The social relations and biophysical flows that link water, food, and energy systems are said to form a ‘nexus’. Efforts to steer or otherwise exert influence on decisions that impact upon these nexus links, including to ignore them, take place at multiple levels, vary in complexity, and have implications for who benefits and who is burdened by those relations and flows. This paper examines how nexus links have been governed, using four medium- to large-scale water infrastructure projects in Laos and Thailand as probes into problematic issues of coordination, anticipation, inclusion, and attribution. Project documents, media reports, and published analyses were coded to extract information about nexus links, narratives, and decisions. Nexus interactions were summarized using a novel symbolic notation and then classified along a scale of increasing structural complexity as pairs, chains, and loops. The key finding from the analysis of the four projects was that nexus governance was fragmented, reactive, exclusive, and opaque. Coordination among ministries was limited with inter-ministerial bodies, and integrated development plans ineffective at guiding project design or operation decisions in the presence of bureaucratic competition. Anticipation of cross-sectoral concerns was rare, despite scope to identify them early in feasibility studies, and assessment activities; instead they were only acknowledged after public pressure. Inclusion of the needs of vulnerable and affected groups was limited, although poverty alleviation, and other social benefits were a significant element in project justification narratives. Attribution of responsibility was difficult as many key decisions took place behind closed doors, while project information was withheld, raising further governance issues of transparency and accountability. Structural complexity in the nexus links made addressing governance problems even more challenging.