Pharmaceutical substances present at low concentrations in the environment may cause effects on biological systems such as microbial consortia living on solid riverbed substrates. These consortia are an important part of the river ecosystem as they form part of the food chain. This case study aims to contribute to an increased understanding of how low levels of pharmaceuticals in freshwater streams may influence sessile bacterial consortia. An important point source for pharmaceutical release into the environment is treated household sewage water. In order to investigate what types of effects may occur, we collected water samples as well as riverbed substrates from a small stream in the south of Sweden, Knivstaån, upstream and downstream from a sewage treatment plant (STP). Data from these samples formed the base of this case study where we investigated both the presence of pharmaceuticals in the water and bacterial composition on riverbed substrates. In the water downstream from the STP, 19 different pharmaceuticals were detected at levels below 800 ng/dm³. The microbial composition was obtained from sequencing 16S rRNA genes directly from substrates as well as from cultivated isolates. The cultivated strains showed reduced species variability compared with the data obtained directly from the substrates. No systematic differences were observed following the sampling season. However, differences could be seen between samples upstream and downstream from the STP effluent. We further observed large similarities in bacterial composition on natural stones compared to sterile stones introduced into the river approximately two months prior to sampling, giving indications for future sampling methodology of biofilms.