Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO 2 and N 2

Rivers in climatic zones characterized by dry and wet seasons often experience periodic transitions between losing and gaining conditions across the river‐aquifer continuum. Infiltration shifts can stimulate hyporheic microbial biomass growth and cycling of riverine carbon and nitrogen leading to major exports of biogenic CO 2 and N 2 to rivers. In this study, we develop and test a numerical model that simulates biological‐physical feedback in the hyporheic zone. We used the model to explore different initial conditions in terms of dissolved organic carbon availability, sediment characteristics, and stochastic variability in aerobic and anaerobic conditions from water table fluctuations. Our results show that while highly losing rivers have greater hyporheic CO 2 and N 2 production, gaining rivers allowed the greatest fraction of CO 2 and N 2 production to return to the river. Hyporheic aerobic respiration and denitrification contributed 0.1–2 g/m 2 /d of CO 2 and 0.01–0.2 g/m 2 /d of N 2 ; however, the suite of potential microbial behaviors varied greatly among sediment characteristics. We found that losing rivers that consistently lacked an exit pathway can store up to 100% of the entering C/N as subsurface biomass and dissolved gas. Our results demonstrate the importance of subsurface feedbacks whereby microbes and hydrology jointly control fate of C and N and are strongly linked to wet‐season control of initial sediment conditions and hydrologic control of seepage direction. These results provide a new understanding of hydrobiological and sediment‐based controls on hyporheic zone respiration, including a new explanation for the occurrence of anoxic microzones and large denitrification rates in gravelly riverbeds.