Advances in Water Resources 26 (2003) 901–905

www.elsevier.com/locate/advwaters

Preface

Modeling hyporheic zone processes

1. Introduction

Stream biogeochemistry is influenced by the physical

and chemical processes that occur in the surrounding

watershed. These processes include the mass loading ofsolutes from terrestrial and atmospheric sources, the

physical transport of solutes within the watershed, and

the transformation of solutes due to biogeochemical

reactions. Research over the last two decades has iden-

tified the hyporheic zone as an important part of the

stream system in which these processes occur. The

hyporheic zone may be loosely defined as the porous

areas of the stream bed and stream bank in whichstream water mixes with shallow groundwater. Ex-

change of water and solutes between the stream proper

and the hyporheic zone has many biogeochemical im-

plications, due to differences in the chemical composi-

tion of surface and groundwater. For example, surface

waters are typically oxidized environments with rela-

tively high dissolved oxygen concentrations. In contrast,

reducing conditions are often present in groundwatersystems leading to low dissolved oxygen concentrations.

Further, microbial oxidation of organic materials in

groundwater leads to supersaturated concentrations of

dissolved carbon dioxide relative to the atmosphere.

Differences in surface and groundwater pH and tem-

perature are also common. The hyporheic zone is

therefore a mixing zone in which there are gradients in

the concentrations of dissolved gasses, the concentra-tions of oxidized and reduced species, pH, and temper-

ature. These gradients lead to biogeochemical reactions

that ultimately affect stream water quality. Due to the

complexity of these natural systems, modeling tech-

niques are frequently employed to quantify process

dynamics.

This special issue of Advances in Water Resources

presents recent research on the modeling of hyporheiczone processes. To begin this preface, a brief history on

modeling hyporheic zone processes is presented. This

background information is by no means complete; ad-

ditional information may be found in Streams and

Groundwaters [17] and the references therein. The

preface concludes with an overview of current re-

0309-1708/$ - see front matter � 2003 Published by Elsevier Ltd.

doi:10.1016/S0309-1708(03)00079-4

search needs and a summary of the articles in the special

issue.

2. Background

Twenty years ago, Bencala and Walters [1] analyzed

the results of a stream tracer experiment using a tran-

sient storage solute transport model (also know as a

�dead zone� model, e.g. [32]). Subsequent work by Ben-

cala, Jackman, McKnight, and coworkers [2,3,16,20]

established the use of stream tracers and the transient

storage model as a standard approach to quantifyingsmall stream hydrodynamics. In its simplest form, the

transient storage model consists of a one-dimensional

advection–dispersion equation [24] with an additional

term to account for transient storage. Transient storage

is defined as the movement of solutes from the free-

flowing main channel into zones of stagnant water,

temporary retention in the stagnant zones, and the

subsequent movement of solute mass back into the mainchannel. Stagnant zones include both surface features

(pools and eddies) and water within the hyporheic zone.

These stagnant zones are lumped together as a concep-

tual storage zone within the transient storage model.

Exchange of solute mass between the main channel and

the transient storage zone is controlled by an exchange

coefficient, a, and the cross-sectional area of the storage

zone, As.Concurrent with the establishment of the transient

storage paradigm, researchers began to recognize the

ecological importance of the hyporheic zone and the

effects of groundwater/surface water interaction on

biogeochemical reactions. In particular, studies of nu-

trient cycling [12,23,34] illustrated the close coupling

between hydrologic transport and biogeochemical pro-

cesses. The transient storage solute transport modelprovided a means to quantify this coupling, with the

transient storage parameters (a and As) providing a

means of quantifying hyporheic exchange [30]. In addi-

tion, the use of conservative stream tracers allowed re-

searchers to distinguish between the effects of hydrologic

and biogeochemical processes. Since the time of the

902 Preface / Advances in Water Resources 26 (2003) 901–905

Stream Solute workshop [30], numerous applications of

stream tracers and the transient storage model have

appeared in the literature [4,5,8,9,14,18,21,22,26,35]. In

addition, advances have been made in regard to field

techniques and modeling tools, e.g. [6,25].

3. Areas of research

Although much progress has been made in model-ing hyporheic zone processes, many challenges remain.

Three areas of research relevant to this special issue

are described here. As discussed by Bencala and

Walters [1], the transient storage model is an empirical

approach that does not attempt to model exchange in

a mechanistic manner. Further, surface storage and

hyporheic exchange are lumped together in a single

storage zone. Although it is sometimes possible to ruleout one of the mechanisms (e.g., a reach affected by

beaver dams may be dominated by surface storage,

whereas a shallow reach with a well defined channel

and porous streambed may be dominated by hypo-

rheic exchange), it is often difficult to distinguish be-

tween surface and subsurface storage. This distinction

is of paramount importance given the differences in

surface and groundwater biogeochemistry noted ear-lier and the ultimate goal of studying stream water

quality. On one hand it may seem trivial to formulate

model equations for multiple storage zones, but it is

quite another matter to develop practical field tech-

niques to correctly parameterize such a model. The

existing stream tracer approach [1] is unlikely to

provide sufficient information for the separation of

surface storage and hyporheic exchange.A second research issue is that of scale. Harvey

et al. [15] conclude that the standard modeling ap-

proach is only capable of identifying hyporheic ex-

change over relatively short-time scales (minutes to

hours). Exchange processes at longer time scales (tens

of hours to days), while important chemically, may

not be properly identified using stream tracer data.

Characterization of long time scale exchange has im-portant implications as solutes entering long hyporheic

flow paths have extended contact with reactive sur-

faces and attached microorganisms that conceivably

leads to enhanced biogeochemical transformation. In

addition to the issue of temporal scale, further work is

needed to identify the spatial scales at which hypo-

rheic exchange is important. With some notable ex-

ceptions [9,18], most investigations of hyporheicexchange have been conducted in low-order streams.

The importance of exchange in these small systems is

presently clear, e.g. [22]. Additional research in higher-

order streams will be needed before similar conclu-

sions can be drawn at larger spatial scales.

The final research issue discussed here is the need for

improved field and modeling techniques to more accu-

rately quantify biogeochemical processes. Biogeochem-

ically reactive solutes may undergo transformation in

the main channel and/or storage zone and the rates oftransformation may vary considerably given the bio-

geochemical gradients noted above. Although separa-

tion of main channel and storage zone processes is

possible using first-order rate coefficients [25], further

refinement in quantifying process dynamics remains a

challenge due to the possible range of storage zone

microenvironments. Processes and rates in surface

storage zones may be significantly different than thoseassociated with the hyporheic zone, and the residence

time (and thus reaction time) of solutes undergoing

short-time scale hyporheic exchange may be consider-

ably less than that for solutes entering longer hyporheic

flow paths. As noted above, multiple storage zone

models may be formulated, but estimation of the phys-

ical and biogeochemical parameters for each storage

zone may not be tractable using existing tracer tech-niques. At the other extreme, lumping the multiple

hydrologic and biogeochemical processes into a single

storage zone with average, aggregate properties may

not provide meaningful results for heterogeneous sys-

tems.

4. Overview of the special issue

The papers in this special issue address many areas

of needed research. With respect to the issues raised

above, several comments are in order. First, the pa-pers of Gooseff et al. [11] and Salehin et al. [27] em-

ploy alternate models of transient storage that may

provide a means of distinguishing between surface

storage and hyporheic exchange. Second, the papers of

Fox and Durnford [10] and Lin and Medina [19]

present approaches that more accurately describe the

groundwater system; these approaches may allow for

the consideration of hyporheic exchange at longertemporal and larger spatial scales. Third, Thomas et al.

[33] present a technique for distinguishing between

main channel and storage zone nutrient uptake, while

Sheibley et al. [29] present a modeling approach for

the transformation of nitrogen in hyporheic sediments.

Additional details on all of the papers in the special

issue are provided below.

Edwardson et al. [7] quantified hyporheic zone in-teractions in seven streams, ranging from first to fifth

order, in the Alaskan tundra. Despite the constraints of

cold temperatures and permafrost, they found that

hyporheic zone interactions were substantial from a

hydrologic and biogeochemical perspective. The hypo-

Preface / Advances in Water Resources 26 (2003) 901–905 903

rheic zone was a zone of degradation of dissolved or-

ganic nitrogen and a source of nitrate, carbon dioxide,

and ammonium in upwelling areas. Concurrent sam-

pling of interstitial waters indicated that parts of the

hyporheic zone did not fully equilibrate with the in-jected stream tracer during the duration of the exper-

iment.

Fox and Durnford [10] investigated the occurrence of

partially saturated conditions within the hyporheic zone

that occur when the water table in the aquifer drops

below the stream bed. Stream–aquifer interaction was

analyzed and the stream depletion rate was quantified

for three types of partially saturated conditions. Streamdepletion rates were incorporated into an analytical

solution of a pumping well adjacent to a stream, re-

sulting in partially saturated conditions beneath the

stream. The transient solution tracked the length along

the stream over which perched conditions develop.

Unsaturated conditions within the hyporheic zone may

lead to higher dissolved oxygen concentrations, limiting

transformation processes that are favored under anaer-obic conditions.

Gooseff et al. [11] characterized hyporheic exchange

processes in three reaches of Lookout Creek (Oregon,

USA). Parameters describing storage and exchange were

estimated using tracer data and two transport models: a

transient storage model with an exponential residence

time distribution and an alternate model based on a

general power-law residence time distribution. Resultssuggest that the transient storage model fit the short-

time tracer response adequately, but not the longer-term

behavior. The long tails in the tracer response were fit

reasonably well by the generalized residence time dis-

tribution model, except at very late times, when the

observed concentrations drop off steeply in contrast to

the model predictions.

Harvey et al. [13] analyzed changes in hydrologicretention by the hyporheic zone in a small desert stream.

During a five year period, growth of aquatic macro-

phytes resulted in a decreased flow rate and average

velocity and an increase in stream width. These hydro-

logic changes were associated with an order of magni-

tude increase in hydrologic retention. Temporal changes

in hydrologic retention in this desert stream and in other

streams were shown to correlate well with the Darcy–Weisbach friction factor, providing a potential guide for

evaluating changes in hyporheic zone characteristics

over time or at other locations.

Lin and Medina [19] developed a conjunctive stream–

aquifer model that couples the transient storage equa-

tions with modules for groundwater flow, groundwater

transport, and unsteady streamflow routing. The resul-

tant modeling framework considers the large-scale ex-change of solute between the stream and the underlying

aquifer and the effects of flood waves on groundwater/

surface water interaction. The coupled model was used

to illustrate the potential contamination of the ground-

water system during high flow events, and the subse-

quent release of solutes back into the stream during

recession of a flood wave.Salehin et al. [27] compared solute transport and

hyporheic exchange in vegetated and unvegetated

reaches of an agricultural stream using tracer data and

the advective storage path model. The stream reaches

analyzed were subject to extreme variations in vegeta-

tion and morphology due to seasonal effects and channel

excavation. Variation of solute storage time in non-

excavated reaches was attributable to differences instream flow depth, velocity, and hydraulic conductivity

of the streambed. Excavation altered stream channel

geometry, increasing the storage time and reducing the

effective exchange rate. Reach comparisons were facili-

tated by scaling model exchange parameters.

Schmid [28] developed analytical expressions for the

temporal moments of the transient storage equations,

for the case of an arbitrary upstream boundary condi-tion. Whereas previous expressions for the temporal

moments were developed for the case of an instanta-

neous slug release, the new expressions allow for the

specification of any concentration-versus-time distribu-

tion at the upstream boundary. Given the upstream

boundary values, the temporal moments may be routed

downstream for comparison with field data or as a check

on the accuracy of numerical models.Sheibley et al. [29] modeled nitrogen transforma-

tions in sediment perfusion cores from the Shingobee

River in Minnesota over an annual cycle. Their results

indicate that ammonium concentrations in the river

were controlled by nitrification of ammonium from

groundwater in hyporheic sediments, and that the rate

of this process was strongly temperature dependent.

This study shows that hyporheic zone biogeochemi-cal processes can change in potentially predictable

ways due to seasonal shifts in temperature, as well as

hydrology.

Supriyasilp et al. [31] developed a statistical technique

for the calibration of water quality models. The tech-

nique, known as quantitatively directed exploration

(QDE), uses the variance of model input parameters to

identify the parameters and sampling locations thatproduce the most uncertainty in model results. QDE was

applied to a hypothetical problem using a model that

considers advection, chemical reaction, settling, and

hyporheic exchange. Statistical results were used to de-

termine which parameters result in the largest variance

in predicted concentration; these parameters were

identified as the focus of additional data collection ef-

forts.Thomas et al. [33] developed the regression parti-

tioning method (RPM), a method for estimating the

904 Preface / Advances in Water Resources 26 (2003) 901–905

portion of solute uptake occurring within the transient

storage zone. Under RPM, whole stream uptake is de-

termined from the spatial pattern of plateau tracer

concentrations and main channel uptake is determined

using data from the rising limb of the tracer profile.Storage zone uptake is then determined by difference.

The method was demonstrated using data from two

tracer additions, where 44–48% of the nitrate uptake

occurred within the storage zone.

Acknowledgements

Work on this special issue was initiated after con-

versations with Marc Parlange, former co-editor of

Advances in Water Resources. The lead editor was sup-

ported in part by funding from the US Geological

Survey�s Toxic Substance Hydrology Program. Helpful

reviews of this preface were provided by Marisa Cox

and Jim Tesoriero.

References

[1] Bencala KE, Walters RA. Simulation of solute transport in a

mountain pool-and-riffle stream: a transient storage model. Water

Resour Res 1983;19(3):718–24.

[2] Bencala KE. Interactions of solutes and streambed sediments: 2.

A dynamic analysis of coupled hydrologic and chemical processes

that determine solute transport. Water Resour Res 1984; 20(12):

1804–14.

[3] Bencala KE, McKnight DM, Zellweger GW. Characterization of

transport in an acidic and metal-rich mountain stream based on a

lithium tracer injection and simulations of transient storage.

Water Resour Res 1990;26(5):989–1000.

[4] Chapra SC, Wilcock RJ. Transient storage and gas transfer in

lowland stream. J Environ Eng 2000;126(8):708–12.

[5] D�Angelo DJ, Webster JR, Gregory SV, Meyer JL. Transient

storage in Appalachian and Cascade mountain streams as

related to hydraulic characteristics. J N Am Benthol Soc 1993;

12:223–35.

[6] Duff JH, Murphy F, Fuller CC, Triska FJ, Harvey JW, Jackman

AP. A mini drivepoint sampler for measuring pore-water solute

concentrations in the hyporheic zone of sand-bottom streams.

Limnol Oceanogr 1998;43(6):1378–83.

[7] Edwardson KJ, Bowden WB, Dahm C, Morrice J. The hydraulic

characteristics and geochemistry of hyporheic and parafluvial

zones in Arctic tundra streams, north slope, Alaska. Adv Water

Resour 2003;26(9):907–23.

[8] Fellows CS, Valett HM, Dahm CN. Whole-stream metabolism in

two montane streams: contribution of the hyporheic zone. Limnol

Oceanogr 2001;46(3):523–31.

[9] Fernald AG, Wigington PJ, Landers DH. Transient storage and

hyporheic flow along the Willamette River, Oregon: field

measurements and model estimates. Water Resour Res 2001;

37(6):1681–94.

[10] Fox GA, Durnford DS. Unsaturated hyporheic zone flow in

stream/aquifer conjunctive systems. Adv Water Resour 2003;

26(9):989–1000.

[11] Gooseff MN, Wondzell SM, Haggerty R, Anderson J. Comparing

transient storage modeling and residence time distribution (RTD)

analysis in geomorphically varied reaches in the Lookout

Creek basin, Oregon, USA. Adv Water Resour 2003;26(9):

925–37.

[12] Grimm NB, Fisher SG. Exchange between interstitial and surface

water: implications for stream metabolism and nutrient cycling.

Hydrobiologia 1984;111:219–28.

[13] Harvey JW, Conklin MH, Koelsch RS. Predicting changes in

hydrologic retention in an evolving semi-arid alluvial stream. Adv

Water Resour 2003;26(9):939–50.

[14] Harvey JW, Bencala KE. The effect of streambed topography on

surface–subsurface water exchange in mountain catchments.

Water Resour Res 1993;29(1):89–98.

[15] Harvey JW, Wagner BJ, Bencala KE. Evaluating the reliability of

the stream tracer approach to characterize surface–subsurface

water exchange. Water Resour Res 1996;32(8):2441–51.

[16] Jackman AP, Walters RA, Kennedy VC. Transport and concen-

tration controls for chloride, strontium, potassium and lead in

Uvas Creek, a small cobble-bed stream in Santa Clara County,

California, USA: 2. Mathematical model. J Hydrol 1984;75:

111–41.

[17] Jones JB, Mulholland PJ. Streams and ground waters. Academic

Press; 2000.

[18] Laeanen A, Bencala KE. Transient storage assessment of dye-

tracer injections in rivers of the Willamette Basin, Oregon. J Am

Water Resour Assoc 2001;37(2):367–77.

[19] Lin Y, Medina MA. Incorporating transient storage in conjunc-

tive stream-aquifer modeling. Adv Water Resour 2003;26(9):

1001–19.

[20] McKnight DM, Bencala KE. Reactive iron transport in an acidic

mountain stream in Summit County, Colorado: a hydrologic

perspective. Geochim Cosmochim Acta 1989;53:2225–34.

[21] Morrice JA, Valett HM, Dahm CN, Campana ME. Alluvial

characteristics, groundwater–surface water exchange, and hydro-

logic retention in headwater streams. Hydrol Process 1997;11:253–

67.

[22] Mulholland PJ, Marzolf ER, Webster JR, Hart DR, Hendricks

SP. Evidence that hyporheic zones increase heterotrophic metab-

olism and phosphorus uptake in forest streams. Limnol Oceanogr

1997;42(3):443–51.

[23] Newbold JD, Elwood JW, O�Neill RV, Vanwinkle W. Phosphorus

dynamics in a woodland stream ecosystem: a study of nutrient

spiralling. Ecology 1983;64:1249–65.

[24] Runkel RL, Bencala KE. Transport of reacting solutes in rivers

and streams. In: Singh VP, editor. Environmental hydrology.

Kluwer Academic Press; 1995. p. 37–64.

[25] Runkel RL. One-dimensional transport with inflow and storage

(OTIS): a solute transport model for streams and rivers. US

Geological Survey Water-Resources Investigation Report 98-

4018, 1998. Available: http://co.water.usgs.gov/otis.

[26] Runkel RL, McKnight DM, Andrews ED. Analysis of transient

storage subject to unsteady flow: diel flow variation in an

Antarctic stream. J N Am Benthol Soc 1998;17(2):143–54.

[27] Salehin M, Packman AI, Worman A. Comparison of transient

storage in vegetated and unvegetated reaches of a small agricul-

tural stream in Sweden: seasonal variation and anthropogenic

manipulation. Adv Water Resour 2003;26(9):951–64.

[28] Schmid BH. Temporal moments routing in streams and rivers

with transient storage. Adv Water Resour 2003;26(9):1021–7.

[29] Sheibley RW, Jackman AP, Duff JH, Triska FJ. Numerical

modeling of coupled nitrification–denitrification in sediment

perfusion cores from the hyporheic zone of the Shingobee River,

MN. Adv Water Resour 2003;26(9):977–87.

[30] Stream Solute Workshop Concepts and methods for assessing

solute dynamics in stream ecosystems. J N Am Benthol Soc

1990;9(2):95–119.

Preface / Advances in Water Resources 26 (2003) 901–905 905

[31] Supriyasilp T, Graettinger AJ, Durrans SR. Quantitatively

directed sampling for main channel and hyporheic zone water-

quality modeling. Adv Water Resour 2003;26(9):1029–37.

[32] Thackston EL, Schnelle KB. Predicting effects of dead zones on

stream mixing. J Sanit Eng Div Am Soc Civ Eng 1970;96(SA2):

319–31.

[33] Thomas SA, Valett HM, Webster JR, Mulholland PJ. A regres-

sion approach to estimating reactive solute uptake in advective

and transient storage zones of stream ecosystems. Adv Water

Resour 2003;26(9):965–76.

[34] Triska FJ, Kennedy VC, Avanzino RJ, Zellweger GW, Bencala

KE. Retention and transport of nutrients in a third-order stream

in Northwestern California: Hyporheic processes. Ecology

1989;70(6):1893–905.

[35] Valett HM, Morrice JA, Dahm CN, Campana ME. Parent

lithology, surface–groundwater exchange and nitrate retention in

headwater streams. Limnol Oceanogr 1996;41(2):333–45.

Robert L. Runkel

United States Geological Survey

Denver, CO, USA

Tel.: +1-303-236-4882; fax: +1-303-236-4912

E-mail address: runkel@usgs.gov

Diane M. McKnight

Institute of Arctic and Alpine Research

University of Colorado

Boulder, CO, USA

Harihar Rajaram

Department of Civil, Environmental, and

Architectural Engineering

University of Colorado, Boulder, CO, USA