Solar Disinfection (SODIS) has been identified as a relatively cheap method of purifying water against pathogens, therefore providing potable drinking water, an essential component upon which living systems and the human body depends. In this study, the antimicrobial efficacy of solar disinfection of drinking well water was studied. A total of thirty (30) wells was randomly sampled from six (6) local government areas in Benin City, based on accessibility and communal usage. The well water was sampled using transparent 1L polyethylene terephthalate (PET) bottles. Standard microbiological and biochemical test procedures were performed to enumerate, isolate, characterize and identify the isolates to genus level. Antibiotic susceptibility of the isolate was also ascertained. Coliform test was conducted and counts expressed in Most Probable Number (MPN). The study revealed that Staphylococcus sp., Micrococcus sp., and Klebsiella sp. and, Penicillium sp., Fusarium sp. and Candida sp. were the most prevalent heterotrophic bacteria and fungi isolates in the study area in addition to fecal indicators (Escherichia coli and Fecal streptococci) with 83.33% occurrences respectively. The study also revealed that the overall percentage elimination of the identified isolates was recorded as 42.11%, while the percentage elimination of fecal indicators identified was 50%. It was observed that SODIS was very efficacious with a percentage reduction of above 95% for all identified isolates. It was also observed that SODIS is slightly more bactericidal as compared to its being fungicidal. From the study, it could not be ascertained with certainty whether or not, exposure to SODIS alters a microbial pathogens’ antibiotic susceptibility. The use of SODIS did not completely eliminate all the fecal coliforms found in the studied well water, therefore making it unfit for drinking with regards to WHO recommendation. Consequently, the study recommends the use of SODIS only in conjunction with other water purification methods to ensure potability.