Below-ground organic matter, a primary component of mangrove carbon stock, is influenced by long-term sea-level history. Poor representation of organic matter dynamics across carbonate settings, particularly in the Southern Hemisphere, reduces confidence in models of carbon stocks. This study focussed on Low Isles, Great Barrier Reef, Australia; a carbonate platform that developed under millennia of relatively stable sea levels. Geochronology and sedimentation rates were quantified using 14C dating, 210Pb dating, and 240+239Pu and 236U bomb-pulse radionuclide dating across a gradient of tidal position, forest age and biomass. Radiometric dating confirmed modern peat development to ~50 cm depth in the older forest, and mapping confirms mangroves established on the reef flat ~200 years ago. This contrasts deep peats in Northern Hemisphere carbonate settings exposed to millennia of sea-level rise. Organic matter accumulation rates were greater in the older forest (~4.5 mm/yr), compared to the intermediate forest (~2.0 mm/yr). Accumulation rates suggest the sea-level rise threshold for mangrove resilience has not been reached but may be exceeded by the end of this century. This study provides information for predicting the response of mangroves to projected sea-level rise and for reconciling the effects on carbon cycling in carbonate settings.