A dynamic change in environmental conditions among floodplain habitats with different geomorphology might be a significant trigger in determining rotifer functional diversity. The aim of the study was to test the importance of environmental differences between several waterbody types, their positions within the floodplain and supporting microcrustacean communities in the structuring of rotifer functional feeding guilds. The study was conducted in Kopački rit floodplain during 2008 at five sites (two lakes, two channels and the main river). ANOSIM showed a significant difference in spatial distribution among rotifer feeding guilds. Redundancy analyses indicated biotic variables to significantly influence rotifer functional diversity in lake systems while in channel environments and the main riverbed guild representation was mainly influenced by limnological variables. Individual guild abundance changed relative to the site position within the floodplain as well, where the increased distance from the main riverbed resulted in increased rotifer numbers, and a different proportion of microfilter-feeders and macrofilter-feeders was recorded. The multiple linear regression showed a significant relation of macrofilter-feeder rotifers with microcrustaceans pointing to notable exploitative competition among these groups. The results highlight the ecological importance of all types of natural floodplain habitats necessary for preserving and maintaining the rotifer diversity.

Floodplains are dynamic interfaces between aquatic and terrestrial ecosystems, where ecosystem functioning is strongly influenced by microbial communities. To investigate the composition of free‐living and particle‐associated prokaryotic and microbial eukaryotic communities, five interconnected study sites were sampled in one of the best‐preserved Danube floodplains and subsequently analyzed using 16S and 18S rRNA gene amplicon sequencing. We compared community dynamics across low‐water periods and minor to moderate floods and observed flooding to increase microbial diversity and promote gradual community shifts depending on flood intensity, whereas low‐water conditions limited microbial exchange and reduced compositional connectivity across floodplain ecosystems. Dispersal effects were particularly pronounced in microbial eukaryotes, including Perkinsea and Fungi, pointing to the importance of hydrological connectivity in structuring micro‐eukaryotic communities. Flooding also facilitated community mixing and more balanced interspecific interactions, while low‐water periods led to more compartmentalized networks. Core microbial community size increased with flooding intensity, reflecting the influence of ecosystem mixing, allochthonous inputs, and increased nutrient availability in shaping floodplain communities. This study highlights the effects of flooding intensity on both prokaryotic and microbial eukaryotic communities, advancing our understanding of how hydrological variability shapes microbial dynamics in riverine floodplains.