The existence of coral reefs is dependent on the production and maintenance of calcium carbonate (CaCO3) framework that is produced through calcification. The net production of CaCO3 will likely decline in the future, from both declining net calcification rates (decreasing calcification and increasing dissolution) and shifts in benthic community composition from calcifying organisms to non-calcifying organisms. Here, we present a framework for hydrochemical studies that allows both declining net calcification rates and changes in benthic community composition to be incorporated into projections of coral reef CaCO3 production. The framework involves upscaling net calcification rates for each benthic community type using mapped proportional cover of the benthic communities. This upscaling process was applied to the reef flats at One Tree and Lady Elliot reefs (Great Barrier Reef) and Shiraho Reef (Okinawa), and compared to existing data. Future CaCO3 budgets were projected for Lady Elliot Reef, predicting a decline of 53 % from the present value by end-century (800 ppm CO2) without any changes to benthic community composition. A further 5.7 % decline in net CaCO3 production is expected for each 10 % decline in calcifier cover, and net dissolution is predicted by end-century if calcifier cover drops below 18 % of the present extent. These results show the combined negative effect of both declining net calcification rates and changing benthic community composition on reefs and the importance of considering both processes for determining future reef CaCO3 production.