Arid and semi-arid regions present special challenges for water management. Streamflow variation in the upstream countries of the international river basins (River Nile basin), due climate changes or anthropogenic activities such as the ongoing construction of the Grand Ethiopian Renaissance Dam (GERD) is making management of water resources in the downstream countries (Egypt) difficult especially with increasing water demands. Groundwater (GW) and surface water (SW) are two interconnected components of one single resource, impacts on of these components will inevitably affect either the quantity or quality of one another, and that is the situation in the study area. Accordingly, not just SW availability will be affected, but also GW. A three-dimensional transient GW model is used to investigate the impacts of expected decreasing in SW supply due to natural (climate change) or artificial (GRED) changes and increasing GW extraction due to increasing population and agricultural development. This model helps to understand the interaction between the River Nile and the main SW canals and the Quaternary aquifer and to study the recharge possibilities of the aquifer as well as prediction of the aquifer behavior under different stresses in Minia Governorate, Egypt. Three scenarios with eleven probabilities were proposed for the prediction simulations and GW budget, levels and flow exchanges between SW and GW were also calculated on year 2050. The first scenario evaluates the impact of decreasing SW levels by 0.5, 1, and 1.5 m due to climate change or the (GRED), the second scenario studies the effect of increasing GW extraction by 25% and 50% from the extraction rate in the current situation due to agricultural development and increasing demand of GW in different uses. The third scenario examines the potential impact of climate change or the (GRED) and pumping scenarios on GW budget and levels in the Quaternary aquifer where it studies the effect of increasing GW extraction by 25% and 50% with decreasing SW levels by 0.5, 1 and 1.5 m on the aquifer. The maximum change in GW budget and levels was found in the third scenario in the case of increasing GW extraction by 50% and decreasing SW levels by 1.5 m in which AS of the aquifer will decrease to - 712821.9 m(3)/day and GW levels will decrease to range from 23.31 to 43.07 m, respectively.