There is an ongoing debate on the fate of mercury (Hg) in areas affected by artisanal and small-scale gold mining (ASGM). Over the last 30 years, ASGM has released 69 tons of Hg into the southeastern Peruvian Amazon. To investigate the role of suspended matter and hydrological factors on the fate of ASGM-Hg, we analysed riverbank sediments and suspended matter along the partially ASGM-affected Malinowski-Tambopata river system and examined Hg accumulation in fish. In addition, local impacts of atmospheric Hg emissions on aquatic systems were assessed by analysing a sediment core from an oxbow lake. Hg concentrations in riverbank sediments are lower (20–53 ng g−1) than in suspended matter (∼400–4000 ng g−1) due to differences in particle size. Elevated Hg concentrations in suspended matter from ASGM-affected river sections (∼1400 vs. ∼30–120 ng L−1 in unaffected sections) are mainly driven by the increased amount of suspended matter rather than increased Hg concentrations in the suspended matter. The oxbow lake sediment record shows low Hg concentrations (64–86 ng g−1) without evidence of any ASGM-related increase in atmospheric Hg input. Hg flux variations are mostly an effect of variations in sediment accumulation rates. Moreover, only 5% of the analysed fish (only piscivores) exceed WHO recommendations for human consumption (500 ng g−1). Our findings show that ASGM-affected river sections in the Malinowski-Tambopata system do not exhibit increased Hg accumulation, indicating that the released Hg is either retained at the spill site or transported to areas farther away from the ASGM areas. We suspect that the fate of ASGM-Hg in such tropical rivers is mainly linked to transport associated with the suspended matter, especially during high water situations. We assume that our findings are typical for ASGM-affected areas in tropical regions and could explain why aquatic systems in such ASGM regions often show comparatively modest enrichment in Hg levels.