A sediment core from the West Spitsbergen continental margin was studied to reconstruct climate and paleoceanographic variability during the last ~9 ka in the eastern Fram Strait (FS). Our multiproxy evidence suggests that the establishment of the modern oceanographic configuration in the eastern FS occurred stepwise, in response to the postglacial sea-level rise and the related onset of modern sea-ice production on the shallow Siberian shelves. The late Early and Mid-Holocene interval (9 to 5 ka) was generally characterized by relatively unstable conditions. High abundance of the subpolar planktic foraminifer species Turborotalita quinqueloba implies strong intensity of Atlantic Water (AW) inflow with high productivity and/or high AW temperatures, resulting in a strong heat flux to the Arctic. A series of short-lived cooling events (8.2, 6.9, and 6.1 ka) occurred superimposed on the warm late Early to Mid-Holocene conditions. Our proxy data imply that simultaneous to the complete postglacial flooding of Arctic shallow shelves and the initiation of modern sea-ice production, strong advance of polar waters initiated modern oceanographic conditions in the eastern FS at ~5.2 ka. The Late Holocene was marked by the dominance of the polar planktic foraminifer species Neogloboquadrina pachyderma, a significant expansion of sea ice/icebergs, and strong stratification of the water column. Although planktic foraminiferal assemblages as well as sea subsurface temperatures suggest a return of slightly strengthened advection of subsurface AW after 3 ka, a relatively stable cold-water layer prevailed at the sea surface, and the study site was probably located within the seasonally fluctuating marginal ice zone during the Neoglacial period.