Artisanal and small-scale gold mining (ASGM) is the primary global source of anthropogenic mercury (Hg) emissions. It has impacted the Amazon rainforest in the Peruvian region of Madre de Dios. However, few studies have investigated Hg's distribution in terrestrial ecosystems in this region. We studied Hg's distribution and its predictors in soil and native plant species from artisanal mining sites. Total Hg concentrations were determined in soil samples collected at different depths (0–5 cm and 5–30 cm) and plant samples (roots, shoots, leaves) from 19 native plant species collected in different land cover categories: naked soil (L1), gravel piles (L2), natural regeneration (L3), reforestation (L4), and primary forest (L5) in the mining sites. Hg levels in air were also studied using passive air samplers. The highest Hg concentrations in soil (average 0.276 and 0.210 mg kg−1 dw.) were found in the intact primary forest (L5) at 0–5 cm depth and in the plant rooting zones at 5–30 cm depth, respectively.Moreover, the highest Hg levels in plants (average 0.64 mg kg−1 dw) were found in foliage of intact primary forest (L5). The results suggest that the forest in these sites receives Hg from the atmosphere through leaf deposition and that Hg accumulates in the soil surrounding the roots. The Hg levels found in the plant leaves of the primary forest are the highest ever recorded in this region, exceeding values found in forests impacted by Hg pollution worldwide and raising concerns about the extent of the ASGM impact in this ecosystem. Correlations between Hg concentrations in soil, bioaccumulation in plant roots, and soil physical-chemical characteristics were determined. Linear regression models showed that the soil organic matter content (SOM), pH, and electrical conductivity (EC) predict the Hg distribution and accumulation in soil and bioaccumulation in root plants.