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Abstract Palynological analyses of sediment core MSM343310 from Disko Bugt (68°38′861°N, 53°49′493°W) document decadal‐ to centennial‐scale variability of sea surface conditions during the last ~ 3,600 years. Dinocyst fluxes (>10 4 cysts/cm 2  yr −1 ) indicate a very high productivity. Dinocyst assemblages dominated by Islandinium minutum , Brigantedinium spp., Islandinium ? cezare , and the cyst of Pentapharsodinium dalei suggest low surface salinity and marked shifts in summer sea surface temperature. The application of the modern analog technique to dinocyst assemblages, using an updated reference data set with new sites from the West Greenland margin, led to reconstruct decadal‐centennial‐scale variations in sea surface salinity and temperature, in phase with the δ 18 O variations in the Camp Century ice core. At ~ 1.5 ka BP, the seasonal sea ice cover records an important regime change, from winter‐only sea ice to more unstable conditions marked by successive cooling pulses with sea ice cover of up to 8 months/yr. The data suggest a close relationship between hydrographic conditions and regional climate over Greenland. Our record shows variations with a mean 200 years periodicity until ~2 ka BP, which supports the hypothesis of climate variations driven by solar variability. After 1.5 ka BP, our data show a variability characterized by a 60–70 year periodicity, which suggests linkages with the Atlantic Multidecadal Oscillation and southwestward migration of the atmospheric polar front. The most recent part of the record, from ~1900 CE to 2007 CE, is characterized by assemblages reflecting warmer surface conditions and reduced sea ice cover. , Key Points Sea surface salinity changes are used as indicators of fresh‐meltwater events and sea ice cover as a diagnostic feature of regional climate Changing sea surface conditions from Disko Bugt are closely related with regional climate over Greenland A marked change in surface waters at about 1.5 ka BP corresponds to enhanced sea ice cover and the onset of unstable conditions