Integrated agriculture and aquaculture systems (IAAS) allow nutrients, energy, and water to flow throughout the components of the system, increasing the efficiency with which inputs are converted to food. Yet effectively designing an IAAS requires understanding how nutrients accumulate and alter the system's productivity. Here we developed a mechanistic model for nitrogen transport and utilization and parameterized it using the IAAS in He'eia, Hawai'i. Of note, we modeled tidal influence, which extends existing IAAS models that often assume aquaculture in tank enclosures. We simulated the impact of nitrogen loading from three possible land use scenarios across agriculture and development priorities on the productivity of the fishpond downstream. We projected that organic nitrogen and nitrate concentrations parallel the successive increases in nitrogen loading across management strategies. Autotroph and fish densities were predicted to follow similar trends in response to increased nitrogen availability, causing fish harvests to increase from the current land use (25 kg/ha) to the restored agriculture (35 kg/ha) and urban (50 kg/ha) alternatives. While fish harvests were predicted to be highest in the urban scenario, modeled caloric production in the restored scenario from agriculture and aquaculture would sustain 235 people (4.3 people/ha) in the He'eia IAAS, 16 and 125 times more than the current or urban land uses, respectively. Restoring diversified agriculture was also predicted to retain a larger proportion of nitrogen inputs (0.43) than urbanizing the region (0.30), which would reduce nitrogen export to the adjacent Kāne'ohe Bay. Several state variables were notably sensitive to tidal flux rates, highlighting the importance of incorporating tidal dynamics into a coastal IAAS model. This model provides valuable insights for the management of existing coastal IAAS and design of new IAAS in coastal regions to improve the sustainability of future food systems.