The STEPPING UP project is a collaboration between researchers at eight universities and research institutes across the UK to understand the interactions of water, energy and food (WEF), and how niche innovations across these systems could be built upon to deliver a STEP-change towards improving sustainability, in the context of a world responding to climate impacts and policies. This paper will present a synthesis existing modelling approaches for managing and understanding the water-energy-food nexus, and highlight key challenges and opportunities. Models of natural resource use and management in water-energy-food systems are becoming prolific and are based on many different paradigms/approaches. There are those that are process based and seek to explore the interdependencies amongst the biophysical components often through a specific water, energy or food security focus. Another emerging approach is the inclusion of disaggregated human decision making, targeted at most to dyadic interdependencies of the WEF, for the purpose of controlling and managing natural resources e.g water and energy. Decision making is complex, with the priorities of different stakeholders requiring consideration during the development of a decision support tool. There are limited models that can be used to understand the WEF, and its interaction and feedback with human decision makers. Of particular interest are the decision makers that produce, consume, manage and control resources at a range of scales. The paper will review the landscape of nexus models and tools from discipline perspectives. The challenges for nexus modelling and decision support tools will be presented and conclusions drawn on the most appropriate approaches for supporting decision making in the WEF Nexus.