Twenty-first-century cities face challenges including potential food shortages, water scarcity, and dependence on nonrenewable energy sources. These are increasingly intensified by global population growth. The development of innovative solutions for the food-water-energy nexus requires transdisciplinary approaches across scales, boundaries, and sectors. The international, interdisciplinary research consortium CITYFOOD investigates the science and practice of aquaponics, an integrated food production system. The three-year research project focuses on the potential for scaling up the integration of aquaponic operations in cities. The team’s goal is to expand the knowledge around aquaponics by applying case study research, modeling, and GIS-based mapping methods across various built environment scales. Through projects like CITYFOOD, the growing understanding of interlinkages between food, water, and energy systems can contribute to a more sustainable future.