We use an innovative methodology to model the socio-economic linkages between water, energy, and food in the East Nile Basin. Based upon a theoretical nexus framework, the methodology is expanded into a quantifiable modeling suite that under-lies the analysis of each of three country case studies. The advantages are that, despite resource shortages being a challenge, the modeling suite aids in devising policies and strategies that formulate these sectoral interdependencies and provide the evidence-based research results necessary for their design in a way that exploits synergies existing across sectors, countries, and regions (Al-Zubari n.d.). This paper lays out the methodology and gives an example of an application and scenarios by focusing on three coun-tries in the East Nile Basin. This methodology paper will be followed by three individual country case studies that highlight the water, energy, and food nexus for each.