Inadequate resource utilization planning can impose considerable stress on ecosystems. It is essential to assess the health of watersheds and strategically manage the consumption of vital water, energy, and food resources. This study evaluated the impact of implementing the water-energy-food (WEF) nexus on the health of the Pishkuh Watershed in Yazd Province, Iran. The watershed's health was conceptualized using the pressure-state-response (PSR) framework alongside problem diagnosis. Various anthropogenic, hydrological, and environmental criteria were gathered or extracted based on data availability and accessibility. The primary crops were optimized through the WEF nexus, considering water and energy consumption, productivity, economic efficiency, and food availability while also considering the limitations of the sub-watershed cultivation area and the availability of water and energy resources. The optimal solution was integrated into the PSR framework at the sub-watershed level. The watershed's health was zoned at this scale, and normalized indicators yielded a health index of 0.53 for the entire watershed. The findings indicated that anthropogenic factors had the most pronounced impact on the region's health status. Furthermore, any decision-making regarding ecosystem management can influence the watershed's health. Consequently, applying the WEF nexus index maximization scenario within the PSR framework enhanced the health status of the Pishkuh Watershed to 0.55, reflecting an improvement of approximately 4%. Although the research results confirm a modest enhancement in watershed health due to applying the WEF nexus, they also suggest a relatively efficient use of water and soil resources. Therefore, it is crucial to maintain the sustainable use of existing resources and to encourage watershed residents to engage in responsible resource management.