The global hydrological cycle is susceptible to climate change (CC), particularly in underdeveloped countries like Pakistan that lack appropriate management of precious freshwater resources. The study aims to evaluate CC impact on stream flow in the Soan River Basin (SRB). The study explores two general circulation models (GCMs), which involve Access 1.0 and CNRM-CM5 using three metrological stations (Rawalpindi, Islamabad, and Murree) data under two emission scenarios of representative concentration pathways (RCPs), such as RCP-4.5 and RCP-8.5. The CNRM-CM5 was selected as an appropriate model due to the higher coefficient of determination (R²) value for future the prediction of early century (2021–2045), mid-century (2046–2070), and late century (2071–2095) with baseline period of 1991–2017. After that, the soil and water assessment tool (SWAT) was utilized to simulate the stream flow of watersheds at the SRB for selected time periods. For both calibration and validation periods, the SWAT model’s performance was estimated based on the coefficient of determination (R²), percent bias (PBIAS), and Nash Sutcliffe Efficiency (NSE). The results showed that the average annual precipitation for Rawalpindi, Islamabad, and Murree will be decrease by 43.86 mm, 60.85 mm, and 86.86 mm, respectively, while average annual maximum temperature will be increased by 3.73 °C, 4.12 °C, and 1.33 °C, respectively, and average annual minimum temperature will be increased by 3.59 °C, 3.89 °C, and 2.33 °C, respectively, in early to late century under RCP-4.5 and RCP-8.5. Consequently, the average annual stream flow will be decreased in the future. According to the results, we found that it is possible to assess how CC will affect small water regions in the RCPs using small scale climate projections.