The ecological condition of the Danube section in Vienna (Austria) has been greatly impaired by urban development, regulation, channel straightening and the construction of a hydroelectric power plant. In 1997, the shoreline of the Danube in this area was restructured by artificial side channels, coves, gravel banks, pools and temporary waters. A monitoring programme has been established focusing on the investigation of the functional integrity of these inshore structures: first results show that the sites isolated from the Danube serve as stepping stone biotopes for dragonflies and amphibians. Particularly amphibians are suitable indicators of the ecological functioning of riparian migration linkages on a (macro-) habitat scale. Rheophilic fish species (e.g. Chondrostoma nasus) colonise side channels connected with the Danube and indicate a longitudinal connectivity on a landscape scale. The role of these structures within an urban greenway is discussed.