Polychlorinated diphenyl ethers (PCDEs) are a group of halogenated aromatic compounds and serious environmental pollutants. In the present study, sediment and water samples from eight sites in Nanjing section of the Yangtze River were characterized with 15 congeners of PCDEs. Concentrations and distributions of these PCDEs in water phase and sediments were analyzed by GC/MS. Results demonstrated that ∑PCDE concentrations were higher in the low water period (1.15-1.80 μg/L) than those in the high water period (0.73-1.30 μg/L) in water phase. Moreover, ∑PCDE concentrations were higher in the low water period (1.58-3.98 μg/kg) than those in the high water period (1.24-3.48 μg/kg) in sediments. A significant linear relationship existed between the ∑PCDE concentrations and TOC contents in sediments, but a poor linearity was found between ∑PCDE concentrations and DOC contents in water phase. Furthermore, the comparison of the percentage compositions in sediments and in water phase showed that CDE-30 (2,4,6-tri-CDE) was the predominant congener in the studied sites, and higher chlorinated congeners accounted for a larger proportion in sediments than those in water phase. In conclusion, the present study demonstrated the prevalent contamination by PCDEs in sediments and water from the Nanjing section of the Yangtze River.