The watershed prioritization of soil erosion-affected areas is an utmost requirement to formulate management and conservation practices. In this study, a geospatial framework integrated with multivariate statistical techniques such as principal component analysis and hierarchical clustering was used to prioritize the fragile ecosystem, i.e., the upper Ghaggar watershed. It is one of the least studied seasonal river watersheds in northern India, which carry substantial monsoon flows. The drainage characteristics were inferred using the interferometrically derived Sentinel 1A/1B digital elevation model (spatial resolution-13.96 m). The study area was further divided into 92 sub-watersheds (32 fourth and 60 third-order) using ArcSWAT. Twenty-seven linear, areal, and relief aspect parameters were exploited to study the watershed's hydrological, lithological, and geomorphological characteristics. The categorization and correlation of these parameters were attempted using principal component/factor analysis, which resulted in five components having an eigenvalue greater than 1. The factor analysis resulted in magnitude, relief, drainage composition, and dissection intensity factor, which accounted for percentage variance of 39.96, 27.70, 10.32, and 9.80%, respectively, which account for 87.78% of the total variance. Finally, the morphometric parameters were grouped into three priority clusters in which 29, 46, and 17 sub-watersheds fall in high, medium, and least priorities clusters, respectively. The methodology adopted in this study provides vital information for watershed characterization and prioritization, which can serve as a criterion for the decision-makers in sustainable planning and management of the resources prevalent within the watershed.