Riverbank filtration systems are important drinking water resources. Aquifers of riverbank filtration systems are subjected to considerable dynamics concerning the quantity and quality of the infiltrating water. The microbiological quality is mainly jeopardized by faecal contamination of the main river. Besides, water quality can be impacted by growth of natural water-borne bacteria due to the input of nutrients resulting in the proliferation of opportunistic pathogens, impairment of odour and taste or bio-corrosion. The occurrence of such phenomena indicates a biological instability. For highly dynamic riverbank filtration systems, it is thus of high relevance to assess the biological stability of the groundwater resource.