Over the past few decades, a significant amount of agricultural land has been lost due to soil degradation/desertification. In addition, the increasing frequency of extreme events, such as intense droughts and forest fires, has negatively impacted various ecosystem services. Two of the main Brazilian biomes—the Cerrado and the Caatinga—have been affected by increased rainfall variability, leading to desertification, increased fire frequency, and, consequently, rising concerns regarding the water and food security of the local population. In this study, we develop a methodology to assess these impacts using a Socio-Environmental Vulnerability Index (SEVI) that combines physical, environmental, and socio-economic indicators related to exposure, sensitivity, and adaptation, as well as including socio-environmental feedback. The developed SEVI is then applied to the São Francisco and Parnaíba river basins. The proposed index is based on the MEDALUS methodology and is adapted to include multiple biological, physical, and socio-economic indicators, allowing for the discrimination of areas characterized by different levels of vulnerability. We also analyze the effectiveness of governmental policies, such as the creation of conservation areas and the rural registration of properties, in reducing vulnerability. The SEVI analysis highlights that adaptive capacity is the main constraint for reducing socio-environmental vulnerability in the Parnaíba basin, while exposure and sensitivity are the greater challenges in the São Francisco basin. The results of this study are crucial for the prioritization of recovery actions in degraded areas.