The historic pandemic faced by the international community today boldly demonstrates the complexity and interconnectedness of the resource challenges we must better understand and address in the future. Further complexity is observed when accounting for the impact of compounded shocks related to natural disasters and forced migration around the world. Effectively addressing these challenges requires the development of research that cuts across disciplines and innovates at their interfaces, in order to develop multifaceted solutions that respond to the social, economic, technological, and policy dimensions of these challenges. Water, energy, and food systems are tightly interconnected. They are faced with pressures of varying natures and levels of urgency which need to be better understood, especially as nations work toward achieving the UN 2030 Agenda’s Sustainable Development Goals by 2030. This paper will review existing models and knowledge gaps related to water-energy-food (WEF) nexus models, as well as models for quantifying the impact of migration, pandemics, and natural disasters on this resource nexus. Specifically, this paper will: (1) explore the WEF nexus literature and identify gaps in current assessment tools and models; (2) explore the literature on tools and models for predicting the shocks of migration, natural disasters, and pandemics; (3) identify interconnections between water, energy, and food systems and the identified shocks; (4) develop a common framework that provides a road map for integrating those shocks in WEF nexus analysis; (5) provide recommendations for future research and policies moving forward.