In this paper, we describe a numerical model for unsteady stratified flow without mixing at the interface (halocline), which was applied for the calculation of salinization in the Neretva River (Croatia) i.e. the first line of penetration. The mathematical model is based on the principles of conservation of mass and momentum. Since, the set of equations does not have analytical solution it is solved numerically, e.g. through finite element method (FEM). Computed variables are water discharges and elevations for each layer separately in each point of finite element mesh. Calibration of the model is based on in-situ measurements. The most important factor for salt water intrusion in an estuary is the fresh water discharge. In the Neretva estuary, salt water was found in Metkovic (22km from the sea) for freshwater flows of less than 180m(3)/s, while for flows greater than 500m(3)/s salt water was completely extruded from the riverbed. The plan is to build a mobile barrier (gate) in the Neretva River to protect it against sea water penetration. Additionally, upstream of the barrier, fresh water would be provided in the riverbed that could be primarily used for irrigation. The same numerical model has been also successfully applied to the estuary of the Jadro River, a small river near Split. Since the model is general, it can be applied on any river mouth with stratified conditions. The projections of sea level changes in the Adriatic Sea shows increase of a few decimeters in 21(st) century. Generally, rising sea levels will increase salt water pressure on the coast, estuaries, water resources, aquifers and farmland. Therefore, the management of estuaries will require even greater engagement of experts from different areas to successfully deal with future difficulties.