Groundwater quality deterioration in arid regions is an increasingly critical concern due to over-extraction and limited recharge. One of the critical challenges in aquifers located near saline desert regions is the excessive groundwater extraction, which leads to the reversal of flow direction-from the desert into the aquifer, causing salinity intrusion. This phenomenon is a major limitation in arid zones where high exploitation pressure persists. In this study, the groundwater flow behavior at the outlet fronts of a desert aquifer was assessed through numerical modeling using the MODFLOW and MT3DMs models. Prediction of the qualitative results of the aquifer showed that the TDS and Chloride concentrations have almost doubled due to the continuous extraction of groundwater wells. Investigations in this model show that, in addition to the effect of groundwater extraction on concentration, another factor also affects the amount of TDS and chloride predicted by the model. The investigations carried out show that with the drop in the groundwater level in the outlet fronts and the reduction of the hydraulic gradient, the flow of groundwater toward the aquifer has been reversed. This transition is accompanied by a high concentration of salts, which has aggravated the salinity of the aquifer. An important issue in the exploitation of desert aquifers is the balance between recharge and discharge in the aquifer; the disturbance of this balance causes a change in the flow of underground water. This causes the influx of salty water from the desert to the aquifer. The results of reducing the withdrawal from the aquifer in this study showed that exploitation management is effective in addition to the quantity over the quality in the desert aquifer.