Datasets produced as a result of analyses on calypso giant gravity core (CASQ) AMD-117Q and box core (BC) AMD16-117Q-BC1-1 onboard the CCGS Amundsen GreenEdge/ArcticNet 2016 Leg 1a expedition. Marine sediment cores cover the Holocene period and were recovered off the coast of Qaanaaq, northernmost Baffin Bay. Discrete subsamples were taken from U-channels for analysis of geochemical, palynological and micropaleontological analysis, with the aim of reconstructing palaeoceanographic conditions in the region of the North Water Polynya.