Baffin Bay is a semi-enclosed basin connecting the Arctic Ocean and the western North Atlantic, thus making out a significant pathway for heat exchange. Here we reconstruct the alternating advection of relatively warmer and saline Atlantic waters versus the incursion of colder Arctic water masses entering Baffin Bay through the multiple gateways in the Canadian Arctic Archipelago and the Nares Strait during the Holocene. We carried out benthic foraminiferal assemblage analyses, X-ray fluorescence scanning, and radiocarbon dating of a 738 cm long marine sediment core retrieved from eastern Baffin Bay near Upernavik, Greenland (Core AMD14-204C; 987 m water depth). Results reveal that eastern Baffin Bay was subjected to several oceanographic changes during the last 9.2 kyr. Waning deglacial conditions with enhanced meltwater influxes and an extensive sea-ice cover prevailed in eastern Baffin Bay from 9.2 to 7.9 ka. A transition towards bottom water amelioration is recorded at 7.9 ka by increased advection of Atlantic water masses, encompassing the Holocene Thermal Maximum. A cold period with growing sea-ice cover at 6.7 ka interrupts the overall warm subsurface water conditions, promoted by a weaker northward flow of Atlantic waters. The onset of the neoglaciation at ca. 2.9 ka is marked by an abrupt transition towards a benthic fauna dominated by agglutinated species, likely in part explained by a reduction of the influx of Atlantic Water, allowing an increased influx of the cold, corrosive Baffin Bay Deep Water originating from the Arctic Ocean to enter Baffin Bay through the Nares Strait. These cold subsurface water conditions persisted throughout the Late Holocene, only interrupted by short-lived warmings superimposed on this cooling trend.