Oceans worldwide are undergoing acidification due to the penetration of anthropogenic CO2 from the atmosphere. The rate of acidification generally diminishes with increasing depth. Yet, slowing down of the thermohaline circulation due to global warming could reduce the pH in the deep oceans, as more organic material would decompose with a longer residence time. To elucidate this process, a time-series study at a climatically sensitive region with sufficient duration and resolution is needed. Here we show that deep waters in the Sea of Japan are undergoing reduced ventilation, reducing the pH of seawater. As a result, the acidification rate near the bottom of the Sea of Japan is 27% higher than the rate at the surface, which is the same as that predicted assuming an air–sea CO2 equilibrium. This reduced ventilation may be due to global warming and, as an oceanic microcosm with its own deep- and bottom-water formations, the Sea of Japan provides an insight into how future warming might alter the deep-ocean acidification.