Libya has experienced progressive seawater intrusion in the coastal aquifers since 1930s because of its ever increasing water demand from underground water resources. Tripoli City and its hinterland are located in the coastal region of the Gefara Plain, where the agricultural activity entirely depends on rainfall and groundwater. In recent years, the risk of seawater intrusion is continuously threatening coastal parts of the Gefara Plain that form one of the economically most significant area in the country. Hydrogeo chemistry of the aquifer system was studied and a numerical assessment of the problem has been accomplished applying a two-stage finite element simulation algorithm. First, an areal, two-dimensional model was formulated in order to perform a steady-state calibration for the physical parameters, and boundary conditions of the hydrodynamic system. In the second stage, the mechanism of the seawater intrusion was analyzed using a cross-sectional finite element model. Simulation runs have been accomplished to study location of the interface and its temporal migration. The groundwater resource in the Tripoli region has been progressively contaminated by seawater intrusion. Simulation results indicate that the proposed scheme successfully simulates the intrusion mechanism. The seawater/freshwater interface would migrate landward leading to a very critical problem if the present groundwater production policy continues operating in the area.