This paper aims to summarize in detail the results of the climate models under various scenarios by temporal and spatial analysis in the semi-arid Karkheh Basin (KB) in Iran, which is likely to experience water shortages. The PRECIS and REMO models, under A2, B2 and A1B scenarios, have been chosen as regional climate models (RCMs). These regional climate models indicate an overall warming in future in KB under various scenarios. The increase in temperature in the dry months (June, July and August) is greater than the increase in the wet months (January, February, March and April). In order to perform climate change impact assessment on water resources, the Arc-SWAT 9.3 model was used in the study area. SWAT (Soil and Water Assessment Tool) model results have been obtained using present and future climate data. There is an overall reduction in the water yield (WYLD) over the whole of the KB. The deficit of WYLD is considerable over the months of April to September throughout KB due to the increase in average temperature and decrease in precipitation under various emission scenarios. Statistical properties in box-and-whisker plots have been used to gain further understanding relevant to uncertainty analysis in climate change impacts. Evaluation of uncertainty has shown the highest uncertain condition under B2.