The abundance and community structure of viruses and heterotrophic bacteria were investigated along a natural continuous salinity gradient (18 to 155 PSU) in a South Australian temperate coastal lagoon using flow cytometry. The brackish waters of the lagoon (18 to 25 PSU) were characterised by high viral concentrations (1.3 x 10(8) to 1.5 x 10(8) ml(-1)) and elevated virus to bacteria ratios (11.7 to 15.5), suggesting high viral infection rates and long persistence of viruses in the water. The increase in salinity above 25 PSU resulted in a decrease in viral abundance without a significant modification of bacterial abundance. A concomitant increase in viral and bacterial abundances with salinity was observed from 50 to 150 PSU, where the highest abundances were observed (1.4 x 10(8) and 2.5 x 10(8) ml(-1), respectively). Prokaryote cytometric richness also varied greatly along the salinity gradient, suggesting a modification of the phylogenetic composition and/or variability in the activity level of the bacterioplankton community along the salinity gradient. The most cytometrically diversified bacterial community (6 to 7 subpopulations) was observed between 50 and 150 PSU. BIOENV analysis identified salinity as the main factor structuring the distribution of bacteria throughout the lagoon. The effect of salinity on viral populations appeared to be more indirect, as the distribution of viruses was mainly driven by host abundance (i.e. bacteria) along the salinity gradient. The complex patterns described here represent the first observation of viral and microbial dynamics along a continuous salinity gradient from 18 to 155 PSU.