The aim of this paper is to present the results of a 3D numerical hydrodynamics and sediment transport study for the navigation channel of the Port of Santos. A comprehensive study on the environmental impacts of dredging deep in the Santos estuary was carried out, including the effects of seasonal meteorological variations (surge), and seasonal runoff conditions. The study consider the effect of the deepening on the general hydrodynamics including changes in current conditions for navigation and especially on the effect on the salinity conditions in the estuary before and after the deepening.