Changes in high latitude ocean gateways and atmospheric CO2 are thought to be main drivers of Cenozoic climate evolution during the last 65 million years. However as yet, especially the link between climate changes and the opening history of the North Polar Seas via the subsidence of the Greenland-Scotland Ridge is poorly understood. Here we use a coupled ocean–atmosphere general circulation model for early Miocene boundary conditions to reveal a threshold behaviour for the ventilation of the North Polar Seas controlled by the Greenland-Scotland Ridge subsidence. Our model simulations show that a deepening of the ridge from 200 to 300 meters below sea-level induces major reorganizations in North Atlantic-Arctic Ocean circulation with an abrupt regime shift from restricted estuarine conditions to a bi-directional flow regime similar to today. Close to critical gateway depths, additional scenarios with different atmospheric CO2 concentrations indicate that realistic Oligocene-Miocene CO2 changes actively modulate the transition between the two circulation regimes via the impact of the atmospheric hydrological cycle. Taking uncertainties in timing into account this suggest that tectonic changes starting at ~33-30 Myrs controlled the circulation of the Nordic Seas. Thereafter superposed changes in CO2 delayed an abrupt transition to a modern prototype North Atlantic-Arctic exchange by millions of years until CO2-levels finally dropped to preindustrial levels at ~25-24 Myrs. This concept and the associated mechanism bridges tectonic processes with much shorter time-scales in the coupled atmosphere-ocean system that differ by three orders of magnitude, which provides an unanticipated new perspective on abrupt climate changes during the Cenozoic era.