Dinocyst assemblages and the physical properties of two sediment cores collected in the easternmost part of the main axis of the Northwest Passage, Canadian Arctic Ocean (cores 2004-804-009 BC and 2004-804-009 PC, 74°11.2′N, 81°11.7′W) were used to reconstruct changes in sea-surface conditions and to characterize changes in the depositional environment. Core 2004-804-009 PC spans the last 12 180 calibrated (cal) years BP, with sedimentation rates ranging from 45 to 122 cm/ka. Quantitative estimates of sea-surface parameters reveal relatively large hydrographic variability at millennial time scale. Before 11 000 cal years BP, our records suggest terrigenous inputs related to the last deglaciation. Between 11 000 and 9600 cal years BP, harsh conditions prevailed with August sea-surface temperatures <2 °C and the dominance of heterotrophic taxa. This episode was followed by a gradual increase in the relative abundance of phototrophic taxa and the establishment of milder condition with sea-surface temperature (SST) reaching ∼2 °C ∼8300 cal years BP, possibly related to increased exchange between the Arctic Ocean and the North Atlantic Ocean. From 6000 cal years BP to the late Holocene, climate variability could be the results of changes in the synoptic-scale atmospheric pattern such as the Arctic oscillation.