1. Viruses are a pervasive component of microbial food webs in both marine and freshwater systems. The abundance of viruses in individual aquatic systems appears to be independent of salinity but related to the biomass of primary and secondary producers as well as seasonal effects. Burst size, virus production rate and the percentage of microbial cells carrying a viral burden also appear to be more closely correlated to trophic status than to salinity. 2. In marine environments, the roles of planktonic viruses as regulators of carbon and nutrient cycling as well as microbial community structure have been a focus of numerous studies, yet the roles of freshwater virioplankton remain much less studied. Nevertheless, a survey of published freshwater studies demonstrates that virioplankton recycle important quantities of growth-limiting nutrients from hosts via generation of dead particulate and dissolved organic matter during cell lysis, and suggests that both the chemical speciation and concentration of these organic compounds and nutrients may have important influences on the microbial community. 3. Parallel observations on the spatial patterns and dynamics of microbial mortality due to viruses or grazing are more advanced in freshwaters than in marine environments. However, the constraints that determine whether virus- or grazer-mediated mortality dominates are not yet understood in either environment. 4. Application of molecular approaches has facilitated the examination of the diversity and ecological dynamics of specific viral populations and entire communities. The depth of detail achieved in marine environments towards characterizing these populations and communities is just beginning to be matched in freshwater systems. The few available data suggest that viruses targeting-related hosts in freshwater and marine systems may be genetically distinct. 5. Although the role of viruses in aquatic systems is complex and remains insufficiently studied, our survey of the literature indicates that, despite some differences, many of the controls on virioplankton activity and diversity are similar in marine and freshwater environments.