At the Sulm River, an Austrian lowland river, an ecologically orientated flood protection project was carried out from 1998-2000. Habitat modeling over a subsequent 3-year monitoring program (2001-2003) helped assess the effects of river bed embankment and of initiating a new meander by constructing a side channel and allowing self-developing side erosion. Hydrodynamic and physical habitat models were combined with fish-ecological methods. The results show a strong influence of riverbed dynamics on the habitat quality and quantity for the juvenile age classes (0+, 1+, 2+) of nase (Chondrostoma nasus), a key fish species of the Sulm River. The morphological conditions modified by floods changed significantly and decreased the amount of weighted usable areas. The primary factor was river bed aggradation, especially along the inner bend of the meander. This was a consequence of the reduced sediment transport capacity due to channel widening in the modeling area. The higher flow velocities and shallower depths, combined with the steeper bank angle, reduced the Weighted Useable Areas (WUAs) of habitats for juvenile nase. The modeling results were evaluated by combining results of mesohabitat-fishing surveys and habitat quality assessments. Both, the modeling and the fishing results demonstrated a reduced suitability of the habitats after the morphological modifications, but the situation was still improved compared to the pre-restoration conditions at the Sulm River.