The Scheldt watershed is characterized by a high population density, intense industrial activities and intensive agriculture and breeding. Due to these anthropogenic pressures, microbiological water quality of the main rivers of the Scheldt drainage network is low as demonstrated by our recent monitoring survey. An evaluation of the sources of microbiological pollutions at the scale of the watershed showed that the release of treated urban wastewaters was the major cause of faecal contamination. The Zenne river, a small stream crossing the Brussels area where it receives the treated effluents of more than one million inhabitants, is a typical example of a river strongly impacted by wastewater release. Studies, as the present one, leading to understand the microbial contamination are important for both industrialized and developing countries where the low microbiological water quality is responsible for numerous waterborne diseases.