[1] Exchange of water and solutes across the stream-sediment interface is an important control for biogeochemical transformations in the hyporheic zone (HZ). In this paper, we investigate the interplay between turbulent stream flow and HZ flow in pool-riffle streams under various ambient groundwater flow conditions. Streambed pressures, derived from a computational fluid dynamics (CFD) model, are assigned at the top of the groundwater model, and fluxes at the bottom of the groundwater model domain represent losing and gaining conditions. Simulations for different Reynolds numbers (Re) and pool-riffle morphologies are performed. Results show increasing hyporheic exchange flows (m 3 /d) for larger Re and a concurrent decrease in residence time (RT). Losing and gaining conditions were found to significantly affect the hyporheic flow field and diminish its spatial extent as well as rates of hyporheic exchange flow. The fraction of stream water circulating through the hyporheic zone is in the range of 1 Â 10 À5 to 1 Â 10 À6 per meter stream length, decreasing with increasing discharge. Complex distributions of pressure across the streambed cause significant lateral hyporheic flow components with a mean lateral travel distance of 20% of the longitudinal flow paths length. We found that the relationship between pool-riffle height and hyporheic exchange flow is characterized by a threshold in pool-riffle amplitude, beyond which hyporheic exchange flow becomes independent of riffle height. Hyporheic residence time distributions (RTD) are log-normally distributed with medians ranging between 0.7 and 19 h.

At the interface between stream water, groundwater, and the hyporheic zone (HZ), important biogeochemical processes that play a crucial role in fluvial ecology occur. Solutes that infiltrate into the HZ can react with each other and possibly also with upwelling solutes from the groundwater. In this study, we systematically evaluate how variations of gaining and losing conditions, stream discharge, and pool-riffle morphology affect aerobic respiration (AR) and denitrification (DN) in the HZ. For this purpose, a computational fluid dynamics model of stream water flow is coupled to a reactive transport model. Scenarios of variations of the solute concentration in the upwelling groundwater were conducted. Our results show that solute influx, residence time, and the size of reactive zones strongly depend on presence, magnitude, and direction of ambient groundwater flow. High magnitudes of ambient groundwater flow lower AR efficiency by up to 4 times and DN by up to 3 orders of magnitude, compared to neutral conditions. The influence of stream discharge and morphology on the efficiency of AR and DN are minor, in comparison to that of ambient groundwater flow. Different scenarios of O 2 and NO 3 concentrations in the upwelling groundwater reveal that DN efficiency of the HZ is highest under low upwelling magnitudes accompanied with low concentrations of O 2 and NO 3 . Our results demonstrate how ambient groundwater flow influences solute transport, AR, and DN in the HZ. Neglecting groundwater flow in stream-groundwater interactions would lead to a significant overestimation of the efficiency of biogeochemical reactions in fluvial systems.

Hyporheic exchange transports solutes into the subsurface where they can undergo biogeochemical transformations, affecting fluvial water quality and ecology. A three-dimensional numerical model of a natural in-stream gravel bar (20 m 3 6 m) is presented. Multiple steady state streamflow is simulated with a computational fluid dynamics code that is sequentially coupled to a reactive transport groundwater model via the hydraulic head distribution at the streambed. Ambient groundwater flow is considered by scenarios of neutral, gaining, and losing conditions. The transformation of oxygen, nitrate, and dissolved organic carbon by aerobic respiration and denitrification in the hyporheic zone are modeled, as is the denitrification of groundwater-borne nitrate when mixed with stream-sourced carbon. In contrast to fully submerged structures, hyporheic exchange flux decreases with increasing stream discharge, due to decreasing hydraulic head gradients across the partially submerged structure. Hyporheic residence time distributions are skewed in the log-space with medians of up to 8 h and shift to symmetric distributions with increasing level of submergence. Solute turnover is mainly controlled by residence times and the extent of the hyporheic exchange flow, which defines the potential reaction area. Although streamflow is the primary driver of hyporheic exchange, its impact on hyporheic exchange flux, residence times, and solute turnover is small, as these quantities exponentially decrease under losing and gaining conditions. Hence, highest reaction potential exists under neutral conditions, when the capacity for denitrification in the partially submerged structure can be orders of magnitude higher than in fully submerged structures.

In this study, we investigate the impact of single stream discharge events on water exchange, solute transport, and reactions in the hyporheic zone below a natural in‐stream gravel bar. We set up a reactive transport groundwater model with streamflow scenarios that vary by event duration and peak discharge. A steady ambient groundwater flow field is assumed that results in losing, neutral, or gaining stream conditions depending on the stream stage. Across the streambed dissolved oxygen, organic carbon, and nitrate are transported into the subsurface. Additional nitrate is received from upwelling groundwater. Aerobic respiration and denitrification are simulated for scenarios with different stream solute concentrations. Results show that hyporheic exchange flux, solute transport, and consumption increase during events. However, their intensities depend highly on the interplay between event characteristics and ambient groundwater conditions. During events where reversals in the hydraulic gradient occur stream water and solutes infiltrate deeper into the aquifer where they have more time to react. For those events, the reactive efficiency of the hyporheic zone (solute consumption as fraction of influx) for aerobic respiration and denitrification is up to 2.7 and 10 times higher compared to base flow conditions. The fraction of stream nitrate load consumed in the hyporheic zone increases with stream discharge (up to 150 mg/m2/h), but remains below the value under base flow conditions for weak events. Events also increase denitrification of groundwater borne nitrate, but groundwater nitrate flux to the stream decreases by up to 33% due to temporary gradient reversals.

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Riparian zones are important buffer zones for streams as they are hotspots of nitrate transformation and removal in agricultural catchments. However, mixing of water from different sources and various transformation processes can complicate the quantification of nitrate turnover in riparian zones. In this study, we analyzed nitrate concentration and isotope data in riparian groundwater along a 2-km stream section in central Germany. We developed a mathematical model combining end-member mixing and isotope modeling to account for mixing of river water and groundwater and quantify nitrate transformation in riparian groundwater. This enabled us to explicitly determine the extent of denitrification (as process leading to permanent nitrate removal from riparian groundwater) and transient nitrate removal by additional processes associated with negligible isotope fractionation (e.g., plant uptake and microbial assimilation) and to perform an extensive uncertainty analysis. Based on the nitrogen isotope data of nitrate, the simulations suggest a mean removal of up to 27% by additional processes and only about 12% by denitrification. Nitrate removal from riparian groundwater by additional processes exceeded denitrification particularly in winter and at larger distance from the river, underlining the role of the river as organic carbon source. This highlights that nitrate consumption by additional processes predominates at the field site, implying that a substantial fraction of agricultural nitrogen input is not permanently removed but rather retained in the riparian zone. Overall, our model represents a useful tool to better compare nitrogen retention to permanent nitrogen removal in riparian zones at various temporal and spatial scales. Plain Language SummaryNitrogen is an important nutrient for agricultural crops. However, excessive nitrogen input into surface water in the form of nitrate can lead to algae blooms and lack of oxygen. The riparian zones of rivers are important buffer zones where groundwater is connected to soils, which are rich in soil organisms and organic matter pools fueling reaction processes. Hence, plants and bacteria can remove nitrate from riparian groundwater before it reaches the river. Bacterial consumption of nitrate (denitrification) leads to complete removal of nitrogen via release of nitrogen gas into the atmosphere. In contrast, other biogeochemical processes such as nitrate uptake by plants merely result in nitrogen retention within riparian zones. To quantify the role of denitrification relative to other processes, we developed a novel model combining concentration and isotope data of nitrate and applied it to a groundwater study site in Central Germany. We found that nitrate removal from riparian groundwater by additional processes largely exceeded denitrification. Hence, a major fraction of nitrogen inputs was retained in the riparian zone and may eventually end up in the river. Such information is highly relevant for many river ecosystems at risk of eutrophication because of high nitr...

Aerobic respiration is an important component of in‐stream metabolism. The larger part occurs in the streambed, where it is difficult to directly determine actual respiration rates. Existing methods for determining respiration are based on indirect estimates from whole‐stream metabolism or provide time invariant results estimated from oxygen consumption measurements in enclosed chambers that do not account for the influence of hydrological changes. In this study we demonstrate a simple method for determining time‐variable hyporheic respiration. We use a windowed cross‐correlation approach for deriving time‐variable travel times from the naturally changing electrical conductivity signal that is transferred into the sediment. By combining the results with continuous in situ dissolved oxygen measurements, variable oxygen consumption rate coefficients in the streambed are obtained. An empirical temperature relationship is derived and used for standardizing the respiration rate coefficients to isothermal conditions. For demonstrating the method, we compare two independent measurement spots in the streambed, which were located upstream and downstream of an in‐stream gravel bar and thus exposed strongly diverse travel times. The derived respiration rate results are in accordance with findings of other stream studies. By comparing the travel time and respiration rate coefficient (i.e., Damköhler number) we estimate the contribution of each to the oxygen consumption in the streambed.

Abstract. Spatial patterns of water flux in the stream bed are controlled by the distribution of hydraulic conductivity, bedform-induced head gradients and the connectivity to the adjoining groundwater system. The water fluxes vary over time driven by short-term flood events or seasonal variations in stream flow and groundwater level. Variations of electrical conductivity (EC) are used as a natural tracer to detect transient travel times and flow velocities in an in-stream gravel bar. We present a method to estimate travel times between the stream and measuring locations in the gravel bar by nonlinearly matching the EC signals in the time domain. The amount of temporal distortion required to obtain the optimal matching is related to the travel time of the signal. Our analysis revealed that the travel times increase at higher stream flows because lateral head gradients across the gravel bar become significantly smaller at the time.