Lowland floodplains are complex ecosystems comprised of standing and flowing waters interacting with terrestrial habitats, and the main force creating, shaping and influencing, both habitats and biotic communities, is a hydrological regime and water supply from the parent river. In areas not much altered by anthropogenic influence, the Danube creates such floodplain areas, and temporary shallow water bodies within represent biodiversity important habitats. In the Kopački Rit Nature Park floodplain in Croatia, diversity based on Chironomidae (Diptera) in both benthic and epiphytic communities was studied in eight ponds (temporary shallow water body) and at two channel locations (permanent shallow water body). At each location samples of sediment and macrophytes were taken at three sites. The benthic chironomid community was comprised of 29 taxa, most abundant being representatives of the Chironomus genus and Tanypus kraatzi in ponds, and Polypedilum nubeculosum and Cladotanytarsus sp. in channel samples. Cricotopus gr. sylvestris, Paratanytarsus sp. and Endochironomus tendens were dominant epiphytic chironomids (18 taxa). Non-metric multidimensional scaling and analysis of similarity analyses showed there was a clear grouping of sampling locations based on their position in the park and the distance from each other, more evident in the case of benthic chironomid communities. Furthermore, when the water bodies were compared based on the community structure from different locations and substrates, there was also a statistically significant separation. Community composition indicates high productivity and organic matter production of studied water bodies, but moreover, the differences in substrate preferences evident in 16 common out of 31 recorded chironomid taxa, indicate the importance of habitat complexity preservation in a floodplain.