Space and Naval Warfare Systems Center Pacific (SSC Pacific) performed the studies described in this report to develop a new National Pollutant Discharge Elimination Systems (NPDES) Permit for the discharge of effluents from the Apra Harbor Wastewater Treatment Plant (WWTP) in Agat, Guam, into Tipalao Bay of the Philippine Sea. The technical approach adhered to proposed U.S. Environmental Protection Agency (USEPA) guidelines to develop and apply mixing zone analysis, recalculation procedure, water effect ratio (WER), and translator. Naval Facilities Engineering Command (NAVFAC) Marianas recognized the requirements and conditions within the National Pollutant Discharge Elimination System Permit No. GU0110019 and initiated a study to develop site-specific discharge limitations using appropriate methods and guidance documents from the USEPA. This study incorporates the results from multiple lines of evidence to examine copper, nickel, and aluminum criteria applied in the permit. The objective is to establish new regulatory discharge limits based on the current state of the science, including the use and application of a mixing zone analysis, a recalculation procedure, a chemical translator study, a WER procedure, and the Biotic Ligand Model. Based on the data generated from these studies, we recommend new NPDES discharge limits for copper and nickel as outlined below, while a separate rationale exists to justify the removal of aluminum from further regulatory limits.