In Alpine streams, humans have strongly modified the interactions between hydraulic processes, geomorphology and aquatic life through dams, flow abstraction at water intakes and river channel engineering. To mitigate these impacts, research has addressed both minimum flows and flow variability to sustain aquatic ecosystems. Whilst such environmental flows might work downstream of dams, this may not be the case for water intakes. Intakes, generally much smaller than dams, are designed to abstract water and to leave sediment behind. Sediment accumulation then results in the need to flush intakes periodically, often more frequently than daily in some highly glaciated basins. Sediment delivery downstream is then maintained through short duration floods with very high sediment loads. Here we tested the hypothesis that sediment flushing, and the associated high frequency of bed disturbance, controls in-stream habitat and macroinvertebrate assemblages. We collected macroinvertebrates over a 17-month period from an Alpine stream as well as a set of lateral unperturbed tributaries that served as controls. In contrast to established conceptual models, our results showed that the stream is largely void of life during summer, but that populations recover rapidly as the frequency of intake flushing falls in early autumn, producing richer and larger populations in winter and early spring. The recovery in autumn may be due to the recruitment of individuals from tributaries. We conclude that intake flushing in summer inverts expected summer-winter macroinvertebrate abundances, and questions the extent to which environmental flows in intake-impacted Alpine streams will lead to improvements in instream macrofauna unless sediment also is managed.