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We document the development and application of a food web bioaccumulation model for polychlorinated biphenyls (PCBs) in San Francisco Bay, California, USA. The model calculates spatial distributions of PCB concentrations in a range of invertebrate, fish, avian, and mammalian organisms, including harbor seals, double-crested cormorants, and Forster's terns. The performance of the model is evaluated against independent empirical PCB concentrations and shows a mean deviation between observed and model-calculated concentrations of 36% for female harbor seals and 5% for benthic invertebrates and jack smelt. The model was applied to produce bay-wide PCB concentration distributions in fish and wildlife species, which were compared with threshold effect concentrations to determine ecological risks and human health risks of fish consumption. Because of their high trophic position in the food web, harbor seals exhibited the highest concentrations of ∑PCBs, which exceeded threshold concentrations for potential adverse effects. The model was also applied to derive bay-wide target sediment concentrations for remediation as part of an ongoing total maximum daily loading characterization. The model calculated bay-wide geometric mean concentrations of ∑PCB in sediments of 1.6 to 73 µg/kg dry weight to meet several ecological and human health risk objectives. The bay-wide geometric ∑PCB concentration in the sediments at the time of the study was 11.6 µg/kg dry weight. The model was developed for assessing the behavior and risks of bioaccumulative substances on an ecosystem level. Environ. Toxicol. Chem. 2010;29:1385–1395. © 2010 SETAC [ABSTRACT FROM AUTHOR]