Reservoir sedimentation is a major concern in the operational management of dams and appurtenant structures. The increasing volume of sediments deposited in reservoirs leads to a loss of water storage, undermining the purpose itself of the dam for human use or protection. The deposition of sediments (mostly fine) in the vicinity of the dam’s operational structures, such as bottom outlets and power intakes, may result in partial or total blockage of these structures. To cope with these problems, it is essential to determine the sediment balance of the reservoirs, by assessing the origin and quantity of the in- and out-fluxes of sediments. This paper presents a methodology to determine the annual sediment balance of a system of interlinked reservoirs across several decades, as well as its application to the alpine hydropower cascade formed by the Oberaar, Grimsel and Räterichsboden reservoirs located in Switzerland. At that aim, the annual sediment fluxes and the sedimentation rates of each reservoir were characterized. Also, the percentage of fine sediments (dm < 10 μm) included in the total sedimentation rate was estimated. The results reveal that the annual sedimentation rate of the lowermost reservoir of the system (Räterichsboden) is highly altered by the flushing operations of the reservoir upstream (Grimsel). Also, for the uppermost reservoir of the system (Oberaar), the volume of fine sediments deposited annually can reach up to 46% of the total sedimentation rate.