Oceanic stratification represents an effective mechanism to reduce vertical mixing of the water column, thereby locking up carbon dioxide (CO2) in the deep sea and preventing air–sea exchange of CO2. It has been proposed that enhanced stratification of the upper water column in polar oceans during late Cenozoic cooling episodes limited the upwelling of CO2-rich deep waters and thus CO2-release to the atmosphere, resulting in a net global drawdown of atmospheric CO2. Increased stratification in the Subarctic Northwest Pacific, during both the onset of Northern Hemisphere glaciation at 2.73 Ma and late Quaternary glacial periods, has been recently linked to enhanced ocean stratification south of the Antarctic Polar Front (APF) in the Pacific and Atlantic sectors of the Southern Ocean. Increased stratification of Southern Ocean surface waters was mainly deduced from a reduction of biological production during these cooling episodes, manifested by the decrease of geochemical proxies for productivity, such as biogenic opal and barium, in the marine sediment records. However, the records chosen from the Southern Ocean do not provide evidence for a more stratified upper water column, rather the observed decrease in biological productivity is likely to have resulted from an expansion of annual sea-ice coverage. The sediment records suggest that south of the APF in the Pacific and Atlantic sectors of the Southern Ocean, extensive sea ice may have contributed to the global CO2-drawdown during glacial periods, with hypothetical glacial increase of stratification in today’s permanent open-ocean zone merely being an “add on“ caused by this expansion.