Over the past four decades, the decline in groundwater levels has accelerated in 30% of the world's regional aquifers, resulting in over-exploitation and threatening billions of people's health and well-being. Good groundwater governance is becoming more widely recognized as a prerequisite for addressing aquifer depletion. Despite advocacy for inclusive governance and the involvement of community-based institutions and market mechanisms, governance modes have mainly relied on state-run strategies to control groundwater (over)abstraction. Nevertheless, existing research indicates that state-centered groundwater governance is predominantly ineffective. In addition to existing "in the shadow of hierarchy," the growing complexity of problems necessitates a shift towards polycentric governance. However, none of the ideal types of governance mode has proven to result in sustainable groundwater use. A holistic and interconnected view of the entire agri-food water system is crucial for addressing water resource limitations, reducing poverty, building local socio-economic system adaptive capacity, and capturing market opportunities. An integrated value chain diagnostic approach can facilitate such analysis. This study aims to develop a framework for bridging the gap between the value chain (VC) approach and groundwater governance, using the Institutional Analysis and Development framework (IAD) as a lens. The framework addresses the VC selection, measuring VC performance, understanding the root causes of underperformance, and improving the VC. The framework is applied empirically to the Najaf-Abad aquifer in Iran. The findings indicate that despite several value-chain analysis tools, economic considerations continue to be prioritized over environmental impacts. The conceptual frameworks of these guides cover various aspects, including VC upgrading (process, product, function, chain), VC governance (market, modular, relational, captive, hierarchy), market context and power dynamics, as well as synergy, efficiency, and competitiveness. Diagnosing VC governance can reveal various institutional arrangements that facilitate coordination processes, assess vulnerabilities and hotspots within the VC, and identify leverage points for interventions. However, the improvement of VC alone is insufficient to address the ineffectiveness of state-centered groundwater governance, which arises from a lack of political will and state capacity. Consequently, a synergistic interplay of governance modes is of the utmost importance.