Model predictions suggest that the saturation state of surface ocean waters with respect to carbonate minerals will decline during the twenty-first century owing to increased invasion of atmospheric CO2. As a result, calcareous organisms may have difficulty calcifying, leading to production of weaker skeletons and greater vulnerability to erosion. Alternatively, it has been suggested that there will be no significant impact on coral reef ecosystems because any changes in saturation state and pH will be restored by dissolution of metastable carbonate minerals. To resolve this controversy, we employ a physical-biogeochemical box model representative of the shallow-water ocean environment. Numerical simulations demonstrate that the carbonate saturation state of surface waters could significantly decrease and hamper the biogenic production of CaCO3 during the twenty-first century. Similarly, the average saturation state of marine pore waters could decline significantly, inducing dissolution of metastable carbonate phases within the pore-water–sediment system. Such dissolution could buffer the carbon chemistry of the pore waters, but overlying surface waters of reefs and other shallow-water carbonate environments will not accumulate sufficient alkalinity to buffer pH or carbonate saturation state changes owing to invasion of atmospheric CO2.