Floodplains have been strongly altered by human activities such as channelization and other river regulations. Globally, there is a growing interest in their restoration because of an increasing understanding of the ecological importance of these habitats for feeding, spawning, nursery or overwintering of aquatic species. In this study, a large floodplain restoration project of the upper Danube River was used to investigate colonization and succession patterns of fish, macroinvertebrates, macrophytes and periphyton in relation to abiotic habitat variables that can be restored through ecosystem management. Highest species diversity was detected near the contact zones of the floodplain channel to the main stem of the Danube, and in the transition zones of river sections (RS) and oxbow lakes (OS). The highest proportions of all taxa (82%) and of distinctive species (22%) were detected in RS, followed by OS (66% of all taxa, 8% distinctive species) and floodplain ponds (FP, 47% of all taxa, 5% distinctive species). The habitat types RS, OS and FP significantly differed in overall community composition and their colonization processes comprising fast colonization of current-adapted specialists in RS, and mostly generalist species in OS and FP. Our results indicate that restoration of floodplain habitats should not only consider the re-establishment of maximum connectivity, but also provide a mosaic of distinct habitat types with different degrees of connectivity and disturbance. Each habitat type in the floodplain supported a unique assemblage of species, which suggests that such habitat mosaics can facilitate exceptionally diverse ecosystems.