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 (n = 96) were collected over a period of five months to determine the levels of enteric bacteria and to perform a Quantitative Microbial Risk Assessment (QMRA) of drinking water quality. Sanitary risk scores revealed `medium' and `low' overall risks for the wells and boreholes, respectively. Three risk factors (faulty fence; small apron; pollution sources) exhibited high significant (p < 0.01) association with the presence of E. coli and thermotolerant 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 detection limit in water from the boreholes. Shigella and Campylobacter were detected in all water samples. Estimated risks of infection associated with Shigella (2.1 × 10-2 to 2.3 × 10-1) were higher than those of Campylobacter (6.7 × 10-2 to 1.9 × 10-1) and Salmonella (1.9×10-3 to 5.6×10-3). Adaption 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 diarrheal illness to humans.