From 1.25 million to 700,000 years ago, the ice age cycle deepened and lengthened from 41,000- to 100,000-year periodicity, a transition that remains unexplained. Using surface- and bottom-dwelling foraminifera from the Antarctic Zone of the Southern Ocean to reconstruct the deep-to-surface supply of water during the ice ages of the past 1.5 million years, we found that a reduction in deep water supply and a concomitant freshening of the surface ocean coincided with the emergence of the high-amplitude 100,000-year glacial cycle. We propose that this slowing of deep-to-surface circulation (i.e., a longer residence time for Antarctic surface waters) prolonged ice ages by allowing the Antarctic halocline to strengthen, which increased the resistance of the Antarctic upper water column to orbitally paced drivers of carbon dioxide release.