With increasing stress on our water resources and recent waterborne disease outbreaks, understanding the epidemiology of waterborne pathogens is crucial to build surveillance systems. The purpose of this study was to explore techniques for describing microbial water quality in rural drinking water wells, based on spatiotemporal analysis, time series analysis and relative risk mapping. Tests results for Escherichia coli and coliforms from private and small public well water samples, collected between 2004 and 2012 in Alberta, Canada, were used for the analysis. Overall, 14.6 and 1.5% of the wells were total coliform and E. coli-positive, respectively. Private well samples were more often total coliform or E. coli-positive compared with untreated public well samples. Using relative risk mapping we were able to identify areas of higher risk for bacterial contamination of groundwater in the province not previously identified. Incorporation of time series analysis demonstrated peak contamination occurring for E. coli in July and a later peak for total coliforms in September, suggesting a temporal dissociation between these indicators in terms of groundwater quality, and highlighting the potential need to increase monitoring during certain periods of the year.