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Mercury contamination from gold mining in the Amazon poses significant environmental and health threats to the biome and its local populations. The recent expansion of non-industrial mining areas has severely impacted territories occupied by traditional communities. To address the lack of sampling data in the region and better understand mercury dynamics, this study used the probabilistic model SERAFM to estimate the mercury distribution and bioaccumulation in fish. The analysis covered 8,259 sub-basins across three major Amazonian basins: the Branco, Tapajós and Xingu rivers. The findings revealed increasing downstream mercury levels, with notable accumulations in the main watercourses influenced by methylation processes and mining releases. The projected concentrations showed that an average of 27.47% of the sub-basins might not comply with Brazilian regulations, rising to 52.38% in the Branco and Tapajós river basins separately. The risk assessment of fish consumption based on the projections highlighted high mercury exposure levels among traditional communities, particularly indigenous populations, with an average of 49.79% facing an extremely high risk in the Branco and Tapajós river basins. This study demonstrated SERAFM's capacity to fill information gaps in the Amazon while underscoring the need for enhanced data collection, culturally sensitive interventions and regulatory updates to mitigate mercury contamination in gold mining-affected areas. [ABSTRACT FROM AUTHOR]