Abstract Continuous sea salt and mineral dust aerosol records have been studied on the two EPICA (European Project for Ice Coring in Antarctica) deep ice cores. The joint use of these records from opposite sides of the East Antarctic plateau allows for an estimate of changes in dust transport and emission intensity as well as for the identification of regional differences in the sea salt aerosol source. The mineral dust flux records at both sites show a strong coherency over the last 150 kyr related to dust emission changes in the glacial Patagonian dust source with three times higher dust fluxes in the Atlantic compared to the Indian Ocean sector of the Southern Ocean (SO). Using a simple conceptual transport model this indicates that transport can explain only 40% of the atmospheric dust concentration changes in Antarctica, while factor 5–10 changes occurred. Accordingly, the main cause for the strong glacial dust flux changes in Antarctica must lie in environmental changes in Patagonia. Dust emissions, hence environmental conditions in Patagonia, were very similar during the last two glacials and interglacials, respectively, despite 2–4 °C warmer temperatures recorded in Antarctica during the penultimate interglacial than today. 2–3 times higher sea salt fluxes found in both ice cores in the glacial compared to the Holocene are difficult to reconcile with a largely unchanged transport intensity and the distant open ocean source. The substantial glacial enhancements in sea salt aerosol fluxes can be readily explained assuming sea ice formation as the main sea salt aerosol source with a significantly larger expansion of (summer) sea ice in the Weddell Sea than in the Indian Ocean sector. During the penultimate interglacial, our sea salt records point to a 50% reduction of winter sea ice coverage compared to the Holocene both in the Indian and Atlantic Ocean sector of the SO. However, from 20 to 80 ka before present sea salt fluxes show only very subdued millennial changes despite pronounced temperature fluctuations, likely due to the large distance of the sea ice salt source to our drill sites.