A mass budget of polybrominated diphenyl ethers (PBDEs) in San Francisco Bay is developed as a first step towards understanding the local sources and transport processes controlling PBDE fate in a highly urbanized estuary. Extensive monitoring of PBDEs in estuarine water and sediment, freshwater tributaries, air, and wastewater effluents and sludges were integrated with a mass budget model to provide a synthetic view of these emerging contaminants. The Bay inventories of BDE 47 and BDE 209 in 2006 were estimated to be 33+/-3 kg and 153+/-45 kg, respectively. Empirically derived estimates of annual inputs of BDE 47 and BDE 209 from all quantifiable external sources ranged from 11 to 28 kg/y and 22 to 24 kg/y, respectively. BDE 47 loads were dominated by wastewater while runoff from local tributaries represented the largest contributor to BDE 209 loads. Model results suggest the Bay PBDE inventory is highly sensitive to changes in external loads, with degradation and outflow being the major processes governing PBDE fate. The mass budget presented provides a framework for integrating future monitoring and modeling efforts.