A large population depends on runoff from Himalayan rivers. They provide enough water for drinking, domestic, industrial, and irrigation. Also, these rivers have a high hydropower potential. A lack of in-depth studies has made it difficult to understand how these rivers respond hydrologically to climate change and, thus, impact the environment. In this paper, modelling the Alkhnanda river system using the Soil and Water Assessment Tool (SWAT) has been conducted to understand the hydrological response and assess its water balance components. The result shows that the basin’s water yield and Evapotranspiration (ET) vary from 58-63% and 34-39% of precipitation, respectively. The amount of lateral runoff contributed by snowmelt to the Alkhnanda River ranged from 20-24%. SFTMP, TLAPS, SMTMP, CN2, SMFMX, and GW_DELAY is found most sensitive at the significance level less than 0.05, shows the contribution of the snowmelt is significant in streamflow while delay in the groundwater will affect the contribution of surface runoff and groundwater in the streamflow. Based on the results, it is highly recommended that the study area’s spatial and temporal hydro-meteorological data be strengthened to improve modelling.