Despite a richly-documented history of metallurgy following Hispanic conquest of the Inca, little is known concerning the loci and intensities of earlier metallurgical activities. Lake sediments offer one strategy to reconstruct this history because the deposition of trace elements associated with smelting form a continuous archive that can be assessed in the context of regional archaeology. To reconstruct regional histories of late Holocene atmospheric pollution, two lake sediment cores were collected from mining areas in the central Peruvian Andes. Lake sediment stratigraphies of elemental concentrations and isotopic ratios preserve a regional record of pre-Incan, Incan, and Colonial smelting practices. Our records provide the first evidence for intensive, pre-Colonial smelting in the central Peruvian Andes, and corroborate earlier findings from Bolivia. Surprisingly, smelting appears to have operated independent of oversight from the Wari (500 to 1000 AD) or Inca (1460 to 1532 AD) Empires. With Spanish arrival, smelting activity increased dramatically, only to be superseded by post-industrial pollution.The two central Andean records were compared to two Bolivian records of atmospheric pollution. Initial Pb enrichment in Bolivia occurs contemporaneously with records from Peru ca. 400 AD. In Bolivia, this coincides with the expansion of the Tiwanaku Empire (ca. 400 to 1000 AD). Inca expansion across both Peru and Bolivia (~1450 AD) led to increased metallurgical activity at all four study sites. Our findings demonstrate the usefulness of paleolimnological methods for reconstructing the timing and magnitude of smelting activity throughout the New World, and thus contribute directly to a fragmentary archaeological record