These data represent estimations of densities of naturally-occurring populations of the species complex “Pseudomonas syringae” in surface water that flows through the Durance watershed. Population densities were quantified in samples obtained at 21 sites along the river during 2 years, based on a combination of platings on microbiological media to count and isolate colonies of putative P. syringae and validation of their identities via phylogenetic analyses of the sequences of a conserved housekeeping gene determined with NGS technology.