Middle East and North Africa (MENA) regions are increasingly concerned about water scarcity. Egypt, one of the arid MENA nations that relies primarily on Nile water, faces a water scarcity issue because of a mismatch between demand and supply. This study presents an integrated executive system for managing water resources in two regions of Egypt that have traits with many MENA regions facing water scarcities. Hydrological modeling is required for the modeling of water resources, and model calibration procedures should be implemented to compare the simulated values to the observed and measured values to minimize model errors. The Water Evaluation and Planning (WEAP) model was used in this study to simulate the network systems of Egypt’s Minia Governorate on the western bank of the Nile’s narrow valley and Nubariya in the West Nile Delta, the lower reaches of the Nile. Using field data and experience, as well as other inputs, geographic information system (GIS) software digitized streams using satellite-interpreted data. The models were run, calibrated, and validated. The main calibration objective was to reduce the discrepancy between the actual and modeled flows as much as possible. Nash–Sutcliffe efficiency (NSE), percentage BIAS (PBIAS), volumetric efficiency (VE), and agreement index (d) values were calculated for three calibration cases. For anticipating water shortages until 2050, two scenarios were examined: (1) climate change scenarios based on historical climatic data from 1960 to 1990 and from 1991 to 2020, which led to a prediction scenario (2021–2050) of increasing temperature in the areas leading to evapotranspiration (ET) increases of 5.42% and 5.13% and (2) canal lining scenarios, which found a flow saving in the areas, showing that we can overcome the anticipated water shortage progress if canal lengths are rehabilitated by 10% and 25% in Minia and Nubariya.