The mouth of the Seine River estuary (France) has undergone marked morphological evolution over several decades mainly due to engineering works aimed at improving access to Rouen and Le Havre harbours. The intertidal areas are decreasing in size and the lower estuary is accumulating sediment and prograding. In order to understand and better describe the major morphological behaviours of the estuary, a morphodynamic numerical model was developed within the Seine-Aval program. At the end of the 1st part of the research program, a validated fine sediment transport model (3D) was available (Le Hir et al., 2001b). As the present morphological study addresses medium-term issues (a few decades), and because of the need to investigate impacts of local structures or events, we chose to use the so-called "process-based approach" starting from the existing model. First, the existing model was upgraded to account for (suspended) sand transport, and to achieve coupling between morphological changes and sediment transport. Erodability of the sediment accounts for the respective proportions of mud and sand. Simulations starting from an arbitrary surficial sediment cover show that the model is able to reproduce realistic sediment patterns. For example, it is able to change the sediment nature on the intertidal flat near Le Havre from sand to mud. Observed structures of suspended sediment are also reproduced: fine particles mainly follow the turbidity maximum whereas significant concentrations of sand grains in suspension are found where the hydrodynamic stresses are intense. Concerning morphodynamics, simulations with real forcing over one year are discussed. The effect of waves on the bathymetric evolution of the mouth is shown and the sensitivity of morphodynamics to the coupling procedure is tested.