In order to study the prevalence of enteric pathogens capable of causing infection and disease in the rural communities of Nkonkobe, bacterial isolates were collected from several surface water and groundwater sources used by the community for their daily water needs. By making use of selective culture media and the 20E API kit, presumptive Escherichia coli, Salmonella spp. and Vibrio cholerae isolates were obtained and then analysed by polymerase chain reaction assays (PCR). The PCR successfully amplified from water samples a fragment of E. coli uidA gene that codes for β-D-glucuronidase which is a highly specific characteristic of enteropathogenic E. coli, enterotoxigenic E. coli and entero-invasive E. coli. The PCR also amplified the epsM gene from water samples containing toxigenic V. cholerae. Although E. coli was mostly detected in groundwater sources, toxigenic V. cholerae was detected in both surface and groundwater sources. There was a possibility of Salmonella typhimurium in Ngqele and Dyamala borehole water samples. The presence of these pathogenic bacteria in the above drinking water sources may pose a serious health risk to consumers.