It is assumed that the regulations of rivers in general and hydropeaking in particular provides elevated degrees of fine sediments in river beds, which affect negatively the habitat quality for juvenile salmonids. The first objective in the present study was to find a better and clear connection between the available shelter for juvenile Atlantic salmon and the grain size distribution. The second was to implement this linear relationship in a 1D numerical model in order to predict the development of shelters over time. In the case of the flow scenarios, first hydrograph consisted of an unregulated runoff series with daily resolution, while the second hydrograph was hydropeaked based on the current operation. The natural alterations of aggradation and degradation was shown at unregulated scenarios, while operated flows led to several anomalies, such as in relation of selective transport and increased embeddedness.