Polybrominated diphenyl ether (PBDE) concentrations in sediment and fish from 12 principal rivers in Taiwan were investigated to determine their association with water quality parameters as well as the biota-sediment accumulation factor (BSAF) in fish with different living patterns. The highest PBDE concentration in sediment was found in the Bajhang River (261 ng g?1 dry weight (d.w.)) and the lowest in the Beinan River and the Da-an River (0.17 ng g?1 d.w.). The PBDE concentrations in fish samples ranged from 1.28 ng g?1 d.w. (Oreochromis niloticus niloticus) in the Yanshuei River to 33.7 ng g?1 d.w. (Varico rhinos barbatulus) in the Da-an River. We conclude that PBDEs contamination in sediment was significantly affected by NH3–N, pH, and DO. The BSAF results showed a parabolic trend from low- to high-brominated BDEs. Fish easily accumulated the congeners BDE-47, -100, -119, -126, and -154 from sediment. The BSAF decreased in the following order: PeBDE > HxBDE > TeBDE > other BDEs. Principle component analysis showed that demersal fish have different PBDE sources than do pelagic fish. We conclude that living and feeding habits are critical factors affecting PBDE accumulation in fish.