Background: Boreholes are principal sources of drinking water in Benin city. This water can become contaminated by runoffs, especially during the rainy season, resulting in outbreaks of waterborne diseases. Objectives: This study aimed at assessing the microbiological and physicochemical qualities of borehole water from four crowded areas of Benin city, Nigeria. Methods: The Total Coliform Count (TCC) and antibiotic susceptibility test of the bacterial isolates were assessed using standard microbiological methods. The colour, turbidity, pH, total dissolved solid (TDS), nitrate, iron, chromium, copper, and fluoride of the samples were compared with national and international standards for drinking water. Results: Most physicochemical parameters were within acceptable limits. The mean TCC values of all the samples were higher when compared to standards. The isolated bacteria were Pseudomonas aeruginosa (38%), Escherichia coli (32.3%), Staphylococcus aureus (20%), Klebsiella pneumoniae (4.2%), and Enterococcus sp. (5.5%). Isolates were sensitive to amoxicillin + clavulanic acid, yet showed high resistance to ampicillin and low resistance to ceftriaxone; the predominant pattern of resistance was DOCRAMPR. Conclusions: Despite the fact that the physicochemical parameters were within acceptable limits when compared to the standards, the water sources still pose health risks. Consequently, constant microbiological monitoring of borehole water is necessary, especially during rainfalls in Benin city.