Groundwater is the main water source in arid climate regions. Climate change and extensive groundwater exploitation will stress the groundwater resources in the upcoming decades. Therefore, groundwater quantity and quality should be assessed. In this study, we focused on groundwater quantity, including recharge and storage (using groundwater level as an indicator) to predict system vulnerability. The northern portion of El-Qaa Plain was chosen as a case study because the aquifer is coastal, arid, over-exploited, and naturally replenished via seasonal precipitation events. To project groundwater recharge under climate change and future exploitation, Water and Energy Transfer between Soil, Plants, and Atmosphere under quasi-steady State (WetSpass) was applied. Modular Finite Difference Groundwater Flow Model (MODFLOW) was utilized to project the groundwater level. Future climate ensembles were acquired from Regional Climate Models (RCMs) of Coordinated Regional Downscaling Experiment (CORDEX) datasets for the EURO 11 domain. The ensembles were bias-corrected using the Delta Change Factor (DCF) method. The results indicate that groundwater resources will be severely affected by climate change, as recharge might drop by nearly 35% to 75% during 2071–2100 for moderate and severe change ensembles. The mean groundwater level might decline by around 7–8 m by 2100 for the same ensembles. Regarding over-exploitation, the maximum drawdown will rise to approximately 16 m (no change in abstraction rate), to 36 m (increase in abstraction rate), and 7 m (decrease in abstraction rate). The results might aid decision-makers and stakeholders developing sustainable water resource management plans for the area.