Different types of water bodies in lowland river floodplains represent vital biodiversity havens and encompass diverse microhabitats, which are essential for structuring different macroinvertebrate communities. Chironomidae larvae (Diptera) are an inseparable part of these communities, with their high richness and abundance. In three water body types within the Danube floodplain Kopački Rit in Croatia, over the course of four sampling campaigns, we recorded 51 chironomid taxa in periphyton on macrophytes, twigs, and glass slides. The most diverse were chironomid communities on macrophytes, whilst month-old periphyton on twigs supported the least taxa. Cricotopus gr. sylvestris, Dicrotendipes lobiger, Dicrotendipes spp., Endochironomus albipennis, Glyptotendipes pallens agg., Polypedilum sordens and Polypedilum spp. were present in all studied microhabitats. The type of substrate is a very important factor influencing Chironomidae diversity and abundance, which was evident in the presence and dominance of Corynoneura gr. scutellata and Monopelopia tenuicalcar in the dense macrophyte canopy epiphyton. Finding pristine floodplains such as Kopački Rit can be very challenging, as such areas are increasingly altered by human activities. Studies of resident species and the extent to which changes in the parent river influence floodplain communities are important for the protection and restoration of the floodplains.