Flow homogenization, the removal of natural flow events such as floods and droughts, can be detrimental to the functioning of riverine habitats. In rivers with beaver (Castor canadensis), flow homogenization can facilitate unchecked beaver dam construction due to lack of dam removal from floods, leading to physical effects such as channel widening and deepening. In this study, I investigated the consequences of a 6-year period of flow homogenization on the aquatic invertebrate communities of the Bill Williams River in the Sonoran Desert of the United States. I found that the aquatic invertebrates of this community shifted in composition and structure, and that flow homogenization did not adversely affect diversity measures such as species richness. However, the proportion of aerial dispersers, which are an important food subsidy for riparian and terrestrial consumers, decreased with increasing water depth associated with flow homogenization and beaver activity. These compositional shifts can have negative effects for how ecosystems function, and managers of threatened and endangered riparian species should consider potential changes in invertebrate food supply due to river management policies. I present a conceptual model to illustrate how the interactive effects of flow homogenization and beaver activity can be quantified and monitored.