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The complexity of understanding the groundwater resources in relation to climate change is caused by direct and indirect effects of climate change on hydrological processes. The study herein aims at implementing a physically based groundwater model to investigate the effects of climate change on groundwater system under 15 general circulation models (GCMs) in a semi-arid region from 2020 to 2044. A non-parametric probability density function estimator was used to quantify the level of uncertainties in the simulations. The method was applied to an area of 2073 km(2) in southwest Iran, consisting of five plains: western Dez, eastern Dez, Sabili, Deymche and Lor. The results indicate that there is a decline in the recharge in April, May, June and October. The range of changes in the recharge was determined to be between -10% and +13% in the Sabili plain, -6% and +10% in the Deymche plain, -4% and +10% in the western-Dez plain, -6% and +26% in the eastern-Dez plain, and -40% and +100% in the Lor plain. The most significant decline in the groundwater level occurred in the Sabili plain in September. The largest uncertainty in the simulation of recharge under GCM scenarios was determined to be in August, September and December. This study highlights that climate change can have a significant effect on groundwater resources in the region that reinforces the need for groundwater management plans and a long-term perspective.