Owing to the heterogenous distribution of contaminated sediments in urban estuaries, contaminant residues, such as polychlorinated biphenyls (PCBs), in fish tissue can vary widely. To investigate the relationship between PCBs in fish tissue and heterogeneity of PCBs in sediment, we developed a geospatial Biota-Sediment Accumulation Factor (BSAF) model for an urban estuary. The model predicts whole fish total PCB residues at a scale of 0.1 km2 by incorporating sediment chemistry, fish home range, and habitat type. The model predicted concentrations from across the estuary ranging from 0 to 161,456 ng/g lipid. An estuary-wide (50+ km2) and a project-scale (1+ km2) field validation of the model demonstrated it produced values that were slightly skewed to low concentrations; performance improved with increased sediment data spatial coverage. We conclude this approach has potential for determining PCBs "hot spot," estimating remediation project footprints, and evaluating potential remediation improvements to the quality of a fishery.