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Although the impacts of large dams on freshwater biota are relatively well known, the effects of small hydropower plants (SHP) are not well investigated. In this work, we studied if mercury (Hg) concentrations in fish rise in two tropical SHP reservoirs, and whether similar effects take place during impoundment. Total Hg concentrations in several fish species were determined at two SHP in the Upper Guaporé River basin floodplain, Brazil. In total, 185 specimens were analysed for Hg content in dorsal muscle and none of them reported levels above the safety limit (500 μg kg -1 ) for fish consumption recommended by the World Health Organisation (WHO). The highest levels of Hg (231 and 447 μg kg -1 ) were found in carnivorous species in both reservoirs. Mercury increased as a function of standard length in most of the fish populations in the reservoirs, and higher Hg concentrations were found in fish at the reservoir compared with fish downstream. The high dissolved oxygen concentrations and high transparency of the water column (i.e. oligotrophic reservoir) together with the absence of thermal stratification may explain low Hg methylation and low MeHg levels found in fish after flooding. Overall, according to limnological characteristics of water, we may hypothesise that reservoir conditions are not favourable to high net Hg methylation.