Soil degradation is one of the most important issues all over the world. Characterizing and describing a watershed is key to develop action plans that prevent soil degradation. Morphometric analysis and its quantitative description are commonly used to describe a watershed and its drainage system; however, these methodologies are long, and their accuracy can be contested. In this paper, we present an alternative for watershed prioritization by coupling principal component analysis (PCA) with geographic information systems (GIS) for watershed prioritization using morphometric parameters and land cover with Normalized Difference Vegetation Index (NDVI). We use data of the Huehuetan river sub-basin, in Chiapas, Mexico, to operationalize our methodology. We found that the principal components (PC01, PC02, and PC03) had a variance more than the 92% in relation to morphometric parameters such as stream frequency (Fs), drainage density (D), elongation ratio (Re), and drainage texture (Dt). The highest priority was found in the upper part of the sub-basin; watersheds 07, 08, and 06 had the 1st, 2nd, and 3rd priority ranks, respectively, reflecting the importance to establish preventive and corrective measurements to reduce soil degradation and mitigate the effects in lower parts of the sub-basin. From our research, we concluded that the use of PCA is a good tool to discriminate the insignificant parameters from the analysis and improve quality of results. In addition, our methodological proposal saves time on the analysis of morphometric parameters and together with NDVI could be a good methodology for watershed prioritization in tropical and sub-tropical areas like basins located in the southeast part of Mexico. © 2021, Saudi Society for Geosciences.