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We examined the effects of flooding and prolonged drying on interstitial water chemistry in the hyporheic zone of a Sonoran Desert stream at three sites with different flow regimens. Sampling began immediately after a winter flood rewetted the previously dry stream, and ended when a summer flash flood destroyed many sampling wells 170 days later. Nitrate-N, soluble reactive phosphorus (SRP), and dissolved oxygen concentrations were high whereas ammonium-N was low at all sites at the beginning of the study period. As discharge declined and drying began, nutrient and dissolved oxygen concentrations declined in phreatic (> 50 cm deep) and parafluvial (lateral to the active channel) subsystems while shallow hyporheic (< 50 cm) samples remained well-oxygenated. Hyporheic water chemistry in areas lacking surface flow (the dry channel hyporheic) varied between sites; nitrate-N and dissolved oxygen decreased at one site but increased at another. With continued drying, phreatic and parafluvial habitats became extremely hypoxic (< 0.50 mg/L dissolved oxygen) and low in nitrate-N (< 0.02 mg/L) due to reduced hydrologic exchange between surface and hyporheic waters. The increased area of hypoxia apparently enhanced nitrate-reducing transformations in phreatic and parafluvial habitats because interstitial nitrate-N concentrations often were lower than surface values; thus, drying caused a functional shift in this N-limited stream as the hyporheic zone changed from a nitrate source to a nitrate sink. Boundaries of hyporheic subsystems fluctuated considerably in response to flooding and drying, underscoring the importance of hydrologic extremes to the strength of chemical linkages between the surface stream and the hyporheic zone.