Managed aquifer recharge using bank filtration is an important approach to produce sustainable drinking water in regions with limited groundwater resources. Gillefalk et al. (2018) provide an overview of the global usage of induced river bank filtration (RBF). For example, RBF provides about 60% of the total drinking water demand in the city of Berlin (Germany, 3.6 Mio. inhabitants), while it is used to serve almost 100% of the population of Düsseldorf (Germany, 0.6 Mio inhabitants) with drinking water (Gillefalk et al., 2018). The RBF concept is based on natural remediation (or attenuation), that is, on the processes occurring in groundwater (such as dispersion and biodegradation) lowering contaminant concentrations, thus reducing the need for additional treatments to obtain drinking water quality.Pathogens, for example, viruses or some bacteria, are mainly released to the environment by wastewater discharge into streams (Xagoraraki et al., 2014). Lakes and rivers around big cities or near large urban areas are often documented to be severely polluted by pathogens, resulting in a high risk of pathogen contamination of groundwater, including RBF sites. Pathogens in drinking water can cause a variety of diseases in humans. The number of pathogen particles which are necessary to cause an infection (also termed infective dose) can vary between a few particles to thousands of particles, depending on the pathogen species (Schmid-Hempel & Frank, 2007). Accurate assessment of pathogen fate and transport are especially relevant for pathogens with a low infective dose. Bacteria concentrations serve as primary indicators for drinking water quality, as set in the World Health Organization guidelines (WHO, 2017) and regulations in several countries (e.g., EU Drinking Water Directive 98/83/EC). Measured bacteria are either pathogens (e.g., some Escherichia coli strains, or the genus Enterococcus) or pathogen/wastewater indicators (e.g., coliforms).