In this contribution, we apply data from an ocean observing and modeling system to examine boundary influences driving phytoplankton ecology in Monterey Bay, CA, USA. The study was focused on species that may cause harmful algal blooms (HABs). During September - October 2010, autonomous molecular analytical devices were moored at two locations characterized by different degrees of stratification and exposure to upwelling dynamics. The time-series revealed multiple transitions in local HAB phytoplankton communities, involving diatoms [Pseudo-nitzschia spp.}, dinoflagellates [Alexandrium catenella), and raphidophytes [Heterosigma akashiwo). Observational and model results showed that the biological transitions were closely related to environmental changes that resulted from a variety of boundary processes - responses of oceanic circulation to wind forcing, influxes of different water types that originated outside of the bay, and emergence of strongly stratified nearshore waters into the greater bay.