Lakes and reservoirs worldwide are increasingly experiencing depletion of dissolved oxygen (anoxia) in their bottom waters (the hypolimnion) because of climate change and eutrophication, which is altering the dynamics of many freshwater ecological communities. Hypolimnetic anoxia may substantially alter the daily migration and distribution of zooplankton, the dominant grazers of phytoplankton in aquatic food webs. In waterbodies with oxic hypolimnia, zooplankton exhibit diel vertical migration (DVM), in which they migrate to the dark hypolimnion during the day to escape fish predation or ultraviolet (UV) radiation damage in the well‐lit surface waters (the epilimnion). However, due to the physiologically stressful conditions of anoxic hypolimnia, we hypothesized that zooplankton may be forced to remain in the epilimnion during daylight, trading oxic stress for increased predation risk or UV radiation damage. To examine how anoxia impacts zooplankton vertical migration, distribution, biomass, and community composition over day–night periods, we conducted multiple diel sampling campaigns on reservoirs that spanned oxic, hypoxic, and anoxic hypolimnetic conditions. In addition, we sampled the same reservoirs fortnightly during the daytime to examine the vertical position of zooplankton throughout the summer stratified season. Under anoxic conditions, most zooplankton taxa were predominantly found in the epilimnion during the day and night, did not exhibit DVM, and had lower seasonal biomass than in reservoirs with oxic hypolimnia. Only the phantom midge larva, Chaoborus spp., was consistently anoxia‐tolerant. Consequently, our results suggest that hypolimnetic anoxia may alter zooplankton migration, biomass, and behavior, which may in turn exacerbate water quality degradation due to the critical role zooplankton play in freshwater ecosystems.