Riverbank filtration (RBF) systems along rivers are widely used as public water supplies. In these systems, many organic micropollutants (OMPs) are attenuated, but some compounds have shown to be rather persistent. Their fate and transport has been studied in RBF sites along lakes and small rivers, but not extensively along large and dynamic rivers. Therefore, the influence of flood events on OMP behavior in these large and dynamic RBF sites was investigated. Monthly samples were taken from surface- and groundwater up to a distance of 900 m from the riverbank of the Danube from March 2014 till May 2016. Two flood events were sampled more extensively nearby the river. Results showed that changes in flow conditions in the river not only caused changes in OMP concentrations, but also in their load. It was seen that the load of benzotriazole, carbamazepine and sulfamethoxazole in the river increased with increasing river discharges. After a relatively long, oxic groundwater passage, several OMPs were reduced. In contrast to previous work, we found that benzotriazole was almost fully removed under oxic conditions. When entering the aquifer, benzotriazole concentrations were significantly reduced and at a distance of 550 m from the river, >97% was degraded. Carbamazepine and sulfamethoxazole showed relatively persistent behavior in the aquifer. The concentrations measured during flood events were in the same range as seasonal sampling. Furthermore concentrations in the groundwater were higher during these events than in the Danube and can reach further into the aquifer. During flood events some highly degradable compounds (i.e. diclofenac) were found up to a distance of 24 m from the river. These results implied that drinking water utilities with RBF wells in oxic, alluvial aquifers located close to highly dynamic rivers need to consider a potential reduction in groundwater quality during and directly after flood events.