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Abstract This study aimed at supporting robust decision-making for planning and management of water–energy–food Nexus systems in the country of Jordan. Nexus priority challenges in Jordan were identified as (1) water scarcity, (2) agricultural productivity and water quality, and (3) shift to energy independence. We created a water–energy–food Nexus model that integrates three modelling frameworks: (1) the Water Evaluation and Planning system WEAP model to estimate water demands, supplies and allocation; (2) the MABIA model to estimate crop production, and, (3) a GIS-based energy modelling tool to estimate energy requirements of the water system. Through a set of scenario runs, results show how desalination is needed to address water scarcity, but it has to be coupled with low-carbon electricity generation in order to not exacerbate climate change. Improving water productivity in agriculture improves most of the studied dimensions across the water–energy–food security nexus; however, it does little for water scarcity at the municipal level. Reducing non-revenue water can have positive effects on municipal unmet demand and reduction of energy for pumping, but it does not improve agricultural water productivity and may have negative feedback effects on the Jordan Valleys aquifer levels. Energy efficiency can support energy-intensive projects, like desalination, by substantially reducing the load on the energy system, preventing increased emissions and achieving a more resilient water system. Finally, when all interventions are considered together all of the major drawbacks are reduced and the benefits augmented, producing a more holistic solution to the WEF Nexus challenges in Jordan.