Viruses are abundant and diverse in aquatic environments; their activities influence biogeochemical cycling, population dynamics throughout the ecosystem and genetic transfer. In turn viral abundance and diversity are influenced by physiochemical factors such as salinity, pH and temperature.  The Coorong lagoon system exhibits an intense environmental gradient increasing in salinity, organic and inorganic matter, and nutrients with distance from the Murray River mouth. The Coorong is an ecosystem of international significance yet the viral community is yet to be fully investigated. Here we investigated how the viral community changes in response to increasing salinity and impacts upon the bacterial and phytoplankton communities present by determining the contribution of viral lysis to mortality. Significant shifts in viral diversity (as determined by morphology) and contribution to bacterial and phytoplankton mortality were observed as salinity increased along the Coorong. An increase in morphotypes common to extreme environments was observed while viral induced mortality was found to be heterogeneous, at both the total community and sub-population level.  This indicates that salinity impacts strongly upon the viral community in natural environments yet the effect of the viral community on other members of the microbial community is varied shifting with prey community composition and physiochemical properties.