The presence of Total coliform, Eschericha coli and enterococci were enumerated in the cattle farming areas of the Oconee Watershed using colilert TM and enterolert TM IDEXX plates, respectively. Microbial Source Tracking (MST) using Bacteroidales molecular markers for ruminant (RuBac) and human (HuBac) specific bacterial groups were used to determine the source of the fecal pollution in the watershed. In the cattle farming regions of the watershed higher levels of fecal bacteria were detected compared to the levels of fecal bacteria at the forested and residential sites. MST indicated that the cattle farming regions (except DC2) of the lake was impacted by fecal pollution from a ruminant source such as cattle. In addition, qPCR for the tuf gene of E. coli and the stx2 gene that is commonly found in enterohemorragic E. coli O157:H7 were used to evaluate the presence of these bacteria in the study area. E. coli O157:H7 (stx2 gene) was detected only in the beef cattle regions of the watershed. The presences of E. coli and stx2 gene in the Oconee Watershed represent a potential public health risk because Lake Oconee and its tributaries are used for recreational activities as well as crop irrigation.