The paper introduces a framework and set of methodologies that define the linkages between the interconnected resources of water, energy and food, and enable explicit corresponding quantifications. The paper presents a new water–energy–food (WEF) Nexus modelling tool (WEF Nexus Tool 2.0) based on that framework which offers a common platform for scientists and policy-makers to evaluate scenarios and identify sustainable national resource allocation strategies. The tool is applied to a case study focusing on Qatar, a hyper-arid Gulf country.