Saltwater intrusion caused by groundwater over-exploitation from coastal aquifers poses a severe problem in many regions. The Fum Al Wad aquifer is located between Atlantic Ocean in the West and Laayoun in the East. This aquifer covers an area of 250 Km², and represents an essential water resource for Laayoun city and the periphery regions. It is heavily exploited for water supply, agriculture and industry. The freshwater-saltwater interface is affected by groundwater extraction by public supplies, irrigation wells, and domestic wells in the coastal of this aquifer. The position of the interface is controlled by several factors: these include precipitation, recharge rate, dryness, evapotranspiration, hydraulic conductivity and hydraulic head. Landward migration of the interface freshwater-saltwater often results in a significant decrease in the water resources available for coastal communities. The volume pumped by public for irrigation and the domestic usage in 2010-2011 is estimated 2.5 Mm³/year, and in 2015 about 2.91 Mm³/year only for domestic usages. The objectives of this work are to model the groundwater flow and saltwater intrusion in the coastal aquifer of Fum Al Wad, by SEAWAT-2000 program which coupled both the version of MODFLOW-2000 and MT3DMS. They are designed to simulate variable-density groundwater flow and solute transport in three dimensions. The model is calibrated for hydraulic conductivity, specific yield, porosity, and recharge rate as well as dispersivity coefficient. The result of simulation of the hydrodynamic model during the period of 1986-2015 has revealed a piezometric drawdown with 2.3 m approximately at the level of the pumping zone. Furthermore, this piezometric depression is caused by excessive pumping of the various uses of water and its corresponding that has resulted in the migration of the saltwater intrusion into freshwater with 4.3 km approximately. The simulations result for scenarios 2020 and 2030 of Fum Al Wad aquifer showed a vertical decrease of the piezometric head (about 2.5 m) in 2030, but the saltwater intrusion has advanced diagonally to reach 4.7 km under the freshwater of groundwater of this aquifer.