Governance has become a cornerstone in addressing complex linkages between multiple resources such as water, energy, and food. However, contributions of governance research in interdisciplinary research projects are either lacking or highly controversial. Drawing on Integrated Water Resources Management-related experiences of German research projects in emerging and developing countries, we demonstrate how to strengthen NEXUS-related governance analyses: There has to be a stronger focus on the analyses of existing and useful governance strategies as well as of conditions for governance transitions; governance analyses should refer to different types of problems, instead of only focusing on single cases and abstract analyses; and answers must be based on a more elaborate practice of inter- and transdisciplinary research. These suggestions should be implemented on the level of single researchers, but should also require incentives on an institutional level.