Circumpolar Deep Water (CDW) intrudes from the mid-layers of the Antarctic Circumpolar Current onto the shelf of the western Antarctic Peninsula, providing a source of heat and nutrients to the regional ocean. It is well known that CDW is modified as it flows across the shelf, but the mechanisms responsible for this are not fully known. Here, data from underwater gliders with high spatial resolution are used to demonstrate the importance of detailed bathymetry in inducing multiple local mixing events. Clear evidence for overflows is observed in the glider data as water flows along a deep channel with multiple transverse ridges. The ridges block the densest waters, with overflowing water descending several hundred metres to fill subsequent basins. This vertical flow leads to entrainment of overlying colder and fresher water in localised mixing events. Initially this process leads to an increase in bottom temperatures due to the temperature maximum waters descending to greater depths. After several ridges, however, the mixing is sufficient to remove the temperature maximum completely and the entrainment of colder thermocline waters to depth reduces the bottom temperature, to approximately the same as in the source region of Marguerite Trough. Similarly, it is shown that deep waters of Palmer Deep are warmer than at the same depth at the shelf break. The exact details of the transformations observed are heavily dependent on the local bathymetry and water column structure, but glacially-carved troughs and shallow sills are a common feature of the bathymetry of polar shelves, and these types of processes may be a factor in determining the hydrographic conditions close to the coast across a wider area.