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.