Understanding oceanic processes, both physical and biological, that control atmospheric CO 2 is vital for predicting their influence during the past and into the future. The Eastern Equatorial Pacific (EEP) is thought to have exerted a strong control over glacial/interglacial CO 2 variations through its link to circulation and nutrient-related changes in the Southern Ocean, the primary region of the world oceans where CO 2 -enriched deep water is upwelled to the surface ocean and comes into contact with the atmosphere. Here we present a multiproxy record of surface ocean productivity, dust inputs, and thermocline conditions for the EEP over the last 40,000 y. This allows us to detect changes in phytoplankton productivity and composition associated with increases in equatorial upwelling intensity and influence of Si-rich waters of sub-Antarctic origin. Our evidence indicates that diatoms outcompeted coccolithophores at times when the influence of Si-rich Southern Ocean intermediate waters was greatest. This shift from calcareous to noncalcareous phytoplankton would cause a lowering in atmospheric CO 2 through a reduced carbonate pump, as hypothesized by the Silicic Acid Leakage Hypothesis. However, this change does not seem to have been crucial in controlling atmospheric CO 2 , as it took place during the deglaciation, when atmospheric CO 2 concentrations had already started to rise. Instead, the concomitant intensification of Antarctic upwelling brought large quantities of deep CO 2 -rich waters to the ocean surface. This process very likely dominated any biologically mediated CO 2 sequestration and probably accounts for most of the deglacial rise in atmospheric CO 2 .