Socio-ecological systems are vital for integrated urban and rural environments. Causal loop diagrams (CLDs) help identify system connections and future planning and policy interventions. This article applies graph theory to the assessment of a CLD of the Food – Energy – Water nexus in integrated urban – rural regions, drawn within a participatory modeling effort with domain experts. We applied well-known measures and developed a new method that considers the loop-based structure of the system. The loop-based structure complements well-established node- and network-based metrics by identifying hidden leverage points that may play a crucial role in disseminating systemic change. Our multi-method approach allows us to identify the most transformative lever points, distinguishing between initiators (e.g., non-commodity local food products, urbanization, and local budgets) from reinforcers of change capable of cementing these transitions by bridging across the system (e.g., climate activism, recreational space, and water pollution). Our analysis confirms some insights derived through the conversations shaping and shaped by the collaborative causal loop diagramming. With our approach, we also find that some policies, while popular in the literature and professional circles, may not be transformative due to their location within the interconnected system. Our approach thus strengthens the contribution of participatory CLD processes to complex problem-solving and policy design.