The combination of a Recirculation Aquaculture System (RAS) and Integrated Multi-trophic Aquaculture (IMTA) aims to optimize the utilization of nutrient input by recycling aquaculture wastes through use as food resources for co-cultured species. The coupling of RAS and IMTA also allows the development of new aquaculture products, potentially increasing economic return. A dynamic nutrient mass balance model was developed for a seawater-based RAS system with a hypothetical IMTA component. The model incorporated a three-dimensional trophic food web (Atlantic salmon, Ulva lactuca and an invertebrate grazing species) alongside traditional mechanical and biological (nitrification) filtration processes. The model simulated different waste treatment methods using biological and mechanical filtration only and further incorporating macroalgae filtration. Simulations showed that RAS in combination with macroalgae IMTA could reduce dissolved inorganic nitrogen (DIN) by 66% and dissolved inorganic phosphorus (DIP) by 31% compared with just RAS biological filtration. Using an optimal harvesting strategy, DIN and DIP waste removal rose to 94% and 45% respectively, and an increase in by-products biomass of 41%. The dynamic nutrient mass balance model provides a quantitative tool to better understand the fate of nutrients, and to optimize the design of the system. Although the commercial-scale development of this type of aquaculture system will depend on feasibility and profitability, the concept of combining RAS and IMTA provides important potential for sustainable aquaculture in the future.