The Bheri River Basin (BRB) in Nepal, located in the Himalayan region, is currently experiencing significant hydrological shifts due to climate change. This research aims to evaluate the potential impacts of climate change on the hydrological patterns of the BRB using future climate projections derived from downscaled CMIP6 GCM models. The Soil and Water Assessment Tool (SWAT) hydrological model was employed to simulate hydrological processes. The model demonstrated strong performance on both monthly and daily time scales. Projections indicate that the average annual temperature in the basin will increase by 0.8°C and 1.9°C under the SSP245 and SSP585 scenarios, respectively, for the future period (2071–2100) compared to historical values (1985–2014). Additionally, precipitation is expected to increase slightly, by approximately 10% under both scenarios. These findings suggest that the combination of increased rainfall and enhanced snowmelt due to higher temperatures will lead to a rise in the discharge of the Bheri River. Specifically, projected discharge is estimated to increase by 12% under SSP245 and 22% under SSP585. Overall, the results indicate an increase in average annual discharge, with more pronounced changes under the high-emission scenario. However, on a monthly scale, river discharge is expected to decrease by 10% in January, February, and March, while it could increase by up to 60% in June. This shift in runoff patterns poses challenges for water users, particularly for planned storage/peaking hydropower and irrigation projects during the dry season. In conclusion, this study highlights the importance of understanding potential hydrological shifts driven by climate change in the Bheri River Basin.