Hyporheic flow in aquatic sediment controls solute and heat transport thereby mediating the fate of nutrients and contaminants, dissolved oxygen, and temperature in the hyporheic zone (HZ). We conducted a series of numerical simulations of hyporheic processes within a dune with different uniform temperatures, coupling turbulent open channel fluid flow, porous fluid flow, and reactive solute transport to study the temperature dependence of nitrogen source/sink functionality and its efficiency. Two cases were considered: a polluted stream and a pristine stream. Sensitivity analysis was performed to investigate the influence of stream water [NO 3 À ]/[NH 4 + ]. The simulations showed that in both cases warmer temperatures resulted in shallower denitrification zones and oxic-anoxic zone boundaries, but the trend of net denitrification rate and nitrate removal or production efficiency of the HZ for these two cases differed. For both cases, at high [NO 3 À ]/[NH 4 + ], the HZ functioned as a NO 3 À sink with the nitrate removal efficiency increasing with temperature. But at low [NO 3 À ]/[NH 4 +] for the polluted stream, the HZ is a NO 3 À sink at low temperature but then switches to a NO 3 À source at warmer temperatures. For the pristine stream case, the HZ was always a NO 3 À source, with the NO 3 À production efficiency increasing monotonically with temperature. In addition, although the interfacial fluid flux expectedly increased with increasing temperature due to decreasing fluid viscosity, the total nitrate flux into the HZ did not follow this trend. This is because when HZ nitrification is high, uniformly elevated [NO 3 À ] lowers dispersive fluxes into the HZ. We found that there are numerous confounding and interacting factors that combined to lead to the final temperature dependence of N transformation reaction rates. Although the temperature effect on the rate constant can be considered as the dominant factor, simply using the Arrhenius equation to predict the reaction rate would lead to incomplete insight by ignoring the changes in interfacial fluid and solute fluxes and reaction zone areas. Our study shows that HZ temperature and stream [NO 3 À ]/[NH 4 + ] are key controls for HZ sink/source functions.

The water quality and ecosystem health of river corridors depend on the biogeochemical processes occurring in the hyporheic zones (HZs) of the beds and banks of rivers. HZs in riverbeds often form because of bed forms. Despite widespread and persistent variation in river flow, how the discharge‐ and grain size‐dependent geometry of bed forms and how bed form migration collectively and systematically affects hyporheic exchange flux, solute transport, and biogeochemical reaction rates are unknown. We investigated these linked processes through morphodynamically consistent multiphysics numerical simulation experiments. Several realistic ripple geometries based on bed form stability criteria using mean river flow velocity and median sediment grain size were designed. Ripple migration rates were estimated based primarily on the river velocity. The ripple geometries and migration rates were used to drive hyporheic flow and reactive transport models which quantified HZ nitrogen transformation. Results from fixed bed form simulations were compared with matching migrating bed form scenarios. We found that the turnover exchange due to ripple migration has a large impact on reactant supply and reaction rates. The nitrate removal efficiency increased asymptotically with Damköhler number for both mobile and immobile ripples, but the immobile ripple always had a higher nitrate removal efficiency. Since moving ripples remove less nitrogen, and may even be net nitrifying at times, consideration for bed form morphodynamics may therefore lead to reduction of model‐based estimates of denitrification. The connection between nitrate removal efficiency and Damköhler number can be integrated into frameworks for quantifying transient, network‐scale, HZ nitrate dynamics.

Stream temperature often varies diurnally and seasonally, and these variations propagate into hyporheic zones (HZs), forming dynamic and heterogeneous thermal patterns. The complex thermal distribution creates potential biogeochemical hotspots and hot moments. Yet, how diel temperature variations affect HZ nitrogen cycling is unknown. We thus conducted a series of multiphysics numerical simulations of nonisothermal fluid flow and multicomponent reactive solute transport to investigate this problem. We imposed a sinusoidally varying stream temperature representing diel warming and cooling and studied the effects of different temperature means and amplitudes on HZ nitrate removal efficiency inside a streambed with a dune. The results showed that the time-variable nitrification, denitrification, and nitrate removal efficiency responded differently to the diel stream temperature signal. The temporal variation of spatially averaged nitrification rate tracks the stream temperature signal, whereas the spatially averaged denitrification variation pattern has a more complex connection to temperature. We observed a persistent hotspot where significant denitrification rates are present over the 24-hr period. We further evaluated and estimated the bulk nitrate removal efficiency calculated by time integration of spatially averaged reaction rates over a day. For denitrification-dominant systems, the bulk nitrate removal efficiency for cases with dynamic stream temperature was effectively the same as those with an equivalent constant mean temperature. Therefore, the bulk removal efficiency of a thermally dynamic diel system may be represented by an equivalent isothermal system given stable flow conditions. However, since large instantaneous variations in various rates were observed, the results imply that randomly timed field measurements are unlikely to be representative. This has to be considered for both past and future synoptic observational studies. Plain Language Summary Stream temperature naturally varies over daily and seasonal periods.This could cause temperature-dependent chemical and biological processes to vary simultaneously. Within the permeable streambed are areas called hyporheic zones where stream water circulates through in and out of the bed. The heat carried by this hyporheic flow that originates from the stream forms dynamic and complex temperature distributions in the hyporheic zone. The thermal patterns within the streambed could determine the presence of denitrification hotspots and hot moments since the hyporheic zone is an important site for many chemical reactions including nitrogen cycling. Through modeling the flow and reaction transport processes within the hyporheic zone, we found that denitrification hotspots persisted despite dynamic and complex hyporheic zone thermal patterns. Our simulation results can help explain previous observations of warmer stream temperature corresponding to lower in-stream nitrate concentrations. The results also imply that instantaneous snapshots through synoptic che...

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