The cause of the rise in atmospheric pCO2 over the last deglaciation has been a puzzle since its discovery in the early 1980s. It is widely believed to be related to changes in carbon storage in the deep ocean, but the exact mechanisms responsible for releasing CO2 from the deep-ocean reservoir, including the role of ocean density stratification, remains an open question. Here we reconstruct changes in the intermediate-deep density gradient in the South Atlantic across the last deglaciation and find evidence of an early deglacial chemical destratification and a late deglacial density destratification These results suggest that other mechanisms, besides deep-ocean density destratification, were responsible for the ocean–atmosphere transfer of carbon over the deglacial period