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The Marin Municipal Water District (MMWD) conducted an 11-month Seawater Desalination Pilot Program (Program) of advanced pretreatment and SWRO technologies for desalting estuarial water from San Francisco Bay during the period from June 2005 to May 2006 with the objective of developing preliminary design criteria and costing for a full-scale desalination facility and to demonstrate that seawater desalination could produce a finished water quality comparable to or better than Marin's current, conventionally treated surface water supply. The program comprised two independently operated treatment trains to enable concurrent testing of the alternative pretreatment technologies and associated SWRO units. Each SWRO unit consisted of three subtrains, each containing six elements utilizing different high rejection RO membrane types. One SWRO unit was fed with combined filtrate from submerged MF and submerged UF units. The second SWRO unit was fed with effluent from a two-stage granular media filter system preceded by ferric coagulation, flocculation and sedimentation. In addition to normal monitoring of SWRO performance during operation, a post-operation autopsy of selected RO elements can be a useful tool in investigating the cause(s) of performance declines. The information from the autopsy analysis can assist in determining mass of foulant deposited, and to identify the nature of the foulant with respect to how much is inorganic versus organic, and to what extent the organic fouling is microbially derived. Following completion of pilot plant testing, selected elements from one manufacturer's array were autopsied by: the element manufacturer using industry-typical methods including element wet test for water flow and salt rejection determination, internal visual inspection, dye/Fujiwara test for oxidant uptake, inductively coupled plasma emission spectroscopy (ICP) for metals, and loss on ignition (LOI) for inorganic versus organic content; and, by more specialized analysis by the Orange County Water District (OCWD) focusing on microbial fouling including high resolution visual microscopy, visual color enhancement of foulant distribution, ATR/FTIR spectroscopy, protein and carbohydrate content analysis, and total bacterial count. These analyses indicate that the SWRO elements operated on conventional treatment effluent exhibited greater particulate, inorganic and organic fouling than those receiving MF/UF filtrate despite generally comparable levels of filtrate turbidity and SDI. However, the latter elements had greater microbial levels with a more monoculture-like appearance, suggesting differences in the pretreated feed chemistry due to the use or non-use of coagulation affected microbial community structure. This paper describes the autopsy results and how the results help to explain differences in SWRO performance and fouling based on different pretreatment as well as provide insight into operational strategies for minimizing fouling in a full-scale facility. Includes reference, tables, figures.