A storm surge barrier and two additional dams have been built across the Eastern Scheldt estuary in the Netherlands. The storm surge barrier can be closed during severe storms to provide flood protection for the adjacent areas. The storm surge barrier restricts the tidal flow in the estuary, but as the dams reduce the tidal area, an acceptable tidal range can be maintained for environmental purposes. For the sake of ecology and the aquaculture, it is important that the present salinity distributions be retained and, for this reason, an extensive investigation of the mixing processes in the estuary has been undertaken. A numerical two-dimensional model of the estuary simulates the water movements and the movements of dissolved substances and computes water levels, velocities, and the salinity at discrete intervals in time and space. An extensive analysis has been presented of the applicability of the model for different regions of the estuary. In the present paper, some of the experience gained in the use of this numerical model is reported.