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Historical records of trace elements in lake sediments provide source-to-sink information about potentially toxic pollutants across space and time. We investigated two lakes located at different elevations in the Ecuadorian Andes to understand how trace element fluxes are related to (i) geology, (ii) erosion in the watersheds, and (iii) local point sources and atmospheric loads. In remote Lake Fondococha (4150 m a.s.l.), total Hg fluxes stay constant between ca. 1760 and 1950 and show an approximately 4.4-fold increase between pre-1950 and post-1950 values. The post-1950 increase in fluxes of other trace elements (V, Cr, Co, Ni, Cu, Zn, As, Cd, and Pb) is lower (2.1–3.0-fold) than for Hg. Mostly lithogenic sources and enhanced soil erosion contribute to their post-1950 increase (lithogenic contribution: > 85%, Hg: ~ 58%). Average post-1950 Hg fluxes are approximately 4.3 times higher in peri-urban Lake Llaviucu (3150 m a.s.l.) than in the remote Lake Fondococha. Post-1950 fluxes of the other trace elements showed larger differences between Lakes Fondococha and Llaviucu (5.2 < 25– 29.5-fold increase; Ni < Pb–Cd). The comparison of the post-1950 average trace element fluxes that are derived from point and airborne sources revealed 5–687 (Hg–Pb) times higher values in Lake Llaviucu than in Lake Fondococha suggesting that Lake Llaviucu’s proximity to the city of Cuenca strongly influences its deposition record (industrial emissions, traffic, caged fishery). Both lakes responded with temporary drops in trace element accumulations to park regulations in the 1970s and 1990s, but show again increasing trends in recent times, most likely caused by increase in vehicular traffic and openings of copper and gold mines around Cajas National Park.