The Moghra aquifer has shown promise in land reclamation projects conducted in the Western Desert of Egypt. Although this aquifer has hundreds of pumping wells in new urban communities built to meet the needs of the increased population, the system is threatened by the phenomenon of seawater intrusion (SWI). The present study evaluates the degree to which these pumping wells will attract seawater to the aquifer system in the Western Desert region under different pumping conditions. Using the SEAWAT module of Groundwater Modeling System (GMS) software, a three-dimensional (3D) finite-difference model is built to simulate the flow and salinity distribution in the Moghra aquifer considering the geological and hydrogeological characteristics of the aquifer system. The procedure used to solve the mathematical model relied on merging two different approaches. The first approach described the dividing lines of the transition zone due to the SWI. The second approach was applied to conduct the perfect calibration process for the aquifer system. The results show that the flow and quality of the groundwater aquifer are affected by pumping. The water level and salinity are predicted under different pumping rates, a fivefold increase in the pumping rate results that the salinity increased between 4% and 26.8% according to the well location. Moreover, the drawdown values reached 162 m, which is about 46.3% of the saturated thickness.