In this study, we investigated the microbiological quality of the small urban Zenne River which flows through the city of Brussels (Belgium). The abundances of faecal indicator bacteria (FIB) (Escherichia coli and intestinal enterococci) revealed high levels of faecal contamination of the Zenne River, especially in Brussels area and downstream from this area where FIB were in the range of what is usually observed in secondary treated wastewaters. The origin of this faecal contamination is mainly attributed to the effluents of the two wastewater treatment plants (WWTPs) located along the river in Brussels. Comparison of the present situation with the 1990s situation (before the implementation of Brussels WWTPs) showed a sharp improvement of the river microbiological quality. This improvement should however be regarded with care as it was also observed that, during rain events, combined sewer overflows (CSO) outfalls were responsible of a strong increase of faecal contamination in the river downstream from Brussels, and such CSO occur frequently in Brussels. Altogether, these results document the variations of the microbiological quality of a sewage-polluted urban river in relation with long-term changes (implementation of WWTP) and the short-term disturbances (CSO).