Abstract Flash floods are a defining feature of desert streams, but flow records are not always available to characterize long-term flood dynamics. In this study, rainfall data spanning 100 years were used as a proxy to quantify long-term flood regimes for southeastern Arizona (USA) streams. The frequency and seasonal timing of severe floods (>50% substrate movement) were highly variable at short temporal scales (days to several years), but clear patterns emerged in the long-term (several years to a century). To explore the ecological effects of flood timing, populations of the caddisfly Phylloicus aeneus (Calamoceratidae) were monitored in 2 streams over 3 years. The timing of individual floods relative to the long-term average strongly affected P. aeneus populations: early and timely floods had little effect on population size in the next year, but late floods significantly reduced population size in the next year. Thus, flood timing might play a role in regulating populations of desert stream organisms.