The onset of the North Atlantic Deep Water formation is thought to have coincided with Antarctic ice-sheet growth about 34 million years ago (Ma). However, this timing is debated, in part due to questions over the geochemical signature of the ancient Northern Component Water (NCW) formed in the deep North Atlantic. Here we present detailed geochemical records from North Atlantic sediment cores located close to sites of deep-water formation. We find that prior to 36 Ma, the northwestern Atlantic was stratified, with nutrient-rich, low-salinity bottom waters. This restricted basin transitioned into a conduit for NCW that began flowing southwards approximately one million years before the initial Antarctic glaciation. The probable trigger was tectonic adjustments in subarctic seas that enabled an increased exchange across the Greenland–Scotland Ridge. The increasing surface salinity and density strengthened the production of NCW. The late Eocene deep-water mass differed in its carbon isotopic signature from modern values as a result of the leakage of fossil carbon from the Arctic Ocean. Export of this nutrient-laden water provided a transient pulse of CO2 to the Earth system, which perhaps caused short-term warming, whereas the long-term effect of enhanced NCW formation was a greater northward heat transport that cooled Antarctica.