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The seafloor depths under the Cook Ice Shelf and Ninnis Glacier Tongue have not been directly measured, despite their importance for understanding ocean circulation and ice shelf change. We model the bathymetry underneath the floating ice and surrounding ocean using airborne gravity data. Our model is constrained by few ship‐based seafloor measurements near the ice front and by ice‐base measurements over areas of grounded ice from radar data. Localized basins (∼1,400 m deep) are found beneath both ice shelves. The shallowest modeled bathymetry (∼200 m) represents the offshore extension of Cape Freshfield. Near the grounding line, seafloor depths are found to be deeper than the observed depth of the modified Circumpolar Deep water in the region (<350 m), key factor for basal melt analyses. From transit flight gravity anomalies, we suggest the relocation of the mapped edge of the continental shelf and a narrowing of the Cook Shelf Depression. Plain Language Summary: The knowledge of how deep the ocean floor is under the floating ice shelves that connect to grounded ice sheets, is crucial for understanding how ocean water circulates and interacts with the overlying ice. We present a new bathymetric model of the seafloor beneath two ice shelves located in East Antarctica: Cook Ice Shelf and Ninnis Glacier Tongue. Both ice shelves are inaccessible to ships due to heavy sea ice conditions, so the data used in our model were collected from airborne surveys. Our bathymetry model shows new information on the depth and shape of the seafloor that will help understanding the ocean circulation in the area and how this might impact ice thickness changes. Key Points: High resolution bathymetry model of Cook Ice Shelf, Ninnis Glacier Tongue, and surrounding open ocean from airborne gravity inversionNew bathymetry model improves the understanding of water pathways between the ice shelves and the continental shelf edgeTransit flight gravity anomalies suggest relocation of the edge of the continental shelf northwards of the currently attributed position [ABSTRACT FROM AUTHOR]