Potentially pathogenic viruses within freshwater reserves represent a global health risk. However, knowledge about their diversity and abundance in deep groundwater reserves is currently limited. We found that the viral community inhabiting a deep confined aquifer in South Australia was more similar to reclaimed water communities than to the viral communities in the overlying unconfined aquifer community. This similarity was driven by high relative occurrence of the ssDNA viral groups Circoviridae, Geminiviridae, and Microviridae, which include many known plant and animal pathogens. These groups were present in 1500 year-old water situated 80 m below the surface, which suggests the potential for long-term survival and spread of potentially pathogenic viruses in deep, confined groundwater. Obtaining a broader understanding of potentially pathogenic viral communities within aquifers is particularly important given the ability of viruses to spread within groundwater ecosystems.