Total alkalinity (TA) is the oceanic capacity to store CO₂. Estuaries can be a TA source. Anaerobic metabolic pathways like denitrification (reduction of NO₃⁻ to N₂) generate TA and are a major nitrogen (N) sink. Another important N sink is anammox that transforms NH₄⁺ with NO₂⁻ into N₂ without TA generation. By combining TA and N₂ production, we identified a TA source, denitrification, occurring in the water column and suggest anammox as the dominant N₂ producer in the bottom layer of the Ems.