Description: Highlights • Neogloboquadrina pachyderma morphotypes can have different isotope compositions. • Isotopic offsets between morphotypes depend on environmental background conditions. • Thin-shelled Neogloboquadrina pachyderma are good recorders of near-surface salinity. • A strong freshwater event off NE Greenland at 12.7 ka may be related to deglaciation. Abstract We report on stable oxygen and carbon isotope data obtained on two different morphotypes of polar planktic foraminifers, i.e., fully encrusted and minor encrusted Neogloboquadrina pachyderma, from a sediment core taken on the NE Greenland continental margin. These morphotypes are supposed to live at different water depths of the upper water column in the area which today is strongly stratified, with a low-saline, cold-water layer at the surface. The paired isotopic data sets inform on temporal variations of past water salinity and temperature in the preferred water depth ranges of the investigated morphotypes and allow conclusions on the stratification of the upper water column. The radiocarbon-dated sediment core covers the time interval from 21 to 4 cal-ka, but the early part of the deglacial interval (18.5–12.7 cal-ka) is not represented, probably due to intense erosion by bottom currents. In sediments from the late last glacial maximum, oxygen isotope differences between thin-shelled and thick-shelled N. pachyderma are low and point at a weaker stratification with less freshwater than today near the surface. The carbon isotopes indicate a dense, perennial sea ice cover, very limited bioproduction, and the presence of a subsurface Atlantic Water layer. In the late deglaciation until ∼10.3 cal-ka, the stable isotope values of both analyzed morphotypes are considerably lower, with significantly stronger amplitudes in the record of thin-shelled specimens than later on. The high-amplitude record stems from a laminated sediment sequence whose older part was deposited within just a few decades. The data are evidence of a strong freshwater event in the research area that probably started before 12.7 ka and may have reduced sea surface salinities by 4–5 practical salinity units. As freshwater sources we discuss both the disintegration of NE Greenland shelf ice and export from the Arctic Ocean interior. The event may have contributed to the weakening of the Atlantic meridional overturning circulation during the Younger Dryas cold event. For the early and mid-Holocene (10-4 cal-ka), the isotope data suggest a structure of the upper water column similar to today, with a well-developed halocline separating low-saline near-surface waters from the underlying Atlantic Water layer. A seasonally disintegrated sea ice cover allowed for a considerable planktic bioproduction.