Understanding the relative importance of dispersal and environmental selection in shaping aquatic mycoplankton communities can help to predict fungus-driven ecological processes such as mycoflux or mycoloop and to maintain biodiversity in river ecosystems. In the presented study, a transect of the Elbe River (7th stream order number) that extended from the shallow freshwater zone through the estuary up to the river plume, and to the adjacent ocean waters, was sampled. Mycoplankton community structure and underlying assemblage processes were investigated using tag sequencing and Quantitative Process Estimates (QPE) analysis. Mycoplankton communities formed three significantly different biomes, by which the most structuring factor of salinity was superimposed by secondary effects of the Elbe deepening works. The underlying processes differed drastically: migrations of taxa played only a minor role. Instead, the species present in upstream sections responded to the strong physico-chemical environmental changes and a change from an autotrophic to a heterotrophic system was observed. Downstream, neither selection nor dispersal dominated but microbial features such as the cell tolerance to salinity variability, host dependency, and life strategy could help to explain the observed patterns. The results showed that the assemblage processes can change over relatively short distances. It indicates that the processes are not static and that the relative importance of a process can vary under different conditions and between members of a community.++