The bioaccumulation of mercury by fish was studied in three natural lakes lining the Tapajós River, Brazilian Amazon. The Hg content variations are also reported between the rainy and the rising water seasons. Position of fish in the food chain and the source of carbon at the base of the food chain were determined using nitrogen and carbon stable isotopes ratios respectively. During the two seasons, the effect of the Hg biomagnification between the non-piscivorous and piscivorous fish of the three lakes is observed. The correlation between the mercury concentrations and the nitrogen isotopic ratios suggests that the fish mercury content variability is connected with the trophic position and size. Aside from classic observations on mercury biomagnification by certain species of fish (i.e. contents increase with size or trophic status), novel results were revealed as well, such as some species decrease of mercury contents with size of fish. Aquatic organisms in the Amazon are adapted to the complexity of trophic webs coupled with changes in environmental variables, depending on the location and/or the season, which results in a wide range of mercurial contamination among the Tapajós ichthyofauna.