Aquaponics is a technique that combines aquaculture with hydroponics, i.e. growing aquatic species and soilless plants in a single system. Commercial aquaponics is still in development. The main challenge consists in balancing the conditions required for the growth of multiple species, leading to dynamic a system with high complexity. Mathematical models improve our understanding of the complex dynamics in aquaponics, and thus support the development of efficient systems.We developed a water and nutrient management strategy for the production of Nile tilapia (Oreochromis niloticus) and tomato (Solanum lycopersicum) in an existing INAPRO aquaponic demonstration system in Abtshagen, Germany. This management strategy aims for improved water and nutrient efficiency. For this purpose, we developed a system-level mathematical model and simulation.In our simulations, we found that the existing configuration and water management of the Abtshagen aquaponic system results in an excessive amount of water discharged from the RAS. Therefore, sending more nutrient-rich water from fish to plants can help reducing water and fertilizer consumption. However, this water transfer may lead to excess concentrations of some nutrients, which could stress fish, plants or both. For the Abtshagen system, our simulations predicted excess concentrations of total suspended solids (TSS) for the fish, and sodium (Na+) and ammonium nitrogen (NH4+-N) for the plants. Furthermore, our simulations predicted excess calcium (Ca2+) and magnesium (Mg2+) for plants, due to the use of local fresh water with relatively high concentrations of those ions.Based on our simulations, we developed an improved management strategy that achieves a balance between resource efficiency and water quality conditions. This management strategy prevents excess levels of TSS for fish, and Na+ and NH4+-N for plants. Under the improved management strategy, simulated water requirements (263 L/kg fish and 22 L/kg tomato) were similar to current commercial RAS and greenhouse horticulture. Simulated fertilizer requirements for plants of N, Ca and Mg (52, 46 and 9 mg/kg tomato, respectively) were one order of magnitude lower than in high efficient commercial closed greenhouse production.