Water, energy, and food resource systems are under increasing stress. As we prepare to move toward more sustainable resource allocation and management strategies, it is critical that we quantify and model the interconnections that exist between these sectors. Such action will help guide decision making and planning for the future of these resources and related strategies. While there is no single cookbook method for “modeling the nexus,” this chapter provides a list of seven guiding questions to help conceptualize a nexus case, model it, and then assess it. The 7-Question nexus modeling guideline is demonstrated using three case studies that represent a wide spectrum of critical questions, involving stakeholders, at different scales.