The rise in atmospheric CO2 concentrations observed at the end of glacial periods has, at least in part, been attributed to the upwelling of carbon-rich deep water in the Southern Ocean. The magnitude of outgassing of dissolved CO2, however, is influenced by the biological fixation of upwelled inorganic carbon and its transfer back to the deep sea as organic carbon. The efficiency of this biological pump is controlled by the extent of nutrient utilization, which can be stimulated by the delivery of iron by atmospheric dust particles. Changes in nutrient utilization should be reflected in the δ13C gradient between intermediate and deep waters. Here we use the δ13C values of intermediate- and bottom-dwelling foraminifera to reconstruct the carbon isotope gradient between thermocline and abyssal water in the subantarctic zone of the South Atlantic Ocean over the past 360,000 years. We find millennial-scale oscillations of the carbon isotope gradient that correspond to changes in dust flux and atmospheric CO2 concentrations as reported from Antarctic ice cores. We interpret this correlation as a relationship between the efficiency of the biological pump and fertilization by dust-borne iron. As the correlation is exponential, we suggest that the sensitivity of the biological pump to dust-borne iron fertilization may be increased when the background dust flux is low. © 2013 Macmillan Publishers Limited. All rights reserved.