Waterborne pathogens are still considered a threat to human health. Wastewater treatment plants (WWTPs), contain a high populace and diversity of viruses that can significantly affect the aquatic ecosystem. Subsequently, the occurrence and recurrence of viral pathogens are alarming that exist in human populations, which are potentially discharged into sewage systems. This study investigated the distribution and diversity of the viral communities from three WWTPs in Gauteng Province, South Africa using next-generation sequencing technology. The results uncovered that most of the viral populaces in the wastewater plants belong to the families Siphoviridae, Microviridae, and Myoviridae of the order Caudovirales. Other families including Baculoviridae, Partitiviridae, Virgaviridae, and Tymoviridae were likewise recorded. On the other hand, enteric pathogens detected were Astroviridae, Reoviridae, and Coronaviridae. The predicted functional features for the viromes revealed that the DNA metabolism was the major function within the community followed by carbohydrate and amino acid metabolism, suggesting that the treatment plants provide a rich biological environment for the growth of diverse viral species and other processes. The overall results in this study highlight the biological significance of WWTPs as a hotspot for some viral agents. The contamination routes of these viral agents are needed for efficient and cost-effective management strategies in water systems. Further, viral metagenomics ought to be considered as a key approach for revealing the diversity and early warning of emerging disease outbreaks.