This geographical study aimed to show natural or water-processing-related factors of faecal contamination incidents (FCIs) of drinking water in continental France. We defined a FCI as the occurrence of at least 20 colony-forming Escherichia coli or enterococci among all the 100 mL samples collected for regulatory purpose within one day from a given drinking water supply zone (SZ). We explored correlations between the standardized number of FCIs per département (N_Pols) and various indicators related to weather, land cover, topography, geology and water management for three SZ size sub-classes. In 2003–2004, 2,739 FCIs occurred in SZs supplying fewer than 2,000 people, mainly with simply disinfected groundwater. N_Pols correlates with four covariates: (1) precipitation; (2) the extension of the karst outcrops; (3) the extent of disinfection; and (4) catchment protection. One hundred millimetres of yearly excess in precipitation increases the pollution risk by 28–37%, depending on the sub-class. A 10% extension of the karst areas, a 10% increase of unprotected resources, or of SZs with no disinfection, could entail a higher risk of FCI by about 10%. The correlations are reproducible over the three sub-classes and corroborate expert appraisals. These results encourage the ongoing effort to generalize disinfection and catchment protection.