Based on the assumption that the water, energy and food sectors are linked, the nexus concept drives research into the integration of governance systems. Nexus governance requires actors to engage across policy domains, governance levels and public, private and civic spheres. There is a need for a better understanding of how stakeholders navigate the inter‐organisational networks constituting a given nexus. A three‐dimensional relational framework and corresponding methods for investigating nexus governance is presented in the article. Drawing on mixed‐methods network research with organisations implementing water, energy,agricultural and environmental policies in the Upper Blue Nile basin of Ethiopia, the authors demonstrate how their framework for investigating network structure, relations and narratives can inform a relational understanding of nexus governance.