River channelization and the construction of high-head storage schemes have been the basis of agricultural and socio-economic development in many alpine regions. One example is the Upper-Rhone River in Switzerland. The Upper-Rhone's morphology changed considerably between 1863 and 1960 as a result of two major channelizations and, from 1950 on, the construction of a large number of high-head storage hydropower schemes in the catchment. These modifications have brought large benefits to the local population, at the cost, however, of substantial disturbances in aquatic and terrestrial ecosystems in and along the river. A primary factor behind these disturbances is the alteration of the natural flow regime, namely hydropeaking due to the operation of the high-head storage hydropower plants. For sustainable river-restoration projects on regulated rivers, scientists and engineers now widely accept the necessity of integrated management of the river. Different aspects such as river morphology, sediment management, water quality, temperature, and the naturally variable flow regime should be considered simultaneously. Mitigation of non-natural, subdaily flow fluctuations due to hydropeaking is a crucial step in restoring natural flow regimes, but is especially challenging due to the economic constraints such mitigation places upon hydropower plants. With the goal of addressing this challenge, this paper proposes three indicators to describe the flow regime of rivers in alpine catchments with and without high-head storage hydropower plants. The indicators quantify: (1) the seasonal distribution and transfer of water, (2) sub-daily flow fluctuations, and (3) the intensity and frequency of flow changes. Indicators are evaluated in a case study of the Upper-Rhone River for preand post-impact situations, and the benefit of a multipurpose project reducing hydropeaking on hydrologic conditions is quantified. Furthermore, the paper explores the possibility of using these indicators to link aquatic and terrestrial ecosystem well being to their hydrology