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Mercury (Hg) is a toxic metal that is transported globally through the atmosphere. Emissions of Hg from mineral reservoirs and recycling between soil/biomass, oceans, and the atmosphere are fundamental to the global Hg cycle, yet past emissions from anthropogenic and natural sources are not fully constrained. We use a sediment core from Yanacocha, a headwater lake in southeastern Peru, to study the anthropogenic and natural controls on atmospheric Hg deposition during the Holocene. From 12.3 to 3.5 ka, Hg fluxes in the record are relatively constant (mean ± 1σ: 1.4 ± 0.6 μg m-2 a-1). Past Hg deposition does not correlate with changes in regional temperature and precipitation or with most large volcanic events that occurred regionally (~300-400 km from Yanacocha) and globally. In 1450 B.C. (3.4 ka), Hg fluxes abruptly increased and reached the Holocene-maximum flux (6.7 μg m-2 a-1) in 1200 B.C., concurrent with a ~100 year peak in Fe and chalcophile metals (As, Ag, Tl) and the presence of framboidal pyrite. Continuously elevated Hg fluxes from 1200 to 500 B.C. suggest a protracted mining-dust source near Yanacocha that is identical in timing to documented pre-Incan cinnabar mining in central Peru. During Incan and Colonial time (A.D. 1450-1650), Hg deposition remains elevated relative to background levels but lower relative to other Hg records from sediment cores in central Peru, indicating a limited spatial extent of preindustrial Hg emissions. Hg fluxes from A.D. 1980 to 2011 (4.0 ± 1.0 μg m-2 a-1) are 3.0 ± 1.5 times greater than preanthropogenic fluxes. Key Points Hg deposition did not vary with past precipitation, temperature, and volcanism Maximum Holocene Hg fluxes occurred ~3 thousand years ago Modern Hg fluxes are 3 times greater than natural fluxes.