Recent observations are showing incursions of warm modified Circumpolar Deep Water (mCDW) reaching several East Antarctic ice shelves. However, large areas of the East Antarctic continental shelf remain poorly observed, making it challenging to determine if the supply of oceanic heat to the ice shelves is changing or has been consistent over time. Here, we use temperature and salinity profiles to the west of the Shackleton Ice Shelf (SIS; ≈100°E) spanning 60 years to assess the variability of the water masses in the context of a changing climate. We document warming and freshening of shelf waters. Prior to 1996, cold mCDW water (θ <−1.6°C) was found below the surface mixed layer and Dense Shelf Water (DSW) with a salinity of >34.5 dominated the water column. After 2010, warm mCDW (≥−1.0°C) was widespread over the continental shelf and DSW with salinity over 34.5 was no longer present. The mixing ratio of glacial meltwater indicates that warm mCDW observed in 2011 caused basal melting of the SIS, freshening DSW. These observations suggest a shift occurred prior to 2011 that increased the ocean heat supply to the continental shelf and to the SIS, increasing basal melt and reducing DSW formation.