The demand for energy, water and food in Africa continues to increase, resulting in growing pressure on contentious multisector resource systems like the River Nile. The ongoing dispute over Nile resources could become a zero-sum game if addressed from a water-centric viewpoint. Understanding how energy system management impacts water infrastructure introduces new opportunities to solve water conflicts. Although benefit-sharing of water resources in the Nile Basin has been promoted to counteract water volume disputes, it has not yielded actionable solutions to the toughest negotiations over the past two decades. Here we develop a detailed and integrated energy–river basin system simulator of 13 East African countries, including the Nile Basin, and show how new electricity trade agreements between Ethiopia, Sudan and Egypt could help resolve the ongoing water dispute over the Grand Ethiopian Renaissance Dam. The results show that increasing energy trade can reduce Egyptian water deficits, reduce regional greenhouse gas emissions, increase hydropower generation in all three countries, reduce energy curtailment in Sudan and increase Ethiopia’s financial returns from electricity. This study underscores how spatial quantification of river–energy system interdependencies can help decision-makers find actionable multisector benefit-sharing solutions.