Current global models predict a hotter and drier climate in the southwestern United States with anticipated increases in drought frequency and severity coupled with changes in flash flood regimes. Such changes would likely have important ecological consequences, particularly for stream and riparian ecosystems already subject to frequent hydrologic disturbance. This study assessed the potential response of aquatic macroinvertebrates to interannual variation in hydrology in a spatially intermittent desert stream (Sycamore Creek, AZ). We compiled data on the recovery of macroinvertebrate communities following spring floods, with successional sequences captured 11 times over a 16-year period (1983–1999). This period encompassed a transition from perennial to intermittent flow in this system, and included a record drought in 1989–1990. Results show that while the size of floods initiating sequences had little explanatory power, changes in macroinvertebrate community structure during postflood succession were closely associated with antecedent flooding and drought. Year-to-year differences in benthic communities integrated taxon-specific responses to antecedent disturbance, including differential resistance to channel drying, use of hyporheic refugia, and variable rates of recovery once stream flow resumed. The long-term consequences of drying on community structure were only evident during later stages of postflood succession, illustrating an interaction between flood and drought recovery processes in this system. Our observations highlight the potential for predicted climate changes in this region to have marked and long-lasting consequences for benthic communities in desert streams.