Our objective was to evaluate the temporal evolution of mercury exposure in two riverside communities, Barreiras and São Luiz do Tapajós, downstream of gold mining areas in the Tapajós basin, Brazilian Amazon. The quantification of mercury in hair sample was made by atomic absorption spectrophotometry in the period between 1994 and 2010. In São Luiz do Tapajós the mercury exposure varied, in log units, from the peak of 1.21 ± 0.03 μg/g in 1996 to 1.16 ± 0.07 μg/g in 2007. Mercury exposure in Barreiras varied, in log units, from 1.25 ± 0.04 μg/g in 1994 to 1 ± 0.03 μg/g in 2010, peaking in 1995 at 1.25 ± 0.06 μg/g. Total mercury concentration found in both communities had no statistical differences across the years (p > 0.05) and they were higher than non-mercury exposed communities in Brazil and in South America. We concluded that the mercury exposure in the Tapajós basin is more than regulatory levels or higher than the general population.