Wastewater and treatment plants harbor a large number of bacteria, viruses, fungi, and parasites including worms and protozoans, that are known to pose the most health risk against humans. However, traditional methods that monitor the microbial quality of wastewater have not changed since the early century and often disregard the presence of other types of significant waterborne pathogens such as viruses. Over the years, technology in microbial research has advanced tremendously enabling the detection of a broader scope of micro-organisms that may be present in our wastewater. Our study aims to characterize the taxonomy, functional profiling, and seasonal patterns of viral DNA and RNA community structures using metagenomics and quantitative PCR to establish the virome distribution in aquatic environments receiving wastewater discharge.