Global environmental changes, such as climate change and reclamation alterations, significantly influence hydrological processes, leading to hydrologic nonstationarity and challenges in managing water availability and distribution. This study introduces a conceptual underpinning for the rational development and sustainability of groundwater resources. As one of the areas intended for the development projects within the Egyptian national plan for the reclamation of one and a half million acres; hundreds of pumping wells were constructed in the Moghra area to fulfill the reclamation demand. This study investigates the long-term impacts of exploiting the drilled pumping wells under climate change. The approach is to monitor the groundwater levels and the salinity values in the Moghra aquifer with various operational strategies and present proposed sustainable development scenarios. The impact of global warming and climate change is estimated for a prediction period of 30 years by using satellite data, time series geographical analysis, and statistical modeling. Using MODFLOW and Solute Transport (MT3DMS) modules of Visual MODFLOW USGS 2005 software, a three-dimensional (3D) finite-difference model is created to simulate groundwater flow and salinity distribution in the Moghra aquifer with the input of forecast downscaling (2020–2050) of main climatic parameters (PPT, ET, and Temp). The optimal adaptation-integrated scenario to cope with long-term groundwater withdrawal and climate change impacts is achieved when the Ministry of Irrigation and Water Resources (MWRI) recommends that the maximum drawdown shouldn’t be more significant than 1.0 m/ year. In this scenario, 1,500 pumping wells are distributed with an equal space of 500 m, a pumping rate of 1,200 m3/day and input the forecast of the most significant climatic parameters after 30 years. The output results of this scenario revealed a drawdown level of 42 m and a groundwater salinity value of 16,000 mg/l. Climate change has an evident impact on groundwater quantity and quality, particularly in the unconfined coastal aquifer, which is vulnerable to saltwater intrusion and pollution of drinking water resources. The relationship between climate change and the hydrologic cycle is crucial for predicting future water availability and addressing water-related issues.