Waterborne diseases are influenced by sewage inputs to drinking and recreational waters. For molecular tools to advance decision-science for public health protection, sample concentration, hazard characterization, quantification, and/or viabililty will need to be addressed for waterborne pathogens in environmental waters. Human viruses are pathogens responsible for many disease idiopathies ranging from mild gastroenteritis to more severe neurological symptoms. Their presence at high numbers in human excreta has been well documented and their high potency and resistance to wastewater treatment makes them of great concern relative to many bacterial pathogens. The Great Lakes are a unique coastal environment, used not only as a source of fresh water for municipal, agricultural and industrial use, but they support a significant commercial and sport fishing industry. Every year millions of people visit the 500 plus recreational beaches in the Great Lakes. Pollution, beach closures and recreational disease are all of notable occurrence in the Great Lakes and the data to date suggests that viral pollution in these waters is part of the problem. Current detection methods are limited in their ability to detect and evaluate multiple virus types from single samples. PCR-integrated cell culture, qPCR, and viral microarrays to screen municipal wastewaters and beaches for the presence of enteric human viruses have been used to address public health risks. Adenoviruses were commonly observed, but RNA viruses were more frequently detected in sewage compared to DNA viruses when analyzed by microarrays. Some seasonality among certain viral groups was observed; other viral groups were shown to be ubiquitously present in sewage. The occurrence on beaches was related predominantly to wind.