The Himalayan rivers are the major source of freshwater resources and have a tremendous potential for hydroelectric generation. However, assessing the water availability under climate change is challenging due to data scarcity, undulating topography, and complex climatic conditions. SWAT modeling investigates all potential consequences of variations in climate on the hydrological fluxes in the Upper Bhagirathi River Basin. Two global circulation models (GCMs) with three different climatic scenarios were employed. Quantile mapping has been used to correct the bias of GCM data. The developed model accurately simulated streamflow during calibration and validation at daily (NSE = 0.79 − 0.74, r = 0.89–0.87, and RMSE = 61.95 m3/s–79.75 m3/s) and monthly (NSE = 0.92 − 0.93, r = 0.96–0.97, and RMSE = 34.19 m3/s–37.39 m3/s) time steps. The analysis of the outcomes from MIROC6 and NorESM2-LM revealed that the rise in streamflow, surface runoff, lateral flow, and baseflow is more pronounced in MIROC6 across all three climatic scenarios. Under all scenarios, both MIROC6 and NorESM2-LM models show significant variations in snowfall and snowmelt patterns, with the area under snowfall reaching up to 51.65% for MIROC6 under SSP1-2.6 and snowmelt area peaking at 64.30% for MIROC6 under SSP2-4.5. This study’s findings will offer essential insights for policymakers, practitioners, and water resource managers in developing climate-resilient strategies for sustainable water management in Himalayan catchments.