Groundwater is of great importance in our daily life, and its importance is due to its multiple uses, whether in agriculture, industry or other uses. Increasing the Groundwater Levels (GWL) in any area is a great benefit for its importance and multiplicity of uses, but in the city of Aswan, it is different, as the increase in the GWL causes severe damage to buildings and leads to poor quality of agricultural land and the destruction of infrastructure due to the lack of good management. The main objective of this study is to develop a conceptual model of the groundwater system to gain better understanding of water dynamics in the study area and to investigate different management scenarios of the use of groundwater. The model was developed using MODFLOW code to achieve the objective of the study, where the necessary field data were collected to feed the model from the study area, such as Surface Water Levels (SWL) in the Aswan Dam lake and the Nile River, GWL in the Aswan Aquifer and the different characteristics of the layers constituting the aquifer, such as porosity and recharge for different periods to ensure obtaining the most accurate and best results from the model. The model was calibrated with mean residual and absolute mean residual which reached −0.08 and 0.629 m, respectively, with a Root Mean Square Error (RMSE) of 0.737m and a normalized RMSE of 4.319%. Two future scenarios have been developed to arrive at a future vision of GWL in the Aswan aquifer. The first scenario investigated GWL in the study area by changing the values of recharge to the aquifer resulting from an increase in the drinking water and sewage networks’ leakage values, which were predicted in the future for years 2025, 2030, 2035 and 2040. The GWL in the study area are increasing as a result of the increase in the amount of leakage in the years 2025, 2030, 2035 and 2040 compared to the GWL in the study area for the year 2020 by 0.29%, 1.31%, 2.01% and 3.16%, respectively. The second scenario investigated GWL by changing the water levels in El hebs (the lake between the High Dam and the Aswan Dam) as follows (108 m, 110 m, 112 m, 114 m, 116 m and 118 m), where the groundwater levels were calculated in the Aswan Aquifer corresponding to each level. The percentage of increase in groundwater levels corresponding to the levels 108 m, 110 m, 112 m, 114 m, 116 m and 118 m compared to the groundwater levels at the level of 106 m was found as follows: 0.92%, 2%, 2.87%, 4.05%, 4.91% and 5.67%, respectively. The simulation results are intended to support integrated groundwater modeling for the components of the hydrological water budget in the city of Aswan. Furthermore, the model provides us with a better understanding of long-term scenarios for the waterlogging in the city. The results are useful for managing the water logging problems and planning the future infrastructure in the city of Aswan.