In this paper, the results of mercury concentrations in two abiotic compartments (river water and suspended particles) and two biotic compartments (fish and human hair) from the upper Madeira rivers of the Bolivian Amazon basin are presented. Because of the local hydrological regimes and a high deposition rate in the plain, due to the presence of a subsidence zone at the bottom of the Andean piedmont, in the dry season, the highest mercury concentrations and fluxes were not found in rivers where mining activities took place (2.25–6.99 ng l −1; and 1.07–8.67 mg Hg d −1 km −2), but at the outlet of the Andean basins exploited for their alluvial gold (7.22–8.22 ng l −1; and 9.47–9.52 mg Hg d −1 km −2). The total mercury concentrations measured in surface waters of the upper Beni basin varied during the dry season, from 2.24 to 2.57 ng l −1 in the glacial waters of the Zongo river, to 7.00 ng l −1 in the Madeira River at Porto Velho and 9.49–10.86 ng l −1 at its confluence with the Amazon. The results obtained from fish indicate, on one hand, that 86% of the piscivorous fishes collected in the Beni river were contaminated, and, on the other hand, their high mercury concentrations could exceed by almost four times the WHO (1976) safety limit. In the Beni River, the mercury concentrations found in omnivorous and mud-feeding fish ranged from 0.02 to 0.19 μg g −1 (wet wt.), and in piscivorous fish, from 0.33 to 2.30 μg Hg g −1 (wet wt.). The mercury accumulated by carnivorous fishes was mainly present in its organic form; methylmercury represented 73–98% of the total mercury analysed. Eighty persons were studied in the entire Bolivian Amazonian basin. Unlike the gold miners, who are more affected by tropical diseases, such as malaria and yellow fever, the indigenous people living on the banks of the Beni river, present elevated levels of mercury (9.81 μg g −1 on average). We observed an increase in contamination in young children still being breast-fed, confirming that hair mercury concentration in babies was significantly affected by maternal mercury contamination during pregnancy. These results show that the major health impacts caused by mercury affect people who are not working directly in gold mining activities but who have a regular fish diet.