Aquatic ecosystems in eastern China are suffering threats from heavy metal pollution because of rapid economic development and urbanization. Heavy metals in surface sediments were determined in five different aquatic ecosystems (river, reservoir, estuary, lake, and wetland ecosystems). The average Cd, Cr, Cu, Ni, Pb, and Zn concentrations were 0.716, 118, 37.3, 32.7, 56.6, and 204 mg/kg, respectively, and the higher concentrations were mainly found in sediment samples from river ecosystems. Cd was the most anthropogenically enriched pollutant, followed by Zn and Pb, indicated by enrichment factors >1.5. According to consensus-based sediment quality guidelines, potential ecological risk indices, and risk assessment codes, all five types of aquatic ecosystems were found to be polluted with heavy metals, and the most polluted ecosystems were mainly rivers. Cd was the most serious pollutant in all five aquatic ecosystems, and it was mainly found in the exchangeable fraction (about 30% of the total Cd concentration, on average). The results indicate that heavy metal contamination, especially of Cd, in aquatic ecosystems in eastern China should be taken into account in the development of management strategies for protecting the aquatic environment.