Both cinnabar (HgS) and metallic mercury (Hg0) were important resources throughout Andean prehistory. Cinnabar was used for millennia to make vermillion, a red pigment that was highly valued in pre-Hispanic Peru; metallic Hg0 has been used since the mid-16th century to conduct mercury amalgamation, an efficient process of extracting precious metals from ores. However, little is known about which cinnabar deposits were exploited by pre-Hispanic cultures, and the environmental consequences of Hg mining and amalgamation remain enigmatic. Here we use Hg isotopes to source archeological cinnabar and to fingerprint Hg pollution preserved in lake sediment cores from Peru and the Galápagos Islands. Both pre-Inca (pre-1400 AD) and Colonial (1532-1821 AD) archeological artifacts contain cinnabar that matches isotopically with cinnabar ores from Huancavelica, Peru, the largest cinnabar-bearing district in Central and South America. In contrast, the Inca (1400-1532 AD) artifacts sampled are characterized by a unique Hg isotopic composition. In addition, preindustrial (i.e., pre-1900 AD) Hg pollution preserved in lake sediments matches closely the isotopic composition of cinnabar from the Peruvian Andes. Industrial-era Hg pollution, in contrast, is distinct isotopically from preindustrial emissions, suggesting that pre- and postindustrial Hg emissions may be distinguished isotopically in lake sediment cores.