Bioavailability-based probabilistic risk assessment is an effective approach for risk characterization of trace metals towards aquatic species. However, it has not been routinely applied in lake management due to limited research. In this study, Chaohu Lake (Anhui Province, China) was selected as a case study, and total and bioavailable concentrations of trace metals in surface sediment were investigated using chemical extraction and diffusive gradients in thin films (DGT). Probabilistic risk assessment (PRA) was performed using Monte Carlo simulation. In addition, the species sensitivity distribution (SSD) was constructed using acute toxicity data to model the sensitivity of aquatic species towards metals. Three evaluation methods, namely, toxic units based on total content, modified potential ecological risk index (RI) based on chemical fractionation and DGT-SSD coupled PRA, were implemented and compared. Results showed that trace metals, especially Cd, were significantly affected by anthropogenic activities. Chemical fractionation analysis revealed that the majority of Cd was readily available to aquatic organisms, while Cr was stable under normal conditions. Toxic units based on the total content demonstrated that metals in sediment were at 91.6 % low and 8.4 % medium toxicity levels, while the modified RI based on chemical fractionation found toxicity levels of 84.1 % low and 15.9 % medium. Furthermore, the combined toxicity calculated from DGT-SSD coupled PRA showed that trace metals in sediment had a 24.8 % probability of toxic effects towards aquatic organisms, with Cu, Zn, Cd, and Ni being the main contributors. Comparative analysis suggested that the DGT-SSD coupled PRA could provide a more objective and scientific evidence for lake management with regard to metal contamination.