Fish stranding in rivers, due to rapid shoreline dewatering, often occurs during the down-ramping phases of hydropeaks enabling peak energy production. Multiple hydrological characteristics of hydropeaking and river morphology influence stranding, but little is known about their relative effects. The goal of our study is to identify how the combination of hydropeaking characteristics and the occurrence of morphological microstructure (e.g., puddles, scour pools) influence fish stranding. For this purpose, we used an extensive dataset of fish stranding observations collected over 3 years in spring at 48 stations along a 50 km-long river reach. We aimed (1) to characterize stranding events and their associated fish assemblages, and (2) to identify the spatial and temporal determinants of stranding. We found that the occurrence of morphological microstructures of the riverbed was the main factor explaining fish stranding. Scour pools are the most impacting microstructures, followed by scour puddles, humid zones, and alluvial puddles. Then, hydropeaking characteristics interact with morphology and modulate the intensity of stranding. Low flow ranges (low peak flow, low base flow) occurring after periods without hydropeaks induce particular “salmonid” and “super-stranding” events and other flow ranges induce regular stranding events. Salmonids are particularly subject to stranding at the beginning of the sampling period. Recommendations that emerged are (1) to act in priority on stations where stranding is most likely, by morphological operations or by installing attractive structures in the perennial area, and (2) to maintain attractive, perennial habitats in the low flow range of hydropeaks.