The effects of hydropeaking in the habitat of the Iberian barbel (Luciobarbus bocagei) a native cyprinid fish species of the Iberian Peninsula, was investigated. Two study sites were selected in the Ocreza River, Mid-Eastern Portugal. A regulated site located immediately downstream from a hydropower dam, and an unregulated site located on a lotic undisturbed segment upstream the reservoir. The habitat preferences were determined based on field data collection and displayed by means of fuzzy sets and rules for juvenile and adult life-stages of barbel. The River2D and CASiMiR Fish 2D model were applied to both river sites in the Ocreza River to simulate how physical habitat conditions vary with powerhouse operation. Results indicate that hydropeaking impact is strongly dependent on river morphology. The more heterogeneous the river is the better it can support areas of suitable habitat, including shelters. Whatsoever, stranding is an associated risk. Furthermore, shifts in the array of habitats were due to occur between the base and peak flow. The study outcomes provide comprehensive information on the barbel response to hydropeaking. Understanding how hydropeaking influences both habitat availability and population dynamics is a crucial point to help guiding hydropower managers towards more sustainable practices.