A pronounced pollution of surface water bodies in the Western Bug River Basin, Ukraine, has been caused by outdated or overloaded wastewater treatment plants, agriculture, industry and coal mining. These pressures have led to a generally poor state of both chemical and microbiological variables creating health risks of various kinds. The state of surface water quality for the Western Bug and five main tributaries was assessed by measuring physical, chemical and microbiological indicators during field campaigns in autumn 2009 and spring 2010. Longitudinal profiles were sampled to identify major sources of pollution and to reveal dominant processes of matter turnover. In addition, the occurrence of antibiotic resistant strains in isolates from stations along the Bug River was investigated. Results clearly underpin the negative impact of the Poltva River as a major source of pollution for the Bug River and further outline an elevated potential health risk from pathogenic bacteria originating from this source. Despite these devastating impacts, a high elimination potential of the Bug River with respect to primary organic loads as well as elimination of pathogenic bacteria was observed particularly at Dobrotvir Reservoir. Further downstream, pollution is kept high because of untreated waste effluents and phytoplankton mass developments due to high phosphorus concentrations.