The Buffalo River and its dams are major surface water sources used for fresh produce irrigation, raw water abstraction and recreation in parts of the Eastern Cape Province in South Africa. Over a 12-month period (August 2010 to July 2011), we assessed the bacteriological qualities of water from the river and 3 source water dams along its course. Faecal indicator bacteria (FIB), including total coliform (TC), faecal coliform (FC) and enterococci (ENT) counts, were high and ranged as follows: 1.9 × 102–3.8 × 107, 0–3.0 × 105 and 0–5.3 × 105 cfu/100 ml for TC, FC and ENT, respectively. Significantly (P < 0.05) higher concentrations of FC and ENT were observed at the sampling sites located at the lower reaches of the river compared to the upper reaches, and at Bridle Drift Dam compared to the other two dams. FIB counts mostly exceeded the recommended maximum values suggested by national and international guidelines for safe fresh produce irrigation, domestic applications, full-contact recreation and livestock watering. These results show that the bacteriological qualities of the Buffalo River and dams were poor, and suggest that sewage was dumped into the Buffalo River during the study period. Urban runoffs and effluents of wastewater treatment plants appear to be important sources of faecal contamination in the river. We conclude that these water bodies represent significant public health hazards. Provision of adequate sanitary infrastructure will help prevent source water contamination, and public health education aimed at improving personal, household and community hygiene is imperative.Electronic supplementary materialThe online version of this article (doi:10.1007/s11356-012-1348-4) contains supplementary material, which is available to authorized users.