<p>Vulnerability assessment is crucial for water resource management, particularly within the context of climate change. This study develops an innovative methodology for assessing watershed vulnerability in data-scarce regions by integrating the Analytical Hierarchy Process (AHP) and the Group Method of Data Handling (GMDH). This developed approach addresses the limitations of traditional methods, which often struggle with data scarcity and fail to capture the complex, non-linear interactions between climatic, hydrological, and socio-economic factors. To address this, we developed a Vulnerability Index (VI) for two different cases, integrating 11 different hydrometeorological variables and socio-economic factors. The VI quantifies watershed vulnerability under distinct climate change scenarios (SSP1-2.6 and SSP5-8.5) with sensitivity analysis. To demonstrate the method, four major river basins, namely Gomati, Haora, Khowai, and Manu in the Northeast India (NEI) are considered. The method is able to quantify the level of vulnerability through VI values, and identify catchments that are highly vulnerable. For instance, the Haora and Gomati Rivers are highly vulnerable indicating VI value more than 0.85 under the SSP5-8.5 scenario. Sensitivity analysis identifies rainfall, runoff, and temperature as the most responsive parameters, highlighting their critical role in watershed vulnerability. The method can be applied to basins in other regions as well, and the results provide valuable information for watershed management and secure water availability amidst the challenges posed by climate change and increasing population.</p>