The water resources carrying capacity (WRCC) is a crucial indicator for assessing the sustainability of regional development. This study integrates the gray water footprint (GWF) into the WRCC evaluation, constructing a comprehensive framework that encompasses five subsystems: water resources, society, economy, ecology, and climate. Using the CRITIC-TOPSIS model, the WRCC of Yunnan Province from 2012 to 2022 is analyzed, and a dynamic assessment is conducted through spatiotemporal hotspot and obstacle factor coupling analyses. The results show that the comprehensive WRCC of Yunnan decreased from 0.489 in 2012 to 0.477 in 2022, displaying an overall fluctuating downward trend with uneven spatial distribution. The per capita GWF and GWF load significantly impacted the WRCC within the social and ecological subsystems, respectively, highlighting the importance of water quality in the WRCC evaluation. The results reveal differing development trends in the dynamic changes of WRCC cold- and hotspots across various regions in Yunnan. Through coupling the obstacle factors of each regional subsystem, the main challenges and key measures for sustainable water resource development in each area are identified. This study optimizes the traditional evaluation framework by addressing shortcomings in water quality considerations, enriching the WRCC assessment, and providing a more comprehensive and accurate decision-support tool for regional development.