Although viruses play key roles in the environments such as in regulating host abundance and diversity, and in the recycling of nutrients, they remain an understudied fraction of natural ecosystems. The St Lawrence River is characterised by waters with a physicochemical gradient namely in terms of salinity and therefore represents a model system to study the change in biological communities in this salinity gradient. For this study, high-throughput sequencing was used to characterize the viral and potential host communities in 6 sampling sites along the St Lawrence River.