Observations and model experiments highlight the importance of ocean heat in forcing ice sheet retreat during the present and geological past, but past ocean temperature data are virtually missing in ice sheet proximal locations. Here we document paleoceanographic conditions and the (in)stability of the Wilkes Land subglacial basin (East Antarctica) during the mid-Miocene (~17–13.4 million years ago) by studying sediment cores from offshore Adélie Coast. Inland retreat of the ice sheet, temperate vegetation, and warm oligotrophic waters characterise the mid-Miocene Climatic Optimum (MCO; 17–14.8 Ma). After the MCO, expansion of a marine-based ice sheet occurs, but remains sensitive to melting upon episodic warm water incursions. Our results suggest that the mid-Miocene latitudinal temperature gradient across the Southern Ocean never resembled that of the present day. We demonstrate that a strong coupling of oceanic climate and Antarctic continental conditions existed and that the East Antarctic subglacial basins were highly sensitive to ocean warming.