Hydroelectric reservoirs are often responsible for releasing total mercury (THg) into aquatic ecosystems. There is limited information on the influence of hydrosystem gradients and fluvial regimes on THg distribution. This study aimed to investigate the influence of vertical gradients, hydrosystem gradients, and fluvial regime on THg distribution in water and plankton in the Curuá-Una reservoir, Brazilian Amazon. Samplings were carried out in four fluvial periods: low-water, rising-water, high-water, and falling-water periods. THg levels were determined by cold vapor atomic fluorescence spectroscopy. Physicochemical conditions of the reservoir varied between lacustrine, transition, and riverine zones. Water transparency was greatest in the lacustrine zone (2.5 m), where the depth reaches 18 m. Conductivity (46.8 μS cm-1) and dissolved oxygen (7.7 mg L-1) were higher in the riverine zone in the falling-water period. During the rising-water period, THg was higher in the hypolimnion (8.8 ng L-1) than in the epilimnion (6.2 ng L-1). THg increased in the low-water period (7.9 ± 1.2 ng L-1). The results demonstrate the influence of water stratification, hypoxia, and fluvial regime on THg dynamics. In the low-water period, the hypoxic hypolimnion favored the increase in HgT. Hg release was also found to be influenced by deforestation and human activities, with higher concentrations observed in pasture and agricultural areas, affecting local aquatic biota. THg dynamics are influenced by hydrological and hydrometric processes. Therefore, these factors should be considered in environmental studies aimed at preserving Amazonian biodiversity.