Although shelf seas account for only 7% of the oceanic surface area, recent observations demonstrate that they host significant ocean-atmosphere CO₂ fluxes. A mechanism implicated in driving a significant CO₂ sink in the temperate shelf seas is the Continental Shelf Pump. Here we present an analysis of the impact of sea-level rise, and the consequent flooding of continental shelves, on the growth of the continental shelf CO₂ pump over the last deglacial transition. We combine reconstructions of shelf palaeogeography, bathymetry and tides, with contemporary shelf sea – atmosphere CO₂ flux estimates, to demonstrate the potential of the expanding shelf seas to have impacted on the global carbon cycle, via the continental shelf CO₂ pump, over the past 21,000 years and, by inference, earlier glacial-interglacial cycles.