Climate change (CC) is impacting the hydrology in the basins of the Himalayan region. Thus, this could have significant implications for people who rely on basin water for their lives and livelihoods. However, there are very few studies on the Himalayan river basins. This study aims to fill this gap by presenting a water balance for the Brahmaputra River Basin using the Soil and Water Assessment Tool (SWAT). Results show that snowmelt contributed about 6% of the total annual flow of the whole Brahmaputra, 21% of the upper Brahmaputra, and 5% of the middle Brahmaputra. The basin-wide average annual water yield (AWY) is projected to increase by 8%, with the maximum percentage increase in the pre-monsoon season. The annual snowmelt is projected to decrease by 17%, with a marked decrease during the monsoon but an increase in other seasons and the greatest percentage reduction in the upper Brahmaputra (22%). The contribution of snowmelt to AWY is projected to decrease while rain runoff will increase across the entire Brahmaputra and also in the upper and middle Brahmaputra. The impact assessment suggests that the upper Brahmaputra will be most affected by CC, followed by the middle Brahmaputra. The results can be used to support future water management planning in the basin taking into account the potential impact of CC.