Fifty years of hyporheic zone research have shown the important role played by the hyporheic zone as an interface between groundwater and surface waters. However, it is only in the last two decades that what began as an empirical science has become a mechanistic science devoted to modeling studies of the complex fluid dynamical and biogeochemical mechanisms occurring in the hyporheic zone. These efforts have led to the picture of surface-subsurface water interactions as regulators of the form and function of fluvial ecosystems. Rather than being isolated systems, surface water bodies continuously interact with the subsurface. Exploration of hyporheic zone processes has led to a new appreciation of their wide reaching consequences for water quality and stream ecology. Modern research aims toward a unified approach, in which processes occurring in the hyporheic zone are key elements for the appreciation, management, and restoration of the whole river environment. In this unifying context, this review summarizes results from modeling studies and field observations about flow and transport processes in the hyporheic zone and describes the theories proposed in hydrology and fluid dynamics developed to quantitatively model and predict the hyporheic transport of water, heat, and dissolved and suspended compounds from sediment grain scale up to the watershed scale. The implications of these processes for stream biogeochemistry and ecology are also discussed.

Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications

an upland agricultural stream. We measured solute concentrations ( 15 NO3 , 15 N2 (g), as well as NO3 ,N H3, DOC, DO, Cl − ), and hydraulic transport parameters (head, flow rates, flow paths, and residence time distributions) of the reach and along HZ flow paths of an instrumented gravel bar. HZ exchange was observed across the entire gravel bar (i.e., in all wells) with flow path lengths up to 4.2 m and corresponding median residence times greater than 28.5 h. The HZ transitioned from a net nitrification environment at its head (short residence times) to a net denitrification environment at its tail (long residence times). NO3 increased at short residence times from 0.32 to 0.54 mg‐ NL −1 until a threshold of 6.9 h and then consistently decreased from 0.54 to 0.03 mg‐ NL −1 . Along these same flow paths, declines were seen in DO (from 8.31 to 0.59 mg‐O2 L −1 ) and DOC (from 3.0 to 1.7 mg‐ CL −1 ). The rates of the DO and DOC removal and net nitrification were greatest during short residence times, while the rate of denitrification was greatest at long residence times. 15 NO3 tracing confirmed that a fraction of the NO3 removal was via denitrification as 15 N2 was produced across the entire gravel bar HZ. Production of 15 N2 across all observed flow paths and residence times indicated that denitrification microsites are present even where nitrification was the net outcome. These findings demonstrate that the HZ is an active nitrogen sink in this system and that the distinction between net nitrification and denitrification in the HZ is a function of residence time and exhibits threshold behavior. Consequently, incorporation of HZ exchange and water residence time characterizations will improve mechanistic predictions of nitrogen cycling in streams.

/pdf/dynamics-of-nitrate-production-and-removal-as-a-function-of-4j0djsn9tk.pdf

Dynamics of nitrate production and removal as a function of residence time in the hyporheic zone

[1] The fate of biologically available nitrogen (N) and carbon (C) in stream ecosystems is controlled by the coupling of physical transport and biogeochemical reaction kinetics. However, determining the relative role of physical and biogeochemical controls at different temporal and spatial scales is difficult. The hyporheic zone (HZ), where groundwater–stream water mix, can be an important location controlling N and C transformations because it creates strong gradients in both the physical and biogeochemical conditions that control redox biogeochemistry. We evaluated the coupling of physical transport and biogeochemical redox reactions by linking an advection, dispersion, and residence time model with a multiple Monod kinetics model simulating the concentrations of oxygen (O2), ammonium (NH4), nitrate (NO3), and dissolved organic carbon (DOC). We used global Monte Carlo sensitivity analyses with a nondimensional form of the model to examine coupled nitrification-denitrification dynamics across many scales of transport and reaction conditions. Results demonstrated that the residence time of water in the HZ and the uptake rate of O2 from either respiration and/or nitrification determined whether the HZ was a source or a sink of NO3 to the stream. We further show that whether the HZ is a net NO3 source or net NO3 sink is determined by the ratio of the characteristic transport time to the characteristic reaction time of O2 (i.e., the Damkohler number, DaO2), where HZs with DaO2 < 1 will be net nitrification environments and HZs with DaO2 ≪ 1 will be net denitrification environments. Our coupling of the hydrologic and biogeochemical limitations of N transformations across different temporal and spatial scales within the HZ allows us to explain the widely contrasting results of previous investigations of HZ N dynamics which variously identify the HZ as either a net source or sink of NO3. Our model results suggest that only estimates of residence times and O2uptake rates are necessary to predict this nitrification-denitrification threshold and, ultimately, whether a HZ will be either a net source or sink of NO3.

/pdf/coupled-transport-and-reaction-kinetics-control-the-nitrate-1ax6sieb17.pdf

Coupled transport and reaction kinetics control the nitrate source-sink function of hyporheic zones

Nitrous oxide from streams and rivers: A review of primary biogeochemical pathways and environmental variables

Increased loading of nitrogen (N) and phosphorus (P) from agricultural and urban intensification has led to severe degradation of inland and coastal waters. Lakes, reservoirs, and wetlands (lentic systems) retain these nutrients, thus regulating their delivery to downstream waters. While the processes controlling N and P retention are relatively well-known, there is a lack of quantitative understanding of how these processes manifest across spatial scales. We synthesized data from 600 lentic systems around the world to gain insight into the relationship between hydrologic and biogeochemical controls on nutrient retention. Our results indicate that the first-order reaction rate constant, k [T−1], is inversely proportional to the hydraulic residence time, τ [T], across 6 orders of magnitude in residence time for total N, total P, nitrate, and phosphate. We hypothesized that the consistency of the relationship points to a strong hydrologic control on biogeochemical processing, and validated our hypothesis using a sediment-water model that links major nutrient removal processes with system size. Finally, the k-τ relationships were upscaled to the landscape scale using a wetland size-frequency distribution. Results suggest that small wetlands play a disproportionately large role in landscape-scale nutrient processing—50% of nitrogen removal occurs in wetlands smaller than 102.5 m2 in our example. Thus, given the same loss in wetland area, the nutrient retention potential lost is greater when smaller wetlands are preferentially lost from the landscape. Our study highlights the need for a stronger focus on small lentic systems as major nutrient sinks in the landscape.

/pdf/biogeochemical-hotspots-role-of-small-water-bodies-in-j818q2nlq5.pdf

Biogeochemical hotspots: Role of small water bodies in landscape nutrient processing

The effect of retention time on redox sequences along the hydrological flow path of groundwater discharging through low-relief coastal stream sediments and the subsequent impact on the fate of NO3  carried in the groundwater was examined in two intact cores. Rates of denitrification were determined for the organic-rich streambedsediments, and a macroscopic, multispecies, reactive transport model based on multiple Monod kinetics was developed to interpret and extend the experimental results. Regionalized sensitivity analysis and parameter estimation were used to determine a set of parameters that best describe the experimental data for one column. The calibrated model successfully replicated the spatial profiles of nitrate under both steady and transient conditions in the second column operated under different conditions. A dimensionless form of the model was used to examine how coupled biogeochemical reactions and hydrological transport processes operate within the stream sediments could be understood in terms of Peclet (ratio of advection to dispersion) and Damkohler numbers (the ratio ofthe characteristic time of transport to the characteristic time for reaction). At the study site, the Peclet number and the Damkohler numbers for both oxygen and nitrate are high (Pe = 25, DaN = 47.5, and DaO = 40). When Pe > 5, Damkohler numbers explain observed variations in nitrate removal rates; as the flow rate increases, the solute residence time in the reactive zone is shortened resulting in a lesser extent of reaction, such that more NO3  is delivered to the stream water.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2007WR006027

Nitrate Reduction In Streambed Sediments: Effects Of Flow And Biogeochemical Kinetics

Groundwater that bypasses the riparian zone by travelling along deep flow paths may deliver high concentrations of fertilizer-derived NO3− to streams, or it may be impacted by the NO3− removal process of denitrification in streambed sediments. In a study of a small agricultural catchment on the Atlantic coastal plain of Virginia's eastern shore, we used seepage meters deployed in the streambed to measure specific discharge of groundwater and its solute concentrations for various locations and dates. We used values of Cl− concentration to discriminate between bypass water recharged distal to the stream and that contained high NO3− but low Cl− concentrations and riparian-influenced water recharged proximal to the stream that contained low NO3− and high Cl− concentrations. The travel time required for bypass water to transit the 30-cm-thick, microbially active denitrifying zone in the streambed determined the extent of NO3− removal, and hydraulic conductivity determined travel time through the streambed sediments. At all travel times greater than 2 days, NO3− removal was virtually complete. Comparison of the timescales for reaction and transport through the streambed sediments in this system confirmed that the predominant control on nitrate flux was travel time rather than denitrification rate coefficients. We conclude that extensive denitrification can occur in groundwater that bypasses the riparian zone, but a residence time in biologically active streambed sediments sufficient to remove a large fraction of the NO3− is only achieved in relatively low-conductivity porous media. Instead of viewing them as separate, the streambed and riparian zone should be considered an integrated NO3− removal unit. Copyright © 2011 John Wiley & Sons, Ltd.

Travel time controls the magnitude of nitrate discharge in groundwater bypassing the riparian zone to a stream on Virginia's coastal plain

Evapotranspiration (ET) can cause diel fluctuations in the elevation of the water table and the stage in adjacent streams. The diel fluctuations of water levels change head gradients throughout the day, causing specific discharge through near-stream sediment to fluctuate at the same time scale. In a previous study, we showed that specific discharge controls the residence time of groundwater in streambed sediment that, in turn, exerted the primary control on removal from groundwater passing through the streambed. In this study, we examine the magnitude of diel specific discharge patterns through the streambed driven by ET in the riparian zone with a transient numerical saturated–unsaturated groundwater flow model. On the basis of a first-order kinetic model for removal, we predicted diel fluctuations in stream concentrations. Model results indicated that ET drove a diel pattern in specific discharge through the streambed and riparian zone (the removal zones). Because specific discharge is inversely proportional to groundwater travel time through the removal zones and travel time determines the extent of removal, diel changes in ET can result in a diel pattern in concentration in the stream. The model predictions generally matched observations made during summertime base-flow conditions in a small coastal plain stream in Virginia. A more complicated pattern was observed following a seasonal drawdown period, where source components to the stream changed during the receding limb of the hydrograph and resulted in diel fluctuations being superimposed over a multi-day trend in concentrations. Copyright © 2013 John Wiley & Sons, Ltd.

Diel patterns in coastal‐stream nitrate concentrations linked to evapotranspiration in the riparian zone of a low‐relief, agricultural catchment

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2014WR015904

Comment on “Hydraulic fracturing in faulted sedimentary basins: Numerical simulation of potential contamination of shallow aquifers over long time scales” by Claire Gassiat et al.

Generality of Nitrate Removal in Streambed Sediment on the Southern Delmarva Peninsula

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