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The hydrological and biogeochemical properties of the hyporheic zone in stream and riverine ecosystems have been extensively studied over the past two decades. Although it is widely acknowledged that sediment heterogeneity can influence biogeochemical reactions, little effort has been made to understand the role of heterogeneity on the spatiotemporal variability of riverbed redox conditions under changing flow dynamics at different timescales. Here we integrate a mechanistic model and field data to demonstrate that heterogeneity in permeability plays a vital role in modulating sediment redox conditions at both seasonal (annual) and event (daily‐to‐weekly) timescales, whereas heterogeneity in particulate organic carbon (POC) content only has a comparable influence on redox conditions at the seasonal timescale. These findings underscore the importance of accurately characterizing sediment heterogeneity, in terms of permeability and POC content, in quantifying biogeochemical dynamics in the riverbed and hyporheic zones of riverine ecosystems. Plain Language Summary The redox condition of riverbed sediments is subject to the combined influence of hydrologic exchange flow and biogeochemical processes and is important for regulating the functioning of riverine ecosystems. Current understanding of the spatiotemporal pattern of sediment redox conditions especially with heterogeneity in consideration is limited, partially due to the lack of measurements and quantitative models. In this study, we integrate a mechanistic model and field data to reveal the role of sediment heterogeneity in controlling the redox condition under dynamic flow conditions. We demonstrate that heterogeneity in permeability modulates sediment redox condition at both seasonal and event timescales, and heterogeneity in particulate organic carbon is most prominent over multi‐month time intervals that reflect the balance between particulate organic carbon (POC) metabolism and time‐integrated oxygen influx. These findings highlight the importance of accurate characterization of sediment heterogeneity in both permeability and POC for predicting the dynamic redox shifts in riverbed sediments. Key Points A reactive transport model was developed to quantify the impact of heterogeneity in permeability and particulate organic carbon (POC) concentration on sediment redox conditions Heterogeneity in permeability controls sediment redox conditions at both seasonal (annual) and event (daily‐to‐weekly) timescales The effects of heterogeneity in POC occur over the monthly timescale, reflecting a balance between POC metabolism and the influx of oxygen

Hyporheic exchange (HE), fine particle deposition and clogging are tightly coupled processes that control ecosystem services in rivers. While HE is assumed to be induced primarily by riverbed topography, surface flow turbulence also drives significant exchange. We show that turbulence‐driven HE produces large interfacial fluxes and drives long‐term feedback between HE and fine suspended particles via bed clogging. Turbulence significantly increases total HE fluxes as it rapidly delivers suspended particles into porewater over the entire interface, whereas advective pumping exchange only delivers particles into focused downwelling regions on the upstream side of bedforms. While turbulence is associated with rapid fluctuations and shallow HE, it is key on longer‐timescale outcomes, namely bed clogging. However, beyond the general effect of clogging in attenuating HE, turbulence‐driven HE will also be important for other river‐borne materials that are retained and transformed within hyporheic zones, such as nutrients and organic pollutants. Plain Language Summary Fine natural sediments like clay particles are transported in rivers and deposited in riverbeds. Clay deposition is important to river ecosystems because it controls habitat conditions within riverbeds. In this research, new computational simulations show that turbulent river flow controls clay deposition in riverbeds. These new simulations incorporate turbulence, and they are able to correctly predict patterns of clay deposits. They also predict how clay deposits clog the riverbed and reduce the exchange of water between the river and bed. These simulation capabilities are important to protect river ecosystems and to manage contaminants that interact with riverbeds, because clogging is a common process that damages river ecosystems. Key Points Turbulence accounts for a significant fraction of fine particle delivery to the hyporheic zone Turbulent transport of fine particles contributes substantially to interfacial clogging that attenuates Hyporheic exchange (HE) A numerical model is presented that integrates interfacial turbulence, HE of suspended particles and bed clogging

The influence of bioturbation induced by bottom‐dwelling macrozoobenthos on nitrogen dynamics in lotic stream sediments remains unclear. In this work, we advance the understanding of faunal bioturbation in lotic environments by developing a fully‐coupled flow and multicomponent reactive transport model and investigate the influence of sediment reworking and burrow ventilation processes on nitrogenous transformations. The model results indicate that sediment reworking and burrow ventilation significantly increase nitrate (NO3−) influx, penetration depth, and reaction rates in the streambed. Denitrification rates were observed up to three times higher in beds with U‐shaped burrows compared to flatbeds. The ratio of mound height to stream water depth ratio (h/H0) is a dominant control on determining the relative importance of the sediment reworking and burrow ventilation processes in modulating nitrogenous reactions. A power‐law scaling framework is ultimately proposed to predict NO3− removal efficiency based on the Damköhler number in bioturbated lotic streambeds. Plain Language Summary The increase in nitrate (NO3−) levels can harm rivers by causing problems like eutrophication, toxic algal blooms, and low oxygen levels. Microbes, like those involved in denitrification, can help reduce NO3− levels in the riverbed, where surface water and groundwater mix. Creatures like macroinvertebrates that live in the riverbed also play a role in how NO3− moves and is used. We wanted to know if these creatures, by disturbing the sediment and irrigating it, change how NO3− behaves in the riverbed. Our computer modeling showed that having U‐shaped burrows in the sediment can enhance the rate at which NO3− is removed, up to three times more than in flatbed sediments. As the ratio of the mound height to the total depth becomes less than 0.1, the influence of sediment reworking on NO3− influx and consumption rates decreases, and burrow ventilation becomes more important. We also came up with a way to predict NO3− removal efficiency in bioturbated riverbeds under flowing water conditions. These findings underscore the significance of bioturbation in rivers with moving water and have important implications for managing and restoring rivers. Key Points Developing a Navier‐Stokes‐Brinkman‐Darcy‐Reaction fully‐coupled approach to study interplay between nitrogen cycling and faunal bioturbation Sediment reworking and burrow ventilation processes could significantly alter the nitrogenous transformations in low flow environments A power‐law scaling framework can be used to predict nitrate removal efficiency within the bioturbated sediments from the Damköhler number

Anthropogenic deterioration of streams and rivers has affected their surface-subsurface linkages. This has led to the degradation of hyporheic zones, a sensitive interface between a stream channel and its surrounding sediments, responsible for transforming pollutants, natural solutes and supporting benthic communities. Several authors have reported the influence of stream restoration measures on hyporheic exchanges and have called for the inclusion of hyporheic zone restorations in stream management. Engineered Hyporheic Zones (EHZ) are the creation of artificial transition areas due to induced hyporheic flows, brought about by some feature modifications done to the stream channel or its subsurface. These feature modifications and their implications have been investigated through lab experiments, outdoor flumes, modelling and field studies for several years. This paper attempts to summarize the endeavours made in the study of EHZ and its applications in water quality improvement and habitat restoration. A comprehensive review of up-to-date literature with specific focus on the influence of engineered structures on hyporheic exchanges is presented, followed by the comparison of preferences opted for different studies and their limitations. The paper ends with suggestive future scope in EHZ studies and its potential as a low cost alternative treatment technology for river restoration.

Hydrodynamic and morphodynamic forces interacting across the sediment‐water interface control the biogeochemistry in the hyporheic zone. When investigating the redox zonation within streambeds, dissolved oxygen (O2) is considered a key solute to the understanding of river ecosystems. However, no field studies have measured the spatiotemporal O2 distribution linked to bedform celerity induced by changes in stream water velocity. Therefore, we developed and tested an innovative in situ setup in the River Erpe, Germany. The setup combines a planar O2 optode and O2 flow‐through cells for eight sediment depths to capture the variability in O2 dynamics, and a laser scanner to capture bedform morphodynamics, which was used to calculate bedform celerity. The setup was tested under different stream water velocities between 0.1 and 0.5 m/s. We found that O2 patterns in the streambed depend on stream water velocity. At low velocities, bedforms were stationary and a stable redox zonation with limited O2 penetration in the streambed (up to 4 cm) was observed. As we increased the velocity up to 0.3 m/s, the spatiotemporal variability of O2 distribution across the bedform increased, with anoxic patches moving along the migrating bedforms. At the highest velocity tested (0.5 m/s), the sediment bed was constantly oxygenated with deeper O2 penetration as compared to slower velocities. The present study provides proof of concept for in situ O2 measurements in small rivers, which helps to refine laboratory and mesocosm experiments, improve the knowledge of the processes involved in natural environments, and develop more sustainable river management strategies.

The fate of nutrients and contaminants in fluvial ecosystems is strongly affected by the mixing dynamics between surface water and groundwater within the hyporheic zone, depending on the combination of the sediment's hydraulic heterogeneity and dune morphology. This study examines the effects of hydraulic conductivity stratification on steady‐state, two‐dimensional, hyporheic flows and solute residence time distribution. First, we derive an integral transform‐based semi‐analytical solution for the flow field, capable of accounting for the effects of any functional shape of the vertically varying hydraulic conductivity. The solution considers the uneven distribution of pressure at the water‐sediment interface (i.e., the pumping process) dictated by the presence of dune morphology. We then simulate solute transport using particle tracking. Our modeling framework is validated against numerical and tracer data from flume experiments and used to explore the implication of hydraulic conductivity stratification on the statistics and pdf of the residence time. Finally, reduced‐order models are used to enlighten the dependence of key residence time statistics on the parameters characterizing the hydraulic conductivity stratification. Key Points A new integral transform‐based semi‐analytical solution for hyporheic flows in stratified sediments is provided and tested against data The impact of hydraulic conductivity stratification on residence time distribution and its statistics is quantitatively analyzed ROMs are used to approximate key residence time statistics in the space of variability of parameters characterizing the conductivity profile

Streambed biogeochemical processes strongly influence riverine water quality and gaseous emissions. These processes depend largely on flow paths through the hyporheic zone (HZ), the streambed volume saturated with stream water. Boulders and other macroroughness elements are known to induce hyporheic flows in gravel‐bed streams. However, data quantifying the impact of these elements on hyporheic chemistry are lacking. We demonstrate that, in gravel‐bed rivers, the amount of dissolved oxygen (DO) in the bed depends chiefly on changes in bed shape, or morphology, such as the formation of scour and depositional areas, caused by the boulders, among other factors. The study was conducted by comparing DO distributions across different bed states and hydraulic conditions. Our experimental facility replicates conditions observed in natural gravel‐bed streams. We instrumented a section in the bed with DO sensors. Results generally indicate that boulder placement on planar beds has some effects, which are significant at high base flows, on increasing hyporheic oxygen amount compared to the planar case without boulders. Conversely, boulder‐induced morphological changes noticeably and significantly increase the amount of oxygen in the HZ, with the increase depending on sediment inputs during flood flows able to mobilize the sediment. Therefore, streambeds of natural, plane‐bed streams may have deeper oxic zones than previously thought because the presence of boulders and the occurrence of flood flows with varying sediment inputs induce streambed variations among these elements. Plain Language Summary What happens beneath a riverbed can have a big impact on water quality and the release of gases like carbon dioxide or methane. One key area is the hyporheic zone (HZ), which is the layer just under the streambed where river water flows within the sediment voids. This zone supports important chemical reactions that clean water and cycle nutrients. In this study, we looked at how large rocks (boulders) affect the amount of oxygen in this underground layer. It turns out, just placing boulders on a flat streambed increase oxygen content a little bit. But when those boulders actually change the shape of the bed, like creating sediment holes and humps on the streambed, they make a big difference. These changes can boost the oxygen levels in the HZ, especially when flooding moves sediments around the boulders and less sediment comes from upstream. So, natural rivers that look fairly flat on the surface might still have deep, oxygen‐rich zones below, thanks to hidden changes caused by large rocks and floods. This finding helps us better understand how riverbeds support healthy ecosystems and manage water quality. Key Points Boulders expand the hyporheic aerobic zone in plane‐bed rivers under high, yet commonly occurring, flow conditions Boulder‐induced morphological changes significantly deepen oxygen‐rich zones in otherwise planar gravel‐bed streams Reduction of upstream sediment supply during floods can enhance hyporheic oxygenation by promoting the formation of boulder‐driven bedforms

Hyporheic zones are commonly regarded as resilient and enduring interfaces between groundwater and surface water in river corridors. In particular, bedform‐induced advective pumping hyporheic exchange (bedform‐induced exchange) is often perceived as a relatively persistent mechanism in natural river systems driving water, solutes, and energy exchanges between the channel and its surrounding streambed sediments. Numerous studies have been based on this presumption. To evaluate the persistence of hyporheic zones under varying hydrologic conditions, we use a multi‐physics framework to model advective pumping bedform‐induced hyporheic exchange in response to a series of seasonal‐ and event‐scale groundwater table fluctuation scenarios, which lead to episodic river‐aquifer disconnections and reconnections. Our results suggest that hyporheic exchange is not as ubiquitous as generally assumed. Instead, the bedform‐induced hyporheic exchange is restricted to a narrow range of conditions characterized by minor river‐groundwater head differences, is intermittent, and can be easily obliterated by minor losing groundwater conditions. These findings shed light on the fragility of bedform‐induced hyporheic exchange and have important implications for biogeochemical transformations along river corridors. Plain Language Summary The hyporheic zone is a small veneer connecting surface water and groundwater systems, which supports vital ecosystem services along river corridors. The current paradigm assumes this exchange zone is ubiquitous and relatively stable over space and time. Yet, the dynamic nature of the surface and subsurface process driving and modulating the exchange can lead to complex spatiotemporal dynamics where bedform‐induced hyporheic zones are only present for short periods or are absent. In this study, we investigated how persistent hyporheic zones are under typical groundwater dynamics. We found that bedform‐induced hyporheic zones are not as stable as usually assumed, and their presence is restricted to a narrow range of hydrological conditions. The findings reveal the fragility of hyporheic zones and offer new perspectives to conceptualize river connectivity processes. Key Points We explore bedform‐induced hyporheic exchange under various seasonal‐ and event‐scale groundwater table fluctuation scenarios Bedform‐induced exchange is intermittent and limited to a narrow range of conditions where river‐groundwater head differences are small Bedform‐induced exchange fragility highlights the need for better representations of turbulence and turnover drivers in water quality models

The hyporheic zone (HZ), where surface water (SW) and groundwater (GW) interact and mix, acts as a critical interface that attenuates contaminants through enhanced biogeochemical cycling. While bedform migration significantly influences hyporheic exchange and non-mixing-driven reactions of solutes from upstream SW, the effects of bedform migration on SW-GW mixing dynamics and mixing-triggered biogeochemical reactions – particularly under gaining stream conditions – remain poorly understood. Establishing a coupled hydrodynamic and reactive transport model that incorporates bedform migration, this paper systematically examines nitrogen processing for scenarios of variable sediment grain size, stream velocities, and upwelling GW fluxes. Results of this study reveal that SW-GW mixing and mixing-triggered denitrification zones progressively transition from crescent shapes into uniform band-like configurations as bedforms migrate. Both hyporheic exchange flux and mixing flux increase with increasing stream velocity and associated bedform celerity. The mixing proportion and mixing zone size increase at the start of migration, while they reach approximately stable when turnover becomes the dominant hyporheic exchange mechanism. Slow to moderate migrated bedforms with enhanced mixing dynamics facilitate mixing-triggered denitrification, whereas fast stream flows and migrating bedforms shorten solute residence timescales and limit denitrification potential. Consequently, in fine to medium sandy sediments, groundwater-borne nitrate removal efficiency declines significantly with bedform migration. The self-purification capacity of the HZ, and particularly its functioning as a natural barrier against GW contamination, is hindered under such dynamic bedform conditions. These findings highlight the need to maintain stable bedform conditions in restoration projects to enhance the capacity of HZ contaminant attenuation.

Biochemical transformations of organic matter (OM) are a primary driver of river corridor biogeochemistry, thereby modulating ecosystem processes at local to global scales. OM transformations are driven by diverse biotic and abiotic processes, but we lack knowledge of how the diversity of those processes varies across river corridors and across surface and subsurface components of river corridors. To fill this gap we quantified the number of putative biotic and abiotic transformations of organic molecules across diverse river corridors using ultra-high-resolution mass spectrometry. The number of unique transformations is used here as a proxy for the diversity of biochemical processes underlying observed profiles of organic molecules. For this, we use public data spanning the contiguous United States (ConUS) from the Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS) consortium. Our results show that surface water OM had more biotic and abiotic transformations than OM from shallow hyporheic zone sediments (1–3 cm depth). We observed substantially more biotic than abiotic transformations, and the numbers of biotic and abiotic transformations were highly correlated with each other. We found no relationship between the number of transformations in surface water and sediments and no meaningful relationships with latitude, longitude, or climate. We also found that the composition of transformations in sediments was not linked with transformation composition in adjacent surface waters. We infer that OM transformations represented in surface water are an integrated signal of diverse processes occurring throughout the upstream catchment. In contrast, OM transformations in sediments likely reflect a narrower range of processes within the sampled volume. This indicates decoupling between the processes influencing surface water and sediment OM, despite the potential for hydrologic exchange to homogenize OM. We infer that the processes influencing OM transformations and the scales at which they operate diverge between surface water and sediments.