This study aims to show how future groundwater recharge (GR) simulations in arid areas respond to uncertainty in climatic parameters—a question, if explored, that bridges a gap in water resources management plans. To this aim, eight regional climate models (RCMs) under two representative concentration pathways (RCP4.5 and RCP8.5) projected four climatic parameters [surface air temperature, precipitation, wind speed, and potential evapotranspiration (PET)] over Qatar during the period of 2071–2100. Using topographic and groundwater data, a physically based water balance model was built to simulate future GR under these 16 scenarios. Results show high uncertainty in climatic parameters. Relative to the reference period (1976–2005), values varied under RCP4.5 (RCP8.5) from +1.8 to +3.4 (+3.8 to +5.6)°C for average temperature, −48% to +15% (−60% to +6%) for annual precipitation, −0.23 to +0.1 (−0.27 to +0.04) m/hour for wind speed, and from −5.7 to +12.8 (+4.3 to +17) mm for annual PET. Uncertainty in climatic parameters caused great uncertainty in future GR estimations. During the late 21st century, GR simulations varied from −67% to +64% with an average value of −20% under RCP4.5, and from −81% to +8% with an average value of −36% under RCP8.5. The greatest uncertainty resulted from the driving model, whereas the choice of emission scenario had a secondary impact. Since GR is a critical component of feeding arid aquifers, the study's findings emphasize the importance of both considering the uncertainty associated with climatic parameters and the regional climatic information chosen.