Due to the high diversity of enteric viruses in the environment, there is an increasing need for methods enabling the multiple detection of different pathogens. Quantitative, emerging digital PCR and isothermal amplification approaches are capable of the quantification of multiple targets, and hence are suitable for long-term monitoring and source tracking of enteric viruses in the aquatic environment. The combination of culturing with PCR-based detection enables rapid viral risk assessment, especially with host tissues capable of the propagation of several viral strains. Viability assays may provide a better understanding on viral survival than PCR-based approaches alone, however, the usefulness of these assays in wastewater and environmental water samples should be further investigated. Undoubtedly, emerging sequencing-based technologies provide invaluable data on the ecology and diversity of viruses, and, along with rapid on-site technologies, e.g. biosensors, may be implemented in viral risk assessment in the aquatic environment in the near future.