Geochemical measurements on well-dated sediment cores from Lake Er (Erhai) are used to determine the timing of changes in metal concentrations over 4500 years in Yunnan, a borderland region in southwestern China noted for rich mineral deposits but with inadequately documented metallurgical history. Our findings add new insight into the impacts and environmental legacy of human exploitation of metal resources in Yunnan history. We observe an increase in copper at 1500 BC resulting from atmospheric emissions associated with metallurgy. These data clarify the chronological issues related to links between the onset of Yunnan metallurgy and the advent of bronze technology in adjacent Southeast Asia, subjects that have been debated for nearly half a century. We also observe an increase from 1100 to 1300 AD in a number of heavy metals including lead, silver, zinc, and cadmium from atmospheric emissions associated with silver smelting. Culminating during the rule of the Mongols, known as the Yuan Dynasty (1271-1368 AD), these metal concentrations approach levels three to four times higher than those from industrialized mining activity occurring within the catchment today. Notably, the concentrations of lead approach levels at which harmful effects may be observed in aquatic organisms. The persistence of this lead pollution over time created an environmental legacy that likely contributes to known issues in modern day sediment quality. We demonstrate that historic metallurgical production in Yunnan can cause substantial impacts on the sediment quality of lake systems, similar to other paleolimnological findings around the globe.