Heavy metal pollution is now widely recognized to pose severe health and environmental threats, yet much of what is known concerning its adverse impacts on ecosystem health is derived from short-term ecotoxicological studies. Due to the frequent absence of long-term monitoring data, little is known of the long-tem ecological consequences of pollutants such as arsenic. Here, our dated sediment records from two contaminated lakes in China faithfully document a 13.9 and 21.4-fold increase of total arsenic relative to pre-1950 background levels. Concurrently, coherent responses in keystone biota signal pronounced ecosystem changes, with a >10-fold loss in crustacean zooplankton (important herbivores in the food webs of these lake systems) and a >5-fold increase in a highly metal-tolerant alga. Such fundamental ecological changes will cascade through the ecosystem, causing potentially catastrophic consequences for ecosystem services in contaminated regions.