Volcanism is one of the major natural processes emitting mercury (Hg) to the atmosphere, representing a significant component of the global Hg budget. The importance of volcanic eruptions for local-scale Hg deposition was investigated using analyses of Hg, inorganic elemental tracers, and organic biomarkers in a sediment sequence from Lake Chungará (4520 m a.s.l.). Environmental change and Hg deposition in the immediate vicinity of the Parinacota volcano were reconstructed over the last 2700 years, encompassing the pre-anthropogenic and anthropogenic periods. Twenty eruptions delivering large amounts of Hg (1 to 457 μg Hg m−2 yr−1 deposited at the timescale of the event) were locally recorded. Peaks of Hg concentration recorded after most of the eruptions were attributed to a decrease in sedimentation rate together with the rapid re-oxidation of gaseous elemental Hg and deposition with fine particles and incorporation into lake primary producers. Over the study period, the contribution of volcanic emissions has been estimated as 32% of the total Hg input to the lake. Sharp depletions in primary production occurred at each eruption, likely resulting from massive volcaniclastic inputs and changes in the lake-water physico-chemistry. Excluding the volcanic deposition periods, Hg accumulation rates rose from natural background values (1.9 ± 0.5 μg m−2 yr−1) by a factor of 2.3 during the pre-colonial mining period (1400–900 yr cal. BP), and by a factor of 6 and 7.6, respectively, during the Hispanic colonial epoch (400–150 yr cal. BP) and the industrial era (~140 yr cal. BP to present). Altogether, the dataset indicates that lake primary production has been the main, but not limiting, carrier for Hg to the sediment. Volcanic activity and climate change are only secondary drivers of local Hg deposition relative to the magnitude of regional and global anthropogenic emissions.