Flow intermittency occurs naturally in alpine streams. However, changing rainfall patterns and glacier retreat are predicted to increase the occurrence of flow intermittency in alpine catchments, with largely unknown effects on ecosystem structure and function. We conducted a flow manipulation experiment within a headwater stream of Val Roseg, a glacierized alpine catchment, to determine the effects of increased flow intermittency on aquatic macroinvertebrates, periphyton, benthic organic matter, and trophic structure. Compared to an adjacent reference channel, an increase in flow intermittency reduced macroinvertebrate density, taxa richness, and the proportion of rheophilic taxa. Density and richness remained low in the manipulated channel after resumption of natural flow. Flow intermittency did not affect organic matter standing stocks, but increased assimilation of periphyton by aquatic macroinvertebrates. Predation on aquatic invertebrates by riparian spiders also increased. We attribute many of these patterns to the timing of drying, which likely excluded summer-growing cohorts of rheophilic, aerial dispersers. This study suggests that reductions in summer glacial melt and rainfall events might increase flow intermittency and lead to fundamental changes in diversity and function of alpine fluvial networks.