We present a millennial-scale multi-proxy reconstruction of changes in properties of the upper water column near the East Antarctic ice shelf based on planktonic foraminifera from a unique sedimentary archive spanning the glacial period from 75,000 to 20,000 years. Our results imply that variations in the thermohaline structure between Antarctic Surface Water and Warm Deep Water (WDW) may have resulted in either strengthening the stratification of the upper water column or promoting polynya formation (convective overturning). Oceanic subsurface warming during glacial Antarctic stadials and periods of low obliquity, combined with increased salinity and nutrient content, suggests the breakdown in stratification and polynya presence. This glacial polynya formed off Dronning Maud Land (DML) reflects a hybrid coastal-open-ocean polynya mode. We attribute the development of the Glacial DML Polynya to sea-ice induced subsurface warming of WDW and a decrease in density stratification in combination with circulation changes in the atmosphere and ocean. The polynya-driven oceanic heat release during the glacial stadials may have increased the moisture supply to Antarctica and thus promoted the accumulation of ice and the thickening of an advancing ice sheet at the continental shelf margin.