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Natural archives have been used to reconstruct mercury atmospheric deposition at different spatial and temporal scales during the Holocene in the Northern Hemisphere. In this study, we present the results from a Brazilian mountain mire (Pinheiro mire, Minas Gerais, SE Brazil), extending back to similar to 57 ka. The core was analyzed for mercury concentration, organic matter content, organic carbon isotopic composition, and tracers of mineral matter flux. Principal components analysis followed by principal components regression enabled us to determine the evolution of the weight of the latent processes governing the accumulation of mercury through time. We show that climate change was the main driver for the variations of mercury concentrations, either indirectly by (i) enhancing soil erosion in the mire’s catchment, which led to a decrease in mercury concentration due to dilution by low mercury-containing mineral matter, (ii) increasing regional dust deposition, which resulted in increased concentrations, or directly, by long-term changes in atmospheric wet deposition (arid vs humid periods). Internal peat processes (i.e., decomposition and mass loss) had a minor influence at the time scale represented by the core.