A robust hydrological assessment is a challenging task in regions of limited hydro-climatological information. This level of uncertainty is further augmented in studies of flood hydrology for regions like the Brahmaputra River basin, where spatial variations of topography, land use, soil, and weather components are very high. The present study describes the development of a suitable hydrologic model for the data-scarce transboundary Brahmaputra River basin occupying an area of more than 5,42,000 km2. The main objective is to provide hydrologic assessment of the Brahmaputra River basin, even at locations having hardly any historical records. The Soil and Water Assessment Tool (SWAT) model is calibrated and validated using observed discharge of three sections located on the main stem. The results show a fair strength of the statistical parameters. Moreover, the model has been found to produce a satisfactory replica of historical flows at the tributaries with a fair value of correlation (R2 = 0.77) at Golaghat. The results of this model would facilitate the ability of the local authorities with science-based elements to carry out decisions on the management of water resources at the main basin, and even at the sub-basin level.