Every year, Taiwan endures typhoons and earthquakes; these natural hazards often induce landslides and debris flows. Therefore, watershed management strategies must consider the environmental vulnerabilities of local basins. Because many factors affect basin ecosystems, this study applied multiple criteria analysis and the analytical hierarchy process (AHP) to evaluate seven criteria in three phases (geographic phase, hydrologic phase, and societal phase). This study focused on five major basins in Taiwan: the Tan-Shui River Basin, the Ta-Chia River Basin, the Cho-Shui River Basin, the Tseng-Wen River Basin, and the Kao-Ping River Basin. The objectives were a comprehensive examination of the environmental characteristics of these basins and a comprehensive assessment of their environmental vulnerabilities. The results of a survey and AHP analysis showed that landslide area is the most important factor for basin environmental vulnerability. Of all these basins, the Cho-Shui River Basin in central Taiwan has the greatest environmental vulnerability.