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As the world increasingly runs up against physical constraints of energy, land, water, and food, there is a growing role for policy to reduce environmental pressures without adversely affecting increases in prosperity. There is therefore a need for policy makers to understand the potential trade-offs and/or synergies between the uses of these different resources, i.e., to encompass the water–energy–food–land nexus for policy and decision making, where it is no longer possible to ignore the limitations in land availability and its links to other natural resources. This paper proposes a modelling approach to help to assess various policies from a nexus perspective. The global macro-econometric model (E3ME) explores a low-carbon transition through different sets of energy and climate policies applied at different spatial scales. The limitations of the E3ME model in assessing nexus interactions are discussed. The paper also argues and offers an explanation for why no single traditional or classic model has the potential to cover all parts of the nexus in a satisfactory way, including feedback loops and interactions between nexus components. Other approaches and methodologies suitable for complexity science modelling (e.g., system dynamics modelling) are proposed, providing a possible means to capture the holistic approach of the nexus in policy-making by including causal and feedback loops to the model components. Based on three case studies in Europe, the paper clarifies the different steps (from policy design towards conceptual model) in modelling the nexus linkages and interactions at the national and regional levels. One case study (The Netherlands) considers national low-carbon transitions at national level. Two other case studies (Latvia and southwest UK) focus on how renewable energy may impact the nexus. A framework is proposed for the generic application of quantitative modelling approaches to assess nexus linkages. The value of the nexus concept for the efficient use of resources is demonstrated, and recommendations for policies supporting the nexus are presented.