The extent to which stochastic and deterministic processes influence variations in species communities across space and time remains a central question in theoretical and applied ecology. Despite their high dispersal ability, the composition of phytoplankton communities displays striking spatial variations among lakes even at small spatial scale. To investigate the mechanisms underlying the distribution of phytoplankton species, we evaluate the contribution of stochastic, spatial and environmental processes in determining β‐diversity patterns of phytoplankton at a regional scale. Phytoplankton communities were surveyed in 50 different lakes from north‐central France, a region characterised by strong environmental heterogeneity. The regional species pool was characterised by extremely high β‐diversity levels, which were mainly explained by species replacement (i.e. turnover) rather than by differences in species richness (i.e. nestedness). Null models of random species distribution and spatial processes failed to explain observed β‐diversity patterns. At the opposite, local environmental conditions strongly influenced the degree of uniqueness of local phytoplankton communities, with the most contrasted environments, including human‐dominated areas, promoting highly distinct phytoplankton communities. Our results suggest that species‐sorting mechanisms that arise from variations in local environmental conditions drive high species turnover at the region scale. Thus, in a landscape strongly impacted by cultural eutrophication, further anthropogenic impacts on aquatic ecosystems would likely induce regional homogenisation of phytoplankton communities. Overall, our study supports the fact that the management of lakes and reservoirs in anthropic landscapes should aim at maintaining environmental heterogeneity while preventing further eutrophication in order to favour the maintenance of high phytoplankton β‐ and γ‐diversity.