The complexity involved in the sustainable management of coastal zones, associated with its economic and socio-environmental relevance, requires a sound knowledge of their morphodynamic characteristics. The use of numerical models for simulation of sediment transport patterns represents an efficient methodology that allows assessing different environmental scenarios and proposing sustainable solutions for integrated estuarine management. The main aim of this work was to characterize the morphodynamics of the river Lima estuary (NW Portugal), which extends between its mouth at Viana do Castelo city and the upstream weir of Ponte de Lima town. The Delft3D software was applied in this study. This software has been widely used throughout the world, and can perform simulations of hydrodynamics, sediment transport, waves propagation, water quality, morphological studies and ecological processes in coastal, river and estuarine areas. It consists of several modules that can interact with each other. After calibration the model was applied to simulate water levels, current velocities and sediment transport for different environmental scenarios and tidal regimes, allowing the characterization of the erosion and deposition patterns within the estuary.