Sanitary inspection and quantitative microbial risk assessment (QMRA) are complementary tools that provide comprehensive risk-based assessment of drinking water quality. This study set out to determine the sanitary risk scores and microbial health risks associated with wells and boreholes in Ilara-Mokin and Ibule-Soro, Nigeria. Water samples were collected over a period of 5 months and sanitary inspection forms were used to determine the sanitary risk scores. The risks of infections were estimated using dose-response models. The sanitary risk scores revealed ‘medium’ and ‘low’ overall risks for the wells and boreholes, respectively. Three risk factors exhibited a highly significant (p < 0.01) association with the presence of Escherichia coli and faecal coliforms in water samples from the wells. E. coli and Salmonella ranged from 1.82 to 2.28 and 2.15 to 2.63 log10 CFU/100 ml, respectively, in water from the wells but were below the detection limit in water from the boreholes. Estimated risks of infection associated with Shigella (2.1 × 10−2 to 2.3 × 10−1) were higher than Campylobacter (6.7 × 10−2 to 1.9 × 10−1) and Salmonella (1.9 × 103 to 5.6 × 10−3). Adoption of water safety plans may be advantageous in these settings, since intentional ingestion of water from the wells and boreholes may pose potential risks of diarrhoeal illness to humans.

  • Sanitary risks and water samples were collected from wells and boreholes.

  • Microbial risk assessment was used to evaluate human dose-response data.

  • Sanitary risk scores correlated positively with microbial water quality.

  • Risk factors exhibited significant association with the presence of E. coli.

  • Estimated risks of infection associated with Shigella were higher than those of Campylobacter and Salmonella.

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