Understanding Food–Energy–Water (FEW) systems is crucial in order to plan for a resilient and sustainable future of interdependent urban–rural regions. While research tends to focus on urban transitions, the topic remains understudied relative to urban-rural regions. The often conflicting pressures in these regions (e.g., urbanization and growing crop production) may pose distinctive challenges where large urbanizations are adjacent to sparsely populated rural areas. These systems may further shift in response to local and global economic and demographic trends, as well as climate change. Identifying these complex system trajectories is critical for sustainability and resilience planning and policy, which requires the pooling of both urban and rural expertise across multiple disciplines and domains. We convened panels of subject matter experts within a participatory causal loop diagramming (CLD) approach. Our workshops were facilitated by our research team to collaboratively construct the web of connections among the elements in the urban–rural FEW system. The CLDs and the discussions around them allowed the group to identify potentially significant lever points in the system (e.g., support for minority farmers to enhance food security while reducing waste), barriers to sustainability (e.g., laws restricting the sale of water treatment biosolids), and potential synergies across sectors (e.g., food and green energy advocacy jointly pressing for policy changes). Despite the greater understanding of urban–rural interdependence afforded by participatory CLD, urban factors were consistently prioritized in the representation of the integrated system, highlighting the need for new paradigms to support sustainable urban–rural transitions.