The semi-arid regions of Iran have experienced severe water resources stress due to natural (e.g., drought) and anthropogenic (e.g., depletion of water in various sectors) factors. Assessing the impact of climate change on water resources and crop production could significantly help toward better water management and hence prevention of land degradation in this area. A hydrological model of the Razan–Ghahavand basin was used as a representative case study of a semi-arid region of Iran. Future climate scenarios in the mid-21st century were generated from four global circulation models (GCMs) with three scenarios under the fourth assessment report of Intergovernmental Panel on Climate Change emission projections. The GCMs have been downscaled based on observed data at 10 climate stations across the basin. The results showed that for the basin as a whole, the mean annual precipitation is likely to decrease while the maximum temperature increases. The changes in these two climate variables resulted in substantial reduction in groundwater recharge as the main source of water supply in this area. Furthermore, soil water content was decreased which resulted in the reduction of crop yield in rain-fed areas. Indeed, the risk of drought in the south and flooding in the north was high.