Abstract. The coastal ocean is a crucial link between land, the open ocean and the atmosphere. The shallowness of the water column permits close interactions between the sedimentary, aquatic and atmospheric compartments, which otherwise are decoupled at long time scales (≅ 1000 yr) in the open oceans. Despite the prominent role of the coastal oceans in absorbing atmospheric CO₂ and transferring it into the deep oceans via the continental shelf pump, the underlying mechanisms remain only partly understood. Evaluating observations from the North Sea, a NW European shelf sea, we provide evidence that anaerobic degradation of organic matter, fuelled from land and ocean, generates total alkalinity (A_T) and increases the CO₂ buffer capacity of seawater. At both the basin wide and annual scales anaerobic A_T generation in the North Sea's tidal mud flat area irreversibly facilitates 7–10%, or taking into consideration benthic denitrification in the North Sea, 20–25% of the North Sea's overall CO₂ uptake. At the global scale, anaerobic A_T generation could be accountable for as much as 60% of the uptake of CO₂ in shelf and marginal seas, making this process, the anaerobic pump, a key player in the biological carbon pump. Under future high CO₂ conditions oceanic CO₂ storage via the anaerobic pump may even gain further relevance because of stimulated ocean productivity.