Numerical simulation were carried out for studying seawater intrusion in Khan-Younis coastal areas with SEAWAT code: a, Computer Program for Simulation of Three-Dimensional Variable- Density Ground-Water Flow coupled to solute transport using a finite difference method 'MODFLOW-MT3DMS). The conceptual model and groundwater data was collected for this study from previous projects such as the SWIMCA (Salt Water Intrusion Management in Coastal Aquifers) project. In the SWIMCA project, the same hydrological logical cross section was simulated using the SUTRA code, which uses a finite element method. In this paper, the SEAWAT code was used in order to estimate the extent of solute migration in depth and time in Khan-Younis area in the south of Gaza Strip-, and to compare it with SUTRA results. This work is being conducted in the framework of the SWIMED (Sustainatble Water management In Mediterranean coastal aquifers) regional project. A finite difference grid was developed to adequately discretize the model domain. For the Khaii--Youins cross section, an irregularly spaced grid was constructed with 178 cells in horizontal direction and 19 cells (layers) in the vertical direction. The total number of cells is 3382. The horizontal size of cells in x direction is 25m in the 1.5 km zone near the sea, increases to 50m between 1.5-3 km, and becomes 100m in the last zone (3-11 km) near the eastern boundary. The results generated by the SEAWAT code showed very good agreement with SUTRA results. The extent of saltwater intrusion for 1997 (based on 1g/l of chlorides) was simulated to be 1300m and 1350m in the middle sub-aquifer by SEAWAT and SUTRA, respectively. Predictive simulations by both codes SEWAT and SUTRA for the year 2006 showed that the saltwater intrusion would be 1.500m and 1750m respectively.