Consistent with recent observations, Coupled Model Intercomparison Project 5 Earth System Models project highest acidification rates in subsurface waters. Using seven Earth System Models, we find that high acidification rates in mode and intermediate waters (MIW) on centennial time scales (−0.0008 to −0.0023 ± 0.0001 yr−1 depending on the scenario) are predominantly explained by the geochemical effect of increasing atmospheric CO2, whereas physical and biological climate change feedbacks explain less than 10% of the simulated changes. MIW are characterized by a larger surface area to volume ratio than deep and bottom waters leading to 5 to 10 times larger carbon uptake. In addition, MIW geochemical properties result in a sensitivity to increasing carbon concentration twice larger than surface waters (ΔH+ of +1.2×10−4 mmol m−3 for every mmol m−3 of dissolved carbon in MIW versus +0.6×10−4 in surface waters). Low pH transported by mode and intermediate waters is likely to influence surface pH in upwelling regions decades after their isolation from the atmosphere.