Following early hypotheses about the possible existence of Arctic ice shelves in the past1,2,3, the observation of specific erosional features as deep as 1,000 metres below the current sea level confirmed the presence of a thick layer of ice on the Lomonosov Ridge in the central Arctic Ocean and elsewhere4,5,6. Recent modelling studies have addressed how an ice shelf may have built up in glacial periods, covering most of the Arctic Ocean7,8. So far, however, there is no irrefutable marine-sediment characterization of such an extensive ice shelf in the Arctic, raising doubt about the impact of glacial conditions on the Arctic Ocean. Here we provide evidence for at least two episodes during which the Arctic Ocean and the adjacent Nordic seas were not only covered by an extensive ice shelf, but also filled entirely with fresh water, causing a widespread absence of thorium-230 in marine sediments. We propose that these Arctic freshwater intervals occurred 70,000–62,000 years before present and approximately 150,000–131,000 years before present, corresponding to portions of marine isotope stages 4 and 6. Alternative interpretations of the first occurrence of the calcareous nannofossil Emiliania huxleyi in Arctic sedimentary records would suggest younger ages for the older interval. Our approach explains the unexpected minima in Arctic thorium-230 records9 that have led to divergent interpretations of sedimentation rates10,11 and hampered their use for dating purposes. About nine million cubic kilometres of fresh water is required to explain our isotopic interpretation, a calculation that we support with estimates of hydrological fluxes and altered boundary conditions. A freshwater mass of this size—stored in oceans, rather than land—suggests that a revision of sea-level reconstructions based on freshwater-sensitive stable oxygen isotopes may be required, and that large masses of fresh water could be delivered to the north Atlantic Ocean on very short timescales.