Freshwater pearl mussels have high ecological demands on their habitat. For natural reproduction and distribution, they need a colmation-free porespace in the substrate and sufficient host fish for their parasitic stage of life. In Austria, river alterations and anthropogenic activities in the catchments are causing habitat degradation for both, the freshwater pearl mussel Margaritifera margaritifera and its host fish Salmo trutta. Due to the lack of reference stretches, sediment transport and sediment deposition in the main channel cannot be measured directly. In (semi-) natural river sections as well as in sections with anthropogenically caused over-width of the river bed, however, it can be observed that the river itself forms a two-stage ditch within a few years. This study examines the deposits of those rivers and describes hydraulic and sedimentological processes influencing the geometry within the main channel below bankfull stage. A possible correlation between the mean annual discharge and the instream geometry could be determined. A simple formula is given as a recommendation for action, which can be used for pre-dimensioning of channel geometry below the bankfull stage in case of river restoration of freshwater pearl mussel habitats. This equation also allows authorities to review planning services for ecologically negative interventions and to recommend a method of implementing measures below bankfull stage.