Glacier retreat is a worldwide phenomenon with important consequences for the hydrological cycle and downstream ecosystem structure and functioning. To determine the effects of glacier retreat on aquatic communities, we conducted a 4-year flow manipulation in a tropical glacier-fed stream. Compared with an adjacent reference stream, meltwater flow reduction induces significant changes in benthic fauna community composition in less than 2 weeks. Also, both algal and herbivore biomass significantly increase in the manipulated stream as a response to flow reduction. After the flow reduction ceased, the system requires 14-16 months to return to its pre-perturbation state. These results are supported by a multi-stream survey of sites varying in glacial influence, showing an abrupt increase in algal and herbivore biomass below 11% glacier cover in the catchment. This study shows that flow reduction strongly affects glacier-fed stream biota, prefiguring profound ecological effects of ongoing glacier retreat on aquatic systems.