Hydropeaking is a common phenomenon of water courses that are affected by peak energy production of hydro power plants. It may cause severe impacts on the biodiversity of a stream. In fact, due to hydropeaking fishes, macroinvertebrates and aquatic plants undergo a major stress and frequently they are not able to survive these frequent water level fluctuations. In this paper a case study is presented where several mitigation measures for an affected river are evaluated. Abiotic indicators representing the hydropeaking phenomenon and responsible for an impaired biodiversity are calculated and compared. Furthermore a cost-benefit analysis of the mitigation measures is carried out allowing to define the measures to be realized. Facing the challenge of a holistic approach the study is embedded in a project with public participation of all concerned stakeholders addressing also the need of flood protection and ecologically sound river restoration.