Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition.Almost all large rivers in Europe are greatly affected by pollution, alterations in the catchment, and hydraulic engineering (30). The greatest impact of damming and regulation on the connectivity, thermal heterogeneity, and biodiversity of a river system becomes visible in the lowland region of a river. Side arms, dead side arms, separated meander segments, and expansive floodplains, as they naturally appear in the lowland reach of a river, create a broad range of lotic, lentic, and semiaquatic habitats, leading to hot spots of biodiversity (37). Natural floodplains serve as sinks, sources, or transformers of dissolved and particulate organic matter, inorganic nutrients, and biota and thus contribute greatly to the self-purification ability of a river. The driving force of exchange processes between the river and its floodplains is hydrological connectivity, via both surface and groundwater inflow (36).The National Park of the River Danube (Austria) is one of the last remnants of a natural floodplain and one of the largest in Europe. It is located downstream of Vienna and extends to the Slovakian border. Due to regulation of the Danube River and the construction of hydropower dams upstream of Vienna, large parts of the floodplains have been drained or disconnected from the river, and the hydrology and limnology of the whole river-floodplain system has been changed. The freeflowing section of t...