Most of the large rivers are heavily degraded and lack near‐natural conditions due to high human pressure (agricultural use and settlements) especially on former inundation areas. Hence, it is rarely possible to ‘restore’ predisturbance conditions of rivers and their floodplains. Further, river or floodplain restoration programs are often based on type‐specific reference conditions. Those reference conditions are mainly determined on the basis of historical maps not giving any information of, for example, sediment supply, flood frequency and vegetation cover (density). Especially for improving the ecological status of rivers with abandoned channel features, key habitats for target fish species have to be restored by reconnecting floodplains and their secondary channel system. In addition, because of the necessity of improving the ecological status, there is growing interest in interdisciplinary river restoration techniques. Within the presented article, an integrative concept is derived based on Light Detection and Ranging measurements and numerical modelling with respect to river dynamics (hydrologic and morphological). Further habitat modelling, based on unsteady depth‐averaged two‐dimensional hydrodynamics, is applied with a focus on the mesounit scale. For testing the conceptual model, various river reaches at the Morava River were selected, featuring different morphological characteristics. It was found that the applied management concept allows considering the important issues of river dynamics (morphological/hydrologic) using a flow‐ and flood‐pulse approach for identifying bottlenecks of target species at the Morava River. The reconnection of abandoned channels will result in an increase of hydromorphological heterogeneity and/or woody debris within the study reach. This might be of high relevance for habitat features (e.g. backwater habitats) especially for flow pulses between low flow and mean flow and/or in reaches without abandoned channels between low‐flow and the bankfull stage. Copyright © 2012 John Wiley & Sons, Ltd.