We present results of one year observations in highly heterotrophic and oxygen-depleted rivers of the polluted Scheldt basin. Monthly measurements revealed a high variability for dissolved inorganic carbon and nitrogen, with the following strong parallelism: highest alkalinity and NH 4 + were associated with lowest NO 3 − and oxygen and vice-versa . In river water incubations, nitrification lowered the alkalinity whereas denitrification raised it; in an anoxic, NO 3 − -free incubation an increase of alkalinity was observed, partially due to ammonification. A stoichiometric analysis, taking into account the amount of protons produced or consumed by each process involving nitrogen, revealed that monthly variations of NO 3 − and NH 4 + with ammonification, nitrification and denitrification could explain the 28 and 62% alkalinity variations at all stations, except one. The remaining part of the alkalinity variations was attributed to other anaerobic processes (Mn-, Fe- and SO 4 -reductions). This trend seems to be the result of the whole catchment metabolism (riverine waters and sediments, sewage networks and agricultural soils). The observed HCO 3 − concentrations in the Scheldt basin were 2–10 times higher than the representative concentrations reported in pristine basins and used in chemical weathering models. This suggests the existence of an anthropogenic source, originating from organic matter decomposition. We conclude that in highly polluted basins, nitrogen transformations strongly influence the acid–base properties of water.