the use of 
plastic materials, such as pyramat, in or near stream banks. Although tightly woven to 
minimize the likelihood of entanglement issues with reptiles and amphibians, DFG staff has 
observed portions of pyramat becoming unanchored within less than one-year of 
installation. Plastic materials such as this may be dislodged during high flows. This may 
lead to entanglement issues, water quality issues, and the introduction of plastic debris into 
the stream channel. DFG also has concern with the use of chain link fencing, as this too 
may become dislodged during high flows and result in washing downstream. 

Pages 3.3-64-3.3-67 - Tables 3.3-5 and 3.3-6: Tables 3.3-5 and 3.3-6 show the projected 
impact acreages due to sediment removal and vegetation management by habitat type and 
activity (non-tidal reaches and tidal reaches, respectively). The habitat types include 
woodlands, herbaceous (non-wetland), sediment wetland, aquatic (wetland), herbaceous 
(wetland), shrub, and misc. DFG is not clear what is meant by sediment wetland, aquatic 
wetland, and herbaceous wetland. Please clarify. For example, DFG assumes that if 
sediment is in the channels, that impacts of sediment removal would result in some level of 
impact to aquatic wetlands. However, the tables show the column of impact to aquatic 
wetland to be 0 in most watersheds. Please define these terms and describe what 
information the tables are meant to convey. 

Pages 3.3-68, 3.3-107, 3.3-112, 3.3-159, and 3.3-183 - Work area percentage: See 
General Comment 5 at the beginning of the letter. 

Page 3.3-69 - Canals and other wetlands: The draft SEIR states that the majority of 
wetlands and aquatic habitats providing important ecological functions and values are 
jurisdictional waters of the United States by the U.S. Army Corps of Engineers (USACE), 
and canals subject to SMP activities are not expected to be considered waters of the United 
States. DFG has adopted the USFWS’ one-parameter definition of a wetland, and has 
adopted the State’s no net-loss policy on wetlands (Fish and Game Code, 2011-Wetland 
Resources page 578). DFG requests that the District map and assess impacts to canals 
and other wetlands meeting the one-parameter definition and proposed appropriate 
mitigation. 



Ms. Sunny Williams 
October 5, 2011 
Page 12 


Page 3.3-72 - Inoperable canals: The draft SEIR states that no mitigation is necessary for 
impacts to non-jurisdictional “other waters,” which are limited to unvegetated areas of 
inoperable canals. Any canals holding water may be considered a wetland under the one- 
parameter definition of a wetland. See the comment for page 3.3-69 above for discussion 
pertaining to canals. 

Page 3.3-72 - Wetland impacts: See the comment for page 2-36 above pertaining to the 
District choosing between mitigation in perpetuity versus pay-as-you-go mitigation. 

Page 3.3-72 - In perpetuity mitigation: The draft SEIR says “For permanent impacts and, at 
the discretion of SCVWD, repetitive impacts to wetlands or other waters in a specific area, 
the District will provide mitigation in perpetuity via one or more of the following methods.” 
The document lists various methods of in perpetuity mitigation as well as pay-as-you-go 
mitigation. DFG advises the District to implement in perpetuity mitigation for permanent 
impacts. Please revise the text to ensure that in perpetuity mitigation is implemented for 
permanent impacts. 

Pages 3.3-72, 3.3-73, and 3.3-79 - In perpetuity mitigation ratios: The draft SEIR presents 
the mitigation ratios for in perpetuity mitigation. They are in-kind restoration/creation 
(1.5:1), in-kind preservation and enhancement (3:1), and out-of-kind preservation of 
watershed lands (8:1). In-kind restoration does not provide the equivalent level of mitigation 
as in-kind creation, and therefore the two types of mitigation should be accounted for 
separately and corresponding mitigation ratios should be proposed to adequately reflect 
their differing mitigation values. In addition, please provide the rationale for proposing a low 
mitigation ratio of 1.5:1 and describe why this ratio is lower than that provided for in-kind 
preservation and enhancement (3:1). In-kind creation will require a longer timeline to 
achieve the functions and values equivalent to habitat that would be restored, preserved, 
and enhanced. Note that DFG does not generally approve out-of-kind mitigation. DFG is 
willing to review this proposal on a case-by-case basis. The 8:1 mitigation ratio for land 
acquisition in watershed lands out of kind is acceptable. 

The last item in the list of possible in perpetuity mitigation refers to the District collaborating 
with owners of land that is currently managed for open space or passive recreation. DFG 
does not approve enhancement or management of land that is in public ownership as 
mitigation. The District needs to focus in perpetuity mitigation on lands not in public 
ownership. 

Page 3.3-73 - Pay-as-you-go mitigation: Please provide the rationale for the low mitigation 
ratio for the pay-as-you-go mitigation of 1.2:1. How does the proposed mitigation ratio 
adequately compensate for impacts from sediment removal and vegetation management, in 
terms of the temporal loss of habitat due to the time it would take for riparian plantings to 
effectively match the functions and values of habitat lost during maintenance activities? 


Ms. Sunny Williams 
October 5, 2011 
Page 13 


Page 3.3-75 - Mitigation for bank stabilization impacts: The draft SEIR states that impacts 
to non-tidal wetlands and aquatic habitats resulting from bank stabilization will be provided 
using the mitigation ratios identified in Table 2-4. See the comment to pages 2-25 and 
2-26 with regard to the mitigation ratios in that table. The text on page 3.3-75 describes 
softscape repairs as self-mitigating because they will not result in long-term adverse effects. 
The ratios for softscape repairs in Table 2-4 are generally 1:1, which is not self-mitigating. 

A self mitigating mitigation ratio is 0:1, which would not be appropriate for these repairs. 
Please revise the text on page 3.3-75 to accurately describe the ratios. 

Pages 3.3-77 and 3.3-80 - Table 3.3-9: Table 3.3-9 shows the estimated impacts to 
riparian woodland, forest, and scrub-shrub from projected vegetation management in each 
watershed. The total amount of pruning projected for all the watersheds is shown as 
13.4 acres. However, the first paragraph on page 3.3-77 and the fourth paragraph on page 

3.3- 80 refer to 40 acres of pruning. Page 3.3-80 also discusses 12 acres of pruning, based 
on a mitigation factor of 0:3. It is unclear how the 13.4 acres was calculated in Table 

3.3- 9 and how this relates to the 40 acres and 12 acres discussed in the text. Please 
clarify. 

Page 3.3-77 - Repetitive riparian impacts: The draft SEIR implies that impacts to woody 
riparian vegetation would mostly be considered temporary. However, the document 
acknowledges that impacts to riparian vegetation that are repetitive will prevent re-growth. 
Please clarify. 

Pages 3.3-80 and 3.3-105 - Tree replacement ratios: The draft SEIR describes tree 
replacement ratios for removed trees (6 to 12 inches dbh) at either 1:1,2:1, or3:1, 
depending on the overall quality and function of the removed trees. After reviewing 
Attachment C (Tree Scoring for Removal of Trees and Shrubs < 12” dbh) of Appendix A 
(2012 SMP Manual), DFG does not consider the tree replacement ratios to adequately 
compensate for removal of trees up to 12 inches dbh. The methodology described in 
Attachment C of Appendix A does not appear to consider dbh or the fact that planting 
between 1 and 3 acorns or seedlings in place of a tree with a stem diameter up to 12 inches 
dbh will not adequately account for the temporal loss of habitat provided by that tree. 
Depending on the tree species, it may take several years for the newly planted trees to 
achieve comparable stature and habitat value to that of the lost tree. DFG advises the 
District to implement tree replacement ratios such that native trees are replaced at a 
minimum ratio of 3:1. 

Page 3.3-82 - Impacts to sensitive plant communities: The draft SEIR describes projected 
acreages of impacts to various sensitive plant communities such as coast live oak and 
valley oak woodlands, sycamore-dominated woodland, and serpentine communities. 

Please provide this data in the form of a table to facilitate reference. 



Ms. Sunny Williams 
October 5, 2011 
Page 14 


Pages 3.3-82 and 3.3-89 - Repetitive serpentine impacts: The draft SEIR states that 
impacts to serpentine plant communities would be considered temporary despite the 
repetitive nature. Impacts to serpentine plant communities that are repetitive should be 
considered permanent due to the fact that the ability for the serpentine plant communities to 
regenerate may be limited with repeated disturbance. Please clarify this point in the text. 

Pages 3.3-88, and 3.3-234 through 3.3-243 - Plant surveys: The draft SEIR refers to plant 
surveys that the District conducted in 2004 and 2008. DFG considers plant surveys older 
than two years generally outdated. DFG requests that the District conduct updated 
focused-species rare plant blooming-period surveys according to the Protocols for 
Surveying and Evaluating Impacts to Special-Status Native Plant Populations and Natural 
Communities (CDFG 2009). The survey protocol can be accessed at 
http://www.dfq.ca.qov/bioqeodata/cnddb/pdfs/Protocols for Surveying and Evaluating Im 

pacts.pdf . 

Pages 3.3-88 through 3.3-100 - Mitigation for special-status plants: The draft SEIR 
describes the impacts and proposed mitigation for special-status plants. Note that under 
Section 15380 of the CEQA Guidelines, DFG will require mitigation for any impacts to rare 
or sensitive plant species, regardless of the portion of the population size impacted. As part 
of the mitigation required for impacts to sensitive plant species, DFG will require the District 
to 1) acquire or protect through a conservation easement land containing the target 
sensitive plant species; 2) implement a minimum 5-year monitoring plan with adaptive 
management to document the success of reintroducing seed propagules to a mitigation site; 
and 3) ensure that seeds of any-rare plant species not already in a seed conservation bank 
be placed into a seed conservation bank repository for long-term storage for availability of 
genetic research and reintroduction conservation work. Any transplanting of special-status 
plants shall be coordinated with the appropriate wildlife agencies. 

Page 3.3-93 - HMMP for special-status plants: The draft SEIR describes elements that will 
be included in the HMMP for special-status plants. In the last bullet on the page, there is a 
description of numerous monitoring measures to be included in the HMMP. Please include 
monitoring to address necessary remediation for any exotic plants that are accidentally 
introduced into the mitigation site. 

Page 3.3-105 - Impact BIO-7: Impact BIO-7 describes the loss of ordinance trees that may 
result from project activities. The document acknowledges that some ordinances may be 
size-based, while some may be species-based and that there isn’t always a distinction 
between native and non-native species. DFG advises the District to work with the 
appropriate municipality to ensure that trees used to replace impacted ordinance trees are 
native species. 

Page 3.3-107 - Fish Relocation Guidelines: The draft SEIR refers to the Fish Relocation 
Guidelines, which were developed in coordination with the NMFS and DFG as a reference 
for properly relocating fish during project dewatering activities. Please include a copy of 
these guidelines as an attachment in the Final SEIR. 










Ms. Sunny Williams 
October 5, 2011 
Page 15 


N61 


Pages 3.3-123 and 3.3-124 - Mitigation Measure BIOS: Augmentation of Spawning Gravel: 
The draft SEIR states that if more than 500 square feet of sediment removal is proposed 
along steelhead streams, a District fisheries ecologist will assess the sediment removal site 
for spawning and rearing habitat quality before the initiation of work. If it is determined to be 
of high quality, compensatory mitigation will be provided by the installation of spawning 
gravel along the creek at a ratio of 1:1. There is no rationale for why this assessment and 
mitigation would not be applied to areas where sediment removal is less than 500 square 
feet. DFG has concerns with this approach, given the limitations of spawning gravel in the 
watersheds below the reservoirs, and the relatively low numbers of spawning steelhead and 
Chinook salmon in District streams. The District’s proposed approach would essentially 
disregard the value of spawning gravels that the District does not deem to be of high quality 
(by only applying mitigation for the loss of high quality gravel), and does not adequately 
compensate for the loss of spawning gravel (a limited but necessary resource for 
salmonids) when the impacts measure less than 500 square feet. DFG advises the District 
to revise this mitigation measure to eliminate the 500 square feet minimum threshold, and 
apply mitigation to spawning gravel that may be deemed less than high quality under the 
District’s assessment. 


N62 


N63 


Page 3.3-125 - Mitigation Measure BIOS: Augmentation of Instream Complexity for Non- 
Tidal Stream Fish: The draft SEIR states that the District will provide mitigation for loss of 
high-quality instream complexity. The document lists criteria for determining whether 
features are considered high quality. Please clarify if only one or all of the listed features 
must be present for the District to deem features of instream complexity high quality. As 
described in the comment above for pages 3.3-124 and 3.3-125, the District’s proposed 
approach appears to disregard the value of instream complexity that may be compromised 
and does not adequately compensate for the loss of these features, which are limited in the 
watersheds below the reservoirs. DFG advises the District to revise this mitigation measure 
to provide adequate compensation for those features of instream complexity that may be 
deemed less than high quality under the District’s assessment. 

In addition, DFG advises the District to increase the proposed mitigation ratio for instream 
complexity, which is currently proposed in the document as 0.5:1. The document says the 
ratio is proposed at less than 1:1 due to erosion, deposition, tree-falls, and debris 
mobilization that is expected to occur within a few years that will naturally reintroduce 
instream complexity. DFG does not agree with this approach, as this does not take into 
account the temporal loss of this habitat that may take several years to be naturally 
reintroduced into the stream. 


N64 


Pages 3.3-130 and 3.3-245 - California tiger salamander: The DSEIR incorrectly identifies 
the California tiger salamander as state endangered. Please revise to show the correct 
status which is state threatened. 


N65 



Pages 3.3-131 and 3.3-144 - Nonbreeding habitat for California tiger salamander and 
California red-legged frog: The draft SEIR does not adequately address the impact of loss 
of upland refugia habitat for the California tiger salamander and the California red-legged 



Ms. Sunny Williams 
October 5, 2011 
Page 16 


a frog due to the loss of burrows. The District’s Dam Maintenance Program also proposes to 
destroy and fill rodent burrows which serve as habitat for these species. Either program by 
itself may have a significant impact on the loss of upland habitat for California tiger 
salamander and California red-legged frog. In tandem, the two programs could have 
N65 devastating impacts for these species due to the inability to find upland refugia within 

dispersal distance of breeding habitat. Please assess the impacts of the SMP Update on 
the non-breeding portion of the California tiger salamander and California red-legged frog 
life cycles and propose a mitigation plan to adequately compensate for the loss of upland 
refugia habitat. 

Pages 3.3-133 through 3.3-135, 3.3-147, and 3.3-148 - Color schemes on mapping: 

Figures 3.3-10 and 3.3-13 show projected vegetation management activities in red and 
N66 sediment removal activities in green. Please use the same color scheme in Figures 3.3-11, 

3.3- 12, and 3.3-14 to avoid confusion, rather than changing between red and green among 
the different maps. 

Page 3.3-142 - Mitigation Measure BIO-10: Implement Compensatory Mitigation for the 
California Tiger Salamander: Mitigation Measure BIO-10 describes the District’s intent to 
tally impacts to California tiger salamander habitat on a yearly basis, provide mitigation at a 
ratio of 2:1 on an acreage basis, and choose between preservation, management, and 
enhancement of occupied habitat, or restoration and enhancement of currently unsuitable 
habitat. See the comment above for pages 3.3-42, 3.3-72, 3.3-79, and 3.3-142 regarding 
tallying impacts on a yearly basis and applying mitigation based on this annual assessment. 
DFG advises the District to focus on mitigation based on preservation, management, and 
N67 enhancement of habitat occupied by California tiger salamander, rather than restoring or 

enhancing currently unsuitable habitat. DFG may consider this second type of mitigation 
(assuming the land was protected in fee title or with a conservation easement in perpetuity) 
on a case-by-case basis with a caveat that DFG would require the District to monitor the 
acquired land and be able to demonstrate occupation of the enhanced or restored habitat 
by California tiger salamander within 5 years. If occupation within 5 years cannot be 
demonstrated, DFG would require additional mitigation equal to or greater than the original 
requirement to account for temporal loss of habitat. 

Pages 3.3-143 and 3.3-144 - California tiger salamander: The last paragraph on page 

3.3- 143 states that if lands that the District currently owns, such as mitigation lands 
acquired for the California red-legged frog for the 2002-2012 SMP, can be enhanced in 

N68 such a way as to substantially improve their value to California tiger salamander, then the 

District may use those lands as mitigation for the California tiger salamander. This 
approach would be unacceptable to DFG, as those mitigation lands are already protected in 
perpetuity via a conservation easement. Compensatory mitigation for California tiger 
salamander must be implemented on land not already under conservation. 

Pages 3.3-162 and 3.3-163 - Mitigation Measure BIO-11: Implement Compensatory 
N69 Mitigation for the California Red-Legged Frog: Mitigation Measure BIO-11 describes the 
Y District’s intent to tally impacts to California red-legged frog habitat on a yearly basis, 



Ms. Sunny Williams 
October 5, 2011 
Page 17 


N69 



provide mitigation at a ratio of 2:1 on an acreage basis, and choose between preservation, 
management, and enhancement of occupied habitat, or restoration and enhancement of 
currently unsuitable habitat. See the comment above for pages 3.3-42, 3.3-72, 3.3-79, 
3.3-142, 3.3-162 and 3.3-163 regarding tallying impacts on a yearly basis and applying 
mitigation based on this annual assessment. DFG advises the District to focus on 
mitigation based on preservation, management, and enhancement of habitat occupied by 
California red-legged frog, rather than restoring or enhancing currently unsuitable habitat. 
DFG may consider this second type of mitigation (assuming the land was protected in fee 
title or with a conservation easement in perpetuity) on a case-by-case basis with a caveat 
that DFG would require the District to monitor the acquired land and be able to demonstrate 
occupation of the enhanced or restored habitat by California red-legged frog. If occupation 
cannot be demonstrated, DFG would require the District to implement mitigation elsewhere 
on occupied habitat. 


N70 


N71 


Page 3.3-164 - Table 3.3-19: The text on page 3.3-164 incorrectly states that Table 3.3-19 
indicates the acreage of projected sediment removal in potential foothill yellow-legged frog 
habitat. Table 3.3-18 shows acreage of projected sediment removal in areas of potential 
foothill yellow-legged frog, whereas Table 3.3-19 shows projected vegetation management 
impacts in areas of potential foothill yellow-legged frog. Please revise. 

Page 3.3-191 - Mitigation Measure BIO-12: Implement Compensatory Mitigation for the 
Least Bell's Vireo: BIO-12A states that vegetation management will occur no more than 
every three years in the reach of lower Llagas Creek from Southside Drive downstream to 
the confluence with the Pajaro River (with the exception of levee tops and lower 
maintenance roads), to allow for the re-growth of shrubs and taller forbs. In addition, the 
measure states that vegetation management will occur along no more than half (measured 
longitudinally along the creek) of the reach downstream of Southside Drive. DFG finds BIO- 
12A to be a minimization measure, rather than an adequate mitigation measure to 
compensate for the loss of habitat for least Bell’s vireo. Please specify the linear feet of 
creek extending from Southside Drive to the confluence with the Pajaro River. 


N72 


BIO-12B states that the District will create or restore conditions similar to those currently 
present along lower Llagas Creek by acquiring land, an easement on land, or permission 
from landowners along the Pajaro River, or along Carnadero Creek downstream from 
Highway 25, and managing a strip 50 feet wide outside of the woody riparian canopy to 
enable tall forbs and shrubs to grow. The 50 foot strip would be managed such that 
portions are disturbed every 3 to 4 years, with no more than half disturbed in a specific year. 
While DFG finds BIO-12B to be a more appropriate mitigation measure in as much as it 
includes acquisition of vireo habitat, it is inadequate since it allows disturbance to least 
Bell’s vireo habitat. 


N73 



The document states that the District may choose between either BIO-12A or BIO-12B. 
DFG does not agree that this is appropriate for the reasons stated above, that BIO-12A is a 
minimization measure, and that both measures allow some level of disturbance in what is 



Ms. Sunny Williams 
October 5, 2011 
Page 18 


a supposed to be compensatory mitigation for the loss of least Bell’s vireo habitat. DFG 
N73 advises the District to develop more protective compensatory mitigation that includes 

conservation in perpetuity either via fee title or a conservation easement. 

Page 3.3-199 - Impacts to species preying on burrowing rodents: The draft SEIR states 
that small mammal control may reduce prey availability for species such as the bald eagle 
and golden eagle, but that such effects would be localized and because of the low numbers 
of eagles that forage in the project areas, activities are not expected to impact eagle 
N74 populations. DFG does not agree with this assessment, and considers this impact in 

tandem with the District’s Dam Maintenance Program, which also includes burrowing rodent 
control, to be significant on a local level. In addition, other predatory species that typically 
prey on small mammals may similarly be impacted by a reduction in small mammal prey 
base. 

Page 3.3-218- San Francisco dusky-footed woodrats: The draft SEIR refers to GEN-14 
which pertains to the protection of the San Francisco dusky-footed woodrat. GEN-14 states 
that if woodrat nests are present and would be affected by maintenance activities, the 
District will develop a site-specific woodrat management plan. DFG requests that any 
woodrat management plans be submitted to DFG for review and approval prior to 
finalization. 

Pages 3.3-218 and 3.3-219- Pallid bats: The draft SEIR identifies Impact BIO-37 Impacts 
on the Pallid Bat due to the removal of smaller trees used as breeding or roosting sites as 
well as disturbance-related impacts to maternity roosts. The District identifies BMP GEN-4: 
Minimize the Area of Disturbance and BMP GEN-13: Protection of Bat Colonies to reduce 
the impacts to pallid bats. BMP GEN-13 refers to the implementation of a buffer zone to 
reduce or eliminate the possibility of disturbance (among measures such as avoidance, 
etc.). Please describe what buffer would be used in the event that maintenance activities 
will take place in the vicinity of a pallid bat (or any other species of bat) colony. 

The District proposes Mitigation Measure BIO-15: Provide Alternative Bat Roost to be 
implemented in the event a tree containing a pallid bat maternity roost will be removed. 
Please describe what type of alternative roost structure the District proposes to implement. 
Note that loss of a maternity roost will likely result in fragmentation of the maternity roost, 
resulting in a less successful regional breeding pool. It should not be expected that 
installation of an alternative bat roost will result in the successful recolonization of a 
maternity bat roost in the near future. DFG advises the District to avoid removal of any 
trees that contain an active maternity roost. If avoidance is not possible for bat roosting 
areas, DFG advises the District to a) provide any alternative roost structure designs to DFG 
for review and approval, and b) locate and protect an extant colony of pallid bats of the 
same quality. 

Page 3.3-223 - Ringtail: The draft SEIR states that bank stabilization and vegetation 
N77 management activities may affect ringtails by disturbing individuals in dens and by small¬ 
's!/ scale habitat loss or modification, but also states that due to the very low number and 





Ms. Sunny Williams 
October 5, 2011 
Page 19 


N77 



limited distribution of ringtails estimated to be in the project area and the low probability of 
presence of the species, the effect to this species is expected to be less-than-significant 
and no mitigation is being proposed. Note that the ringtail is a fully protected species, for 
which there is not a permitting mechanism for their take (Fish and Game Code Section 
4700). Therefore, additional avoidance measures must be developed and implemented. 


N78 


Page 3.3-227 - Mitigation Measure BIO-16: Invasive Species Management Plan: The draft 
SEIR states that the primary goal of the Invasive Species Management Plan (IPMP) is to 
preserve and improve habitat within the streams and riparian corridors by reducing the 
population of invasive plant species. DFG requests that the IPMP be submitted to the 
appropriate wildlife agencies for review and approval prior to finalization. 


N79 


Page 3.3-230 - Significant and unavoidable impacts: The draft SEIR states that habitat 
fragmentation caused by proposed SMP activities to be significant and unavoidable. Please 
disclose where fragmentation is anticipated to occur and how the District proposes to 
ameliorate impacts of fragmentation. 


N80 


Chapter 5 

After reviewing the alternatives analysis provided in the chapter, DFG agrees that the 
Proposed Project is the appropriate recommended alternative, provided that the issues 
stated in our letter can be adequately addressed. 


Appendix A 2012 Stream Maintenance Program Manual 

Note that many of the comments brought up in Chapters 2 and 3 also pertain to Appendix A 
[Stream Maintenance Program Manual (Program Manual)] and Appendix C (2012-2022 
SMP Update Mitigation Approach Memorandum). Any changes that are made in Chapters 
2 and 3 as a result of CEQA comments should be made accordingly in Appendices A and 
C. 


N82 


Pages 3, 22, 24, 25, 41 - Mitigation chapter: There are several references to a Mitigation 
chapter in the Program Manual. The Program Manual does not appear to contain a 
Mitigation chapter. 


Page 4 - Capital improvement projects: The Program Manual states that future capital 
improvement projects will analyze and account for long-term maintenance impacts under 
their own environmental review documents, and that any environmental effects of new 
capital improvement projects will be compared to the 2002 SMP projections for that reach of 
N83 creek. The Program Manual also states that mitigation for capital improvement projects will 

only be required if there are impacts from the capital project that were not projected in the 
2002 SMP. This section is unclear why maintenance under future capital improvement 
projects will be compared to 2002 projections, when the maintenance will be conducted 
between 2012 and 2022. In addition, as is discussed under the comment for pages 2-35, 
3.3-42, 3.3-43, 3.3-72, 3.3-73, 3.3-79, 3.3-87, 3.3-99, 3.3-144, and 3.3-163 regarding 
V mitigation in perpetuity, the 2012 SMP is a new project with a new project term. Therefore, 



Ms. Sunny Williams 
October 5, 2011 
Page 20 


N83 

N84 

N85 

N86 

N87 

N88 

N89 

N90 

N91 


A any impacts due to maintenance activities during the new project term should be mitigated 
appropriately. Revise the discussion to clearly state whether maintenance for future capital 
improvement projects will be addressed and mitigated under each capital improvement 
project CEQA document, or under the 2012 SMP. 


Pages 5 and 9 - Maintenance Guidelines: The Program Manual refers to the District’s 
Maintenance Guidelines. There does not appear to be a copy of the Maintenance 
Guidelines in the document. Please provide as an attachment in the Final SEIR. 

Pages 7and 28 - Instream herbicide use: The Program Manual states that instream 
herbicide use will occur between June 15 and October 15. Please modify this work window 
to end August 15 in the Guadalupe and Coyote watersheds to minimize impacts to 
upmigrating Chinook salmon. 

Pages 7 and 29 - Upland herbicide work: The Program Manual states that upland 
herbicide work may occur year-round, weather permitting. Please define what is meant by 
“upland” in this context. 


Page 7 - Sediment removal work window: The Program Manual states that sediment 
removal may occur during the work window of June 15 through October 15 (or until 
December 31 using a 24-hour forecast). See comment for page 2-40 regarding work 
windows. 


Pages 8 and 41 - Bank stabilization: The Program Manual states that bank stabilization 
work is allowed during the work window of June 15 through October 15, and that if it is more 
than 50 percent complete on October 15, it may continue until completion, December 31, or 
until the first 5-day forecast that includes significant rainfall. See comment for pages ES-10 
and 2-26 regarding the bank stabilization work window. 

Pages 18, 20, 24, 26, 30, 32, 37, 41, 53, and 61 - Appendix A: The Program Manual 
contains numerous references to a list of BMPs in Appendix A. The Program Manual does 
not appear to contain Appendix A. 


Pages 21 and 28- Stump treatment: The Program Manual describes stump treatment as 
hand removal rather than including it in herbicide use. See comment for page 2-44. 

Pages 23 and 31 - QEMS procedure: The Program Manual refers to the District’s OEMS 
procedure with regard to tree removal. DFG is unfamiliar with this procedure. Please 
describe and include as an attachment in the Final SEIR. 


N92 


Page 24 - Native trees on channel banks: The Program Manual states that native trees are 
generally undesirable on some channel banks. Please describe what is meant by this 
statement. 



Ms. Sunny Williams 
October 5, 2011 
Page 21 


N93 

N94 

N95 

N96 

N97 

N98 

N99 

N100 


Page 24 - Vegetation on levees: The Program Manual describes vegetation maintenance 
on levees. Please clarify whether the 2012 SMP assumes that the District will be following 
the USACE's guidance on maintaining levees such that they do not contain woody 
vegetation and allow only herbaceous vegetation. Note that the USACE guidance has not 
been finalized. 

Page 26 - Large woody debris: The Program Manual refers to a large woody debris (LWD) 
Program document. DFG is unable to locate a LWD Program document or further 
discussion of the LWD Program anywhere in the Program Manual or the rest of the draft 
SEIR. Please describe and provide a copy in the Final SEIR. 

Page 29 - Herbicide use in serpentine areas: The Program Manual states that herbicides 
may be permitted in serpentine areas when approved by a qualified plant biologist and with 
the incorporation of measures to protect sensitive biological resources. Herbicide use 
should be avoided in serpentine areas to avoid inadvertent impacts that could result from 
drift or from use during nonblooming periods when identification of special-status plants 
may be difficult. 

Pages 30 and 52 - California red-legged frog and California tiger salamander mapped 
areas: The Program Manual refers to range maps for sensitive amphibians, including 
California red-legged frog, California tiger salamander, and foothill yellow-legged frog. 
Please describe how these range maps were developed. DFG advises the District to avoid 
the use of all pesticides, including bait stations, in the range of these species. 

Page 30 - Indicator dye: The Program Manual describes the use of an indicator dye to be 
used to help the herbicide applicator identify areas that have been treated and better 
monitor the overall application. Please discuss what the indicator dye is composed of and 
whether the use of this indicator dye in aquatic herbicides may pose a water quality issue 
for aquatic species. 

Page 32 - Mowing work window: The Program Manual describes a mowing work window 
of February 1 through November 30. Please describe the rationale for this work window 
and how it would avoid impacts to burrowing owl. 


Page 32 - Discing work window: The Program Manual describes a discing work window of 
February 1 through October 15. DFG advises the District to revise this work window to 
June 15 through October 15 to avoid erosion issues and the introduction of sediment into 
adjacent water bodies. 

Page 35 - Equipment in stream channels: The Program Manual describes the possibility of 
lowering small equipment into a stream channel from a nearby stream crossing to minimize 
impacts associated with sediment removal operations. Please clarify that equipment will not 
be operated in wetted streams. 



Ms. Sunny Williams 
October 5, 2011 
Page 22 


N101 

N102 

N103 

N104 

N105 

N106 


Page 37 - Sediment removal work window: The Program Manual states that sediment 
removal may occur between June 15 and October 15, with an extended work window 
through December 31 based on a 24-hour forecast. See comment for page 2-40 regarding 
work windows and weather forecasts. 

Page 37 - Continuing sediment removal after significant rainfall: The Program Manual 
states that additional sediment removal work may continue after significant rainfall on 
Berryessa Creek, Lower Silver Creek, Thompson Creek, Canoas Creek, Ross Creek, 
Calabazas Creek, and San Tomas Aquino Creek. Please provide a clear rationale for 
continuing sediment removal activities in these locations after significant rainfall and why 
the District feels the measures described will adequately avoid erosion issues and protect 
water quality. Also see the comment for page 2-40 regarding weather forecasts. 

Pages 37 and 43 - Monitoring and Reporting: The Program Manual refers to a Monitoring 
and Reporting chapter. There does not appear to be a chapter on Monitoring and Reporting 
in the Program Manual. 

Page 44 - Bank stabilization methods: Table 1 in the Program Manual lists bank 
stabilization methods and their proposed mitigation ratios. See the comment for pages 2-15 
and 2-16 on adequate mitigation ratios and the need to eliminate some of the methods from 
the SMP. 

Pages 52 and 60 - Carcass surveys: The Program Manual states in the Management of 
Animal Conflicts portion of the SMP, carcass surveys will occur daily with the use of acute 
toxins (zinc phosphide and strychnine), and weekly with the use of anticoagulant baits 
(chlorophacinone and diphacinone are listed as examples). DFG does not agree that 
waiting one week after exposure to anticoagulant bait would be appropriate to avoid impacts 
of secondary poisoning to other species that may prey on poisoned target species. This 
approach would also not be consistent with what is proposed in the District’s Dam 
Maintenance Program. DFG provided extensive comments on the District's Dam 
Maintenance Program Draft Program EIR, and DFG advises the District to ensure that 
methods proposed in both the Dam Maintenance Program and SMP are consistent where 
applicable. Please clarify when carcass surveys would begin after initial implementation of 
acute toxins and anticoagulant baits. In addition, please clarify whether the District 
anticipates using anticoagulant baits other that the two listed. 

Page 56 - Minor maintenance: The Program Manual states that regulatory agency staff will 
receive information regarding potential Minor Maintenance projects that require review and 
approval for minor activities that have an impact exceeding 0.05 acres per activity per site. 
Activities exceeding 0.05 acres do not qualify under the category of Minor Maintenance, and 
instead should be reported in the Notice of Proposed Work under the appropriate category 
of sediment removal, bank stabilization, etc.? 


Ms. Sunny Williams 
October 5, 2011 
Page 23 


N107 

N108 

N109 

N110 

Nlll 

N112 

N113 


Page 57 - Footnote 1: The first paragraph on the page has a footnote at the end of the last 
sentence. The explanation for the footnote is missing in the document. 

Attachment A - Bank Stabilization Methods: See comment for pages 2-15 and 2-16 
regarding adequate mitigation ratios and DFG’s recommendation to eliminate some of the 
bank stabilization methods from the SMP. 

Attachment B - Mitigation Feasibility Assessment Field Protocol: There is a formatting 
issue with the first page of Attachment B, which makes it difficult to read. Please correct the 
formatting. DFG is unfamiliar with the proposed Mitigation Feasibility Assessment (MFA) 
Field Protocol. Please describe how the method of MFA ranking was developed, and how 
the scoring and it’s relation to success criteria was developed. Is there literature on this 
methodology and/or any examples of the success of its use elsewhere? 

Attachment C - Tree Scoring for Removal of Trees and Shrubs < 12” dbh: Please describe 
how this method of determining mitigation ratios for trees was developed. Is there literature 
on this methodology and/or any examples of the use of this methodology to adequately 
compensate for tree loss elsewhere? It is unclear why this method does not take stem 
diameter (dbh) into consideration at all. 

On page 1, bullet 1 (Canopy cover), step B(c) indicates that width X length = square 
footage, whereas the Metric table says to assess canopy cover at the widest dripline 
extension point and square that value. These two statements appear to conflict with each 
other. Please clarify as to how the canopy cover is supposed to be measured. 

On page 2, bullet 3 (Ecosystem Benefits), there should be the ability to score the attribute 
called “Used by wildlife” with more than one point, depending on the different elements of 
wildlife use the tree would provide. Some trees provide a wide variety of wildlife uses, and 
those that provide either unique uses or a high number of wildlife uses should be scored 
higher. By only attributing one point for wildlife use, the tree may be undervalued in terms 
of habitat, and therefore, mitigation may be developed that does not adequately 
compensate for its loss. 

On page 3, bullet C (Mitigation Calculation), the highest mitigation ratio of 3:1 may not 
adequately compensate for the loss of certain types of trees with high habitat value. An 
example is a small stature oak tree. Planting one to three acorns or seedlings in its place 
will not adequately compensate for the loss of that tree due to the long period of time it will 
take for those acorns or seedlings to reach a similar stature. Please revise this section with 
appropriate mitigation ratios that will adequately compensate for the loss of trees resulting 
from the SMP. For oak trees, DFG recommends planting three acorns for each inch of 
stem diameter (dbh) that is removed per oak tree. For example, to compensate for the 
removal of an eight inch dbh oak tree, the District shall establish eight planting holes, each 
containing three acorns. 



Ms. Sunny Williams 
October 5, 2011 
Page 24 


DFG appreciates the opportunity to comment on the District’s Stream Maintenance Program 
Update draft SEIR. Any questions or comments regarding this letter and any further 
coordination on this project should be directed to Ms. Tami Schane, Environmental 
Scientist, at (415) 831-4640; or Mr. Liam Davis, Senior Environmental Scientist, at 
(707) 944-5529. 



Regional Manager 
Bay Delta Region 


cc: State Clearinghouse 

Ms. Cori Mustin 
U.S. Fish and Wildlife Service 
2800 Cottage Way, W-2605 
Sacramento, CA 95825 

Mr. Gary Stern 

National Marine Fisheries Service 
111 Sonoma Avenue, Room 325 
Santa Rosa, CA 95404 


3. Responses to Comments and DSEIR Revisions 


Response to Comment N-l 

SCVWD has a series of Quality Environmental Management System (QEMS) documents, 
including Q751D02. Control of Oversight of Pesticide Use and WW75100— Vegetation Control 
Work Instructions, that define the process for evaluating pesticide/herbicide use and 
making modifications to the pesticide/herbicide program. These documents meet all state 
and federal regulations for pesticide use. SCVWD is unaware of the need to prepare a 
Pesticide/Pest Management Plan for wildlife agency review and approval, or of the 
authority under which DFG may require such a plan. In comparison, if SCVWD is working on 
modified channels, these same techniques may be used, but SCVWD also may use broadcast 
spray (for instance, on access roads) or foliar application techniques. 

Response to Comment N-2 

Please refer to the response to Comment N-l. SCVWD is unaware of the legal requirement to 
prepare an Herbicide Management Plan for wildlife agency review and approval, or of the 
authority under which DFG may require such a plan. 

Response to Comment N-3 

As described in the 2012-2022 SMP Manual in Appendix A and on page 2-28 of the DSEIR, 
SCVWD may use sheep, goats, or other appropriate species to provide weed control in 
limited circumstances and in limited areas. SCVWD does not need to prepare, and obtain 
wildlife agency review and approval of, a Grazing Management Plan. Grazing management 
on any conservation lands that are managed as mitigation for impacts to special-status 
species or sensitive communities (such as serpentine communities) would be described in a 
Habitat Mitigation and Management Plan for the specific mitigation site, as described for 
applicable mitigation measures in Section 3.3 (e.g., Mitigation Measure BIO-3, -4, -5, and 
others). Because grazing management may vary somewhat among mitigation sites, 
depending on site conditions and focal species for which management is being performed, a 
single grazing management plan for all mitigation lands would not be appropriate. 

Response to Comment N-4 

The comment describes DFG's emphasis and need for land acquisition-based mitigation. 
SCVWD agrees with DFG on the important role that land acquisition-based mitigation serves 
to provide long-term suitable mitigation for maintenance program impacts. Land 
acquisition-based mitigation would continue to serve as mitigation for program impacts 
projected in 2002. For new work areas identified for the 2012-2022 program period that 
do not yet have mitigation, mitigation would be developed as described in Appendix C to the 
DSEIR, including both “pay as you go" annually developed mitigation, as well as longer-term 
acquisition-based mitigation. SCVWD understands that impacts to state-listed species must 
be addressed through acquisition-based mitigation, rather than “pay as you go" mitigation. 

Regarding the text that the comment requests to be added to the DSEIR, SCVWD is unable to 
add this exact text passage because of the District's legal and operational mandate that 
prevents making such endowment commitments without a clearly defined source of long- 


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3. Responses to Comments and DSEIR Revisions 


term funding. A variety of financial mechanisms meet this objective. SCVWD instead adds 
the following text to the FSEIR that achieves the majority of the intent of the comment, 
which is to clarify the District's commitment to supporting acquired lands as well 
functioning mitigation, on Page 2-35, second paragraph: 

As described in Appendix C to the DSEIR (Mitigation Approach Memorandum). 
SCVWD would provide compensatory mitigation for SMP Update activities requiring 
mitigation by acquiring or protecting appropriate mitigation lands (including 
populations of special-status species, where impacts are to such species), using 
conservation easements or other vehicles as appropriate, or would provide suitable 
ecological services-based mitigation as needed to compensate for annual impacts. 
SCVWD would identify funding mechanisms to support the long-term maintenance 
and conservation of such mitigation lands and projects. 

Response to Comment N-5 

Work area percentage refers to the proportion of a given reach that would be subject to a 
specific maintenance activity. For instance, sediment removal within a 1,000-square foot 
area of a 10,000-square foot reach would have a work area percentage of 10 percent. In 
some cases, work area percentage is calculated based on linear feet of channel, rather than 
area. 

Response to Comment N-6 

Where such plans are part of mitigation for impacts to resources under DFG's jurisdiction, 
the District would follow the process as outlined in DFG's permit conditions. 

Response to Comment N-7 

The DSEIR recognizes the distinction between temporary impacts (those that do not result 
in irreversible modification of habitat; when those impacts cease, habitat regenerates or can 
be restored) and permanent impacts (those that result in irreversible modification of 
habitat, precluding the regeneration of the habitat type that was previously present) to 
biological resources. Where appropriate, the DSEIR discusses that some temporary impacts 
are repetitive, resulting in longer-term effects (at least over the course of the 10-year SMP 
Update). References to these distinctions, such as discussion of the effects of repetitive 
impacts, appear in a number of locations throughout the DSEIR (e.g., on pages 3.3-39, -70, - 
72, -77, -80, -83, and many others). Because of the varying frequencies with which different 
reaches may undergo SMP Update activities, drawing a clearer distinction between multiple 
categories of impacts (e.g., one-time, short-term, repetitive, and permanent) as suggested by 
the comment is infeasible. Furthermore, drawing such a distinction is unnecessary for 
impacts to be mitigated to less-than-significant levels, as the mitigation program has been 
established to account for differences in frequency (or permanence) of impacts, by 
requiring more mitigation or more permanent mitigation for permanent impacts or 
repetitive impacts than for one-time or short-term impacts. 

The comment suggests that the FSEIR should identify additional incremental mitigation for 
repetitive impacts. The mitigation program described in the DSEIR already takes the 


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3. Responses to Comments and DSEIR Revisions 


additional impact resulting from repetitive impacts into account by requiring either for 
SCVWD to provide in perpetuity mitigation for such impacts or that mitigation be provided 
repeatedly if the same area was repeatedly impacted. As a result, the mitigation provided 
for repetitive impacts would be greater (e.g., repeated pay-as-you-go mitigation, or in 
perpetuity mitigation instead of pay-as-you-go) than for a one-time impact. 

The various temporal categories of impacts were considered in the impact assessment for 
each of the species and resources evaluated in the DSEIR. SCVWD recognizes that each of 
the biological resources evaluated in the DSEIR could be affected by one-time, short-term, 
repetitive, or permanent impacts. 

The comment suggests that if special-status species re-establish in impact areas between 
impact events, additional mitigation beyond one-time compensation should be provided. 
The mitigation program described in the DSEIR would be adequate to provide mitigation in 
the event that re-establishment occurred, for several reasons. First, mitigation for impacts 
to some species, such as the California tiger salamander and California red-legged frog, and 
for impacts to sensitive communities, would be provided in perpetuity at a 2:1 
(mitigatiomimpact) ratio; enhancement, preservation, and management of the mitigation 
sites would offset SMP Update impacts, even repetitive impacts, by protecting and 
enhancing populations elsewhere. Second, mitigation for impacts to wetland and riparian 
habitats would be provided, either in perpetuity (to fully compensate for the impact) or on a 
repeated basis if impacts to those habitats were repetitive, thus providing the additional 
mitigation suggested by the comment. Although species re-occupying a maintenance area 
may be impacted by subsequent maintenance, that subsequent maintenance may affect only 
a small proportion of the originally impacted area, or may occur years after the initial 
maintenance. The ability of plants and animals to colonize and use such areas for several 
generations is expected to benefit the populations more than permanently impacting those 
areas, even if subsequent maintenance disturbance were to occur. Finally, for many species 
associated with early-successional habitats (such as the San Francisco common 
yellowthroat), SMP Update activities would help to maintain suitable habitat, and periodic 
disturbance would be a short-term impact, necessary to maintain populations of those 
species. 

The comment's definitions of temporary, short-term, and permanent impacts are noted. 
However, SCVWD does not agree with all the components of these definitions. For example, 
DFG would include activities that would remove habitat for more than two growing seasons 
as a permanent impact. If conditions for regeneration of the habitat were maintained, then 
SCVWD would not consider this impact to be permanent. Furthermore, as described above, 
the mitigation program would provide adequate compensatory mitigation for such an 
impact. 

The comment recommends that all permanently impacted habitat types be mitigated at a 
ratio of at least 1:1, and that additional mitigation be provided if the habitat is sensitive or 
supports special-status species. SCVWD does not agree that impacts to non-sensitive habitat 
types, such as ruderal, developed, landscaped, or other land uses and habitat types, would 
require mitigation, as impacts to these habitats would be less than significant. Mitigation for 
all sensitive and regulated habitats, and mitigation specifically targeting many special- 


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3. Responses to Comments and DSEIR Revisions 


status species, would be required (at a ratio of at least 1:1), as described in Section 3.3 of 
the DSEIR. 

SCVWD is working with DFG to obtain a CESA Incidental Take Permit and appreciates DFG's 
assistance with these biological resources issues. 

Response to Comment N-8 

No additional sediment reuse sites have been identified, beyond those described in the 
DSEIR. The District acknowledges that further CEQA compliance could be required in 
association with new sites. 

Response to Comment N-9 

The rationale for the SMP Update to increase its tree removal size limit from 6 to 12 inches 
is based on the extremely rapid growth rates of certain trees in SCVWD-maintained 
channels. This rationale has been developed using several years' experience during the 
original SMP period (2002-2012); if trees targeted for removal were not cut and removed 
while still at a 3-5-inch-diameter stage, they would quickly grow beyond 6 inches in 
diameter and be off-limits for removal. This situation was particularly limiting for channels 
with aggressive Eucalyptus stands, which grew very rapidly beyond the 6-inch size limit. 
Raising the vegetation size limit for removal would be necessary to prevent SMP Update 
channels from becoming dense forests with insufficient flow capacity. The decision-making 
process to remove trees would be based on several factors, including: 

• Is the tree infected or diseased, and is removal necessary for the improved ecologic 
health of the greater area? 

• Does the tree have structural defects, insect infestation, or pathogens that threaten 
the surrounding area? 

• Is the tree a potential or likely danger because of a high probability for falling that 
would result in potential property damage, human risk, or increased flood threat? 

Response to Comment N-10 

For minor maintenance activities, the number of such grading areas would be small. Minor 
maintenance activities are defined as being activities that result in removing less than 0.05 
acres of wetland or riparian vegetation. Annually, minor maintenance activities would not 
result in impacting more than 0.2 acres of wetlands/riparian vegetation per year. This 
specific type of minor grading typically would occur in areas above the top of bank that 
would not have vegetation and would require small-scale drainage or erosion 
improvements. Minor grading activities to improve local drainage or reduce erosion are not 
projected maintenance activities because of their small size and unknown locations at the 
time of maintenance work projecting. Although estimates are not available concerning how 
much of this type of maintenance activity would occur during the SMP Update program 
period (2012-2022), based on SCVWD's experience to date (under the SMP between 2002- 


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3. Responses to Comments and DSEIR Revisions 


2010), it is estimated that the total area for this type of activity would be in the 1-2-acre 
range during the 2012-2022 period. 

Response to Comment N-ll 

SCVWD would ensure that the canal was dry when conducting sediment removal activities. 
In cases where the channel was not dry during the maintenance period, SCVWD would 
accomplish dewatering by shutting off the appropriate upstream valves or by implementing 
one of the techniques outlined in BMP GEN-33 or BMP GEN-34. 

Response to Comment N-12 

Please refer to responses to Comments D-2, D-6, and D-8. 

Response to Comment N-13 

As stated in the Section 7, Bank Stabilization of the Mitigation Memorandum (in Appendix C 
of the DSEIR, replaced in entirety in Volume II of this FSEIR), SCVWD's preference would be 
to first consider use of softscape approaches, and only use hardscape where absolutely 
necessary. Between 2002 and 2009, the District used softscape techniques over 80 percent 
of the time for bank stabilization activities (32,088 linear feet of softscape treatment versus 
7,383 linear feet of hardscape treatment). See also responses to Comments M-7 and M-8. 

Response to Comment N-14 

Thank you for your comment. The footnote of Table 2-2 is revised as follows: 

Notes: 

1. Certain locations may have been the subject of s e dim e nt channel hand removal 
more than once during the 2002-2009 period, but their lengths are only counted 
once in this column. 

Response to Comment N-15 

The following types of in-kind bank repairs have been conducted under existing SMP: 
maintenance road repair of potholes and toe damage to restore drivability: limited levee 
reconstruction; concrete panels (both in-channel and not); wing walls; certain gage 
structures; in-channel scour of concrete facilities; weirs; outfalls; tide gates; turnouts; and 
various channel bank revetments (both hardscape and not). On revetments, SCVWD has 
allowed in-kind repairs to be replaced with similar features (i.e., replacing sacked concrete 
with rock). However, under no circumstances does SCVWD consider the use of hardscape to 
replace softscape as an “in-kind" repair. 

Response to Comment N-16 

The Dam Maintenance Program would cover activities that affected the structures and 
facilities of outlet structures. The SMP Update would address instream issues. Impacts 


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resulting from maintenance activities would be tracked and mitigated according to the 
process and requirements of the appropriate program. 

Response to Comment N-17 

The comment references Table 2-4, which identifies the SMP Updates' 13 bank stabilization 
treatment methods and their mitigation ratio requirements. The comment notes that 
several of the bank stabilization methods had higher mitigation ratios under the 2002 SMP 
FEIR and regulatory approval than what is shown in Table 2-4. For example, treatments 2A 
(live construction with boulder toe), 3A (contour wattling with boulder toe), 4A (brush 
mattress with boulder toe), and 5A (surface matting with boulder toe) have mitigation 
ratios assigned of 1.5:1 (mitigation-to-impacted area) under the SMP Update 2012-2022, 
whereas in the 2002 SMP FEIR, these treatments had mitigation requirements of 3:1 
(mitigation-to-impacted area). Other treatments including 7 (cellular confinement), 8 (rock 
blanket), 8A (boulder revetment), and 9A (articulated concrete blocks with planted trees) 
are treatments with a proposed mitigation ratio of 2:1, whose mitigation ratios were 3:1 
under the original SMP EIR. The comment indicates that no rationale is provided for why 
these mitigation ratios have decreased from the original program. The comment requests 
that SCVWD restores these bank stabilization mitigation ratios to the higher ratios of the 
original SMP EIR. 

The rationale for lowering bank stabilization mitigation ratios (as described above) is 
rooted in SCVWD's 10 years of SMP experience (2002-2011), when SCVWD has observed 
that the resource values and functions of streambank sites requiring repair and stabilization 
typically is very low. Bank stabilization sites typically exhibit conditions of unstable earthen 
erosion, with no vegetation or vegetation of low value (such as early serai invasive 
vegetation colonizing the destabilized site). SCVWD biologists and geomorphologists have 
observed that historically, bank stabilization sites have poor baseline conditions. Based on 
several years' observations of typically poor quality existing conditions at bank stabilization 
sites, SCVWD is proposing to use mitigation ratios that would more accurately represent the 
mitigation requirement for the loss of ecologic functions/values resulting from maintenance 
activities. SCVWD's primary concern is that the relative baseline of functions/values 
provided at eroded bank sites may be lower than justified by the 3:1 mitigation ratios 
currently in use for certain bank treatments. The proposed revised mitigation ratios, 
including ratios of 1:5 and 2:1, would be more appropriate for the specific baseline 
conditions. 

The comment also suggests that SCVWD should eliminate certain hardscape bank 
stabilization methods including 9 (articulated concrete blocks), 9A (articulated concrete 
blocks with planted areas), 10 (concrete crib walls), and 12 (gunite slope protection) 
because SCVWD has little or no need to use these techniques and superior methods to these 
could achieve stabilization objectives and also provide habitat. SCVWD acknowledges that 
these techniques have had little or zero application in the existing SMP. However, SCVWD 
staff engineers prefer to retain such techniques in the event that specific hydraulic 
conditions at a bank stabilization site may require such hardscape approaches. Any use of 
such techniques would be subject to agency review as part of the Notice of Proposed Work. 
As evidenced by SCVWD's past record of prioritizing softscape or hybrid approaches over 
full hardscape bank approaches (see Table 2-3 of the DSEIR), having such hardscape 


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techniques available for the SMP Update would not necessarily lead SCVWD to their use and 
application. As Table 2-3 suggests, softscape or hybrid solutions were used by SCVWD about 
77 percent of the time during the 2002-2010 period. 

Response to Comment N-18 

SCVWD appreciates DFG's provision of information regarding the need to notify DFG within 
14 days after beginning emergency repair work. 

Response to Comment N-19 

The comment references text in the last paragraph on page 2-27 of the DSEIR that describes 
hard structures providing examples of concrete, sacked concrete, and gabions. The 
comment notes that as gabions are not included as an SMP bank stabilization technique as 
listed in Table 2-4, they should not be referenced in this text on page 2-27. SCVWD agrees 
with this comment. The reference to gabions is removed from the text on page 2-27 of the 
DSEIR as follows: 

As summarized in Table 2-4, the SMP Update would include several bank 
stabilization approaches, ranging from "soft structures" (e.g., willow brush 
mattresses, log crib walls, and pole plantings), to "hard structures" (e.g., concrete, 
and sacked concrete , and gabions ), or a combination of hard and soft structures. 

Response to Comment N-20 

The following definition of hybrid bank stabilization is added as a second paragraph under 
Bank Stabilization on page 2-28 of the DSEIR as follows: 

Hybrid bank stabilization refers to a combination approach whereby softscape bank 
stabilization approaches like live construction, contour wattling, brush mattresses, 
or surface erosion matting are combined with a limited amount of rock toe 
protection at the base of the bank stabilization site. Additional boulders at the toe of 
the bank treatment is only applied if necessary, if there are hydraulic shear forces 
affecting the bank site, or geologic slumping or mass wasting forces affecting the site 
(because of the site's position or slope) that require the additional presence of 
mass/rock at the base of the slope. 

The use of hybrid bank stabilization techniques would be consistent with SCVWD's 
commitment that no more than half of in-kind bank repair projects would consist of 
impervious hardscape each year. This would be true for the following reasons. Boulder toe 
applications would not occur on all soft-scape treatments. When used, boulder toe 
applications typically would occupy less than 20 percent of the overall bank stabilization 
site, focusing on the lower "toe" of the slope. Very often, boulder toe applications are 
constructed with a soil matrix between rocks, which is then vegetated. When this occurred, 
the boulder toe application would not be an impermeable surface, and soil development and 
additional biological functioning would occur. Yes, the "no more than half" commitment 
would include localized hardscape, such as boulders/rocks placed at the toe of the slope. 
Because the "no more than half" commitment would be tracked based on the aerial extent of 


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the bank repairs, a hybrid approach would be accounted for by measuring the area of the 
bank repair that consisted of hardscape versus softscape. 

Response to Comment N-21 

The comment questions the DSEIR's description of the ongoing SMP mitigation program. 
More specifically, the comment references Margaret Paul, who participated in the EIR 
review and 1601 permit development for DFG during the 2001-2002 SMP FEIR approval 
process. The comment suggests Ms. Paul believed that the original mitigation program 
provided mitigation for repeated maintenance programs only within the term of the first 
10-year period of the SMP, 2002-2012. The comment further suggests that the terms and 
conditions of the 2002 SMP FEIR and permit approvals only apply to the original permit 
period (2002-2012). The comment states that “mitigation in perpetuity” was not intended 
to last beyond the 10-year term of the original permits. 

This recollection that “mitigation in perpetuity” was intended to apply only for the first 10 
years of the SMP is not supported on the basis of the record. The District disagrees with 
DFG's interpretation of the original mitigation program for the following reasons: 

• The SMP is a continuous program. It is true that project planning and environmental 
compliance processes typically occur for some specific action or interval. However, 
from its inception, the SMP was organized and described as a long-term, continuous 
maintenance program, not as an individual, short-term project. The State CEQA 
Guidelines confirm that the “project” is the underlying activity being approved and 
does not refer to each governmental approval for the underlying activity (State 
CEQA Guidelines, Section 15378[a] and [c]), and because the SMP is a continuous 
program, it is not a new project for purposes of CEQA. 

• The original mitigation program that was developed for the SMP (2001-2002) was 
anchored on the concept of providing mitigation in perpetuity, meaning mitigation 
that would address repeated impacts in the same locations for the duration of the 
program, not just for the initial permit term. 

• Because the original mitigation program was providing mitigation in perpetuity, it 
used land acquisition and restoration activities as the central components to 
provide mitigation. The land acquisition and restoration mitigation commitments 
included in the original SMP EIR were expansive and very costly to SCVWD. SCVWD 
agreed to pursue such expansive mitigation because it would serve the program in 
perpetuity. 

The District's understanding of the 2001-2002 permit negotiations is supported by text 
contained in the Joint Aquatic Resource Permit Application (JARPA) dated February 14, 
2001; DFGSAA Notification R3-2001-0119 ; RWQCB Order R2-2002-0028; U.S. Army Corps of 
Engineers Permit, File Number 22525S, August 7, 2002 (Corps permit); and the 2002 SMP 
FEIR. Excerpts from these documents are included in this response as follows: 

• The Joint Aquatic Resource Permit Application (JARPA), submitted in 2001 with the 
original SMP permit applications to the San Francisco RWQCB, DFG, USACE, USEPA, 


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USFWS, and NMFS, includes a specific reference and a description of the original 
SMP mitigation program as serving mitigation in perpetuity. The JARPA is provided 
as Appendix D to Volume I of this FSEIR). The first paragraph on page 12 of the 
JARPA (Box 9) describes this issue specifically and succinctly, stating, "For the 
Program, permanent mitigation (see Box 13) is proposed for temporary, repetitive 
impacts." 

• Several of the individual permit authorizations from the original SMP approval 
process (2001-2002) specifically describe the permanent aspect of the original SMP 
mitigation program, that mitigation was intended to last and have a net beneficial 
effect beyond the initial permit term. That the District intended and demonstrated 
the project to be continuous is a determining factor to whether this project would be 
considered as new or not under CEQA. Key permit terms include: 

o DFG SAA Notification R3-2001-0119, pages 1-2 - “Project impacts will be counted 
on a one-time basis. Repetitive or overlapping stream maintenance activities in the 
same section or areas of creek are not progressively added to the total area of 
impact” 

o USACE: as stated under Special Condition 4 in the USACE Permit No. 22525S, 
(Long-Term Stream Maintenance Program, Santa Clara Valley Water District), 
“...impacts in locations at which repeated maintenance activities occur do not have 
to be compensated for more than once for the duration of the permit. Unless new 
information comes to light , such as a new species listing, for example , this 
arrangement is expected to continue for the duration of any subsequent permits 
covering the same program .” [emphasis added] 

o Regional Board: as stated under Finding 13 in the RWQCB Order R2-2002-0028 
(Multi-Year Stream Maintenance Program), “The permanent mitigation installed 
as part of the SMP in the first 10 years is intended to provide mitigation for 
temporary but repetitive impacts caused by similar maintenance activities in 
subsequent years, provided that the work is consistent with the environmental 
effects evaluated in the Final EIR.” [emphasis added] 

o NMFS: as stated in the Biological Opinion of July 3, 2002, Effects of the Proposed 
Actions, Section E Mitigation, “The proposed compensatory mitigation measures 
include a substantial investment towards the protection and enhancement of the 
watersheds and streams of Santa Clara County. Enhancement and restoration of 
999 to 1349 acres of wetlands and riparian areas will be a beneficial effect of the 
proposed SMP.” 

• In addition, the 2002 SMP FEIR states the following: 

o 2002 SMP FEIR Page II-5 - “The maintenance activities described in this program 
EIR are ongoing and will remain effective for an indefinite period of time as long 
as the nature of the work or environmental conditions do not substantially change. 
Because permits from other agencies will need to be renewed in 10 years, the 


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District will reexamine the applicability of the Program EIR at that time and make 
revisions as needed'." 

o 2002 SMP FEIR Pages 11-29 and 11-30 - “The SMP is intended to establish an 

indefinite , ongoing District program. The SMP and the Program EIR use a 20-year 
planning timeframe to evaluate cumulative impacts. Permits from the Corps and 
other agencies are expected to last for a period of 10 years, after which time the 
District would apply for renewal. The program will be reviewed in 10 years and 
the EIR amended if necessary." 

o 2002 SMP FEIR Page IV-B-62 - “A one-time accounting method for potentially 
significant impacts was developed for the program because impacts to stream 
vegetation from routine sediment removal and vegetation management are 
temporary but repetitive. The approach of this impact analysis is to count future 
impacts to any one section of creek one time only. Repetitive or overlapping stream 
maintenance activities in the same section of creek are not progressively added to 
the total impact acres. The one-time accounting assessment method is relevant to 
assessing the impacts of the program because work is spread out over many years, 
routine maintenance takes place in only a portion of the total program work area 
in any given year, and stream vegetation regrows between cyclical maintenance 
events. This approach determines that a one-time assessment of impacts from 
routine maintenance activities adequately represents significant impacts of all 
future maintenance work in that same area, and the compensatory mitigation 
program is designed accordingly. For the program, permanent mitigation is 
proposed for these temporary, repetitive impacts." 

• To help facilitate review and approval of the SMP Update, a multi-agency, Inter- 
Agency Working Group (IAWG) was formed with representatives from SCVWD's 
SMP team, SCVWD consultants, and representatives from the USACE, USEPA, 
USFWS, NMFS, DFG, San Francisco RWQCB, and Central Coast RWQCB. The IAWG 
has met three times to review and discuss key program updates (as discussed 
below). The IAWG members have received several program status reports, meeting 
notes, and other program documents via e-mail distribution. 

o At the first IAWG meeting (held on August 26, 2010), the topic of program 
mitigation was discussed with all participating agency representatives. This 
discussion included a review of the fundamental components of the original SMP 
mitigation program that was developed in 2002. The IAWG discussion also 
described and confirmed that the original (and ongoing) mitigation program 
provides mitigation for repeated and ongoing maintenance work in the locations 
that were projected in 2002. This discussion verified that continued 
maintenance work in the streams and work areas included in the original 2002 
SMP projections would not need to be mitigated beyond the original 
commitments. As discussed at this meeting, maintenance work in new program 
areas that were not included in the original projections would require additional 
mitigation. IAWG members, in particular those who participated in the original 
SMP development process (such as Luisa Valiela of USEPA), confirmed that the 
original intention of the program's mitigation approach was to provide 


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mitigation in perpetuity for the channels/creeks included in the original 
projections. SCVWD's consultant, Ken Schwarz of Horizon Water and 
Environment specifically raised this point for clarification, comment, and 
approval by IAWG members. Ken asked the entire IAWG assembly if there was 
consensus that the original SMP mitigation provided mitigation in perpetuity. 
The IAWG jointly agreed that the original SMP provided mitigation in perpetuity. 
For reference, please see topic #5 in the attached IAWG meeting notes this 
meeting (provided in Appendix E, Volume I of this FSEIR). 

o At the second IAWG meeting (held on October 20, 2010), agenda item #5 was a 
discussion of the SMP Update's mitigation program. This discussion included a 
brief review of the mitigation status to date for the original 2002 SMP mitigation 
requirements. The discussion also reviewed the original mitigation assumptions, 
as summarized at the first IAWG meeting. SCVWD Consultant Ken Schwarz 
stated that SCVWD would be developing a mitigation package for the 2012- 
2022 SMP Update, to provide mitigation for impacts associated with newly 
projected maintenance work. Ken confirmed that the original SMP mitigation 
program would continue to provide ongoing mitigation for the work areas 
projected and identified by the original SMP EIR, and that for the SMP Update, 
mitigation would need to be developed to address new work areas not projected 
in the original SMP EIR (2002). Consensus was reached by the IAWG members 
that this was the necessary approach; SCVWD would need to provide mitigation 
for new work areas. (Refer to the meeting notes from the second IAWG meeting, 
provided in Appendix E, Volume I of this FSEIR). 

o At the third IAWG meeting (held on July 21, 2011), the entire agenda focused on 
a review and discussion of the SMP Update's mitigation approach, as provided in 
Appendix C of the DSEIR. Consistent with the first and second IAWG meetings, 
the discussion at this meeting included review of the fundamental assumption 
that the original SMP mitigation program (2002) provides ongoing mitigation in 
perpetuity for maintenance activities projected during the original program 
development. The discussion confirmed that the additional mitigation required 
for the 2012-2022 SMP Update would be to provide mitigation for newly 
identified work areas. The majority of the third IAWG meeting focused on 
SCVWD's proposed approach to provide mitigation for new work areas. (Refer 
to the meeting notes from the third IAWG meeting, provided in Appendix E, 
Volume I of this FSEIR). 

At no time during the SMP Update planning process or interactions with the IAWG (before 
receipt of this comment from DFG on the DSEIR) was this issue raised that the original 
SMP's mitigation program was not somehow providing mitigation in perpetuity. SCVWD 
developed Appendix C to the DSEIR as a suitable and appropriate mitigation approach for 
newly projected work areas associated with the SMP Update, based on the assumption that 
the existing and ongoing SMP mitigation program will continue to provide mitigation in 
perpetuity for the originally projected work areas. 

Response to Comment N-22 


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The comment requests clarification on what is meant by “new programmatic mitigation" 
and how instream complexity and gravel augmentation mitigation programs differ from the 
other proposed ecological service-type mitigation. SCVWD agrees that as written in Chapter 
2, Project Description, and Appendix C of the DSEIR, the distinction between "ecologic 
services" type mitigation and "new programmatic mitigation" is confusing. Appendix C of 
the DSEIR is revised to remove the category of "new programmatic mitigation" (see revised 
Appendix C in Volume II of the FSEIR). Text on page 2-36 in Chapter 2 of the DSEIR is 
deleted as follows: 

&— N e w Programmatic Mitigation. In addition to th e mitigation approach e s 
d e scrib e d abov e , th e District would provid e additional programmatic habitat 
mitigation through th e instr e am compl e xity and grav e l augm e ntation mitigation 
programs. 

In addition, instream complexity and gravel augmentation mitigation are included within 
the ecological-services type mitigation category, although in the case of gravel 
augmentation, it would be focused on sediment removal activities in steelhead creeks. 

Response to Comment N-23 

SCVWD has applied for an Incidental Take Permit from DFG, for anticipated take of the 
longfin smelt and California tiger salamander resulting from SMP Update activities, a 
separate process from the CEQA review process. For both species, SCVWD would provide 
in-perpetuity mitigation, consistent with DFG's requirements as described in this comment. 
For the longfin smelt, such mitigation would occur via restoration of tidal habitat at the 
Island Ponds, whereas for the California tiger salamander, appropriate mitigation lands 
would be identified. SCVWD does not anticipate that take of any other state-listed species 
would occur. 

Response to Comment N-24 

The comment requests clarification and an explanation for the mitigation ratios provided in 
Table 2-9. Table 2-9 summarizes the mitigation approaches that are described more 
completely in Appendix C of the DSEIR (Mitigation Approach Memorandum). The mitigation 
approaches listed in Table 2-9 apply to temporary but repetitive impacts to riparian and 
aquatic habitats, caused by sediment removal and vegetation management activities. The 
comment includes a specific reference to the 0.5:1 ratio for instream habitat complexity 
features. Based on further review, SCVWD has revised the mitigation ratio for instream 
complexity mitigation to 1:1 (mitigation-to-impacts) (see revised Appendix C in Volume II 
of the FSEIR). 

Explanations for the various mitigation ratios are provided as follows: 

• Land acquisition (in-kind preservation/enhancement) would have a 3:1 ratio, 
meaning that 3 acres of land would be acquired, preserved, and/or enhanced for every 
1 acre of impacted habitats resulting from SMP maintenance activities. Ecological 
enhancement activities would recognize a site's existing physical and biological 
processes and would seek to enhance or improve those processes that may be currently 


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functioning at a less than optimal performance. Enhancement activities also may include 
improving the site's functions and values, either for the ecosystem as a whole or 
targeting a particular species or group of species. For this class of land acquisition, a 3:1 
mitigation-to-impact ratio was based on professional practice and experience, 
consistent with other regional land conservation and acquisition programs, including 
habitat conservation plans and natural community conservation plans. 

• Land acquisition (in-kind restoration) would have a 1.5:1 ratio. In this case, the 
acquired lands would be selected because they would have good potential to provide 
similar ecologic functions and values to habitat areas impacted by SMP maintenance 
activities. However, restorative actions would be necessary to lift the quality, functions, 
and values of the lands, to provide a net improvement/benefit and, therefore, to serve 
as mitigation for SMP Update-impacted habitats. Because additional restoration 
activities would be necessary to lift the quality of such acquired lands, to provide 
functions/values that would serve as appropriate mitigation, the mitigation ratio would 
be lower, to reflect that the purchase and acquisition of the land was not the sole 
mitigation effort of SCVWD, but that additional and possibly robust restorative actions 
would be necessary and provided by SCVWD. Ecological restoration activities would 
evaluate a site's existing physical and biological processes and compare those 
conditions to either past on-site processes (or conditions at a suitable reference site) 
and seek to restore (or reintroduce) such processes and forms on-site that would have 
been previously lost or degraded. Although restoration activities could look to a site's 
past or to a suitable reference site, an effective restoration project would operate within 
the context of the existing system and what processes that system would support 
sustainably. Similar to enhancement activities, restoration activities also may include 
restoring the site's functions and values, either for the ecosystem as a whole or 
targeting a particular species or group of species. 

Furthermore, the mitigation ratio for this type of mitigation would be lower than for 
land acquisition and management because restoration-type mitigation would create 
new areas of higher quality habitat in the county, rather than simply preserving existing 
habitat areas, and hence would provide more incremental benefit per unit. 

In summary, for this class of land acquisition, the 1.5:1 mitigation-to-impact ratio was 
based on professional practice and experience, consistent with other land acquisition 
programs where subsequent restoration analysis, design, implementation, monitoring, 
and permitting all occurred to lift the habitat functions and values of the parcel to 
provide suitable mitigation. 

• Land acquisition (watershed lands out of kind) would have an 8:1 ratio. These would 
be acquired lands that would provide more general conservation, open space, and 
habitat values, but the acquired lands would not be specifically tied or matched in-kind 
to wetland or riparian habitats impacted by SMP maintenance activities. Acquired 
watershed lands may include broader habitat communities, such as woodland and 
grassland. Ecologic enhancement activities may be applied to provide further lift in 
functions and values. Owing to the broader open space nature of these general 
watershed lands, a higher mitigation ratio was set. For this class of land acquisition, the 
8:1 mitigation-to-impact ratio was based on professional practice and experience, 


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consistent with other general land acquisition programs where implemented. These 
other programs would include the initial (and ongoing) SMP mitigation program, which 
had higher ratios set for the acquisition of general watershed-type lands. 

• Invasive Plant Management Program would have a 1.2:1 ratio. The primary goal of 
this program would be to preserve and improve habitat in County streams and riparian 
corridors, by reducing the population of ecologically impacting invasive plant species. 
This program would address impacts by improving riparian habitat quality. Controlling 
the spread of invasive plant species is a critical element in improving the ecological 
health of streams and watersheds. Invasive plants thrive and spread aggressively, 
negatively altering resource allocation regimes, wildlife patterns, soil stability, and 
water quality, and thus degrading habitat quality and the overall ecological value of a 
site. In addition, invasive plants can exacerbate flooding and fire danger, undermine 
structural assets, and impact access to roads, levees, and trails. The program would 
provide compensatory mitigation for SMP vegetation impacts to upland, riparian, 
freshwater, and tidal wetlands, by eliminating or significantly reducing the population 
of invasive plant species from these affected habitats. A key determinant of setting the 
ratio at 1.2 acres mitigated to every 1 acre of maintenance impacts was to recognize that 
the loss of instream wetland vegetation and habitat resulting from SMP maintenance 
activities would be temporary. SCVWD studies indicate that instream wetland 
vegetation and habitats impacted by sediment removal and vegetation management 
activities recover on average within 1-2 years following maintenance activities. 1 
Because the impacts would be temporary and self-recovering, a mitigation ratio of 1:1 
may be appropriate. However, because a temporal loss or gap would occur between the 
time when the habitat was impacted and when the mitigation was applied, an additional 
20 percent mitigation requirement would be applied, resulting in a 1.2:1 mitigation 
ratio. This additional 20 percent is believed to be adequate to address the temporal gap. 
The mitigation ratio is not higher than 1.2:1, to account for the temporary nature of 
impacts to which it would be applied (e.g., if the impacts stopped, the wetland or 
riparian habitat in the impact area would be re-established). The 1.2:1 ratio is based on 
SCVWD's experience with other flood protection channel maintenance programs, such 
as in Sonoma County where similar routine vegetation management and sediment 
removal activities are mitigated at a 1.1:1 ratio. The Sonoma County Stream 
Maintenance Program was approved by DFG and the other regulatory agencies 
authorizing the County SMP. 

• Riparian Restoration and Planting Program would have a 1.2:1 ratio. The primary 
goal of the riparian planting component of the SMP Update mitigation package is to 
compensate for the loss of quality and quantity of native-dominated riparian habitat 
caused by sediment removal and vegetation management. Riparian planting would 
enhance habitat for birds, amphibians, and other wildlife, using terrestrial riparian 
areas while providing shading, sources of organic matter, coarse woody debris, and 
water quality benefits to aquatic species. Restoration would be accomplished primarily 
via the revegetation of creek banks, benches, and floodplains within the Project Area 
where the existing physical conditions (i.e., topography, hydrology, and soils) were 
suitable for the establishment of native-dominated riparian habitat. This program 


1 Santa Clara Valley Water District. 2002 (July). Op. cit. 


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would address maintenance impacts by improving riparian habitat quality. The 1.2:1 
ratio was set for the same rationale as described above for the invasive plant 
management program, notably that the maintenance activities would be temporary and 
self-recovering but additional mitigation would be necessary to accommodate for the 
temporal gap until the mitigation work was implemented. Similar to the invasive plant 
management program, the 1.2:1 ratio for riparian restoration also would be consistent 
with other permitted stream maintenance programs, such as at Sonoma County, where 
a 1.1:1 ratio has been approved by DFG and other regulatory agencies. 

• Tree Plantings for Removal of Trees Less Than or Equal to 12 inches dbh. 

Removing trees sized 6-12 inches dbh would be mitigated through the individual 
planting of replacement trees. Appendix C of the DSEIR (the appendix regarding Tree 
Scoring for Removal of Trees and Shrubs 6 - 12”DBH - April, 2011) provides a specific tree 
appraisal and evaluation protocol to determine how replacement planting would occur. 
The protocol in Appendix C would involve carefully assessing targeted tree removals for 
their existing conditions and functions, including their canopy cover, local area value, 
ecosystem benefits, and ecosystem detriments. Using a cumulative ranking method, tree 
replacement mitigation ratios for removed trees (6-12 inches dbh) would occur at 
either 1:1, 2:1, or 3:1 (replacement tree to removed tree), depending on the overall 
quality and function of the removed tree. These tree replacement ratios are consistent 
with other tree replacement ratios, approved by regulatory agencies for the Sonoma 
County Stream Maintenance Program (whereby removed native vegetation is replaced 
at 2:1 ratio, removed non-native vegetation that provides some benefits is replaced at a 
1.5:1 ratio, and removed problematic non-native vegetation does not require 
replacement mitigation). Chapter 2 of the SMP Update Manual (Appendix A, Volume II of 
the FSEIR) describes SCVWD's vegetation management and tree removal activities in 
detail. 

• Instream Habitat Complexity Features (1:1). SCVWD would develop, enhance, or 
provide in-kind installation of instream habitat complexity features, to mitigate for the 
loss of instream complexity caused by annual sediment removal and vegetation 
management activities, including large woody debris removal. Examples of potential 
instream complexity activities includes: enlarging an existing large woody debris 
feature; geomorphically shaping an instream bar or bed feature for improved habitat; 
and enhancing a pool feature threatened by sedimentation. These mitigating activities 
would occur at a 1:1 ratio to where such features would be removed because of SMP 
maintenance activities. 

• Gravel Augmentation in Steelhead Creeks (1:1). The ratio for gravel augmentation 
mitigation activities were developed, reviewed, and approved in close coordination with 
representatives from NMFS. The 1:1 ratio represents a target mitigation objective. Also 
important, the actual process for identifying high quality and appropriate sediment for 
use in gravel augmentation projects was reviewed and approved through NMFS 
coordination, and this would include the following process: 

1. An SCVWD biologist would visit sediment removal sites (where more than 

100 square feet of sediment were to be removed), to assess the extent and quality of 
the sediment proposed for removal. Once the extent of sediment removal was 


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understood, the biologist then would assess if high quality sediment would be 
impacted. 

2. If the biologist determined that as much as 100 square feet of spawning quality 
gravel may be present throughout the sediment removal area as a whole, then 
sediment would be evaluated for its suitability for gravel augmentation-type 
activities. 

3. Sediment suitability evaluation would focus on median sediment size (D 50 texture), 
as well as on percent fines, and would be performed only for the sediment removal 
areas that were thought to provide potential spawning gravel. Areas obviously not 
suitable for providing spawning quality sediment would not be included in the 
suitability evaluation. 

4. If the evaluated sediment qualified as “high quality” and suitable for augmentation- 
type activities, then augmentation activities would follow the description as stated 
in the Mitigation Memo (Appendix C as revised in Volume II of the FSEIR). 

5. If less than 100 square feet of gravel qualified as high quality, no mitigation would 
be necessary. 

Response to Comment N-25 

SCVWD appreciates having this information. Because of the language in Table 2-10, listing 
the extension dates on permit R3-2001-0119 is unnecessary. Table 2-10 is revised as 
follows, adding permit number 1600-2009-0361-R3 and the accompanying issue date and 
expiration, as requested: 


Table 2-10. Agency Approvals 


Agency 

Applicable 
Law/Regulations 
Guiding Jurisdiction 

Current or Prior Permits or Approvals for Maintenance 

Description 

Original Date of 
Issuance 

Date of 
Expiration 

California 
Department of 
Fish and Game 
(DFG) 

Fish and Game 

Code Section 1602 

Lake and Streambed 
Alteration Agreement, 
Notification No. R3- 
2001-0119 

July 8,2002 

Dec 31, 

204410 

Lake and Streambed 
Alteration Agreement 
Notification No. 1600- 
2009-0361-R3 

lan 21. 2011 

Dec 31. 2014 

Fish and Game 

Code Section 2081 

(California 

Endangered 

Species Act) 

N/A 

N/A 

N/A 


Response to Comment N-26 


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The work windows and rain forecasts for the various SMP Update activities are as indicated 
in Table 2-12 of the DSEIR. Similarly, as indicated in Table 2-12, a 72-hour weather forecast 
for substantial rain events would be applicable for most activities unless otherwise 
specified. SCVWD has determined that a 72-hour forecast window would be an appropriate 
amount of time to avoid or adequately prepare sites for rainfall. As suggested, Table 2-11 on 
page 40 of the DSEIR is revised as follows, with the changes to the work windows and rain 
forecasts for bank stabilization: 


Table 2-11. Comparison of Key Differences between 2002 SMP and 2012 SMP 
Update 


Description of 
Activity 


Bank Stabilization 


2002 SMP 


2012 SMP Update 


Work Window 


Generally between July 1 and 
October 15, 50 percent completed 
project may extend to October 30. 


Ju l y 1 June 15 to October 15. Projects may 
continue until the approved date stated below 
50 p e rc e nt comp le t e d proj e cts by Octob e r 15 
may continu e unti l comp le tion, or until the first 
5 - day 72-hour forecast that includes significant 
rainfall (greater than 0.5 inch/24 hours). 


• In Creeks Supporting Anadromous Fish 

o An extended work window may occur 
until October 31 st for bank stabilization 
projects that will be 50% complete by 
October 15 th . 

• In Creeks Not Supporting Anadromous Fish 
o An extended work window may occur 

until November 30 th for projects that 
will be 50% complete by October 15 th 
or until significant rainfall. 

An extended work window may occur until 
November 30 th for new bank stabilization 
projects that will be completed in five (5) days 
or less, or until significant rainfall. 


Description of 
Activity 

2002 SMP 

2012 SMP Update 

Sediment Removal 


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Work Window 


Instream work limited to June 15- 
October 30 or first significant rainfall 
after October 15 (greater than 0.5 
inch/24 hours), whichever occurs first. 


June 15-October 15, with extended work 
window under the following conditions: 

♦ Creeks Supporting Anadromous Fish: 

An extended work window may occur from 
October 15 through October 31, or until local 
rainfall of 0.5 inches or greater falls within 
the subject watershed within a 24-hour 
period, whichever occurs first . 

♦ Creeks Not Supporting Anadromous Fish: 

An extended work window may occur from 


October 15 through November 30 th , or until 
local rainfall of 0.5 inches or greater falls 
within the subject watershed within a 24- 
hour period, whichever occurs first. 


• In lower quality areas, w Work may occur 
after a significant rainfall event but no later 
than stops at first significant rainfa ll (0.5 
inch e s of rain in a 2 4- hr p e riod) or December 
31 , p e r wat e rsh e d 

o Additional conditions needed for work 
on Berryessa Creek (0-88+80; 232+70- 
236+00; 284+30-288+00), Lower Silver 
Creek (Reach 3 between Stations 37+40 
and 381+19), Thompson Creek (0+00- 
10+00), Canoas Creek (0+00-390+00), 
Ross Creek (0+00-86+30), Calabazas 
Creek (35+00-105+00), and San Tomas 
Aquino Creek (80+00-100+00), after a 
rainfall event (0.5 inch/24 hours) 

Sites maintained in a winterized state during 
extended work window 


The text on pages 14 and 63, respectively, of the 2012-2022 SMP Manual (Appendix A of 
the DSEIR) also is revised as follows: 

3. Bank Stabilization 

Bank stabilization work is allowed during the work window of June 15 - October 15. 
If a work extension is granted proi e ct is mor e than 50% compl e t e on Octob e r 15 . it 
may continue until the approved date stated below compl e tion. D e c e mb e r 31 . or 
until the first 72-houn 5-4awforecast that includes significant rainfall. Significant 
rainfall is local rainfall 0.5 inches or greater that falls within a 24-hour period in the 
subject watershed. 

L In Creeks Supporting Anadramous Fish 

An extended work window may occur until October 31 st for bank stabilization 
projects that will be 50% complete by October 15 th . 

2. In Creeks Not Supporting Anadramous Fish 


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a. An extended work window may occur until November 30 th for projects that 
will be 50% complete by October 15 th or until significant rainfall. 

b. An extended work window may occur until November 30 th for new bank 
stabilization projects that will be completed in five (5) days or less, or until 
significant rainfall. 

and 


D. Work Window 

Bank stabilization work is allowed during the work window of June 15 - October 15. 
If a work extension is granted proj e ct is mor e than 50% compl e t e on Octob e r 15 . it 
may continue until the approved date stated below compl e tion. D e c e mb e r 31 . or 
until the first 72-hour 5 - dav forecast that includes significant rainfall. Significant 
rainfall is local rainfall 0.5 inches or greater that falls within a 24-hour period in the 
subject watershed. 

3. In Creeks Supporting Anadramous Fish 

An extended work window may occur until October 31 st for bank stabilization 
projects that will be 50% complete by October 15 th . 

4. In Creeks Not Supporting Anadramous Fish 

c. An extended work window may occur until November 30 th for projects that 
will be 50% complete by October 15 th or until significant rainfall. 

d. An extended work window may occur until November 30 th for new bank 
stabilization projects that will be completed in five (5) days or less, or until 
significant rainfall. 


Response to Comment N-27 

The statement in Table 2-11 that "No rodenticide or fumigant application within the current 
mapped potential range of sensitive amphibians" would occur is incorrect. SCVWD proposes 
to use ingestible rodenticides, though not fumigants, within the range of special-status 
amphibians. Table 2-11 is revised to reflect this intent, consistent with BMP ANI-4, which 
states that no fumigants would be used within the habitat areas of special-status 
amphibians. Table 2-11 (on page 2-41 of the DSEIR) also is revised as follows to include the 
measure described in BMP ANI-3 that would implement a 656-yard buffer around known 
burrowing owl locations where no rodenticides or fumigants would be used: 

• No rod e nticid e s or fumigant application within the current mapped 
potential range of sensitive amphibians. 

• Specifically designed bait stations to prevent entry of California Ttiger 
Ssalamander, California Rred-Llegged Ffrog, or Ffoothill Yyellow-tlegged 
Ffrog species, or Salt Marsh Harv e st Mous e 

• Live traps will be designed to allow salt marsh harvest mouse to enter 
and exit easily. 

• Minimization of secondary poisoning impacts including cleanup and 
disposal of spilled bait. 

• A 656-vard buffer will be established around known burrowing owl 
locations where no rodenticides or fumigants (including smoke bombs) 


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will be used. A 0.5-mile buffer will be established around known bald 
eagle and golden eagle nesting locations where no rodenticides will be 
used. 


Per BMP ANI-4, any bait stations used within potential habitat areas of special-status 
amphibians would be designed to prevent entry by special-status amphibians. Per BMP 
ANI-2, no bait stations (i.e., containing rodenticides) would be used in salt marsh harvest 
mouse habitat. Rather, any rodent control within salt marsh harvest mouse habitat would 
be limited to live trapping, using traps designed for larger rodents, such as ground squirrels. 
Such traps would allow any animal as small as a salt marsh harvest mouse that entered the 
trap to easily exit. 

Response to Comment N-28 

SCVWD agrees with the comment that snags can be important wildlife habitat components. 
Row 2 of Table 2-11 (on page 2-45 of the DSEIR) is revised as follows to remove the 
reference to snag removal from the "Ecological Health/Stewardship" justification category. 

Greater description of activity includes: 

• Hand-removal of woody vegetation occurs for the following reasons: 

- Maintenance (retain conveyance capacity) 

- Bank Stabilization 

- Ecological Health/Stewardship (includes habitat improvement 7 
snag r e moval ) 

• Stump treatment is included as hand removal (not considered 
Herbicide work). 

• Tree/shrub removal 6-12 inches dbh. Tree removal is subject to 
removal assessment process and criteria. 

• Timing same as described for Pruning Activities 

• "Pay as you go" mitigation 

• Additional requirements include supervision by qualified specialist 
for certain pruning types, and 

Response to Comment N-29 

Stump treatment is included under the work activity of hand removal to fully account for 
the needs of the work. To meet the objectives for removing the vegetation, stump treatment 
would be required to prevent regrowth. The two activities would occur together to meet the 
work objective. Defining these as paired work activities also ensures that the appropriate 
biological pre-construction surveys would occur for both work activities. 

Response to Comment N-30 

As discussed on page 3.3-134 of the DSEIR, fall-run Chinook salmon in the Project Area have 
been tested genetically and have been demonstrated to be derived from hatchery stock, and 
thus, this species is not considered native to the Project Area. Further, studies have found 
conditions for successful spawning are marginal and as a result, the Project Area is not 
important to this species' populations, and any SMP Update impacts to this species would be 


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3. Responses to Comments and DSEIR Revisions 


considered less than significant Therefore, mitigation measures to restrict the instream 
herbicide window to the extent suggested by this comment are not required by CEQA. 
Restricting instream herbicide use throughout the extensive Guadalupe River and Coyote 
Creek watersheds to only a 2-month period, as this comment suggests, would be infeasible 
for SCVWD, and it would be unnecessary because of the less-than-significant nature that the 
impact would have on fall-run Chinook salmon. 

The comment also refers to text on page 3.3-128; no text on that page discusses the Chinook 
salmon or what the work window for herbicide application is, and thus the comment's 
reference is unclear. 

Response to Comment N-31 

BMP GEN-2 in Table 2-12 of the DSEIR is revised as follows, to include DFG review and 
approval: 

Instream herbicide applications will take place between June 15 and October 31 for 
streams with steelhead. with an e xt e nsion through and lune 15 to December 31 for 
non-steelhead streams or until the first occurrence of any of the following 
conditions; whichever happens first: 

• local rainfall greater than 0.5 inches is forecasted within a 24-hour period from 
planned application events; or 

• when steelhead begin upmigrating and spawning in the 14 steelhead creeks, as 
determined by a qualified biologist (typically in November/December), 

o A qualified biologist will determine presence/absence of sensitive 
resources in designated herbicide use areas and develop site-specific 
control methods (including the use of approved herbicide and 
surfactants). Proposed herbicide use would be limited to the aquatic 
formulation of glyphosate (Rodeo or equal). Surfactant would be limited 
to non-ionic products such as Agri-dex. Competitor, or another brand 
name using the same ingredients. Any modifications to these materials 
would require review and approval by NMFS and DFG . 
o A qualified fisheries biologist will review proposed herbicide application 
methods and stream reaches. The fisheries biologist would conduct a 
pre-construction survey (and any other appropriate data research) to 
determine whether the proposed herbicide application is consistent 
with SMP approvals concerning biological resources and determine 
which BMPs would be instituted for work to proceed. 

Response to Comment N-32 

SCVWD disagrees that nesting-bird surveys need to be conducted within one week prior to 
starting work or conducted again if a lapse of only one week occurs. The BMPs designed to 
protect nesting birds that SCVWD has been implementing for the SMP during the period 
2002-2012 have used a 2-week survey period, and SCVWD has found this period to be 
adequate to minimize impacts to nesting birds. Maintenance crews are well trained in the 
implementation and intent of the BMPs, and they look for nesting birds while maintenance 


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work is being performed. Only on relatively few occasions have nests become established 
within the period between the initial pre-activity survey and the commencement of work, 
and on those occasions, maintenance staff have contacted SCVWD biologists and established 
the appropriate buffer around the nests. Reducing the pre-activity survey window from 
2 weeks to 1 week would not result in a substantial reduction in impacts to nesting birds, 
yet it would severely impinge on the feasibility of SMP activities because of the additional 
survey effort and reduced flexibility that would result from requiring a survey within 
1 week before the start of SMP Update activities. 

Also, SCVWD disagrees that the buffer around the nests of ground-nesting birds should be 
increased from 25 feet to 50 feet. Based on SCVWD's experience performing maintenance 
activities around the nests of birds such as killdeer (the main ground-nesting species for 
which nests are detected in and around SMP work areas), a 25-foot buffer has been 
adequate to avoid causing nest abandonment or other impacts resulting in take of these 
birds. 

Response to Comment N-33 

SCVWD understands that DFG does not recommend or approve burrowing owl eviction or 
relocation. SCVWD proposes to only evict owls from their burrows during the non-breeding 
season, if necessary to avoid injury or mortality of individual owls because of the necessity 
to perform SMP Update activities that could physically harm owls (e.g., within burrows) if 
eviction did not take place. SCVWD also understands that DFG does not formally approve 
the use of artificial burrows. However, H. T. Harvey & Associates 12 and others have found 
that owls will use artificial burrows if they are properly constructed and maintained. As a 
result, SCVWD would retain the option of providing artificial burrows to serve as alternative 
roosting or nesting sites for evicted owls, as appropriate. However, eviction of owls and 
construction of artificial burrows does not constitute the full mitigation for impacts to 
burrowing owls; such mitigation is described in detail in the DSEIR under Mitigation 
Measure BIO-13, and is consistent with the process of impact avoidance, minimization, and 
compensation, described in Comment N-33. 

BMP GEN-7 will continue to include the statement that SCVWD will consult with DFG and 
USFWS before evicting owls and/or establishing alternative burrows, so that SCVWD may 
consider any input these agencies may have on the relocation process and on any 
recommendations for the establishment of alternative burrows for evicted owls. Any 
mitigation measures implemented in consultation with these agencies would be at least as 
protective as those outlined in BMP GEN-7. 

Response to Comment N-34 


1 California Department of Fish and Game. 1999. 3COM Burrowing Owl Relocation and Management Plan. 
Prepared by H. T. Harvey & Associates. 

2 H.T. Harvey developed a mitigation plan for borrowing owls on a parcel of land owned by the 3COM 
Corporation of San Jose, California, that was scheduled for construction during the 1997 breeding season. H. 
T. Harvey successfully relocated the birds in early spring 1997, before the onset of the breeding season; 
monitoring and mitigation continued until October 2000. See H. T. Harvey Endangered and Special-Status 
Species Studies & Consultations online at www.harveyecology.com. 


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SCVWD disagrees that focused-species, rare plant surveys necessarily must be performed 
during the blooming period, as some special-status plants are readily identifiable when in 
fruit or even in a vegetative condition. In this respect, BMP GEN-9 is consistent with DFG's 
survey protocol (cited in the comment), as the protocol states that field surveys should be 
conducted "... at the time of year when species are both evident and identifiable. Usually this 
is during flowering and fruiting." Nevertheless, for the purpose of clarification, BMP GEN-9 
(on page 2-53 of the DSEIR) is revised as follows, to indicate that surveys would be 
conducted during the appropriate time of year to adequately identify special-status plants 
that potentially could occur on the site in question : 

3. Surveys will be conducted during the appropriate time of the year to adequately 
identify special-status plants that could potentially occur on the site of proposed 
maintenance activities . 

SCVWD botanists perform special-status plant surveys in general accordance with DFG's 
survey protocol. However, deviations from this protocol are appropriate in certain 
instances. For example, the protocol suggests that "multiple visits to the same site (e.g. in 
early, mid, and late-season for flowering plants) to capture the floristic diversity at a level 
necessary to determine if special status plants are present" may be necessary and 
recommends the use of reference sites to determine whether a species is identifiable. 
Because of the experience of SCVWD botanists in the Project Area, a single, appropriately- 
timed visit to look for a particular species or group of species often would be adequate to 
determine that a species was absent from a particular area. As a result, SCVWD respectfully 
declines to follow only the DFG protocol to conduct surveys but rather prefers to use a 
combination of the DFG protocol and the CNPS Botanical Survey Guidelines. 1 The guidelines 
are more applicable to the region. Therefore, the introductory text to BMP GEN-9 is revised 
as follows: 

A qualified botanist will identify special status plant species and sensitive natural 
vegetation communities and clearly map or delineate them as needed in order to 
avoid and/or minimize disturbance, using the DFG protocols and the CNPS Botanical 
Survey Guidelines to formulate the following protocols: 

Response to Comment N-35 

Per the comment, BMP GEN-12 is revised as follows to indicate that the buffer established 
around any active western pond turtle nest would be 50 feet. 

C. If an active western pond turtle nest is detected within the activity area, a Z5 50- 
foot buffer zone around the nest will be established and maintained during the 
breeding and nesting season (April 1 - August 31). The buffer zone will remain 
in place until the young have left the nest, as determined by a qualified biologist. 


1 California Native Plant Society. 1983 (December 9). CNPS Botanical Survey Guidelines. Available: 
http://www.cnps.org/cnps/rareplants/pdf/cnps_survey_guidelines.pdf. Revised June 2, 2001. 


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However, with implementation of this buffer, SCVWD believes that no monitoring would be 
needed around such a nest because no work would occur within the buffer as long as the 
nest was active. 

Response to Comment N-36 

Per the comment, the first paragraph under Impact BIO-40 is revised as follows, to indicate 
the status of the San Joaquin kit fox as state-threatened: 

In the Project Area, the San Joaquin kit fox (federally listed as endangered and state 
listed as threatened ) is expected to occur only as an occasional dispersant in the 
vicinity of Pacheco Creek and the uppermost reaches of the Pajaro River, upstream 
from the Llagas Creek confluence. Even in those areas, kit fox occurrence is expected 
to be extremely infrequent, and at most, very low numbers of individuals would 
move through those areas during dispersal, between areas of known breeding 
activity well outside the Project Area. No SMP Update activities are projected in the 
portion of the county where kit foxes could occur, and SCVWD has easements in 
only two limited areas in this part of the county. Thus, this species would not be 
impacted by projected SMP Update activities, and very low potential would exist for 
even unprojected activities to impact this species. 

Also, BMP GEN-15.5 (on page 2-58 of the DSEIR) is revised as follows, to indicate that take 
authorization from DFG would be necessary if take (as defined by the CESA) occurred: 

3. If take of the San loaquin kit fox will occur, take authorization from the USFWS 
and CDFG will be necessary. 

Response to Comment N-37 

The discussion of state-listed species on page 3.3-10 of the DSEIR does not explicitly state 
that a CESA incidental take permit would be needed for the fully protected species noted in 
this comment (i.e., California clapper rail, California black rail, California condor, bald eagle, 
or salt marsh harvest mouse). Rather, it states that these and others are "state-listed species 
potentially occurring in the Project Area." Nevertheless, the CESA section is revised as 
follows, per this comment, to clarify that these five species would be fully protected and that 
SCVWD would avoid all take of these species: 

Project Applicability. Maint e nanc e activiti e s may r e sult in th e tak e of a numb e r of 
stat e- list e d sp e ci e s. A CESA tak e p e rmit or oth e r form of authorization may b e 
r e quir e d for Stat e- list e d wildlif e sp e ci e s occurring (or pot e ntially occurring) in th e 
Proj e ct Ar e a. State-listed species potentially occurring in the Project Area include 
the Tiburon paintbrush, longfin smelt ( Spirinchus thaleichthys ), California tiger 
salamander, bank swallow [Riparia riparia ), California condor, bald eagle 
[Haliaeetus leucocephalus ), Swainson's hawk ( Buteo swainsoni), California clapper 
rail, California black rail [Laterallus jamaicensis coturniculus ), California least tern, 
least Bell's vireo, salt marsh harvest mouse, and San Joaquin kit fox. Th e only stat e- 
list e d plant sp e ci e s known to occur in th e Proj e ct Ar e a is th e stat e- thr e at e n e d 
Tiburon paintbrush. Of these, the California clapper rail. California black rail. 


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California condor, bald eagle, and salt marsh harvest mouse are also listed as fully 
protected species: take of such species must be avoided. Maintenance activities may 
result in the take of other state-listed species, including the California tiger 
salamander and longfin smelt: a CESA Incidental Take Permit would be required for 
take of these species. 

Response to Comment N-38 

The sentence referred to in this comment (in the last paragraph on page 3.3-39 of the 
DSEIR) contains a typo and is revised as follows, both to correct the typo and to provide 
further clarification: 

Finally, there are some areas where work activities were projected in 2001 for the 
period 2002-2012, and where activities are also projected for the period 2012- 
2022, but where the type and extent of activities may differ somewhat. For example, 
a reach subjected to manual vegetation management during the period 2002-2012 
may undergo herbicide treatment during the period 2012-2022. In general, 
herbicide has less impact on vegetation than hand removal because hand r e moval 
herbicide application is targeted to specific individual plants. However, careful 
application of herbicide also is targeted and can reduce the effects on surrounding 
vegetation. Furthermore, hand removal makes it possible to remove larger diameter 
vegetation that fills a somewhat different ecological niche than herbicide 
application. To compound the difficulty of estimating the relative increase or 
decrease in the magnitude of the impacts resulting from these SMP Update 
activities, the projections in 2002 were based on linear extents and approximate 
widths while the 2012 projections were based on actually located polygons. Thus, a 
detailed comparison of the relative effects of these activities is infeasible. 

Response to Comment N-39 

The method of quantifying mitigation needs and providing mitigation at the end of a year's 
maintenance activities would result in some temporal loss of habitat functions and values. 
This temporal loss is one of the reasons why mitigation ratios for impacts to wetland and 
riparian habitat are greater than 1:1 (e.g., 1.2:1 for riparian restoration and planting or 
invasive plant management, 1.5:1 for in-kind restoration and creation). 

SCVWD acknowledges that DFG requires mitigation for impacts to state-listed species be 
provided in advance of the impact. SCVWD would work with DFG during the CESA 
consultation process to identify the timing of the mitigation that would need to be provided 
for CESA compliance purposes. However, the DSEIR finds that the mitigation approach 
described in Appendix C would be adequate to reduce impacts to less-than-significant levels 
as required by CEQA. Please see response to Comment N-24 for a complete discussion of the 
rational for mitigation ratios, specifically for impacts to wetland vegetation and riparian 
habitat. 

Response to Comment N-40 


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SCVWD is aware of the potential for Pyramat®, and even heavier materials such as chain- 
link fencing, to become dislodged during high flows. However, it relies on these materials in 
some areas for erosion control and to prevent burrowing animals from establishing new 
burrows, and it has had success with these materials with proper anchoring. Because 
SCVWD is aware of the potential for these materials to become dislodged, it anchors the 
materials as well as possible and monitors areas where these materials are used during and 
after high flows to address any problems posed by loosened materials. SCVWD would train 
all staff on proper installation and use of Pyramat® and chain link fencing. In addition, 
SCVWD would continue to monitor sites where these materials have been installed and 
make any repairs immediately. 

Response to Comment N-41 

In Tables 3.3-5 and 3.3-6 of the DSEIR, "sediment wetland" refers to wetland and aquatic 
habitats (combined), projected to be impacted by sediment removal, based on calculations 
performed by SCVWD that took into account the length of reaches where sediment removal 
is projected and the approximate widths of the wetland/aquatic habitat within those 
reaches. SCVWD then identified additional areas (i.e., outside the "sediment wetland" 
polygons) where the various SMP Update activities are projected in areas mapped by AIS as 
aquatic habitats (which are summarized in those tables as "aquatic (wetland)" impacts) and 
vegetation types that are considered herbaceous wetlands (summarized in those tables as 
"herbaceous (wetland)" impacts). The impacts to "aquatic (wetland)" habitats are projected 
as zeros for most watersheds, simply because all of the habitat mapped by AIS as aquatic 
already is included in the "sediment wetland" impact area or because AIS's mapping 
captures relatively little area as aquatic because of the prevalence of overhanging riparian 
vegetation. 

Both Tables 3.3-5 and 3.3-6 of the DSEIR are revised as follow, with the addition of a 
footnote beneath the four existing footnotes to clarify these distinctions: 

5. "Sediment wetland" refers to wetland and aquatic habitats (combined) 
projected to be impacted by sediment removal, based on calculations performed 
by SCVWD, taking into account the length of reaches where sediment removal is 
projected and the approximate widths of the wetland/aquatic habitat within 
those reaches. SCVWD then identified additional areas (i.e., outside the 
"sediment wetland" polygons) where the various SMP Update activities were 
projected in areas mapped by AIS as aquatic habitats (summarized in those 
tables as "aquatic [wetland]" impacts) and vegetation types that are considered 
herbaceous wetlands (summarized in those tables as "herbaceous [wetland]" 
impacts). 

Response to Comment N-42 
See response to Comment N-5. 

Response to Comment N-43 


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Although the discussion on page 3.3-68 of the DSEIR states that the canals subject to SMP 
Update activities are not expected to be considered waters of the U.S., it also states that this 
determination would have to be made by the USACE. 

Within native creeks and flood protection channels such as those in the Project Area, 
SCVWD expects that areas that are considered jurisdictional wetlands and other waters of 
the U.S. by the USACE would show virtually complete overlap with any areas that may be 
considered "wetlands" using a one-parameter definition. As a result, the only potential 
discrepancy between the areas identified as sensitive habitats (e.g., waters of the U.S. plus 
vegetated wetlands within canals) and areas that may be identified as wetlands using a one- 
parameter definition would be unvegetated sections of canals that would hold water long 
enough to meet the criterion for wetland hydrology. 

Many sections of these canals do not possess any wetland characteristics; these sections 
may convey stormwater runoff from upslope areas for brief periods following rain events, 
but such runoff conveyance does not meet any criteria for wetland hydrology, and these 
sections do not support hydrophytic vegetation (instead having upland-dominant 
vegetation) or hydric soils. Also, SCVWD believes that the unvegetated portions of canals 
that pond water long enough to meet the criterion for wetland hydrology provide little in 
the way of ecological functions and values, and maintenance activities such as sediment 
removal have little effect on the biological importance of such areas. Furthermore, the one- 
parameter approach to identifying "wetlands" followed by the USFWS, as referenced in this 
comment, is based on Cowardin et al. 1 . Cowardin et al. classified wetlands as including areas 
with hydrophytes (which were considered wetlands, and thus sensitive habitats, by the 
DSEIR), areas with hydric soils (which have certainly not truly developed in these canals), 
and "wetlands without soil and without hydrophytes, such as gravel beaches or rocky 
shores without vegetation." SCVWD believes that unvegetated sections of inoperable canals 
do not possess ecological functions and values that even approach the gravel beaches or 
rocky shores envisioned by Cowardin. Furthermore, because Cowardin's definition of 
wetlands does not include objective criteria for determining when unvegetated features 
such as canals should be considered wetlands, nothing in Cowardin's definition of wetlands, 
on which the USFWS's (and evidently the DFG's) one-parameter wetland definition is based, 
suggests that unvegetated segments of SCVWD canals meet Cowardin's definition of a 
wetland. 

Response to Comment N-44 

The DSEIR indicates that any impacts to vegetated wetlands within canals would be 
considered a substantial impact because of the functions and values provided by those 
wetlands, whether or not they are considered jurisdictional waters of the U.S. However, 
unvegetated sections of inoperable canals would provide minimal ecological functions and 
values, and instead would serve merely to convey stormwater runoff that was captured 
from upslope areas. Thus, impacts to such areas (e.g., from removal of sediment) would not 


1 Cowardin, L. M., V. Carter, F. C. Golet, and E. T. LaRoe. 1979. Classification of wetlands and deepwater 
habitats of the United States. U.S. Department of the Interior, Fish and Wildlife Service, Washington, D.C. 
131pp. 


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have a substantial ecological impact, and mitigation would not be necessary for such an 
impact. 

Please also refer to the response to Comment N-43 regarding the one-parameter definition 
of a wetland. Considering an unvegetated reach of an inoperable canal that conveys 
stormwater runoff for brief periods a "wetland" because it occasionally holds water would 
be no different from considering a concrete-lined roadside ditch or a puddle as a "wetland," 
yet neither of those types of features provides important ecological functions and values 
that would necessitate mitigation because of maintenance activities. 

Response to Comment N-45 

Please refer to the response to Comment N-23 pertaining to the use of in-perpetuity 
mitigation to compensate for impacts to state-listed species. 

Response to Comment N-46 

According to the comment, DFG advises SCVWD to implement in-perpetuity mitigation for 
permanent impacts. As stated on page 3.3-71 of the DSEIR, SCVWD would provide in- 
perpetuity mitigation for permanent impacts. However, repetitive impacts are not 
considered permanent impacts for the reasons discussed in the response to Comment N-7. 
Because habitat in repetitively impacted areas would have the potential to become restored 
(even without intentional restoration efforts), SCVWD would not consider impacts to such 
areas to be permanent. As a result, for repetitively impacted areas, SCVWD would retain the 
options of either providing one-time, in perpetuity mitigation for impacts or providing pay- 
as-you-go mitigation each time that area was impacted. 

Response to Comment N-47 

Please see the response to Comment N-24 that addresses all of the mitigation ratios 
proposed for vegetation management and sediment removal activities, including a 
description of the rationale for the land acquisition ratios. 

Response to Comment N-48 

SCVWD is proposing to collaborate with land owners whose land is managed for open space 
or passive recreation, and to provide them with additional habitat enhancement, 
restoration, acquisition services, or funding. In this situation, SCVWD would not acquire the 
mitigation lands but would enter into an agreement with the landowners to provide 
management and financial support toward preserving or improving lands for beneficial 
outcomes, including improved habitats. In such case, this mitigation would result in these 
lands providing functions and values that they currently do not provide, resulting in an 
incremental improvement for which mitigation credit could be taken. 

A detailed management plan for the species or habitat to be protected/improved would be 
the responsibility of SCVWD and would not necessarily be managed by the landowner. The 
mitigation accounting for such "partnership projects," and how much mitigation would be 
provided to account for SMP activities, would be reviewed and developed with regulatory 


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staff on a case-by-case basis. This approach is seen as a unique method to address special 
opportunities that may arise. This method would not be the focus of SCVWD's acquisition 
mitigation effort, but could provide additional flexibility in achieving good mitigation 
results. This type of mitigation partnership with other watershed landowners/stakeholders 
has proven to be effective in Sonoma County in reducing erosion source areas, and thereby 
reducing the need for downstream sediment removal in flood protection channels. 

Response to Comment N-49 

Please see the response to Comment N-24 that discusses the rationale for these mitigation 
ratios and their relationship to addressing temporal impacts. 

Response to Comment N-50 

As per the comment, first paragraph beneath the bullets on page 3.3-74 of the DSEIR is 
revised as follows: 

Mitigation for Bank Stabilization Impacts. Impacts to non-tidal wetlands and 
aquatic habitats resulting from bank stabilization will be provided via the methods 
described in Appendix C and using the mitigation ratios identified in Table 2-4. 
Softscap e r e pairs will b e s e lf - mitigating b e caus e th e y will not r e sult in long - t e rm 
adv e rs e e ff e cts. Mitigation may occur through a combination of replacement of 
“hard" stabilization measures with soft, biotechnical measures (either on the 
stabilization site or off-site) or out-of-kind via riparian revegetation as determined 
by a Mitigation Feasibility Assessment, as described in Appendix C. These measures 
will reduce impacts to wetlands and aquatic habitats resulting from bank 
stabilization by increasing the functions and values of existing wetland and aquatic 
habitats. 

Response to Comment N-51 

The pruning projections in Table 3.3-9 of the DSEIR, totaling 13.4 acres, were derived from 
SCVWD's database of reach-by-reach projected SMP Update activities. However, additional 
pruning is expected to be necessary in areas that are not yet completely defined, to restore 
conveyance capacity of a creek reach, to provide visual inspection of SCVWD facilities, and 
to provide access clearance on roadways, for bank stabilization projects and 
ecological/stewardship purposes. As a result, SCVWD has allowed for the possibility that 
pruning may affect considerably more acreage than has been indicated in Table 3.3-9 and 
has set a cap of 40 acres of pruning for the entire 10-year 2012-2022 program. Impact BIO- 
2 is revised as follows to clarify the reason for this apparent discrepancy, both in the text 
(the last paragraph on page 3.3-77 of the DSEIR) and as a footnote to Table 3.3-9: 

Hand pruning has b ee n proj e ct e d in 40 acr e s of n e w work ar e as. Pruning will occur 
on woody v e g e tation in ord e r to r e stor e conv e yanc e capacity of a cr ee k r e ach, 
provid e visual insp e ction of District faciliti e s, and to provid e acc e ss cl e aranc e on 
roadways (not proj e ct e d in 2002) and for bank stabilization proj e cts. Hand pruning 
may—also—be— p e rform e d —for—e cological/st e wardship — purpos e s. The pruning 
projections in Table 3.3-9, totaling 13.4 acres, were derived from SCVWD's database 


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of reach-bv-reach projected activities. In addition, additional pruning are expected 
to be necessary in areas that are not yet completely defined, to restore conveyance 
capacity of a creek reach, provide visual inspection of SCVWD facilities, and provide 
access clearance on roadways, for bank stabilization projects and for 
ecological/stewardship purposes. As a result. SCVWD has allowed for the possibility 
that pruning may affect considerably more acreage than has been indicated in Table 
3.3-9 and has set a cap of 40 acres of pruning for the entire 10-vear 2012-2022 
program. 


and 


Note: 

Some of the activities in this table overlap within a specific area. Also. SCVWD may 
perform additional pruning that could affect up to 40 acres during the period 2012- 
2022 . 

Source: Data compiled by Horizon Water and Environment in 2011 based on 
information from SCVWD 

The reference to 12 acres on page 3.3-80 of the DSEIR pertains to the mitigation for 40 
acres of pruning impacts, based on the methodology described on that page. 

Response to Comment N-52 

Repetitive impacts to riparian habitat would prevent regrowth for as long as the impacts 
continued. For the sake of the 10-year SMP Update, repetitive mowing or herbicide 
application, for example, would prevent riparian habitat from regrowing. However, 
following the cessation of such vegetation management, riparian vegetation is expected to 
naturally regenerate or recolonize the affected area. As a result, the impact would not be 
considered permanent (which would imply that the maintenance activity had irreversibly 
altered habitat conditions), but instead was repetitive. Please also refer to the response to 
Comment N-7. 

Response to Comment N-53 

Tree Scoring for Removal of Trees and Shrubs <12” dbh (in Appendix A of the DSEIR) was 
developed with a collaborative team of professional revegetation specialists and 
International Society of Arboriculture-certified arborists. Common forestry practices and 
ecological assessments look at the ecological value provided by individual species. The Tree 
Scoring protocol does this by defining ecological attributes and assigning scores to those 
values. A literature review resulted in a wide variety of assessment tools. These protocols 
were specifically designed to account for the ecological values that can occur within 
urbanized creek systems. 

Stem dbh is taken into consideration under "Ecosystem Benefits," whereby trees and shrubs 
6-12" dbh are assigned an additional score to account for the enhanced ecological benefits 
larger trees can provide. 


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SCVWD based its proposed mitigation ratios not only on the tree scoring protocol, but also 
on the success of its riparian mitigation plantings. As a subsequent and continuing program 
from the 2002-2012 SMP, mitigation ratios of 3:1, 2:1, and 1:1 were determined to continue 
to be adequate ranges to appropriately mitigate for the loss of vegetation within urbanized 
stream systems. SMP Update revegetation projects would replant with saplings and not 
with acorns or seedlings, as the comment indicates. 

Response to Comment N-54 

Per the comment's request, Impact BIO-3 is revised as follows, to include a tabulated 
summary (the new Table 3.3-10) of projected impacts to sensitive communities by 
community type: 


Table 3.3-10. Estimated Impacts to Northern Coastal Salt Marsh, 
Sycamore Alluvial Woodland, and Serpentine Communities from 
Projected SMP Update Activities, 2012-2022 


Community 

Projected Impact 
(acres) 

Northern Coastal Salt Marsh 

8.3 

Svcamore Alluvial Woodland 

17.6 

Coast Live Oak 

27.3 

Valiev Oak 

7.2 

Serpentine 

24.4 


Note: 

Source: Data compiled by Horizon Water and Environment in 2011 based on 
information from SCVWD and AIS. 


The first paragraph under Impact BIO-3 (on page 3.3-81 of the DSEIR) is revised as follows, 
to incorporate this table: 

Sensitive plant communities (see Regulated and Sensitive Natural Communities 
above) often are of limited distribution within a region and frequently support 
special-status species or high numbers of common species. Thus, the conservation 
of these natural communities is integral to maintaining biological diversity. 
However, as described above under Determination of Impacts on Aquatic and 
Wetland Communities and Determination of Impacts on Non-instream Sensitive Plant 
Communities, Proposed Project activities may affect sensitive plant communities 
through direct disturbance of vegetation and disturbance, modification, or 
destruction of habitat. Impacts to wetlands and aquatic habitats in general, which 
are considered sensitive communities, are described under Impact BIO-1, and 
impacts to riparian habitats (also sensitive communities) are described under 
Impact BIO-2. Impact BIO-3 focuses on specific sensitive communities, such as 
northern coastal salt marsh, sycamore alluvial woodland, oak woodland, and 
serpentine communities. Table 3.3-10 summarizes estimated impacts of projected 
SMP Update activities on these latter communities, based on mapping by AIS and 
SCVWD projections for maintenance activities during the period 2012-2022. 


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As a result of inserting this new Table 3.3-10, the table numbering (and table references 
thereto) for all subsequent tables in Chapter 3.3 of the DSEIR are revised in the FSEIR. 

Response to Comment N-55 

SCVWD is unaware of any evidence that the ability of serpentine communities to regenerate 
may be limited with repeated disturbance. The discussion on page 3.3-83 of the DSEIR 
states that the repetitive nature of impacts in some areas would result in longer-term 
effects over the 10-year duration of the SMP Update. However, if such disturbances were to 
cease, the plant communities in these areas would be expected to return to conditions 
similar to baseline conditions. 

Nevertheless, Mitigation Measure BIO-3 requires in-perpetuity mitigation, via preservation, 
enhancement, and management, of off-site serpentine communities, to compensate for any 
impacts to high-quality serpentine communities, whether permanent or temporary. 

Response to Comment N-56 

BMP GEN-9 describes pre-activity surveys for special-status plants that would be conducted 
by SCVWD before any maintenance activities in areas that could support special-status 
plants. These surveys would be conducted within 1 year before the initiation of 
maintenance activities in those areas, which would be within the 2-year period within 
which DFG considers surveys to be valid. Please also refer to the response to Comment N-34 
regarding the protocol to be used for special-status plant surveys. 

Response to Comment N-57 

Neither the DSEIR nor the comment identifies significant impacts to species qualifying as 
“rare" under State CEQA Guidelines, Section 15380. Thus, the suggested mitigation is 
unnecessary. 

No state-listed plants would be impacted by the Proposed Project, as described under 
Impacts BIO-4 and BIO-5 of the DSEIR. Thus, the “required" mitigation elements listed in 
this comment are noted, but SCVWD intends to implement the mitigation that is described 
in Mitigation Measure BIO-4 and Mitigation Measure BIO-5. These measures would include 
permanent preservation and monitoring of the mitigation lands, as recommended by the 
comment. The comment suggests that any transplantation of special-status plants should be 
coordinated with the appropriate wildlife agencies. With the exception of state and federally 
listed species, as noted above, SCVWD is unaware of any regulatory requirement for 
consultation with wildlife agencies regarding the transplantation of special-status plants 
(e.g., those appearing only on CNPS rare plant lists). 

Response to Comment N-58 

Per the comment, the contents of the HMMP for Mitigation Measure BIO-4 and Mitigation 
Measure BIO-5 are revised, to include monitoring to address necessary remediation for any 
non-native plants that are accidentally introduced onto the mitigation site. Specifically, the 


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first bullet on page 3.3-90 of the DSEIR, and the sixth bullet at the bottom of page 3.3-93are 
revised identically as follows (changes were also made in Volume II, Appendix L): 

• A description of species monitoring measures on the mitigation site, including 
specific, objective goals and objectives (including enhancement of 
populations of focal special-status species on the mitigation site). 
performance indicators and success criteria (including increasing the 
abundance of the focal species by at least as many individuals as were 
impacted), monitoring methods (including sampling for the focal species). 
data analysis, reporting requirements, and monitoring schedule. Determining 
other specific performance/success criteria requires information regarding 
the specific mitigation site, its conditions, the biological resources present on 
the site, the specific plant species for which mitigation is being provided, and 
the specific enhancement and management measures tailored to the 
mitigation site and its conditions. As a result, thos e additional specific criteria 
will be defined in the HMMP rather than in this SEIR. Nevertheless, the 
performance/success criteria described in the HMMP will guide mitigation to 
manage and protect high-quality serpentine habitat for, and populations of, 
the impacted species. The HMMP will include monitoring for non-native plant 
species and remediation measures in the event that such species are detected 
on the site. 

Response to Comment N-59 

All trees planted by SCVWD as mitigation for impacts resulting from SMP Update activities 
would be native trees. 

Response to Comment N-60 

The Fish Relocation Guidelines are included in the FSEIR as Appendix M. 

Response to Comment N-61 

Please refer to response to Comment M-6. 

Mitigation Measure BIO-8 has defined “high-quality" spawning gravel to include gravel with 
characteristics that typically are used by spawning steelhead. As a result, SCVWD fisheries 
ecologists believe that the criteria for “high-quality" spawning gravel represent the 
conditions where steelhead typically spawn in the Project Area, and these biologists do not 
believe that extensive areas that actually are used for spawning by steelhead would be 
excluded from evaluation and from the mitigation requirement. SCVWD has reduced the 
minimum threshold to removal of 100 square feet of high-quality gravel (from 500 square 
feet, as referenced in the last paragraph of Mitigation Measure BIO-8 on page 3.3-107 of the 
DSEIR. 

Response to Comment N-62 

Per the comment, Mitigation Measure BIO-9 (on page 3.3-107 of the DSEIR) is revised as 
follows, to indicate that instream habitat complexity features would be considered of “high 


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quality/' based on one or more of the criteria listed (rather than requiring the presence of 
all criteria): 

SCVWD will provide mitigation for loss of instream complexity, which provides 
habitat heterogeneity, cover, and refugia during high flows, by in-kind installation of 
structures that provide such complexity. Before sediment removal, bank 
stabilization, or large woody debris removal activities, the affected area will be 
surveyed by an SCVWD fisheries ecologist to identify any features that provide high- 
quality instream complexity for fish. The ecologist will determine that such features 
are of "high quality" based on a combination the presence of one or more of the 
following criteria: 

SCVWD disagrees that providing mitigation only for impacts to high-quality instream 
complexity features would inadequately mitigate this impact, as the availability of lower 
quality features in SMP Update streams would be much greater than that of high-quality 
features, and thus SMP Update activities are not expected to substantially reduce the 
regional availability of lower quality features. 

Response to Comment N-63 

Please see response to Comment D-23. 

Response to Comment N-64 

The first paragraph under BIO-11 on page 3.3-113 of the DSEIR is revised as follows, to 
indicate that the California tiger salamander is state-listed as threatened rather than 
endangered. 

The California tiger salamander (federally and state listed as threatened and stat e 
list e d as e ndang e r e d ) has been largely extirpated from the valley floor, and extant 
populations in the Project Area are now limited primarily to areas with seasonal 
pools and stock ponds around the periphery of the Project Area, particularly in the 
less heavily developed areas and areas that have not been heavily cultivated. 
Because of its distribution in the Project Area, potential impacts to California tiger 
salamanders would be relatively limited. However, they may pass through work 
sites during seasonal movements to and from breeding ponds and may use upland 
burrows within work sites as refugia (e.g., to prevent dehydration during the dry 
summer and autumn months). In addition, some potential would exist for California 
tiger salamanders to breed in portions of canals, particularly inoperable canals such 
as the Coyote and Coyote Extension Canals. 

Response to Comment N-65 

SCVWD disagrees that the DSEIR does not adequately address the impact of the loss of 
upland refugia on the California tiger salamander and California red-legged frog because of 
the loss of burrows. This impact on the California tiger salamander is discussed throughout 
the paragraph from the end of page 3.3-113 and beginning of page 3.3-114 of the DSEIR, 
and on the California red-legged frog throughout the paragraph spanning the end of page 


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3.3-121 and beginning of page 3.3-122. These paragraphs discuss the impact on individuals 
during burrow removal and the impact of the reduced availability of burrows on these 
species. The DSEIR analysis considers that the loss of habitat, including upland habitat and 
burrows, would be significant impacts for both species. 

SCVWD disagrees that the SMP Update and SCVWD's Dam Maintenance Program 
collectively would have "devastating" impacts on these species because of the loss of upland 
refugia. As discussed for the California tiger salamander under Impact BIO-11 and the 
California red-legged frog under Impact BIO-12, the vast majority of SMP Update activities 
would occur in areas where these species are not known or expected to occur, and the 
DSEIR takes a conservative approach in discussing the areas where these species could 
occur, including a number of areas quite distant from known occurrences. As a result, the 
extent of impacts to these species, including impacts to upland refugial habitat, as projected 
in the DSEIR, likely overestimates what would be the actual impacts to occupied habitat. 
Furthermore, SCVWD surveyed all burrows on all of its dams in winter 2009-2010, and 
again in 2010-2011 for special-status species using a combination of fiber-optic scoping 
and burrow excavation; no California tiger salamanders or California red-legged frogs were 
found on any dams, indicating that these species occur on SCVWD infrequently and/or in 
low numbers, at best. Because of the low magnitude of impacts of these two projects on 
these species, coupled with the extremely small proportion of the species' regional (e.g., 
County) ranges in which activities from either of these projects would occur, these projects 
would not be expected to have "devastating" impacts on either habitat availability or 
populations of these species. 

Nevertheless, mitigation for impacts to both of these species is provided in the DSEIR, in 
Mitigation Measure BIO-10 and Mitigation Measure BIO-11. Such mitigation would include 
upland refugial habitat. These two mitigation measures are revised as follows, to emphasize 
the need for upland refugia within the mitigation habitat to be provided for impacts to these 
two species. 

Specifically, the second paragraph on page 3.3-120 of the DSEIR is revised as follows: 

Because most, if not all, impacts to California tiger salamander habitat will consist of 
modification of upland refugial/dispersal habitat (rather than aquatic breeding 
habitat), mitigation lands will also consist of upland habitat for this species. All 
mitigation lands for this species must be located within Santa Clara County and 
within the area where the species is thought to be extant as shown in Figure 3.3-10 
(or as otherwise modified over the course of 2012-2022, based on any new 
information that may modify the understanding of the species' potential range in the 
Project Area). SCVWD will develop an HMMP describing the measures that will be 
taken to manage the property and to monitor the effects of management on the 
California tiger salamander. That plan will include, at a minimum, the following: 

Similarly, the second paragraph on page 3.3-132 of the DSEIR is revised as follows: 

Because much of the impact to California red-legged frog habitat will consist of 
modification of upland refugial/dispersal habitat (rather than aquatic breeding or 
foraging habitat), the mitigation lands will include upland habitat for this species. All 


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mitigation lands for this species must be located within Santa Clara County and 
within the area where the species is thought to be extant as shown in Figure 3.3-13 
(or as otherwise modified over the course of 2012-2022, based on any new 
information that may modify the understanding of the species' potential range in the 
Project Area). SCVWD will develop an HMMP describing the measures that will be 
taken to manage the property and to monitor the effects of management on the 
California red-legged frog; the HMMP will include components similar to those 
described for California tiger salamanders. Determining specific 
performance/success criteria for this mitigation requires information regarding the 
specific mitigation site, its conditions, and the specific enhancement and 
management measures tailored to the mitigation site and its conditions. For 
example, performance criteria for a mitigation site providing only upland habitat for 
California red-legged frogs would include the maintenance of grassland habitat of a 
suitable height and density for use by dispersing frogs, whereas a mitigation site 
providing red-legged frog breeding habitat would also include criteria related to 
adequate depth and hydroperiod of breeding habitat and suitable vegetative cover. 
As a result, those specific criteria will be defined in the HMMP rather than in this 
SEIR. Nevertheless, the performance/success criteria described in the HMMP will 
guide the mitigation to manage and protect high-quality habitat for the California 
red-legged frog, adequate to compensate for impacts. 

Response to Comment N-66 

SCVWD agrees that maintaining consistency in the color schemes among figures would be 
ideal, but different color schemes are necessary on these figures to allow the information to 
be readily apparent at the scale of these figures. On the maps for California, tiger 
salamander and California red-legged frog that show both sediment removal and vegetation 
management (Figures 3.3-10 and 3.3-13 in the DSEIR), the color scheme is the same, with 
red for vegetation management and green for sediment removal. On Figures 3.3-12 and 3.3- 
14, which depict different categories of the same type of activity, the use of both red and 
green is necessary to differentiate between the different categories. The color scheme for 
Figure 3.3-11 is revised as per the inserted new figure in the FSEIR, to indicate sediment 
removal as green instead of red for consistency with the way sediment removal is shown in 
Figures 3.3-10 and 3.3-13. 

Response to Comment N-67 

Regarding the comment about how impacts and mitigation requirements would be tallied 
and mitigation would be provided, please refer to the response to comment N-39. SCVWD 
understands DFG's emphasis on mitigating impacts to California tiger salamanders via 
preservation, management, and enhancement of currently occupied habitat and, via the 
CESA Incidental Take Permit, SCVWD would obtain DFG's approval of any mitigation lands 
for this listed species. 

Response to Comment N-68 

SCVWD understands that DFG objects to mitigation of impacts to the California tiger 
salamander on lands that are already under conservation. However, SCVWD would retain 


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the option to provide mitigation for impacts to this species, via enhancement of already 
conserved lands, if the enhancement would be substantial enough to provide important 
benefits to the species' populations. For example, if connectivity between two California 
tiger salamander populations on existing conservation lands could be linked by 
management of non-native vegetation, changes in grazing management to benefit 
burrowing mammals, or construction of breeding ponds, the benefits to the species' 
persistence and recovery could outweigh the benefits of preservation and management of 
currently occupied land elsewhere. SCVWD would like to continue to discuss such 
mitigation options with DFG, through the CESA Incidental Take Permit process, but 
meanwhile is retaining this mitigation option in the FSEIR as an adequate precaution to 
reduce impacts to the species to less-than-significant levels. 

Response to Comment N-69 

Regarding the comment about how impacts and mitigation requirements would be tallied 
and mitigation would be provided, please refer to the response to Comment N-39. SCVWD 
understands DFG's emphasis on mitigating impacts to California red-legged frogs via 
preservation, management, and enhancement of currently occupied habitat. However, 
restoring or enhancing currently unsuitable or unoccupied habitat, followed by 
demonstration of colonization of that habitat, also could provide substantial benefits to the 
species, and SCVWD is retaining this mitigation option in the FSEIR as an adequate 
precaution to reduce impacts to the species to less-than-significant levels. SCVWD would 
work closely with DFG to determine what monitoring and mitigation would be required for 
this species. 

Response to Comment N-70 

Per the comment, Impact BIO-13 (the last paragraph on page 3.3-131 of the DSEIR) is 
revised as follows, to indicate that Table 3.3-19 in the DSEIR (changed to Table 3.3-20 in the 
FSEIR) summarizes the acreage of projected vegetation management activities: 

Table 3.3-4R19 indicates the linear miles of creek in which sediment removal 
activities are projected in potential foothill yellow-legged frog habitat, and Table 
3.3-4920 indicates the acreage of projected s e dim e nt — r e moval vegetation 
management in potential foothill yellow-legged frog habitat. As shown in these 
tables, impacts to areas where this species may occur would be very limited. Since 
2004, SCVWD has conducted annual surveys for the presence or absence of 
amphibians in numerous locations before the application of instream herbicides 
(see Table 3.3-3); yellow-legged frogs have never been found at any of the locations 
listed in Table 3.3-3, suggesting that the distribution of these species in and near the 
Project Area is so limited that impacts would be very low. 

Response to Comment N-71 

SCVWD disagrees that Mitigation Measure BIO-12A is only a minimization measure for 
impacts to the least Bell's vireo rather than a mitigation measure to compensate for 
alteration of the species' habitats. The least Bell's vireo typically is associated with early- 
successional habitat, generally nesting in dense, often "weedy" vegetation associated with 


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such habitat. As a result, mature, undisturbed riparian woodland is not this species' typical 
habitat, and some level of disturbance, such as is described in Mitigation Measure BI0-12A, 
would be necessary to maintain conditions that may be suitable for use by nesting least 
Bell's vireos. 

Llagas Creek is approximately 2.4 miles in length, extending from Southside Drive to the 
confluence with the Pajaro River. 

Response to Comment N-72 

SCVWD disagrees that disturbance (in the form of limited vegetation management) of any 
riparian habitat areas managed for the least Bell's vireo would make it unsuitable for the 
species. Rather, as described in the response to comment N-71, periodic disturbance would 
be necessary to maintain the "weedy" edges and relatively early-successional conditions 
with which this species typically is associated. Thus, the disturbance described in Mitigation 
Measure BI0-12B would be intended to maintain suitable conditions for the species. 

Response to Comment N-73 

Please refer to the responses to Comments N-71 and N-72 regarding why both of these 
mitigation options are adequate to reduce impacts to least Bell's vireo habitat to less-than- 
significant levels and why some level of disturbance would be desirable in the mitigation 
area. 

Response to Comment N-74 

SCVWD disagrees that impacts of animal conflicts management on the bald eagle, golden 
eagle, and other raptors would be significant because of a reduction in prey availability, 
either on a project-specific basis or in combination with activities of SCVWD's Dam 
Maintenance Program. On the County landscape, the footprint of the areas in which 
management of burrowing mammals would occur would be limited to streams in the 
Project Area, and thus no population-level impacts on predatory species would result from 
management of burrowing mammals. Because of the extensive home ranges of large 
raptors, such as eagles in particular, as well as the very low number of eagle nests located 
near areas where SMP Update activities are projected, controlling mammals on SCVWD- 
maintained levees is not expected to affect the reproductive success or survivorship of any 
eagles. 

Response to Comment N-75 

SCVWD would consult with DFG regarding appropriate measures to include in woodrat 
management plans to minimize impacts to woodrats, in the event a woodrat nest must be 
relocated. Woodrat nests often are encountered in the same types of situations repeatedly, 
so that the same types of management actions would be repeatedly implemented by 
SCVWD. A buffer distance between work activities that may disturb woodrats would be set 
by a qualified SCVWD biologist for each individual project. 

Response to Comment N-76 


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The dimensions of the buffer zone around a bat maternity colony may vary, depending on 
the presence or absence of screening vegetation or structures between the roost and the 
SMP Update activity, the type of SMP Update activity, and the level of existing disturbance 
(including noise and vibration) to which bats already would be habituated in the vicinity of 
the roost. As a result, the buffer dimensions would be determined by a qualified biologist on 
a case-by-case basis, and BMP GEN-13 (bullet 3b on page 2-57 of the DSEIR) is revised as 
follows, to include this site-specific determination: 

b. There is a need for a buffer zone to prevent disturbance to the bat colony, and 
implementation of the buffer zone (determined on a case-bv-case basis by a 
qualified biologist) will reduce or eliminate the disturbance to an acceptable level. 

A typical buffer for a bat roost may range from 50 feet (e.g., for low-intensity activities 
performed on the ground near a high roost in an area that already has a lot of human 
activity) to 250 feet or more for a large pallid bat maternity roost in a relatively exposed 
area that lacks intensive ambient human activity. 

Response to Comment N-77 

Very few reliable records exist for ringtail in the Project Area, indicating both that its 
distribution in the vicinity is very limited and that it occurs in very low numbers here. 
Existing records are from the margins of the Project Area, where SMP Update activities 
would be limited. As a result, SMP Update activities would affect few, if any, ringtails, and 
thus the SMP Update would not substantially affect the species' regional populations, and 
impacts would be less than significant. Therefore, no mitigation measures would be 
necessary for CEQA purposes. The comment suggests that because a species is fully 
protected, mitigation is necessary. However, just because the Fish and Game Code contains 
a requirement does not mean that a low probability impact becomes a significant impact 
under CEQA that would require mitigation. In addition, SCVWD does not believe that the 
Proposed Project would result in take, as defined in the Fish and Game Code, of ringtail. 

Response to Comment N-78 

SCVWD agrees that the Invasive Plant Management Program (IPMP) is an integral 
component of the mitigation for impacts to resources, such as riparian habitats that are 
regulated by DFG. An attachment has been added to the Program Manual to further explain 
the IPMP. 

Response to Comment N-79 

Habitat fragmentation would occur as a result of SMP Update activities whenever 
substantial habitat removal (e.g., removal of riparian or wetland vegetation) would occur 
along a reach of creek where habitat restoration or creation was not feasible (e.g., because 
of the need for flood protection) and where the surrounding landscape did not provide 
adequate connectivity for movement of animals or plants among habitat patches. In many 
areas, habitat mitigation could be implemented within the impacted reach, thus helping to 
offset the effects of habitat fragmentation. In other areas, vegetation in surrounding areas 
outside of the channel may provide connectivity. However, in some flood protection 


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channels, particularly in urban areas where the need for flood protection is paramount, 
habitat mitigation would not be feasible within the reaches where extensive sediment 
removal and/or vegetation removal would occur, and the surrounding land uses may not 
provide adequate habitat connectivity, thus resulting in significant and unavoidable 
impacts. Examples of areas where habitat fragmentation may occur include the lowermost 
reaches of Stevens, Calabazas, San Tomas Aquino, Berryessa, Lower Penitencia, and 
Thompson creeks. Such fragmentation may be temporary in some areas, as regeneration of 
vegetation would provide connectivity over time. However, repeated sediment removal and 
vegetation management in some of these reaches would contribute to this habitat 
fragmentation. SCVWD would ameliorate impacts of fragmentation, when feasible, by 
providing mitigation within or near impacted reaches where habitat fragmentation was of 
particular concern. However, because of the need for adequate flood protection, such 
measures are not expected to be able to reduce fragmentation impacts to less-than- 
significant levels. 

Response to Comment N-80 

SCVWD appreciates the positive feedback given in this comment and agrees that the 
Proposed Project is the appropriate recommended alternative. 

Response to Comment N-81 

All revisions resulting from the comments received on the DSEIR will be incorporated into 
the appropriate sections of the 2012-2022 SMP Manual (Appendix A) and 2012-2022 SMP 
Update Mitigation Approach Memorandum (Appendix C of the DSEIR, replaced in entirety in 
this FSEIR). A revised version of the Draft SEIR (including appendices) is provided as 
Volume II of this FSEIR. 

Response to Comment N-82 

On further consideration, SCVWD has determined that the Mitigation chapter will be most 
appropriately written after SCVWD has been issued all relevant regulatory permits, so that 
the chapter is consistent with the requirements contained in those permits. The chapter will 
be a part of the Implementation Plan, rather than the SMP Manual. In the interim, please 
refer to Appendix C, which describes current mitigation approaches. 

Response to Comment N-83 

The impacts from the construction of capital projects would be addressed through separate 
CEQA and permitting processes from the SMP Update. However, any necessary mitigation 
may follow the processes and requirements of the SMP Update because these mitigation 
approaches will have been previously vetted through the CEQA process and 
reviewed/approved by the regulatory agencies. To the extent that future maintenance work 
requirements are not covered by the Permanent Mitigation Areas in the 2002 SMP FEIR and 
incorporated projects, the long-term incremental maintenance needs, including the scale 
and frequency of work needed, must be analyzed and accounted for under a capital 
improvement program (CIP)/other new project. The mitigation required for those impacts 
would need to be included in the CIP environmental document and would need to provide 


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up front permanent mitigation for repeated maintenance impacts in perpetuity. Only then 
would those incremental future maintenance activities be added to the SMP Permanent 
Mitigation Area projections. 

Please also refer to the discussion in response to Comment N-21. 

Response to Comment N-84 

SCVWD's Maintenance Guidelines are numerous and lengthy, and it is not feasible to attach 
them to the FSEIR. Examples of those applicable to specific creeks/reaches can be provided 
to DFG on request. 

Response to Comment N-85 

Please refer to the response to Comment N-30. 

Response to Comment N-86 

"Upland" in this context refers to locations outside of the active water body. 

Response to Comment N-87 

See response to Comment N-26. 

Response to Comment N-88 

See response to Comment N-12. 

Response to Comment N-89 

Please refer to the BMPs presented in Table 2-12 of the DSEIR. 

Response to Comment N-90 

Please refer to the response to Comment N-29. 

Response to Comment N-91 

The QEMS procedure referenced in the comment was included as Attachment C, Tree 
Scoring for Removal of Trees and Shrubs < 12 “ dbh of Appendix A in the DSEIR. 

Response to Comment N-92 

The following statement on page 40 of the 2012-2022 SMP Manual (Appendix A of the 
DSEIR) is revised as follows: 

Native trees are given a higher level of consideration for preservation than non¬ 
native trees. Native tree species are g e n e rally more desirable and their presence is 


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encouraged over non-native species. Th e y continu e , how e ver, to b e g e n e rally 
und e sirabl e on cr ee k bottoms and som e chann e l banks and l e v ee s. Non-native 
species and invasive non-natives especially are less desirable. (Please see the 
Invasive Plant Removal section for a description of a program designed to 
comprehensively address these species.) Trees, native or non-native, located within 
a creek channel, channel bank, or levee may require removal if flow conveyance 
capacity is reduced, the structural integrity is compromised, and where needed for 
visual inspection of levees. 

Response to Comment N-93 

SCVWD recognizes that USACE's Vegetation Guidelines have not been finalized. However, 
USACE is using the draft guidelines to conduct annual inspections of USACE levees. The 
District anticipates that some vegetation work would be performed to meet USACE 
guidelines. 

Response to Comment N-94 

The Large Woody Debris (LWD) program document will be written after SCVWD is issued 
the final permits, and will be included as part of the SMP Implementation Plan. 

Response to Comment N-95 

With implementation of the appropriate measures, SCVWD believes that herbicide could be 
used in serpentine areas appropriately and in a way that would avoid or minimize impacts 
to sensitive species. Herbicide use only would be implemented in such areas if special- 
status plant surveys had been performed to identify the locations of plants to be avoided, 
thus minimizing the potential for inadvertent impacts. Furthermore, compensatory 
mitigation would be provided for any impacts to high-quality serpentine communities, 
including impacts of herbicide use. 

Some invasive plants, such as barbed goatgrass, have become particularly noxious weeds in 
some serpentine communities in the Project Area. Thus, some herbicide use by SCVWD may 
be directed at the management of this and other invasives. 

Response to Comment N-96 

The range maps for the California tiger salamander, California red-legged frog, and foothill 
yellow-legged frog that are used in the DSEIR were based on similar maps prepared for 
SCVWD by H. T. Harvey & Associates in the late 1990s. Those maps were prepared by 
experienced herpetologists, based on: the locations of all known occurrences of those 
species (e.g., from the California Natural Diversity Database, museum accession records, 
SCVWD data, and other sources); consideration of any data regarding whether populations 
associated with those occurrences were still extant or whether they had been extirpated; 
consideration of habitat suitability in areas that lacked recent records; and consideration of 
land use, dispersal barriers, and other factors that would contribute to a determination of 
whether these species were likely extant in or extirpated from a given area. The 


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approximate ranges of these three species were then mapped conservatively (i.e., erring on 
the side of considering the species to be present in areas where uncertainty existed). 

For the SMP Update, H. T. Harvey & Associates herpetologists overlaid all new records from 
these sources (mentioned above that had accumulated since the late 1990s) on the 
previously mapped range. They then considered new information that has come to light 
since the late 1990s on the dispersal capabilities of these species, and considered changes in 
land use that occurred over the previous decade, to determine where changes to the 
extant/extirpated boundary needed to be made. For all three species, this boundary was 
shifted in many areas to be even more conservative (i.e., including much more area where 
these species were considered likely extant) than in the original maps. Thus, these maps 
truly represent a conservative view of the likely range of these species in the County. 

SCVWD cannot commit to avoiding the use of all pesticides, including bait stations, within 
the ranges of these species. As discussed in the DSEIR, only a small percentage of SMP 
Update activities would occur within the ranges of these species, and thus the effect of SMP 
Update activities would be very low in the context of the entire county, or these species' 
entire ranges. However, SCVWD may need to use pesticides, including bait stations, in areas 
where these species may occur, and as a result, the DSEIR requires compensatory 
mitigation for such impacts in the form of habitat preservation and management. In 
addition, SCVWD would implement BMPs such as GEN-8 and ANI-4 to minimize impacts to 
these special-status amphibians. 

Response to Comment N-97 

Applications would be performed consistent with the USEPA bulletin, Protecting 
Endangered Species: Measures for Use of Pesticides in Santa Clara County. 

More specifically, the indicator dyes are a colorant, the specific composition is listed as 
proprietary. Dyes are not listed as hazardous material by USEPA, do not have a registered 
USEPA number, and are not requested by the Agricultural Commissioner. Therefore, 
SCVWD does not believe that they pose a risk to aquatic species. They would be used to 
specifically identify treatment areas, which would minimize over-treatment or treatment in 
undesired areas. 

Response to Comment N-98 

Mowing is proposed within the work window of February 1 through November 30, to 
include the season in which vegetation would grow to a height that it would hinder 
maintenance and inspection of SCVWD facilities. This period also would include the 
burrowing owl nesting season, extending approximately from February 1 through August 
31. However, per BMP GEN-7, no work would be done near occupied burrowing owl 
burrows during the nesting season, to avoid impacts to nesting owls, except for mowing. 
H. T. Harvey & Associates has observed that mowing (e.g., at the Santa Clara Valley 
Transportation Authority's Cerone facility) is beneficial to burrowing owls; by maintaining 
short vegetation, the visibility that owls require around their nests during the breeding 
season is provided. H. T. Harvey has observed owls on other sites that have abandoned 
burrows during the breeding season, when vegetation became very tall and dense because 


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of a lack of vegetation management, such as mowing. As a result, SCVWD would mow 
around burrowing owl burrows during the breeding season, taking precautions not to cause 
excessive breeding-season disturbance or to collapse burrows. For example, in accordance 
with BMP GEN-7, burrows would be marked immediately before mowing, and within the 
250-foot buffer zone around a nest, mowing may be done to within 10 feet of an active 
burrow, provided no burrowing owls are active on the surface. An on-site monitor would 
observe the area in front of the mower from a safe vantage point while it was in operation. 
In areas within 10 feet of active burrows, the vegetation may be removed by hand (e.g., with 
weed whackers). All mowing and hand-removal of vegetation within 250 feet of a burrow 
would be done as quickly as possible, to minimize disturbance of burrowing owls. 

Response to Comment N-99 

Discing activities typically are performed to meet the directives of the County Fire Marshall 
for fire protection purposes. Discing is performed on flat land where erosion and 
sedimentation concerns are minimal. Delaying the work to June 15 would limit staff and 
equipment resources from performing other necessary work that required resource 
protection measures, delaying a work activity (discing) that would not be posing a threat to 
water quality. 

Response to Comment N-100 

Such equipment would not be operated within wetted streams. 

Response to Comment N-101 

See response to Comment N-26. 

Response to Comment N-102 

Berryessa, Lower Silver, Thompson, Canoas, Ross, Calabazas, and San Tomas Aquino creeks 
are identified because these areas require frequent maintenance for flood protection and 
they do not support habitat for sensitive aquatic species. 

Work only would be allowed to continue at these sites after a significant rainfall if the 
following criteria were met: 

• clearance was provided after a preconstruction biological survey; 

• site conditions were dry; 

• work-related vehicles would not impact roadways; 

• no water diversions were to be used; 

• work would be stopped in the event of any immediate rainfall forecast within 3 days 
(72 hours); and 

• e-mail notification was provided to regulatory agencies 2 days before start of work. 

In addition, relevant work sites would be maintained in a "winterizable” state, with 
measures described in BMP GEN-20 in place to the extent feasible to allow the work to 
proceed. Because of the necessary measures described above, the fact that erosion controls 


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would be established on-site, and that work would stop within 72 hours before the onset of 
a significant rainfall, SCVWD is confident that water quality and habitat would be 
adequately protected within the specific reaches of the seven creeks listed in BMP GEN-1. 

Please see responses to Comments D-2, D-6, D-8, and N-26 regarding weather forecasts. 

Response to Comment N-103 

As also stated in the response to Comment N-82, SCVWD has been determined that the 
Mitigation chapter will be most appropriately written after SCVWD has been issued ah 
relevant regulatory permits, so that the chapter is consistent with the requirements 
contained in those permits. The chapter will be a part of the Implementation Plan, rather 
than the SMP Manual. In the interim, please refer to Appendix C, which describes current 
mitigation approaches. 

Response to Comment N-104 

Please see the response to Comment N-17 that addresses this topic. 

Response to Comment N-105 

With respect to the frequency of carcass surveys, please see the revisions to BMP ANI-1 
described in response to Comment M-9, which are expected to provide adequate protection 
against secondary poisoning. Although this approach is largely consistent with the Dam 
Maintenance Program, because of the different nature of the two programs, SCVWD does 
not believe that complete consistency between the two programs is necessary or 
appropriate. 

With respect to which anti-coagulants may be used, chlorophacinone and diphacinone are 
the two anti-coagulants currently permitted in California and in use by SCVWD. Appendix J 
in the DSEIR has assessed the impact, from the effects of first-generation anti-coagulant 
usage in general and not solely from the two identified types. Therefore, the DSEIR analysis 
would be applicable to other first-generation anti-coagulants that act in the same manner as 
chlorophacinone and diphacinone. The DSEIR analysis would be similarly applicable to 
other first-generation anti-coagulants that may be produced and permitted for use on 
California ground squirrels in the future in California. 

Response to Comment N-106 

The FSEIR and 2012-2022 SMP Manual (included as Appendix A of the FSEIR) are revised to 
state that a Minor Maintenance activity is defined as work that results in the removal of less 
than 0.05 acres (2,178 square feet) of wetland or riparian vegetation. 

In Appendix A of the DSEIR (the 2012-2022 SMP Manual), page 85, below H. Annual 
Notification and Reporting is deleted, as follows: 


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R e gulatory ag e ncy staff will — r e c e iv e— information — r e garding pot e ntial — Minor 
Maint e nanc e proj e cts that r e quir e th e ir r e view and approval for minor activiti e s 
that hav e an impact e xc ee ding 0.05 acr e p e r activity p e r sit e . 

Response to Comment N-107 

The Footnote 1 notation is unnecessary and reference to it is deleted on page 87 of the 
2012-2022 SMP Manual (Appendix A of the DSEIR), and the last sentence in the first 
paragraph on page 55 is deleted as follows: 

During the first nine (9) years of the SMP, 2002 - 2010, the average length of a sediment 
job was 16A3 feet; removing an average of 661 cubic yards of sediment annually. 4 

Response to Comment N-108 

Please see the response to Comment N-17 that addresses this topic. 

Response to Comment N-109 

The Mitigation Feasibility Assessment (MFA) protocol formatting has been corrected. The 
MFA was developed after a lengthy literature search, interagency inquiries, and 
collaboration among SCVWD staff (i.e., biologists, arborists, and vegetation specialists). The 
goal of the MFA is to increase the efficacy and sustainability of District mitigation and 
revegetation plantings. The experience of implementing the 2002 SMP bank protection 
mitigation requirements resulted in revegetating in low-quality habitat conditions. Low 
habitat quality planting areas reduce the ability for plants to meet the required success 
criteria, minimize the ecological effectiveness of the mitigation, and increase District time 
and resources to manage the site to try to meet the success criteria. Thus, the District's 
resources have been inefficiently used and expended. 

Therefore, a more prudent ecological approach has been created. The attributes included in 
the MFA are standard ecological assessment parameters, enhanced by District specific 
considerations of bank repair characteristics, facility maintenance, and potential damage 
caused by wildlife/rodents. The scoring assigned to the attribute rankings apply years of 
professional experiences, observations, and applied ecological assessment methodology. 

The success criterion builds on the current mitigation requirements and expands the 
efficacy of the success criteria to consider each site individually. The success criteria vary, 
depending on the value of the site condition. The objective is for each revegetation site to be 
ecologically appropriate and valuable. Where site conditions are favorable, success criteria 
can be higher and more easily achieved. Poor site conditions may still be revegetated, in an 
effort to create some ecological value. However, because of the difficulty to establish plants 
in poor site conditions, the success criteria would be appropriately reduced. The MFA 
would provide the mechanism to assess an individual site and provides a success criterion 
appropriate to the site's condition. 

Response to Comment N-110 


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Tree Scoring for Removal of Trees and Shrubs <12" dbh (included in Attachment C of 
Appendix A in the DSEIR) was developed with a collaborative team of professional 
revegetation specialists and International Society of Arboriculture-certified arborists. In 
this document, common forestry practices and ecological assessments look at the ecological 
value provided by individual species. The Tree Scoring protocol does this by defining 
ecological attributes and assigning scores to those values. A literature review resulted in a 
wide variety of assessment tools. These protocols were specifically designed to account for 
the ecological values that can occur within urbanized creek systems. 

Stem dbh is taken into consideration under "Ecosystem Benefits/' whereby trees and shrubs 
6-12" dbh are assigned an additional score to account for the enhanced ecological benefits 
that larger trees can provide. 

Response to Comment N-lll 

The calculation for canopy cover is clarified in the Tree Scoring for Removal of Trees and 
Shrubs <12" dbh protocols (included in Attachment C of Appendix A in the FSEIR). 
Specifically, Appendix A of the FSEIR (the Program Manual), page 1, is revised as follows: 

DSEIR Attachment C pg 1 

B. Ranking 

1. Canopy cover 

a) Square footage of canopy is measured at the widest dripline extension of 
the subject tree. 


Metric: Choose 1. Assess at widest dripline extension point and-s quare that value . 


Attribute 

Score 

0-100 Square Feet of Canopy (< 10’ diameter) 

0 points 

101-400 Square Feet of Canopy (10-20’ 
diameter) 

+ 1 points 

>401 Square Feet (> 20’ diameter) 

+ 2 points 


0-2 points 


Response to Comment N-112 

The "Used by Wildlife" attribute in Tree Scoring for Removal of Trees and Shrubs <12" dbh 
(included in Attachment C of Appendix A in the FSEIR) encompasses broad ecological 
attributes. Each tree/shrub can provide a wide range of food, habitat, perching, roosting, 
and ground cover litter. Without lengthy monitoring of each individual tree/shrub species 
over a period of time, it would be difficult to ascertain the breadth of benefits potentially 
provided or actually provided by that individual tree species. Because the goal of the 
assessment is to determine the ecological value of an individual, the scoring either increases 
or decreases that value, and the determination of actual versus potential usage would be 
onerous. The result of increasing the overall scoring was determined to meet the objective 
of increasing the value because of "use by wildlife." 


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The other three attributes of “3. Ecosystem Benefits" also account for use of wildlife. SRA 
(shaded riverine aquatic habitat), cover/structure, and larger tree dbh incorporate the 
various and different uses that trees/shrubs provide for wildlife. 

Response to Comment N-113 

The mitigation calculation for Tree Scoring for Removal of Trees and Shrubs <12" dbh 
(included in Attachment C of Appendix A in the FSEIR) applies an ecological assessment for 
determining appropriate mitigation ratios by assessing four attributes: canopy cover, local 
area value, ecosystem benefits, and ecosystem detriments. As a subsequent and continuing 
action from the 2002 Stream Maintenance Program, mitigation ratios of 3:1, 2:1, and 1:1 
were determined to continue to be adequate ranges to appropriately mitigate for the loss of 
vegetation within urbanized stream systems. 

In addition, ongoing SMP revegetation projects replant with saplings and not acorns. A 
mitigation ratio of 3:1 would equate to three saplings being planted per one tree removed. 


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3.4 Other Revisions to the DSEIR 

Other modifications are noted as follows. 

The DSEIR is revised in the following locations, to reflect that the "plant" portion of 
Mitigation Measure BIO-16 is included (i.e., Invasive Plant Management Program [IPMP]): 

Table ES-1, for Mitigation Measures to BIO-44 
Section 3.3, Mitigation Measure BIO-16 heading 

Section 3.3, Mitigation Measure BIO-16, first line in fourth paragraph under Invasive 
Plant Management Mitigation Requirement 

Chapter 4, under Cumulative Impact BIO-1, under Mitigation Measures (under 
Conclusion) 

Appendix L, MMRP Table, row describing Mitigation Measure BIO-16 
Appendix L, page L-24, Mitigation Measure BIO-16 heading 

Appendix L, Page L-25, first line in fourth paragraph under Invasive Plant 
Management Mitigation Requirement 

Executive Summary 

The Proposed Project Overview paragraph on page ES-1 of the DSEIR is revised as follows: 

The SMP Update has been prepared to provide guiding policies, specific direction on 
approach, and regulatory authorization for routine stream and canal maintenance 
activities. The Proposed Project would update the 2002 SMP, as necessary, to meet 
new conditions or maintenance needs of SCVWD. The SMP Update (including the 
2012 SMP Manual [Appendix A] and this CEQA document) is an ongoing and 
continuous program with an indefinite time horizon: int e nd e d to cov e r th ea 10-year 
planning period beginning in 2012 and ending in 2022 has been used for the 
purposes of the regulatory permitting . These SMP Update documents are intended 
to fully replace the original documents that guided the SMP from its inception 
through 2012. The 2012 SMP Manual (included as Appendix A in this DSEIR) and 
the contents of the DSEIR are meant to be read as companion volumes. The DSEIR 
references or summarizes information (including figures and tables) presented in 
the 2012 SMP Manual frequently to avoid repeating information. The reader is 
encouraged to review the 2012 SMP Manual while reviewing the DSEIR. 

The heading on page ES-9 of the DSEIR is revised as follows: 

Activities Not Covered in the SMP Update 
Table of Contents 

The Table of Contents contains a variety of miscellaneous changes, such as correcting 
references to page numbers, which are not shown here. 

An appendix is amended to those listed in the DSEIR, as follows: 

Appendix M Fish Relocation Guidelines 


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The following acronym is revised in the Acronyms list: 

NPW Notification Notice of Proposed Work 

SCVWD requested revisions to the DSEIR Glossary are noted as follows: 

Modifi e d Natural Chann e l — A wat e rcours e that has had improv e m e nts, 

such as bank prot e ction ( e .g., gabions, rip rap, oth e r 
r e v e tm e nts), and s e l e ct e d ar e as of historical 
chann e lization ( e .g., wid e ning, straight e ning) and/or 
oth e r capacity or passag e improv e m e nts. 

Natural Chann e l - A wat e rcours e without any significant improv e ments 

or modifications and v e ry littl e e vid e nc e of historical 
alt e rations. 

The following definition has been added to the Glossary: 

Upland Terrestrial, referring to habitats that are not wetland 

or aquatic habitats. 

The definition of Winterization on page xxxiii is revised as follows: 

Winterization Winterization is the process to maintain project sites 

with the appropriate BMPs to prevent erosion, 
sediment transport, and protect water quality. 
Winterization occurs upon completion of bank 
repairs or on incomplete projects after October 15 
and prior to the forecast of significant rainfall, 0.5 
inches or greater of rainfall within 24 hours in the 
subject watershed. Winterization shall be completed 
prior to the occurrence of such actual significant 
rainfall. Winterization materials will be available and 
on-site when rain falls after October 15. 

Executive Summary 

Additional wording has been added under Maintenance Timing on ES-10 to clarify work 

windows. 

Work windows for sediment removal, in-stream vegetation and herbicide 
application, and bank stabilization generally would be conducted between June 15 
and October 15. However, if the fall season remained dry, work could continue until 
the first significant rainfall event occurred. Sediment removal may occur after a 
significant rainfall under special circumstances but only in low quality areas. A 
significant rainfall event is defined as local rainfall of 0.5 inches or greater within 
the watershed over a 24-hour period. Even if no significant rainfall occurred, no 
instream work (excluding hand pruning and hand removal in non-steelhead 
streams) would continue later than December 31. 


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Chapter 1, Introduction 

An additional library, the Alviso Library, was available for the Proposed Project public 
review documents. Thus, page 1-6 of the DSEIR is revised as follows: 

All documents mentioned herein or related to the Proposed Project can be reviewed 
on any SCVWD business day between the hours of 8:00 a.m. and 5:00 p.m. Monday 
through Friday at SCVWD headquarters, located at the address shown above, or on 
the SCVWD Web site at www.valleywater.org under Quick Links, Public Review 
docs. The documents also will be available at the libraries listed below during their 
normal operating hours. 

Dr. Martin Luther King, Jr. Library 
150 E. San Fernando Street 
San Jose, CA 95112 

Morgan Hill Public Library 
660 W. Main Avenue 
Morgan Hill, CA 95037 

Palo Alto Public Library 
1213 Newell Road 
Palo Alto, CA 94303 

Cupertino Public Library 
10800 Torre Avenue 
Cupertino, CA 95014-3207 

Milpitas Public Library 
160 N. Main Street 
Milpitas, CA 95035 

Alviso Library 
5050 N. 1st St. 

San lose. CA 95134 


Headings of subsections 1.4.2 and 1.4.3 are revised as follows: 

1.4.2 Draft EIR DSEIR Comment Period 

1.4.3 Preparation of Final EIR FSEIR and Public Hearing 

Chapter 1, Introduction 

The first paragraph on page 1-2 of the DSEIR is revised as follows: 

Although the SMP is an ongoing program, the initial 2002 SMP Manual and Final 
Environmental Impact Report used a 20-year planning horizon to forecast SMP 


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activities and consid e r pot e ntial e nvironm e ntal e ff e cts . In 2009, SCVWD initiated an 
SMP Update process to renew necessary SMP permits as well as to review and 
update the SMP Manual and environmental compliance documentation. For the 
purposes of regulatory permitting, Tthe SMP Update (including the 2012 SMP 
manual and this CEQA document) is intended to cover the 10-year planning period 
beginning in 2012 and ending in 2022. These SMP Update documents are intended 
to fully replace the original documents that guided the SMP from its inception 
through 2011. In general, the SMP Update is a continuation of past routine creek and 
canal maintenance activities in most of the same areas, using many of the same 
techniques. The SMP Update includes some new work areas and new work 
activities. More details regarding the SMP Update are provided in Chapter 2, Project 
Description. 

The last line of Section 1.5 of the DSEIR is revised as follows: 

Appendix M Fish Relocation Guidelines 

Chapter 2, Project Description 

The second paragraph in Section 2.1 of the DSEIR is revised as follows: 

Although the SMP is an ongoing , continuous program (with an indefinite time 
horizon), the 2002 SMP Manual and Final Environmental Impact Report used a 20- 
year planning horizon to forecast SMP activities and— consid e r — pot e ntial 
e nvironm e ntal e ff e cts . The proposed SMP Update (including the revised SMP 
manual and this document) is intended to address cov e r the 10-year planning period 
from 2012-2022 for the purposes of regulatory permitting . The updated SMP 
documents are intended to fully replace the original documents that have guided the 
SMP from its inception in 2002 through the present. 

The Applicable Ends Policies of the Board of Directors on page 2-2 has been revised, 

based on the July 2011 update: 

Applicable Ends Policies of the Board of Directors (as of June 2010 J uly 2011) 

E-l Mission and General Principles 

The mission of SCVWD is to provide for a healthy, safe, and enhanced quality of 
living in Santa Clara County through watershed stewardship and comprehensive 
management of water resources in a practical, cost-effective, and environmentally- 
sensitive manner for current and future generations. 

E-2 Water Supply: There is a reliable, clean water supply for current and future 
generations. 

Goal 2.1 _ Current and future water supply for municipalities, 

industries, agriculture and the environment is reliable. 

Objective 2.1.1 Aggressively protect groundwater basins from the threat of 

contamination and maintain and develop the groundwater 


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basins to optimize reliability and to minimize land subsidence 
and salt water intrusion. 


E-3 


E-4 


Objective 2.1.2 Protect, maintain and develop local surface water. 


Natural Flood Protection: There is a healthy and safe environment for residents, 
businesses and visitors, as well as for future generations. 

Goal 3.1 _ Natural flood protection for residents, businesses and visitors 

Objective 3.1.1 Balance environmental quality and protection from flooding. 

in a cost e ff e ctiv e mann e r 

Objective 3.1.2 Preserve flood conveyance capacity. 

Water Resources Stewardship: There is water resources stewardship to protect 
and enhance watersheds and natural resources and to improve the quality of life in 
Santa Clara County. 

Goal 4.1 _ Healthy creek, and-bav and other aquatic ecosystems 

Objective 4.1.1 Balance water supply, flood protection and environmental 

stewardship functions. 

Objective 4.1.2 Protect and improve watersheds, streams, and natural 

resources. 


Objective 4.1.3 


Goal 4.2 


Promote awar e n e ss the protection of aquatic cr ee k and bay 
ecosystem functions. 

Clean, safe water in creeks and bay 


Objective 4.2.1 Preserve or improve surface and ground water quality for 

beneficial uses. 

Objective 4.2.2 Promote awar e n e ss the protection of water quality and 

stream stewardship. 


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ID No 13 and the footnote in Table 2-4 of the DSEIR are revised as follows: 


13 


Earth with Rock Toe on Grass Lined 
Channels 1 


2:l 2 Non e if rock is b e low 
bankfull d e pth, and 
includ e s som e e l e m e nt of 
instr e am compl e xity. 
For ar e as abov e bankfull 
d e pth, us e mitigation 
ratios as sp e cifi e d in ID 
Nos.l thru 12 abov e . 


Soft/Hybrid 


No 


1 Grass lined channels are those where grass is the predominant or sole vegetation, and that contain no significant 
riparian structure. The NPW submittal will include photographs and descriptions to justify use of this line item. 

2 None if rock is below bankfull depth and includes some element of instream complexity. 

Source: Data compiled by Horizon Water and Environment in 2011 


The text on pages 2-26 and 2-27of the DSEIR is revised as follows: 

■ Bank Stabilization: 

- Projects that w e r e mor e than 50 p e rc e nt compl e t e on Octob e r 15 may continue 
until the approved date stated below compl e tion or until the first 3-day forecast 
that includeds significant rainfall. 

- In Creeks Supporting Anadromous Fish 

o An extended work window may occur until October 31 st for bank 
stabilization projects that will be 50% complete by October 15 th . 

- In Creeks Not Supporting Anadromous Fish 

o An extended work window may occur until November 30 th for projects that 
will be 50% complete by October 15 th or until significant rainfall. 

o An extended work window may occur until November 30 th for new bank 
stabilization projects that will be completed in five (5) days or less, or until 
significant rainfall. 

a 

- After October 15, all incomplete bank repair projects would be winterized before 
the date when the forecast included significant rainfall. 

■ Sediment Removal: 

- Work may occur until December 31. 


1 Winterization is the process to prepare and maintain work sites with the appropriate BMPs to prevent erosion, 
sediment transport, and protect water quality during the rainy season. Winterization occurs on completion of bank 
repairs or on incomplete projects after October 15 and before the forecast of significant rainfall, 0.5 inches or greater 
of local watershed rainfall within 24 hours. Winterization would be completed before the occurrence of such actual 
significant rainfall. 


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- Additional sediment removal work may occur aft e r th e first significant rainfall 
e v e nt — only within Berryessa Creek (0-88+80; 232+70-236+00; 284+30- 
288+00), Lower Silver Creek (Reach 3 between Stations 37+40 and 381+19), 
Thompson Creek (0+00-10+00), Canoas Creek (0+00-390+00), Ross Creek 
(0+00-86+30), Calabazas Creek (35+00-105+00), and San Tomas Aquino Creek 
(80+00-100+00), if clearance was provided through a preconstruction biological 
survey; site conditions were dry; vehicles would not impact roadways; no water 
diversions were used; and work would stop in the event of any rainfall forecast 
3 days in the future ; and e- mail notification of work would b e provid e d to 
r e gulatory ag e nci e s 2 days b e for e start of work . 

- Sites would be maintained in a winterized state during extended work windows. 

- Work may occur after a significant rainfall event but no later than December 31. 

■ Vegetation Management: 

- As a non-ground disturbing activity, instream hand pruning may occur year- 
round except where equipment would need to access the site by crossing a creek 
or otherwise affect water quality, or in steelhead creeks wh e r e th e g e n e ral work 
window would apply to Dec 31 or significant rainfall . As described above, 
mechanized equipment would not cross an active (wet) creek. 

The heading for Section 2.2.7 on page 2-24 of the DSEIR is revised as follows: 

2.2.7 Activities Not Includ e d in the SMP Update 

The second sentence in the first paragraph of Section 2.3.1 of the DSEIR is revised as 
follows: 

Annual administration of the SMP Update would occur in three phases (as shown in 
Figure 2-41). In the winter and early spring, maintenance needs would be assessed 
and prioritized, the annual maintenance work plan would be developed, and the 
regulatory agencies would be notified through the Notification Notice of Proposed 
Work (NPW) document. 

The fourth and fifth bullets under Maintenance Timing on page 2-26 are revised as follows: 

■ Coyote Watershed ( Penitencia Water Treatment Plant, station located at Anderson 
Dam.) 

■ Pajaro Watershed ( Church Ave percolation ponds, station located in Morgan Hill) 

The first and third paragraphs of Section 2.4.3 of the DSEIR are revised as follows: 

SMP mitigation measures were developed in 2002 to compensate for anticipated 
impacts caused by SMP activities. Mitigation for sediment removal and vegetation 
management was based on a comprehensive accounting in 2002 of the potential 
impacts from maintenance activities on instream wetlands, tidal wetlands, riparian 
vegetation, and other sensitive habitats in the program area. Table 2-8 summarizes 


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the existing mitigation requirements for ongoing SMP activities. The SMP mitigation 
program includes land acquisition, habitat protection, and wetland 

restoration/creation;—and— invasiv e— sp e ci e s — control — activiti e s to mitigate for 
maintenance activities. 

An important aspect to the original mitigation approach was that the 

“programmatic" or “up front" mitigation was calculated based on the maximum 
work projections. The programmatic mitigation included coverage for repeat 
maintenance work at sites in perpetuity. Impacts from other non-projected 
maintenance activities such as bank stabilization projects are mitigated on an “as- 
needed" basis using defined mitigation ratios as maintenance projects occur. 

As shown in Table 2-8, to date not all of the SMP's mitigation requirements have 
been met. The District is committed to completing all remaining mitigation 
requirements. Appendix A of the Mitigation Approach Memorandum (which is 
included in the DSEIR as Appendix C) includes a letter from the District to San 
Francisco Bay RWOCB that describes the current status of the SMP mitigation 

program and presents a plan to meet all of the District's SMP mitigation 

requirements identified in the 2002 SMP and the associated permits for the 2002- 
2012 program period. The District Board has recently approved the purchase of a 
property (known as the “Castle & Cooke property"). The District continues to pursue 
land acquisition opportunities for Stream and Watershed Protection. In addition, a 
propos e d proj e ct to r e stor e w e tlands at Laguna S e ca is curr e ntly und e r t e chnical 
r e vi e w. If f e asibl e , this proj e ct could provid e som e or all of th e r e maining n ee d e d 
wetland mitigation cr e dit. 

The footnote in Table 2-8 of the DSEIR is revised as follows: 

* With the purchase of the Castle & Cooke property, some of the mitigation 
requirements not yet complete as shown above would be completed. Also, this 
status summary does not include achievement of final success criteria through 
at completion of the monitoring period. 

The first paragraph beneath 2012 Update to the 2002 SMP Mitigation Program on page 2- 

35 of the DSEIR is revised as follows: 

The proposed SMP Update process includes reviewing and revising the existing 
compensatory mitigation package that was established in 2002. The 2002 SMP 
Mitigation Program that covers the original projected activities (sediment removal 
and vegetation management) would remain in place to provide compensatory 
mitigation in perpetuity for the channels identified in the 2002 work projections. 
The channel reaches shown in red in the maps at the end of this chapter (Figures 2- 
14 through 2-38) have all had their mitigation provided for through the original 
mitigation program. Because the original programmatic mitigation was developed 
to address compensatory mitigation for the 2002 SMP identified channels based on 
full work projections, the mitigation provided for these reaches (shown in red and 
gold colors in the maps) continues in perpetuity. No new significant environmental 


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effects or a substantial increase in the severity of previously identified significant 
effects are anticipated under the SMP Update in these locations. 

The first paragraph, bullets, and second paragraph on page 2-36 of the DSEIR are revised as 
follows: 

As a result of this revised approach, thr ee two key changes are being made to the 
existing programmatic mitigation program (for sediment removal and vegetation 
management) for the 2012 SMP Update: 

1. Ecologic Services. In addition to land acquisition-based mitigation projects 
that provide mitigation in perpetuity (i.e., mitigate for repeat impacts in the 
same work location), programmatic mitigation for sediment removal and 
vegetation management also would include ecologic services-based 
mitigation projects for individual maintenance projects. These approaches 
would provide mitigation on a “pay as you go” or incremental basis. Ecologic 
services-type mitigation projects would only mitigate for an individual work 
activity. Service-based “pay as you go" mitigation would be identified 
annually based on the annual maintenance work plan, provided in the 
annual NPW, and verified in the end of year annual PCR. 

2. Project Specific Accounting. Rather than identifying all the necessary 
mitigation areas (acreages) for sediment removal and vegetation 
management activities “up front" in 2012 for the new work sites where 
maintenance would occur between 2012 and 2022, mitigation criteria and 
metrics would be identified by standard unit measures (typically acreages). 
The specific extent of mitigation required for any given year's work will be 
defined annually when the work areas are precisely identified. This annual 
mitigation analysis will clearly distinguish mitigation requirements for new 
work areas from mitigation already accomplished for work in areas 
projected in 2002. Th e actual mitigation r e quir e m e nt would b e calculat e d 
annually wh e n th e work sit e s w e r e mor e pr e cis e ly d e fin e d. 

th — N e w Programmatic Mitigation. In addition to th e mitigation approach e s 
d e scrib e d abov e , th e District would provid e additional programmatic 
habitat — mitigation — through —the— instr e am — compl e xity —and— grav e l 
augm e ntation mitigation programs. 

These two thr ee adjustments to the programmatic mitigation program are further 
described in Appendix C (2012-2022 SMP Update Mitigation Approach 
Memorandum). The District would be able to use “pay as you go" mitigation 
projects/services to provide incremental mitigation annually on an as-needed basis. 
The District also could continue to purchase lands to provide longer-term mitigation 
needs. In this way, the District would have more flexibility to pursue suitable 
mitigation opportunities through either long-term land acquisition or annual 
mitigation project approaches. Mitigation credits from the 2002 SMP mitigation 
program (Stream and Watershed Protection) may potentially be applied to new 
work areas in need of mitigation support. The District would work with the 


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appropriate regulatory staff to identify, review, and approve the potential 
application of existing mitigation credit toward new work areas. 

The paragraph starting at the bottom of page 2-37 of the DSEIR is revised as follows: 

In addition to the programmatic mitigation described in Table 2-9 for sediment 
removal and vegetation management, mitigation would be provided to compensate 
for impacts to individual special-status species resulting from SMP Update activities. 
The species for which compensatory mitigation would be provided, and the form 
that this mitigation would take, is identified in Section 3.3, Biological Resources and 
will be further described in pending Biological Opinions (BOs) for the 2012 SMP 
Update to be issued by the National Marine Fisheries Service (NMFS) and the U.S. 
Fish and Wildlife Service fUSFWS) , as well as the Incidental Take Permit that will be 
issued by the California Department of Fish and Game fDFG) . The impact analysis in 
this document is intended to provide CEQA coverage for all mitigation activities 
under the Proposed Project, to the extent that the mitigation projects would not 
result in any new or more significant impacts than those disclosed in this DSEIR. 

The heading for Section G on Table 2-12, on page 2-73 of the DSEIR is revised as follows: 

SECTION G - Management of Animal Damag e Conflict BMPs 

The list of creeks as well as information regarding work windows in BMP GEN-1: In-Channel 
Work Window, in Table 2-12 has been updated for consistency with the SMP Manual. 

All ground-disturbing maintenance activities (i.e., sediment removal, bank stabilization, tree 
removal, and mechanized vegetation management) occurring in the channel (below bankfull) 
will take place between June 15 and October 15. Requests for work window extensions must be 
submitted to the regulatory agencies by October 1 st , listing the creek names and reaches where 
a work extension will occur. Work extensions vary per work activity. The agencies will provide a 
single response within one week. Significant rainfall applies after October 15. An extension 
through December 31 may apply if the following requirements are met and regulatory agency 
approval is received: 

For ground-disturbing activities: 

■ Work may continue if no significant rainfall, defined as greater than 0.5 inches per 24 
hours within a local watershed, is either forecasted 1 or observed. Following October 
15 th , maintenance work shall cease for the season if such a rain event is forecasted or 
observed. 

Sediment removal 

■ Extended Work Window: 

1. Creeks Supporting Anadromous Fish: 

An extended work window may occur from October 15 through October 31, or until 
local rainfall of 0.5 inches or greater falls within the subject watershed within a 24- 
hour period, whichever occurs first. 

2. Creeks Not Supporting Anadromous Fish: 

An extended work window may occur from October 15 through November 30 th , or 
until local rainfall of 0.5 inches or greater falls within the subject watershed within a 
24-hour period, whichever occurs first. 


1 Weather Forecasts. No phase of the project may be started if that phase and its associated erosion control 
measures cannot be completed prior to the onset of a storm event if that construction phase may cause the 
introduction of sediments into the stream. Seventy-two-hour weather forecasts from the National Weather Service or 
other localized and more detailed weather forecast service will be consulted prior to start up of any phase of the 
project that may result in sediment runoff to a stream. 


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■ Extended Work Window in Lower Quality Areas: 

1. Aft e r a s i gnif i cant ra i nfa ll e v e nt (0.5 i n/2'1 hrs), sSediment removal work may occur 
until December 31. 

2. Work will only occur on Berryessa Creek (0-88+80; 232+70-236+00; 284+30- 
288+00) , Lower Silver Creek (Reach 3 between Stations 37+40 and 381+19) , 
Thompson Creek (0+00-10+00), Canoas Creek (0+00-390+00) , and-Ross Creek 
(0+00-86+30), Calabazas Creek (35+00-105+00), and San Tomas Aquino Creek 
(80+00-100+00) can cont i nu e with the following conditions: 

o site conditions are dry and access for all construction equipment and vehicles 
will not impact waterways; and 

o all work will stop if any rainfall is forecast for the next 72 hour period.T-auct 
e —e ma il not i f i cat i on of work status w ill b e prov i d e d to r e gu l atory ag e nc ie s two days 
i n advanc e of sch e du le d work. 

3. Work may occur after a significant rainfall event but no later than December 31. 

4. Sites must be maintained in a rapidly winterizable 1 state (implement control 
measures BMP GEN-20). 

Bank stabilization projects that ar e 50% comp le t e by Octob e r 15 may continue until the 
approved date stated below comp le t i on or unt il 0.5 i nch e s of ra i n i s pr e d i ct e d i n th e n e xt 2d-hr 
p e r i od . Prior to a forecasted significant rainfall event (0.5 in/24 hrs), all incomplete bank 
stabilization projects must be winterized. 

1. In Creeks Supporting Anadromous Fish 

o An extended work window mav occur until October 31 st for bank stabilization 

^ j.i_ 

projects that will be 50% complete by October 15 . 

2. In Creeks Not Supporting Anadromous Fish 

o An extended work window mav occur until November 30 th for projects that will 
be 50% complete by October 15 th or until significant rainfall. 
o An extended work window mav occur until November 30th for new bank 
stabilization projects that will be completed in five (5) days or less, or until 
significant rainfall. 

■ Instream hand pruning and hand removal of vegetation will occur year round, except 
when: 

o Wheeled or tracked equipment needs to access the site by crossing a creek, 
ponded area, or secondary channel; or 

o Work occurs in streams that support steelhead. In these streams instream 
vegetation maintenance will cease on December 31 or when local rainfall 
greater than 0.5 inches is predicted within a 24-hour period of planned 
activities, whichever happens first. 

Modification and removal of instream large woody debris will occur at any time of the year, and 
as further described in the NMFS Biological Opinion, i f i mm i n e nt dang e r of a f l ood thr e at 
pr e c l ud e s le av i ng th e wood i n p l ac e . 

Additional language has been added to Table 2-12 under BMP GEN-2 and BMP GEN-8 for 
clarification of the types of proposed herbicides as well as herbicide application 
requirements. 

BMP GEN-2: Instream Herbicide Application Work Window 

Instream herbicide applications will take place between June 15 and October 1534, with an 
extension through December 31 or until the first occurrence of any of the following conditions; 
whichever happens first: 

■ local rainfall greater than 0.5 inches is forecasted within a 24-hour period from planned 
application events; or 

■ when steelhead begin upmigrating and spawning in the 14 steelhead creeks, as 
determined by a qualified biologist (typically in November/December), 


1 Winterization is the process to maintain work sites with the appropriate BMP’s to prevent erosion, sediment 
transport, and protect water quality. Winterization occurs upon completion of bank repairs or on incomplete projects 
after October 15 and prior to the forecast of significant rainfall, 0.5 inches or greater of local watershed rainfall within 
24 hours. Winterization shall be completed prior to the occurrence of such actual significant rainfall. 


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o A qualified biologist will determine presence/absence of sensitive resources in 
designated herbicide use areas and develop site-specific control methods 
(including the use of approved herbicide and surfactants). Proposed herbicide 
use would be limited to the aquatic formulation of glyphosate (Rodeo or 
equal). Surfactant use would be limited to non-ionic products, such as Agri- 
dex, Competitor, or another brand name using the same ingredients. Any 
modifications to these materials would require review and approval by NMFS 
and CDFG . 

o A qualified fisheries biologist will review proposed herbicide application 
methods and stream reaches. The fisheries biologist would conduct a pre¬ 
construction survey (and any other appropriate data research) to determine 
whether the proposed herbicide application is consistent with SMP approvals 
concerning biological resources and determine which BMPs would be 
instituted for work to proceed. 

In addition, herbicide application requirements are as follows: 

■ no direct application into water; 

■ herbicide application shall not occur when wind conditions may result in drift; 

■ herbicide shall only be applied after the surfactant has a “wet” appearance on the 
target plants in order to avoid run off; and 

■ where permitted, surfactants shall be added to the spray solution prior to application. 


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A new best management practice, BMP GEN-6.5: Protection of Nesting Least Bell’s Vireos has been added to Table 2-12: 


GEN-6.5 


Protection of Nestinq Least 



To the extent feasible, SMP activities within woody riparian habitat along portions of lower Llagas Creek 
downstream from Highway 152, the Pajaro River from Llagas Creek downstream, and lower Uvas/Carnadeo 
Creek downstream from Hecker Pass Road shall be scheduled to occur outside of the least Bell’s vireo nesting 
season (March 15 - July 31). 

For activities within woodv riparian habitat along the aforementioned creek reaches that will occur between 


March 15 and July 31, anv work will be preceded bv a focused survey for least Bell’s vireos. Pre-activitv 


surveys will consist of two site visits, conducted on separate days within 14 days before the initiation of 


maintenance activities in the given area, with at least one of these surveys occurring within 7 days before the 


initiation of such activities. Surveys will be conducted between dawn and 11:00 a.m., during mild weather 


conditions (i.e., not during excessive cold, heat, wind, or rain), within all riparian habitat in and within 250 feet 


roposed maintenance location along these reaches. The surveys will be conducted bv a qualified 


biologist who is familiar with the visual and auditory identification of this species. 


To minimize impacts to nestinq least Bell’s vireos and other birds, the biologist will not initially be looking for 


Bell’s vireo nests during these surveys. Rather, the biologist will look and listen for individual vireos. If a least 


Bell’s vireo is detected, it will be observed to determine whether it is actively nestinq. The biologist will note the 


nest location, or if finding the actual nest could result in excessive disturbance or risk damaging the nest, the 


biologist will determine the approximate location, based on observation of birds carrying nesting material, 


carrying food, or repeatedly visiting a certain area. 


If an active nest is found, a minimum 250-foot no-activity buffer will be established around the nest. If a 
territorial male is found but no nest can be detected, then the approximate centroid of the bird’s area of activity 
will be the point from which the buffer will be applied. The required buffer may be reduced in areas where 
dense riparian forest occurs between the construction activities and the active nest or where sufficient barriers 
or topographic relief exists to protect the nest from excessive noise or other disturbance. The biologist will 
coordinate with the USFWS and CDFG to evaluate exceptions to the minimum no-activity buffer distance on a 
case-bv-case basis. 

No work will occur within the buffer without verification bv a biologist that the nest is inactive and until anv 
fledged young are no longer dependent on adults for food. 


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BMP GEN-7: Protection of Burrowing Owls, in Table 2-12 is revised as follows: 


1. I f burrow i ng ow l s ar e pr e s e nt, th e n w Work within 250 feet of an occupied burrow will be delayed until after the 
nesting season. 

2. If suitable burrowing owl habitat is identified where mowing is proposed, or active burrows are found, they will 
be marked in such a way that the mower can identify the locations of such burrows. Mowing can then occur 
anywhere beyond the 250 foot buffer zone. Within the 250 foot buffer zone mowing may be done to within 10 
feet of an active burrow provided there are te no burrowing owls active on the surface. An on-site monitor will 
observe the area in front of the mower from a safe vantage point while it is in operation. In areas within 10 ft of 
active burrows the vegetation may be removed by hand (e.g., weed-whackers). All mowing and hand-removal 
of vegetation within 250 ft of a burrow will be done as quickly as possible to minimize disturbance of burrowing 
owls. 

BMP GEN-8: Protection of Sensitive Fauna Species from Herbicide Use 

■ A qualified biologist will determine presence/absence of sensitive resources in designated herbicide use 

areas and develop site-specific control methods (including the use of approved herbicide and surfactants). 

Proposed herbicide use would be limited to the aquatic formulation of glyphosate (Rodeo or equal). 

Surfactant use would be limited to non-ionic products, such as Agri-dex, Competitor, or another brand name 

using the same ingredients. Any modifications to these materials would require review and approval by 

NMFS and CDFG . 

BMP GEN-9 in Table 2-12 of the DSEIR is revised as follows: 

4. The qualified botanist will ensure avoidance and/or minimize impacts by implementing one or more of the 
following, as appropriate per the botanist’s recommendation: 

7. All impacts to sensitive natural communities and special status plants identified by the qualified botanist will be 
avoided and/or minimized. 

BMP GEN-10 of the DSEIR is revised as follows: 

1. Areas supporting Bay checkerspot larval host plants will be identified by a qualified botanist and protected from 
disturbance to the extent feasible, by establishing buffer zones around individual plants or populations. The 
size of the buffer will be determined by a qualified botanist; the actual distance will depend on the plant species 
potentially affected and the type of disturbance. No herbicide will be applied to the buffer area, and to the 
extent feasible, maintenance personnel and equipment will not operate within such areas. 

BMP GEN-11 of the DSEIR is revised as follows: 

4. Specific habitat areas are vegetated areas of cordgass (Spartina spp), marsh gumplant (Grindelia spp.), 
pickleweed (Sarcocornia pacifica), alkali heath, (Frankenia sp.), and other high marsh vegetation, brackish 
marsh reaches of creek with heavy accumulations of bulrush thatch (old stands), and high water refugia 
habitat that may include annual grasses, and shrubs immediately adjacent to channels. 

BMP GEN-13 of the DSEIR is revised as follows: 


F. If an active western pond turtle nest is detected within the activity area, a 2550 ft-buffer zone around the 
nest will be established and maintained during the breeding and nesting season (April 1 - August 31). The 
buffer zone will remain in place until the young have left the nest, as determined by a qualified biologist. 

BMP GEN-13 of the DSEIR is revised as follows: 


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b. There is a need for a buffer zone to prevent disturbance to the bat colony, and implementation of the 
buffer zone (determined on a case-by-case basis by a qualified biologist) will reduce or eliminate the 
disturbance to an acceptable level. 

BMP GEN-15.5 of the DSEIR is revised as follows: 

3. If take of the San Joaquin kit fox will occur, take authorization from the USFWS and CDFG will be necessary. 

Number 4 and number 5 have been switched and updated in BMP GEN-33 of the DSEIR is 
revised as follows: 

4. §^lnstream cofferdams will only be built from materials such as sandbags, earth fill, clean gravel, or rubber 
bladders which will cause little or no siltation or turbidity. 

5. 4^Plastic sheeting will be placed over k-rails, timbers, and earth fill to minimize water seepage into and out of 
the maintenance areas. The plastic sheets will be firmly anchored, using sandbags, to the streambed to 
minimize water seepage. 

BMP VEG-2 of the DSEIR is revised as follows: 

Invasive species (e.g. cape ivy [De/a/rea odorata/ Senecio mikanoides], arundo \Arundo don ax 1 ) will be 
disposed of in a manner that will not contribute to the further spread of the species. Cape ivy removed 
during a project shall be bagged and disposed of in a landfill. Arundo canes will be prevented from floating 
downstream or otherwise entering the creek or waterway. 

BMP HM-4 of the DSEIR is revised as follows: 

5. A District staff contact phone number will be posted on the sign, including a paq e r cellular phone number. 

The introductory paragraph for SECTION C- Sediment Removal BMPs has been updated as 
follows: 

This group of BMPs is intended to be implemented specifically during sediment removal activities^ 
Tto avoid potential impacts on biological resources , non e of th e s e m e asur e s w ill b e i mp le m e nt e d 
unt il author i zat i on from th e SMP I mp le m e ntat i on Proj e ct Manag e r i s r e c ei v e d . 

The introductory paragraph for SECTION E- Bank Stabilization BMPs has been updated as 
follows: 

These BMPs provide additional guidance during implementation of bank stabilization projects^ 
Tto avoid impacts on biological and cultural resources , non e of th e s e m e asur e s w ill b e 
i mp le m e nt e d unt il author i zat i on from th e SMP I mp le m e ntat i on Proj e ct Manag e r i s r e c ei v e d . 


Chapter 3, Environmental Setting and Impact Analysis 
Section 3.0, Introduction 

The second sentence in the first paragraph on page 3.0-2 of the DSEIR is revised as follows: 

Therefore, the project description for the SMP Update is comprehensive, and 
includes activities under both the existing SMP and the proposed changes to the 
SMP. This SEIR uses existing conditions at the time of the Notice of Preparation as 


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the environmental setting and baseline, and analyzes the 2012 - 2020 impacts of the 
comprehensive SMP Update against this baseline. This conservative approach to the 
Subsequent EIR baseline and impact analysis scope represents an exception to 
established District CEQA practice due to the unique nature of the proposed SMP 
changes. It will not necessarily be employed in future District Subsequent EIRs for 
other projects in the absence of similar unique circumstances. 

Section 3.3, Biological Resources 

Language has been added to the bottom of pages 3.3-65 in order to provide examples for 

Habitat Mitigation and Monitoring Plans as follows: 

• A description of community monitoring measures on the mitigation site, 
including specific, objective goals and objectives (such as maintaining or 
increasing abundance of sensitive species), performance indicators (such as 
presence of suitable habitat structure), success criteria (such as residual dry 
matter levels or abundance of target sensitive species), monitoring methods 
(such as residual dry matter monitoring or sampling for target sensitive 
species), data analysis, reporting requirements, and monitoring schedule 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 

DSEIR. 

Language has been added to the bottom of page 3.3-120 in order to provide examples for 

Habitat Mitigation and Monitoring Plans as follows: 

• a description of species monitoring measures on the mitigation site, including 
specific, objective goals and objectives (including maintaining or improving 
habitat suitability for California tiger salamanders), performance indicators 
and success criteria (including maintaining or increasing the abundance of 
upland refugia for California tiger salamanders), monitoring methods (such 
as sampling of the abundance of upland refugia). data analysis, reporting 
requirements, and monitoring schedule. Determining other specific 
performance/success criteria requires information regarding the specific 
mitigation site, its conditions, and the specific enhancement and management 
measures tailored to the mitigation site and its conditions. For example, 
performance criteria for a mitigation site providing only upland habitat for 
California tiger salamanders would include the maintenance of grassland 
habitat of a suitable height and density for burrowing mammals, and 
maintenance of suitable burrowing mammal populations, whereas a 
mitigation site providing salamander breeding habitat would also include 
criteria related to adequate depth and hydroperiod of breeding habitat. As a 
result, thos e additional specific criteria will be defined in the HMMP rather 
than in this SEIR. Nevertheless, the performance/success criteria described in 
the HMMP will guide the mitigation to manage and protect high-quality 
habitat for the California tiger salamander, adequate to compensate for 
impacts. 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 

DSEIR. 


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Language has been added to the second to last paragraph on page 3.3-153 in order to 
provide examples for Habitat Mitigation and Monitoring Plans as follows: 

• a description of species monitoring measures on the mitigation site, including 
specific, objective goals and objectives (including maintaining or restoring 
suitable habitat for the least Bell's vireo). performance indicators and success 
criteria (including maintenance or improvement of habitat structure suitable 
for use by least Bell's vireos). monitoring methods (including least Bell's vireo 
surveys), data analysis, reporting requirements, and monitoring schedule. 
Determining other specific performance/success criteria requires 
information regarding the specific mitigation site, its conditions, and the 
specific enhancement and management measures tailored to the mitigation 
site and its conditions. As a result, additional thos e specific criteria will be 
defined in the HMMP rather than in this SEIR. Nevertheless, the 
performance/success criteria described in the HMMP will guide the 
mitigation to manage and protect habitat at least as suitable for use by the 
least Bell's vireo as the habitat that is impacted. 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

Language has been added to the last paragraph on page 3.3-157 in order to provide 
examples for Habitat Mitigation and Monitoring Plans as follows: 

This mitigation may be provided via the management of suitable habitat on SCVWD 
lands (either existing lands or lands that are acquired), purchase of credits in a 
mitigation bank (if one is available), or contribution of funds toward the 
management of the required amount of suitable habitat owned by another entity. If 
SCVWD provides habitat mitigation on its own lands, either on existing SCVWD 
lands or on lands that are acquired for mitigation purposes, an HMMP will be 
prepared detailing the areas to be preserved for owls; the methods for managing on¬ 
site habitat for owls and their prey (including vegetation management to maintain 
low-statured herbaceous vegetation) : methods for enhancing burrow availability 
within the mitigation site (potentially including the provision of artificial burrows, 
although long-term management for ground squirrels will be important as well); 
measures to minimize adverse effects of development on owls on-site; and a 
monitoring program and adaptive management program. The monitoring program 
will include performance indicators and success criteria, including maintenance of 
short vegetation supporting California ground squirrels and maintenance of 
increase in burrowing owl numbers on the mitigation site. Determining other 
specific performance/success criteria requires information regarding the specific 
mitigation site, its conditions, and the specific enhancement and management 
measures tailored to the mitigation site and its conditions. For example, 
performance criteria for a site where burrowing owls are known to occur (including 
maintaining or increasing burrowing owl abundance) may differ from those for an 
unoccupied site adjacent to occupied burrowing owl habitat (including attracting 
owls to use the mitigation site) . As a result, those specific criteria will be defined in 
the HMMP rather than in this SEIR. Nevertheless, the performance/success criteria 


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described in the HMMP will guide the mitigation to manage and protect high-quality 
habitat for burrowing owls, adequate to compensate for impacts. 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

The discussion of mitigation for impacts to tidal wetlands and other waters under 
Mitigation Measure BIO-1 (on pages 3.3-71 of the DSEIR) is revised as follows: 

The compensatory mitigation package, which is detailed in Appendix C, 2012-2022 
SMP Update Mitigation Approach Memorandum, shall be implemented to 
compensate for new impacts (i.e., work areas not included in the 2002-2012 work 
projections) on wetlands (both jurisdictional and non-jurisdictional) and on 
jurisdictional "other waters"; no mitigation is necessary for impacts to non- 
jurisdictional "other waters", which are limited to unvegetated areas of inoperable 
canals. For work areas included in the 2002-2012 work projections, previously 
provided mitigation would continue to serve as mitigation in perpetuity, as no new 
significant environmental effects or a substantial increase in the severity of 
previously identified significant effects are anticipated under the SMP Update. 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

The discussion of mitigation for impacts to tidal wetlands and other waters under 
Mitigation Measure BIO-1 (on pages 3.3-74 and 3.3-75 of the DSEIR) is revised as follows: 

Mitigation for Impacts to Tidal Wetlands and Other Waters. SCVWD will 
continue to implement mitigation measures adopted to reduce impacts for the SMP. 
Although the 2012 project description has changed, this FSE1R has examined the 
Proposed Project changes and determined that the existing tidal marsh restoration 
mitigation measures will continue to reduce the Proposed Project impacts to less 
than significant. The 2012 SMP Update will be a continuation from the 2002 SMP, 
with some program modifications: although the work activities are updated, the 
original mitigation remains, along with the resulting benefits. 

As mitigation for impacts to tidal habitats and tidal marsh species predicted to 
result from the 2002-2012 SMP work activities. SCVWD restored the "Island Ponds" 
(Ponds A19, A20, and A21), located between Coyote Slough and Mud Slough near 
Alviso, to tidal action. Restoring these ponds provided 30 acres of tidal habitat that 
is used by a variety of tidal marsh species. Monitoring has documented achievement 
of all performance criteria appropriate for the development of both vegetated tidal 
salt/brackish marsh and tidal aquatic habitat, includin g with the formation of 
nascent tidal marsh habitat, including extensive channel networks, within these 
ponds. 

The 2002 SMP work projections provided the basis for determining the SMP's 
initial, upfront compensatory mitigation. As a result of those projections, impacts to 
tidal habitats for the 2002-2012 SMP Update were calculated with a mitigation 


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requirement of 30 acres of tidal restoration. SCVWD already has met this obligation 
by restoring 30 acres of tidal habitat with the “Island Ponds.” Thirty acr e s of tidal 
r e storation within th e Island Ponds was int e nd e d to s e rv e as mitigation for impacts 
to tidal habitats for th e 2002 - 2012 SMP. However, not all of the 2002 projected 
work has actually been performed. Thus, the 2002 mitigation of 30 acres of restored 
tidal habitat paid for more work than was conducted. Based on the actual impacts 
from activities conducted between 2002-2012 Propos e d Proj e ct activiti e s , only 9 
acres of tidal mitigation will b efs needed to compensate for those impacts. 

The 2002-2012 SMP created an upfront compensatory mitigation package to 
account for SMP impacts in perpetuity. The 2012-2022 SMP Update has modified 
the project description to refine maintenance work activity needs. The updated 
project description in this FSE1R is a continuation, with modifications, of the 2002- 
2012 SMP. 


SCVWD will remove the 2002 work activity projections that would have resulted in 
the need for 21 tidal habitat mitigation acres. The removal of these projections, 
therefore, will equate to having 21 acres of tidal habitat mitigation that is not 
attributed to ongoing SMP impacts. Th e r e for e . SCVWD cr e at e d 21 acr e s of e xc e ss 
tidal habitats. SCVWD will use the 21 acres of e xc e ss tidal marsh habitat restoration 
as available mitigation for impacts to tidal wetlands and aquatic habitats, as well as 
tidal marsh species, that may occur under the 2012-2022 SMP Update . Physical 
br e aching of th e Island Pond l e v ee s and oth e r physical work r e quir e d for this tidal 
r e storation has alr e ady occurr e d, and no furth e r activiti e s (oth e r than continu e d 
monitoring —of— marsh — d e v e lopm e nt —per—the— 2002 - 2012 —SMP— monitoring 
r e quir e m e nts) ar e propos e d by SCVWD. 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

The third paragraph under Mitigation Measure BIO-3 on page 3.3-85 of the DSEIR is revised 
as follows: 

Compensation for unavoidable effects to high-quality serpentine communities will 
be provided via the protection, enhancement, and management of serpentine 
communities outside SMP work sites at a 2:1 f mitigation: impact :mitigation ) ratio, 
on an acreage basis. SCVWD will acquire land supporting serpentine communities 
via fee title or purchase of a conservation easement. Compensatory mitigation may 
be carried out through one or both of the following methods, in order of preference: 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

The last bullet on page 3.3-85 of the DSEIR is revised as follows: 

• A description of community monitoring measures on the mitigation site, 
including specific, objective goals and objectives (including maintaining or 
increasing native plant species diversity), performance indicators and success 


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criteria (including maintaining or increasing the relative abundance of native 
vs. non-native species), monitoring methods (including vegetation sampling 
for plant species composition), data analysis, reporting requirements, and 
monitoring schedule 

(Determining other specific performance/success criteria requires 
information regarding the specific mitigation site, its conditions, the 
biological resources present on the site, and the specific enhancement and 
management measures tailored to that site and its conditions. As a result, 
additional those specific criteria will be defined in the HMMP rather than in 
this SEIR. Nevertheless, the performance/success criteria described in the 
HMMP will guide the mitigation for management and protection of high- 
quality serpentine communities to adequately compensate for the functions 
and values of the impacted communities.) 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

The first sentence in the second paragraph of the conclusion under Impact BIO-10 on pages 
3.3-112-113 is revised as follows: 

As discussed under Impact BIO-1, Mitigation Measure BIO-1 includes mitigation for 
impacts to tidal wetlands and other waters, which would be the habitats in which 
the longfin smelt and green sturgeon could potentially occur. SCVWD would use the 
21 acres of e xc e ss tidal marsh restoration that it has accomplished at the Island 
Ponds as available mitigation for impacts to tidal wetlands and aquatic habitats, as 
well as tidal species such as the longfin smelt and green sturgeon. 

The second paragraph under Mitigation Measure BIO-10 on page 3.3-119 has been revised 
as follows: 

Compensation for these effects will be provided via the protection, enhancement, 
and management of habitat that currently supports, or can support, this species at a 
2:1 ( mitigation: impact :mitigation ) ratio, on an acreage basis. Compensatory 
mitigation may be carried out through one or both of the following methods, in 
order of preference: 

The second paragraph under Mitigation Measure BIO-11 on page 3.3-130 of the DSEIR is 
revised as follows: 

Compensation for these effects will be provided via the protection, enhancement, 
and management of habitat that currently supports, or could support, this species at 
a 2:1 ( mitigation: impact :mitigation ) ratio, on an acreage basis. Compensatory 
mitigation may be carried out through one or both of the following methods, in 
order of preference: 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 


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The conclusion under Impact BIO-20, in the last paragraph on page 3.3-145 of the DSEIR, is 
revised as follows: 

Mitigation Measure BIO-1 includes mitigation for impacts to tidal habitats and tidal 
marsh species. As mitigation for impacts to tidal habitats and tidal marsh species 
was predicted to result from the 2002-2012 SMP, SCVWD restored the "Island 
Ponds" (Ponds A19, A20, and A21), located between Coyote Slough and Mud Slough 
near Alviso, to tidal action. Monitoring has documented the formation of nascent 
tidal marsh habitat, including extensive channel networks, within these ponds. 
Thirty acres of tidal restoration within the Island Ponds was intended to serve as 
mitigation for impacts to tidal habitats for the 2002-2012 SMP. However, based on 
the actual impacts from 2002-2012 SMP activities, only 9 acres of tidal mitigation 
was needed to compensate for those impacts. Furth e rmor e As a result. SCVWD 
created 21 acres of e xc e ss tidal habitats beyond what was needed to mitigate for the 
actual impacts from 2002-2012 SMP activities . SCVWD would use the 21 acres of 
e xc e ss tidal marsh restoration as available mitigation for impacts to tidal wetlands 
and aquatic habitats, as well as tidal marsh species, under the 2012-2022 SMP 
Update. 

The applicable best management practices under Impact BIO-23 on page 3.3-152 of the 
DSEIR are revised as follows: 

Applicable Best Management Practices 

BMP GEN -4 : Minimiz e th e Ar e a of Disturbanc e 

BMP GEN - 6: Minimiz e Impacts to N e sting Birds via Sit e Ass e ssm e nts and Avoidanc e 
M e asur e s 

BMP GEN-6.5: Protection of Nesting Least Bell's Vireos 

The last paragraph under Mitigation Measure BIO-13 on page 3.3-157 of the DSEIR is 
revised as follows: 

Th e HMMP will b e submitt e d to th e CDFG for r e vi e w. If a mitigation bank providing 
credits for burrowing owls is established within the aforementioned mitigation area 
(i.e., in Santa Clara County, or in areas of San Mateo or Alameda counties adjacent to 
San Francisco Bay), then mitigation may take the form of the purchase of credits 
equivalent to the number of acres of mitigation required. 

This revision is also reflected in the full mitigation text in Volume II, Appendix L of the 
DSEIR. 

The conclusion under Impact BIO-35, on the last paragraph on page 3.3-173 of the DSEIR, is 
revised as follows: 

As described under Impact BIO-3, management of the invasive perennial 
pepperweed in the Coyote Creek Bypass area would benefit the northern coastal salt 
marsh community, and salt marsh harvest mouse habitat, and thus would not 
require mitigation. Otherwise, as mitigation for impacts to tidal habitats and tidal 
marsh species predicted to result from the 2002-2012 SMP, SCVWD would 


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implement Mitigation Measure BIO-1 that (as described) restored the "Island 
Ponds" (Ponds A19, A20, and A21), located between Coyote Slough and Mud Slough 
near Alviso, to tidal action. Monitoring has documented the formation of nascent 
tidal marsh habitat, including extensive channel networks, within these ponds. 
Thirty acres of tidal restoration within the Island Ponds was intended to serve as 
mitigation for impacts to tidal habitats for the 2002-2012 SMP. However, based on 
the actual impacts from 2002- 20120^ SMP activities, only 9 acres of tidal mitigation 
were needed to compensate for those impacts. In addition As a result. SCVWD 
created 21 acres of e xc e ss additional tidal habitats compared to what was needed to 
mitigate for the actual impacts from 2002-2012 SMP activities . SCVWD would use 
the 21 acres of e xc e ss tidal marsh restoration as available mitigation for impacts to 
tidal wetlands and aquatic habitats, as well as tidal marsh species, under the 2012- 
2022 SMP Update. 

The heading for Mitigation Measure BIO-16 on page 3.3-183 and in Appendix L of the DSEIR 
has been revised as follows: 

Mitigation Measure BIO-1 6; Invasive Plant Species Management Program 

Chapter 4: Other Statutory Considerations 

The list of applicable best management practices under Cumulative Impact BIO-1 on page 4- 
20 is revised as follows: 

GEN-4: Minimize the Area of Disturbance 
GEN-5: Mitten Crab Control Measure 

GEN-6: Minimize Impacts to Nesting Birds via Site Assessments and Avoidance 
Measures 

GEN-6.5: Protection of Nesting Least bell's vireo 
GEN-7: Protection of Burrowing Owls 

GEN-8: Protection of Sensitive Fauna Species from Herbicide Use 
GEN-9: Avoid Impacts to Special-Status Plant Species and Sensitive Natural 
Vegetation Communities 

GEN-10: Avoid Impacts to Bay Checkerspot Butterfly and Associated Critical Habitat 
GEN-11: Protection of Salt Marsh Harvest Mouse and California Clapper Rail 
GEN-12: Protection of Special-Status Amphibian and Reptile Species 
GEN-13: Protection of Bat Colonies 

GEN-14: Protection of San Francisco Dusky-Footed Woodrat 
GEN-15: Salvage Native Aquatic Vertebrates from Dewatered Channels 
GEN-15.5: Avoidance of Impacts on the San Joaquin Kit Fox 

Appendix A, 2012 Stream Maintenance Program Manual 

The draft 2012 SMP Manual has been replaced with a final version. 

Appendix C, 2012-2022 SMP Update Mitigation Approach Memorandum 

The draft 2012-2022 SMP Update Mitigation Approach Memorandum has been replaced 
with a final version. 


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Appendix L, Mitigation and Monitoring Report Program 

The reference to the DSEIR is revised as follows: 

[Under Introduction, in the first sentence of the second paragraph:] 

The purpose of discussing the MMRP in the DSEIR (DSEIR) FSEIR is to appropriately 
assign the mitigation responsibilities for implementing the Proposed Project. The 
mitigation measures listed in the MMRP are required by law or regulation and will 
be adopted by SCVWD as a condition of the primary SMP Update approval. 

[Under Introduction, in the first sentence of the second paragraph:] 

Mitigation measures provided in this MMRP were initially identified in Chapter 3, 
Environmental Setting and Impact Analysis of the DSEIR Draft Subsequent 
Environmental Impact Report (DSEIR). as feasible and effective in mitigating 
Proposed Project-related environmental impacts. As a result of comments received 
during public review of the DSEIR, these mitigation measures will b e have been 
revised as necessary. 

Figures 

The following text has been added to all maps showing work projections (as indicated in the 
Table of Contents) in the FSEIR: 

Project area maps provide a general description of work type and area for the 2012- 
2022 SMP and are not intended to represent the exact locations of future work. 

In addition, the contents of Figures 3.3-11, 3.3-19, 3.3-10, and 3.3-22 have been updated. 


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Volume I, Appendix A 

Notice of Completion and Environmental Document 

Transmittal for the DSEIR 


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Appendix C 


Notice of Completion & Environmental Document Transmittal 

Mail to: State Clearinghouse, P.O. Box 3044, Sacramento, CA 95812-3044 (916) 445-0613 
For Hand Delivery/Street Address: 1400 Tenth Street, Sacramento, CA 95814 


sch #2000102055 


Project Title: Stream Maintenance Program Update 2012-2022 _ 

Lead Agency: Santa Clara Valley Water District _ Contact Person: Sunny Williams 

Mailing Address: 5750 Almaden Expressway _ Phone: (408) 265-2600 _ 

City: San Jose _ Zip: 95118 County: Santa Clara _ 


Project Location: County: Santa Clara _City/Nearest Community: San Jose, etc (see Figure 2-1) 


Cross Streets: Multiple (see Program Area Map, Figure 2-1) 


Zip Code: 95118 

Longitude/Latitude (degrees, minutes and seconds'): 37 ° 20 

-27 "n / 

121 ° 53 '43 

W Total Acres: 

Assessor's Parcel No.: Multiple 

Section: 

Twp.: 7S 

Range: IE Base: Mt. Diablo 

Within 2 Miles: State Hwy #: 101, 880, 237,17,152, 9 

Waterways: 

Guadalupe/Pajaro Rivers, and more (Figure 2-1) 

Airports: San Jose Int'l, Moffett Field 

Railways: Amtrak 

Schools: Multiple 


Document Type: 


CEQA: 



NOP 


Draft EIR NEPA: 


NOI Other: 


Joint Document 


Early Cons 

_/ 

Supplement/Subsequent EIR 


EA 


Final Document 


Neg Dec i 

(Prior SCH No.) . 


Draft EIS 


Other: 


Mit Neg Dec Other: 


FONSI 




Local Action Type: 



General Plan Update 


Specific Plan 


Rezone 



General Plan Amendment 


Master Plan 


Prezone 


□ 

General Plan Element 


Planned Unit Development 

□ 

Use Permit 

□ 

□ 

Community Plan , | 


Site Plan 

□ 

Land Division (Subdivision, etc.) 

0 


Annexation 
Redevelopment 
Coastal Permit 
Other: Maint. Program 


Development Type: 


— 

Residential: Units Acres 

Office: Sq.ft. Acres Emplovees 

— 

f 

Transportation: Type 


Commercial: Sq.ft. Acres Employees 


Mining: Mineral 


Industrial: Sq.ft. Acres Employees 


Power: Type MW 


Educational: 


Waste Treatment: Type MGD 


Recreational: 


Hazardous Waste:Type 


Water Facilities:Type MGD 


Other: 


Project Issues Discussed in Document: 


PI Aesthetic/Visual 


Fiscal 

7 

Recreation/Parks 

7 

Vegetation 

0 

Agricultural Land 

V 

Flood Plain/Flooding 

7 

Schools/Universities 

7 

Water Quality 

b 

Air Oualitv 

ar 

7 

Forest Land/Fire Hazard 

7 

Septic Svstems 

X V 

7 

Water Supplv/Groundwater 

xx v 

/_ 

Archeological/Historical 

7 

Geologic/Seismic 

7 

Sewer Capacity 

7 

W etland/Riparian 

V 

Biological Resources 


Minerals 

7 

Soil Erosion/Compaction/Grading 

7 

Growth Inducement 

□ 

Coastal Zone 

7 

Noise 

7 

Solid Waste 

7 

Land Use 

PI Drainage/Absorption 

7 

Population/Housing Balance 

7 

Toxic/Hazardous 

7 

Cumulative Effects 

f~l Economic/Jobs 

7 

Public Services/Facilities 

7 

Traffic/Circulation 


Other: 


Present Land Use/Zoning/General Plan Designation: 

Varies 

Project Description: (please use a separate page if necessary) 

See attached Chapter 2 "Project Description", in accompanying Draft Subsequent EIR 


Note: The State Clearinghouse will assign identification numbers for all new projects. If a SCH number already exists for a project (e.g. Notice of Preparation or 
previous draft document) please fill in. 


Revised 2008 










Reviewing Agencies Checklist _ 

Lead Agencies may recommend State Clearinghouse distribution by marking agencies below with and "X". 
If you have already sent your document to the agency please denote that with an "S". 


X 


X 

X 


X 


X 


X 

X 


X 

X 


Air Resources Board 

Boating & Waterways, Department of 

California Highway Patrol 

Caltrans District # 4 

Caltrans Division of Aeronautics 

Caltrans Planning 

Central Valley Flood Protection Board 
Coachella Valley Mtns. Conservancy 
Coastal Commission 
Colorado River Board 
Conservation, Department of 
Corrections, Department of 
Delta Protection Commission 
Education, Department of 
Energy Commission 
Fish & Game Region # 3 
Food & Agriculture, Department of 
Forestry and Fire Protection, Department of 
General Services, Department of 
Health Services, Department of 
Housing & Community Development 
Integrated Waste Management Board 
Native American Heritage Commission 


X 

X 


X 


X 

X 

X 


X 


X 


X 

X 


Office of Emergency Services 
Office of Historic Preservation 
Office of Public School Construction 
Parks & Recreation, Department of 
Pesticide Regulation, Department of 
Public Utilities Commission 
Regional WQCB # 2 & 3 
Resources Agency 

S.F. Bay Conservation & Development Comm. 

San Gabriel & Lower L.A. Rivers & Mtns. Conservancy 

San Joaquin River Conservancy 

Santa Monica Mtns. Conservancy 

State Lands Commission 

SWRCB: Clean Water Grants 

SWRCB: Water Quality 

SWRCB: Water Rights 

Tahoe Regional Planning Agency 

Toxic Substances Control, Department of 

Water Resources, Department of 


Other: 

Other: 


Local Public Review Period (to be filled in by lead agency) 

Starting Date August 8, 2011 _Ending Date September 21,2011 


Lead Agency (Complete if applicable): 

Consulting Firm: Horizon Water and Environment Applicant: Santa Clara Valley Water District 

Address: 1330 Broadway, Ste 424 Address: 5750 Almaden Expressway 

City/State/Zip: Oakland, CA 94612 _ City/State/Zip: San Jose, CA 95118 

Contact: Michael Stevenson Phone . (408) 265-2600 

Phone: (510) 986-1850 


Signature of Lead Agency Representative: 



Date: 


. 0-V-// 


Authority cited: Section 21083, Public Resources Code. Reference: Section 21161, Public Resources Code. 


Revised 2008 






Volume I, Appendix B 

DSEIR Distribution List 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 





SCVWD DSEIR Distribution List 


Address 

Contents 

Kristen O'Kane 

Santa Clara Valley Water District 

Winfield Warehouse 

5905 Winfield Blvd 

San Jose, CA 95123-2428 

408-265-2604x2692 

1 Hard Copy (HC) 

1 CD 

State Clearinghouse 

1400 Tenth Street 

Sacramento CA 95814 

916-322-2318 

15 Exec Sum 

15 CD 

1 NOA 

1 Signed NOC 

Dr. Martin Luther King, Jr. Library 

150 E. San Fernando St. 

San Jose, CA 95112 

408-808-2000 

1 HC 

1CD 

1 NOA 

1 transmittal 

Keye Luke 

Alviso Branch Library 

5050 N 1st St. 

San Jose, CA 95134 

408-263-3626 

1 HC 

1CD 

1 NOA 

1 transmittal 

Peggy Tomasso 

Morgan Hill Public Library 

660 W. Main Ave 

Morgan Hill, CA 95037 

408-779-3197 

1 HC 

1CD 

1 NOA 

1 transmittal 

Monique le Conge 

Palo Alto Public Library 

1213 Newell Rd. 

Palo Alto, CA 94303 

650-329-2436 

1 HC 

1CD 

1 NOA 

1 transmittal 

Mark Fink 

Cupertino Public Library 

10800 Torre Avenue 

Cupertino, CA 95014-3207 

408-446-1677 

1 HC 

1CD 

1 NOA 

1 transmittal 

Linda Arbaugh 

Milpitas Public Library 

160 N. Main Street 

Milpitas, California 95035 

408-262-1171 

1 HC 

1CD 

1 NOA 

1 transmittal 

Kristen O'Kane 

Santa Clara Valley Water District 

Winfield Warehouse 

5905 Winfield Blvd 

San Jose, CA 95123-2428 

408-265-2604x2692 

10 HC 

10 CD 

10 NOA 














SCVWD DSEIR Distribution List 


Address 

Contents 

John Rohrbough 

Central Coast Water Board 

895 Aerovista Place, Suite 101 

San Luis Obispo, CA 93401-7906 
[805] 549-3458 

1 HC 

1CD 

1 NOA 

Tami Schane 

California Department of Fish and Game 

P.O.Box 29398 

San Francisco, CA 94129-0398 
[415) 831-4640 

1 HC 

1CD 

1 NOA 

Liam Davis 

California Department of Fish and Game 

Bay Delta Region 

7329 Silverado Trail 

Napa, CA 94558 
[707)944-5529 

1 HC 

1CD 

1 NOA 

Luisa Valiela 

USEPA Region 9 

75 Hawthorne Street 

San Francisco, CA 94105 
[415) 972-3400 

1 HC 

1CD 

1 NOA 

Vincent Griego 

U.S. Fish and Wildlife Service 

Coast- Bay Branch 

2800 Cottage Way, Room W-2605 

Sacramento, CA 95825 
[916) 414-6493 

1 HC 

1CD 

1 NOA 

Gary Stern 

NOAA National Marine Fisheries Service 

North Central Coast Office 

777 Sonoma Avenue, Rm. 325 

Santa Rosa, CA 95404 
[707) 575-3152 

1 HC 

1CD 

1 NOA 

Margarete Beth 

San Francisco Bay Regional Water Control Board 

1515 Clay Street, Suite 1400 

Oakland, CA 94612 

510-622-2338 

1 HC 

1CD 

1 NOA 

Ian Liffman 

Regulatory Division USACE, South Branch 

1455 Market Street, 16th Floor 

San Francisco, CA 94103-1398 
[415) 503-6769 

1 HC 

1CD 

1 NOA 













SCVWD DSEIR Notice of Availability (NOA) Distribution List 


Alviso Collaborative 

SCVWD Environmental Advisory Committee 
SCVWD Flood Protection Committee 
SCVWD Watershed Advisory Committee 


Cities and Counties 
City, State, Zip 

San Jose, CA 95110 
San Jose, CA 95113-1905 
Gilroy, CA 95020 
Morgan Hill, CA 95037 
Santa Clara, CA 95050 
Sunnyvale, CA 94086 
Sunnyvale, CA 94086 
Cupertino, CA 95014-3202 
Saratoga, CA 95070 
Los Gatos, CA 95030 
Palo Alto, CA 94301 
Los Altos, CA 94022 
Los Altos Hills, CA 94022 
Campbell, California 95008 
Milpitas, CA 95035 
Monte Sereno, CA 95030 
Mountain View, CA 94039 


Name 

Jody Hall Esser, Director 
Joseph Horwedel, Director 
David Bischoff, Planning Manager 
Planning Director 
Kevin L. Riley, Director 
Shaunn Mendrin 
Lorrie Gervin 
Director 

John Livingstone, Director 
Wendie Rooney, Director 
Curtis Williams, Director 
Director 

Debbie Pedro, Director 

Kirk E. Heinrichs, Community Development Director 
James Lindsay, Director 
Planning Director 
Planning Director 


Individuals 

Name 

Trish Mulvey 

(received hard copy of DSEIR) 
Libby Lucas 


Organization Address 

Clean South Bay 527 Rhodes Drive 

174 Yerba Santa Drive 


City, State, Zip 

Palo Alto, CA 
94303 

Los Altos, CA 
94022 



This page intentionally blank 



Volume I, Appendix C 

August 22,2011SCVWD Watershed 

Stewardship Division Letter 
to the San Francisco Regional Water Quality 

Control Board 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 





Santa Ctaro Volley 
Water District A 






6 






5750 ALMADEN EXPWY 
SAN JOSE, CA 95118-3686 
TELEPHONE (408) 265-2600 
FACSIMILE (408) 266-0271 
www.valleywater. org 

AN EQUAL OPPORTUNITY EMPLOYER 


August 22, 2011 


Shin-Roei Lee 

California Regional Water Quality Control Board 
San Francisco Bay Region 
1515 Clay Street, Suite 1400 
Oakland, CA 94612 

Subject: Stream Maintenance Program 2002 Compensatory Mitigation Status and Commitment 
Dear Ms. Lee: 

This letter provides a current status of the Santa Clara Valley Water District’s (District) 2002 
Stream Maintenance Program (SMP) compensatory mitigation elements, and a plan for meeting 
the District’s mitigation obligations as described in the Final Environmental Impact Report and 
Stream Maintenance Program Report for the Multi-Year Stream Maintenance Program (August 
2001) and the following regulatory permits: 

• San Francisco Bay Regional Water Quality Control Board (SF RWQCB): Waste Discharge 
Order No. R2-2002-0028 (March 5, 2002) 

• Central Coast Regional Water Quality Control Board (CC RWQCB): Waste Discharge Order 
No. R3-2002-008 (March 22, 2002) 

• California Department of Fish and Game (CDFG): 1601 Agreement No. R3-2001-0119 (July 

8 , 2002 ) 

• U.S Army Corps of Engineers (USACE): Permit No 22525S (August 7, 2002) 

• U.S. Fish and Wildlife ^Service (USFWS): Formal Endangered Species Consultation 
Biological Opinion: PN 22525S (July 5, 2002) 

Summary 


The Stream Maintenance Program (SMP) was developed in 2001 to provide multi-year 
regulatory agency permits for conducting annual routine stream and canal maintenance 
activities for District property and easement areas. Activities include sediment removal, 
vegetation management, bank stabilization, management of animal conflicts, and minor 
maintenance. The District is in the process of updating its California Environmental Quality Act 
(CEQA) document and renewing regulatory permits, which will expire prior to the 2012 work 
season. 

The existing SMP programmatic mitigation program was developed in 2002 to include defined 
“up front” programmatic mitigation for sediment removal and vegetation management activities. 
This original programmatic mitigation continues to serve the SMP in perpetuity for maintenance 
activities and work areas identified in the 2002 program work projections. Impacts from other 



The mission of the Santa Clara Valley Water District is a healthy, safe and enhanced quality of living in Santa Clara County through watershed 
stewardship and comprehensive management of water resources in a practical, cost-effective and environmentally sensitive manner. 




Ms. Shin-Roei Lee 
Page 2 

August 22, 2011 


non-projected maintenance activities such as bank stabilization projects are mitigated on an “as- 
needed” basis using defined mitigation ratios as maintenance projects occur. 

The District’s compensatory mitigation program for the SMP provides mitigation in perpetuity for 
impacts to tidal wetland, freshwater wetland, and riparian habitats; and California red-legged 
frog. A summary of the mitigation types, requirements, and current status is presented as 
Attachment 1 to this letter. To date, the tidal wetland mitigation, tidal wetland restoration, and 
invasive smooth cordgrass control have been completed, except for long-term monitoring which 
is progressing as required. The giant reed control program was 93% complete at the end of the 
2010 work season. The freshwater wetland creation and restoration program, and the Stream 
and Watershed Protection program are partially complete. A summary of each of the mitigation 
programs, their status, and plan and commitment for completion is provided. 

Status of Stream Maintenance Program mitigation programs 

1. Tidal wetland restoration 

Purpose: Provides mitigation for impacts to tidal wetlands. 

Status: 100% Complete. In March 2006 the District in conjunction with the USFWS Don 
Edwards National Wildlife Refuge breached 3 former salt ponds known as the Island Ponds 
(Ponds A19- A21) to restore tidal action to the 475 acre complex. Year 5 (of the 15 year 
requirement) of the collaborative mitigation monitoring program was completed by the 
District and USFWS, in 2010. The restoration is progressing as anticipated with 
sedimentation rates higher than predicted and tidal wetland vegetation starting to take hold 
in all three ponds. 

Plan/commitment for completion: The District will continue to collaborate with USFWS to 
continue annual monitoring until year 15, or until the success criteria have been met. 

2. Freshwater wetland creation and restoration 

Purpose: Provides mitigation for impacts to non-tidal freshwater wetlands by converting 
areas to seasonal or perennial wetlands. 

Status: 100% Complete for Pajaro Basin. 70% complete for Santa Clara Basin. 

The Pajaro Basin Freshwater Wetland was constructed in 2007 providing 4.65 acre credits 
of compensatory mitigation for the Pajaro Basin requirement of 4 acres. The third year of 
mitigation monitoring was completed in 2010. 

The Coyote Parkway Freshwater Wetland was constructed in 2006-2007 providing 7 acre 
credits of compensatory mitigation for the Santa Clara Basin requirement of 10 acres. The 
fourth year of mitigation monitoring was completed in 2010. 




Ms. Shin-Roei Lee 
Page 3 

August 22, 2011 


Plan/commitment for completion: 

The plan for fulfilling this requirement is found in Stream and Watershed Protection Section 
of this letter. 

3. Stream and Watershed Protection (S&WP) 

Purpose: Provides compensatory mitigation for impacts to non-tidal freshwater wetlands and 
California red-legged frog (CRLF) through land preservation and protection. Mitigates for 
impacts to 92 acres of wetlands and 26 acres of CRLF habitat. 

Status: For wetlands: 100% complete for Pajaro Basin; 12% complete for Santa Clara 
Basin. 

The Program has met 100% of its wetland mitigation requirements in the Pajaro Basin, and 
all remaining needed credits are for the Santa Clara Basin. Of the total program 
requirement, projects completed thus far have obtained 21 of the 92 required wetland 
mitigation credits for 23 percent of the total obligation. 

For CRLF: 52% complete. 

52% (56 of the required 108 acres) of CRLF mitigation has been obtained. An additional 52 
acres within Santa Clara County are needed. 

Completion of SMP mitigation for CRLF was required by July 5, 2007. The USFWS has 
granted one-year extensions annually since 2007 to continue working on meeting the CRLF 
mitigation commitment. In August 2011 the District submitted a request for a 6-month 
extension beyond September 1, 2011 to USFWS. 

Additional status information is provided in the Ninth Annual Mitigation Monitoring Report 
(2010), included as Attachment 2 to this letter. Annual reports are required to be submitted 
to the relevant agencies for 10 years or until all required mitigation credit is obtained. 

Plan/commitment for completion: 

The District is actively pursuing both wetland restoration alternatives and land preservation 
opportunities in order to meet the remaining 74 acres of wetland mitigation credit in Santa 
Clara Basin. The following are options the District is actively pursuing. 

Wetland restoration options: 

The Laguna Seca Freshwater Wetland project commenced planning in 2007 and was 
expected to begin construction in 2010. Until early 2009, this project was expected to 
provide all or a large portion of the remaining acres of wetland mitigation for the SMP in lieu 
of all or a portion of S&WP Program land acquisition. However, prior to moving forward with 










Ms. Shin-Roei Lee 
Page 4 

August 22, 2011 


design, information indicating potential uncertainty in future groundwater conditions was 
obtained. Further data collection and modeling commenced, the purpose being to ensure 
viable long-term success. Project feasibility is currently under review and pending further 
information; the project may be revised or abandoned. The groundwater evaluation to re¬ 
consider long-term feasibility and adjust project design is expected to be completed in late 
summer 2011, followed by a reassessment of the project in fall 2011. 

Following the delay of Laguna Seca in 2009 the District proposed an option to more quickly 
provide some of the needed wetland mitigation acreage by restoring wetlands at an 
alternative site on the Carnadero Preserve, the site of the successful Pajaro Basin 
Freshwater Wetlands project for the SMP. If this proposal had quick acceptance, the initial 
construction was projected to begin as early as summer 2010. The proposal was not 
accepted by the San Francisco Regional Water Quality Control Board due to the site being 
located in a different basin (Pajaro) than the impacts (Santa Clara). In the most recent 
communication on this topic, SF RWQCB staff indicated that this option may be revisited 
pending information about past and projected SMP impacts as part of the SMP renewal 
review. This project could restore approximately 25-37 acres of historic wetland and 
riparian habitat. The District would like to re-open consideration of this option. 

Land Preservation options: 

Work on two properties, described below, is currently in progress. 

The large Castle and Cooke (C&C) property east of the valley floor in the Mt. Hamilton 
Range was first identified in 2010 and reviewed by the District and regulatory agencies in 
early 2011. This property has approximately 457 acres of S&WP lands and would provide 
approximately 37 credits and the remaining required 52 acres of CRLF habitat. The District 
was in close and frequent communication with the owner’s representative during several 
months of studies and real estate work on the property leading up to the submission of a 
formal purchase offer in June 2011. However, contrary to our communications over those 
several months, it is currently not clear whether or not C&C wishes to sell to the District. We 
remain in contact with the C&C representative, trying to work this out with them as quickly as 
possible. 

The Hendry Creek Property located in the Lexington Reservoir vicinity is currently under 
review. The property would provide approximately 100 acres of S&WP land, over 8 wetland 
credits and the remaining required 52 acres of CRLF habitat. An agency site visit is 
scheduled for late August 2011. This is a partnership project with Midpeninsula Regional 
Open Space District (MROSD) and Peninsula Open Space Trust (POST). The property 
would quickly be purchased by POST in phases, from October 2011 through January 2012. 
MROSD and the District would then acquire the property from POST soon thereafter. 

Although the mitigation requirements for freshwater wetlands (in the Santa Clara Basin), and 
California red-legged frog will not be achieved by the end of 2011, the District is committed 
to completing this mitigation and is working diligently on acquiring acceptable properties. 



Ms. Shin-Roei Lee 
Page 5 

August 22, 2011 


The District continues to actively work to identify and evaluate suitable Stream and 
Watershed Protection mitigation acquisition opportunities. 

4. Giant reed ( Arundo donax) control 

Purpose: Provides mitigation for impacts to riparian vegetation. 

Status: On target for 100% completion in 2011. As of 2010, 116 acres (93% of 125 acres) 
have received initial treatment. 

Plan/commitment for completion: The remaining 9 acres will be completed in 2011 to meet 
the requirement of 125 acres of treatment. Retreatment of re-growth areas will continue for 
an additional three years through December 2015. 

5. Invasive smooth cordgrass ( Spartina alterniflora) control 

Purpose: Provides mitigation for the time lag associated with implementation of the tidal 
wetland restoration component discussed in number 1. 

Status: 100% Complete. In 2007 the District completed its 5 year monitoring commitment for 
the smooth cordgrass mitigation element. From 2008- 2010 the District completed 3 
additional years of re-treatment work in the program area. In total, 10 acres of invasive 
smooth cordgrass was treated throughout the program area from 2004 - 2010. 

Plan/commitment for completion: While the 2002 SMP mitigation obligation to monitor and 
treat 10 acres of smooth cordgrass has been achieved, the District applied for and received 
a $75,000 grant in June 2011 to continue assisting the regional Invasive Spartina Program 
(funded by the CA Coastal Conservancy) in control of invasive smooth cordgrass in South 
Bay marshes and creeks for 5 additional years. 

SMP work completed to date 

It is important to note that as of year 9 of the first 10 years of implementation, the District has 
not conducted all of the work that was projected in 2002 and therefore, has not incurred all of 
the impacts anticipated. As of the end of the 2010 work season (including years 2002-2009), 
the District had provided an excess of mitigation in both the Santa Clara and Pajaro Basins. 
These numbers, presented in the table below, were calculated by comparing the actual work 
completed to the mitigation obligation. 


Excessr SF Bay Mitigation: 

Freshwater wetland 

9.41 acres 


Tidal wetland 

21.35 acres 



Freshwater wetland 

6.20 acres 












Ms. Shin-Roei Lee 
Page 6 

August 22, 2011 


Next steps 

The District is committed to continue monitoring those mitigation program elements that have 
already been constructed. The District is also committed to completing its obligations for both 
the freshwater wetland creation and restoration, and the Stream and Watershed Protection 
programs, and will continue to work with the agencies as opportunities for land acquisition 
become available. 

If you have any questions, or require additional information please contact me at 408-265-2607, 
extension 2665. 


Sincerely, 





Ann Draper, AssfistdnfOfficer 
Watershed Stewardship Division 


Attachments: 

1. Summary table of SMP Mitigation Programs 

2. Stream and Watershed Protection Ninth Annual Mitigation Monitoring Report (2010) 

cc: Bruce Wolfe, Bill Hurley, Maggie Beth (SFB RWQCB) 

Jon Rohrbough (CC RWQCB) 

Liam Davis, Tami Schane (CDFG) 

Cameron Johnson, Paula Gill, Ian Liffman (US Army Corps of Engineers) 

Gary Stern, Darren Howe (NMFS) 

Ryan Olah, Vincent Griego (USFWS) 

Luisa Valiela (USEPA, Region IX) 

B. Goldie, L. Lee, C. Elias, S. Dharasker, K. O’Kane, N. Nguyen, G. Rankin, M. Wander, J. 
Castillo (SCVWD) 



Attachment 1: Summary table of SMP Mitigation Program 



asWMtas'ii 

.C6 


. '■«&?.izxzjr; . .. 

^C-' Ay/,; ff■>■ v 





1 

Tidal Wetland 
Restoration 

Restore Bay salt ponds to tidal 
marsh conditions. 

Provides mitigation for tidal 
wetland impacts. 

30 acres 

30 acres 

100% 

2 

Freshwater 

Wetland 

Creation/ 

Restoration 

Convert or restore areas to 
seasonal or perennial 
wetlands. Provides mitigation 
for non-tidal wetland impacts. 

10 ac Santa Clara Basin 

4 ac Pajaro Basin 

7ac Santa Clara Basin 

4ac Pajaro Basin** 

70% Santa Clara 

Basin 

100% Pajaro Basin 

3 

Stream and 
Watershed 
Protection 

Preserve, protect, and 
improve streams and 
associated watersheds. 

Provides mitigation for non- 
tidal wetland and CRLF 
impacts 

Freshwater wetland habitat: 
820-1080 ac acquired 
(81 ac credit) for Santa Clara 
Basin 

11 ac credit for Pajaro Basin 

CRLF Habitat -108 ac credit 
District wide 

Freshwater wetland habitat: 

10 ac credit (125 ac total) for 
Santa Clara Basin 

11 ac credit (138 ac total) for 
Pajaro Basin** 

CRLF Habitat - 56 ac credit 

12% Santa Clara 

Basin 

100% Pajaro Basin 

52% CRLF Habitat 


Giant reed 
(Arundo donax) 
Control 


Invasive smooth 
cordgrass 
Control (Spartina 
alterniflora) 


Control giant reed outbreaks; 
map, revegetate, educate, 
and coordinate reed control 
efforts in County. 

Provides mitigation for 

riparian impacts. _ 

Control invasive cordgrass 
along tidal shorelines. 
Provides mitigation for time 
lag until tidal wetland 


125 ac District wide 


116 ac District wide 


93% 


Up to 10 acres in tidal areas 


10 acres 


100 % 


_ _ mitigation is established. _|_|_ 

*Does not include monitoring period and achievement of final success criteria. 

** Rough acreages - slightly more wetland acreage and less S&WP acreage were credited in order meet the required 15 credit total in Pajaro 
Basin 


Page 1 of 1 


























STREAM AND WATERSHED PROTECTION PROGRAM 


COMPENSATORY MITIGATION FOR THE 
SANTA CLARA VALLEY WATER DISTRICT’S 
MULTI-YEAR STREAM MAINTENANCE PROGRAM 

NINTH ANNUAL MITIGATION MONITORING REPORT 

CALENDAR YEAR 9 (2010) 


Prepared by 


Gale Rankin 

Environmental Services Unit 
Watershed Stewardship Division 
Santa Clara Valley Water District 


Santa Clara Valley Water District 
5750 Almaden Expressway 
San Jose, CA 95210 


May 2011 




Table of Contents 


Executive Summary i 

1.0 Introduction 1 

1.1 Program Overview 1 

1.2 Acreage Requirements 1 

2.0 Summary of Actions in Calendar Year 9 (2010) 2 

2.1 Properties Considered in 2010 2 

2.2 Properties Acquired in 2010 4 

3.0 Summary of S&WP Program Milestones, Credits, and 4 

Success Criteria 

4.0 References 6 

TABLES 

Table 1 Summary of S&WP Program Credits (2010) 5 







Eighth Annual S&WP Mitigation Monitoring Report 


EXECUTIVE SUMMARY 

The Stream and Watershed Protection (S&WP) Program (Program) provides compensatory 
mitigation for impacts to 92 acres of freshwater wetlands, and also the California red-legged frog 
(CRLF), under the Santa Clara Valley Water District’s (District) Stream Maintenance Program 
(SMP). This report constitutes the ninth annual report for the S&WP Program. Under the 
S&WP MMP, annual reports are required to be submitted to the relevant agencies for 10 years 
or until all required mitigation credit is obtained. This report covers calendar year 2009 
(approximately 8 Vi years of the Program). 

The first acquisition project for the S&WP Program, the Camadero Preserve, was initiated in 
2002 and acquired in 2004. This project supplied almost all required Pajaro Basin S&WP 
wetland credit (10.7 of 11 credits) within the 138-acre S&WP stream buffer areas. 
Implementation of the required Camadero Preserve management plan began in winter-spring of 
2007-08. Construction of the Pajaro Basin Freshwater wetland mitigation project on the 
Camadero Preserve was completed in early 2008 and provides the additional 0.3 acres of 
mitigation credit needed for the S&WP Program in South County, thus all S&WP Program 
credits for the Pajaro Basin have been fulfilled. The District retains fee-title of the property. 

The second property, Stevens Canyon Ranch, was acquired in 2006. The property provides 5.4 
Santa Clara Basin wetland mitigation credits within the 69-acre S&WP stream buffer areas. 

The property is now owned by the Midpeninsula Regional Open Space Authority with a riparian 
conservation easement on the mitigation area held by the District. 

The third acquisition, the “Moore Property” along Upper Penitencia Creek, was completed in 
2009. The property provides 4.5 Santa Clara Basin wetland mitigation credits within the 56- 
acre S&WP stream buffer areas. The property also provides 56 acres of California red-legged 
frog (CRLF) mitigation credit. The property is now owned by the Santa Clara County Open 
Space Authority with a riparian conservation easement on the mitigation area held by the 
District. 

The Laguna Seca Freshwater Wetland project commenced planning in 2007 and was expected 
to begin construction in 2010. Until early 2009, this project was expected to provide all or a 
large portion of the remaining acres of wetland mitigation for the SMP in lieu of all or a portion of 
S&WP Program land acquisition. However, project feasibility is currently under review and 
pending further information the project may be revised or abandoned. The groundwater 
evaluation required to re-evaluate feasibility and adjust project design is expected to be 
completed in 2011. A 2009 District proposal to, in the meantime, more quickly provide some of 
the needed wetland mitigation acreage by restoring wetlands at an alternative site was not 
accepted by the San Francisco Regional Water Quality Control Board due to the site being 
located in a different basin (Pajaro) than the impacts (Santa Clara), but may be revisited 
pending information about past and projected SMP impacts as part of the SMP renewal review. 

A large property east of the valley floor in the Mt. Hamilton Range was first identified in 2010 
and reviewed by the District and regulatory agencies in early 2011. This approximately 670 
acre property has approximately 457 acres of S&WP lands and would provide approximately 37 
S&WP credits and the remaining required 52 acres of CRLF habitat. The District plans to begin 
negotiations with owner for acquisition of the property. 


Page i 




■" ' f *e»v * -j i 


Eighth Annual S&WP Mitigation Monitoring Report 


Projects completed thus far have obtained of 21 of the 92 required wetland mitigation credits for 
23 percent of the total obligation. The Program has met its wetland mitigation requirements in 
the Pajaro Basin, and all remaining needed credits are for the Santa Clara Basin. 

Just over 50% (56 of the required 108 acres) of CRLF mitigation have been obtained. An 
additional 52 acres within Santa Clara County are needed. Completion of SMP mitigation for 
CRLF was required by July 5, 2007. One-year extensions were granted by USFWS in 2007, 
2008, and 2009 to continue working on meeting the CRLF mitigation commitment. In 2009 the 
USFWS directed the District to continue to pursue CRLF property acquisition, and rejected a 
District proposal for an alternative approach to meeting the mitigation requirement by managing 
an existing CRLF population on public lands. In 2010 the USFWS granted a 1-year extension, 
with a requirement to obtain the remaining mitigation property by September 1 st ' 2011 or have a 
20 acre increase in required acquisition. 

The District continues to actively work to identify and evaluate suitable S&WP mitigation 
acquisition opportunities. 


Page i 


Eighth Annual S&WP Mitigation Monitoring Report 


1.0 INTRODUCTION 

1.1 Program Overview 

The Stream and Watershed Protection (S&WP) Program (Program) provides compensatory 
mitigation for impacts to 92 acres of freshwater wetlands under the Santa Clara Valley 
Water District’s (District) Stream Maintenance Program (SMP). The remaining 14 acres of 
the total 106 acres of SMP freshwater wetland impacts are to be mitigated by other projects 
(e.g., Coyote Parkway Freshwater Wetland and Pajaro Basin Freshwater Wetland). In 
addition to wetland mitigation, the S&WP Program will also provide mitigation for SMP 
impacts to red-legged frog. The S&WP Program Mitigation and Monitoring Plan (MMP) is 
Attachment A of Appendix J of the SMP Final EIR (SCVWD 2001b), and SMP wetland 
impacts are detailed in the SMP Draft EIR (SCVWD 2001a). The S&WP Program is 
required under SMP permits from: 

• U.S Army Corps of Engineers (USACE): Permit No 22525S (August 7,2002) 

• San Francisco Bay Regional Water Quality Control Board (SF RWQCB): Waste 
Discharge Order No. R2-2002-0028 (March 5, 2002) 

• Central Coast Regional Water Quality Control Board (CC RWQCB): Waste 
Discharge Order No. R3-2002-008 (March 22, 2002) 

• California Department of Fish and Game (CDFG): 1601 Agreement No. R3-2001- 
0119 (July 8, 2002) 

• U.S. Fish and Wildlife Service (USFWS): Formal Endangered Species Consultation 
Biological Opinion: PN 22525S (July 5, 2002) 

This report constitutes the ninth annual report for the S&WP Program. Under the MMP, 
annual reports are required to be submitted to the relevant agencies for 10 years or until all 
required mitigation credit is obtained under the S&WP Program. This report covers 
calendar year 2010 (approximately 8.5 Program years). Some updated information through 
April 2011 is also included, as appropriate. 

The S&WP Program supports the overall SMP compensatory mitigation program goal to 
“balance opportunity, feasibility, and cost to provide the maximum benefit to the natural 
function of the watersheds and streams of Santa Clara County". The S&WP Program will 
provide long-term protection and improvement of unique and valuable local steam 
resources together with their watersheds, in a largely self-sustaining setting. The primary 
focus is on streams that are in a fairly undisturbed state and generally good ecological 
condition. Streams that are currently degraded, but that can be returned to good ecological 
condition, can also be included in the Program. 

The S&WP Program consists primarily of land acquisition, but also provides for some 
restoration, rehabilitation and/or management projects (restoration projects). Properties 
containing streams and their immediate watersheds will be acquired. Restoration projects 
that would benefit stream resources would be conducted on selected acquisition projects or 
other qualifying lands, as described in the MMP. 

1.2 Acreage Requirements 

Of the 92 acres of mitigation to be provided by S&WP, acquisition is projected to provide 
82 acres of credit, and restoration projects are projected to provide 10 acres of credit. The 


Page 1 of 6 




Eighth Annua! S&WP Mitigation Monitoring Report 


relative contributions of these sub-components may be adjusted based on opportunity and 
resource needs identified as the mitigation program progresses. The 92 acres of 
mitigation must be located within the basins in which the impacts occur; thus 81 acres of 
credit are required for the Santa Clara Basin, and 11 acres are required for the Pajaro 
Basin. 

Based on credit ratios of 15 to 1 and 10 to 1, approximately 820 to 1,080 acres are to be 
acquired to meet the 82 acres of required mitigation with an estimated 720-950 acres in 
the Santa Clara Basin, and 100-130 acres in the Pajaro Basin. Of these, 108 acres are 
required to also provide mitigation for California red-legged frog (CRLF) and western pond 
turtle. These acres must be located within Santa Clara County with at least one site in the 
Santa Cruz and one site in the Hamilton mountain ranges. 

2.0 SUMMARY OF ACTIONS IN CALENDAR YEAR 9 (2010) 

2.1 Properties Considered in 2010 

Properties 1-4 were carried forward from prior years. Status updates are provided and more 
detailed descriptions are available in prior year's annual reports. 


1. Laguna Seca Wetland Project. The Laguna Seca wetland project is proposed to provide 
mitigation for SMP freshwater wetland impacts in-lieu of all or part of the remaining S&WP 
Program needs and in-lieu of the 3-acre Los Capitancillos Freshwater Wetland Project (74 acres 
of mitigation credit total). 

Planning of this project began in July 2007. In 2006, regulatory agency staff encouraged District 
staff to pursue the Laguna Seca Wetland Project. Construction was estimated to begin in June 
2010. However, recent information and regional groundwater modeling in the Coyote Valley 
indicated that groundwater conditions might change substantially in the near future, making the 
proposed design infeasible. In early 2009, the District proposed, with the agreement of the 
regulatory agencies, that further studies be conducted prior to proceeding with either the 
proposed project or a modified project suited to altered future conditions. The plan was to 
conduct three years of site-specific studies to calibrate the predictive regional Coyote Valley 
groundwater model and determine its sensitivity to conditions at the project site. Based upon 
these results, project feasibility would be re-evaluated and possible modifications to the site 
design would be made. 

Site-specific groundwater monitoring began in June 2008; three years of data collection would 
conclude in June 2011. However, the property owner declined to extend permission for 
SCVWD to collect groundwater information beyond December 2010. The preliminary results 
from the regional groundwater modeling effort indicate that the model corresponds well with the 
observed site conditions. With the current water supply and increased groundwater extraction 
in the Coyote Sub-basin, the model predicts that groundwater at the site could drop more than 
15 feet within five years after onset of a severe drought. Levels would recover after cessation 
of the drought, but only to about 2 feet below the pre-drought elevation. It is worth noting that 
as yet, groundwater levels have dropped only slightly within the proposed project area, and 
currently remain within workable elevations for wetland restoration. The District is currently 
evaluating the projected effects to groundwater at the site due to possible changes in 
management of Coyote Creek from FAHCE requirements or from re-operation of the Coyote 
Canal. It is anticipated that this additional evaluation will be completed in September 2011 and 
a recommendation will be made on the feasibility of the proposed wetland. 


Page 2 of 6 



Eighth Annual S&WP Mitigation Monitoring Report 


An alternative proposal to provide additional wetlands at the District’s Carnadero Preserve was 
made in 2009. Staff from SF RWQCB indicated that although the other reviewing agencies 
would consider this proposal, the SF RWQCB would likely not approve mitigation in the Pajaro 
Basin for Santa Clara Basin impacts. However, the SF RWQCB staff has stated that pending 
reporting by the SMP renewal project on actual impacts incurred to date by the SMP, the 
proposal may be revisited. 

2. Guadalupe Watershed Parcel. The Mid-Peninsula Regional Open Space District (MROSD) 
continued to discuss purchase of this 153-acre property with a confluence of two perennial 
streams with the private owner. The MROSD first proposed a joint acquisition and rehabilitation 
project with the District in 2004. This property is described in Rankin 2005. This property 
cannot be purchased by the MROSD without assistance of a partner due to high costs of site 
rehabilitation. 

A meeting and field review of this property with regulatory agency staff in 2005 concluded that 
the site may be considered for the S&WP Program or as alternative mitigation for S&WP 
pending an evaluation of the costs versus benefits of purchase and restoration. 

A review of this property in 2008 indicated that the high cost of removing multiple old stream- 
side cabins and bridges and re-vegetating the site could make this project infeasible. However, 
because the only viable alternative for achieving conservation ownership and rehabilitation of 
this resource-valuable property appears to be this public agency partnership, the District 
planned to re-examine the costs and benefits of this potential project in 2010. 

There is no confirmed CRLF on site, but 2010 surveys determined that the property has good 
habitat features including a nearby pond on MROSD property, good in-stream features suitable 
for CRLF and a documented 1996 CRLF sighting 1.14 miles downstream in 1996. However, 
2010 review of work needed on the property reaffirmed the high cost of rehabilitation. In 
addition, in summer 2010 USFWS (Cay Goode, by phone conference) commented that the 
property appeared to have high complexity for use as CRLF mitigation and suggested 
consideration of other properties instead. The District doesn’t plan to pursue this project 
further. 

3. San Jose Water Company property. Talks with SJWC representatives resumed last year 
with tentative and uncertain interest expressed in exploring a potential easement. 

Subsequently, SJWC informed the District that it does not intend to place any easements on the 
property. 

4. Coyote Watershed Property #1. In years past there were indications that the owner might 
consider selling a portion of this property that would be of interest primarily for CRLF. The 
owner has not recently indicated any interest in selling; this property is currently inactive. 

5. Hamilton Range Property - southeast Santa Clara County. This property was 
investigated for provision of CRLF mitigation only. A CRLF breeding pond was confirmed on 
this large ranch property. The District proposed to the owner and USFWS the placement of a 
conservation easement on the pond and its watershed. However, the value of the property, 
based on an appraisal report obtained for the purposes of this project, was not unacceptable to 
the owner, and the easement could not be purchased. 


Page 3 of 6 




Eighth Annual S&WP Mitigation Monitoring Report 


6. Coyote Watershed Property #2. A large property east of the valley floor in the Mt. 

Hamilton Range was first identified in 2010 and reviewed by the District and regulatory agencies 
in early 2011. This approximately 670 acre property has approximately 457 acres of S&WP 
lands and would provide approximately 37 S&WP credits and the remaining required 52 acres 
of CRLF habitat. The District plans to begin negotiations with the owner for acquisition of the 
property. 

7. Other properties considered. Several other parcels were considered at a preliminary level for 
provision of CRLF mitigation. Most of these were in south county or had little stream footage and 
were therefore of possible interest for CRLF rather than wetland mitigation. A Pacheco Creek 
watershed parcel appeared to have good potential for CRLF, and although on the market, the 
owner did not wish to entertain proposals from the District. An Isabel Creek watershed property in 
the eastern part of the county had potentially suitable CRLF habitat, but no confirmed presence of 
CRLF or CRLF breeding within dispersal distance. A southwest county parcel has reported CRLF 
habitat. The owner claimed to have an interest in a conservation easement, then ceased contact. 

2.2 Properties Acquired in 2010 

No properties were acquired in 2010 

3.0 SUMMARY OF S&WP PROGRAM MILESTONES, CREDITS, AND SUCCESS CRITERIA 

The S&WP Program will be implemented over 10 years. Acquisition will be completed, and 
restoration project will be identified in order to meet the interim milestones. Per the MMP, the 
milestones are: 

• % of the mitigation credit obtained (23 credits) by completed acquisition of property 
and/or identification of approved restoration projects by year 3 

• !4 of credit (46 credits) obtained by year 6 

• all of credit (92 credits) obtained by year 10 

A summary of the wetland credits obtained and in progress by end of 2010 is shown in Table 3. 
There is no change since 2009. Property and credits pending and under consideration in 2011 
are not included in the table. Projects in Table 3 are at 91 percent of the year 3,46 percent of 
the year 6 and 23 percent of the final year 10 milestone. The remainder of all required wetland 
credits for the Program is for the Santa Clara Basin. 

Fifty-six of the required 108 acres of CRLF mitigation were covered by the Moore Property and 
52 more acres are needed. CRLF mitigation was required for completion by Year 5 of the SMP 
Program. One-year extensions were granted by USFWS in 2007, 2008, and 2009 to continue 
working on meeting the CRLF mitigation commitment. USFWS granted a 1-year extension in 
2010, with the stipulation that if acquisition of mitigation land was not completed by September 
1, 2011 an additional 20 acres of land would be required. 

The Laguna Seca wetland project was expected until spring 2009 to provide all or a large 
portion of the remaining acres of wetland mitigation for the SMP, in lieu of all or a portion of the 
S&WP Program and the Los Capitancillos wetland project (see Section 2.1). Project feasibility 
is currently under review and pending further information, expected in fall 2011, the project may 
be revised or abandoned. A 2009 District proposal to provide alternative wetland mitigation for 
Santa Clara Basin impacts in the Pajaro Basin was not originally acceptable to the SF RWQCB, 
but may be reconsidered pending evaluations of SMP impacts to date. 


Page 4 of 6 




HMMNMMM 


Eighth Annual S&WP Mitigation Monitoring Report 


The District plans to begin negotiating acquisition of Coyote Watershed Property #2. If the 
property is acquired it will satisfy the remaining 52 acres of required CRLF mitigation and 
provide approximately 37 S&WP program credits, leaving a remainder of 34 credits to be 
achieved. 

The District continues to work with its acquisition partners and search for other S&WP 
acquisition opportunities. Suitable acquisition opportunities in the Santa Clara Basin have been 
limited since the inception of the Program. Opportunities in the Pajaro Basin continue to be 
more abundant. 

The MMP final success criteria are: 

1) Completed acquisition of fee title or easements on land selected in accordance with the 
Requisite Criteria and the Priority Evaluation Considerations in the amount required to fulfill 
total mitigation obligations (MMP Section 3.4), and 

2) All projects required to the meet the S&WP Restoration, Rehabilitation and Management 
element have met their individual success criteria (MMP Section 4.4). 

Table 3 

Summary of S&WP Program Credits (2010) 



Total 

Credits 

Required 

Acquisition Credits 

Percent 
of 3 year 
milestone 

Percent 
of 6 year 
milestone 

Percent 
of final 

In 

Progress 1 

Completed 

Total 

Credits 

Pajaro 

11 

0 

11.0 

II 2 

NA 

NA 

100 

Santa 

Clara 

81 

0 

10.0 

10.0 

49 

25 

12 

Total 

92 

0 

21.0 

21.0 

91 

46 

23 


1 Acres under consideration beginning 2011 not included 

2 0.3 acres of 11 acres of credit in the Pajaro basin are provided by the Pajaro Basin Wetland Project for a total of 
100% of final mitigation 


Page 5 of 6 
































Eighth Annual S&WP Mitigation Monitoring Report 


4.0 REFERENCES 

Ecological Services Unit (Santa Clara Valley Water District). 2003. Lower Uvas-Carnadero 
Riparian and Wetland Habitat Improvement Opportunities and Constraints Analysis; 
Supporting Biological Resources, Surface Water and Soils Information. Santa Clara Valley 
Water District. San Jose CA. 

Philip Williams and Associates. 2003. Lower Uvas-Carnadero Creek Property Wetland and 
Riparian Habitat Improvement Opportunities: Hydrologic and Hydraulic Evaluation. For 
Santa Clara Valley Water District. San Jose, CA. 

Rankin, G. 2003. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: First Annual 
Mitigation Monitoring Report, Calendar Year 1 (2002). Santa Clara Valley Water District. 
San Jose, CA. 

Rankin, G. 2004. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Second 
Annual Mitigation Monitoring Report, Calendar Year 2 (2003). Santa Clara Valley Water 
District. San Jose, CA 

Rankin, G. 2005. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Third Annual 
Mitigation Monitoring Report, Calendar Year 3 (2004). Santa Clara Valley Water District. 
San Jose, CA 

Rankin, G. 2006. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Fourth 
Annual Mitigation Monitoring Report, Calendar Year 4 (2005). Santa Clara Valley Water 
District. San Jose, CA 

Rankin, G. 2007. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Fifth Annual 
Mitigation Monitoring Report, Calendar Year 5 (2006). Santa Clara Valley Water District. 
San Jose, CA. 

Rankin, G. 2008. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Sixth Annual 
Mitigation Monitoring Report, Calendar Year 6 (2007). Santa Clara Valley Water District. 
San Jose, CA. 

Rankin, G. 2009. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Seventh 
Annual Mitigation Monitoring Report, Calendar Year 7 (2008). Santa Clara Valley Water 
District. San Jose, CA. 

Rankin, G. 2010. Stream and Watershed Protection Program: Compensatory Mitigation for the 
Santa Clara Valley Water District’s Multi-Year Stream Maintenance Program: Seventh 
Annual Mitigation Monitoring Report, Calendar Year 8 (2009). Santa Clara Valley Water 
District. San Jose, CA. 


Page 6 of 6 



Eighth Annual S&WP Mitigation Monitoring Report 


Santa Clara Valley Water District. 2001a. Draft Environmental Impact Report for the Multi-Year 
Stream Maintenance Program. San Jose, CA. 

Santa Clara Valley Water District 2001b. Final Environmental Impact Report for the Multi-Year 
Stream Maintenance Program. San Jose, CA. 


Page 7 of 6 






Volume I, Appendix D 

Joint Aquatic Resource Permit Application 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 





/'U*' fV\ H I \ \ I isp ' i * UV V'] 

Jt ^¥' M ^ o^O ciS 4 «-NrTcrn^AY r a ^' 01 

|Tfc: lili& 9 aiotA GiAeto SANTRANCISCO BAY AREA 

% ^ JOINT AQUATIC RESOURCE PERMIT APPLICATION 

I ‘ V prvuei Muiti-Year Stream Maintenance Program Q (2 JEz S 

L \jOIPf^STQ- Santa Clara Valley Water District CVw « 

L-l San Jose, CA r-ntffl 

PLEASE TYPE OR PRINT IN BLUE OR BLACK INK_ K - H S3 


Contact Name Phone # Application #(if known’ 


Agency Information__ 


□ I have applied to my local agency 
(i.e. City or County Planning 
Department), and special local 
district (i.e. flood control) if 
applicable, for CEQA compliance to 
meet local permitting requirements. 
Based on the instructions, I am 
sending copies of this application to 
the following federal, state, and 
regional agencies 

□ San Francisco Bay Conservation and 

Development Commission (BCDC) for 

□ A "Notice of Intent to Proceed:" with routine 

maintenance under BCDC regionwide or 
abbreviated regionwide permit 

# _ _ 

Q An administrative permit application for minor 
repair or improvement 

□ A federal consistency determination or 

certification (federal agencies only) 

□ A major permit application for a new project 

□ An application for a material amendment to 

BCDC permit#._ 

13 San Francisco Bay Regional Water 
Quality Control Board for Section 401 or 
Waste Discharge Requirements 
13 California Department of Rsh and 
Game for 1601 1603_ 

□ Timber Harvest Plan #_ 

□ Gravel Extraction #_ 

□ Water App #_ 

□ California State Lands Commission* 

□ California Coastal Commission 

13 US Army Corps of Engineers for Section 
404 or Section 10 Individual or Nationwide 
Permits 

13 US EPA for 404 Individual Permits* 

13 US Fish and Wildlife Service for 404 
Individual Permits* 

13 National Marine Fisheries Service 

□ US Coast Guard for Section 9 Bridge 
Permit 

G Federal Funding Agency _ 


* See Instructions 




Applicant is lead agency under California Environmental Quality Act 
(CEQA) 


Bob Batha 


Loretta K. Barsamian 
Lee Miies 


415) 352-3600 Permit No. M77-113 


was amended on July 21, 2000 
and is effective through June 1, 2005. 


(510) 622-2300 
(510) 622-2429 


Carl Wilcox 

Margaret Roper 

(707) 944-5525 
(408) 842-8917 

Revision of MOU's 
1408-90 and 331-89 

Molly Martindaie 

(415) 972-8462 


Becky Tuden 

(415) 744-1991 


Sheila Larson 

(916) 414- 6600 


Maura Eagan 

(707) 575-6092 




AGENCY CONTACT INFO INSTRUCTIONS 




SFBA JARPA VERSION 1.2 


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W:\SMP\PemnitsVARPAAPP.doc 






SECTION ONE - TO BE COMPLETED BY ALL APPLICANtS 

Attach additional sheets, if needed _ • _ ; _ 


Box 1 Applicant Name 

Santa Qara Valley Water District 


Mailing Address 

5750 Almaden Expressway, San Jose, CA 95118-3686 


Work' Phone 
(408) 265-2600 


Home Phone 


Fax # 


•E-mail Address 


Relationship of applicant to property: 

□ Owner Q Purchaser Q Lessee 


Other Chief Executive Officer 


Application is hereby made for a permit or permits to authorize the activities described herein. I 
certify that I am familiar with the information contained in this application, and that to the best of my 
knowledge and belief, such information is true, complete, and accurate. I further certify that I 
possess the authority to undertake the proposed activities. I hereby grant to the agencies to which 
this application is made, the right to enter the above-described location to inspect the proposed, in¬ 
progress or completed work. I agree to start work only after all necessary permits have been 
received. 


Stanley M. Williams, Chief Executive Officer 



Date 

2-/V-0/ 


Box 2 Authorized Agent Name and Signature (Jfan agent is acting for the applicant during the permit process) 
Cindy Roessler, Proiect Manager, Santa Clara Valley Water District 

Mailing Address 

5750 Almaden Expressway, San Jose, CA 95118-3686 



Work Phone 

Home Phone 

Fax # 

E-maii Address 

(408) 265-2607, ext. 2765 

— 


Cindroes@scvwd .dstica. us 


I hereby designate the above named authorized agent to act as my agent in matters related to this 
application for permit(s). I understand that I am bound by the actions of my agent and I understand 
that if a federal or state permit is issued, I, or my agent, must sign the permit. 

Signature of applicant 



Date 

2-/4-©l 


I certifythat I am familiar with the information contained in this application, and that to the best of 
my knowledge and belief, such information is true, complete, and accurate. _ 


Signature of authorized agent 





Date 


Box 3 Name of property owner(s), if other than applicant. 

n/a 


Mailing Address 



Work Phone 

Home Phone 


I understand I am bound by actions of authorized agent and/or the applicant 


Signature of property owner (except public entity landowners) 

Date 


This page must be signed by the applicant, property owner and agent to 
be considered complete. 


SFBA JJARPA VERSION 1.2 


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Box 4 Location, including street address, city, county, zip code where proposed activity will occur: 

The location of work is the streams, water delivery canals, and any adjacent property in Santa Clara County 
(County), California that the Santa Clara Valley Water District (District) owns or holds an easement for access 
and maintenance. The Multi-Year Stream Maintenance Program (Program) area, as shown in Figure 1, consists 
of 191 streams for approximately 828 miles and 9 canals for approximately 41 miles. The District's jurisdiction 
on a stream begins at that point where 320 acres of watershed drain to the stream; stream reaches and 
tributaries above that point are not included in the Program area. The property the District owns adjacent to 
streams and canals typically consists of an approximately 20-foot wide strip of land on tire outside edge of both 
tops of bank. Creeks with constructed levees and flood bypass channels may include a wider access area 
outside of the top of bank. 

The Program area is divided into two major hydrologic basins: the Santa Clara Basin draining the northern 
portion of the County to San Francisco Bay, and the Pajaro River Basin draining the southern portion of the 
County to Monterey Bay. Streams in the northeast portion of the County are not in the jurisdiction of the 
District, and are not in the Program area. 

Although the Program area covers ali streams, canals, and adjacent right-of-way within the District's 
jurisdiction, projections of routine maintenance work are for a smaller area, consisting of approximately 240 
miles of 75 streams and 29 miles of 9 canals. The areas in which work is projected are shown in Rgure 1. 

Not ail of these locations are within the jurisdiction of regulatory agencies. Refer to Table 1 for a summary of 
agency jurisdiction by work type and location. The District requests the agencies review this table and advise 

us to any changes that are relevant to permitted activities. ___ _ 

Waterbody (if known): 

The 58 streams where work is projected in the Santa Clara Basin, the 17 streams where work is projected in 
the Pajaro River Basin, and the 9 canals where work is projected are shown in Table 2. See Box 7 below for 
additional information on the projected work area. 


Tributary of: 


Latitude 8i longitude if known: 

From approximately 36° 55 ’ to 37° 30 latitude and 
122° 20 ’ to 121° 15 * longitude. See Figure 2_ 


Assessors parcel number: 


Zoning Designation: 




Section, Township, Range, USGS Quadrangle Map: 
See Figure 2 for index 


Box 5 Existing site conditions: Describe the existing condition of the site, including wetlands, channels, 
streams, ponds, seeps and ditches, and other jurisdictional features. Include information on elevations, 
vegetation, property use, and structures. Use additional pages if necessary. If any portion of the proposed 
activity has already been initiated or completed on this property, indicate type of activity and month and year of 

completion, if applicable: n/a Month / n/a. Year 


Streams in the Program area have been modified by historical land uses for many decades, including 
encroachment of development upon the stream corridors, and construction of flood control projects. Many of 
the streams in the urbanized portions of the flat valley floor have been straightened and confined to narrow 
channels with homes and businesses built up to the edge of the stream bank. Some of the streams modified 
for flood control purposes have concrete channel bottoms, and may have either concrete or earthen channel 
banks. Some streams, primarily at the upstream end of the Program area, are in a more natural condition with 
any flood control modifications made within the floodplain, but the stream channel and banks remaining in an 
earthen condition with no modifications for flood control. Another category of streams is of a mixed condition 
where the channel bottom is earthen, but the banks have been modified for flood and erosion control purposes, 
and consist of a variety of conditions including excavated earth, earth levees, rock, gabions, sack concrete or 
concrete flood walls. Stream channel types are estimated in Table 3. 


SFBA JARPA VERSION 1.2 


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Existing Site Conditions: BO* 5 (CONTINUED) 

Routine stream maintenance activities will affect saltmarsh, brackish marsh, freshwater marsh, seasonal 
wetlands, riparian forest, ruderal/nonnative grassland, and open water habitat types. These habitat types, as 
they occur within the projected work area, are briefly described below. Additional description will be provided 
in the Draft Environmental Impact Report (DEIR) to be submitted to agencies in March 2001. 

Salt marsh occurs in the intertidal zone of creeks near San Francisco Bay. Typically, salt marsh in the work 
area consists of stands of pickleweed ( Saiicornia Virginia ), associated with other halophytes such as spearscale 
0 Atripiex triangularis, alkali heath {Frankenia grandifolia), salt grass {DistichUs spiata ), and brass buttons 
(Cotuia coronopifofia). Occasionally, the work area contains California cordgrass ( Spartina foliosa). 

Brackish marshes occur where freshwater inflow reduces the salinity of tidal water. In the County, tidal 
influence generally does not extend upstream of Highway 101 or Highway 237. Alkali bulrush {Scirpus 
robustus) and California bulrush ( Scirpus californicus ) dominate the more saline brackish marshes, often 
occupying a narrow strip adjacent to the low flow channel. California bulrush and cattails {Typha spp.) 
dominate lower salinity marshes. Perennial pepperweed ( Lepidium iatifoiiurri), an invasive, nonnative plant, is 
commonly found in brackish marshes of the projected work area in the upper zone of the marsh and along 

levee slopes. 

Upstream of the influence of tides, freshwater marshes are common on perennial streams, or in more localized 
areas where culverts or other drainage features create inundation of the channel or saturation of its sediments. 
Typical species include cattails and bulrushes {Scirpus spp.). Seasonal wetlands occur in areas that are 
inundated in the rainy season but are dry for some part of the growing season. As a result of these fluctuating 
conditions, annuals and perennials, some which are wetland species and some which are weedy nonnatives, 
variously dominate seasonal wetlands. 

During surveys of the projected work area, 3 categories of freshwater and seasonal marshes were recognized, 
primarily defined by the dominant vegetation type: cattail-bulrush dominated wetlands consisting of tall, erect, 
monotypic stands with other species relegated to the edges; creeping, emergent, native dominated wetlands 
with primrose {Ludwigias p.) and water cress {Rorippa sp.), usually in areas with summer water; and nonnative 
dominated wetlands with Italian ryegrass {Lo/ium multiflorurri), dail/s grass {Paspalum dilatatium), cockiebur 
{Xanthium sp.) and water smartweed {Polygonum amphibium), in slightly drier areas especially in the summer, 

or sometimes on sediment bars. 

Riparian forests along Program area streams tend to be long and narrow strips along the edges of the channel 
and on the stream banks. Typical riparian tree species along these streams are: Fremont cottonwood {Populus 
fremontii), arroyo, red, and narrow-leaved willows {Salix laevigata, S. lasiolepls, 5. exigua ), box elder {Acer 
negundo californicum), western sycamore {P/atanus racemosa), . and blue elderberry {Sambucus caerulea). 
Further upstream or further up the bank, coast live oak and valley oak {Quercus agrifolia and Q. lobata), big- 
leaf maple {Acermacrophyllum) and California bay {Umbellularia California) occur. It is common in the project 
area for riparian forests to intergrade with ornamental landscaping from adjacent land uses. Because the 
Program areas have been routinely maintained for flood control purposes for decades, the actual projected 
work a reas do not contain any mature riparian trees, although sapling riparian trees are often present, and 
mature riparian trees may be present immediately adjacent to the maintenance work areas. 

Channel banks, levee slopes, and upland areas adjacent to streams and canals are often vegetated with 
ruderal/nonnative grasslands. Common annual grasses are wild oats {Avena fatua), ripgut brome {Bromus 
diandrus), Italian ryegrass, and smilo grass {Piptatherum miliaceum) with annual ruderal species such as black 
mustard {Bra ssi ca nigra), wild radish {Raphanus sativus), yellow star thistle {Centaurea solstitialis) and sweet 
fennel {Foeniculum vu/gare). Site conditions and repeated maintenance activities tend to keep these areas in a 
ruderal/annual grassland condition. For example, flood control levees are highly compacted in order to provide 
structural stability, and they are maintained with low vegetative cover to allow inspection of their surfaces for 
cracks or other structural problems. Adjacent upland areas need to be maintained with low vegetation cover to 
allow a ccess of maintenance equipment and inspection vehicles, and to control the potential for fires. 

Canals can support freshwater marshes, seasonal wetlands, or open water. _ 


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Box 6 Proposed starting date: lulv 2QQ1 Estimated duration of activity: 10-vears 

Will the project be constructed in stages? □ Yes _ 1*1 No Maintenance work is repeated in years 

Box 7 Description of the proposed project: Use as many pages as necessary to describe the project as 
completely as possible. Describe the area within the project site that will be used each for development 
features and open space. Include construction plans pertaining to the project. For additional guidance on what 
to include, refer to the instructions. 

The three major types of routine stream maintenance activities are sediment removal, vegetation management, 
and bank protection. Minor maintenance activities include trash removal at trash racks and more generalized 
locations; repair and installation of fences and gates; grading and other repairs to restore the original contour 
of access roads and levees; grading small areas without vegetation above stream banks to improve drainage 
and reduce erosion; repair of structures with in-kind materials within the same footprint (such as replacement 
of concrete lings, culverts, pipes, valves or similar structures); cleaning and minor sediment removal at stream 
gages, outfalls, culverts, flap gates, tide gates, inlets, grade control structures, fish ladders, fishnets and 
screens; graffiti removal; tree pruning along maintenance roads and fence lines to provide access and to 
remove hazards; irrigation, weeding, replanting and other types of ongoing maintenance at mitigation sites; 
removal of obstructions to flow in the immediate vicinity (not to exceed 100 feet) of bridges, streamflow 
measuring stations, box culverts, storm drain outfalls and drop structures to maintain functions of such 
structures; removal of trees or branches that are in imminent danger of falling, fallen trees, and associated 
debris to maintain channel design capacity; and ground squirrel and rodent control with traps, smoke bombs, 
and pesticides. 

Not all of these activities are within the jurisdiction of regulatory agencies. Refer to Table 1 for a summary of 
agency jurisdiction by work type and location. 

Table 4 provides information on the amount of work projected for different lengths of time by work type and by 
basin. 

The District implements Best Management Practices (BMPs) to ensure that routine stream maintenance work 
has the least impact possible. The District's equipment and work methods are updated as new equipment or 
better methods become available. Sediment removal projects and vegetation management are also revised as 
new designs are implemented through Capital Improvement Projects. Table 5 lists the BMPs currently 
implemented for routine stream maintenance activities. 


SEDIMENT REMOVAL 

Sediment removal is the act of mechanically removing sediment deposited within a stream or canal. Typically, 
sediment is removed when it: (1) reduces capacity; (2) prevents facilities or appurtenant structures from 
functioning as intended; or (3) impedes fish passage and access to fish ladders. Sediment is usually removed 
from channels modified for flood control. Sediment is removed from some natural creeks to provide proper 
functioning of outfalls, culverts, bridge crossings and stream gauging stations. Occasionally, sediment is 
removed from canals to maintain their function as water conveyance facilities. 

The method of sediment removal is dependent on channel configuration and geometry, equipment reach and 
rate of production, channel type (tidal or non-tidal, concrete or earth bottom), moisture content of the silt, 
ramp location and access road width. Sediment is removed by a dragline or an excavator positioned on the top 
of the creek bank on wide access roads for tidal reaches with a channel bottom of wet bay muds that will not 
support equipment require silt removal. Concrete-lined channels may be cleaned by pushing sediment into a 
pile with a bulldozer and using a loader to place the material in trucks for removal to an approved disposal site. 
The trucks are located at strategic points either in the channel bottom or at the top-of-bank depending on the 
method of routing the trucks. Another example is cleaning or creating a low flow channel with excavation 


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Description of Proposed Project: BOX 7 (CONTINUED) 

equipment working in the channel bottom, loading trucks either in the channel bottom or moving the sediment 
to trucks at the top-of-bank. 

Although work is usually conducted during the summer dry season (3uly 1 to October 15), streamflow, when 

present in the proposed work area, is usually bypassed around the work area to protect water quality. 

■ 

Saturated sediments may be temporarily placed adjacent to the work site to dry out before being removed to a 
landfill or to other suitable disposal or reuse sites. Figures A-l, A-2, A-3, and A-4 are typical plan views and 
cross-sectional views of sediment removal work in tidal and freshwater areas. 

Typical equipment used for sediment removal includes excavators, draglines, loaders, and 10- or 20-cubic-yard 
dump trucks. Water pumps and piping, and cofferdams of earth, gravel, sandbags, hay bales, rubber or other 
appropriate material may be used for bypassing water around the work area. In some cases, a bypass channel 
or detention basin is appropriate to isolate a site. 

The District estimates that it removes an average of 80,000 cubic yards of sediment on about 16 miles of 
channel per year in the County (14 miles and 73,000 cubic yards in the Santa Clara Basin; 2 miles and 7,000 
cubic yards in the Pajaro River Basin). This average includes both concrete-lined and earth-lined channels. 
This is an average annual quantity and will vary from year-to-year depending, in part, on rainfall conditions of 
the past season. Sediment is removed from streams on an estimated frequency of two to ten years, depending 
on the channel design and site conditions. Sediment is removed from canals on an infrequent basis, usually 

consisting of less than 1,000 cubic yards per year. 

When removing sediment in the past, the District has conducted sediment testing and monitored for water 
quality. The District's sediment testing program allows the District to (1) effectively plan for disposal of the 
sediments (2) ass ist with determining the BMPs for implementation, and (3) efficiently monitor the water 
quality impacts from the sediment removal operation. It is anticipated that the large amount of data generated 
under the sediment testing program in previous years (1997 to 1999) will provide valuable information 
regarding the general nature of sediments in Santa Clara County and will reduce the quantity of sampling and 
analysis which is required for future sediment removal projects. Exhibits A and B contain an example Sediment 
Characterization Plan and an example Self-Monitoring Program Water Quality Sampling Plan. 


VEGETATION MANAGEMENT 

Vegetation management occurs in creeks, canals, and adjacent uplands (Figures B-l, B-2, B-3, and B-4). It 
consists of controlling vegetation for the purpose of maintaining flood control capacity of and access to 
streams, and maintaining water conveyance capacity of and access to canals. Vegetation management is also 
conducted to maintain revegetation sites, control invasive plants, and for public safety purposes. 

Dense vegetation can adversely affect the ability of a stream, modified as a flood control channel, to contain 
the volume and velocity of floodwaters for which it was designed. Therefore, most flood control facilities 
require some type of periodic vegetation removal. Depending on the original design and the characteristics of 
the channel, the frequency of vegetation management varies from annually to every few years, and may occur 
across the entire channel bottom, or just a portion of it. Channel vegetation management often occurs in the 
same location as channel sediment removal, but in intervening years. 

The District plants and maintains revegetation or mitigation projects, often along creeks. Because it is 
important to control weeds at revegetation sites in the first few years as the planted native trees and shrubs 
are establishing, the District includes revegetation sites in its Vegetation Management Program. Currently, the 
District also removes invasive, nonnative plants from streams and canals and their adjacent upland areas on an 
occasional basis where they may cause a flooding problem and from revegetation sites. 

The District manages vegetation for other purposes including the protection of levees, and concrete linings 
from plant roots; meeting local fire codes requiring the control of combustible weeds and grasses; providing 


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BOX 7 (CONTINUED) 


-Description of Proposed Project: 
visual clearance to inspect the condition of a facility; and providing access along maintenance roads. 

The three basic methods of vegetation management utilized by the District are: hand removal (chain saws, 
weed-eaters, etc.), mechanical (mowing and discing), and chemical control through the use of herbicides. A 
method or combination of methods is chosen for each site depending on the maintenance requirements of the 
facility. Efficiency, economics, and the protection of public health and environmental resources are all 

considered in the selection of methods. 

Herbicides often are more effective at controlling vegetation than mechanical or hand removal methods. This is 
because of the ability of the herbicide chemicals to spread into and damage the roots of the target plants, thus 
preventing resprouting. When treated with mechanical or hand methods, some woody plants, such as willows, 
will resprout with multiple stems. The multiple sprouts result in a greater flood control problem and require 
annual control. With herbicides, annual retreatment is often necessary; however, the treatment area is greatly 
reduced, as only a small percentage of regrowth will occur. As a result, this Program includes herbicides as the 
primary method by which vegetation is controlled in channels and on stream banks. Herbicides are currently 
not used for vegetation management in the Pajaro River Basin, but in the Program are proposed for use in both 

basins. 

Herbicides are not broadcast sprayed across the channel, but are selectively sprayed at the plants targeted for 
removal by the design parameters of each particular stream reach. The phrase treated area is used to refer 
to the smaller area within the larger work area in which herbicides are actually sprayed. In some streams, only 
woody saplings are removed in the target area, while other streams require removal of both herbaceous and 
woody vegetation. The woody saplings which are treated with herbicides are no greater than 2 in diameter at 

breast height. 

The District only uses herbicides according to the label directions and for uses approved by the U.S. 
Environmental Protection Agency (USEPA) and the California Department of Pesticide Regulation. Currently, 
the primary herbicides which the District uses in channels and on the inside of levee slopes are Roundup Pro 
and Rodeo®. These herbicides are formulations of the chemical glyphosate, which is a non-se!ective broad 
spectrum herbicide. Rodeo® is approved for use in aquatic areas, whereas Roundup" Pro is not approved for 
application directly in water or to areas where surface water is present. 

Other herbicides which are used by the District for routine maintenance in channel and upland areas are shown 
in the Table 6. 

Hand removal of vegetation is undertaken in a few locations where it is not possible to access the area with 
spray equipment, or where cutting woody saplings (no greater than 6" in diameter at breast height) is more 
effective than herbicide spraying. In some cases, the vegetation is sprayed with herbicides, and then 
approximately 6 months later, the dead material is removed by hand removal methods. This latter category of 
work is referred to as follow-up hand removal. Follow-up hand removal of vegetation is only necessary when 
herbicide spraying is new to an area and there is a large volume of vegetation created in the first year or two. 
In subsequent years, the amount of vegetative regrowth is reduced and follow-up hand removal is necessary 

much less frequently. 

The five types of vegetation management in upland areas are: discing, mowing, herbicide application, hand 
removal, and removal of overhanging growth. 

Upland discing occurs on upland parcels outside of the streambanks and is conducted to create firebreaks. 
Upland mowing consists of operating a flail mower to eliminate or reduce grasses that would cause a fire 
hazard during the summer. Mowing can occur from one to three times annually at each location, usually 
between May and October. Mowing is conducted on the inside slope of some levees or streambanks. 

Upland herbicide spraying is used on levees, unpaved maintenance roads, and along some property lines. On 
levees, herbicides are used primarily to keep woody vegetation and broadleaf weeds from becoming 
established where they will interfere with flood control capacity, damage the levees, or hinder their inspection. 


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Description of Proposed Project:. 


BOX 7 (CONTINUED) 


Weeds and grasses are sprayed on maintenance roads to dearly define and keep open the access route. 
Herbicide spraying along property lines assists in establishing a firebreak. Pre* and post-emergent herbicides 
are sprayed from a truck-mounted rig or by a controlled drop applicator. 

Hand removal of vegetation is conducted in upland areas where mowers cannot access, and herbicides are 
either not practical due to steep terrain or not allowed. Hand removal of vegetation is generally used in upland 
areas along property lines to establish fire breaks. Removal of overhanging growth consists of pruning trees 

branches that impede access roads or hang over fence lines. 

The frequency of vegetation management activities varies from semi-annually to once every several years, 
depending on the method used. Generally, channel herbicide and channel hand removal of vegetation are 
conducted once every year near the end of the growing season. 


On average vegetation management work is annually performed on roughly 4,000 acres. Within this larger 
work area, the targeted treatment area consists of approximately 2,000 acres. These totals include the 

following approximate levels of activity: 

• 923 acres on which vegetation management work is conducted in 222 miles of stream channels with 132 

acres of the total actually receiving treatment (585 work acres or 75 acres of treated area on 166 miles in 
the Santa Clara Basin, and 338 acres or 57 acres of treated area and 56 miles in the Pajaro River Basin) 

• 23 acres on which vegetation management work is conducted on 27 miles of canals with 6 acres of the total 


actually receiving treatment ^ . .. 

3021 acres of uplands on which vegetation management work is performed, with 1885 acres actually 

receiving treatment. Upland vegetation management is outside of the area of inundation, and generally 

has a buffer of grass or vegetation on the slopes between the right-of-way and the stream 


RANK PROTECTION 


Bank protection involves an action by the District to repair stream banks that are eroding or are in need of 
preventative erosion protection. The District implements bank protection when the problem (1) causes or could 
cause significant damage to a property or adjacent property, (2) is a public safety concern, (3) negatively 
affects transportation or recreational use, (4) negatively affects water quality, or (5) negatively affects riparian 
habitat. Repairs may take several forms from installing "hard" structures (e.g., rock, concrete, sack concrete, 
gabions) to "soft" structures (e.g., willow brush mattresses, log crib walls, pole plantings). 

Stream bank erosion is a natural process, which mostly happens during major storm events. Erosion can occur 
because of hydraulic forces and geotechnical instabilities, and can be accelerated by human intervention and 
land uses. Accelerated erosion is typically a result of particular land uses that affect the stream corridor, 
including grazing, agriculture, and road and utility construction. In a constrained urban setting, erosion of 
banks can result in increased sediment deposition, which can lead to decreased flood flow capacities and 
potential flood hazards. Erosion on banks may also cause vegetation and soil loss, damage to private or public 
property, transportation impacts, safety hazards, and turbidity injurious to fish and aquatic life. Levee erosion 

may lead to failure of the structure and flooding. 


Bank protection work may either occur as repair of an existing bank protection project which is failing, or as 
new work along a bank which is eroding. The new work is considered routine maintenance because it is either 
restoring the flood control function of a modified channel or it is repairing a natural bank to its approximate 
condition prior to becoming an erosion problem. 

Repair of existing bank protection structures occurs when these structures fail and are replaced with in-kind, in- 
place materials. New bank protection projects are those that repair or protect the watercourse from fortha- 
degradation or erosion using the softest method appropriate. This type of protection is considered 
maintenance if the maintenance does not significantly alter the flood conveyance capacity of the streams. 



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Description of Proposed Project: 


BOX 7 (CONTINUED) 


Equipment used for bank protection may ^wate^mus^be^byp'assed around^hesiteduring 

“ tev bate ° r r“S Z£Z 

sukabif material may be used. In some cases, a bypass channel or detent™ basrn is appropnate to isolate a 
site Most often, bank protection projects are implemented in the dry season. 

»ss sag g 

"Son" ™s Se“rn,y°W, upofe method of bank protect used, but *. the 
physical properties of the stream where the repair is taking place. 

T e , r- <-r>nHiHnn< where there are no flow capacity requirements, vegetation components for 
sfteamt nk repair are selected. In modified creek channels where the flow requirements must be reBined 
S3! as for JheTc»-year flood), this will often necessitate a roughness max,mum whrch, depending on the 
channel design, may limit the vegetation component of the design. 

A ranae of methods is used for bank protection, as can be exemplified by several District bank Pfot^on 
projects. Many of the following examples demonstrate how soft methods can be combined with harder 

methods when site conditions cannot maintain a purely natural solution. 

Fnr ail bank Detection projects, the District makes an inspection of the stream upstream and downstream of a 
Si*3?? there is an identifiable cause of the erosion. In some cases, the cause of eros.cn .s 

S fSStafc tTSSSi « flows are being directed toward the bank from a srxtrce 

upstream, whether the channel Invert Is down cutting, or If Htega! drainage rs causing the problem. These 
factors can affect the bank protection approach implemented by the District. 

ThP District estimates that an average of 5,000 linear feet of banks may be repaired annually based on 
StoriJalrecords District experience, and current levels of funding. This is an average annual quantity andwili 

' car FariiH-ipc; ^rp in^nected after the winter storms for damage and maintenance needs. 

ssrs s&szrsssss* ** v- «—-«- **» «* 

balanced with annual budget constraints. 

Unlike sediment remuval and vegetation management, the historical location of bankpru^n tenot 

n „nSf nrSr bf where future bank protection will be required. The quantity and location of bank protecbon 
l£Sm gre^om year-to-year, based upon watershed conditions, degree of safety hazard, work 

load, budget, and quantity of other priority work to be done in a given year. 

Attach fiqures maps, and directions to the project site. See instructions for completing the drawings. One set" 
of original or good quality reproducible drawings must be attached to each agency. Applicants are encouraged 
to submit photographs of the project site, but these do not substitute for drawings. BCDC, die Corps 
Engird and <£a* Guard require at least one set of drawings on 8-1/2 x 11 inch sheets Urge, drawings 
may also be required. Fish and Game requires a USGS map. For a complete list of required drawings, refer to 

the instructions. __ 


Reason (s) for the proposed work: 

The District routinely removes sediment from streams and associated facilities to restore their 
SSlwateS and tarn canals to restore their water delivery function. Vegetation rs routmely removal tarn m 
a^areund'ieams and canals for the same reasons, and to provide access and fire prevenhon. Hie District 
conducts bank protection activities to restore eroded flood control facilities and to protect property. 


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Impacts on Wetlands: : BOX 9 (CONTINUED) 

impacts to 29 acres of tidal wetlands as shown in Figure 4. Channel Vegetation Management will impact an 
additional acre of tidal wetlands. 

' * 

TYPFS OF IMPACT 

As sediment is removed, so is any vegetation that is growing on it. The type of vegetation removed can vary 
from entirely herbaceous wetland species, to a mix of wetland and upland species, or almost entirely upland 
species depending on the location of the stream channel (e.g., tidal versus freshwater), spatial relationship of 
the low-flow channel to sediment benches, presence or absence of year-round water, and the duration 
between and overlap of different types of maintenance activities. The amount of vegetation present can also 
vary based on these conditions. At some locations in some years, sediment levels are high enough or the 
ephemeral condition of a stream may result in no stream vegetation being present on the channel bottom at 
the time of sediment removal. 

Channel Vegetation Management involves the application of herbicide to targeted vegetation or the hand 
removal of such vegetation. Target vegetation primarily consists of either tall emergent herbaceous wetland 
vegetation, such as cattails and bulrush, or woody vegetation consisting of native riparian species such as 
willows and box elder and nonnative species such as eucalyptus. The woody riparian vegetation removed is 
comprised of seedlings and saplings no greater than 6" in diameter at breast height. Neither sediment removal 
or vegetation management results in the removal of large stature, mature riparian vegetation. 

The projected impacts to stream vegetation are based on field surveys, calculations, and a special method for 
evaluating impacts from temporary but repetitive activities which was developed for this Program. These 
factors are described below. Field surveys were conducted in 1997 and 2000 to determine wetland extent in 
projected sediment removal areas (District 1999a; District 1999b; District 1999c). Freshwater wetland impacts 
were estimated through a randomly selected 10% sample of environmentally homogeneous reaches of 
proposed work areas. The extent of wetlands in each sample area was directly measured or estimated in the 
field. Results from the sample were extrapolated to provide an estimate of total sediment removal impacts to 
freshwater wetlands. Most freshwater wetland surveys were conducted in 1997; however, a few additional 
areas were surveyed in 2000. This same method was used to estimate freshwater wetlands in canals in 2000. 

Impacts to tidal wetlands were estimated in projected sediment removal work areas in 1997 using a different 
method. All proposed sediment removal work areas were surveyed in tidal areas rather than a representative 
sub-sample, as the total work areas in tidal reaches are much smaller than freshwater reaches. In each 
projected work location, the extent of wetland vegetation was measured directly or estimated in the field. 

Areas of impact to stream vegetation from the Vegetation Management Program were not measured in the 
field, but were based primarily on records of the existing Vegetation Management Program which identify areas 
and type of target vegetation by stream reach (District 1999c). Because herbicide spraying in the stream 
channel specifically targets either wetland or riparian vegetation (rather than broadcast spraying the entire 
channel bottom), the projected treated area is a good estimate of future wetland and riparian impacts. 
Therefore, no field surveys were necessary to estimate the amount of wetland and riparian vegetation 
potentially impacted by the Vegetation Management Program. 

Projected vegetation management areas were refined to include the Pajaro River Basin areas where herbicides 
are not currently used, but are proposed for herbicide treatment as part of the Program. For those areas, 
future herbicide use was projected based upon the area of existing hand removal and mowing operations and 
known target vegetation. 

ONE-TIME ACCOUNTING METHOD 

A one-time accounting method of impacts was developed for the Program because impacts to stream 
vegetation from routine maintenance are temporary but repetitive. The approach of this impact analysis is to 
count future impacts to any one section of creek one time only. Repetitive or overlapping stream maintenance 
activities in the same section of creek are not progressively added to the total impact acres. 


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Impact on Wetlands BOX 9 (CONTINUED) 

The one-time accounting assessment method is relevant to assessing the impacts of the Program because 
permanent mitigation is provided, current conditions are probably an overestimate of the typical amount of 
stream vegetation, work is spread out over many years, and stream vegetation regrows between maintenance 
events. Basically, this approach determines that a one-time assessment of impacts from, routine maintenance 
activities adequately represents significant impacts of all future maintenance work in that same area, and a 
mitigation program is designed accordingly. For the Program, permanent mitigation (see Box 13) is proposed 
for temporary, repetitive impacts. Current conditions in the stream channels are not typical and may represent 
a greater amount of stream vegetation since routine level of maintenance has not been undertaken over the 
past five or more years during development of the Program. Furthermore, routine maintenance work takes 
place in only a portion of the total Program work area in any given year, allowing vegetation re-establishment 

in other areas. 

District studies have found that wetland vegetation often quickly re-establishes following sediment removal. 
Rankin and Hillman (District 2000) found 98% average regrowth within two years after sediment removal at 
eight freshwater study sites, and 29% regrowth at five tidal study sites. Vegetation dominance and quality (as , 
represented by vegetation type, total percent cover of vegetation, and relative percent cover of native and 
invasive species) were similar between reference sites on which routine maintenance activities had not recently 
been conducted and the regrowth study sites. At most sites, one of these neutral or positive vegetation shifts 
occurred: full or partial transition from one native-dominated vegetation type to another, disappearance of a 
nonnative vegetation type, or increased total percent cover. The study found that potentially negative changes 
occurred less frequently: increased invasive species cover, appearance or increase in amount of a nonnative 
vegetation type, and decrease in total percent cover. The regrowth study primarily measured the results of 
sediment removal only, and did not assess the combined affect of sediment removal and subsequent 

vegetation management. 

In many creek sections, both sediment removal and aquatic herbicide application are undertaken, but in 
different years within the facility's particular maintenance cycle. For example, sediment removal may be 
conducted in year one. The following year, herbaceous wetland vegetation may begin to establish where the 
sediment was removed. In year three, vegetation may be sufficiently established to pose a potential flood 
hazard, so herbicide is applied to kill the targeted vegetation. Herbicide applications may continue in 
subsequent years. In the meantime, sediment accumulates until it eventually reaches a point where flood 
capacity is significantly reduced and sediment removal is again required. 

In those sections of creek where both sediment removal and vegetation management activities are undertaken, 
sediment removal was designated as the primary effect and therefore used to project the future impacts. This 
is because sediment removal tends to affect all or most of the channel bottom whereas herbicide treatment is 
more selective and affects a smaller area of the channel bottom. Likewise, only the first time that either 
sediment removal or a herbicide treatment is conducted on a section of creek is counted as an impact, and 
repeat treatments at that same location in subsequent years are not counted as additional impacts. The 
impact projections from vegetation management provided in Table 4 represent sections of creek where only 
channel vegetation management work is undertaken. Vegetation management impacts to stream vegetation 
appear relatively small compared to sediment removal because sediment removal numbers include the areas of 

overlap. 

Unlike sediment removal and vegetation management, locations for future bank protection work cannot be 
predicted. Routine bank protection can be done anywhere it is needed within District jurisdiction. Routine bank 
protection activities may after the biological resource values the stream environment by changing the conditions 
in the stream itself or by changing the vegetation surrounding the stream. Impacts from bank protection to 
biological species and stream functions vary depending on locations of each work site; values and function of 
riparian vegetation before and after project construction; quality of stream environment (i.e., fisheries) before 
and after project construction; and types of bank protection techniques used. Exhibit C describes the 
programmatic impact assessment and mitigation for routine bank protection activities. 


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Impact on Wetlands: 

IMPACTS AND MITIGATION COMMITMENTS FROM PRIOR YEARS 


uua 9 (CONTINUED) 


During preparation of the Program, the District has assessed impacts to stream vegetation on an annual basis 
since 1996, and committed to several mitigation projects. These commitments are identified in Table 10. The 
District and regulatory agencies have agreed that the mitigation commitments made under these recent annual 
projects can be incorporated into the mitigation package for the Program. 

♦ If a wetlands delineation has been completed, please submit it with application - attached Q Yes E No 

♦ If a geology or soils report has been prepared, please subm it with application - attached Q Yes Enq 




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Box 13 Mitigation . . . d mitiaate detrimental impacts, and provide proper protection of 

- - "TESST ,ine for lmptemenoaon - 

Define buffer areas as appropriate. Include the monitoring component, if applicable. 

If an Alternatives Analysis has been prepared, please attach it- attached IS Yes □ No 

Additional analysis regarding alternatives will be provided in CEQA document in March 2001. 

MITIGATION 

^"^nnpnte^ritdal^etland mstorSon; (2)leshwater wetland creation; (3) stream and watershed protection; 
and (4) control of giant reed. The 4 components of the stream vegetation mitigation package are summanzed in 

Table 7, and proposed sites are shown in Figure 5. 

~ mitiaation oackage for stream vegetation compensates for the same or similar functions as those impacted, 

and Game, San Francisco Bay Regional Water 
9 •* pm,Mnaw agreements made 

SSKrifcWt agenctes, Witt many of the agreements assisting in the development of 
a mitigation package for stream vegetation. 

sS 1=5 

mitigationdesign and implementation will be spread out over a period of approximately 10 years. 

This section ends with a proposal for annual reporting and a discussion of alternatives. 

TIDAL WETLAND R ESTORATION 

Management). 

Thpa nwrirt mans to create self-sustaining tidal wetlands by restoring a diked salt evaporation pond, Cargill Pond 
U SfStafal tidal marsh conditions. The restored tidal marsh is expected to support wetland habitat similar to 
or of higher quality than the habitat impacted by repetitive maintenance activities. 

_ 0 nnnH te located in the Cities of San Jose and Sunnyvale along South San Francisco Bay in the Santa Clara 
It is tordeS by Sunnyvale West Channel to the west, Guadalupe Slough to the northeast, and Sunnyvale 
Ea^nnd"tt?soutt^em comer. The pond Is under owr^hip of tte District, and . currency leased 

to Cargill Salt Division to continue their salt production operations until 20UZ. 
and for duck hunting. 


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Currently. Pond A-4 is a low salinity pond (0 to 60 parts per thousand) with shallow and stable water levels. The 
perimeter of the pond is bordered by narrow bands of mudflat and pickleweed. The levees surrounding the pond 
support broad, relatively large areas of upland ruderai vegetation. The sloughs adjacent to the pond levees are 

densely vegetated with California and alkali bulrush. 

Weeklv surveys by District biologists between March 1999 and February 2000 recorded 82 species of birds utilizing 
the open water and levees of Pond A-4 for roosting, foraging and nesting. The majority of observed birds were 
waterfowl (70%) with the highest use recorded in November and early March. Shorebirds accounted for less than 
8% of the birds observed. Resident bird species included Black-necked Stilts {Himantopus mexicanus), American 
Avocets ( Recurvirostra americana), Northern Shoveiers ( Anas dypeata), Ruddy Ducks ( Oxyura jamaicensis), 
California Gulls ( Larus ca/ifornicus), and Caspian Terns ( Sterna caspia). Two species of mammals were observed, 
California Ground Squirrel {Spermophilus beecheyi) and Black-tailed Jackrabbit (Lepus ca/ifornicus). 

The pond was sampled in August 2001 to determine what fish species were present. Two species were recovered 
during the 3-day sample period: Fish likely to occur in the pond included Yellowfin Gobie {Acanthogobius 
flarimanus) and Longjaw Mudsucker ( GiHichthys mirabilis). Associated invertebrates likely to occur in the pond 
include Brine Shrimp {Artemia franciscana) and various copepods, annelids and others. 

The restoration concept consists of lowering the outboard levees or breaching them in several strategic locations 
to provide full tidal action to the site. It is anticipated that a mosaic of mud flat, tidal wetland and upland habitats 
will be created. A combination of natural sedimentation processes and placement of dredge fill is proposed to 
accelerate restoration of wetland function to the site and create beneficial re-use of clean sediment excavated 
from tidal streams. Modification of Sunnyvale East Channel may be included in the design to improve its hydraulic 
performance and eliminate the need for future sediment removal and vegetation management for flood control 

purposes. 

Planning and design of the Pond A-4 tidal restoration are currently underway, and construction is expected to 
begin in 2006. The first phase of restoration will consist of 40 or more acres. A mitigation banking instrument and 
funding strategy will be developed, as well as a monitoring program. 

The design process will address several potential issues. Few large-scale tidal marsh restoration projects have 
been undertaken, and essentially no long-term studies exist to guide design and implementation of new sites. The 
Pond A-4 project will need to be coordinated with other large-scale tidal marsh restoration projects proposed for 
South San Francisco Bay. Because of ground subsidence, re-use of clean fill material may be necessary to 
supplement natural sedimentation in order for higher elevation features (high marsh) to develop in the short term. 
Control of perennial peppergrass, an invasive species that has infested brackish and freshwater marshes in the 

South San Francisco Bay, may be problematic. 

A Hazardous Substances' Assessment indicates the presence of low concentrations of arsenic in the levee, and 
arsenic and copper in the soils on the pond perimeter. The concentrations of these metals preclude the use of 
some soils for wetland cover material but not as noncover material according to the Sediment Screening Cnteria 
for Wetland Creation and Upland Beneficial Re-use developed by the San Francisco Bay RWQCB (Resolution 92 

145). 

FRFSHWATER WETLAND CREATION 

The Freshwater Wetland Creation component and the Stream and Watershed Protection component (described in 
next section) are proposed to compensate for impacts to 116 acres of freshwater wetlands (109 acres of impacts 
from work in freshwater stream channels and 7 acres of impacts from work in canals). The Freshwater Wetlan 
Creation component is proposed for compensation of 14 acres of freshwater wetland impacts in stream channels. 

The District would create 14 acres of freshwater wetlands (also known as non-tidal wetlands) at locations near 
streams in the Santa Clara (10 acres) and Pajaro River (4 acres) Basins. Although the freshwater wetland creation 
sites will not be instream as the impacted freshwater wetlands, they have an advantage of not being subject to 
routine disturbance from flood cont rol maintenance as the impacted sites ar e . These created wetlands will provide 

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Mitigation:- B0X 13 (CONTINUED) 

habitat for common local wildlife and wetland-related plants in a streamside setting. Because of their offstream 
location, they will rely on water supplied from off-site sources, and will require management of water levels. 

Proposed locations for freshwater wetland creation are: 

• Los Capitancillos Site — (3 acres) along Guadalupe Creek in the Santa Clara Basin 

• Coyote Lakes Park Site 10A — (7 acres) along Coyote Creek in the Santa Clara Basin 

• Church Pond Number 2 — (4 acres) along Uagas Creek in the Pajaro River Basin 

The District will continue searching for additional sites for freshwater wetland creation. An ©(tensive search 
initially conducted in 1997 will be reviewed. If additional freshwater wetland sites are located, then the Stream 
and Watershed Protection component of the mitigation package would be reduced. The sites currently identified 
for freshwater wetland creation are described further below. 

Los Capitancillos Site 

The Los Capitancillos freshwater wetland creation site will consist of approximately 3 acres of off-stream 
freshwater seasonal or perennial wetlands adjacent to Guadalupe Creek in the Santa Clara Basin. The site, 
located near Coleman Road and Redmond Avenue in the City of San Jose, is currently an upland field of annual 
grasses and is owned by the District The Los Capitancillos site is currently under design, and is expected to be 

installed in the year 2002. 

To create suitable conditions for development of a wetland, the site will be excavated. Water will be provided 
from the Almaden Valley pipeline and water control structures will be constructed to allow for adjustments of 
water depth and duration of inundation. Native hydrophytic species will be planted. 

This site will be developed in coordination with an adjacent project, the restoration of a meander configuration 
and shaded riparian aquatic habitat on Guadalupe Creek for fisheries values. The Guadalupe Creek project is not 

part of the Program. 

Preliminary investigations indicate that mercury levels are elevated in surface and shallow-depth soils on the Los 
Capitancillos site. The elevated levels are well below hazardous materials levels, but exceed wetland creation 
cover material levels recommended by the Regional Water Quality Control Board. This situation is being 
investigated further; however, the likely solution is that soils not suitable for wetland surfaces will be removed 
from the site and replaced with dean soils. 

Coyote Lakes Park Site 10A 

Coyote Lakes Park Site 10A is located in the City of San Jose in the Santa Ciara Basin. The land is owned by the 
County and under the management of County Parks and Recreation Department. The District has discussed 
potential use of this site for mitigation of the District's Program with staff of the County Parks Department. County 
Parks staff has preliminarily indicated that development of the site would be consistent with their park and 
recreation goals, and they are considering the site for this use. 

The Coyote Lakes Park site is situated on the northeast bank of Coyote Creek, just upstream of the interchange of 
Highways 101 and 85. The site is bounded to the northeast by Highway 101, an abandoned gravel pond to the 
west, and Coyote Creek and a District percolation pond to the south. 

The site currently consists of nonnative annual grassland habitat. The adjacent gravel pond, percolation pond, 
and Coyote Creek contain open water, emergent wetland, and mixed riparian forest. Soils on the potential site 
appear to be heavily disturbed by former highway and levee construction activities, however, their low 
permeability is suited for wetland creation. 

Depending on the final design, the site could be developed as 7 to 17 acres of perennial freshwater wetland. The 


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wetland habitat wouid be dominated by tali emergent marsh species such as California bulrush, common tule 
(Scfrpus acutus ), and narrow-leaved and broad-leaved cattail (Typha augustifolia, T. latifoHa). The design could 
also provide shallow, ponded areas dominated by short emergent obligate wetland species such as creeping 
spikerush (Eleocharis macrostachya ) and rushes. Riparian species on the fringe could be arroyo, red and 
narrow-leaved willows, western sycamore, and coast live and valley oak. 

Under the excavation option, the site's existing ground surface would be lowered 10 to 15 feet below the bottom 
of the adjacent gravel pond. Connections wouid be made between the restoration site and the gravel pond to 
enable water to passively flow onto the site and create approximately 7 acres of either perennial or nearly 
perennial ponded wetland habitat with a fringe of riparian vegetation. If approved by regulatory agencies, the 
excavated soil could be used to partially fill some of the open water areas of the gravel pond and convert them to 
approximately 10 acres of additional wetland habitat. 

Alternatively, the site would receive minimal grading, and water would be delivered to the site from the adjacent 
percolation pond. Water is supplied to the percolation pond from releases made from Anderson Reservoir and 
delivered via the Coyote Creek Channel. Preliminary calculations indicate that sufficient water exists in this system 
to supply the proposed wetland. Inlet and outlet control structures would regulate the inflow and control the 
water level on the site. Outflow from the site could be either to the gravel pond or Coyote Creek. This option 
would create similar wetland habitat as described for the first option above. 


Currently, there are breaches in the perimeter of the berm separating the gravel pond and Coyote Creek. As 
streamfiow diverts into the gravel pond it may result in higher water temperatures and stranding of fish. The Site 
10A freshwater creation design could include or coordinate with repair of these breaches. 

Additional studies wouid be necessary to assess the relationship between groundwater levels in the gravel pond, 
Coyote Creek, and the proposed mitigation site. Archeological studies may also be necessary. Although no 
archeological resources are known to occur at the site, Native American burials were found during deep excavation 

of a site nearby on Coyote Creek. 

Church Pond Number 2 


The Church Pond freshwater wetland creation site will consist of converting open water at the Church Avenue 
groundwater recharge ponds into approximately 4 acres of freshwater wetland. Currently, three ponds provide 
approximately 42 acres of surface area dedicated to groundwater recharge at the intersection of Uagas and 
Church Avenues in the community of San Martin in the Pajaro River Basin. The property is under the ownership of 

the District. 

The preliminary concept calls for a 4-acre earthen bench to be installed in one pond (Number 2) in a location 
known to be underlain by relatively impermeable soils. Shallow groundwater investigations of the Church Avenue 
Ponds indicate the low-permeability substrates in Pond Number 2 are likely to have relatively low infiltration rates, 
and not contribute substantially to overall recharge performance. Therefore, converting the primary purpose and 
management of this pond from groundwater recharge to wetland mitigation is not expected to result in substantial 
loss of groundwater recharge capability. The remainder of the pond's 15-acre surface area will remain open water 
used for percolation. Currently, the pond is often left dry. 

The project will take advantage of the existing infrastructure, pond configuration, and water management to 
operate the Church pond system for dual percolation and wetland mitigation purposes. For purposes of creating 
the wetland area, water will be supplied to the ponds from Llagas Creek and is not expected to require a 
substantial alteration of recent District reservoir water releases or operations. Under current operation, stored 
water from upstream reservoirs flows downstream as far as Church Ponds during the dry season. The preliminary 
concept calls for water to be routed to the pond system via an existing intake pipe between Pond 1 and Llagas 
Creek. It will be necessary to construct a flashboard dam in the creek in order to divert the water. The 
flashboard dam will be installed and the diversion operated during the summer dry season. The flashboard dam 
will be designed and operated so as to not obstruct fish passage and not cause bank erosion. A fish ladder over 


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the flashboard will be provided if necessary to allow fish passage, and the intake pipe will be screened to prevent 
diversion of fish into the ponds. Alternative water delivery methods, such as an infiltration gallery, will be explored 
during the planning phase. The design will create water levels on the bench of an adequate depth for wetland 
vegetation and will reliably control surface water elevation. 

Construction of the Church Pond wetland creation project is expected to begin in 2003. 


STREAM ANn WATERSHED PROTECTION 

The Stream and Watershed Protection component and the Freshwater Wetland Creation component (described 
above) are proposed to compensate for impacts to 116 acres of freshwater wetlands (109 acres of impacts from 
work in stream channels and 7 acres of impacts from work in canals). If the 3 freshwater wetland creation sites 
are implemented as described above, then actions under the Stream and Watershed Protection component would 
compensate for impacts to 74 acres of impacts in the Santa Clara Basin and 21 acres of impacts in the Pajaro 
River Basin. The Stream and Watershed Protection component would compensate in either basin for an additional 
7 acres of impacts to canals. 

The District will continue searching for additional sites for freshwater wetland creation. If additional freshwater 
wetland sites are located, then the Stream and Watershed Protection component of the mitigation package would 
be reduced by approximately 10 acres for every additional 1 acre of freshwater wetland creation. 

Under this component, the District would purchase approximately 920 to 1,210 acres of land and conservation 
easements to preserve, protect, and improve streams and their associated watersheds in the County. 

The mitigation component will focus on preservation and improvement of streams that are generally in a fairly 
undisturbed state and in good ecological condition. 

This effort consists primarily of land acquisition, but also provides for some restoration and/or management of 
acquired lands. Acquisition will provide 92 acres of mitigation credits and restoration and management on 
selected parcels will provide 10 acres of credit. The relative contribution of these sub-components could be 
adjusted based on opportunity and resource needs identified as the mitigation component progresses. 

Stream and watershed protection provides a logical link to stream maintenance impacts: 

• Impacts occur to habitat within streams. Stream and watershed protection provides for preservation, 
restoration, and management of streams and their related habitats. 

• Stream and watershed protection represents a "trade up" in stream habitat quality: the type of stream habitat 
protected is different, but has a higher quality, than that impacted. 

• The impacted in-stream freshwater wetlands of modified channels are considered to be of lower quality than 
the structurally and functionally more complex native riverine and riparian habitats of less-altered streams. 
In-stream freshwater wetlands of the extent and type impacted occur primarily in modified earthen and 
concrete channels in which stream structure and function has been impaired. 

• Temporary impacts to existing local stream reaches are mitigated by permanently protecting other local 
stream reaches. 

• The impacts consist of repeated but temporary disturbance to existing in-stream wetland. There is no 
reduction in the overall amount of stream habitat present, and the wetland vegetation regrows between 
disturbances. The mitigation program protects other existing stream habitat from effects of human 
disturbance, and, where needed, will improve the stream's environmental condition. 

The acquisition element will be mostly accomplished by donating funds to park and open space agencies, land 


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trusts and other land conservation organizations that will ultimately own title or easements and manage the 
property. The Districts contribution will typically provide partial funding of a larger acquisition, however, in some 
cases the district may choose to purchase and retain sole ownership or easement. Examples of suitable land 
include ranch land, farm land, and other undeveloped or sparsely developed land. 

Potential partners include land management agencies and private land conservation organizations that are active 
in the County. Examples of potential partners include, but are not limited to, the County Parks and Recreation 
Department, Santa Clara County Open Space Authority, Mid-Peninsula Regional Open Space District, California 
State Parks/Land Trust for Santa Clara County, The Nature Conservancy, and Peninsula Open Space Trust. 

The District will evaluate each proposed acquisition under a standard set of criteria established to ensure that the 
mitigation goals are met and mitigation credit is obtained. To qualify for consideration under this Program, the 
land must meet a standard set of core criteria (e.g. the land must include a stream, must be located in a 
watershed related to District streams, would not otherwise be purchased by the District, and is available from a - 
willing seller). Additional criteria will be used to determine the relative priority for acquisition of available parcels. 
Consideration will be given to site specific features (e.g. type and condition of stream resources, presence of 
endangered species or their habitat), transaction-related features (e.g., level of protection gained, time-frame for 
purchase completion, relative cost), and regional considerations (e.g. links with adjacent protected lands, achieves 
multiple agency and community benefits, supports Maintenance Program mitigation goal of maximizing benefit to 
local streams and watersheds by focusing on areas that provide the highest natural resource values). 

Each acquired property will be further evaluated to determine if the stream resources would benefit from 
1 restoration or management actions. Examples of the many types of restoration or management actions that could 
be undertaken to improve stream health include: removal of nonnative riparian plant species and revegetation 
with native species, repair and rehabilitation of denuded or otherwise degraded stream segments, replacement of 
ranch road stream crossings with more environmentally sensitive crossings, installation of erosion control 
measures on roads adjacent to streams (dirt or paved roads run parallel to most sizeable streams in the county), 
and installation of fencing to exclude cattle from the riparian area. 

An annual report will be prepared and submitted to the relevant agencies until all required mitigation credit is 
obtained. The report will include a description of each parcel acquired in the past year, detailing the location, size, 
stream and watershed amount present, summary of the core criteria and priority evaluation criteria analyses, 
mitigation credit earned, the entity that will own the fee title or conservation easement, planned land use (e.g. 
public park or open space, private ranch land, farm land), and planned restoration or management projects. The 
report will summarize all Stream and Watershed Protection Program actions and credits obtained to date. 

Individual monitoring reports will be prepared for restoration and management projects appropriate for the 
particular action taken (e.g. A re-vegetation project would require a standard mitigation and monitoring plan 
including the project description, performance and success criteria measures, schedule, etc). Once land has been 
acquired, the district will conduct periodic surveys to ensure that land use and management is consistent with the 
terms and agreements of the district contribution. Ongoing periodic summary status reports will be prepared. 

Credit for acquisition will be given at a 10:1 or 15:1 ratio (acquisition acreage : impact acreage) for acquisition of 
lands that both contain and are directly adjacent to stream resources as described below. The crediting method 
ensures that a substantial amount of stream and associated riparian corridor will be acquired, that immediately 
adjacent uplands which directly affect stream condition will also be acquired, and that the district's financial 
contribution will be large enough to enable purchase of appropriate parcels. 

• 10:1 ratio: Up to 50 feet from the centerline of 1 st order streams and 150 feet from the centerline of 2 nd order 
and greater streams, and 

• 15:1 ratio: For an additional area from 150 up to 500 feet from the centerline of 2 nd order and greater 
streams. 

Credit for restoration and management will be generated on a dollar value basis as follows: one acre of mitigation 


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credit obtained for each $150,000 of projects funded. The $150,000 figure is based on the approximate per acre 
cost of District riparian mitigab'on projects recently implemented in the lower watershed. Many of the restoration 
or management actions that can provide substantial improvement of the stream environment cannot be quantified 
in the same way as traditional acre-for-acre riparian revegetation mitigation projects. This lump sum crediting 
approach provides the flexibility needed to implement a variety of beneficial actions, as dictated by the needs and 

condition of each property. 

The projected total Program cost is based on an average estimated land value of $15,000 per acre. Most land is 
expected to cost less than this amount. Land cost under this Program is not-to-exceed $25,000 per acre. 

CONTROL OF GIANT REED 

The Giant Reed Control component is proposed to compensate for impacts from vegetation management in 
streams to 77 acres of riparian vegetation (32 impacts in the Santa Clara Basin and 45 acres in the Pajaro River- 
Basin). Overall, this component includes removing giant reed {Arundo donax) from 125 acres along with several 
other associated efforts as described above. Of the total acres from which giant reed is removed, 80 acres would 
be credited towards the 77 acres of impacts to riparian vegetation. An additional 45 acres of giant reed control is 
proposed to compensate for any lag time between maintenance impacts to stream vegetation and implementation 

of the other 3 mitigation components. 

Giant reed is an invasive nonnative plant. Large stands of giant reed degrade wildlife habitat, cause localized 
flooding, and increase the risk of wildland fires. Since giant reed displaces open water and native riparian and 
wetland plant communities of freshwater streams, its control is appropriate compensation for impacts to sapling 
riparian vegetation caused by channel vegetation management 

In the County, substantial infestations of giant reed are known in Coyote, Calabazas, Llagas, and Uvas Creeks, and 
along the Guadalupe River. Currently, the District removes stands of giant reed on an occasional basis where they 
may cause a flooding problem and from revegetation sites. However, neither the District nor any other entity has 
taken a coordinated effort to remove giant reed from the county's streams. 

Under this mitigation component, the District would remove giant reed from 125 acres in the County over a period 
of 10 years. 

This component includes the following associated elements that are necessary to ensure successful control of giant 
reed on a long-term basis. 

• Mapping - Outbreaks of giant reed throughout the county will be mapped. The goal of mapping is to assist in 
assessing the extent of the problem, prioritizing control efforts, and tracking and reporting annual progress. 
The District has already started collecting existing information and conducting field surveys. Additional 
surveys will be conducted in areas for which information is not currently available. Where conditions are 
favorable, remote sensing and aerial photography will be used. A protocol will be developed for locating and 
quantifying the size of existing stands to ensure consistent data collection. Most data will be collected using 
Global Positioning System (GPS) technology. All data collected in the mapping effort will be incorporated into 
a Geographic Information System (GIS) for generating maps and data analysis. The GIS information will be 
made available to non-District persons who are participating in control of giant reed or otherwise conducting 

research. 

• Prioritization and Pilot Site - Subsequent to completion of the initial mapping effort in the first year, areas will 
be identified by a priority system for control. Priority will be given to those locations where sustained control 
efforts will provide the most habitat value, access can be gained to giant reed outbreaks at the top of the 
watershed and for continuous reaches, and multiple benefits can be gained in combination with the other 

mitigation components. 

A pilot control site or sites will be selected in the first few years to experiment with different control methods 


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Construction, and Readiness Division, Directorate of Civil Works, October 10, 1997, Interim Guidance I 
Regarding Mitigation and Other Implementation Requirements for Flood Control Maintenance Activities 
Authorized Under Nationwide Permit 31, Memorandum for Commander, South Pacific, Division.] 

The District therefore interprets this NWP as allowing routine maintenance work in tidal areas to be permitted 
under NWP 31 and to not require mitigation as long as the maintenance work has been conducted on a 
regular basis, and the original construction of the project was after 1970. The District assumes that all District 
flood control projects constructed after 1970 have been reviewed under CEQA and either mitigation was 
offered for the original construction, or the impacts were evaluated at that time as not significant. Therefore, 
no additional mitigation would be required under NWP 31. Almost all of the tidal portions of the District's flood 
control facilities have been constructed or modified after 1970. This standard would only apply to 
maintenance work in tidal areas because, currently, the Corps only regulates sediment removal in tidal areas. 

Under this alternative, it is also assumed that three other categories of maintenance work will qualify for a- 
Regional General Permit currently being proposed by the Corps and San Francisco Bay RWQCB. This proposed 
regulation, referred to as the Minimal Threat Flood Control Channel Maintenance Activities permit, would apply 
to major flood control districts in the San Francisco Bay area, and is expected to be enacted sometime in the 
Year 2001. This permit would allow sediment and debris removal in concrete lined channels and in-channel 
siltation basins, vegetation management, maintenance of structures, and bank protection. Prohibitions under 
the proposed regulation include a condition that there should be no permanent loss or significant temporal loss 
of wetland or riparian habitat in terms of acreage, function or value; however, these conditions have not been 
defined yet. A condition for bank protection activities is that the structure be no longer than 500 feet in 

length. 

According to this proposed Regional General Permit, with implementation of the appropriate BMPs, these 
activities typically would not require mitigation. The District therefore interprets this Regional General Permit 
as allowing these types of activities to occur without mitigation. Therefore, the No Project - Maintenance 
Baseline Alternative does not provide mitigation for sediment and debris removal in concrete lined channels 
and in-channel siltation basins, vegetation management, maintenance of structures, and bank protection. 

2 . No Work Alternative 

This alternative consists of conducting no routine maintenance work in streams and canals within the District's 
jurisdiction. Over time, these facilities would fill with more sediment and vegetation, which would affect their 
functions. No impacts would occur to stream vegetation from routine stream maintenance work. 

3. No Herbicides Alternative 

The No Herbicide Alternative will be the same as the Multi-Year Program Alternative except there will be no 
use of herbicides in routine stream or canal maintenance. Instead, vegetation will be managed by mechanical 
and hand methods in those areas in which herbicides are currently used in the Santa Clara Basin. The use of 
herbicides will continue to be excluded on streams in the Pajaro River Basin. 

4. Modified Pajaro River Basin Alternative 

This alternative is similar to the Program except that it will not include the use of herbicides in stream channels 
of the Pajaro River Basin unless they are for the control of nonnative, invasive plants. Instead, hand and 
mechanical methods will be used to control vegetation in stream channels of the Pajaro River Basin. Herbicides 
will continue to be used in adjacent upland areas in the Pajaro River Basin, and in channels, canals and 
associated upland areas in the Santa Clara basin. All activities will otherwise occur at the same level as the 
multi-year program alternative, with design, BMPs and annual reporting implemented in a programmatic 
manner, and mitigation provided at the same level. 


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Mitigation: 

5. Reduced Herbicides Alternative 

Under the Reduced Herbicides Alternative, sediment removal and vegetation management will occur in 
primarily the same locations as for the Program. Herbicides would be used for vegetation management in and 
adjacent to streams and canals throughout the District's jurisdiction; however, the overall amount of herbicides 
used will be reduced compared to die Preferred Alternative. 

Under this alternative, the following standards will be implemented to reduce the use of herbicides. The use of 
herbicides will be reduced 25% in streams and substituted with hand removal methods. In upland areas, non- 
seiective herbicides will be used only along fence lines and immediately adjacent to structures. In the 
remaining upland herbicide areas, herbicides selective to broadleaf plants will be used, and mowing and hand 
removal methods will be used to control grasses. 

REFERENCES 

District 1999a. Long-term Maintenance Program: 1997 Non-tidai Instream Wetland Extent Survey. Santa Clara 
Valley Water District Memorandum. G. Rankin. October 4,1999. 

District 1999b. Long-term Stream Maintenance Program: 1997 Tidai Wetland Extent in Program Area and in 
Santa Clara County. Santa Clara Valley Water District Memorandum. L. Squires. September 29, 1999. 

District 1999c. Long-term Maintenance Program: Estimated Tidal Umits Used for Environmental Analysis. Santa 
Clara Valley Water District Memorandum. G. Rankin. October 4, 1999. 

District 1999d. Riparian and wetland impacts of the Stream Maintenance Program. Santa Clara Valley Water 
District Memorandum. C. Roesster. October 20, 1999. 

District 2000. Instream Wetland Vegetation Regrowth Study, Second Annual Report: Results for 1999. Gale 
Ranking and Janell Hillman. September 2000. 


Box 14 Environmental Impact Documentation 

National Environmental Protection Act (NEPA) or California Environmental Quality Act (CEQA) compliance 
document provided: Q Yes E No 

Is documentation being prepared? 0 Yes Q No DEIR will be sent in March 2001 

The following is attached: □ EIS □ EIR □ Negative Declaration □ Mitigated Negative Declaration 

□ Categorical Exemption Q Statutory Exemption Q Notice of Exemption Q Notice of Determination 


Box 15 Has any agency denied approval for the activity described herein or for any activity directly 
related to the activity described herein? □ Yes 


No If yes, explain: 


Box 16 Names, addresses and tele 
(Local governments may require c 
Name 

iphone numbers of adjoining property owne 
additional notice - consult your local govern 
Address 

srs, lessees, etc. 
mentj 

Phone number 

Numerous adjacent property owners. Project has been advertised throughout county and will continue to be 
advertised through CEQA process to solicit public comment. 


End of Section One 


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Construction, and Readiness Division, Directorate of Civil Works, October 10, 1997, Interim Guidance 
Regarding Mitigation and Other Implementation Requirements for Flood Control Maintenance Activities 
Authorized Under Nationwide Permit 31, Memorandum for Commander, South Pacific, Division.] 

The District therefore interprets this NWP as allowing routine maintenance work in tidal areas to be permitted 
under NWP 31 and to not require mitigation as long as the maintenance work has been conducted on a 
regular basis, and the original construction of the project was after 1970. The District assumes that all District 
flood control projects constructed after 1970 have been reviewed under CEQA and either mitigation was 
offered for the original construction, or the impacts were evaluated at that time as not significant. Therefore, 
no additional mitigation would be required under NWP 31. Almost all of the tidal portions of the District's flood 
control facilities have been constructed or modified after 1970. This standard would only apply to 
maintenance work in tidal areas because, currently, the Corps only regulates sediment removal in tidal areas. 

Under this alternative, it is also assumed that three other categories of maintenance work will qualify for a* 
Regional General Permit currently being proposed by the Corps and San Francisco Bay RWQCB. This proposed 
regulation, referred to as the Minimal Threat Flood Control Channel Maintenance Activities permit, would apply 
to major flood control districts in the San Francisco Bay area, and is expected to be enacted sometime in the 
Year 2001. This permit would allow sediment and debris removal in concrete lined channels and in-channel 
siitation basins, vegetation management, maintenance of structures, and bank protection. Prohibitions under 
the proposed regulation include a condition that there should be no permanent loss or significant temporal loss 
of wetland or riparian habitat in terms of acreage, function or value; however, these conditions have not been 
defined yet. A condition for bank protection activities is that the structure be no longer than 500 feet in 
length. 

According to this proposed Regional General Permit, with implementation of the appropriate BMPs, these 
activities typically would not require mitigation. The District therefore interprets this Regional General Permit 
as allowing these types of activities to occur without mitigation. Therefore, the No Project - Maintenance 
Baseline Alternative does not provide mitigation for sediment and debris removal in concrete lined channels 
and in-channel siitation basins, vegetation management, maintenance of structures, and bank protection. 

% 

2. No Work Alternative 

This alternative consists of conducting no routine maintenance work in streams and canals within the District's 
jurisdiction. Over time, these facilities would fill with more sediment and vegetation, which would affect their 
functions. No impacts would occur to stream vegetation from routine stream maintenance work. 

3. No Herbicides Alternative 

The No Herbicide Alternative will be the same as the Multi-Year Program Alternative except there will be no 
use of herbicides in routine stream or canal maintenance. Instead, vegetation will be managed by mechanical 
and hand methods in those areas in which herbicides are currently used in the Santa Clara Basin. The use of 
herbicides will continue to be excluded on streams in the Pajaro River Basin. 

4. Modified Pajaro River Basin Alternative 

This alternative is similar to the Program except that it will not include the use of herbicides in stream channels 
of the Pajaro River Basin unless they are for the control of nonnative, invasive plants. Instead, hand and 
mechanical methods will be used to control vegetation in stream channels of the Pajaro River Basin. Herbicides 
will continue to be used in adjacent upland areas in the Pajaro River Basin, and in channels, canals and 
associated upland areas in the Santa Clara basin. All activities will otherwise occur at the same level as the 
multi-year program alternative, with design, BMPs and annual reporting implemented in a programmatic 
manner, and mitigation provided at the same level. 


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BOX 13 (CONTINUED) 


Mitigation: 

5. Reduced Herbicides Alternative 

Under the Reduced Herbicides Alternative, sediment removal and vegetation management will occur in 
primarily the same locations as for the Program. Herbicides would be used for vegetation management in and 
adjacent to streams and canals throughout the District's jurisdiction; however, the overall amount of herbicides 

used will be reduced compared to the Preferred Alternative. 

Under this alternative, the following standards will be implemented to reduce the use of herbicides. The use of 
herbicides will be reduced 25% in streams and substituted with hand removal methods. In upland areas, non- 
selective herbicides will be used only along fence lines and immediately adjacent to structures. In the 
remaining upland herbicide areas, herbicides selective to broadleaf plants will be used, and mowing and hand 

removal methods will be used to control grasses. 

REFERENCES 

District 1999a. Long-term Maintenance Program: 1997 Non-tidal Instream Wetland Extent Survey. Santa Clara 
Valley Water District Memorandum. G. Rankin. October 4, 1999. 

District 1999b. Long-term Stream Maintenance Program: 1997 Tidal Wetland Extent in Program Area and in 
Santa Clara County. Santa Clara Valley Water District Memorandum. L. Squires. September 29, 1999. 

District 1999c. Long-term Maintenance Program: Estimated Tidal Limits Used for Environmental Analysis. Santa 
Clara Valley Water District Memorandum. G. Rankin. October 4, 1999. 

District 1999d. Riparian and wetland impacts of the Stream Maintenance Program.-Santa Clara Valley Water 
District Memorandum. C. Roessler. October 20, 1999. 

District 2000. Instream Wetland Vegetation Regrowth Study, Second Annual Report: Results for 1999. Gale 
Ranking and Janell Hillman. September 2000. 


Box 14 Environmental Impact Documentation 

National Environmental Protection Act (NEPA) or California Environmental Quality Act (CEQA) compliance 
document provided: Q Yes ® No 

Is documentation being prepared? SI Yes Q No DEIR will be sent in March 2001 

The following is attached: □ EIS □ HR □ Negative Declaration □ Mitigated Negative Declaration 

Q Categorical Exemption Q Statutory Exemption Q Notice of Exemption Q Notice of Determination_ 


Box 15 Has any agency denied approval for the activity described herein or for any activity directly 
related to the activity described herein? Q Yes E No If yes, explain: 


Box 16 Names, addresses and telephone numbers of adjoining property owners, lessees, etc. 

(Localgovernments may require additional notice — consult your local government.) 

Name | Address _'_ | Phone number _ 

Numerous adjacent property owners. Project has been advertised throughout county and will continue to be 
advertised through CEQA process to solicit public comment. . . . 


End of Section One 


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txaio - Anpnrv Snecific Requirements for Project Permitting 

Box 17 Depi 
Projects Ad - 

artment of Fish and Game - 

iarpnt to. or Involving a River, Stream, or Lake 


□ This Droiect does not involve this agency (no additional questions completed) 

• _ 

Project Name Multi- 
Proposed compietii 

Project □ Open 
on page 2 Name 

-Year Stream Maintenance Proa ram Project cost $ 8.6 miilion/year Proposed start date July ,2001 1 
rrn date SeDtember 2010 Number of Stream Encroachments 

atorQ Contractor, □ Contact, if different from applicant, agent, and property owner 

2 , address, phone and fax for each 

Attach copies of completed applicable local, state, or federal permits, agreements or authorizations. 

□ Local (describe): . . 

E State (describe): San Francisco Bay Conservation and Development Commission 

□ Federal (describe): ..- - 


Project Questionnaire: Yes 

Maybe/ 

Uncertain 

No 

Please explain if you responded "yes*' or 
"maybe/uncertain” 

1. 

2. 

Will the project or activity involve work on the 
hank riv#ar stream, or lake? 

✓ 



Maintenance work occurs in streams 
throughout Santa Clara County. 

If , * ncu/crcH “ves” to #1. will the Droiect or activity involve any of the following. 


a Removal of any veaetation? 

✓ 



For vegetation management activities. 


b. Excavation of the bank? 

✓ 



For bank protection activities. 


p. Placement of piers? 



✓ 



d. Placement of bank protection or stabilization 
structures or materials (e.g., gabions, 
riD-rao. concrete siurry/sacks)? 

✓ 



For bank protection activities. 

3. 

Will the project or activity take place in, adjacent 
to, or near a river that has been designated as 
"wild and scenic" under state or federal law? 



✓ 

- 


Will the project or activity involve work in the bed 
or channel of a river, stream, or lake? 

✓ 



For ail channel activities. 

9 

Will the project or activity involve the placement 
of any permanent or temporary structure in a 
river, stream, or lake? 

✓ 



Permanent structures for bank protection. 
Temporary coffer dams to divert flow around 
work site for some sediment removal and bank 
protection. 

a 

Will the project involve the use of material from a 
streambed? 



✓ 


1 

Will the project or activity result in the disposal or 
deposition of debris, waste, or other material in a 
river, stream, or lake? 



✓ 


■ 

a. If you answered "yes" to #7, describe the 
material that will be disposed of or 
denosited in the river stream, or, lake: _ 


■ 

Will any type of equipment be used in a river, 
stream, or lake? 

✓ 





a. If you answered "yes" to #8, describe the type 
of equipment that will be used: 

Loaders, dozers, trucks, cranes, and mowers. 

9 

Does the project or activity area flood or 
oeriodicallv become inundated with water? 

✓ 




10. 

Will water need to be diverted from a river, 
stream, or lake for the project or activity? 

✓ 



Water is diverted for some sediment removal 
and bank protection activities. 

Bi 

If um. ancu/ereH "ves” to #10. please answer the following: ...—— 


a. Will this be a temporary diversion? 

✓ 


. 

Stream flow will be diverted around work 
areas. ._ _ 


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BOX 17 (CONTINUED 



b. Will water quality be affected by the 

deposition of silt, an increase in water 
temperature, a change in the pH level, or 
in some other way? 

✓ 



Best Management Practices are included to 
protect water quality. 

. 


c. Will the water be diverted by means of a dam, 
reservoir, or other water impoundment 
structure? 

✓ 



Temporary coffer dams will be used to bypass 
Bows. 

a 

Will the project or activity be done pursuant to a 
water riqht application or permit? 


✓ 


Some sediment will be removed from diversion 
structures. 

13. 

Has a wildlife assessment or study been 
completed for the area where or near where the 
project or activity will take place? (If "yes”, 
attach or enclose a copy of the assessment or 
study.) 

✓ 



Wildlife assessment will be included in Draff 
Environmental Impact Report to be submitted 
in March 2001. BMPs are included to protect 
plant and wildlife species. 

HI 

Will the project or activity affect fish, amphibians, 
insects, or other aquatic resources? 


✓ 


See 13 above. 


Will the project or activity affect terrestrial 
wildlife? 


✓ 


See 13 above. 

16. 

Are any endangered or rare plant species 
thought or known to occur In the area where the 
proposed project or activity will take place? 


✓ 


See 13 above. 

17. 

Are any endangered or threatened fish, bird, or 
animal species thought or known to occur in the 
area where the proposed project or activity will 
take place? 


✓ 


See 13 above. 

18. 

Have you contacted any other local, State, or 
federal agency regarding the project or activity? 

✓ 





a. If you answered "yes” to #18, please list the 
names of the agencies you have 
contacted: 

$F Bay Conservation and Development Commission, SF Bay and 
Central Coast Regional Water Quality Control Boards, CA Department of 
Fish and Game, and U.S. Army Corps of Engineers, U.S. EPA, U.S. Fish 
and Wildlife Service 

i 

Have you applied for or obtained any permit, 
agreement, or other authorization for your project 
or activity from any government agency? 

✓ 

; 

_ _ _ 

' 


p ; |gpfp» 

If you answered "yes" to #19, please list the 
names or describe the permit, agreement, or 
authorization you have applied for or obtained: 

San Francisco Bay Conservation and Development Commission as 
noted on page 1. 

20. 

Have any environmental documents pertaining to 
your project or activity been prepared? 


✓ 


Draft Environmental Impact Report to be 
submitted March 2001. 


a. If you answered "yes" to #20, please list the 
environmental documents that have been 
prepared: 



/ hereby certify that all information contained in this notification is true and correct and that I am authorized to sign this document : I understand that in the 
event this information is found to be untrue or incorrect , / may be subject to civil or criminal prosecution and the Department may consider this notification to 
be incomplete and/or cancel any Lake or Streambed Alteration Agreement issued pursuant to this notification. I understand that this notification is valid only 
for the project described herein and that l may be subject to civil or criminal prosecution for undertaking a project that differs from the one described herein, 
unless I have notified the Department of that project in accordance with section }60l or 1603 of the Fish and Game Code . 

/ understand that a Department representative may need to inspect the property where the project described herein will take place before issuing a Lake or 
Streambed Alteration Agreement pursuant to this notification. Jn the event the Department determines that a site inspection is necessary, I hereby authorize 
the Department to enter the property where the project described herein will take place to inspect the property at any reasonable time and certify that l am 
authorized to grant the Department permission to access the property. 


Q / request the Department to first contact me at (insert telephone number j 


to schedule a date and time to enter the 


propertv where the project described herein will take place and understand that this may delay the Department s evaluation of the project described herein. 

_ 2-lH-ol 


Operator or OperatorrKcp 




Date 


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, II -- 

Box 18 California Coastal Commission - 

Projects in the Coastal Zone _____ 

[xj This project does not involve this ag ency (no additional questions co mpleted)- 

Length of coast line on the project site, in feet: I Length of coast line of any.adjacent.property owned 

s hv t-hp owner of the proiect site, in feet:_ 


Area reserved for non-public access uses, in square feet: j Area reserved for public access, in square feet: 

document proof of applicant' interest in the property by inc luding stamped envelopes and letters.,- 

Types of activities to be undertaken or materials to be placed within coastal zone: 

* 

. Will the project be located within a water-oriented priority use area that is designated in the Coastal Access 
Plan? □ Yes (If yes, please attach an explanation of how the project can be approved despite this inconsistency.) 

• □ No 

Total area within the coastal zone ... square feet. ___ 

Public Access Information _ n „ n.. 

• Does public access or ocean views exist on the project site or on a contiguous property. LI Yes 

If "yes" please attach a description of the public access; if "no" explain what is preventing public access to the 

coastline. 


Area within coastal zone to be reserved for non-public access uses: -- squan 

Area within zone to be reserved for public access: - square feet 

Will the proiect block public views or adversely impact present or future public access? □ Yes 

* J ... . i I __ ^ _ _. .L*. I:_ C/hi* rrt/ 


square feet 


□ No 


If yes please describe why the project will or will not affect public views or public access. For most large projects, 
identify: (1) the existing number of people or employees using the site: and1(2) the existing ™mbero rare, 
bicycles, and pedestrians visiting the site and the level of service of all nearby roads leading to the site. plea *“ 
describe how the project will change these factors. Please describe the impact the imped: theproject ^ ected t0 
have on the existing use of the site and on existing public views or physical public access at the site. Please 
describe the impact the project is expected to have on the public's use of existing nearby parks, public access, 
public parking and other recreational areas on the shoreline and the roads leading to the site. 

. Do public safety considerations or significant use conflicts make it infeasible to provide new public access to the 
shoreline on the project site? □ Yes □ No If "yes", please attach a description of the P^afety 

considerations or significant use conflicts which make it infeasible to provide public access at the projectsite and 
either (1) identify an offsite area where public access to the coast is to be provided as part of the projert and 
describe the proposed public access at a specified offsite location, or (2) provide an explanation as to why no offsite 

public access is proposed as part of the project. 


Summarize the public access to be provided as part of the total project: 

• Total amount of public access - 

• Length of waterfront public access area - 

• Number of parking spaces for public access area - 

• Area and width reserved for view corridor(s) - 


. square feet 
feet 

square feet 


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BOX 18 (CONTINUED 



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Box 19 Bay Conservation and Development Commission — 

Projects on the Shore of the San Francisco Bay or Other BCDC Areas of Jurisdiction 

HI This project does not involve this agency (no additional questions completed) 


Does the project involve development within the primary 
management area of the Suisun Marsh? 

Q Yes Q No 

If "Yes", provide any relevant Duck Club number(s): 


Length of shoreline on the project site, in feet: 


Does the project involve development within the 100- 
foot shoreline band around San Francisco Bay? 

Q Yes Cl No 

San Francisco Bay Plan Shoreline 

Designation _ 

Length of shoreline of any adjacent property owned by 
the owner of the project site, in feet: _ 


Area reserved for public access, in square feet: 


cubic 


Area reserved for non-pubiic access uses, in square feet: 

Total size of underwater and tidal areas of the project site, I ID Numbers) of previous BCDC permits) issued for 
in square feet: _____ work on this site: _ 

Total cost of project. This means the fair market value of the project, including materials, 

labor, machine rentals, etc. $ Process ing Fee -_ 

Bay Fill Information - Fill means earth or any other substance or material, including pilings or structures 
placed on pilings, and structures floating at some or all times and moored for extended periods such as houseboats 
and floating docks. 

• Total Volume of solid fill to be placed in water or marsh areas:_cubic 

■ Area to be covered with solid fill:_.square feet 

■ Area to be covered with floating fill:__ Sd fe®t 

• Area to be covered with pile-supported fill:_sq feet 

• Area to be covered with cantilevered fill:___sq feet 

■ Salt pond area to be filled:___ _ feet 

■ Managed wetland area in the primary management 

■ Area of the Suisun Marsh to be filled: __sq feet 

■ Area on new fill to be reserved for private, commercial, or other uses:_sq feet 

■ Area on new fill to be reserved for public access:_sq feet 

» What is the basic purpose of the new fill in the Bay, salt pond, managed wetland, or certain waterway? 

Information on Fill to be provided in an attachment 

• Please specify the area of fill, in square feet, proposed to be covered in structures; used for roads; used for 
parking; used for pathways and sidewalks; covered with landscaping; used for piers, docks, and other maritime 
related purposes; placed for shoreline protection; and used for other purposes (specify uses). 

■ Please provide dimensions of portions of ail structures to be built on new fill, including length, width, area, height 

and number of stories. 

■ Please provide one or more photographs of existing shoreline conditions. 

Provide the following information to justify the proposed fill in an attachment: 

BCDC can approve new fill for only five purposes: (1) accommodating a water-oriented use; (2) improving shoreline 
appearance; (3) providing new public access to the Bay; (4) accommodating a project that is necessary to the 
health, safety, or welfare of the public in the entire Bay Area; and (5) accommodating a project that is consistent 
with either: (1) the Suisun Marsh Preservation Act and the Suisun Marsh Protection Plan; or (2) the Suisun Marsh 
Local Protection Program. Please explain how the project is consistent with one or more of these purposes. 

■ If the fill is to be used for improving shoreline appearance or providing new public access to the Bay, please explain why 
it is physically impossible or economically infeasible to accomplish these goals without filling the Bay. 

« Please explain how the fill will result in a stable and permanent shoreline. 

• Please explain the steps that will be taken to assure that the project will provide reasonable protection to 
persons and property against hazards of unstable geologic or soil conditions or of flood or storm waters. 

• Please provide the names, addresses, and telephone numbers of any licensed geologists, engineers, or 
architects involved in the project design who can provide technical information and certify to the safety of the 

project. 



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BOX 19 (CONTINUED - ) 


• Please explain: 

1. What possible effects the proposed fill would have on the Bay Area, such as (1) any impact on the volume 
of Bay waters, on Bay surface area, or on the circulation of Bay water; (2) any impact on water quality; (3) 
any impact on the fertility of marshes or fish and wildlife resources; and (4) any impact on other physical 
conditions that exist within the area which would be affected by a proposed project, including land, air, water, 
minerals, flora, fauna, noise, or objects of historic or aesthetic significance; and 

■ 2. How the nature, location, and extent of the proposed fill would minimize any possible harmful conditions or 

effects. 

■ Please explain how the public benefits of the project would exceed the public detriment from the loss of water or 
marshlands. 

■ For marina projects, please indicate how many berths, if any, are to be made available for live-aboard boats and 
explain how these live-aboard boats will contribute to public trust purposes. 

■ Please identify any other specific policies of the McAteer-Petris Act (California Government Code Title 7.2, 

especially Section 66605), the Suisun Marsh Preservation Act (California Public Resources Code Sections 29000- 
29612), the San Francisco Bay Plan and the Suisun Marsh Preservation Plan, and BCDC's regulations regarding minor 
fill for improving public access and shoreline appearance, that are relevant to and offer support for the project and 
explain how the project is consistent with these policies._____ 


Shoreline Band Information - Shoreline band means the land area lying between the bay shoreline and a 
line drawn parallel to and 100 feet from the bay shoreline. The bay shoreline is the mean high water line, or five 
feet above mean sea level in marshlands. 

• Types of activities to be undertaken or materials to be placed within the shoreline band 

• Will the project be located within a water-oriented priority use area that is designated in the San Francisco Bay 

Plan? G Yes O No If "yes", please attach an explanation of how the project can be approved despite 

this inconsistency. If no, complete the questions below: 

• Total shoreline band area within project site:_sq feet 

• Area within shoreline band to be reserved for non-public uses:_sq feet 

• Area within shoreline band to be reserved for public access:_sq feet 

• Information about the shoreline work to be provided in an attachment: 

» Please describe the area, in square feet, to be covered by structures; used for roads; used for parking; 
used for pathways and sidewalks; covered with landscaping; used for shoreline protection; and used for 
other purposes (specify uses). 

■ Please identify the total number of parking spaces in the project and within the shoreline band. 

■ Please provide dimensions of portions of all structures to be built within the shoreline band, including 

length, width, area, height, and number of stories.___ 


Environmental Impact Documentation 

• Is the project statutorily exempt from the need for environmental documentation? □ Yes □ No If "yes", 
please attach a statement supporting this exemption. 

• is the project categorically exempt from the need for environmental documentation? □ Yes □ No If "yes" 

please attach a statement supporting this exemption. 

• Has a government agency other than the lead agency certified a "negative declaration on the project? Q Yes 
□ No If "yes", please attach a copy of the certified negative declaration. If "no", please provide sufficient 
information to allow agencies to make the necessary findings regarding all applicable policies. 

• Has a government agency other than the lead agency, certified an environmental impact document on the 

project? □ Yes □ No If "yes", please attach copies of the certification and the document also, please 
provide a summary of the document if it is longer than 10 pages. If "no", please provide sufficient information to 
allow agencies to make the necessary findings regarding all applicable policies, the certified document must be 
submitted prior to action on the permit_______ 


BOX 19 (CONTINUED) 

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Public Access Information 

- Does public access to the shoreline or views to the bay presently exist on the site of a property contiguous to 
the project? Q Yes Q No 

If "yes", please attach a description of the public access. If "no", explain what is preventing public access to 
the shoreline. 

• Will the project block public views of the bay or adversely impact present or future public access to the 
shoreline? Q Yes Q No 

Please describe why the project will or will not affect public views or public access to the shoreline. For most large 
projects identify: (1) the existing number of people or employees using the site; and (2) the existing number of 
cars bicycles, and pedestrians visiting the site and the level of setvice of all nearby roads leading to the site. Please 
describe how the project will change these factors. Please describe the impact the project is expected to have on 
the existing use of the site and on existing public views or physical public access at the site. Please describe the 
impact the project is expedted to have on the public's use of existing nearby parks, public access, public parking and 

other recreational areas on the shoreline and the roads leading to the site. 

■ Do public safety considerations or significant use conflicts make it infeasible to provide new public access to the 

shoreline on the project site? Q Yes Q No 

If "yes" please attach a description of the public safety considerations or significant use conflicts which make it 
infeasible to provide public access at the project site and either (1) identify an offsite area where public access to 
the shoreline is to be provided as part of the project and describe the proposed public access at a specified offsite 
location, or (2) provide an explanation as to why no offsite public access is proposed as part of the project. 

■ Summarize the public access to be provided as part of the total project: 

■ Total amount of public access _sq feet 

« Length of waterfront public access area -feet 

■ Number of parking spaces for pubiic access area - 

■ Area and width reserved for view corridor (s) -sq feet 

Detailed information about pubiic access to be provided in an attachment: Please describe, in square feet, leng 
and width, when appropriate, the existing and proposed public access areas and improvements, including areas used 
for decks, piers, pathways, sidewalks, landscaping, parking, and other public features. Please describe how the 
public access area facilities would be accessible to handicapped persons. Please describe the connections to existing 
public streets or offsite public pathways. Specify how the public access will be permanently guaranteed (e.g. 
dedication, deed restriction, etc.). --------—- 


Disclosure Of Campaign Contributions 

The following contributions of $250 or more were made by the applicant or applicants agent to a bcul 
commissioner or commissioner's alternate in the preceding twelve months to support the commissioners or 
alternate's campaign for election to a local, state or federal office. 

Contribution made to:___Contribution made by.---- 

Date of contribution: ______ 

□ No such contributions have been made_____ 


END OF FORM 


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Volume I, Appendix E 

Inter-Agency Working Group Meeting Notes 

(August 26,2010; October 20,2010; and July 21,2011) 


Santa Clara Valley Water District 

Stream Maintenance Program Update 2012-2022 

Final Subsequent Environmental Impact Report 


December 2011 
Project 10.005 





Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



Attachments: 

■ PowerPoint presentation from Aug. 26 IAWG meeting 

■ Current 2010 SMP BMP document 


1. Introductions 

- Mike Higgins, CCRWQCB 
Tami Schane, DFG 

- Bill Smith, SCVWD 

- Maggie Beth, SFRWQCB 
Luisa Valiela, EPA 

- Paula Gill, USACE 
Vincent Griego, USFWS 
Shree Dharasker, SCVWD 
Kristen O'Kane, SCVWD 

- Doug Padley, SCVWD 
Sunny Williams, SCVWD 
Devin Mody, SCVWD 
Ken Schwarz, Horizon 
Michael Stevenson, Horizon 
Cameron Johnson, USACE 
Darren Howe, NMFS (phone) 

2. Role of IAWG 

Ken: Introduced the role of the IAWG as shown in Slide 4 as a forum to discuss/guide 
the permitting process for the program renewal. 

Luisa: 

o Why no BCDC at meeting? 

■ Time frame is different, 5-yr permit extension was just conducted, their 
permit expires in 2015 

o Which agency people did you work with for Sonoma project? 

■ USACE: Jane Hicks, Pete Straub, Jim Mazza 

■ SF-RWQCB: Bill Hurley, Abigail Smith, Maggie Beth, Shin-Roei Lee 

■ North Coast RWQCB: Stephen Bargsten, Mark Nealy, John Short, Luis 
Rivera 

■ DFG: Richard Fitzgerald 

■ USFWS: Kim Squires, Ben Solvesky, Ryan Olah 

■ NMFS: Gary Stern, Josh Fuller 

o During original SMP development (1999-2001), the agencies met multiple times, 
including many times without SCVWD there, is that going to be the vision here? 



Horizon 


WATER anef ENVIRQNMENT 







Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



■ This is up to the agencies, and certainly possible if agency staff wish to 
meet additionally. Outcomes of such regulator-only meetings should be 
communicated back to the District. 

■ The vision, as this is a program renewal and not an entirely new 
program, is that fewer agency meetings will be necessary 


Paula: 

o We need one point of contact from the District, please decide who that is and 
let Paula know. 

■ The single point of contact will be Kristen O'Kane as the District's 
project manager. However, the agencies are also welcome to contact 
the consultants at Horizon or other District staff for data requests, 
questions, etc. Though for any formal communications things should be 
addressed to Kristen. 

3. Overview of Existing Program 

Ken provided an overview of the existing program, including the program area and 
watersheds (Slides 6-11), the project setting and typical/routine expected maintenance 
activities (Slides 12-17), sediment removal activities to date (Slides 18-21), vegetation 
management activities to date (Slides 22-23), bank repair and stabilization activities 
(Slides 24-26), and the annual work sequence (Slide 27). Key questions are summarized 
below. 

Mike Higgins - what is post-maintenance condition? This was discussed as illustrated in 
Slides 16 and 17 

Vincent - what are the water velocity/behavior differences between pre- and post¬ 
maintenance condition? 

o Ken: channel conditions are so site specific that we don't have a specific answer 
as to how velocities change with maintenance. The key question is to 
understand how much roughness (in the form of vegetation) and how much 
deposited sediment can the channel accommodate, before its flood conveyance 
capacity is diminished? The original engineering designs for these channels 
most likely assumed no vegetation (or limited vegetation) and very little 
sediment accumulation, that the channels would be maintained per the as-built 
design condition. 

o Ken: Also on velocity, the key variable for velocity will be channel slope, and 
this ranges throughout the program area. The District has conducted some 
hydraulic studies for channels to describe velocities, water surface elevations, 
etc. 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



Higgins: In CEQA analysis, will you be looking at impacts as a system? For example, 
more vegetation provides more shade, moderate temperature provides habitat value, 
promotes biodiversity. Do you consider the relationships between these various factors 
when choosing a design roughness? 

o Ken: Yes, while CEQA documents are typically divided according to disciplines, 
this program does relate to the flood channels and streams as an integrated 
system. We will try to maintain a systems approach in the EIR document. In 
addition to the systematic approach, it is also important to consider the varying 
scales and timeframes involved in the program. For example, for water quality, 
there might be some small-scale local impacts related to the maintenance 
activities. However, the lack of maintenance would increase the flood risk, and 
a bank overtopping flood would have severe water quality impacts to the 
channel/creek system. 

Mike: Can we use newer technologies and analysis tools that can refine our approach to 
the analysis? 

Luisa: On the issue of "new work" vs. "repeated work" as shown on Slide 20. Luisa 
provided some context from the original program development. That the regulators 
wanted to track repeat maintenance so that they could determine the frequency of 
maintenance in particular locations. Locations with high frequency of repeat 
maintenance might be good candidates for source control options to help reduce the 
need for frequently repeated maintenance. 

o Ken related this idea of source control opportunities to mitigation options - that 
seeking projects/sites that would help reduce sediment loading in downstream 
channels may be a very effective and appropriate mitigation approach. 

Ken discussed the herbicide application during 2002-2009 

o Question: was the 2002 Herbicide application number really that large? 

■ Bill Smith: probably so, but note that not the entire area of every linear 
foot was subject to application, so all of these numbers may be 
overstatements. Only a percentage of the work area is sprayed. 

o Mike Higgins: there are no herbicides shown applied in the Pajaro watershed - 
was that a permit condition? 

■ Yes, also arose from CEQA analysis 

Bank stabilization 

o Bill Smith: Appendix A (Bank Protection) includes designs with velocities and 
other design considerations - to help choose which treatments are appropriate 
in given circumstances. 

o "Bank protection mitigation only" category is for projects which are solely 
conducted to provide mitigation for other bank stabilization projects; included 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



on table for accounting purposes. This really isn't bank stabilization per se, and 
is more of a mitigation topic. 

o Locations of repeat failures may be indications of inappropriate design choices 
for the repair, or it could simply be illuminating a design issue with the channel 
(sharp bend in channel, step drop, or other conditions which may make the 
given location more erosive, etc.). 

4. Program BMPs 

Ken reviewed the original intention of the BMPs, to provide a flexible framework that 
could be updated/revised with program improvements. The challenge came when the 
BMPs were codified into the permits of 2002, and these permit terms/conditions 
became hard to adjust. 

Ken provided an overview of the 2002 BMP document. 

Attached is the current 2010 BMP table. 

On the topic of how to maintain flexibility into the BMPs 

o Mike Higgins: for RWQCB, monitoring programs (MRPs) can be updated and 
approved by Executive Officer more easily, without need for permit 
amendment. Perhaps BMPs can be part of that? 
o USACE and USFWS perspective - write the ability to modify the BMPs right into 
the permit, and thereby maintain the flexibility 
o DFG - interim permit (the DFG/District are currently working on) will accept the 
current BMP list that comes out of annual review process. Issues have arisen in 
the past where BMPs were tied into a variety of conditions in the permit which 
cannot all be changed, so they got hardwired in that manner. 

Bill Smith: Regarding the 2002 BMP list, some BMPs were actually project description or 
mitigation topics and therefore not appropriate for the BMP document. We want to 
now clean this up and have BMPs be operationally focused, with other non-operational 
or program items not being located here, but in a more appropriate location in the 
program manual or elsewhere. 

For example, BMPs 0.2 (minor maintenance work) and 3.19 (biodiversity monitoring 
program) from 2002 - really don't belong in the BMP document. On BMP 0.2 - Smith - 
described that the District wants to move away from acres because for such small areas, 
it is not very clear, and this has become a confusing work impediment. Luisa: why is it 
not clear? Smith: because sometimes the project area is bigger than the area of impact, 
and where just the project area is used, it overestimates the area of impact, etc. Also 
some things were not truly minor activities. In the current renewal process, some things 
will move to other parts of the program (that don't belong in minor maintenance). 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



Paula - how do we account for the jurisdiction of different agencies? E.g., 0.05 acres 
may be a different amount for USACE, RWQCB, DFG - who have different jurisdictions 
and mandates? 

Ken to send the group the 2010 BMP document for their review. Requesting comments 
from IAWG on the BMPs back over next few weeks (Due September 30 th ). 

5. Program Mitigation 

Ken provided an overview of the Mitigation Program to date, reviewing Slides 30-33. 

On the Laguna Seca project - issue with project is the ability of ground water (GW) to 
support the wetlands in light of GW extraction in the area. District is continuing to 
monitor GW levels to determine feasibility - GW levels are looking very encouraging, 
only 1 foot drop as opposed to the 10-15 feet which were predicted in the GW model. 

Smith: What do the agencies think about the Stream and Watershed Protection 
Program? It has been very difficult to implement. Should we continue with this 
program element? If so, could there be different acceptance criteria for potential 
properties, because many properties do not meet the current criteria? Also, most of the 
available land is in south county, but bulk of the maintenance work is in north county, so 
not easy to mitigate in the north. Also landowners are holding out because they see the 
HCP coming and think they can get higher prices. 

o Maggie: about revising the criteria. Is that something that can be changed now, 
or wait for the renewal? 

o Paula: please put the Districts thoughts/proposal regarding potential mitigation 
program revisions together in a comprehensive way and present it to the 
agencies for their review/comment. It is difficult to answer in a blanket way, 
the IAWG is willing to look at these things but not without a specific proposal. 
Ken described that such a "mitigation proposal" would come to the IAWG in the 
coming months, and we will discuss it at upcoming meetings. 

o Bill/Ken described that an alternative approach to acquisition would be more 
"service based" whereby mitigation is provided through providing 
services/activities, etc. but not necessarily through land acquisition. 

o Overall consensus was to tie up the old program mitigation and look fresh at the 
new work and work areas. 

Ken described the original/fundamental assumption to the mitigation program in 2002, 
that the programmatic mitigation provided through the existing program, provides 
mitigation for the work projected in the original program. Continued maintenance work 
in the streams and work areas included in the original projections need not be mitigated 
beyond the original commitments. However, for "new program areas" that were not 
included in the original projections, these lands will require additional mitigation. The 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 


Santa Clara Valley 


Water Distric 



Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


question now becomes what will be the best way to provide that mitigation? The IAWG 
confirmed the original intention of the program's mitigation approach so as to provide 
mitigation in perpetuity for the channels/creeks included in the original projections. 

Maggie: Does the District have a plan to satisfy the prior mitigation requirements that 
have not been met? 

o Smith: It is a complicated question. HCP is on its way, a lot of things up in the 


air. 


o Maggie: I would like to see something about this. 

o Luisa: Does the District plan to advance a proposal that the mitigation 
completed to date adequately addresses the work performed to date? 

■ Ken: that was me speaking, not the District, and was more of an 
observation than a proposal, that it appears that the mitigation 
provided to date does exceed the relative mitigation requirement based 
on how much maintenance work was conducted. We can revisit this 
issue within the framework of the mitigation proposal for the new work 


areas. 


o Cameron: on the topic of no net loss of functions and values to wetlands. There 
is no agreement or standard approach within Corps on how to 
quantify/measure the replacement mitigation for losses to wetlands. There are 
ways to do it. It may be easier for fluvial systems than wetlands, although fluvial 
system mitigation is more difficult to find. So, not to discourage the District 
from pursuing this approach, but there would need to be agreement on the 
methodology beforehand. 

■ Higgins: District/consultants should develop a robust methodology and 
propose it for RWQCB approval. You're the experts, not us. 

■ Ken: We could use CRAM or some other functional assessment tool. 

■ Ken: But, there may be excellent mitigation opportunities through 
funding of local projects (RCDs, etc.) that provide land stewardship, 
environmental enhancement/restoration. Such "watershed 
partnerships" were successfully used in Sonoma County to provide off¬ 
site mitigation. 

• Paula: before you spend a lot of time investing in that kind of 
watershed partnerships type mitigation, let's be sure that the 
regulatory agencies can buy off on it at the end of the day. That 
you don't go too far down that path without a clear path for 
approval. 

■ Cameron: From the Corps' perspective, taking an approach that has an 
objective measurement that no one can argue about would be best. 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



Best to avoid subjective interpretations of data. Not to discourage the 
District from doing good things, but measuring/crediting it is important. 

■ Tami: As an agency, DFG prefers an acquisition approach, so may be 
difficult for DFG to go down alternative paths. Ken - ok, but DFG did 
approve Sonoma County's mitigation approach which was not 
acquisition oriented, and used a combination of on-site, and funding of 
watershed projects to achieve mitigation for maintenance projects. 

6. Overview of 2010 Program Revisions 

Ken: reviewed the anticipated program revisions (Slides 34-35). 

Mike Higgins: the proposed changes to the Program from 2002 should be justified in 
detail. 

Luisa: Regarding Corps levees, since timeframe for these issues might exceed the 
permit renewal process, how do we handle that? 

o Smith: defer this to a subsequent/supplemental CEQA analysis 
o Stevenson: CEQA document cannot entirely defer analysis, but needs to make a 
good-faith effort at disclosing what we do know, while also acknowledging the 
uncertainties. 

Luisa: why no stream gages or arundo identified as program changes? 

o Smith: stream gages are wrapped into other aspects of program (sediment 
removal, vegetationmanagement). Didn't want to include as minor 
maintenance since the actual activities fall into other categories. To have it in 
minor maintenance raises problems because as minor maintenance, there is not 
clear guidance (e.g., how veg mgmt is to be performed). In other words, the 
District wants to be more upfront about the specific type of activity and 
categorize it as such. 

o Williams: no arundo because we're wanting to move in the direction of a more 
comprehensive invasive management program. Arundo removal will fall under 
the mitigation umbrella, not a change to program activities. 


7. Program Timeline 

Ken: Reviewed project timeline graph shown in Slide 36 

Vincent: Corps needs to reinitiate USFWS/NMFS consultations. Green sturgeon, EFH, 
CTS are now under consideration. We need the permit package and BAs to move 
forward. 

o Perhaps have a more focused meeting on species issues, 
o Tami: include DFG in CTS discussions. 

o Vincent: does CRLF critical habitat designation affect SMP? Padley: no. 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 1: Thursday, August 26, 2010 
Summary Meeting Notes 


Santa Clara Valley 
Water District 



8. Wrap Up 

Scheduling future meetings: Higgins only available T, W, Th. Should we bounce back 
and forth between San Jose and Oakland? IAWG members expressed interest in an 
Oakland meeting location. This isn't a problem, we can use Horizon's conference room. 

Teleconference, web conference as options. USFWS is in Sacramento. 

Email will get circulated to schedule the next meeting. October/November timeframe 
for next meeting. Meeting #3 in Feb/March timeframe. 

o Luisa: at least two meetings on each of the topics that Ken has identified would 
be better. A little concerned about spacing things out too much, keep the 
conversation fresh. Schedule 2 meetings at a time so we're doing well to look 
ahead. 

o Bring your calendars to future meetings for scheduling purposes. 

PowerPoint presentation will be provided as part of meeting notes. 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 2: Wednesday, October 20, 2010 

1330 Broadway, Oakland - 4 th Floor Conference Room 

Summary Meeting Notes 


Santa Clara Valley 
Water District 



Handouts: 

■ PowerPoint presentations from Oct. 20 IAWG meeting (attached) 

■ Current 2012 SMP BMP document (distributed at meeting) 

■ Current 2012 SMP Project Description (distributed at meeting) 


Attendees: 

Michael Stevenson, Horizon 

- Maggie Beth, SFB RWQCB 
John Rohrbough, CC RWQCB 
Sunny Williams, SCVWD 
Kristen O'Kane, SCVWD 

- Bill Smith, SCVWD 
Luisa Valiela, USEPA 

- Doug Padley, SCVWD 
Ginger Bolen, H.T. Harvey 
Steve Rottenborn, H.T. Harvey 

- Paula Gill, USACE 
Tami Schane, CDFG 
Ken Schwarz, Horizon 
Sandy Devoto, Horizon 

Devin Mody, SCVWD (conference call) 


1. Review Agenda and Introductions 

2. SMP Program Renewal 

Ken provided an overview of the existing program, including the program area, the 
project setting and typical/routine expected maintenance activities (Slides 3-5), and 
activities to date (Slides 6-9), examples of work activities (10-13), and work projections 
for 2012-2022 (Slide 14-15). 

Question regarding the intensity of sediment removal work in repeated areas. 

o Bill: In general, where repeat maintenance has occurred, it typically has 
happened 2-3 times at the repeated site, but it can vary greatly. Some sites 
have been visited up to 5 times, though this is rare. 

Ken reviewed a sequence of maps that summarized the 2002 work projections, 2002- 
2009 actual work conducted, and 2012 work projections for sediment removal and 
vegetation management. Map sequence included: 1) a description of where work was 



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WATER anef ENVIRONMENT 








Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 2: Wednesday, October 20, 2010 

1330 Broadway, Oakland - 4 th Floor Conference Room 

Summary Meeting Notes 


Santa Clara Valley 
Water District 



projected in 2002 and conducted; 2) where work was projected in 2002 and not 
conducted; and 3) where work was conducted in 2002 but not projected. The maps 
reviewed were draft and are currently under internal District review. 

3. Revised Program BMP Document 

Ken provided a walk-through of the revised BMP document (copies distributed at 
meeting). 

Luisa: is agency approval needed to extend work window? 

o No. For the five watersheds, as currently written there is a notification 
requirement (but not an approval). 

o Paula is concerned about the existing notification process, because they get 
buried in e-mails, and it is hard to keep all the messages straight. Paula asked if 
some sort of consolidated request was possible? 

o Team to revisit whether advance notification and/or approval is something that 
is important to notify in regard to the extended work window, or whether they 
can be notified after the fact in the PCR. Luisa mentioned that it is probably a 
topic that the IAWG will need to discuss independently. 

Luisa: on BMP VEG-8, will it be generic or plant-specific? 

o Bill/Ken: The non-native species plant removal issue will be integrated into a 
broader Invasive Species Management Program, and will not be a BMP. 

District will provide further guidance on how/when to comment on the BMPs. 


4. Species Discussion 

Steve Rottenborn provided an overview of special-status species in the Program Area 
(see second Powerpoint). 

Maps will be created to show where areas of projected work overlap with habitat areas. 

Team mentioned Vincent Griego's absence and lack of participation in this meeting. 

Paula pointed out that we will not get much attention from USFWS until a formal 
consultation begins. 

Tami: least bell's vireo had been sighted in Santa Clara County. 

o Steve confirmed that there had been one individual heard during one survey 
approximately 4 years ago, and had not been identified since. 

Essential Fish Habitat will be included. 

Process for consultation will be (1) submittal of draft BAs to Services on an informal 
basis, (2) update BAs based on their comments, and then (3) these revised versions will 
be used to initiate formal consultation. 



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Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 2: Wednesday, October 20, 2010 

1330 Broadway, Oakland - 4 th Floor Conference Room 

Summary Meeting Notes 


Santa Clara Valley 
Water District 



On schedule for the BAs, the sooner the better, although it is contingent on several 
factors such as BMP development, what the compensatory mitigation program will look 
like, etc. The EIR analysis, which is currently underway, will support preparation of the 
BA. 

5. Mitigation Program Status and Look Ahead 

Ken: reviewed the status of the current mitigation program (Slides 20-21). 

Tami: Stream and Watershed Protection mitigation - important to note that the 
acreage represents credits at a ratio of 10:1 or 15:1, so the actual acreage needed is 
much greater. 

Tami: erosion control as mitigation - would this address District sources of erosion, or 
other sources? 

o Ken: both 

o Tami: that has been identified as a goal for the HCP, but the District has 
strongly opposed addressing erosion sources outside of District's control. 

o Bill: as a clarification, District would not do work on other people's lands, rather 
provide funds for other entities to do this. 

o Kristen: the SMP program and District supervisor in charge of the SMP support 
this type of approach. 

o Sunny: District staff appreciate the comment and will be cognizant of this in 
other District meetings. 

Bill will be quantifying actual impacts of program to date to compare against mitigation 
requirements and mitigation completed to date. Will be ready within the next few 
months. 

Ken described that the District is developing a mitigation package for the 2012-2022 
program renewal process that seeks to provide mitigation for impacts associated with 
newly projected maintenance work. The mitigation program under development will 
likely have several components (a "basket of goods") that can provide different kinds of 
ecological and watershed functions. 

6. Next Steps 

Email will get circulated to schedule the next meeting. Feb/March timeframe for next 
meeting. 

Topics to be covered at next meeting: 



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WATER anef ENVIRONMENT 






Stream Maintenance Program 
Inter Agency Working Group (IAWG) 

Meeting 2: Wednesday, October 20, 2010 

1330 Broadway, Oakland - 4 th Floor Conference Room 

Summary Meeting Notes 


Santa Clara Valley 
Water District 



o Invasive Species Management approach (includes Arundo donax control 
program. Presented by Bill Smith) 

o Mitigation Accounting for 2002 SMP; and 

o Mitigation Proposal for 2012 SMP. 

PowerPoint presentation will be provided as part of meeting notes. 



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WATER anef ENVIRONMENT 




Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



1. Review Agenda and Introductions 

• Attendees: 

S Luisa Valiela, EPA 

v' Paula Gill and Ian Liftman, Corps 

S Maggie Beth and Shin-Roei Lee, SFRWQCB 

v' Jon Rohrbough, CC RWQCB (on phone) 

v' Greg Martinelli, DFG (on phone) 

v' Gary Stern, NMFS (on phone) 

v' Vincent Griego, USFWS (on phone) 

v' Kristen O'Kane, Sunny Williams, Bill Smith, Melissa Moore (on 
phone), SCVWD 
v' Ginger Bolen, HT Harvey 

v' Ken Schwarz, Michael Stevenson, Jill Sunahara, Horizon 

2. Overview of Project Status and Schedule 

• SMP Manual Update 2012-2022 - printed copies were distributed in 
meeting. The Manual will be included as an appendix to the EIR. 

• Draft EIR - Will be out for public review in August, copies will be sent to all 
IAWG partners. 

• Public oral comments on the Draft EIR will be received at the District Board 
Hearing on September 13 th at 9am. 

3. Review and Discuss the Updated Mitigation Approach 

• Memo Review Process - Responses to IAWG submitted comments received 
will be provided. Responses will be provided for each direct comment 
received, and a revised version of the Mitigation Approach memo will be 
developed and distributed. 

• Foundational issue - the SMP is an on-going program with an existing 
mitigation in place and operational. 

i. The remaining 2002-2012 mitigation requirements and District's 
commitment to complete them will be addressed in a forthcoming 
letter from the District. 


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Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



ii. The District can provide additional data on the status of mitigation 
projects conducted to date. This information has been included in 
the annual SMP Post Construction Reports (PCRs) that are sent to 
regulatory partners. 

• Comment from Paula: the proposal to apply tidal mitigation credits to offset 
future 2012-2022 impacts must be evaluated on a case by case basis. 

• Paula: The Corps will need a supplemental or sub-document that addresses 
only mitigation activities within Corps' jurisdiction to regulate. 

• Luisa: Projected areas, how were these created? How were reaches 
identified for mitigation and maintenance work, how specific are the 
projections? 

i. Michael/Bill/Sunny/Ginger - projections are just a tool to refine 
mitigation numbers (CRLF habitat for example), but program covers 
the whole county (below 1,000 ft) and work can occur anywhere. 

• Paula: We need a clearer procedure for reporting/approval of maintenance 
locations. What happens if work were to occur outside of projected areas? 
How would agencies be notified of that? District needs to develop a 
procedure for reporting, review/approval, and monitoring for any work areas 
outside of the projected maintenance reaches. 

i. Ken/MMS - work tracking will be covered during the annual 
notification process. Example tracking table showing projected, work 
to date, proposed, and total work. If something were to come up 
outside of the projected area it would be included in the notice of 
proposed work. The CEQA and environmental analysis for the BA 
development included a far range of environments within the 
program area, and would most likely cover any project that would 
occur in a "non projected" area. That said, if such an area were to 
arise whereby the base environmental documentation (EIR, BAs, etc.) 
were not adequate, than additional environmental assessment would 
be necessary to ensure that the maintenance reach is consistent with 
the potential impacts as described in the program documents. 

ii. Paula - make sure all activities projected and not projected are 
tracked to ensure consistency with Programmatic coverage. Please 


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Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



develop an accounting system and procedure for tracking work areas 
within and outside of projected work areas. We'll need annual and 
cumulative accounting. 

iii. Luisa - Projected areas vs. projected impacts - what is the difference? 

iv. Paula - concerned about species protection in areas not projected or 
covered by BOs, which are based on projections. 

1. Hope to establish within BOs and DFG "take" approvals 

2. Ken: walked through a tracking example of how work in a new 
work area (not projected) would be tracked. 

3. Paula: We would need to know what resources/species are in 
the new proposed area? Ken/Michael - similar to above, 
team would evaluate new work area (non-projected) to 
ensure it is consistent with information provided in BA, some 
sort of consistent assessment/evaluation of potential effects. 
Basic habitat description. If there are issues, or it is 
inconsistent with existing environmental documentation - 
then the permit coverage would not apply, until it is shown 
that the work site is consistent with the program. If work site 
is consistent with the program, then coverage can be 
approved under the RGP. Recognize that Corps will need 
extra time for review of non-projected work. If we get a 
standard procedure in place, it will expedite review process if 
and when it happens. There should be agency-wide approval 
of standard procedure for considering such work sites 
(NMFS/FWS/RB/DFG). 

4. Shin-Roei: Sonoma Permit example. Regional Board 
established a process to evaluate individual projects one by 
one if necessary. 

• Shin-Roei: Yellow projected areas. What about frequency of maintenance 
projected within existing areas? If maintenance may occur more often in 
existing areas, there will be more impact. 

i. Bill presented a table with the work frequency information 
summarized by reach. 


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Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



ii. Shin-Roei: most work areas are maintained less than originally 
projected. But what is occurring within the areas that are most 
frequently maintained? Are there recurring issues that could be 
addressed through other means? 

iii. Kristen - Asset Management Program will answer those questions. 

iv. Ken - Regional Board applications include discussion of Maintenance 
Guidelines, Asset Management, Geomorph Programs. Addresses 
frequency and causes of maintenance. 

v. Maintenance Guidelines Memo will be distributed to IAWG 
members for their reference. 

• Section 5 

i. Luisa - what is the mitigation prioritization process? Is there a 
hierarchy in selecting which components of the mitigation program 
are implemented? How do each of the components compare to 
benefits? 

ii. Luisa - Is riparian planting a mitigation component? Isn't this a 
standard component of maintenance work? 

iii. Ken - Riparian planting is a mitigation component, and not a 
standard requirement of maintenance work. Of the various 
mitigation options, first priority would to applying on-site mitigation 
directly where maintenance occurred. Ideally, mitigation activities 
(per the memo) would be applied in-kind toward the maintenance 
work sites. If there is not an opportunity to provide such mitigation 
on-site, then off-site opportunities would be evaluated. 

iv. Melissa - described an example of an urban site. Complex and lots of 
variables to consider. 

v. Greg - need to define a process for selection and application of 
mitigation 

vi. Luisa - can a procedure be written up for urban/degraded and higher 
quality streams? 


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Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 



Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 

/ith i-1_~ r_r, 


0 


4 Floor Conference Room 


1. Melissa - no, it's difficult because there are critters even in 
degraded areas. Maybe we can define for "improved" and 
"natural" channels. 

vii. Luisa - Each component in the basket are apples and oranges, so 
application protocols should be defined for each with a decision 
tree. Plus cumulative tracking. 

• 5 year mitigation coverage for repeat maintenance 

x. L. 

i. Herbicides, mitigation required every 5 time 

ii. Sediment, mitigation required every year 

iii. Veg maintenance, ok to return to site to fine tune within 5 yrs w/o 
having to re-mitigate. Mainly for veg maintenance activities. 

iv. Luisa- why does the District need this? 

v. Shin-Roei - why not permanent? 

1. Bill, if frequent enough, then District will mitigate under the 
perpetuity program 

vi. Land acquisition to provide permanent mitigation 

1. Shin-Roei: acquisition must provide some environmental lift, 
not just set aside land. Present a package to restore/enhance 
the parcel too. Address the state's "no net loss" policy 

2. Ken - described in Section 5.1 

3. Ginger - acquisition is only applicable for permanent impacts 
(hardscape for bank stabilization projects). Most other 
maintenance results in temporary impacts. 

vii. Greg - Definition of "perpetuity" 

1. Same as for the existing program, meaning for the life of the 
maintenance program. 

2. Not conservation easements, except on case by case basis 

• Section 6 Species-Specific Mitigation 

i. Gravel Augmentation (described by Melissa) 


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Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



1. Luisa: Projects will be coordinated county-wide/watershed 
wide 

2. Gary: Objective of the program is that the d50 sediment size 
should become coarser. Location, depth, velocity aren't 
necessary criteria. Focus on the removal of fine sediment to 
benefit spawning gravel quality. District conduct d50 analysis, 
and count credit for sed removal of fines. Keep it simple. 

• Bank Stabilization 

i. Shin-Roei: No need to set a maximum on program-wide hardscape at 
50%. Just use site by site approach and always prioritize soft-scape. 

ii. Ken/Bill: Will delete hardscape cap. 

iii. Paula: Yes, but we need to continue to track and report what type of 
bank stabilization projects occur. 

• Mitigation Reporting 

i. Annual accounting of impacts 

ii. Annual accounting of mitigation 

iii. Shin-Roei: additional requirement for completion of Wetland Tracker 
Form, one submittal per year. Document total losses and gains over 
course of program 

• Mitigation Credit for Capital Projects in SMP sites, language described in SMP 
Manual is misleading 

i. Lower Berryessa and other projects 

ii. Paula: problematic for Corps. Mitigation for different activities 
(stream maintenance vs. CIP) 

iii. Bill/Ken: Not the intent. Will clarify language in Manual. Separate and 
add discussion in Mit Memo too. Mitigation is to cover maintenance 
work, not construction activities (Page 4) 


4. Review and Discuss Next Steps for Program Permit Renewals 


6 



Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



• Public Draft ElR will include today's version of the Mitigation Memo. 

• We will revise and respond to the agency comments, and provide the revised 
Mitigation Memo separately, after the Draft EIR (perhaps with the final EIR?) 

• Summary of Key recommendations from today's meeting 

i. Develop protocol for the identification, agency review and application 
of maintenance activities that occur outside of projected work areas. 

ii. Develop protocol to describe the prioritization and selection of 
mitigation activities (for annual pay as you go type mitigation 
projects) 

iii. Need to carefully track mitigation annually and cumulatively, and 
keep regulators updated through annual reporting process. 

iv. District needs to provide IAWG with a letter or memo describing the 
commitment to comply with original program mitigation 
requirements, and also (if possible) describe what planned mitigation 
activities may be implemented to achieve any outstanding 
requirements. 

v. Clarify language in maintenance manual that mitigation is applied for 
maintenance activities, not CIPs who will need their own mitigation. 

• IAWG members to provide any additional comments by next Friday (7/29) 

• Next Steps 

i. Individual agency discussions 

1. Corps, separate mitigation memo to address Corps-specific 
issues 

2. Regional Board, use of the District Maintenance Guidelines 

3. NMFS/FWS, review of Biological Assessments 

4. DFG - will have follow up mtg with Tami in person to review 
mitigation topic and also DFG permitting 

ii. Potential to have another collective meeting (if considered necessary) 
to review/discuss mitigation activities further 


7 



Santa Clara Valley Water District 
Stream Maintenance Program Renewal 

IAWG Meeting #3 

Meeting Agenda 

Thursday, July 21, 2011, 1:00pm- 3:30pm 
1330 Broadway, Oakland 
4 th Floor Conference Room 


Santo Clara Valley 
Water District 



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