The Sao Joao Drainage Basin is a very important and strategic waterbody located in the Lagos Region, Rio de Janeiro State, one of the most popular tourist regions of Brazil. However, the fast economic and subsequent population growth in that region has created untreated wastes from several anthropogenic activities, which include the trace metals disposal into the surface waterbody. This study aims to relate the major ions and trace metals behavior during a 1-year sampling campaign and to provide information about the sources of chemical constituents and the factors that control their concentrations in the three main fluvial compartments of the drainage basin, including the Juturnaiba Reservoir which has a crucial role for water supply in the Lagos Region. The chemical data reveal that rainfall is the main factor responsible for the physicochemical parameters and the water dissolved constituent's variations. The geological and anthropogenic factors which are the main sources of water constituents were assessed by the Inorganic Chemical Index. Those data corroborate the great influence of rainfall and reveal the importance of anthropogenic sources of chemical constituents in some parts of the Juturnaiba Reservoir. The geochemical modeling suggests that hydrolysis reactions are primarily responsible for the trace metals availability in the three fluvial compartments in both dry and wet seasons, followed by carbonate and sulfate complexation.