Groundwater levels vary from region to another and sometimes in different zones in the same country due to different boundary conditions and extraction rates. Therefore, understanding intricate aquifer systems and predicting how they will react to hydrological changes require the use of groundwater models. In Egypt, the groundwater levels in the Nile Delta aquifer decrease causing problems to the delta ecosystem while it is rising in Aswan area due to the presence of Nasser Lake causing several damages to the city’s buildings and infrastructures. In order to maximize its benefits and lessen the harm brought on by inadequate groundwater management in the city of Aswan, the height of the groundwater level in that city was examined, appraised, and groundwater management scenarios were established in this study. To achieve the objectives of the study, a simulation of Aswan aquifer’s groundwater system is built based on a quasi-three-dimensional transient groundwater flow model using MODFLOW. The model was calibrated and verified. Four management scenarios are tested. The fifth scenario, in this scenario, the four scenarios combined together at the same time and with the same conditions and ratios were proposed to be implemented. The results of the proposal to implement the four scenarios together showed that the rates of decline in groundwater levels in the last stage will be 12.44%. The study results reveal that a better understanding of the simulated long-term average spatial distribution of water balance components is useful for managing and planning the available water resources in the Aswan aquifer.