The recognition of the interlinked nature of water, energy and food (WEF) resources has resulted in growing momentum to change the approaches for managing these interlinked resources. Initially, models were developed as a mean of integrated methodology for watershed management. Several frameworks and models have been proposed to help policymakers understand the complexity of the nexus and to assist with planning and regulating these resources. Most countries and governments manage these natural resources with different institutions that have their own mission and objectives, and with their own staff, data, measures and tools. This has mostly led to huge variations in terms of methodological approach to design these models, type of data used and eventually results interpretations and policies design. We conducted a review of current literature on the water–energy–food nexus to understand what’s known and what’s missing and identify key opportunities and challenges facing WEF design and modeling. Our analysis also identified the followings:•Our review reveals that there are a limited number of models and frameworks that address all WEF together and there are even fewer models and frameworks that has diverse methods and transdisciplinary approaches in analyzing the nexus. It’s essential as we design out modeling tools to analyze the nexus to incorporate several dimensions beyond the WEF sectors such as political, social and economic in order to reach nexus thinking and therefore address complexity of the multi-sectoral resources.•Agricultural sectors require significant amounts of energy as an input to production, yet few water–energy–food resource planning approaches have incorporated spatial cropping patterns and land use by combining energy and water requirements.•Policymakers are provided with an effective way to analyze the nexus on an aggregate level using macro-drivers, but these often omit the complexity of managing the resources at a smaller scale where other factors such as climate and geography have tremendous influence on supply and demand.•There are knowledge gaps pertaining the incorporation of spatial–temporal drivers as well as the spatial–temporal dynamics of resource availability or accessibility. This is a significant component in the WEF framework design as natural resources are subject to dramatic changes over space and time.•There are a considerable number of WEF framework and models that demonstrate promising tools to analyze the nexus but some of these models fall short of capturing interactions among nexus components due to lack of data sharing and availability.The increased regional and global variation in natural resources distribution over time and space creates a need to develop more sophisticated models that incorporate these drivers to support the planning and regulatory policy process. These models should also be flexible enough to be applied at varying geographic levels to support resource management at the national, regional, watershed and project levels. Integrating spatial–temporal drivers would result in more comprehensive models that can deliver better policies for sustainable development, increase synergies between institutions and improve social welfare.