The water-energy-food nexus lens highlights the complex relationships and multiple sources of uncertainty that affect the achievement of global sustainable development. Such complexity and uncertainty requires future-oriented research that is effective in gathering experience across disciplines, sectors and scales. Scenario analysis is a proven method for decision support in conditions of uncertainty, shown to provide opportunities for learning that supports transformational change. There are, however, few scenario studies that examine the water-energy-food nexus. This paper presents a novel morphological method for developing and analysing transdisciplinary scenarios that cover the water-energy-food nexus. The method combines existing research to generate of a small suite of scenarios that are able to portray substantial complexity and multidimensionality, yet are fit for use within participatory research. The potential of this method to enhance nexus thinking is discussed, illustrating how it could provide a much-needed platform to support the transition towards sustainability across the nexus. By providing a platform for transdisciplinary dialogue, the scenarios disturb existing assumptions, reintroduce social and justice questions to the technical challenges that face the nexus, and build capacity for sustainable transformation. Further research is required to apply this approach so it can support tangible changes in decision making.