In the twenty-first century, the world's demand for natural resources is more pressing and deeply interconnected than ever before. The Water-Energy-Food (WEF) nexus has gained growing interest as a promising concept for complex resource management challenges. However, knowledge about the root causes of cross-sectoral coordination problems and how they can be shifted towards sustainability is still lacking. This paper fills this gap by conceptualising a WEF nexus case with the Networks of Action Situations approach combined with systems thinking. This approach allows a deep analysis of the root causes of coordination gaps, facilitates a joint understanding of the system dynamics to identify leverage points for shifting the WEF nexus towards sustainability, and to envision the impact of potential interventions on the network of action situations and their outcome. The value and the reciprocal benefits of the combined approach introduced are illustrated for a case in Switzerland, Europe. The results show a coordination gap between the different sectors and that not all sectors were considered equally. This leads to a prioritization of energy production over water-bound biodiversity and food production. The root causes for this outcome are a focus to mitigate climate change and awareness of biodiversity but much less awareness of the impacts of climate change on Swiss water bodies. The study identifies five deep leverage points for interventions, which are expected to ensure a shared systemic problem understanding and more balanced coordination between different sectors resulting in the sustainable and equitable provision and utilization of WEF resources.