There are a multitude of challenges confronting resource-limited, rapidly growing cities that revolve around food-water-energy (FWE) resource issues, and there are a multitude of potential solutions. But such solutions often address one or just a few challenges without regard to their impacts on the entire FWE system. This Working Paper discusses a process in integrating local knowledge on FWE nexus challenges and solutions in Pune and Amman in the development of an integrated systems model. We contextualize the process theoretically and point out why the investigation of complex societal problems such as the provision of FWE resources needs a transdisciplinary research setting. We elaborate on the role of stakeholder engagement in such settings and deepen the understanding of living labs as an approach for stakeholder engagement.