The structure and function of many rivers and streams worldwide are altered by water abstraction. However, this impact is often coupled with changes in flow regimes, water quality, and sediment transport, making it difficult to separate the effects of each of these disturbances. Here, we used a field manipulation to measure the responses of taxonomic and biological trait metrics to a 2-mo experimental water abstraction in an unpolluted mountain stream. We diverted water to reduce discharge by 65% while mimicking the effects of small hydropower plants by maintaining continuous flow in the bypassed impact reach. Water abstraction altered the taxonomic composition of invertebrate assemblages, creating combinations not found before in this stream. Abstraction did not affect total invertebrate density, but by narrowing the wetted channel, it reduced total invertebrate abundance/unit channel length to <1/2 that of control values. Abstraction also changed the density of some dominant taxa and reduced functional dispersion (computed from 9 biological traits related to movement, diet, and respiration mode). This effect was mainly driven by homogenization of diet. Moreover, abstraction affected the relative abundance of 3 biological traits, indicating additional changes in the way the assemblages use the stream. Our results show that abstraction produced rapid and intense reductions in invertebrate abundance, along with functional modifications, even though flow continuity was maintained. Together, these alterations may impair the capacity of the stream ecosystem to process, transform, and export organic matter.