East Dongting Lake and Hong Lake are two typical lakes in the middle watershed of the Yangtze River, China. The differences in the hydrological condition and human activities of the region may result in the differences in concentrations, distribution, and sources of contaminants. The levels, sources, distribution, and ecological risk of OHCs, including 15 OCPs, 7 PCBs, and 7 PBDEs in surface sediments and water from this region, were investigated. OCPs and PCBs were the predominant pollutants in water and sediments samples, respectively. Source analysis showed that HCHs, PBDEs, and PCBs were mainly from the historical input of commercial products, but there were recent discharges of DDT into the water. The spatial distribution of OHCs showed that higher levels of OHCs in sediments and water were found in the sampling sites far away from the estuary of Hong Lake, but such obvious distribution characteristic was not found in East Dongting Lake. TOC played a crucial role in the retention of OCPs in the sediments of Hong Lake, but significant correlation between TOC and OCPs for East Dongting Lake, TOC and PCBs or PBDEs for both lakes were not found. The possible adverse biological effects could be caused by OCPs residues in sediments of both lakes, and it was worse for Hong Lake. The noncarcinogenic and carcinogenic risk assessment of HCHs and DDTs indicated the water quality of both lakes was safe for bathing and drinking. The potential ecotoxicological risks of PBDEs and PCBs of both lakes were rather low.