During the last two decades theoretical and applied limnological research increasingly focused on the investigation of floodplain rivers (Amoros & Roux 1988, Junk et al. 1989, Schiemer 1999, Ward et al. 1999, Findlay et al. 2002). Ecological key prerequisites of such systems are natural fluvial dynamics leading to flood-controlled disturbances, thereby favouring geomorphic processes and successional patterns (e.g. Amoros and Roux, 1988; Junk et al., 1989). A great variety of human activities has led to the longitudinal and lateral fragmentation of large river systems, which is considered to be one of the major threats to running water ecosystems (Dynesius and Nilsson, 1994; Schiemer, 1999). According to the requirements of the EU Water Framework Directive (WFD, 2000/60/EC; European Commission 2000), all surface water bodies should reach at least “good ecological status” (class II within a five class system). In line with the WFD, schemes for assessing the ecological status of floodplain areas were developed for dragonflies (Chovanec & Waringer 2001; Chovanec et al. 2004) and caddisflies (Waringer & Graf 2002). Based on these methods, a multi-species approach is presented including a comprehensive set of indicator groups, which allow to thoroughly explore connectivity patterns of a river-floodplain system: molluscs, caddisflies, dragonflies, amphibians and fish. The assessment procedure was developed for a large, anabranched river system, the Danube in Austria, and tested in a floodplain area of this river upstream of Vienna.