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The San Francisco Bay (California, USA) is a water body listed as impaired because of Hg contamination in sport fish for human consumption, as well as possible effects on resident wildlife. A legacy of Hg mining in local watersheds and Hg used in Au mining in the Sierra Nevada (USA) has contributed to contamination seen in the bay, with additional more recent and ongoing inputs from various sources. Methylmercury is the species of Hg most directly responsible for contamination in biota, so better understanding of its sources, loads, and processes was sought to identify the best means to reduce impacts. A regional scale model of San Francisco Bay was developed to characterize major methylmercury inputs and processes. The model was used to evaluate the potential impact of uncertainties in estimates for methylmercury loading pathways and environmental processes, identify major data gaps, and explore management prospects for reducing methylmercury contamination. External loading pathways considered in the mass balance include methylmercury loads entering via atmospheric deposition to the bay surface, and discharges from the Sacramento/San Joaquin Delta, local watersheds, municipal wastewater, and fringing wetlands. Internal processes considered include exchange between bed and suspended sediments and the water column, in situ production and demethylation, biological uptake, and losses via hydrologic transport to the ocean through the Golden Gate. In situ sediment methylation and demethylation were dominant sources and losses determining ambient steady-state concentrations in the model, with changes in external loads and export causing smaller changes. Better information on methylation and demethylation is thus most critical to improving understanding of methylmercury balances and management. Environ. Toxicol. Chem. 2011;30:88-96. © 2010 SETAC [ABSTRACT FROM AUTHOR]