A comprehensive analysis of heavy metal pollution was conducted in the representative limnetic ecosystems of eastern China, which are subject to rapid economic development and population growth. The results demonstrated that the average contents with standard deviations of Cd, Cr, Cu, Ni, Pb and Zn in the surface sediments were 0.925 ± 0.936, 142 ± 46.8, 54.7 ± 29.1, 60.5 ± 21.6, 61.9 ± 36.0 and 192 ± 120 mg/kg dry wt., respectively, and that higher values were mainly observed in the southern portion of the study area, especially in the basins of Southeast Coastal Rivers (SCRB) and the Zhu River (ZRB). The six heavy metals in the surface sediments all had anthropogenic origins. In addition, the limnetic ecosystems, especially in the southern portion of the study area were found to be polluted by heavy metals, especially Cd. Overall, two hotspots of heavy metal pollution in the limnetic ecosystems of eastern China were found, one that consisted of the heavy pollution regions, SCRB and ZRB, and another composed of Cd pollution. These results indicate that heavy metal contamination, especially Cd, should be taken into account during development of management strategies to protect the aquatic environment in the limnetic ecosystems of eastern China, especially in the two aforementioned basins.