Total contribution of six recently discovered submerged coral reefs in northern Australia to Holocene neritic CaCO3 and CO2 is assessed to address a gap in global budgets. CaCO3 production for the reef framework and inter-reefal deposits is 0.26–0.28 Mt. Holocene CO2 production is 0.14–0.16 Mt. Coral and coralline algae are the dominant sources of Holocene CaCO3 although foraminifers and molluscs are the dominant constituents of inter-reefal deposits. The total amount of Holocene neritic CaCO3 produced by the six submerged coral reefs is several orders of magnitude smaller than that calculated using accepted CaCO3 production values because of very low production, a ‘give-up’ growth history, and presumed significant dissolution and exports. The contribution of submerged coral reefs to global Holocene neritic CaCO3 is estimated to be 0.26–0.62 Gt, which yields 0.15–0.37 Gt of CO2. This amount of CO2 is 0.02–0.05% of the 780 Gt added to the atmosphere since 18 kyr BP. Contributions from Australian submerged coral reefs are estimated to be 0.05 Gt CaCO3 and 0.03 Gt CO2 for an emergent reef area of 47.9 × 103 km2. Based on the growth history of the submerged coral reefs in the Gulf of Carpentaria, maximum global Holocene CaCO3 fluxes could have attained 0.3 Gt yr−1 between 11 and 7 ka BP. This additional CaCO3 would have culminated in a maximum CaCO3 production from all (emergent and submerged) coral reefs of 1.2 Gt yr−1 and neritic CaCO3 production of 2.75 Gt yr−1. The dilemma remains that the global area and CaCO3 mass of submerged coral reefs are currently unknown. It is inevitable that many more submerged coral reefs will be found. Our findings imply that submerged coral reefs are a small but fundamental source of Holocene neritic CaCO3 and CO2.