Aquatic insects exhibit complex life cycles that include egg, larval, adult, and, in some instances, pupal stages. Disturbances at any of these life stages can affect overall population dynamics. Yet, efforts to understand the effects of disturbances, such as hydrologic alterations, overwhelmingly focus on the larval life stage of aquatic insects. We evaluated the potential for load-following flows associated with hydroelectric power production to act as a population bottleneck for aquatic insects via reductions in the availability and temporal persistence of optimal oviposition habitats. Specifically, we quantified the oviposition habitat selectivity of Baetis spp. (Baetidae), Brachycentrus occidentalis (Brachycentridae), Chironomidae (Diptera), and Hydropsyche occidentalis (Hydropsychidae) downstream of Flaming Gorge Dam, Utah, USA. We found that all taxa except H. occidentalis preferentially laid eggs on large emergent substrates located along the river edge. Peak discharge associated with load-following flows substantially reduced the number of emergent substrates available for oviposition, and daily low flows exposed eggs in these habitats to desiccation and drying. When subjected to experimental drying, both Baetis and H. occidentalis eggs experienced nearly 100% mortality after 2 h, whereas most B. occidentalis remained viable after 8 h. Our paired field and experimental results are consistent with the hypothesis that load-following flows from hydroelectric dams produce a population bottleneck for aquatic insects by short circuiting recruitment processes. Environmental flows that seek to improve the health of tailwater aquatic insect populations would benefit from consideration of habitat requirements for all life stages of aquatic insects.