AbstractIn this study, we successfully implemented a total alkalinity (TA) analyzer in a flow‐through setup, in combination with a FerryBox. The high‐frequency (10 min) measurements along our ship's route revealed that in coastal systems, where carbon fluxes are dynamic, TA can differ significantly (by up to 100 μmol kg−1) between the nearshore and adjacent coastal regions. Even though this study could not account for the net yearly TA production in the coastal region, it demonstrated that there was a seasonal increase in TA of 100–150 μmol kg−1 in coastal waters of the North Sea, equivalent to TA production of 11.7–26.8 mmol m−2 d−1 during the spring and summer months. This seasonal change could not be accounted for by riverine contributions, but instead was probably related to seasonal organic matter production and processing in coastal and nearshore regions. Bottom sediments and the tidally coupled biogeochemical reactor between coastal (North Sea) and nearshore (Wadden Sea) regions are mediating this TA change, and the ~ 4 months lag between the seasonal increase in alkalinity and the peak organic matter production could be explained by the supply of (labile) organic matter and its temperature‐dependent remineralization via both aerobic and anaerobic pathways.