A total of one hundred and twenty-two water samples were obtained from hand-dug wells and boreholes in Ogbomoso metropolis, Oyo State, Nigeria. Physico-chemical, most probable number technique, direct culture methods, and water quality index were used to assess the drinking water quality in this region. Some of the physicochemical parameters were within the acceptable limits, with the exemption of conductivity (940 μscm−1), total dissolved solids (1120 mgL−1) total hardness (404 mg CaCO3L−1), and Cl− ion (220 mg/L). Escherichia coli, Klebsiella sp, Staphylococcus aureus, Shigella dysenteriae, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella sp, and Serratia sp are some of the isolates obtained from the water samples. Total coliform count in the well water samples was higher than those from boreholes, with E. coli having up to 180 and 45 CFU/mL for well and borehole water samples respectively. The calculated water quality index indicated poor drinking water quality. Some of the isolates were resistant to nothing less than three antibiotics and a maximum of ten antibiotics. All approaches used for assessing the water samples emphasize the need for improvement in water quality to safeguard public health. Drinking water from hand-dug wells and boreholes in this region requires treatment by chlorination, filtration, and boiling before consumption. Government bodies saddled with environmental and health responsibilities in the region should provide a potable water supply.