Hydraulic engineering is increasingly relied upon to provide the necessary dry-season discharge for Peru’s hydroelectricity generation. Redirecting stream flow can yield unintended consequences, however, and here we document the wholesale contamination of the Lake Junín National Reserve by acid mine drainage from the Cerro de Pasco mining district. Since construction of the Upamayo Dam in 1932, the Río (river) San Juan, which drains the Cerro de Pasco region, has been seasonally redirected into Lake Junín.