A detailed geochemical groundwater survey was conducted within a carbonate sand subterranean estuary (STE) system on the tropical island of Rarotonga, Cook Islands, to identify N sources and transformation along the groundwater flow paths. There were two distinct sources of N to the STE: (1) local organic material which produced NH4+ in the anoxic deeper groundwater (3.5 - 4 m below the aquifer surface), and (2) an NO3- rich upper saline plume located in the shallow groundwater near the high tide mark of the STE. Ammonium concentrations decreased away from the organic source and the δ15N-NH4+ signature became increasingly enriched. The calculated kinetic fractionation factor for NH4+ loss was much less than that reported for nitrification in other systems, implying that mixing was important in reducing concentration. A simple fractionation/mixing model showed that NH4+ loss via nitrification increased towards the surface where it contributed up to 80% of the observed decrease in NH4+ concentration. A fast moving (~ 2 m d- 1) upper saline plume of shallow NO3- rich groundwater was a major feature of the studied STE. Denitrification was estimated to account for up to 88 % of the decrease in NO3- concentration in this plume. The potential denitrification rate based on an isotope tracer addition experiment was 270 μmol L- 1 d- 1. Assuming that similar NO3- rich plumes occur all along the foreshore of the studied lagoon, we estimate that groundwater can contribute 4 - 15 % of the daily lagoon N standing stock. We conclude that submarine groundwater discharge of shallow N rich porewater into the studied lagoon system is strongly regulated by denitrification within the STE.