This paper presents a general system for the reconstitution of natural flows series to support the SNIRH (Brazilian acronym for National Water Resources Information System). There is a need for system structuring due to the fact that streamflows may suffer human modifications which difficult to carry out water resources management. In order to make a reliable assessment, it is essential to determine the socalled “natural flow series” i.e. the flows that would have occurred prior to human action. The SisVazNat system was applied in the Tocantins watershed, located in the Amazon Region, and in order to validate the proposed methodology, the results were compared with those published by the Electric System National Operator (ONS). The mean percent differences obtained in each hydropower plant were, respectively: UHE Serra da Mesa (3.2%); UHE Cana Brava (5.6%); UHE Lajeado (4.2%) and UHE Tucuruí (4.4%), allowing the validation of the tool.