In a small river catchment, microbiological quality of different sewage treatment plants under regular conditions and in case of heavy rainfall, when combined sewage overflow basins (CSOs) are activated, was examined regarding microbial indicators and pathogens. In the watercourse, no self-cleaning effects could be observed. Small compact treatment plants discharge treated wastewater with a poor microbiological quality compared to river water quality and the quality of treated wastewater of larger plants. During storm water events, concentrations of microorganisms downstream of sewer overflows were approximately two logs higher than during dry weather conditions. Concentrations of parasites decreased slowly during the overflow, in parallel to filterable matter and particle-bound substances. The annual load of microorganisms originating from CSOs significantly exceeds the load from treated effluent of the sewage plants. Thus, an improved hygienic quality of the water course could be achieved by preventing overflows and by enhancing sewage treatment plants.