Terrestrial records from the Canadian Arctic Archipelago indicate that a temperate and moist climate prevailed during the Pliocene, i.e., before the intensification of Northern Hemisphere glaciations, but the controlling factors causing these conditions remains elusive. Here we present marine seismic reflection evidence of contiguous kilometer-scale sedimentary drifts, or contourites, buried below the West Greenland shelf, which relates high-latitude Pliocene warmth to intense geostrophic currents along the eastern Baffin Bay margin. Seismic to borehole correlation indicates that enhanced current-induced deposition began during the middle Miocene, ca. 17–15 Ma, and terminated during the late Pliocene onset of global cooling. The transition from along-slope sediment transport to trough-mouth fan progradation designates the onset of Greenland Ice Sheet glaciers advancing across the continental shelf and coincides with increasing iceberg productivity in Baffin Bay and the Nordic Seas from 3.3 to 2.7 Ma. Our results suggest that the Baffin Bay–West Greenland margin formed a late Neogene passageway for persistent ocean boundary currents, and we infer that the Pliocene high-latitude warmth was to a significant extent caused or enhanced by advection of subtropical heat and moisture to the Arctic regions. Attenuation of the poleward heat flux conveyed by the paleo–current system may have been critical for allowing glacial buildup in the Canadian Arctic and northern Greenland during the late Pliocene. We further surmise that vertical tectonic adjustments of the continental margin played a role in this attenuation, which eventually caused the demise of meridional ocean circulation through Baffin Bay.