We assessed the occurrence of Vibrio pathogens in the final effluents of five wastewater treatment plants (WWTPs) located in Amathole and Chris Hani District Municipalities in South Africa over a 12 months period between September 2012 and August 2013 using standard membrane filtration technique followed by cultivation on thiosulphate citrate-bile salts-sucrose (TCBS) agar. The identities of the presumptive Vibrio isolates were confirmed using polymerase chain reaction (PCR) including delineation into V. parahaemolyticus, V. vulnificus and V. fluvialis pathotypes. The counts of Vibrio spp. varied with months in all the study sites and ranged in the order of 101 and 104 CFU/100mL. Vibrio distribution also showed seasonality with high counts being obtained in autumn and spring (p < 0.05). Prevalence of Vibrio spp. among the five WWTPs also differed significantly (p < 0.05). Of the 300 isolates that were confirmed as belonging to the Vibrio genus, 29% (86) were V. fluvialis, 28% (84) were V. vulnificus and 12% (35) were V. parahaemolyticus. The isolation of Vibrio pathogens from the final effluent suggests that this pathogen is in circulation in some pockets of the population and that the WWTPs under study do not efficiently remove bacterial pathogens from the wastewater and consequently are threats to public health.