Fourteen and 17 sediment samples were collected from three main rivers of Shanghai in July and November, respectively. Eight polybrominated diphenyl ether (PBDE) congeners (BDE-28, BDE-47, BDE-99, BDE-100, BDE-153, BDE-154, BDE-183, and BDE-209) were detected in these samples to clarify the pollution status in the metropolis. Instrumental analyses showed that the concentrations of ∑8PBDEs ranged from 10.97 to 64.05 ng/g dry weight (dw), with an average value of 29.71 ng/g dw. BDE-209 was the predominant congener accounting for more than 97% of total PBDEs, followed by BDE-47 and BDE-99. Remarkable spatial and seasonal distributions of PBDE concentrations were observed, suggesting that local sources, seasonal climates, and hydrologic conditions might be the influencing factors. Moderate correlations (r (2) = 0.28-0.51, p < 0.05) were found between total organic carbon and PBDEs, which indicated that organic carbon content influenced the distributions of PBDEs in sediment of Shanghai at some extent. Hazard quotients revealed PBDEs posed no potential risk to benthic organisms in the study area at present.