Groundwater is considered one of the important sources in Egypt. However, it is expected to face many challenges in the next few decades. The Eastern Nile delta fringes region, the current area of interest, is one of the most highly developed areas in Egypt for more than three decades. Special attention will be given to the existing large reclamation lands (surface water/groundwater) in the high desert lands and low ones which are adjacent and surrounding the Ismailia canal. Under the expected stress of extensive shortage in surface water of the Nile water system, as a result of the construction of GERD, the rapid population and urbanization, a direct impact on the groundwater system in terms of groundwater levels and water budget will be expected. The main research question of the present study is: what is the response of the Nile Delta Aquifer in the south Eastern Nile Delta Fringes in the case of crisis for the sustainability of existing large projects? Visual MODFLOW was used to simulate the existing condition of the irrigation canals and the expected changes under different scenarios of water shortage. The model was simulated and calibrated for the initial hydrogeological conditions throughout the period . The model was tested for scenarios based on the final calibration as an initial condition. Four scenarios were proposed and simulated for the calibrated regional groundwater model at the study area to evaluate and predict the response of the quaternary aquifer during the decrease of surface water levels for 20 years. These scenarios are: 1. Decrease of the surface water levels by 10% against drainage surplus this expression represents the net recharge to the aquifer all the year, 2. Decrease of the surface water levels by 10% against seasonal drainage surplus for six months (summer, winter), 3. Decrease of the surface water levels by 20% against drainage surplus all the year and 4. Decrease of the surface water levels by 20% against seasonal drainage surplus for six months (summer, winter). The results of simulated scenarios showed a change and fluctuation in the groundwater levels, while the maximum value of the change in storage was found in scenario 4.in which this value was decreased by 52.9 % between 2017 and 2037. but in all scenarios, the change in storage of the aquifer still stable and continuously increase, by 36.5% under scenario 2 and 29 % under scenario 4. This volume of storage will be available for pumping by extraction wells in case of surface water reduction.