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Mercury (Hg) is a chemical element that, depending on its concentration, may become toxic to living organisms due to the ability of Hg to bioaccumulate in food chains. In this study, we collected samples of soil, litter and organisms in the Middle Araguaia floodplain, Brazil. Total mercury (THg) concentrations in litter were significantly higher (p < 0.0001) than that in soil, ranging from 10.68 ± 0.55 to 48.94 ± 0.13 and 20.80 ± 1.07 to 55 .19 ± 1.59 ppb, respectively. Total mercury concentration levels in soil showed a linear, inversely proportional relationship with soil organic matter (SOM) contents and soil pH, which is consistent with the geochemical behavior of chemical elements in flooded environments. Ten orders of organisms were identified and the average THg concentrations determined in their bodies were up to 20 times higher than those in soil and litter. We found a significant linear relationship between the levels of THg in litter and the levels found in soil organisms, thereby allowing the prediction of THg concentration levels in soil organisms through the analysis of litter at the sample units. The different dynamics and feeding habits of soil organisms, the concentration of THg in these organisms may be influenced by the course of the river. The bioaccumulation factor (BAF) calculated based on litter indicated the formation of trophic guilds, thus, BAF is a strong indicator of the trophic level of the sample units.