Polybrominated diphenyl ethers (PBDEs) were found in water, surface sediments, and bivalve samples that were collected from the San Francisco Estuary in 2002. sigmaPBDE concentrations in water samples ranged from 3 to 513 pg/ L, with the highest concentrations found in the Lower South Bay (range 103-513 pg/L) region, which receives approximately 26% of the Estuary's wastewater treatment plant effluents. The sigmaPBDEs in sediments ranged from below detection limits to 212 ng/g dry wt, with the highest concentration found at a South Bay station (212 ng/g dry wt), which was up to 3 orders of magnitude higher than other stations. The sigmaPBDE concentrations ranged from 9 to 64 ng/g dry wt in oysters (Crassostrea gigas), from 13 to 47 ng/g dry wt in mussels (Mytilus californianus), and from 85 to 106 ng/g dry wt in clams (Corbicula fluminea). Only three PBDE congeners were detected in bivalves, BDE-47, BDE-99, and BOE-100; these are the most bioaccumulative congeners from the commercial Penta-BDE mixture.