Coral reefs in the southwest Indian Ocean cover an area of ca. 18530 km2 compared with a global reef area of nearly 300000 km2. These regions are important as fishing grounds, tourist attractions and as a significant component of the global carbon cycle. The mass of calcium carbonate stored within Holocene neritic sediments is a number that we are only now beginning to quantify with any confidence, in stark contrast to the mass and sedimentation rates associated with pelagic calcium carbonate, which have been relatively well defined for decades. We report new data that demonstrate that the reefs at Rodrigues, like those at Réunion and Mauritius, only reached a mature state (reached sea level) by 2–3 ka: thousands of years later than most of the reefs in the Australasian region. Yet field observations show that the large lagoon at Rodrigues is already completely full of carbonate detritus (typical lagoon depth less than 1 m at low spring tide). The presence of aeolian dunes at Rodrigues indicates periodic exposure of past lagoons throughout the Pleistocene. The absence of elevated Pleistocene reef deposits on the island indicates that the island has not been uplifted. Most Holocene reefs are between 15 and 20 m in thickness and those in the southwest Indian Ocean appear to be consistent with this observation. We support the view that the CO2 flux associated with coral–reef growth acts as a climate change amplifier during deglaciation, adding CO2 to a warming world. southwest Indian Ocean reefs could have added 7–10% to this global flux during the Holocene.