The Bellingshausen Sea hosts heat transport onto the continental shelf, potentially enhancing ice shelf basal melt. Here, we use the GLORYS12V1 1993-2018 reanalysis to identify physical processes that set seasonal and interannual variability of water mass properties in the Eltanin and Latady Bays on the southern Bellingshausen Sea continental shelf. Annual means of potential temperature from 300m to the seabed reveal interannual variability and allow separation into warm and cold regimes. The Amundsen Sea Low (ASL) is more intense and extends further east during the warm regime than the cold regime. In the warm regime, a wind-induced reduction of sea ice concentration near the coast increases surface heat loss, convection, and formation of cold dense water in winter, associated with a decrease in heat content of the southern Bellingshausen Sea over time and a net northward heat transport. In contrast, in the cold regime, increased sea ice concentration reduces surface heat loss and thus formation of cold, dense water. Combined with an increase in heat content over time and a net southward heat transport, this results in a warming of the southern Bellingshausen Sea. This suggests that variability in the deep water temperature in the southern Bellingshausen Sea is primarily due to local surface heat fluxes above the shelf. The variability of surface heat fluxes is related to the variability of the ASL and its influence on sea ice extent and local formation of cold, dense water in winter.