Enhanced transport of warm subsurface Atlantic Waters (AW) into Greenland fjords has driven glacier mass loss, but the mechanisms transporting AW to the fjords remain poorly characterized. Here, we identify a wind-driver for AW inflow toward Sermilik Fjord abutting Helheim Glacier, one of Greenland’s largest glaciers. Often associated with the passing of cyclones and subsequent sea surface lowering, a weakening or reversal of northeasterly alongshore winds stimulates coastal ocean upwelling that, through interactions with Sermilik’s bathymetric trough on the continental shelf, leads to enhanced AW upwelling and inflow along the trough. These intrusions produce ocean warming at deep moorings near Sermilik Fjord mouth (0.31±0.18°C) and within the fjord (250m: 0.30±0.19°C; 350m: 0.17±0.09°C) that is not diminished by subsequent coastal downwelling. Similar wind-driven processes at other bathymetric trough regions around Greenland may play a substantial role in ocean heat transport towards much of the Greenland Ice Sheet.