We report mercury (Hg) mass-dependent isotope fractionation (MDF) and mass-independent isotope fractionation (MIF) in hair samples of the Bolivian Esse Ejjas native people and in several tropical fish species that constitute their daily diet. MDF with δ202Hg ranging from −0.40 to −0.92 ‰ for fish and +1.04 to +1.42 ‰ for hair was observed. Hair samples of native people with a fish-dominated diet are enriched by +2.0 ± 0.2 ‰ in δ202Hg relative to the fish consumed. Both odd Hg isotopes, 199Hg and 201Hg, display MIF in fish (from −0.14 to +0.38 ‰ for Δ201Hg and from −0.09 to +0.55 ‰ for Δ199Hg) and in hair (from +0.12 to +0.66 ‰ for Δ201Hg and from +0.14 to +0.81 ‰ for Δ199Hg). No significant difference in MIF anomalies is observed between Hg in fish and in human hair, suggesting that the anomalies act as conservative source tracers between upper trophic levels of the tropical food chain. Fish Hg MIF anomalies are 10-fold lower than those published for fish species from midlatitude lakes. Grouping all Amazonian fish species per location shows that Δ199Hg:Δ201Hg regression slopes for the clear water Itenez River basin (0.95 ± 0.08) are significantly lower than those for the white water Beni River basin (1.28 ± 0.12). Assuming that the observed MIF originates from aquatic photoreactions, we calculated limited photodemethylation of monomethylmercury (MMHg) in the Beni River floodplains and insignificant photodemethylation in the Itenez River floodplains. This is possibly related to lower residence times of MMHg in the Itenez compared to the Beni River floodplains. Finally, a significantly negative Δ201Hg of −0.14 ‰ in Beni River fish suggests that the inorganic Hg precursor to the MMHg that bioaccumulates up the food chain defines an ecosystem specific non-zero Δ201Hg baseline. Calculation of photodemethylation intensities from Hg or MMHg MIF, therefore, requires a baseline correction.