Until recently, few water utilities or researchers were aware of possible virus presence in deep aquifers and wells. During 2008 and 2009 we collected a time series of virus samples from six deep municipal water-supply wells. The wells range in depth from approximately 220 to 300 m and draw water from a sandstone aquifer. Three of these wells draw water from beneath a regional aquitard, and three draw water from both above and below the aquitard. We also sampled a local lake and untreated sewage as potential virus sources. Viruses were detected up to 61% of the time in each well sampled, and many groundwater samples were positive for virus infectivity. Lake samples contained viruses over 75% of the time. Virus concentrations and serotypes observed varied markedly with time in all samples. Sewage samples were all extremely high in virus concentration. Virus serotypes detected in sewage and groundwater were temporally correlated, suggesting very rapid virus transport, on the order of weeks, from the source(s) to wells. Adenovirus and enterovirus levels in the wells were associated with precipitation events. The most likely source of the viruses in the wells was leakage of untreated sewage from sanitary sewer pipes.