In order to learn about the status of heavy metals and ecological risks in Chinese lakes, species sensitivity distributions (SSD) method was applied to assess the ecological risk of six kinds of heavy metal (Zn, Cd, Cr, Cu, Hg and Pb) to freshwater organisms, while principal component analysis was applied to analyze the distributions and source of heavy metal. The evaluation indexes are including the potential affected fractions (PAF) and multi-substance PAF (msPAF), which rank the ecological risk levels. The results showed that among the 18 lakes, the average concentrations of Zn, Pb, Cd, Cu, Cr and Hg were 17.06 μg/L (range is 4.03-29.33 μg/L), 9.33 μg/L (range is 0.04-33.7 μg/L), 5.56 μg/L (range is 0.65-40.0 μg/L), 3.71 μg/L (range is 0.02-10.2 μg/L), 1.17 μg/L (range is 0.01-13.6 μg/L) and 0.19 μg/L (range is 0.03-1.04 μg/L), respectively. The distribution of heavy metal in 18 lakes was reflected by three principal components with the contribution rates of F1 (Cu, Zn and Hg), F2 (Pb and Cd) and F3 (Cr, Cu) were 28.50%, 24.17% and 18.40%, respectively, which was less affected by economic and geographical differences. Different kinds of heavy metal have different HC5 values for all freshwater organisms with Cu for the lowest HC5 value (the order is Cu < Cr < Hg < Cd < Pb < Zn), indicating freshwater organisms have the highest sensitivity to Cu. In the selected 18 lakes, the order of msPAF of heavy metal in each lake was:Lake Hulun (67.0%) > Lake Luhu (56.7%) > Lake Erhai (52.7%) > Lake Jinyin (52.3%) > Lake Taihu (40.5%) > Lake Moshui (39.3%) > Lake Gehu (30.2%) > Lake Poyang (26.8%) > Lake Hongze (23.1%) > Lake Gaobao (22.4%) > Lake Chaohu (20.7%) > Lake Wuliangsu (19.7%) > Lake Donghu (19.1%) > Lake Liangzi (4.0%) > Lake Tangxun (2.0%) > Lake Dongting (1.0%) > Lake Honghu (0)=Lake Luoma (0). Based on the above work, the ecological risks of heavy metal pollution in lakes were evaluated, which provided a scientific theoretical basis for lake risk management and protection.