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Sediment plays an important role in controlling biogeochemical cycling of heavy metals in aquatic environment. The Ya-Er Lake is a typical lake which was historically contaminated by heavy metals in Hubei province, China. After industries surrounding the Ya-Er Lake being shut down, oxidation pond treatment and dredging program were conducted for pollution management since 1970s. To date, the Ya-Er Lake has been used for aquaculture for several decades. However, the status of heavy metal levels and ecological risks in this lake remains unclear. Herein, concentrations, chemical fractions, and risk assessment of heavy metals were investigated in the Ya-Er Lake sediment. Results showed that concentrations of heavy metals in the Ya-Er Lake sediment were higher than other reported lake systems, suggesting that heavy metal pollution in the Ya-Er Lake is still serious. Relatively higher proportions of carbonates bound form of Cd and Ni indicated high-risk potential of these two heavy metals, and Cd and Ni should be listed as the primary heavy metal pollutants in the Ya-Er Lake according to the results of potential ecological risk index (PERI) and sediment quality guidelines (SQGs). The risk assessment code (RAC) analysis showed that Ni and Cd poses higher bioavailability and mitigation potential, and may affect the Ya-Er Lake ecosystem and downstream aquatic environment. These findings reflected that oxidation pond treatment and dredging sediment to near place are not effective to control heavy metal pollution, and a long-term ecological risk is still posed to surrounding aquatic environment. Our study provides scientific basis on pollution control and management in aquatic system contaminated by heavy metals. [ABSTRACT FROM AUTHOR]