In the Brazilian Amazon, mercury has being studied due to Artisanal small scale gold mining (ASGM) activities in this area, which increases mercury inputs in this ecosystem. The most toxic form of this element is methyl mercury, which is a potent neurotoxic capable of going through the placental barrier, therefore affecting the fetus development causing irreversible damage in the new born. Riparian populations have a fish-based diet, and depending on the fish trophic levels ingested, this could represent a significant source of methylmercury for these populations. Even though ASGM has been reduced in the last few years, the new projects for economic development could increase the incorporation of Hg-levels into trophic chain as methylmercury. This study assess mercury exposure (blood and hair), during the flooding stage of the hydroelectric power plant at the Madeira river, with focus in children s health of two riparian communities located downstream of the reservoir in areas influenced by the hydroelectric plant in both a direct and an indirect way. In the Hg exposure assessment are included other important factors such as blood Se-levels, diet, hemogram, blood pressure and anthropometric measures. In order to create a baseline information for future monitoring and exposure patterns surveillance plan, to assess health impact in the riparian communities located in this area, after commissioning of the hydroelectric power plant. The results point out, that the values of the health parameters (blood pressure, BMI, hemogram) assessed, were within the normal values for healthy children, and there wasn t significance difference between the communities in the general health conditions. However, about Hg and Se exposure, both elements levels showed significant difference between the two communities. Hg and Se concentrations were higher at RESEX Cuniã.. It was also observed a seasonal pattern in the exposure of these elements. Hg levels were higher during dry season, different from Se levels, that were higher during the wet seasons. It was also observed possible evidence that intake of Se could represent a protector factor on Hg exposure. The information reported in this study, will contribute to the children’s health surveillance programs of the Ministry of Health, for assessment on health impact, in areas where hydroelectric power plant are established.