A detailed model of the ocean circulation and carbon cycle was coupled to a mechanistic model of CaCO3 diagenesis in deep sea sediments to simulate the millennium-scale response of the oceans to future fossil fuel CO2 emissions to the atmosphere and deep sea. Simulations of deep sea injection of CO2 show that CaCO3 dissolution is sensitive to passage of high-CO2 waters through the Atlantic Ocean, but CaCO3 dissolution has a negligible impact on atmospheric pCO2 or the atmospheric stabilization CO2 emission in the coming centuries. The ultimate fate of the fossil fuel CO2 will be to react with CaCO3 on the seafloor and on land. An initial CaCO3 dissolution spike reverses the net sedimentation rate in the ocean until it is attenuated by an enhanced vertical gradient of alkalinity after about 1000 years. The magnitude of the initial spike is sensitive to assumptions about the kinetics for CaCO3 dissolution, but subsequent behavior appears to be less model dependent. Neutralization by seafloor CaCO3 occurs on a timescale of 5–6 kyr, and is limited to at most 60–70% of the fossil fuel release, even if the fossil fuel release is smaller than the seafloor erodible inventory of CaCO3. Additional neutralization by terrestrial CaCO3 restores a balance between CaCO3 weathering and seafloor accumulation on a timescale of 8.5 kyr, while the deficit of seafloor CaCO3 (the lysocline) is replenished with an e-folding timescale of approximately 18 kyr. The final equilibrium with CaCO3 leaves 7–8% of the fossil fuel CO2 remaining in the atmosphere, to be neutralized by the silicate rock cycle on a time frame of hundreds of thousands of years.