Understanding the hydrogeology of aquifers is fundamental to the management of groundwater resources especially in arid and semi-arid regions. However, understanding the responses of hydrogeological processes to climate change is complicated since climate change can affect hydrogeological processes directly and indirectly. This study aims at implementing a physically-based groundwater model to investigate the effects of climate change on groundwater system under fifteen General Circulation Models (GCMs) in a semi-arid region for the period of 2020-2044. A nonparametric method, Probability Density Function (PDF) estimator, was used to quantify the level of uncertainties in the simulations. The methodology was applied in an area of 2073 Km² in south-west Iran, consist of five plains; Western Dez, eastern Dez, Sabili, Deymche and Lor. Results indicate that there is a decline in recharge in April, May, June, and October. The range of changes in recharge were determined 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, -%40 and +%100 in the Lor plain. The most significant decline in groundwater level occurs in the Sabili plain in September. The largest uncertainty in simulation of recharge under GCM scenarios was determined in August, September, and December.