Due to hydropower operation, base flow is periodically disrupted by extreme and short-duration fluctuations of discharge during daily-peaks of energy demand, severely affecting the aquatic ecosystem. To contradict this tendency, structural and operational measures have been proposed. The implementation of operational measures has been neglected due to the economic impact on the electricity producer. Therefore, a better understanding of the impacts of these measures over the economics of electricity production is paramount. The present study investigates the effects of a mini-hydropower plant operation in the fish habitat of brown trout. Thus, the River2D model was applied to the river reach immediately downstream the Ermida hydropower plant, to obtain the hydrodynamic features for different discharges. To perform the habitat modelling with the Casimir Fish 2D, fuzzy sets and rules were developed for brown trout life-stages. The operational scenarios were developed considering the habitat availability and the power production periods according to the electricity selling price. The influence of the hydropower operation on the habitat suitability, as well as the energy revenue losses related with the production scenarios were taken into consideration. Results from this study may help water managers to adapt hydropeaking regimes to reduce the ecological impact of hydropower production.