Ocean acidification affects marine ecosystems and carbon cycling, and is considered a direct effect of anthropogenic carbon dioxide uptake from the atmosphere1–3 . Accumulation of atmospheric CO2 in ocean surface waters is predicted to make the ocean twice as acidic by the end of this century4 . The ArcticOcean is particularly sensitive to ocean acidification becausemoreCO2 candissolveincoldwater5,6 .Herewepresent observations of the chemical and physical characteristics of EastSiberianArctic Shelfwatersfrom1999,2000–2005,2008 and 2011, and find extreme aragonite undersaturation that reflects acidity levels in excess of those projected in this region for 2100. Dissolved inorganic carbon isotopic data and Markov chain Monte Carlo simulations of water sources using salinity andδ18 Odata suggest that the persistent acidification is driven by the degradation of terrestrial organic matter and discharge of Arctic river water with elevated CO2 concentrations, rather than by uptake of atmospheric CO2 . We suggest that East Siberian Arctic Shelf waters may become more acidic if thawing permafrost leads to enhanced terrestrial organic carbon inputs and if freshwater additions continue to increase, which may affect their efficiency as a source of CO2.