A basic objective of hydro-solidarity is the integrated, unified management of shared water resources. As water flows down a gradient across the landscape, the relationship between upstream and downstream entities and the connection between terrestrial (land-based) conditions and water resources must be considered for effective water management. These interlinkages required coordinated management efforts within watershed or river systems not only for the efficient use and conservation of the resources but also to avoid or resolve water-related conflicts and hydrological disasters. Assessment of sediment yield from reach and prioritization of watershed is one of the major concerns in mountainous regions for watershed management and prevention and mitigation of hydrological disaster. In this study, Soil and Water Assessment Tool (SWAT) model is operated to quantify the sediment yield from the Bhagirathi basin and prioritize the sub-basin of high risk. The inputs required for the model are the Digital Elevation Model (DEM), land use land cover, soil, and weather data. Further, the calibration and validation of the model is carried out using the Sequential Uncertainty Fitting (SUFI-2) algorithm in the SWAT Calibration and Uncertainty Program (SWAT-CUP). The model was calibrated for 2005–2014 and validated for 2015–2019 with 4 years of warm-up period. The statistics of indices were up to the mark. R2 and NS for calibration are 0.94 and 00.88, respectively, for validation, it is 0.81 and 0.79. P-factor and R-factor for the calibration period are 0.72 and 0.71, respectively, for validation the values are 0.60 and 0.80, respectively. The research summarizes that the sub-basin 4 is at high risk with a sediment yield of more than 50 metric tons per hour and about 90 × 106 tons of sediment out of the watershed into the reach. The study also highlights how assessment of sediment yield from reach and prioritization can help mitigate and prevent hydro disasters. Also, it augments hydro-solidarity between public and private institutions and governments to tackle future problems.