Providing both fish and plants with optimal environmental conditions is a classical problem in the field of aquaponics. Several studies have tackled this problem by decoupling fish and plant systems. However, in order to achieve both high nutrient levels for the plants and low nutrient and particulate loading in the fish tanks, suspended matter in the aquaculture component needs to be discharged and fertilizer needs to be added to the plants continuously. The present study aims to explore to what degree desalination technology could potentially be used to provide the necessary balance between the two different components based on a theoretical modelling approach using contemporary source material. We suggest how specific desalination engineering approaches can improve the nutrient balances in multi-loop aquaponics systems in order to attain optimal growth conditions for both fish and plants.