In this research, by using participatory approach, governance challenges have been evaluated from the perspective of influential and influenced actors in the Yazd-Ardakan plain. According to the water, food, energy nexus and considering interdependencies of these three sectors, in the first step, key players were identified. In the next step, according to the viewpoints of actors, the factors that led to excessive withdrawal of groundwater resources in each water, food and energy sector were identified as governance challenges. DPSIR framework was then used to assess the governance challenges specified by participatory approach. Eventually, the rules and infrastructure of the water, food, and energy sectors were evaluated. The results showed that in the water, food and energy, respectively, 11, 8, 2 challenges were identified which have led to pressure on groundwater resources. Finally, for the 21 identified challenges, 28 strategies for modifying groundwater governance were introduced that 11, 15 and 2 strategies related to water, food and energy sectors. The most important strategies identified in water, food and energy sectors are include: improvement of legal structures for sealing of all unauthorized wells, establishment of formal water market, empowerment of actors, convergence of assessment criteria of water and food organizations, modify planting plans and food market control, pricing of water and energy resources. The results of this study can help planners and policymakers to reform the laws and infrastructure for modifying groundwater governance and improving the status of aquifers.