Rivers are important transport systems for nutrients and organic material and thus influence biogeochemical cycles and food web structures. Microorganismal biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that freshwater fungi perform important ecological functions, there is scarcely any fungal data available for river systems. In this study, we address the fundamental question of how mycoplankton communities are structured and assembled over a longer river section with strong environmental gradients and anthropogenic pressure and what variables control on it. The mycoplankton communities from the shallow freshwater to the coastal-oceanic transition zone were analyzed based on 18S rRNA gene tag-sequencing and the observed patterns were related to environmental and spatial factors by multivariate statistics. Finally, the underlying assembly processes were revealed by Quantitative Process Estimates (QPE) method. The partitioning of mycoplankton communities deviated from the previously described patterns of fluvial microbial communities, triggered by a strong influence of local environmental conditions, which were partly under spatial control. The deepening of the Elbe River for improved navigation purpose seemed to have a strong secondary effect. The salinity gradient was the most explaining variable and zoosporic fungi showed higher sensitivity to high salinity levels. Consequently, none of the zoosporic taxon groups occurred solely in the marine environment. Significant differences were found in the assemblage processes with a dominance of environmental selection in the upstream region compared to undominated processes in downstream and coastal transition regions. The results suggest that fungi play various ecological roles along the diverse river sections and that their biotic interactions become more complex in the estuary. These results provide an important framework to help predict the functional consequences of changes in mycoplankton community structure and to help conserve microbial biodiversity in river ecosystems.