The surface waters of the modern subarctic Pacific Ocean are isolated from the nutrient-rich waters below by a steep vertical gradient in salinity (halocline), a feature which is a dominant control on upper-ocean stratification in polar environments. The physical processes which maintain the halocline and, in turn, its physical, biological, and geochemical effects have long been subjects of intense inquiry. The stratification of polar surface waters influences the exchange of CO2 between ocean and atmosphere, so the history of the subarctic Pacific halocline may have played a role in past changes in atmospheric CO2 concentration. Here we report opal accumulation rates and nitrogen-isotope data from sediments in this region which indicate that the subarctic Pacific halocline developed abruptly 2.73 million years ago, coincident with the onset of extensive Northern Hemisphere glaciation. The halocline would have reduced the transport of nutrient-rich deep water into the euphotic zone, leading to a decrease in biological production but an increase in the fraction of nutrient stocks utilized. This increase in the efficiency of the 'biological pump' would have lowered the rate of CO2 evasion from ocean to atmosphere, potentially reducing atmospheric CO2 concentrations from the suggested higher level of the preceding mid-Pliocene warm interval.