Planning and alignment of man-made maritime water areas such Damietta Port, have to be carefully designed to guarantee adequate water exchange between the port basin water and the open sea fresh water. Stagnant water areas could consist in isolated areas, artificial canals, islands, connection channels and structures that block the natural water flow. The properties of the water exchange rate of Damietta Port basin has been investigated as a response of relevant natural hydrodynamic drivers. A two-dimensional numerical model uses the equations of continuity and conservation of momentum was used to simulate the flow circulation patterns and tracking the pollutants transport in the port basin, depending on both water levels and wind data. The core of the work was to set up a hydrodynamic model for Damietta port, to determine the port basin hydrodynamic characteristics attitude. The tidal and wind data were used as input to the hydrodynamic model to simulate tidal currents in the port basin. Then, the results of the hydrodynamic model were analyzed to detect the tidal current characteristics and the general current patterns during a typical tidal cycle were simulated. Finally, the transport of pollutant particles in the port basin was simulated using the particle tracking technique in order to predict the pollutant particles movement. The results showed that the attitude of hydrodynamic characteristics of the port basin helps to make a good exchange of the fresh water between the port basin and the Mediterranean Sea.