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The Marin Municipal Water District (MMWD) Seawater Desalination Pilot Program was a successful year-long desalination pilot study of advanced pretreatment and seawater reverse osmosis (SWRO) technologies for desalting water from San Francisco Bay (Bay) from June 2005 to May 2006. Based on the favorable outcome of the pilot program, seawater desalination can be a local, reliable drought-proof source of drinking water supply for Marin, California. The MMWD Seawater Desalination Pilot Program included: determining that microfiltration (MF)/ultrafiltration (UF) is the recommended pretreatment for North San Francisco Bay water; developing preliminary design criteria and conceptual costs for a full scale desalination facility; demonstrating that the desalinated water is safe and meets all state and federal requirements; and, demonstrating that the brine discharge blended with CMSA effluent will not adversely impact the San Francisco Bay environment. The primary objective of the pilot testing program was to compare the performance of high rejection SWRO membranes with two different pretreatment alternatives, MF/UF and conventional pretreatment. This objective was accomplished through the concurrent operation of two parallel SWRO pilot units of identical design, with Unit 1 treating MF/UF filtrate and Unit 2 treating conventional filtrate. The source water for the MMWD SWRO pilot plant, the North San Francisco Bay, is a complex estuarine water body with influences from the ocean, rivers, and bay discharges that affect water quality on a daily as well as seasonal basis. Total dissolved solids (TDS) varied from approximately 25,000 mg/l in the summer to less than 5,000 mg/l in the winter. While both the conventional and MF/UF pretreatment produced suitable quality RO feedwater, MF/UF filtrate was lower in SDI and less impacted by source water variations. Four different high rejection SWRO membranes were tested. All membranes provided satisfactory performance, although differences were observed between element types in both trains. No significant differences were observed in RO performance between the two trains based on changes in normalized permeate flow or salt passage. However, based on normalized differential pressure and autopsy results, elements operated with conventional pretreatment exhibited greater overall particulate, organic, protein and carbohydrate fouling than those with MF/UF filtrate. The pilot program also included analytical testing of over 100 regulated and 500 non-regulated constituents in the Bay water and RO permeate, as well as an evaluation of second pass RO to meet MMWD's stringent finished water boron and sodium requirements. Environmental studies conducted in conjunction with the pilot testing included fish entrainment studies, bioassay studies and California Toxics Rule analysis of the brine discharge and toxicity analysis of the residuals from the pretreatment systems. Includes tables, figures.