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The energy transfer in the aquatic food chain is an important way for mercury (Hg) to enter other trophic levels. The objective of this work was to evaluate the Hg concentrations in plankton upstream and downstream of the Samuel Hydroelectric Reservoir, Rondônia, Brazil. Phytoplankton and zooplankton samples were collected with 20-μm and 68-μm nylon nets. An aliquot was removed for taxonomic analysis and another for total mercury determination, performed by cold vapor atomic absorption spectroscopy. Water physical-chemical parameters were also measured. The Hg concentrations in total plankton (phytoplankton and zooplankton samples) obtained at the three sampling upstream stations showed the same behavior, with the highest values registered in June 2005 (232 μg kg -1 , 118 μg kg -1 , 128 μg kg -1 ). The lowest values at stations J1 and M1 were recorded in November 2005 (4 μg kg -1 and 22 μg kg -1 , respectively), while the lowest values at stations M4 and M8 were recorded in October 2005 (22 μg kg -1 and 5 μg kg -1 , respectively). The Hg results found in the plankton in this study corroborate the results of other recent studies in the same region. The statistical analyses revealed that Hg concentrations in plankton do not explain the distribution of these organisms at the four sampling stations of Samuel Reservoir. Graphical Abstract.