Worldwide harbors are settled inside estuarine areas due the protection function of these environments against oceanic waves and therefore are subjected to the hydrodynamic processes that provide morphodynamic changes in sediment distribution and bed evolution. Understanding the dynamic of sediments and the bed evolution at estuaries is of crucial importance on maintenance of fairways and harbor docks. We modeled using the finite element technique 1005 days of hydro and morphodynamic of the Patos Lagoon estuary, in order to identify the critical deposition areas inside the Rio grande harbor fairway. Therefore, a hydrodynamic model, TELEMAC 3D, and a morphodynamic, Sisyphe, were applied in order to acquire the bed evolution and sediment distribution of the area using different data sources for the oceanic, atmospherical and continental boundary conditions. The results, present that clay is being deposited at deeper parts of the channel. Bed evolution results indicate siltation/erosion process where silt/clay is being deposited. Sedimentation rates were calculated based on the bed evolution results as well. The validation procedure showed good representation by the models of the physical aspects of the environment.