| Summary: | The gradients of hydrological, hydrophysical, and hydrochemical conditions form the transition zones in river mouth areas. These areas are considered ecotones in the presence of the edge effect. Our research aimed to identify the main patterns in the structural organization of zooplankton communities in different types of river mouth areas in lowland reservoir tributaries within the Middle Volga basin. A cluster analysis was performed to structure and determine the zooplankton communities. The identified zooplankton communities were characterized by the noticeable heterogeneity in the species structure. We analyzed the spatial distribution of the structural indicators of zooplankton communities and, on the basis of RDA, determined the factors that significantly affect the organization of the ecotone community. An ecotone was found in all types of river mouth areas where the highest density, biomass, diversity, species, and functional richness of zooplankton were noted, as compared to bordering zooplankton communities. As the morphological structure of the mouth areas became more complex, the values of the main structural parameters of zooplankton communities increased. It was demonstrated that conditions in the ecotones are favorable to the development of zooplankton alien species. The major factors determining the species structure of the ecotone zooplankton community were water electrical conductivity (R<sup>2</sup> = 21.07%, <i>p</i>-value = 0.001), dissolved oxygen content (R<sup>2</sup> = 10.33%, <i>p</i>-value = 0.003), and water transparency (R<sup>2</sup> = 9.77 %, <i>p</i>-value = 0.001).
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