Hydropeaking, resulting from rapid starting and shut-down of turbines, is one of the major hydrological alterations in Alpine streams. The upper Aare River basin in Switzerland comprises a complex high-head storage hydropower scheme. The significant turbine capacities of the two downstream powerhouses produce severe hydropeaking in the Aare River. To reduce the negative impact of the foreseen increase of the turbine discharge, a compensation basin combined with an extended tailrace tunnel downstream of the powerhouses has been designed and is under construction now to facilitate lower flow ramping increasing time for aquatic species to react. The design of the basin and its overall operation had to be defined to reach best ecological as well as economic performance. The retention volume and the operation rules of the basin have been optimized to avoid dewatering of juvenile brown trout. Further, flow ramping has to be limited in order to reduce drifting of macroinvertebrates. The paper presents a consistent approach of a target-oriented process management, including modelling, simulation and comparison of future flow regime without and with mitigation measure. Finally, rules for decision-making as well as the prototype’s final design are addressed.