Microbial indicators are used to infer fecal contamination and the potential presence of enteric pathogens. Since viruses pose one of the greatest health concerns, viral indicators of fecal contamination (e.g., bacteriophage, viruses of commonly consumed plants, and host-associated, non-pathogenic viruses) offer an alternative to bacterial indicators. For instance, crAssphage and Torque teno virus (TTV) are highly prevalent and restricted to the human gastrointestinal (GI) tract, and certain Enterococcus phages exhibit survival rates resembling those of enteric pathogenic viruses. While viral indicators of fecal contamination are often detected using culture- and/or molecular-based methods, emerging technologies, such as viral metagenomics, have also been evaluated for the detection of enteric viruses in sewage and water sources. Here, viral metagenomics is discussed as a potential tool to track sources of fecal contamination and identify enteric pathogenic viruses. Advancements of viral metagenomics in source tracking and surveillance have facilitated the identification of viruses from multiple sources. Viral metagenomics has also enabled the development of assays to identify and characterize novel viral indicators of fecal contamination. Considerations of viral metagenomics to track fecal contamination sources are also discussed. Finally, future perspectives in the areas of viral metagenomics in source tracking and surveillance are also addressed.