Bacteria, which are the most common pathogens in water, gain entrance into water mostly through fecal contamination and this poses significant risks to human and animal health. The causative agent of cholera is globally autochthonous to the aquatic environment and it's not confined to only cholera endemic areas. This study is a survey of the microbiological quality of Oyun River and most importantly using the detection and incidence of Vibrio cholerae as an additional indicator of pollution of faecal origin. Molecular characterization and confirmation of bacterial isolates were done via Polymerase Chain Reaction (PCR) and DNA sequencing. The microbiological and molecular analysis revealed the presence of E. coli, Streptococcus thermophillusTH1435, Vibrio Parahaemolyticus wp_051483013, Enterobacter cloacae strain sugR_1, Vibrio campbellii HYO1 Vibrio cholerae and Thermobaculum terenum in the Oyun River. Further sequence analysis revealed the presence of six new strains of enteric bacteria which was allocated the following accession numbers after deposition at the GenBank (MT275484; MT275485; MT275486; MT275487; MT275488; MT275489). The confirmation of isolates from the Vibrio genus and other enteric bacteria posits that the pollution is of faecal origin and thus, adequate monitoring to control activities along the riverside should be upheld by both the citizens and government authorities to avoid preventable outbreaks.