Seabirds transfer nutrients from the ocean to their nesting island, potentially altering nitrogen (N) cycling within adjacent terrestrial and marine ecosystems. Yet, the processes involved in seabird‐N transfer along the land–sea continuum remain elusive. Using δ15N and δ18O measurements of groundwater nitrate, we demonstrate the role of brackish groundwater located within a coral island's landmass as a major reservoir of nitrate (at millimolar levels). Nearly all of the total dissolved seabird‐derived N leaching into the groundwater (mostly ammonium and uric acid) is converted to nitrate by nitrification, as supported by the relatively low δ18O of the groundwater nitrate (3.97‰ ± 0.30‰). Comparison of nitrate δ15N and δ18O suggests that little denitrification takes place within the groundwater lens, implying that the high δ15N of groundwater nitrate (13.73‰ ± 0.05‰) derives from the high trophic position of seabirds and postdepositional processes that increase the δ15N of seabird excreta. Seawater and coral skeleton samples from a reef flat exposed to groundwater had higher δ15N values than at sites devoid of groundwater influence, indicating that the main source of N at the latter site was the Subtropical Upper Water, while the groundwater nitrate dominated the exposed reef flat N pool up to 200 m from shore. In addition, these results indicate that coral‐bound δ15N can detect seabird‐derived nitrate δ15N, raising opportunities to reconstruct historical seabird‐N inputs to coral reefs in relation to climatic and other changes, such as the introduction of invasive species.