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. As a result, the upper several decimeters of sediment in the lake contain peak concentrations of Cu, Zn, and Pb of ~6000 ppm, ~50,000 ppm, and ~2000 ppm, respectively, with the latter two greatly exceeding the United States Environmental Protection Agency (EPA) limits for the entire 150 km2 lake basin. That the source of the contamination to Lake Junín is acid mine drainage from Cerro de Pasco is supported by spatial gradients in metal concentrations, authigenic calcite (marl) concentrations, and the isotopic record of Junín water. Today, the upper 50 cm of sediment in Lake Junín contain ~60,400, 897,600, and 40,900 metric tons of Cu, Zn, and Pb, respectively, which is equivalent to ~5.1 years’ worth of Zn extraction and ~0.7 years’ worth of Pb extraction from mining operations at Cerro de Pasco at current rates.