Water and nutrient savings can be established by coupling water streams between interacting processes. Wastewater from production processes contains nutrients like nitrogen (N), which can and should be recycled in order to meet future regulatory discharge demands. Optimisation of interacting water systems is a complex task. An effective way of understanding, analysing and optimising such systems is by applying mathematical models. The present modelling work aims at supporting the design of a nearly emission-free aquaculture and hydroponic system (aquaponics), thus contributing to sustainable production and to food security for the 21st century. Based on the model, a system that couples 40 m3 fish tanks and a hydroponic system of 1,000 m2 can produce 5 tons of tilapia and 75 tons of tomato yearly. The system requires energy to condense and recover evaporated water, for lighting and heating, adding up to 1.3 GJ/m2 every year. In the suggested configuration, the fish can provide about 26% of the N required in a plant cycle. A coupling strategy that sends water from the fish to the plants in amounts proportional to the fish feed input, reduces the standard deviation of the NO3− level in the fish cycle by 35%.