There is increasing evidence that environmental degradation may be contributing to an increase in marine-related diseases across a wide range of taxonomic groups. This includes a growing number of reports of both recreational and occupational users of marine waters developing gastrointestinal, respiratory, dermatologic, and ear, nose, and throat infections. The duration and type of exposure, concentration of pathogens, and host immunity determine the risk of infection. Public health authorities may not be able to accurately predict the risk of waterborne disease from marine waters due to the limitations of conventional monitoring, as well as erroneous perceptions of pathogen life span in marine systems. Pathogens undetectable by conventional methods may remain viable in marine waters, and both plankton and marine sediments may serve as reservoirs for pathogenic organisms, which can emerge to become infective when conditions are favorable. In this paper we address the environmental factors that may contribute to illness, the types of associated economic costs, the issues of water quality monitoring and the policy implications raised by the apparent rise in incidence of marine water-related illnesses.