The desert area southeast of Sohag is a target area for development and agricultural expansion, where the Quaternary aquifer is the main water resource. In this study, a groundwater flow model was developed for groundwater management and forecasting groundwater levels and flow under different conditions. This model was calibrated under transient conditions for the period 2017-2021. The calibrated model was used to predict the groundwater conditions in this area through three different scenarios. The first scenario assumes that the groundwater extraction rates remain the same for 20 years, while the second scenario suggests that extraction rates were doubled. The third scenario considers the role of surface water in groundwater recharge. It supposes the decrease in the River Nile and the Eastern Nag Hammadi Canal levels by 1 and 0.5 m, respectively. The results of these scenarios indicated that the most drawdown is always in the southeastern part of the study area where the majority of wells were drilled, while the minimum drawdown is in the western side close to the Nile floodplain area where feeding from both surface water and adjacent aquifer unit is predominant. Moreover, the maximum drawdown of 10.5 m was observed in the second scenario in the eastern and southeastern parts. In contrast, the western part is expected to be significantly affected by the third scenario, where the flux from surface water to groundwater decrease. It is necessary to rationalize irrigated water consumption by using the appropriate irrigation method.