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Nitrification in the hyporheic zone of Sycamore Creek, a Sonoran Desert stream, was examined, focusing on the association between respiration and nitrate production. Subsurface respiration in Sycamore Creek is highest in regions of hydrologic downwelling where organic matter derived from the stream surface is transported into the hyporheic zone. Similarly, nitrification was closely related to hydrologic exchange between the surface and hyporheic zone. Nitrification in downwelling regions averaged 13.1 mu gNO(3)-N . L sediments(-1). h(-1) compared with 1.7 mu gNO(3)-N . L sediments(-1). h(-1) in upwelling regions. Hyporheic respiration also varies temporally as a result of flash floods which scour and remove algae from the stream and thus reduce the pool of organic matter to support subsurface metabolism. Nitrification was also significantly affected by flooding; nitrification increased from an average of only 3.0 mu gNO(3)-N . L sediments(-1). h(-1) immediately following floods to 38.5 mu gNO(3)-N . L sediments(-1). h(-1) late in succession. Nitrification was significantly correlated with hyporheic respiration, supporting the hypothesis that nitrification is fueled by mineralization of organic nitrogen to ammonium. The coupling between subsurface respiration and nitrification is one step in a cyclic interaction between surface and hyporheic zones and serves to transform nitrogen from an organic to inorganic form.