Extreme, short-duration fluctuations caused by storage hydropower plant discharges or ‘hydropeaking’ occur when hydropower is used to cover the peak electrical loading conditions of a power network. The overall effects of hydropeaking can result in serious disturbances to the hydrologic regime, river morphology and the ecological condition of a river. In this study a transient, fuzzy logic based two-dimensional fish habitat model was used to investigate the stranding risk to juvenile European grayling (Thymallus thymallus) corresponding to different river morphologies. The stranding risk was simulated using two 24 hour discharge hydrographs in two alpine gravel bed river reaches. Both reaches were in close proximity to the hydropower plant outlet and were chosen due to their starkly contrasting morphological features. Spatially distributed stranding risk was determined based on a multi-step procedure which took into account the stationary habitat suitability, critical dewatering rates and flow depths. Although the number of reaches used in the investigation was limited in scope, clear distinctions with respect to the stranding risk were found. The reach with wider, flatter cross sections had a larger amount of stranding risk areas as compared to the reach with a steeply incised channel form. Stranding risk was found to be related to a specific set of changes in the discharge than to a particular rate of change or magnitude of the flow fluctuations. The temporal distribution of stranding risk was found to be almost identical for both reaches.