The downstream ecological consequences of two controlled “free flow” flushing operations designed to remove sediments accumulated in an alpine reservoir are described. The main objectives of the study were (a) to verify to what extent the suspended solid concentration (SSC) in the receiving water course can be controlled by flushing operations, (b) to determine the biological consequences of flushing operations, and (c) to produce technical guidelines for the future planning and monitoring of these activities. We found that the flushing of large volumes of accumulated sediment had clear effects on the stream ecosystem due to the unpredictability of short duration SSC peaks (70–80 g L⁻¹) and the high average SSC (4–5 g L⁻¹) within flushing periods. The main impacts were decreased fish densities (up to 73%) and biomass (up to 66%). A greater mortality recorded for juveniles will likely result in long-term impairment of the age-structures of future fish populations. The zoobenthic assemblages, despite exhibiting a drastic reduction in abundance following the first floods, showed substantial recovery within 3 months of the beginning of flushing operations. Regular sediment removal by yearly flushing is recommended in order to avoid SSC peaks and to facilitate the control of scouring effects caused by the water used to wash out sediments. We also recommend maximum allowable SSCs of 10 g L⁻¹ (daily average) and 5 g L⁻¹ (overall average) for flushing operations carried out in similar environmental contexts.