The world is facing serious problems of which population rise, climate change, water scarcity, and food security are among the most important. Aquaponics, consisting of aquaculture and hydroponics elements, could contribute to addressing these problems. In this project, zero-waste coupled and decoupled desert aquaponic systems, including separated anaerobic digestion of fish sludge and plant waste, are investigated through lab-scale experiments and pilot farming. Computer simulations support the design of nutrients and bioenergy recovery processes and are used to compare the coupled and decoupled aquaponics system configuration.