High-head storage hydropower plants are an important renewable source of energy in alpine areas. Kinetic energy released from water, which is stored in reservoir and diverted through turbines, produces electricity. During daily peaks of energy demand, the powerhouse outflow is released in the downstream river, creating artificial flow fluctuation, so-called hydropeaking. This alters the natural flow regime of rivers and has a negative effect on ecosystems and biodiversity. As a result, water discharge, temperature, fine particle load and other abiotic factors are changed. Consequently, river organisms and their habitat are impacted. Resulting from an increased pressure for atmospheric carbon mitigation, hydropower production is expected to increase in the future (e.g. from storage powerplants). In Switzerland this trend is further enhanced by the recent governmental decision to phase out nuclear power production. Thought, the revision of the Swiss water protection act shows the growing awareness to protect natural ecosystems downstream of hydropower facilities. However, there is a strong need for research in this field due to the lack of knowledge on the adverse impacts stemming from hydropower production. This study is part of the interdisciplinary research project “Sustainable use of hydropower – innovative measures to reduce hydropeaking problematic” and it focuses on the impact of hydropeaking on fish and their habitat. Brown trout is used as a target species and important steps in their life cycle are studied. Three target stages of brown trout development were selected: adults, spawning and young-of-the-year. Each different life stage has specific habitat requirements. The latter can be used for identifying potential landscape filters constraining fish population renewal. Landscape filters are determined by the joint influence of river morphology and discharge regimes, such as hydropeaking. In this work, two rivers, with different morphological characteristics, are studied, namely the Vorderrhein and the Hasliaare Rivers. Both rivers show a hydropeaking regime, are situated in alpine areas and have a comparable hydrological regime. The hydrology of the two rivers is characterized by low discharge in winter and high discharge in summer due to snowmelting. Fish species composition is similar and strongly dominated by brown trout. The Vorderrhein River is one of the few natural and morphologically intact rivers found in Switzerland, which allows to isolate the effect of hydropeaking from other potential human-induced stressors. In contrast, the Hasliaare River has been strongly channelized in the past century. Thus, the Hasliaare River system was chosen to investigate the joint effect of hydropeaking and river channelization. In the Vorderrhein River, the seasonal impact of hydropeaking on adult brown trout habitat was modeled using the CASiMiR fish module. Therefore, different critical seasons are defined. Furthermore, the natural reproduction success was assessed and brown trout reproduction and rearing habitat were modeled. Habitat preference of spawning and young-of-the-year are established with specific Habitat Suitability Curves. The habitat model was adapted to the hydropeaking problem and indices measuring habitat dynamics were developed. Moreover, the transferability of Habitat Suitability Curves in habitat models was discussed. In addition, young-of-the-year density as well as egg to hatch survival were monitored. The results show that hydropower operations have an effect on brown trout habitat, whereat spawning and young-of-the-year life stages are more impacted than adults. The impact is seasonal and aggravated in winter. The natural river morphology provides suitable habitat areas at both peak and off-peak discharges. Although these suitable habitat areas are dewatered almost entirely or displaced on a daily basis. In the Hasliaare River system, the joint effect of hydropeaking and channelization on young-of-the-year, lake and stream resident spawning brown trout were studied. Steady and dynamic habitat conditions were evaluated and the habitat was modeled for three different degraded morphologies. Specific preference curves for each investigated life stage were developed. Moreover, the reproduction success was monitored by egg to hatching survival experiments and young-of-the-year density surveys. The results show that channelization aggravates the impact of hydropeaking as no young-of-the-year or spawning habitat is present at peak flow. In addition, egg development was found to be impaired. Therefore, the density of young-of-the-year individuals was negligible in the hydropeaking section. The habitat model shows that in a channelized river such as the Hasliaare River, suitable habitat conditions for fish are restrained at peak flow by the riverbed width. Finally, a tool for evaluating scenarios for mitigating the impact of hydropeaking on the downstream ecosystem was developed. The novel economic-ecological diagnostic and intervention method takes into account financial as well as environmental outcomes of hydropeaking mitigation measures for fish habitat improvement. The approach comprises (1) a hydropower operation model of flow regime generation and cost estimates for different mitigation measures, (2) a 2D hydrodynamic model to simulate the flow conditions in representative river reaches, and (3) a dynamic fish habitat simulation tool to assess the sub-daily changes in fish habitat conditions. This modeling approach gives the possibility to estimate true benefits of rehabilitation measures. The intervention diagnostic method was tested on the Hasliaare River. The developed tools and knowledge will help implement scientifically-based solutions for a sustainable hydropower management. The study may help in supporting the application of river restoration projects at existing and newly developed hydropower facilities in alpine areas.