Ice shelves play a critical role in the long-term stability of ice sheets through their buttressing effect. The underlying bathymetry and cavity thickness are key inputs for modelling future ice sheet evolution. However, direct observation of sub-ice-shelf bathymetry is time-consuming, logistically risky, and in some areas simply not possible. Here we use new compilations of airborne and marine gravity, radar depth sounding, and swath bathymetry to provide new estimates of sub-ice-shelf bathymetry outboard of the rapidly changing West Antarctic Thwaites Glacier and beneath the adjacent Dotson and Crosson ice shelves. This region is of special interest, as the low-lying inland reverse slope of the Thwaites Glacier system makes it vulnerable to marine ice sheet instability, with rapid grounding line retreat observed since 1993 suggesting this process may be underway. Our results confirm a major marine channel >800 m deep extends tens of kilometres to the front of Thwaites Glacier, while the adjacent ice shelves are underlain by more complex bathymetry. Comparison of our new bathymetry with ice shelf draft reveals that ice shelves formed since 1993 comprise a distinct population where the draft conforms closely to the underlying bathymetry, unlike the older ice shelves, which show a more uniform depth of the ice base. This indicates that despite rapid basal melting in some areas, these recently floated parts of the ice shelf are not yet in dynamic equilibrium with their retreated grounding line positions and the underlying ocean system, a factor which must be included in future models of this region’s evolution.