This paper is a reflexive analysis of a three-year participatory water research project conducted in the Upper East Region (UER) of Ghana, whose explicit objective was to initiate a multi-level dialogue to support the national Integrated Water Resources Management (IWRM) policy framework. The transdisciplinary team adopted the Companion Modeling approach (ComMod), using role-playing games and a computerized agent-based model to support the identification of a problemshed centered on issues of river bank cultivation, erosion, and flooding, and initiate a multi-level dialogue on ways that this problemshed could be tackled. On the basis of this experience, we identify three key criteria for transdisciplinary research to support innovative water governance: (1) the iterative adaptation of tools and facilitation techniques based on feedback from participants; (2) a common understanding of the objectives pursued and the approach used among researchers, who need to explicit their posture, and crucially; (3) the co-identification of a problemshed that diverse stakeholders are interested in tackling. Finally, we argue that the context in which research is funded and conducted in the development sector constitutes a challenge for researchers to be “participants like any other” in the projects they coordinate, which constitutes a barrier to true transdisciplinarity.