We used a hydrological model for the Ganges, Brahmaputra, and Meghna River Basins to simulate runoff (streamflow) from the three river systems using the downscaled climate data at different scenarios. We used SWAT+ (Soil and Water Assessment Tool Plus), a process-based, semi-distributed hydrological and environmental model developed by the USDA Agricultural Research Service (ARS) and Texas A&M University. It is designed to simulate the impacts of land use, land management, and climate on water, sediment, and nutrient dynamics in complex watersheds over long periods. SWAT+ introduces a more flexible and modular architecture that allows for detailed representation of landscape units, hydrologic connectivity, reservoirs, channels, and management practices. It divides the watershed into spatially explicit hydrologic response units (HRUs) and landscape elements, enabling simulations of water flow, sediment transport, nutrient cycling, and crop growth. SWAT+ was applied at daily time steps and integrated with downscaled and bias-corrected climate data, soil, topography, and land use data to assess water resources availability in the GBM basins’ outlets in Bangladesh. Its improved structure makes it easier to analyze scenarios for climate change, land management, and policy evaluation. It also makes it easier to develop upstream boundaries for the other hydrodynamics model of the southwest coast region.