Distributions, potential sources and ecotoxicological risks of PCBs and PBDEs in surface water of the Three Gorges Dam (TGD) region (Yangtze River, China) were investigated. Samples were collected from 18 sites from upstream (UTGD) and downstream (DTGD) of the TGD. Thirty-two PCBs and ten PBDEs were analyzed. RPCBs from the UTGD and DTGD ranged from 10.6 to 26.1 and 1.7 to 29.8 ng L-1, respectively. RPBDEs from the UTGD and DTGD ranged from 2.0 to 17.6 and 0.8 to 11.1 ng L-1, respectively. The total concentrations of PCBs and PBDEs showed a declining trend from the UTGD to DTGD. Independent-samples t test analysis showed no statistical significance of RPCBs and RPBDEs between the UTGD and DTGD samples. Principal component analysis indicated the difference of potential sources and levels of PCBs and PBDEs in the study area. The potential eco-toxicological risk of PCBs in surface water of the TGD region is very low, whereas special attention needs to be paid to PBDEs in the study area.