Oceanic heat strongly influences the glaciers and ice shelves along West Antarctica. Prior studies show that the subsurface onshore heat flux from the Southern Ocean on the shelf occurs through deep, glacially carved channels. The mechanisms enabling the export of colder shelf waters to the open ocean, however, have not been determined. Here, we use ocean glider measurements collected near the mouth of Marguerite Trough (MT), west Antarctic Peninsula, to reveal shelf-modified cold waters on the slope over a deep (2,700 m) offshore topographic bank. The shelf hydrographic sections show subsurface cold features (θ <=1.5°C), and associated potential vorticity fields suggest a significant instability-driven eddy field. Output from a high-resolution numerical model reveals offshore export modulated by small (6 km), cold-cored, cyclonic eddies preferentially generated along the slope and at the mouth of MT. While baroclinic and barotropic instabilities appear active in the surrounding open ocean, the former is suppressed along the steep shelf slopes, while the latter appears enhanced. Altimetry and model output reveal the mean slope flow splitting to form an offshore branch over the bank, which eventually forms a large (116 km wide) persistent lee eddy, and an onshore branch in MT. The offshore flow forms a pathway for the small cold-cored eddies to move offshore, where they contribute significantly to cooling over the bank, including the large lee eddy. These results suggest eddy fluxes, and topographically modulated flows are key mechanisms for shelf water export along this shelf, just as they are for the shoreward warm water transport.Plain Language Summary The glaciers and ice shelves of the West Antarctic Peninsula have been rapidly retreating in the past 50 years, believed to be driven by increasing fluxes of heat from the ocean. While knowledge of the mechanisms that drive this heat from the open ocean onto the continental shelves has improved, our understanding of the counterbalancing flows of shelf waters remains limited. In this study, temperature, salinity, and velocity observations from an underwater autonomous vehicle, alongside numerical model output, are used to elucidate the pathway and mechanisms by which shelf waters are moved into the ocean interior. Small spinning vortices-known as eddies-containing shelf water are periodically generated from dynamical instabilities that derive from the horizontal shear of the flow. These small eddies then move offshore to cool a region of elevated topography near the mouth of Marguerite Trough, a deep glacially carved canyon. Here, cold water accumulates in a larger persistent eddy; satellite observations suggest that this water may ultimately be discharged into the Southern Ocean interior. Given that the topographic conditions of the field site are not unique, eddies and topographic flows are likely key mechanisms that balance the onshore flux of ocean heat in the West Antarctic.