This study evaluated the risk to human health from mercury (Hg) exposure through fish consumption in the Pantanal, Brazil. In order to address these risks, Hg concentrations and accumulation patterns were determined in target organs of predatory fish (Crenicichla lepidota and Pygocentrus nattereri). Levels of Hg were analysed during the two phases of the flood pulse (flood and drought) in fish from different local ecosystems, such as the Bento Gomes and Paraguay rivers. Although the former study area is directly affected by gold mining, a higher, but not significantly different, Hg concentration in fish was found compared with fish at the Paraguay River, which is regarded as pristine area. Moreover, no seasonal variability was found in either river. Although total mercury levels in fish did not exceed the maximum FAO/WHO threshold (0.5 μg g(-1)), according to dietary habits in riverine communities of the Pantanal (up to 6 oz of fish per day), there is reason for concern over the potential for deleterious health effects that could be caused by high Hg intake. In fact, the estimated daily intake in the present study ranged from 0.49 to 1.08 μg Hg kg(-1) day(-1), for adults (including women of childbearing age) and children, respectively. Because of high Hg intakes in riverine groups, which exceed the recommended reference dose value, these communities could be considered at risk. Therefore, it is necessary to consider regulatory measures and public education regarding fish consumption, particularly in vulnerable groups (i.e. children, pregnant women and women of childbearing age).