Environmental DNA is a new and emerging approach that has not yet been tested in the Neotropics, where loss of diversity is imminent. Environmental DNA (eDNA) has been used as a way to assess the biodiversity contained within environmental samples for conservation biology. This new approach combines molecular tools in ecological studies, prioritizing management actions that are necessary for the restoration and conservation of native species and the control of invasive species. Species richness does not fully explain diversity. Morphology and functional diversity are limiting in their measurement for more comprehensive ecological inferences. Fish are important bioindicators for the functioning and maintenance of the aquatic environment. Therefore, understanding the impacts caused by dams and how they affect fish diversity in the region is necessary in order to outline conservation strategies. The proposed study will address three aspects of the fish fauna in the Teles Pires River region. First: the effects of the Sinop Hydroelectric Power Plant, identifying which environmental parameters influence the composition and distribution of the ichthyofauna of the Teles Pires River at different levels of environments (streams, rivers and reservoir) using environmental DNA; Second: phylogenetic diversity and structural composition of the ichthyofaunal community in the longitudinal spatial distribution pattern under the influence of the reservoir; Third: seasonal dynamics over two annual hydrological cycles in the variation of the composition of fish assemblages in the Sinop and Colíder reservoirs and adjacent areas. This work aims to corroborate the preservation of ichthyic biodiversity and will be a fundamental instrument using molecular tools in ecological studies for future management actions.