Due to the persistence and the high toxicity of metals to many aquatic organisms, metals in aquatic ecosystems have attracted considerable attention. The objective of the present study was to rank metals in Lake Taihu based on the threat they pose to aquatic organisms. The method involved the assessment of the risks of metals to native aquatic organisms and the potential influence of concentration distributions. Both quotient and probabilistic methods were used to rank the risks of arsenic, cadmium, chromium, copper (Cu), mercury, manganese, nickel (Ni), lead, and zinc (Zn). Based on the probabilistic method, Cu, Ni, and Zn were the metals of great concern, with Cu posing the highest risk.