The retention capacity for biologically available nitrogen within streams can be influenced by dynamic hyporheic zone exchange, a process that may act as either a net source or net sink of dissolved nitrogen. Over 5 weeks, nine vertical profiles of streambed chemistry (NO3− and NH4+) were collected above two beaver dams along with continuous high-resolution vertical hyporheic flux data. The results indicate a non-linear relation of net NO3− production followed by net uptake in the hyporheic zone as a function of residence time. This Lagrangian-based relation is consistent through time and across varied morphology (bars, pools, glides) above the dams, even though biogeochemical and environmental factors varied. The empirical continuum between net NO3− production and uptake and residence time is useful for identifying two crucial residence time thresholds: the transition to anaerobic respiration, which corresponds to the time of peak net nitrate production, and the net sink threshold, which is defined by a net uptake in NO3− relative to streamwater. Short-term hyporheic residence time variability at specific locations creates hot moments of net production and uptake, enhancing NO3− production as residence times approach the anaerobic threshold, and changing zones of net NO3− production to uptake as residence times increase past the net sink threshold. The anaerobic and net sink thresholds for beaver-influenced streambed morphology occur at much shorter residence times (1.3 h and 2.3 h, respectively) compared to other documented hyporheic systems, and the net sink threshold compares favorably to the lower boundary of the anaerobic threshold determined for this system with the new oxygen Damkohler number. The consistency of the residence time threshold values of NO3− cycling in this study, despite environmental variability and disparate morphology, indicates that NO3− hot moment dynamics are primarily driven by changes in physical hydrology and associated residence times. Copyright © 2013 John Wiley & Sons, Ltd.