Since the Industrial Revolution, the North Atlantic Ocean has been accumulating anthropogenic carbon dioxide (CO2) and experiencing ocean acidification1, that is, an increase in the concentration of hydrogen ions (a reduction in pH) and a reduction in the concentration of carbonate ions. The latter causes the ‘aragonite saturation horizon’—below which waters are undersaturated with respect to a particular calcium carbonate, aragonite—to move to shallower depths (to shoal), exposing corals to corrosive waters2,3. Here we use a database analysis to show that the present rate of supply of acidified waters to the deep Atlantic could cause the aragonite saturation horizon to shoal by 1,000–1,700 metres in the subpolar North Atlantic within the next three decades. We find that, during 1991–2016, a decrease in the concentration of carbonate ions in the Irminger Sea caused the aragonite saturation horizon to shoal by about 10–15 metres per year, and the volume of aragonite-saturated waters to reduce concomitantly. Our determination of the transport of the excess of carbonate over aragonite saturation (xc[CO32−])—an indicator of the availability of aragonite to organisms—by the Atlantic meridional overturning circulation shows that the present-day transport of carbonate ions towards the deep ocean is about 44 per cent lower than it was in preindustrial times. We infer that a doubling of atmospheric anthropogenic CO2 levels—which could occur within three decades according to a ‘business-as-usual scenario’ for climate change4—could reduce the transport of xc[CO32−] by 64–79 per cent of that in preindustrial times, which could severely endanger cold-water coral habitats. The Atlantic meridional overturning circulation would also export this acidified deep water southwards, spreading corrosive waters to the world ocean.