Seabirds drive nutrient cycling across ecosystem boundaries by transporting significant quantities of nitrogen from marine to terrestrial environments. However, the fate and transformations of land to sea subsidies remains underexplored. We investigated N subsidies to tropical seabird breeding islands, and the influence on surrounding reef ecosystems. We reconstructed historical seabird populations and modelled N deposition across five islands in the tropical Indian Ocean. We collected and analysed the composition, transformations, and δ15N and δ18O signatures of guano, groundwater, and reef waters. Results indicate submarine groundwater discharge is the primary pathway of ornithogenic N to the reef flat. We demonstrate δ15N and δ18O are critical to interpreting the contribution of ornithogenic nutrients to the nearshore system. Furthermore, we suggest a combination of methods to balance N budgets and trace chemical transformations of N on seabird islands. Our deposition models showed strong species-specific discriminations, suggesting that previously employed methods may misrepresent historical ornithogenic inputs. The trends observed in our study provide the first evidence of seabird N depositions influencing nearshore N cycling across multiple islands. Our findings yield new insights into the ecological significance of seabird nutrients and inform restorations of functional seabird populations and ecosystem-wide nutrient dynamics.