Floods and droughts are a common feature of most lotic ecosystems, presenting both ecological and evolutionary challenges to resident organisms. While some organisms possess adaptations for coping specifically with either flooding or drought, some traits are best characterized as adaptations to flow variability itself rather than to a single disturbance type. Here we report how two aquatic insects use positive rheotaxis to compensate for flow variability due to cycles of flooding and drought in desert rivers. We observed ca. 3,600 adults of the long-toed water beetle Postelichus immsi (Coleoptera:  Dryopidae) crawling upstream concurrent with upstream recession of surface water (caused by a diel peak in evapotranspiration) in the Santa Maria River, Arizona. We also observed larvae of the gray sanddragon Progomphus borealis (Odonata: Gomphidae) burrowing upstream in large densities (690 larvae/m2). Both taxa moved with sufficient speed to arrive at perennial reaches of the river and avoided being overtaken by drought. We also observed these behaviors following a small flood event (28 m3/s), suggesting that individuals displaced into flood-activated side channels have a viable mechanism for returning to perennial reaches during flood recession.