Mercury emissions from artisanal and small-scale gold mining throughout the Global South exceed coal combustion as the largest global source of mercury. We examined mercury deposition and storage in an area of the Peruvian Amazon heavily impacted by artisanal gold mining. Intact forests in the Peruvian Amazon near gold mining receive extremely high inputs of mercury and experience elevated total mercury and methylmercury in the atmosphere, canopy foliage, and soils. Here we show for the first time that an intact forest canopy near artisanal gold mining intercepts large amounts of particulate and gaseous mercury, at a rate proportional with total leaf area. We document substantial mercury accumulation in soils, biomass, and resident songbirds in some of the Amazon's most protected and biodiverse areas, raising important questions about how mercury pollution may constrain modern and future conservation efforts in these tropical ecosystems.