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Large cities worldwide are increasingly suffering from a nexus of food, water, and energy supply challenges. This complex nexus can be analyzed with modern physico-economic system models. Only when practical knowledge from those affected, experts, and decision makers is incorporated alongside various other data sources, however, are the analyses suitable for policy advice. Here, we present a concept for “Sustainability Nexus Workshops” suitable for extracting and preparing relevant practical knowledge for nexus modeling and apply it to the case of Amman, Jordan. The experiences of the workshop participants show that, although water scarcity is the predominant resource problem in Jordan, there is a close connection between food, water, and energy as well as between resource supply and urbanization. To prevent the foreseeable significant degradation of water supply security, actions are needed across all nexus dimensions. The stakeholders demonstrate an awareness of this and suggest a variety of technical measures, policy solutions, and individual behavioral changes—often in combination. Improving the supply of food, water, and energy requires political and institutional reforms. In developing these, it must be borne in mind that the prevalent informal structures and illegal activities are both strategies for coping with nexus challenges and causes of them.