Spatial Periodic Boundary Condition for MODFLOW

Small‐scale hyporheic zone (HZ) models often use a spatial periodic boundary (SPB) pair to simulate an infinite repetition of bedforms. SPB's are common features of commercially available multiphysics modeling packages. MODFLOW's lack of this boundary type has precluded it from being effectively utilized in this area of HZ research. We present a method to implement the SPB in MODFLOW by development of the appropriate block‐centered finite‐difference expressions. The implementation is analogous to MODFLOW's general head boundary package. The difference is that the terms on the right hand side of the solution equations must be updated with each iteration. Consequently, models that implement the SPB converge best with solvers that perform both inner and outer iterations. The correct functioning of the SPB condition in MODFLOW is verified by two examples. This boundary condition allows users to build HZ‐bedform models in MODFLOW, facilitating further research using related codes such as MT3DMS and PHT3D.     

Mixing interfaces,fluxes, residence times and redox conditions of the hyporheic zones induced by dune-like bedforms and ambient groundwater flow

Recent studies highlighted the importance of the interface between streams and their surrounding sediment, known as the hyporheic zone, where stream waters flow through the alluvium. These pore water fluxes stem from the interaction among streambed morphology, stream hydraulics and surrounding groundwater flow. We analytically model the hyporheic hydraulics induced by a spatially uniform ambient groundwater flow made of a horizontal, underflow, and a vertical, basal, component, which mimics gaining and losing stream conditions. The proposed analytical solution allows to investigate the control of simple hydromorphological quantities on the extent, residence time and redox conditions of the hyporheic zone, and the thickness of the mixing interface between hyporheic and groundwater cells. Our analysis shows that the location of the mixing zone shallows or deepens in the sediment as a function of bedform geometry, surface hydraulic and groundwater flow. The point of stagnation, where hyporheic flow velocities vanish and where the separation surface passes through, is shallower than or coincides with the deepest point of the hyporheic zone only due to underflow. An increase of the ambient flow causes a reduction of the hyporheic zone volume similarly in both losing and gaining conditions. The hyporheic residence time is lognormally distributed under neutral, losing and gaining conditions, with the residence time moments depending on the same set of parameters describing dune morphology and stream flow.     

Residence time of bedform-driven hyporheic exchange

Biogeochemical and ecological transformations in hyporheic zones are dependent on the timing of hyporheic exchange. We show through linked modeling of open channel turbulent flow, groundwater flow, and solute transport that the residence time distributions of solutes advected by hyporheic flow induced by current–bedform interaction follow power-laws. This tailing behavior of solutes exiting the sediments is explained by the presence of multiple path lengths coupled with very large variability in Darcy flow velocity, both occurring without heterogeneity in sediment permeability. Hyporheic exchange through bedforms will result in short-time fractal scaling of stream water chemistry.     

Transport of nonsorbing solutes in a streambed with periodic bedforms

Previous studies of hyporheic zone focused largely on the net mass transfer of solutes between stream and streambed. Solute transport within the bed has attracted less attention. In this study, we combined flume experiments and numerical simulations to examine solute transport processes in a streambed with periodic bedforms. Solute originating from the stream was subjected to advective transport driven by pore water circulation due to current–bedform interactions as well as hydrodynamic dispersion in the porous bed. The experimental and numerical results showed that advection played a dominant role at the early stage of solute transport, which took place in the hyporheic zone. Downward solute transfer to the deep ambient flow zone was controlled by transverse dispersion at the later stage when the elapsed time exceeded the advective transport characteristic time t_c (= L/u_c with L being the bedform length and u_c the characteristic pore water velocity). The advection-based pumping exchange model was found to predict reasonably well solute transfer between the overlying water and streambed at the early stage but its performance deteriorated at the later stage. With dispersion neglected, the pumping exchange model underestimated the long-term rate and total mass of solute transfer from the overlying water to the bed. Therefore both advective and dispersive transport components are essential for quantification of hyporheic exchange processes.     

Imaging hyporheic zone solute transport using electrical resistivity

Traditional characterization of hyporheic processes relies upon modelling observed in‐stream and subsurface breakthrough curves to estimate hyporheic zone size and infer exchange rates. Solute data integrate upstream behaviour and lack spatial coverage, limiting our ability to accurately quantify spatially heterogeneous exchange dynamics. Here, we demonstrate the application of near‐surface electrical resistivity imaging (ERI) methods, coupled with experiments using an electrically conductive stream tracer (dissolved NaCl), to provide in situ imaging of spatial and temporal dynamics of hyporheic exchange. Tracer‐labelled water in the stream enters the hyporheic zone, reducing electrical resistivity in the subsurface (to which subsurface ERI is sensitive). Comparison of background measurements with those recording tracer presence provides distributed characterization of hyporheic area (in this application, ∼0·5 m²). Results demonstrate the first application of ERI for two‐dimensional imaging of stream‐aquifer exchange and hyporheic extent. Future application of this technique will greatly enhance our ability to quantify processes controlling solute transport and fate in hyporheic zones, and provide data necessary to inform more complete numerical models. Copyright © 2010 John Wiley & Sons, Ltd.     

Implementation of Solute Transport in the Vadose Zone into the “HYDRUS Package for MODFLOW”

The “HYDRUS package for MODFLOW” is an existing MODFLOW package that allows MODFLOW to simultaneously evaluate transient water flow in both unsaturated and saturated zones. The package is based on incorporating parts of the HYDRUS-1D model (to simulate unsaturated water flow in the vadose zone) into MODFLOW (to simulate saturated groundwater flow). The coupled model is effective in addressing spatially variable saturated-unsaturated hydrological processes at the regional scale. However, one of the major limitations of this coupled model is that it does not have the capability to simulate solute transport along with water flow and therefore, the model cannot be employed for evaluating groundwater contamination. In this work, a modified unsaturated flow and transport package (modified HYDRUS package for MODFLOW and MT3DMS) has been developed and linked to the three-dimensional (3D) groundwater flow model MODFLOW and the 3D groundwater solute transport model MT3DMS. The new package can simulate, in addition to water flow in the vadose zone, also solute transport involving many biogeochemical processes and reactions, including first-order degradation, volatilization, linear or nonlinear sorption, one-site kinetic sorption, two-site sorption, and two-kinetic sites sorption. Due to complex interactions at the groundwater table, certain modifications of the pressure head (compared to the original coupling) and solute concentration profiles were incorporated into the modified HYDRUS package. The performance of the newly developed model is evaluated using HYDRUS (2D/3D), and the results indicate that the new model is effective in simulating the movement of water and contaminants in the saturated-unsaturated flow domains.     

A Comparison of Hyporheic Transport at a Cross‐Vane Structure and Natural Riffle

While restoring hyporheic flowpaths has been cited as a benefit to stream restoration structures, little documentation exists confirming that constructed restoration structures induce comparable hyporheic exchange to natural stream features. This study compares a stream restoration structure (cross‐vane) to a natural feature (riffle) concurrently in the same stream reach using time‐lapsed electrical resistivity (ER) tomography. Using this hydrogeophysical approach, we were able to quantify hyporheic extent and transport beneath the cross‐vane structure and the riffle. We interpret from the geophysical data that the cross‐vane and the natural riffle induced spatially and temporally unique hyporheic extent and transport, and the cross‐vane created both spatially larger and temporally longer hyporheic flowpaths than the natural riffle. Tracer from the 4.67‐h injection was detected along flowpaths for 4.6 h at the cross‐vane and 4.2 h at the riffle. The spatial extent of the hyporheic zone at the cross‐vane was 12% larger than that at the riffle. We compare ER results of this study to vertical fluxes calculated from temperature profiles and conclude significant differences in the interpretation of hyporheic transport from these different field techniques. Results of this study demonstrate a high degree of heterogeneity in transport metrics at both the cross‐vane and the riffle and differences between the hyporheic flowpath networks at the two different features. Our results suggest that restoration structures may be capable of creating sufficient exchange flux and timescales of transport to achieve the same ecological functions as natural features, but engineering of the physical and biogeochemical environment may be necessary to realize these benefits.     

Convergence of Groundwater Discharge through the Hyporheic Zone of Streams

Significant attention has been given to hyporheic water fluxes induced by hydromorphologic processes in streambeds and the effects they have on stream ecology. However, the impact of hyporheic fluxes on regional groundwater flow discharge zones as well as the interaction of these flows are much less investigated. The groundwater-hyporheic interactive flow not only governs solute mass and heat transport in streams but also controls the retention of solute and contamination following the discharge of deep groundwater, such as naturally occurring solutes and leakage from geological waste disposal facilities. Here, we applied a physically based modeling approach combined with extensive hydrologic, geologic and geographical data to investigate the effect of hyporheic flow on groundwater discharge in the Krycklan catchment, located in a boreal landscape in Sweden. Regional groundwater modeling was conducted using COMSOL Multiphysics by considering geologic heterogeneity and infiltration constraint of the groundwater circulation intensity. Moreover, the hyporheic flow was analyzed using an exact spectral solution accounting for the fluctuating streambed topography and superimposed with the regional groundwater flow. By comparing the discharge flow fields with and without consideration of hyporheic flows, we found that the divergence of the discharge was substantially enhanced and the distribution of the travel times of groundwater was significantly shifted toward shorter times due to the presence of hyporheic flow. Particularly important is that the groundwater flow paths contract near the streambed interface due to the hyporheic flow, which leads to a phenomenon that we name “fragmentation” of coherent areas of groundwater upwelling in pinhole-shaped stream tubes.     

Modeling Variably Saturated Subsurface Solute Transport with MODFLOW‐UZF and MT3DMS

The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated‐zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume‐averaged approach in which Lagrangian‐based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF‐MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably‐Saturated Two‐Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two‐ and three‐dimensional simulations also were investigated to ensure unsaturated‐saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large‐scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF‐MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three‐dimensional variably saturated flow and transport simulations revealed UZF‐MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide‐spread use of both MODFLOW and MT3DMS, the added capability of unsaturated‐zone transport in this familiar modeling framework stands to benefit a broad user‐ship.     

A temporal stable isotopic (δ18O, δD,d‐excess) comparison in glacier meltwater streams,Taylor Valley,Antarctica

In this paper, we describe the importance of hyporheic dynamics within Andersen Creek and Von Guerard Stream, Taylor Valley, Antarctica, from the 2010–2011 melt season using natural tracers. Water collection started at flow onset and continued, with weekly hyporheic‐zone sampling. The water δ¹⁸O and δD values were isotopically lighter in the beginning and heavier later in the season. D‐excess measurements were used as an indicator of mixing because an evaporative signature was evident and distinguishable between 2 primary end‐members (glacier meltwater and hyporheic zone). Hyporheic‐zone influence on the channel water was variable with a strong control on streamwater chemistry, except at highest discharges. This work supports previous research indicating that Von Guerard Stream has a large, widespread hyporheic zone that varies in size with time and discharge. Andersen Creek, with a smaller hyporheic zone, displayed hyporheic‐zone solute interaction through the influence from subsurface hypersaline flow. Overall, the evolution of Taylor Valley hyporheic‐zone hydrology is described seasonally. In mid‐December, the hyporheic zone is a dynamic system exchanging with the glacier meltwater in the channel, and with diminishing flow in January, the hyporheic zone drains back into the channel flow also impacting stream chemistry. This work adds new information on the role of hyporheic zone–stream interaction in these glacier meltwater streams.     

The role of the hyporheic zone across stream networks

Many hyporheic papers state that the hyporheic zone is a critical component of stream ecosystems, and many of these papers focus on the biogeochemical effects of the hyporheic zone on stream solute loads. However, efforts to show such relationships have proven elusive, prompting several questions: Are the effects of the hyporheic zone on stream ecosystems so highly variable in place and time (or among streams) that a consistent relationship should not be expected? Or, is the hyporheic zone less important in stream ecosystems than is commonly expected? These questions were examined using data from existing groundwater modelling studies of hyporheic exchange flow at five sites in a fifth‐order, mountainous stream network. The size of exchange flows, relative to stream discharge (Q_HEF:Q), was large only in very small streams at low discharge (area ≈ 100 ha; Q < 10 l/s). At higher flows (flow exceedance probability > 0·7) and in all larger streams, Q_HEF:Q was small. These data show that biogeochemical processes in the hyporheic zone of small streams can substantially influence the stream's solute load, but these processes become hydrologically constrained at high discharge or in larger streams and rivers. The hyporheic zone may influence stream ecosystems in many ways, however, not just through biogeochemical processes that alter stream solute loads. For example, the hyporheic zone represents a unique habitat for some organisms, with patterns and amounts of upwelling and downwelling water determining the underlying physiochemical environment of the hyporheic zone. Similarly, hyporheic exchange creates distinct patches of downwelling and upwelling. Upwelling environments are of special interest, because upwelling water has the potential to be thermally or chemically distinct from stream water. Consequently, micro‐environmental patches created by hyporheic exchange flows are likely to be important to biological and ecosystem processes, even if their impact on stream solute loads is small. Published in 2011 by John Wiley & Sons, Ltd.     

Colloid transport and distribution in the hyporheic zone

Colloids moving from the stream into the hyporheic zone may have a negative impact on aquatic ecosystems as they are potential contaminants or carriers of contaminants. Moreover, retained colloids in the hyporheic zone could not only reduce the exchange flux between the stream and streambed but also change the conditions of the bed, affecting the habitats for aquatic organisms. Previous studies focused on the exchange flux across the sediment–water interface, but the colloid transport processes and distribution of retained colloids in the streambed have received little attention. We conducted experiments within a laboratory flume to examine these processes in a streambed driven by bedform‐induced hyporheic flow. Retained colloids measured in the bed at the end of the experiments revealed colloid retention mainly in the shallow layer of hyporheic zone (0–5 cm below the interface). The results demonstrated significant effects of particle trapping and settling on the colloid transport and distribution in the streambed. Retention leads to the formation of a colloid‐filled shallow layer in the bed. Particle paths based on model simulations showed that colloid settling in pore water modifies the direction of colloid transport and allows the colloid particles to move more deeply in the bed.     

Focused Groundwater Controlled Feedbacks into the Hyporheic Zone During Baseflow Recession

Groundwater surface water interaction in the hyporheic zone remains an important challenge for water resources management and ecosystem restoration. In heterogeneous stratified glacial sediments, reach‐scale environments contain an uneven distribution of focused groundwater flow occurring simultaneously with diffusely discharging groundwater. This results in a variation of stream‐aquifer interactions, where focused flow systems are able to temporally dominate exchange processes. The research presented here investigates the direct and indirect influences focused groundwater discharge exerts on the hyporheic zone during baseflow recession. Field results demonstrate that as diffuse sources of groundwater deplete during baseflow recession, focused groundwater discharge remains constant. During baseflow recession the hyporheic zone is unable to expand, while the high nitrate concentration from focused discharge changes the chemistry of the stream. The final result is a higher concentration of nitrate in the hyporheic zone as this altered surface water infiltrates into the subsurface. This indirect coupling of focused groundwater discharge and the hyporheic zone is unaccounted for in hyporheic studies at this time. Results indicate important implications for the potential reduction of agricultural degradation of water quality.     

A coupled model for simulating surface water and groundwater interactions in coastal wetlands

Coastal wetlands are characterized by strong, dynamic interactions between surface water and groundwater. This paper presents a coupled model that simulates interacting surface water and groundwater flow and solute transport processes in these wetlands. The coupled model is based on two existing (sub) models for surface water and groundwater, respectively: ELCIRC (a three‐dimensional (3‐D) finite‐volume/finite‐difference model for simulating shallow water flow and solute transport in rivers, estuaries and coastal seas) and SUTRA (a 3‐D finite‐element/finite‐difference model for simulating variably saturated, variable‐density fluid flow and solute transport in porous media). Both submodels, using compatible unstructured meshes, are coupled spatially at the common interface between the surface water and groundwater bodies. The surface water level and solute concentrations computed by the ELCIRC model are used to determine the boundary conditions of the SUTRA‐based groundwater model at the interface. In turn, the groundwater model provides water and solute fluxes as inputs for the continuity equations of surface water flow and solute transport to account for the mass exchange across the interface. Additionally, flux from the seepage face was routed instantaneously to the nearest surface water cell according to the local sediment surface slope. With an external coupling approach, these two submodels run in parallel using time steps of different sizes. The time step (Δt_g) for the groundwater model is set to be larger than that (Δt_s) used by the surface water model for computational efficiency: Δt_g = M × Δt_s where M is an integer greater than 1. Data exchange takes place between the two submodels through a common database at synchronized times (e.g. end of each Δt_g). The coupled model was validated against two previously reported experiments on surface water and groundwater interactions in coastal lagoons. The results suggest that the model represents well the interacting surface water and groundwater flow and solute transport processes in the lagoons. Copyright © 2011 John Wiley & Sons, Ltd.     

Impact of watershed topography on hyporheic exchange

Among the interactions between surface water bodies and aquifers, hyporheic exchange has been recognized as a key process for nutrient cycling and contaminant transport. Even though hyporheic exchange is strongly controlled by groundwater discharge, our understanding of the impact of the regional groundwater flow on hyporheic fluxes is still limited because of the complexity arising from the multi-scale nature of these interactions. In this work, we investigate the role of watershed topography on river-aquifer interactions by way of a semi-analytical model, in which the landscape topography is used to approximate the groundwater head distribution. The analysis of a case study shows how the complex topographic structure is the direct cause of a substantial spatial variability of the aquifer-river exchange. Groundwater upwelling along the river corridor is estimated and its influence on the hyporheic zone is discussed. In particular, the fragmentation of the hyporeic corridor induced by groundwater discharge at the basin scale is highlighted.     

Development of a grid‐based version of the SWAT landscape model

Integrated river basin models should provide a spatially distributed representation of basin hydrology and transport processes to allow for spatially implementing specific management and conservation measures. To accomplish this, the Soil and Water Assessment Tool (SWAT) was modified by integrating a landscape routing model to simulate water flow across discretized routing units. This paper presents a grid‐based version of the SWAT landscape model that has been developed to enhance the spatial representation of hydrology and transport processes. The modified model uses a new flow separation index that considers topographic features and soil properties to capture channel and landscape flow processes related to specific landscape positions. The resulting model is spatially fully distributed and includes surface, lateral and groundwater fluxes in each grid cell of the watershed. Furthermore, it more closely represents the spatially heterogeneous distributed flow and transport processes in a watershed. The model was calibrated and validated for the Little River Watershed (LRW) near Tifton, Georgia (USA). Water balance simulations as well as the spatial distribution of surface runoff, subsurface flow and evapotranspiration are examined. Model results indicate that groundwater flow is the dominant landscape process in the LRW. Results are promising, and satisfactory output was obtained with the presented grid‐based SWAT landscape model. Nash–Sutcliffe model efficiencies for daily stream flow were 0.59 and 0.63 for calibration and validation periods, and the model reasonably simulates the impact of the landscape position on surface runoff, subsurface flow and evapotranspiration. Additional revision of the model will likely be necessary to adequately represent temporal variations of transport and flow processes in a watershed. Copyright © 2014 John Wiley & Sons, Ltd.     

Modeling surface and ground water mixing in the hyporheic zone using MODFLOW and MT3D

We used a three-dimensional MODFLOW model, paired with MT3D, to simulate hyporheic zones around debris dams and meanders along a semi-arid stream. MT3D simulates both advective transport and sink/source mixing of solutes, in contrast to particle tracking (e.g. MODPATH), which only considers advection. We delineated the hydrochemically active hyporheic zone based on a new definition, specifically as near-stream subsurface zones receiving a minimum of 10% surface water within a 10-day travel time. Modeling results indicate that movement of surface water into the hyporheic zone is predominantly an advective process. We show that debris dams are a key driver of surface water into the subsurface along the experimental reach, causing the largest flux rates of water across the streambed and creating hyporheic zones with up to twice the cross-sectional area of other hyporheic zones. Hyporheic exchange was also found in highly sinuous segments of the experimental reach, but flux rates are lower and the cross-sectional areas of these zones are generally smaller. Our modeling approach simulated surface and ground water mixing in the hyporheic zone, and thus provides numerical approximations that are more comparable to field-based observations of surface–groundwater exchange than standard particle-tracking simulations.     

Impact of debris dams on hyporheic interaction along a semi‐arid stream

Hyporheic exchange increases the potential for solute retention in streams by slowing downstream transport and increasing solute contact with the substrate. Hyporheic exchange may be a major mechanism to remove nutrients in semi‐arid watersheds, where livestock have damaged stream riparian zones and contributed nutrients to stream channels. Debris dams, such as beaver dams and anthropogenic log dams, may increase hyporheic interactions by slowing stream water velocity, increasing flow complexity and diverting water to the subsurface. Here, we report the results of chloride tracer injection experiments done to evaluate hyporheic interaction along a 320 m reach of Red Canyon Creek, a second order stream in the semi‐arid Wind River Range of Wyoming. The study site is part of a rangeland watershed managed by The Nature Conservancy of Wyoming, and used as a hydrologic field site by the University of Missouri Branson Geologic Field Station. The creek reach we investigated has debris dams and tight meanders that hypothetically should enhance hyporheic interaction. Breakthrough curves of chloride measured during the field experiment were modelled with OTIS‐P, a one‐dimensional, surface‐water, solute‐transport model from which we extracted the storage exchange rate α and cross‐sectional area of the storage zone A_s for hyporheic exchange. Along gaining reaches of the stream reach, short‐term hyporheic interactions associated with debris dams were comparable to those associated with severe meanders. In contrast, along the non‐gaining reach, stream water was diverted to the subsurface by debris dams and captured by large‐scale near‐stream flow paths. Overall, hyporheic exchange rates along Red Canyon Creek during snowmelt recession equal or exceed exchange rates observed during baseflow at other streams. Copyright © 2005 John Wiley & Sons, Ltd.     

Nitrate removal processes in the riverbed during a single-peak flood event

The effect of the interplay between unsteady flow and bedform in a flood event on nitrogen cycling in the hyporheic zone (HZ) remains poorly understood. In this study, a reactive transport groundwater model with different flood hydrographs was proposed to investigate the effect of modified hyporheic flow on nitrate dynamics in the HZ, including nitrate source-sink function, response to the single-peak flood event and removal efficiency. The results demonstrate that there exists an optimal range of river channel gradients that could enhance the biogeochemical reactions (respiration, nitrification and denitrification) in a flood event. The HZ acts as a nitrate sink especially after the flood event, and its source-sink function is independent of the unsteady discharge/stage conditions. The nitrate in the HZ has a hysteretic response to peak stage/discharge, and its removal efficiency is decreased by up to 70% compared to steady flow conditions. These findings not only provide a better understanding of nitrogen dynamics under the effect of unsteady channel flow, but also can be applied for river restoration to efficiently remove nitrate in the HZ by modifying river channel gradients.     

Does streambed heterogeneity matter for hyporheic residence time distribution in sand-bedded streams?

Stream water residence times within streambed sediments are key values to quantify hyporheic processes including sediment thermal regime, solute transient storage, dilution rates and biogeochemical transformations, such as those controlling degassing nitrous oxide. Heterogeneity of the streambed sediment hydraulic properties has been shown to be potentially an important factor to characterize hyporheic processes. Here, we quantify the importance of streambed heterogeneity on residence times of dune-like bedform induced hyporheic fluxes at the bedform and reach scales. We show that heterogeneity has a net effect of compression of the hyporheic zone (HZ) toward the streambed, changing HZ volume from the homogenous case and thus inducing remarkable differences in the flow field with respect to the homogeneous case. We unravel the physical conditions for which the commonly used homogenous field assumption is applicable for quantifying hyporheic processes thus explaining why predictive measures based on a characteristic residence time, like the Damköhler number, are robust in heterogeneous sand bedded streams.