Sediments from Niagara River, an important waterway connecting two of the Great Lakes (Lake Erie to Lake Ontario), were analyzed for 14 congeners of polychlorinated biphenyls (PCBs) and 9 congeners of polybrominated diphenyl ethers (PBDEs) using accelerated solvent extraction and gas chromatography/mass spectrometry. Total concentrations of PCBs ranged from 1.7 to 124.6 ng/g were PCBs 138 and 153 were found in all samples. All sites but one showed PBDE in sediments with total concentrations as high as 148 ng/g, suggesting that PBDE is becoming an important class of POP. A land-use and coverage map was used to trace potential localized sources of PCB and PBDE contamination. Results indicate that the highest levels of PCBs and PBDEs were found in sediments collected from areas closest to the discharge locations of municipal wastewater treatment plants (WWTP) and local industries. This is the first study that suggests the importance of WWTP discharges as a potential source of PBDE contamination in the Great Lakes.