The health and sustainability of a watershed are complex issues that must be evaluated from social, economic, and environmental perspectives using a variety of indicators. The objective of this study is to assess the sustainability and health status of the Khansar watershed in Yazd Province based on the modified WHSI model. This model, developed in accordance with local conditions in Iran and the available variables, includes 34 key variables, comprising 13 social variables, 5 hydrological variables, 10 water quality variables, and 6 land-use–related variables. In this study, ten-year data were collected for each variable and scored using quantitative methods. According to the results, 11 variables were in good condition, one variable was moderate, three variables were weak, and 19 variables were in a critical state. The WHSI model analysis showed that the social indicators were in a relatively better condition, whereas the hydrological, water quality, and land-use variables were predominantly in a critical state. The findings of this study also indicated that the health status of the Khansar watershed in Yazd, with a score of 74, falls within the intermediate health category, while its sustainability, with a score of 12, is classified as unsustainable. The results of this research provide a precise depiction of the critical variables and can serve as a foundation for formulating targeted management policies, improving the quality and quantity of water resources, restoring vegetation cover, controlling unsustainable exploitation, and strengthening climate adaptation programs. In doing so, it can play a significant role in enhancing resilience and improving the health and sustainability of the watershed.