This study evaluated the physicochemical quality, microbial contamination and possible health risks of borehole water samples taken from 12 locations in Benin metropolis, Nigeria. Physicochemical parameters, microbial indicators, and some heavy metals were analyzed in the water samples, and a questionnaire survey was conducted to assess the public perception of water-quality risks. The mean pH of all samples was 5.50 ± 0.36, which was all acidic and 67% of boreholes had total coliforms present, while all physicochemical parameters met World Health Organization (WHO) and Standards Organization of Nigeria (SON) guidelines. The Occurrence of sporadic Escherichia coli suggested faecal contamination. Two general patterns were indicated by exploratory multivariate analysis: mineralization-related and a microbial-turbidity pattern. Heavy metals were found to have low risk of non-carcinogenic and carcinogenic effects, while microbial contamination still poses a public health risk. A validated public awareness questionnaire (Cronbach’s α = 0.780, n = 20) demonstrated societal relevance. Routine monitoring, adjusted pH, enhanced disinfection and public awareness are recommended.