The microbiological quality of 75 private drinking water supply boreholes in Co. Cork, Ireland was assessed in order to determine the incidence of contamination and the potential pathways of such contamination. Microbiological analysis was carried out using the membrane filtration technique for the recovery of thermotolerant (faecal) coliforms. The sanitary protection of the supplies was evaluated by means of systematic inspections and subsequent qualitative sanitary risk assessment. Almost a quarter of all supplies investigated (24%, n = 18) was found positive for thermotolerant coliforms. Weather conditions had a significant impact on microbiological water quality, increasing both contamination incidence and gross contamination frequency. Over half of the supplies had nine or more sanitary hazards and most had rudimentary sanitary protection measures at the head of the borehole. These low sanitary protection measures suggest that boreholes can pose a significant hazard to valuable groundwater resources by providing direct contamination routes.