Numerous seawater lagoons punctuate the southern coastline of France. Exchanges of seawater between these lagoons and the open sea are limited by narrow channels connecting them. Lagoon salinities vary according to evaporation and to the volume of freshwater arriving from influent streams, whose nutrients also promote the growth of algae. We compared Prasinovirus communities, whose replication is supported by microscopic green algae, in four lagoons and at a coastal sampling site. Using high-throughput sequencing of DNA from a giant virus-specific marker gene, we show that the environmental conditions significantly affect the types of detectable viruses across samples. In spatial comparisons between 5 different sampling sites, higher levels of phosphates, nitrates, nitrites, ammonium and silicates tend to increase viral community richness independently of geographical distances between the sampling sites. Finally, comparisons of Prasinovirus communities at 2 sampling sites over a period of 10 months highlighted seasonal effects and the preponderant nature of phosphate concentrations in constraining viral distribution.