The natural flow regime of rivers is being reshaped by numerous global change stressors, such as increasing drought and human water use. Aquatic invertebrates are particularly susceptible to these changes due to their limited mobility and reliance on multiple components of the flow regime for their life history. While the effects of hydrologic alteration on invertebrate communities are commonly viewed through changes in taxonomic identity, linking traits to environmental gradients associated with hydrologic alteration – such as flow reduction – can provide mechanistic insight to community assembly rules in the wake of global change. This may be particularly relevant for regions experiencing severe aridification resulting from consumptive water demands, warming temperatures, and decreased run-off, such as the upper Colorado River basin (UCRB). However, little is known about invertebrate assemblages in the UCRB, including the effect of widespread flow reductions in shaping the taxonomic identity and trait distribution of assemblages. Here, we use a series of univariate and multivariate approaches to investigate the role of flow reductions in shaping the taxonomic structure and trait composition of assemblages across the UCRB. Invertebrate communities were less diverse in rivers that have undergone large flow reductions and characterized by intolerant taxa such as Simuliidae and Ceratopogonidae. Spatial patterns in biodiversity were accompanied by differences in the taxonomic structure of communities and correlated with multiple abiotic factors including flow reduction, flow skewness, baseflow, conductivity, gross primary production, and temperature. However, only a subset of these variables (flow reduction, conductivity, and baseflow) explained variation in trait distributions. In rivers with large flow reductions, invertebrate assemblages were characterized by collector-filterer trophic roles, synchronized emergence strategies, and strong adult flying strengths. We show that flow reductions shape the structure and function of invertebrate communities across the UCRB. As warming temperatures and consumptive water needs continue to intensify, understanding the impact of water scarcity across multiple levels of ecological organization will be needed to conserve freshwater ecosystems in the wake of a hotter, drier future.