Although the production of polybrominated diphenyl ethers (PBDEs) has been phased out over the past decade worldwide, they are still potentially hazardous to the environment due to their persistence and toxicity. This study investigated the levels of 55 PBDEs in water and sediments from the Danjiangkou Reservoir, China. The levels of PBDEs were in the range of not detected (ND)-286.67ng/L in water and ND-236.04ng/g in sediments. BDE209 was the predominant PBDE congener and constituted 15-50% and 44-68% of the total PBDEs in water and sediments, respectively. Commercial pentaBDE products (70-5DE, DE-71) were the dominant source of tetraBDE, pentaBDE, and hexaBDE, while commercial octaBDE (79-8DE) and decaBDE (102E and 82-0DE) products were the main sources of nonaBDE and decaBDE in water. PBDEs in sediments mainly stemmed from commercial decaBDE products and combustion sources. BDE-209 posed high ecological risks to aquatic organisms and dominated the total ecological risks of PBDEs. No cancer risks and non-cancer risks were observed for PBDEs. A ranking method based on four criteria, i.e., detection frequency, concentration, ecological risk, and health risks, was proposed, and 17 PBDEs were identified as high priority PBDEs for future monitoring and management in the Danjiangkou Reservoir.