Ammonium is an undesirable substance in the abstracted water of riverbank filtration (RBF) schemes, due mainly to the complications it causes during post-treatment (e. g. during chlorination). During RBF, ammonium can be formed in the riverbed by mineralization of organic nitrogen. Column experiments with riverbed sediments and river water from the Elbe were performed to evaluate the controls on ammonium concentrations during riverbed infiltration. Concentrations of ammonium went from <0.1 mgN/l in the feed water up to 1 mgN/l in the columns effluent. Higher temperatures and lower infiltration rates led to increased ammonium concentrations in the effluent. This shows higher susceptibility to ammonium increases of RBF settings in warmer climates and points to potential threats of climate change to water quality at RBF sites. In the later phases of the experiments, after the columns have been flushed their pore volumes several times, ammonium concentrations continually decreased. This behavior was attributed to the partial consumption of easily degradable organic material in the sediments, leading to lesser reducing conditions and lower mineralization rates. Based on operation with varied nitrate concentrations (0–11 mgN/l) and ¹⁵N isotopic measurements, dissimilatory nitrate reduction to ammonium (DNRA) was not shown to be relevant in the formation of ammonium. Anaerobic ammonium oxidation (anammox), however, was hypothesized to be an important sink of ammonium inside the columns, which indicates that rivers with high nitrate concentrations, such as the Elbe, may have a buffer of protection against ammonium formation during RBF.