Polybrominated diphenyl ethers (PBDEs) were extensively investigated in water, sediment, and biota samples collected from Chaohu Lake basin in China. The total concentrations of eight PBDEs (Σ8PBDEs) were in the ranges of 0.11–4.48 ng/L, 0.06–5.41 ng/g, and 0.02–1.50 ng/g dry weight (dw) in the water, sediment, and biota samples, respectively. The concentrations showed wide variations in the monitoring area, while the congener profiles in all the water, sediment, and biota samples were generally characterized by only a few compounds, such as BDE-47, BDE-99, and/or BDE-209. The spatial analysis depicted a decreasing trend of PBDEs from west to east Chaohu Lake, consistent with regional industrialization degree. The distributions of PBDE congeners in the biota samples were similar to the compositional profiles in the water, which were dominated by BDE-47 and/or BDE-99. Nevertheless, BDE-47 and BDE-153 in the brain tissue showed a higher accumulative potential than PBDEs in other tissues as well as the whole body, with 96% relative contribution of Σ8PBDEs. The noncarcinogenic risk values estimated for BDE-47, BDE-99, and BDE-153 indicated that the specific risk associated with the studied water and foodstuffs is limited. However, there is a potential mixture ecotoxicity at three trophic levels at some sampling points in the water, which should draw considerable attention.