Land-use and management practices on limed acidic and carbonate-bearing soils can fundamentally alter carbon (C) dynamics, creating an important feedback to atmospheric carbon dioxide (CO2) concentrations. Transformation of carbonates in such soils and its implication for C sequestration with climate change are largely unknown and there is much speculation about inorganic C sequestration via bicarbonates. Soil carbonate equilibrium is complicated, and all reactants and reaction products need to be accounted for fully to assess whether specific processes lead to a net removal of atmospheric CO2. Data are scarce on the estimates of CaCO3 stocks and the effect of land-use management practices on these stocks, and there is a lack of understanding on the fate of CO2 released from carbonates. We estimated carbonate stocks from four major soil types in Australia (Calcarosols, Vertosols, Kandosols and Chromosols). In >200-mm rainfall zone, which is important for Australian agriculture, the CaCO3-C stocks ranged from 60.7 to 2542 Mt at 0–0.3 m depth (dissolution zone), and from 260 to 15 660 Mt at 0–1.0 m depth. The combined CaCO3-C stocks in Vertosols, Kandosols and Chromosols were about 30% of those in Calcarosols. Total average CaCO3-C stocks in the dissolution zone represented 11–23% of the stocks present at 0–1.0 m depth, across the four soil types. These estimates provide a realistic picture of the current variation of CaCO3-C stocks in Australia while offering a baseline to estimate potential CO2 emission–sequestration through land-use changes for these soil types. In addition, we provide an overview of the uncertainties in accounting for CO2 emission from soil carbonate dissolution and major inorganic C transformations in soils as affected by land-use change and management practices, including liming of acidic soils and its secondary effects on the mobility of dissolved organic C. We also consider impacts of liming on mineralisation of the native soil C, and when these transformations should be considered a net atmospheric CO2 source or sink.