We investigated the macrophyte community in a free flowing stretch of the Danube downstream ofVienna, Austria. Aim of the study was to analyze the macrophyte - habitat relationship with respect to depth andconnectivity. Habitat types (HT-1 to HT-5) paralleled those introduced within the Floodplain Index, i.e. they represent a gradient from permanent and lotic to temporary and lentic environments, which were all represented by water bodies inour survey reach. Species number decreased with increasing connectivity to the main channel and temporary waters showed a diminished diversity. Based on community analysis our data confirmed that the macrophyte vegetation can be used as an indicator that separates all the HTs from each other. A high number of indicator species was observed in HT-3, HT-4, and HT-5, indicating the stress on aquatic plants by the water flow in the main channel (HT-1) and in permanently connected side channels (HT-2). With respect to the EC Water Framework Directive, our study partly fills the gap which is still present as regards the deeper knowledge of macrophyte composition in floodplain waters. We also gave numerical proof to the common knowledge that there is a rather great diversity in floodplain water vegetation, determined by connectivity with the main river channel.