The net uptake of carbon dioxide (CO2) from the atmosphere is changing the ocean's chemical state. Such changes, commonly known as ocean acidification, include a reduction in pH and the carbonate ion concentration ([CO32−]), which in turn lowers oceanic saturation states (Ω) for calcium carbonate (CaCO3) minerals. The Ω values for aragonite (Ωaragonite; one of the main CaCO3 minerals formed by marine calcifying organisms) influence the calcification rate and geographic distribution of cold-water corals (CWCs), important for biodiversity. Here, high-quality measurements, collected on thirteen cruises along the same track during 1991–2018, are used to determine the long-term changes in Ωaragonite in the Irminger and Iceland Basins of the North Atlantic Ocean, providing the first trends of Ωaragonite in the deep waters of these basins. The entire water column of both basins showed significant negative Ωaragonite trends between −0.0014 ± 0.0002 and − 0.0052 ± 0.0007 per year. The decrease in Ωaragonite in the intermediate waters, where nearly half of the CWC reefs of the study region are located, caused the Ωaragonite isolines to rapidly migrate upwards at a rate between 6 and 34 m per year. The main driver of the decline in Ωaragonite in the Irminger and Iceland Basins was the increase in anthropogenic CO2. But this was partially offset by increases in salinity (in Subpolar Mode Water), enhanced ventilation (in upper Labrador Sea Water) and increases in alkalinity (in classical Labrador Sea Water, cLSW; and overflow waters). We also found that water mass aging reinforced the Ωaragonite decrease in cLSW. Based on these Ωaragonite trends over the last three decades, we project that the entire water column of the Irminger and Iceland Basins will likely be undersaturated for aragonite when in equilibrium with an atmospheric mole fraction of CO2 (xCO2) of ~880 ppmv, corresponding to climate model projections for the end of the century based on the highest CO2 emission scenarios. However, intermediate waters will likely be aragonite undersaturated when in equilibrium with an atmospheric xCO2 exceeding ~630 ppmv, an xCO2 level slightly above that corresponding to 2 °C global warming, thus exposing CWCs inhabiting the intermediate waters to undersaturation for aragonite.