Most of the world’s large rivers are affected by dams and weirs resulting in serial discontinuity and disconnection from their floodplains. These changes in lateral and longitudinal connectivity of the rivers caused a serious decline of European riverine fish species in the past decade. This contribution analyses the quantitative and qualitative effects of the introduction of weirs and of floodplain restoration measures using case studies in Europe. Abiotic habitat properties as well as the community structures of fishes, macroinvertebrates, macrophytes and periphyton were strongly affected by weirs, exceeding the importance of other factors such as geographic location, geology, and drainage system. All of the tested in-stream habitat restoration measures such as the introduction of gravel, dead wood, and shallow water zones revealed only marginal and short-term effects in highly modified waterbodies. As evident from two case studies on the floodplain reconnection and restoration in the upper Danube and Main/Rhine catchments, the important roles of these habitats as migration corridors, spawning and feeding grounds for juvenile and rheophilic fishes is illustrated. Consequently, these functions of secondary floodplain channels as compensatory habitats should be better considered in river restoration. The evaluation system presented herein, by including several taxonomic groups and physicochemical habitat variables, provides a universally applicable tool for the ecological assessment of serial discontinuity and of floodplain restoration.