Spatial and temporal changes in assemblage structure of the hyporheos of a Sonoran Desert stream were monitored after re-wetting occurred in winter at three sites with different flow regimens. Diverse assemblages of hyporheic invertebrates were found at all sites within two days of re-wetting. At two sites, drying represented a gradual press disturbance to the hyporheos, altering the assemblage composition from a predominance of cyclopoid copepods and chironomids to one dominated by microturbellarians, ceratopogonid larvae, ostracods, nematodes, and, just before the hyporheic zone dried, several species of water mites. There were fewest hyporheic taxa at the most intermittent site where cyclopoid copepods were most numerous. The site that remained inundated during the entire study harbored a speciose hyporheos whose composition varied vertically and laterally. Amphipods, isopods, and bathynellaceans were found in the phreatic (deeper than 50 cm) zone whereas cyclopoids, cladocerans, chironomids, and water mites were common in the shallow (< 50 cm) hyporheic habitat. In wells sunk in the stream bank, nematodes, ostracods, and bathynellaceans characterized the parafluvial zone. Spates temporarily altered the assemblage composition of the parafluvial and shallow hyporheic habitats but recovery was rapid, implying a resilient fauna. Phreatic assemblages were not immediately influenced by spates. At the scale of an individual reach (122m), a distinct longitudinal pattern in assemblage composition was correlated with trends in water chemistry and the gradual transition from zones of hyporheic upwelling (discharge) to downwelling (recharge). Upwelling areas were nitrate-rich, hypoxic, and harbored a typically phreatic fauna whereas downwelling zones were well-oxygenated, low in nitrate, and were characterized by taxa found in the shallow hyporheos. This longitudinal pattern was consistent over time but became truncated as surface water receded upstream, altering the exchange of surface and subsurface water. Recognition of temporal changes in the vertical, lateral, and longitudinal variation in subsurface biota and how they respond to surficial hydrologic extremes is essential to understanding the way these subsystems interact with the surface stream ecosystem; the next goal is to determine the causes of these patterns.