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Late Holocene paleoceanography and climate variability of the Southeastern Beaufort Sea (Canadian Arctic) have been investigated on the basis of sedimentary cores collected over the Mackenzie Slope. Piston, trigger and box cores were sampled at station 803 in 2004 aboard the CCGS Amundsen at 218 m water depth. The chronology of the piston core is constrained by 4 AMS-14C dates, as the sedimentation rate in the box core is assessed from 210Pb data. We obtain a continuous composite sequence covering the last 4600 years, with a sedimentation rate of ~ 140 cm.kyr− 1. Transfer functions (modern analogue technique) based on dinoflagellate cyst (dinocyst) assemblages were used to reconstruct the evolution of sea-surface conditions over the time period covered by the cores. Palynological data reveal that dinocyst assemblages are dominated by Operculodinium centrocarpum sensu lato (mean of 43.3%) throughout the core, with the accompanying taxa Brigantedinium spp. (19.6%), Islandinium minutum (15.6%) and cysts of Pentapharsodinium dalei (13.7%). Four zones have been established on the basis of dinocyst relative abundances. Dinocyst assemblage zone 1 (D1), from 4600 to 2700 cal years BP, is dominated by O. centrocarpum (mean of 49.0%). In zone D2 (2700–1500 cal years BP), the relative abundances of O. centrocarpum decrease (34.4%) in favour of the opportunistic, heterotrophic taxa Brigantedinium spp. (28.8%) and cysts of Polykrikos sp. var. arctic/quadratus (2.8%). Dinocyst zone D3 (1500–30 cal years BP or 450–1920 AD) is characterised by the high relative abundance of the peridinioid taxa I. minutum (19.9%). The last zone (D4), spanning from 1920 to 2004 AD, is again dominated by O. centrocarpum (44.5%), and shows low relative abundances of Brigantedinium spp. and cf. Echinidinium karaense. Quantitative reconstructions of past sea-surface parameters (August sea-surface temperature: SST, August sea-surface salinity: SSS, and duration of sea-ice cover) indicate relatively stable conditions over the last 4.6 kyr, with episodic cooling events (SST of ~ 1.5 °C below the modern value of 6 °C) that took place between 700 and 1820 AD. We associate the last and the longest of these cooling events (1560–1820 AD) with the Little Ice Age. Reconstructed SSS shows decadal oscillations since 1920 AD that we tentatively associate with the accumulation of freshwater by the Beaufort Gyre and the subsequent Great Salinity Anomalies. Our data suggest that similar salinity anomalies could have occurred ca. 1860 and 1790 AD. Stable isotopic data show a slight increase in δ13C values (from ~−27.1‰ at the base to ~−25.8‰ at the top) over the last 4.6 kyr that we associate with the gradual increase in atmospheric CO2 concentration as recorded by Antarctic ice cores. Variations in the δ15N profile suggest variations in Pacific water influence from 4600 to ~ 1300 cal years BP, associated with centennial scale shifts of the Arctic Oscillation phases.