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Stream Ecosystems in a Changing Environment
Stream Ecosystems in a Changing Environment
Stream Ecosystems in a Changing Environment
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Stream Ecosystems in a Changing Environment

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Stream Ecosystems in a Changing Environment synthesizes the current understanding of stream ecosystem ecology, emphasizing nutrient cycling and carbon dynamics, and providing a forward-looking perspective regarding the response of stream ecosystems to environmental change. Each chapter includes a section focusing on anticipated and ongoing dynamics in stream ecosystems in a changing environment, along with hypotheses regarding controls on stream ecosystem functioning. The book, with its innovative sections, provides a bridge between papers published in peer-reviewed scientific journals and the findings of researchers in new areas of study.

  • Presents a forward-looking perspective regarding the response of stream ecosystems to environmental change
  • Provides a synthesis of the latest findings on stream ecosystems ecology in one concise volume
  • Includes thought exercises and discussion activities throughout, providing valuable tools for learning
  • Offers conceptual models and hypotheses to stimulate conversation and advance research
LanguageEnglish
Release dateJul 7, 2016
ISBN9780124059191
Stream Ecosystems in a Changing Environment

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    Stream Ecosystems in a Changing Environment - Jeremy B. Jones

    Stream Ecosystems in a Changing Environment

    First Edition

    Jeremy B. Jones

    Emily H. Stanley

    Table of Contents

    Cover image

    Title page

    Copyright

    Dedication

    Contributors

    Acknowledgments

    Chapter 1: Hydrologic Exchange Flows and Their Ecological Consequences in River Corridors

    Abstract

    Introduction

    Origins of a Hydroecological Perspective in River Corridors

    Delineating Hydrologic Exchange Flows (HEFs)

    Ecological Relevance of HEFs

    Fluvial, Geomorphic, and Biological Influences on HEFs

    Physical Drivers of HEFs

    Temporally Dynamic HEFs

    Understanding Controls and Predicting Consequences Across Scales

    Overview of Modeling Approaches

    Modeling Transport in River Corridors: From Spiraling to Transient Storage

    Modeling Reactive Chemical Transport in Streams with Storage Zones

    Interpretation of HEF Parameters

    Incorporating the Multiple Scales of Exchange Flows in River Network Models

    Modeling Cumulative Effects of HEFs in River Networks

    Synthesis: From Challenges Emerge Opportunities

    Conclusions

    Topics to Stimulate Discussion

    Chapter 2: Shaping the Physical Template: Biological, Hydrological, and Geomorphic Connections in Stream Channels

    Abstract

    Introduction

    Range of Variability in Alluvial Channels

    Disturbance-Recovery Regimes

    Bio-Hydro-Geomorphic Templates for Stream Ecosystems

    Geomorphic Considerations for Environmental Flows

    Looking Forward and Downstream

    Discussion Questions

    Chapter 3: Stream Microbial Ecology in a Changing Environment

    Abstract

    Introduction

    Conclusions

    Future Directions

    Discussion Questions

    Chapter 4: Metabolism of Streams and Rivers: Estimation, Controls, and Application

    Abstract

    Introduction

    Approaches to Measuring Reach-Scale Metabolism

    Balance and Coupling of GPP and ER in Streams

    Primary Controls on Metabolism

    Metabolic Control of Element Cycling in Streams

    From Human Effects on Metabolism to Application

    Looking Ahead

    Discussion Questions

    Chapter 5: Nutrient Spiraling and Transport in Streams: The Importance of In-Stream Biological Processes to Nutrient Dynamics in Streams

    Abstract

    Introduction

    STOICMOD—A Stream Model Based on Spiraling and Ecological Stoichiometry

    Simulations

    Conclusions

    Discussion Questions

    Chapter 6: Dissolved Organic Matter in Stream Ecosystems: Forms, Functions, and Fluxes of Watershed Tea

    Abstract

    Acknowledgments

    Introduction

    DOM Sources

    Molecular Characterization of DOM

    DOM Transformations and Fates

    DOM Contributions to Ecosystem Metabolism

    DOM in the Anthropocene

    Future Research Challenges

    Discussion Topics

    Chapter 7: Stream-Lake Interaction: Understanding Coupled Hydro-Ecological Systems

    Abstract

    Introduction

    Conceptual Frameworks in Stream and Lake Ecology

    The Physical Template of Coupled Stream-Lake Systems

    Implications of Stream-Lake Interactions for Nutrient Spiraling

    Effects of Stream-Lake Interaction on Benthic Invertebrates and Fishes

    Stream-Lake Interactions in a Changing Environment and Future Directions

    Discussion Questions

    Chapter 8: From Headwaters to Rivers to River Networks: Scaling in Stream Ecology

    Abstract

    Acknowledgments

    Introduction

    Mathematical Framework

    Scaling Physical Characteristics

    Scaling Chemical Characteristics: The Terrestrial-Aquatic Linkage

    Scaling Biological Characteristics

    Scaling Heterogeneity and Connectivity

    Impacts of a Changing Environment

    Forward Looking

    Discussion Topics

    Chapter 9: Landscape and Regional Stream Ecology

    Abstract

    Introduction

    Historic Context

    Streams as Landscapes

    Streams in Landscapes

    Streams Across Landscapes

    Conclusion

    Discussion Topics

    Chapter 10: Global Models of River Biogeochemical Functioning

    Abstract

    Introduction

    Challenges in Examining Current and Future Material Fate and Transport Across Regions and Continents

    Modeling Approaches and Limitations to Quantifying River Processing and Export Across Regions

    Future Generation of Models

    Thought Activities and Discussion

    Chapter 11: Human Impacts on Stream Hydrology and Water Quality

    Abstract

    Introduction

    Human Impacts on Stream Environments

    Unifying Themes Across Intensively Managed Landscapes

    Rivers and Their Catchments: A Coupled Natural and Human System

    Conclusion

    Discussion Topics

    Chapter 12: Human-Dominated Rivers and River Management in the Anthropocene

    Abstract

    Introduction

    Towards Sustainable River Management

    Looking Forward: Challenges for Sustainable River Management

    Conclusion

    Discussion Questions

    Chapter 13: Synthesis and Conclusions

    Abstract

    Introduction

    Hydrology and Geomorphology

    Biogeochemistry

    Streams as Components of the Landscape

    Index

    Copyright

    Academic Press is an imprint of Elsevier

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    Notices

    Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary.

    Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.

    To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein.

    Library of Congress Cataloging-in-Publication Data

    A catalog record for this book is available from the Library of Congress

    British Library Cataloguing-in-Publication Data

    A catalogue record for this book is available from the British Library

    ISBN 978-0-12-405890-3

    For information on all Academic Press publications visit our website at https://www.store.elsevier.com/

    Dedication

    In memory of Pat Mulholland for his inspiration, mentoring, and friendship.

    Contributors

    C.D. Arp     University of Alaska Fairbanks, Fairbanks, AK, United States

    M.A. Baker     Utah State University, Logan, UT, United States

    N.B. Basu     University of Waterloo, Waterloo, ON, Canada

    R.M. Cory     University of Michigan, Ann Arbor, MI, United States

    M.W. Doyle     Duke University, Durham, NC, United States

    Z. Easton     Biological Systems Engineering, Blacksburg, Virginia

    S. Ensign     Aquatic Analysis and Consulting LLC, Morehead City, NC, United States

    S. Findlay     Cary Institute of Ecosystem Studies, Millbrook, NY, United States

    K.J. Goodman     NEON Inc., Boulder, CO, United States

    Robert O. Hall, Jr.     Department of Zoology and Physiology, University of Wyoming, Laramie, WY, United States

    J.W. Harvey     U.S. Geological Survey, Reston, VA, United States

    J.B. Heffernan     Duke University, Durham, NC, United States

    E.T. Hester     Virginia Tech, Blacksburg, VA, United States

    J.B. Jones     University of Alaska Fairbanks, Fairbanks, AK, United States

    J.P. Julian     Texas State University, San Marcos, TX, United States

    L.A. Kaplan     Stroud Water Research Center, Avondale, PA, United States

    L. Lin     Virginia Polytechnic Institute and State University, Blacksburg, VA, United States

    R.B. Manners     University of Montana, Missoula, MT, United States

    A.M. Marcarelli     Michigan Technological University, Houghton, MI, United States

    K.M. Meitzen     Texas State University, San Marcos, TX, United States

    K. Van Meter     University of Waterloo, Waterloo, ON, Canada

    J.D. Newbold     Stroud Water Research Center, Avondale, PA, United States

    C.J.P. Podolak     Duke University, Durham, NC, United States

    M. Rogers     Biological Systems Engineering, Blacksburg, Virginia

    T.V. Royer     Indiana University, Bloomington, IN, United States

    D. Scott     Biological Systems Engineering, Blacksburg, Virginia

    R.A. Sponseller     Umeå University, Umeå, Sweden

    E.H. Stanley     University of Wisconsin, Madison, WI, United States

    S.E. Thompson     University of California, Berkeley, CA, United States

    J.R. Webster     Virginia Polytechnic Institute and State University, Blacksburg, VA, United States

    N.A. Wilgruber     Oklahoma University, Norman, OK, United States

    W.M. Wollheim     University of New Hampshire, Durham, NH, United States

    W.A. Wurtsbaugh     Utah State University, Logan, UT, United States

    Acknowledgments

    First and foremost, we would like to thank all of the authors who contributed to this book. The interest and engagement among the authors was contagious, and made working on the project intellectually rewarding. We also wish to give thanks to the staff at Elsevier, Inc., especially Candice Janco for working with us to develop the book, and Rowena Prasad for ushering us through the process. Support from our home institutions, the University of Alaska Fairbanks and the University of Wisconsin, is gratefully acknowledged. Finally, JBJ wishes to thank Diane and Amelia for their support.

    Chapter 1

    Hydrologic Exchange Flows and Their Ecological Consequences in River Corridors

    J.W. Harvey    U.S. Geological Survey, Reston, VA, United States

    Abstract

    The actively flowing waters of streams and rivers remain in close contact with surrounding off-channel and subsurface environments. These hydrologic linkages between relatively fast flowing channel waters, with more slowly flowing waters off-channel and in the subsurface, are collectively referred to as hydrologic exchange flows (HEFs). HEFs include surface exchange with a channel’s marginal areas and subsurface flow through the streambed (hyporheic flow), as well as storm-driven bank storage and overbank flows onto floodplains. HEFs are important, not only for storing water and attenuating flood peaks, but also for their role in influencing water conservation, water quality improvement, and related outcomes for ecological values and services of aquatic ecosystems. Biogeochemical opportunities for chemical transformations are increased by HEFs as a result of the prolonged contact between flowing waters and geochemically and microbially active surfaces of sediments and vegetation. Chemical processing is intensified and water quality is often improved by removal of excess nutrients, metals, and organic contaminants from flowing waters. HEFs also are important regulators of organic matter decomposition, nutrient recycling, and stream metabolism that helps establish a balanced and resilient aquatic food web. The shallow and protected storage zones associated with HEFs support nursery and feeding areas for aquatic organisms that sustain aquatic biological diversity. Understanding of these varied roles for HEFs has been driven by the related disciplines of stream ecology, fluvial geomorphology, surface-water hydraulics, and groundwater hydrology. A current research emphasis is on the role that HEFs play in altered flow regimes, including restoration to achieve diverse goals, such as expanding aquatic habitats and managing dissolved and suspended river loads to reduce over-fertilization of coastal waters and offset wetland loss. New integrative concepts and models are emerging (eg, hydrologic connectivity) that emphasize HEF functions in river corridors over a wide range of spatial and temporal scales.

    Keywords:

    Hydrologic exchange flows (HEFs); Hyporheic zone; Transient storage model (TSM); River Corridor; Floodplain; Groundwater-surface water Interactions

    Contents

    Introduction

    Origins of a Hydroecological Perspective in River Corridors

    Delineating Hydrologic Exchange Flows (HEFs)

    Ecological Relevance of HEFs

    Fluvial, Geomorphic, and Biological Influences on HEFs

    Physical Drivers of HEFs

    Hyporheic Exchange Flows

    Hydrologic Exchange with Off-Channel Surface Waters

    Bioroughness, Burrowing, and Bio-irrigation

    Temporally Dynamic HEFs

    Flood and ET-Driven Vertical Exchange with Streambed

    Bank Storage Exchange Flows

    River-Floodplain Exchanges

    Watershed Influences

    Understanding Controls and Predicting Consequences Across Scales

    Overview of Modeling Approaches

    Modeling Transport in River Corridors: From Spiraling to Transient Storage

    Water Mass Balance

    Combined Water and Chemical Mass Balance

    Reactive Chemical Transport

    The Spiraling Model

    Modeling Reactive Chemical Transport in Streams with Storage Zones

    Dynamic Reactive Transport Simulated by the Transient Storage Model

    Interpretation of HEF Parameters

    Prediction of HEFs Through Statistical Analysis of Published Data Sets

    Prediction of HEFs Using Physically Based Scaling Equations

    Hydrogeologic Modeling of HEFs

    Modeling Dynamic Exchanges with River Banks and Floodplains

    Incorporating the Multiple Scales of Exchange Flows in River Network Models

    Modeling Cumulative Effects of HEFs in River Networks

    Synthesis: From Challenges Emerge Opportunities

    Conclusions

    Topics to Stimulate Discussion

    References

    Introduction

    Rivers are not pipes that passively drain the landscape. Instead, the downstream movement of waters through the channel is punctuated by lateral and vertical exchanges with slowly moving surface waters located in pools, marginal areas of the channel, or in off-channel riparian areas, floodplains, in waters temporarily routed through subsurface flow paths beneath channels, or beneath banks and floodplains (Junk et al., 1989; National Research Council, 2002; Ward, 1989; Winter et al., 1998). Hydrologic exchange flows (HEFs) are broadly defined to include these and all other types of vertical and lateral exchange flows that bring relatively fast moving waters of the channel’s thalweg into prolonged contact with geochemically and biologically reactive surfaces on sediment grains, leaf packs, epiphytic coatings on vegetation, and downed wood in channels, riparian areas, and floodplains.

    Interactions between hydrology and ecology are integral to a functioning river corridor – a zone considerably larger than the main channel that includes flow routed temporarily through the subsurface as well adjacent shallow aquatic areas and intermittently flooded habitats (Harvey and Gooseff, 2015) (Fig. 1). Riparian trees modulate water temperatures (Beschta, 1997) and the fall of leaves and insects enrich the channel (Mulholland et al., 1997), and downed riparian wood adds structure and organic matter that supports specialized foraging and nursery habitats that sustain a diverse and resilient food web (Baxter and Hauer, 2000; Geist, and Dauble, 1998; Junk et al., 1989). Surface and subsurface hydrologic exchanges increase microbial and geochemical opportunities for reactive transformations of organic carbon, nutrients, and other energy-rich substrates in flowing waters that support healthy levels of stream metabolism and other functional values, such as water quality improvement (Hotchkiss et al., 2015; Battin et al., 2008; Bernhardt et al., 2005).

    Fig. 1 River corridors include fast flowing channel waters and more slowly flowing waters at channel sides, in addition to marginal waters in side cavities and off-channel ponds in riparian areas and on floodplains. Hydrologic exchanges through surface pathways interact with subsurface waters moving vertically and longitudinally beneath the channel and horizontally through the bank and beneath the floodplain. Surface and subsurface hydrologic exchange increase microbial and geochemical opportunities for reactive transformations of organic carbon, nutrients, and other energy-rich substrates that support healthy levels of aquatic metabolism and other functional, recreational, and economic values. (From Harvey, J., Gooseff, M., 2015. River corridor science: hydrologic exchange and ecological consequences from bedforms to basins. Water Resour. Res. 58, 6893–6922. http://dx.doi.org/10.1002/2015WR017617 as modified from National Research Council, 2002. Riparian Areas: Functions and Strategies for Management. Washington, DC: National Academy Press).

    HEFs increase contact between flowing water and the biologically and geochemically reactive zones at interfaces and in the subsurface (Bencala, 1993; Stanford and Gonser, 1998; Stanford and Ward, 1993). The key characteristics are chemical compositions and mixing between waters from different sources (eg, river, groundwater, hillslope drainage, direct precipitation, etc.). Also important are water residence times within the marginal surface and subsurface waters and geochemical and biologically reactive surface coatings on sediment in those marginal storage areas. These interactions often increase the rate of transformation of carbon and nutrients and also may perform valued functions such as facilitating precipitation or sorption of trace metals from flowing waters or transforming harmful organic compounds to less mobile forms. The biogeochemical opportunities are generally increased by longer residence times in HEF reaction zones (Battin et al., 2008), although the cumulative effects on river chemistry depend on additional factors such as water exchange rates with HEFs (Findlay, 1995; Harvey and Fuller, 1998), which determine the rate of replenishment to reaction sites, and are also affected by ancillary sedimentary, chemical, and microbiological conditions at the sites of reactions (Hall et al., 2013). The resulting enhancement of chemical reactions influence water chemistry and affect carbon and nutrient cycling in ways that structure aquatic food web and improve water quality and the functional and economic values of downstream waters (Fleckenstein et al., 2004).

    This chapter reviews the concepts, measurement techniques, and integrative mathematical models underlying HEFs and their role in river corridors. Understanding of the physical processes driving HEFs has advanced enormously. Reliable tools for predicting HEFs now exist for specific channel conditions based on relatively simple and easily acquired data. Assessing the cumulative influences of HEFs in large basins over longer timescales is becoming an active area of research. Understanding the effects of HEFs on reactive transformation of dissolved and fine particulates and its influence on downstream chemistry has been elusive, and forecasting how transport and storage of fine sediments will respond to changing future conditions is an even more elusive goal. Meanwhile, assessing and prioritizing the benefits of various types of corrective management practices, such as stream restoration, is a growing priority as the world responds to changing land use, a changing climate, and other natural and human-induced disturbances. The greatest challenge may be at the intersection between physical and biological processes. Complex interactions between physics and biology often produce unanticipated feedbacks that amplify certain effects and that may produce hysteretic (eg, path-dependent) responses of ecosystems to fluvial or geomorphic alterations. All of these topic areas are reviewed with a mindset toward predicting how river corridors will respond to natural and human induced stressors.

    Origins of a Hydroecological Perspective in River Corridors

    Concepts for HEFs originated from the disciplines of stream ecology, civil engineering, and hydrogeology. Hydrologists concentrated on problems such as defining sources of streamflow and controls on timing and volume of outflows from drainage basins using traditional tools, such as stream discharge gaging and chemical sampling of streamflow (Loague, 2010). Classical approaches to studying weathering reactions and acid rain neutralization in watersheds generally treated the stream as a pipe, which drained the catchment without further interactions with the landscape (Fig. 2). At the same time, aquatic ecologists had developed theories of river function, such as the river continuum concept (Vannote et al., 1980) and the flood pulse hypothesis (Junk et al., 1989), which drew inspiration from fluvial geomorphology.

    Fig. 2 The river corridor perspective illustrates a growing understanding that rivers remain in close contact with their surrounding riparian areas, floodplains, and subsurface waters rather than just passively draining the landscape. Traditional watershed and groundwater basin perspectives generally emphasized streams as drains on the landscape and did not recognize the role of river corridors as modifiers of water chemistry and aquatic ecosystem functionality (part A). Early instrumentation such as auto samplers in surface water and groundwater monitoring wells adequately characterized bulk timing and quantity of watershed and basin outflows but were not adequate to delineate zones of enhanced biogeochemical reaction at the interface (part B). (Part A From Harvey, J., Gooseff, M., 2015. River corridor science: hydrologic exchange and ecological consequences from bedforms to basins. Water Resour. Res. 58, 6893–6922. http://dx.doi.org/10.1002/2015WR017617 and part B uses a USGS photo courtesy of Idaho http://toxics.usgs.gov/photo_gallery/metals_variation_all.html and a USGS image of a piezometer courtesy of Skinner, K.D., 2005. Estimating Streambed Seepage Using Heat as a Tracer on the Lower Boise River, Canyon County, U.S. Geological Survey, Scientific Investigations Report 2005–5215).

    Integrative concepts that linked aquatic and terrestrial processes were proposed by stream ecologists, including effects of flow dynamics and prolonged hydrologic residence times of flood waters on carbon processing and food webs (eg, Doyle et al., 2005; Junk et al., 1989; Minshall et al., 1985; Poff et al., 1997; Stream Solute Workshop, 1990). Further connections were made between ecosystems of surface waters with ecosystems below the streambed that possessed distinctive biology and chemistry (ie, hyporheic zone) (see reviews by Boano et al., 2014; Cardenas, 2015; Fleckenstein et al., 2010; Jones and Mulholland, 2000; Larned et al., 2015; Runkel et al., 2003).

    Meanwhile, stream hydrologists were developing river tracer methods (Bencala and Walters, 1983) by adapting quantitative models from civil and chemical engineering (Fischer et al., 1979; Streeter and Phelps, 1925). From those efforts were observations of HEFs with off-channel and subsurface dead zones, which were not easily explained by classical river mixing theory (Thackston and Schnelle, 1970; Valentine and Wood, 1979). Concurrently, groundwater hydrologists became interested in groundwater-surface water interactions and identified processes such as bank storage (Pinder and Sauer, 1971), evapotranspiration (ET) driven depletion of stream flow (Banks, 1973), flood wave attenuation by overbank flow resistance (Knighton, 1998), and the importance of groundwater recharge in ephemeral channels (Moench et al., 1974).

    A key early step in the study of river corridors as a quantitative science was sparked by interactions between stream ecologists and hydrologists that permitted the measurement of whole stream rates of nutrient cycling and contaminant removal in streams (eg, Bencala, 1983; Kennedy et al., 1984; Kimball et al., 1994; Newbold et al., 1981, 1982). From those early efforts emerged the nutrient spiraling and transient hydrologic storage concepts (Stream Solute Workshop, 1990), which have spawned decades of research and produced a broad understanding of material flow and spiraling between physical, chemical, and biological compartments.

    A broader perspective of river corridors is emerging with the concept of hydrologic connectivity playing a central role. Hydrologic connectivity integrates longitudinal transport in rivers with vertical and lateral exchanges with floodplains and subsurface waters (Stanford and Ward, 1988, 1993), inputs from watersheds (Jencso et al., 2010), and exchanges with slowly moving marginal aquatic ecosystems (Larsen et al., 2012). Desirable levels of connectivity are thought to be associated with rivers that are well-connected longitudinally, while also being well-connected vertically and laterally, with marginal waters where carbon and nutrients are efficiently transformed, and where aquatic organisms feed, are reared, or take refuge during floods (Harvey and Gooseff, 2015). The concept of connectivity is playing an increasingly important role by influencing the development of scientifically based policies for protecting the valuable functions of river corridors (eg, Alexander et al., 2007; Nadeau and Rains, 2007).

    Delineating Hydrologic Exchange Flows (HEFs)

    River flow is predominantly oriented with a channel’s main axis, however, gradients in the energy of flow that are oriented normal to the primary stream wise direction can cause river water to be exchanged with more slowly moving waters located outside of the main flow (Fig. 1). HEFs are activated by gradients in water’s energy distribution as it flows over complex topographic features of the river bed, causing exchange between the main channel and waters located vertically in the bottom of pools or within the streambed, and lateral exchange with recirculating waters behind boulders, logs, and in marginal side cavities at channel sides, or subsurface waters within marginal sand and gravel bars, and within alluvial sediments beneath the banks. HEFs also include main channel water flowing through minor side channels or flooding onto sloughs, wetlands, riparian areas, or even higher floodplain surfaces.

    The key defining characteristic of HEFs is a bidirectional exchange flow that begins and returns to the river. HEFs are therefore distinct from watershed and groundwater flows which begin as recharge on the uplands and discharge only once across the surface-subsurface interface. This basic definition of HEFs is intentionally broad to emphasize commonalties; however, there may be good reasons to distinguish specific types of HEFS (eg, surface and subsurface), or to distinguish specific timescales of exchange across the broad continuum of HEFs that may occur. HEFs are not usually studied for the effect that they have on water supply, but rather for their effects on chemical reactions and aquatic organisms.

    Ecological Relevance of HEFs

    HEFs extend opportunities for material processing in watersheds. Surface water from the relatively fast-moving main channel typically has high oxygen concentration, high exposure to light, and has experienced variable temperatures when it enters an HEF. There, surface water mixes with waters with contrasting chemistries resulting from low exposure to light and atmospheric gases, but high exposure to microbial biomass and geochemically active surfaces on sediments (Brunke and Gonser, 1997; Dahm et al., 1998; Fischer et al., 2005; Fisher et al., 1998) (Fig. 3). For example, surface waters may mix with groundwaters in hyporheic zones, a type of subsurface HEF where flow is temporarily routed through the subsurface before returning to the main channel (Harvey and Bencala, 1993). The return flows are typically more stable in temperature and poorer in oxygen content compared to surface waters (Briggs et al., 2015; Duff and Triska, 1990; White, 1990). The lag and attenuation of surface water temperature extremes in hyporheic flow produces a return flow of water to the river that is moderated in temperature (Arrigoni et al., 2008). Hyporheic zones also tend to be focal areas for organic matter degradation (Grimm and Fisher, 1984; Mulholland et al., 1997) and thus may return flows that tend to be enriched in organic and inorganic nutrients that may stimulate primary production in the river by algae and aquatic macrophytes (Valett et al., 1994). In addition to a carbon cycling function, HEFs also provide habitat and other types of support for macroinvertebrates and other primary consumers of detrital-based food webs, as well as nurseries for egg rearing, and other types of habitat for higher level consumers that structure and sustain aquatic ecosystems (Baxter and Hauer, 2000; Briggs et al., 2013; Geist and Dauble, 1998; Malcolm et al., 2005).

    Fig. 3 Steep chemical gradients and high rates of biogeochemical reactions typically define the interface between groundwater and surface water. (From Harvey, J., Gooseff, M., 2015. River corridor science: hydrologic exchange and ecological consequences from bedforms to basins. Water Resour. Res. 58, 6893–6922. http://dx.doi.org/10.1002/2015WR017617)

    HEFs are hot spots for many microbially mediated chemical reactions involving organic carbon, nutrients, metals, and organics (Lautz and Fanelli, 2008). The increased time of contact of river water with sediment interfaces and subsurface zones is probably the most important function of HEFs because of the catalyzing influence of reactive mineral and organic coatings on chemical reactions (McClain et al., 2003). The magnitude of HEFs is important because it influences the rate of delivery of important river solutes to reaction sites and the size of the exchange zones is important because it influences the sediment capacity for reactions (Bencala, 1983).

    Mixing between river surface waters and off-channel waters facilitates steep redox gradients and diversity in microbially mediated reactions (Baker et al., 1999; Hedin et al., 1998), with the resulting metabolism involving not only oxidation of organic carbon (Grimm and Fisher, 1984), but also mineralization of nutrients (Valett et al., 1996), denitrification (Harvey et al., 2013; Jones and Holmes, 1996; Pinay et al., 2009; Sheibley et al., 2003; Zarnetske et al., 2011), and other transformations such as microbial precipitation of metal oxides (Fuller and Harvey, 2000; Von Gunten and Lienert, 1993) or bioremediation of organic compounds (Conant et al., 2004; Kim et al., 1995) and emerging contaminants such as wastewater from nonconventional oil and gas extraction (Warner et al., 2013), and pharmaceuticals (Fick et al., 2009). Such enhancement of biogeochemical reactions in HEFs can be substantial enough to modify the chemistry of water flowing from drainage basins (Harvey et al., 2013; Marzadri et al., 2012; Wörman et al., 2002).

    Often the biogeochemical reactions occur on or just beneath the sediment surface in a reactive surface biolayer, which is bathed with light and rich with algal cells, fine particulate organic matter, and microbes (Battin and Sengschmitt, 1999). Because the biolayer is located on top of the surface sediments (biofilm) and within the surface sediments, the algal community and fine particular organic matter can create a seal that blocks hydrologic exchange (eg, Brunke, 1999; Velickovic, 2005). In some streams, the reactive surface biolayer is easily disturbed, even during small spates (Battin, 2000). Thus, the timescales of flood duration and geomorphic adjustment of the river bedforms are important determinants of the reactive capacity of river corridors (Harvey et al., 2012). Consequently, the flooding of off-channel areas vastly expands the wetted surface area during floods, especially when the channel widens and may overflow its banks (Jung et al., 2004; Poole et al., 2006). Biogeochemical reactions are stimulated as a result of the increase in wetted surface area (Ensign et al., 2008), but also as a result of the prolonged time of exposure of surface waters to finer graded sediments with greater surface area, higher microbial concentrations, and more abundant organic matter (Forshay and Stanley, 2005; Richardson et al., 2004).

    Fluvial, Geomorphic, and Biological Influences on HEFs

    HEFs occur in diverse landscapes ranging from steep mountain streams to lowland rivers, lakes, wetlands, and floodplains, all the way to submarine areas of estuaries and coastal shelves. Surface-subsurface exchange occurs essentially everywhere that surface water flows in contact with permeable sediments (Fig. 4). There is commonality in the driving forces for flow and in the forces that resist flow all the way from mountains to the sea. Although this chapter emphasizes river studies, because of remarkably similar processes, the guiding concepts, models, and tools for studying HEFS used in river corridors have parallel applications across the seemingly disparate environments of lakes, estuaries, and coastal marine settings.

    Fig. 4 Hydrologic exchange flows occur worldwide but are most prevalent in humid regions with abundant rivers, lakes, and wetlands. Land areas with greater river density (part A) and shallower water table depth (part B), and more permeable sediments tend to have larger HEFs. In the ocean it is the continental shelves that have most of the permeable sediments (part C) where there also is sufficient wave energy and bottom currents to drive submarine HEFs. (Part A of figure is from HydroSHEDS (hydrosheds.cr.usgs.gov), part B is from Fan, Y., Li, H., Miguez-Macho, G., 2013. Global patterns of groundwater table depth. Science 339(6122), 940–943. http://dx.doi.org/10.1126/science, and data used for part C is from National Ocean Service, 2013. NOAA/NOS and USCGS Seabed Descriptions from Hydrographic Surveys. National Geophysical Data Center, NOAA, http://dx.doi.org/10.7289/V5BG2KWG[9/18/2013] where red areas are mostly sand and blue areas are mostly clay with colors between representing sand/silt/clay mixtures).

    From a global perspective, hydrologic exchange is expected to be greater in humid regions with greater river runoff, higher soil moisture, more variable topography, and relatively shallow groundwater tables (Fan et al., 2013) (Fig. 4). Data sources from satellite remote sensing are increasingly being used for global and continental-scale modeling of water budgets (Alsdorf et al., 2007) and groundwater-surface water interactions (Wörman et al., 2007). The potential for submarine hyporheic fluxes has been estimated on a global scale with greater exchanges expected in estuaries, nearshore coastal marine areas, and on continental shelves where sediments tend to be sandy and where waves and currents impose greater energy on the ocean bed (Huettel et al., 2014).

    Physical Drivers of HEFs

    The fluvial, geomorphic, and hydrogeologic signatures of drainage basins provide a basis to anticipate HEFs. Foremost among the controls is the river corridor’s overall geomorphic template, as influenced by the valley slope and width, and the extent, shape, and average grain size of the channel and surrounding sediments. Next is the size and frequency of channel-forming flows that determine bankfull width, channel sinuosity, and types, sizes, and spacing of bedforms and barforms that determine how water depth and wetted width vary with lower river discharges. The presence of biological features, such as downed wood, adds flow roughness that interacts with sediment features to increase the exchange between the main channel and zones of separation in off-channel areas and in subsurface hyporheic zones. Transpiration by near-stream vegetation alters the direction and amount of near-stream subsurface flow. Riparian and submerged and emergent aquatic vegetation also contribute substantially to flow roughness and may shield sediments from erosion and add strength to riverbeds and banks.

    The principal work in building the geomorphic template occurs during large, channel-forming flows with additional controls imposed by valley slope, which affects stream power, and by the depth and width of hillslope and valley sediments, which affect sediment supply and channel grain size. Together all of these factors shape the channel’s planform, determining bankfull channel width and height, width to depth ratio, sinuosity, and the size and distribution of specific bars and bedforms (Shumm, 1977).

    HEFs are triggered by flow over and around geomorphic features, and the styles and combinations of geomorphic features that control HEFs are a direct response to flow energetics and the sediment supply (Fig. 5). Fluvial processes build bedforms ranging in size from small grain clusters that protrude slightly above the bed, small ripples and dunes, channel spanning features such as riffles, steps, and cascades, all the way up to alternating bars and meanders that typically are of a size on the order of ten times the channel width (Knighton, 1998). Each of these topographic features may cause HEFs, with the key controls being the size (usually the wavelength) of the associated geomorphic feature, the degree of submergence or emergence above the flow, and the permeability of the sediment (Buffington and Tonina, 2009; Tonina and Buffington, 2009).

    Fig. 5 Styles of geomorphic features and associated hydrologic exchange flows vary with river slope (S). (From Buffington, J.M., Tonina, D., 2009. Hyporheic exchange in Mountain Rivers II: effects of channel morphology on mechanics, scales, and rates of exchange. Geogr. Compass 3, 1038–1062. http://dx.doi.org/10.1111/j.1749-8198.2009.00225.x).

    Hyporheic Exchange Flows

    River water often must steer around geomorphic features ranging from individual boulders and logs, channel-spanning features such as cascades, steps, and riffles, and larger features, including alternating channel margin bars and river meanders within alluvial floodplains (Boano et al., 2014; Buffington and Tonina, 2009; Kasahara and Wondzell, 2003). All of these geomorphic features may drive interactions between rivers and groundwater at many different scales (Ward et al., 2014). For example, geomorphic features that span channels, such as cascades, steps, and riffles, block enough of the main channel’s flow to build up the hydraulic head in a pool just upstream of where the channel gradient steepens, thus increasing the force to drive subsurface flow. Gradients in hydraulic head cause surface water to enter hyporheic flow paths, which re-emerge in more gently sloped sections of the stream (Lautz et al., 2006). At larger spatial scales, hyporheic flow short circuits sinuous pathways by flowing beneath point bars and floodplain terraces of meandering rivers (Cardenas, 2008). The water flux through hyporheic flow paths scales positively with sediment permeability and average slope of the stream and scales negatively with the size of the geomorphic feature (Hester and Doyle, 2008; Larkin and Sharp, 1992). The depth or distance that hyporheic flow penetrates into the bed scales roughly with the topographic feature’s length (Stonedahl et al., 2010). Heterogeneity of streambed hydraulic conductivity is also a control, with the effect tending to increase hyporheic fluxes (Salehin et al., 2004; Vaux, 1968). Other important factors include the height of the geomorphic feature and its effect on local slope of the water surface. For example, the hydrostatically driven hyporheic flow is greater beneath larger bedforms that are partly emergent because those features cause the greatest variation in water-surface slope. As a result, channels spanning geomorphic features, such as steps, have a greater influence on hydrostatically driven fluxes compared with only partially spanning features such as individual boulders, because of the greater local slope in the water surface that is created. Groundwater discharge is also an important control on hyporheic fluxes because the hydraulic forces that drive groundwater discharge are opposing the forces driving hyporheic flow.

    The hydrodynamic forces that drive hyporheic flow, in contrast with the hydrostatic forces, do not depend on flow blockage as much as they depend on the energy of flowing stream water and the shear forces imparted on the bed. Hydrodynamically driven hyporheic flow is greatest over small, submerged geomorphic features that are typically less than a third of the stream’s depth. Rather than blocking and pooling the flow, such conditions accentuate kinetic forces through Bernoulli-type flow effects that impart variable flow velocities and pressures across the bedform surfaces that accentuate the velocity head gradients in the sediment compared with hydrostatic head gradients. Hydrodynamically driven hyporheic flow typically enters the river bed on the upstream face of a small sand dune or ripple where the total hydraulic head is accentuated by the increase in velocity head. Unlike hydrostatically driven flow, the hydrodynamic component can direct hyporheic flow, both in downstream and upstream directions, with subsurface flow re-emerging where total hydraulic head on the bed is lowest in the zone of recirculation located near the peak of the bedform, and just downstream where surface water flow has separated from the main flow (Savant et al., 1987; Thibodeaux and Boyle, 1987). Hydrodynamically driven hyporheic flow scales positively with bed shear stress, height of the roughness feature, and sediment permeability (O’Connor and Harvey, 2008) with the depth of exchange in sediment typically scaling with of the wavelength of the roughness features (typically eighty percent) (Cardenas and Wilson, 2007; Elliott and Brooks, 1997a). The residence time scales positively with length of the roughness feature and negatively with streambed permeability (Elliott and Brooks, 1997a).

    Wood debris on the streambed is another commonly studied roughness feature affecting both hydrostatically and hydrodynamically driven hyporheic flow (Lautz et al., 2006; Endreny et al., 2011a,b). The relative importance of the different components of driving force (ie, contributions from potential and kinetic energy gradients) is determined by the extent to which the topographic feature or log spans the channel and the extent of submergence. Downed trees in small streams tend to fill with leaf packs and often create scour holes and have sufficient blockage ratio to create enough scouring to form small pools. For channel sections with submerged channel-spanning logs, the flow through the underlying sediments beneath the logs exhibits positive scaling with Froude number and wood blockage ratio (ie, the fraction of the channel flow depth blocked by log; Sawyer et al., 2011). The hyporheic flow beneath wood debris tends to be deeper and residence times longer, compared with hyporheic flow beneath streambed ripples (Sawyer et al., 2011), although the resulting hyporheic fluxes may be on the same order of magnitude. Interestingly, the gap ratio (ie, the height of the open area beneath the debris relative to total stream depth) was not found to be an important factor. However, the sediment scour that typically occurs around submerged wood significantly influences the resulting hyporheic flow due to the adjustment of the bed surface topography (Sawyer et al., 2011). With more complex flow situations, such as steps that create hydraulic jumps, even greater complexities in velocity-head driven hyporheic flow are apparent (Endreny et al., 2011a,b). The multiple types of hyporheic flow span orders of magnitude in spatial and temporal scales (Fig. 6).

    Fig. 6 Multiple scales of hyporheic exchange flows driven by small submerged bedforms, barforms, and meanders. (Modified from Stonedahl, S.H., Harvey, J.W., Wörman, A., Salehin, M., Packman, A.I., 2010. A multiscale model for integrating hyporheic exchange from ripples to meanders. Water Resour. Res. 46, W12539. http://dx.doi.org/10.1029/2009WR008865).

    Hydrologic Exchange with Off-Channel Surface Waters

    HEFs connect main channel waters with more quiescent areas at channel sides or recirculating areas behind roughness features in the main channel (Fernald et al., 2001; Jackson et al., 2013a). Types of surface water storage zones include lateral cavities at channel sides, isolated protruding flow obstructions, partially or fully channel-spanning flow obstructions such as steps, cascades, and riffles, aquatic vegetation zones, pools within the main flow, and meander bed mixing layers. The hydraulic exchange between the main channel and surface water storage zones usually involves coherent turbulent motions of river water that that are generally classified either as (1) concentrated jets, (2) small wakes behind individual roughness features, or (3) mixing layers that form at the boundary of separation between main channel and off-channel flows. Inside the storage zone, the flow moves much more slowly as a result of reduced energy and greater flow resistance. Often a gyre-like recirculation pattern forms, which is separated from the main channel. The size of topographic features causing the flow separation, the relative degree of submergence of those features, and their width relative to the full channel width are important features that control HEF fluxes, storage-zone size, and residence time of channel water in storage.

    The size of the surface water storage zones is closely associated with the size of the associated irregularities in channel topography that create a reservoir for more slowly moving surface water. The exchange fluxes into and out of storage zones scale positively with main channel velocity, which tends to increase the turbulence that drives mass exchange across the shear zone. Exchange flux also varies with various shape factors that emphasize how large the interfacial area is relative to the volume of storage. Exchange flux also varies inversely with roughness conditions in the main channel near the boundary that generates frictional forces that retard exchange.

    Water residence time in storage, on the other hand, scales positively with the size of the surface water storage zone with a secondary influence of the ratio between width (normal to flow) and length (parallel to flow), which, above a threshold, creates additional and more slowly circulating gyres at the back of the storage zone, increasing overall residence time (Jackson et al., 2013b). Also, the ratio of average cavity depth to the depth at the cavity opening scales positively with residence time because of the larger fluid volume that must be exchanged through a smaller opening.

    Bioroughness, Burrowing, and Bio-irrigation

    HEFs also may be enhanced by the physical structure and the activity of organisms and plants. Aquatic and emergent macrophytes in channel also increase drag, which typically slows flow and causes deepening and/or widening of channels (Harvey et al., 2003; White, 1990). Macroinvertebrates at the sediment interface may increase shear stress and vertical mixing as a result of bioroughness (Koseff et al., 1993), which enhances hyporheic flow by increasing the topographic variability of the streambed (Huettel et al., 2014). Fish may rework sediments both to bury eggs and to optimize hyporheic exchange flows that bathe eggs with oxygenated waters (Tonina and Buffington, 2007), and burrowing organisms may affect water exchange across the sediment interface as a result of the building or irrigation of tube shelters by macroinvertebrates (O’Riordan et al., 1996). Microbial activity builds biomass on sediment surfaces and may cause buildup of gaseous products of metabolism that reduce the volume fraction of water and decreasing hydraulic conductivity (Battin and Sengschmitt, 1999; Cuthbert et al., 2010), which may limit hyporheic flow and its associated delivery of oxygen, labile organic carbon, and other important substrates that are important for hyporheic-zone reactions. Also, riparian and channel vegetation directly affect streamflow (Griffin et al., 2005; Harvey et al., 2009; Hopkinson and Wynn, 2009) and surface-subsurface water exchange by evapotranspiration-driven pumping (Wondzell et al., 2010). Flow in small streams often varies by 20% or more diurnally, with the subsurface drawdown in the near-stream groundwater system by riparian evapotranspiration causing hyporheic flow to expand during the day and contract at night (Harvey et al., 1991).

    Temporally Dynamic HEFs

    There has been a recent trend toward merging concepts to combine HEFs that occur during low-flow with HEFs that only occur during floods. For example, hyporheic flow occurs all the time, whereas bank storage only occurs when changing channel stage reverses the direction of hydraulic gradients, first into, and then back out of banks. A unified assessment of these processes makes sense given that they all respond to the same fundamental gradients in hydraulic driving forces and flow resistances. Vertical hyporheic exchange with the streambed often is greatest during low flow when streambed topographic features have their maximum effect in producing a variable water-surface slope that accentuates hydrostatically driven head gradients. The stream’s submergence of topographic features during high flow can subdue vertical hyporheic exchange with the streambed, but may accentuate other types of hyporheic flow. Studies by Käser et al. (2009), Francis et al. (2010), Gerecht et al. (2011), Shope et al. (2012), Gariglio et al. (2013), Nowinski et al. (2011), Mwakanyamale et al. (2012) and Zimmer and Lautz (2014) detailed changes in hyporheic flow through gravel bars, pointbars and banks as the flow paths evolved during floods. Another example is the effect of cyclic hydropower dam releases in creating bidirectional circulation patterns in the streambed that were larger than the hyporheic flow that would have occurred without the dam releases (Gerecht et al., 2011; Rosenberry et al., 2013; Sawyer et al., 2009).

    Flood and ET-Driven Vertical Exchange with Streambed

    Vertical exchange of water with the streambed also is affected by relatively minor changes in stream velocity. This is because the velocity-head driven force scales with the square of velocity (Elliott and Brooks, 1997b). Boano et al. (2007, 2010a) modeled the effect of stream velocity variation during floods on hyporheic flow. However, more than just the change in flow velocity is important, because floods cause storm-induced geomorphic adjustments in bedforms that affect hyporheic flow. Lautz (2012) and Bhaskar et al. (2012) built upon methods pioneered by Hatch et al. (2006) and others to quantify temporal patterns of vertical flux through streambeds using heat as a tracer. Field observations were made on tens of minutes to hourly timescales during storms lasting multiple days, as well as on weekly and seasonal timescales to characterize longer-term patterns. Authors found that temporal changes in flux that occur over hours can be accurately characterized using traditional one-dimensional models, with some smoothing effects. A field study by Harvey et al. (2012) identified time-varying hyporheic flow caused by flood-driven growth in size and spacing of sand bedforms and the effect it had in activating deeper hyporheic flow paths. The authors speculated that the storm-driven expansion of hyporheic flow is likely to be most significant for flood timescales that are similar to the residence time of hyporheic flow (Gomez et al., 2012; Harvey et al., 2012).

    Other dynamic effects occur over slower timescales, such as diel variation in hyporheic flow accompanying riparian evapotranspiration (Larsen et al., 2014; Wondzell et al., 2010) or responding to seasonal wetting and drying of the catchment (Harvey et al., 1996). Diel variation in stream temperature adjusts the viscosity of stream water entering hyporheic flow paths, which nominally adjusts the HEF through the effect that viscosity has on hydraulic conductivity of the streambed (Constantz et al., 1994). Temporal variations in HEFs also may occur over longer timescales (ie, months to years) (eg, Wondzell and Swanson, 1999), with some of these changes being periodic (eg, evapotranspiration-driven) and others being episodic (eg, flood pulse-driven; Larsen et al., 2014).

    Bank Storage Exchange Flows

    In addition to driving overbank flows, floods cause bank storage (ie, the flow of water into the bank and streambed bed below the bank; Boano et al., 2014; Sawyer et al., 2014; Gerecht et al., 2011). Analytical model solutions are available for bank storage that predict simple dynamics such as bank storage responding to sinusoidal changes in river stage (eg, Pinder and Sauer, 1971). The bank storage water flux is proportional to the horizontal hydraulic conductivity and the hydraulic head gradient. The penetration distance of bank storage waters is affected by the flooding timescale and by the width of permeable sediments in the valley. Maximum penetration occurs if the flood lasts as long as the characteristic transport time needed for the pressure waves to be transported across the alluvial aquifer, which can be calculated from the hydraulic diffusivity and the floodplain width. Any preexisting gradients in hydraulic head that are associated with gaining (ie, discharging) or losing (ie, recharging) conditions also affect bank storage fluxes. A river receiving groundwater discharge will have a lower volume of bank storage with lesser penetration distance and a shorter residence time (eg, Welch et al., 2014). Bank storage is an effective means of storing and chemically transforming widely used herbicides such as atrazine (Squillace et al., 1993).

    River-Floodplain Exchanges

    During floods, river discharge may increase enough to exceed bankfull, after which river water overtops the banks onto floodplains. Factors such as floodplain width and connectivity of low-lying floodplain areas become important and determine the extent of flooding (Mertes, 1997). Depending on the topography of levees, embankments, and other floodplain features, water may follow channelized flow paths back to the river, or may become ponded and slowly recharge the alluvial groundwater, or slowly evaporate. Floodplain dynamics are affected by topographic variability on the floodplain surface and living vegetation, including grass and grass-like emergent, shrubs, and trees, as well as by stems and trunks of dead vegetation lying horizontally on the floodplain (Bates et al., 1998; Bridge, 2009; Heeren et al., 2014).

    Well-connected floodplains provide out-of-channel water storage for rivers during flood stage, which may have the positive effect of attenuating the height of a flood at points further downstream. However, channels are dynamic features that, depending on the recurrence frequency of channel forming floods, may lead to channel narrowing over time as a result of vegetation ingrowth (Larsen, 2011), which could reduce a river’s bankfull flow capacity, creating a flashier river that floods more often. Although distinct in the details of a particular river, the dynamic processes discussed above all tend to increase contact time of river water with geochemical and microbially active sediments on floodplains (Hoehn and Cirpka, 2006). For example, Forshay and Stanley (2005), Ensign et al. (2008), Scott et al. (2014), and Wollheim et al. (2014) documented the expansion of the wetted sediment surface area during overbank flows and its effects on chemical reactions. Authors found that overbank flows vastly increased the interfacial area of surface water and sediments, which substantially increased the amount of denitrification. Increased understanding about how hydrological variability influences hyporheic exchange, bank storage, and overbank flows will help with the management of the ecological impact of river regulation by dams and other modifications (Jefferson et al., 2013).

    Watershed Influences

    Flows from the watershed typically interact with and are modified by HEFs before they enter the main channels of rivers. Distinguished from HEFs by their upland source, watershed flows include overland flow, subsurface stormflow, and groundwater flow, all of which are usually chemically distinct from river water. Watershed flow paths are varied and may be complicated (National Research Council, 2002). For example, subsurface stormflow may re-emerge on the floodplain surface in a process known as return flow, creating saturated areas with a distinctive chemistry, which may be further modified by direct precipitation before draining to channels. Shallow and deeper groundwater flow may lag considerably in their transport times, for hours, decades, or even centuries, compared to overland flow and subsurface stormflow (Fig. 7). Groundwater contact with soils and weathered bedrock produces a distinctive chemistry in relation to the surface waters that they drain into. As these waters converge by discharging to surface water, the mixing between shallow and deeper flows may enhance certain chemical reactions (eg, Conant et al., 2004; Hedin et; al., 1998; Baker et al., 1999).

    Fig. 7 Cross valley and downvalley watershed influences illustrating (1) infiltration, (2) overland flow, (3) subsurface stormflow, (4) groundwater recharge and discharge, (5) floodplain exfiltration, (6) hyporheic exchange and (7) surface water side-channel exchange. (From Harvey, J., Gooseff, M., 2015. River corridor science: hydrologic exchange and ecological consequences from bedforms to basins. Water Resour. Res. 58, 6893–6922. http://dx.doi.org/10.1002/2015WR017617 as modified from Poole, G.C., 2010. Stream hydrogeomorphology as a physical science basis for advances in stream ecology. J. North Am. Benthol. Soc. 29(1), 12–25).

    Understanding Controls and Predicting Consequences Across Scales

    , where hh is the hydrostatic head potential [L], hp is pressure head potential [L], and z where q is specific discharge in units of water volume per unit area per time [LT− 1], h is hydraulic head [L], l [L] is distance through sediment over which the change in head is measured, and K is a rate constant known as hydraulic conductivity [LT− 1], which is a measure of sediment’s ability to transmit water. K is a function of grain size, pore size distribution, soil-water content, and viscosity of water, and accounts for the effect of flow path tortuosity and drag on rough granular surfaces within the subsurface. The minus sign in Darcy’s Law is a convenience that defines flow as occurring from areas of higher to lower hydraulic head.

    , where hv is velocity head [L], v is stream velocity [LT− 1], and g is gravity [LT− 2]. Thus the total potential, his expected to grow dramatically across the range of flow from quiescent coastal rivers to steeper conditions simply because of the velocity head contribution. Also, there are many types of flow resistance that may need to be quantified in surface water including form drag on geomorphic features and vegetation as well as drag on granular surfaces (Prestegaard, 1983; Bathurst, 1988), with the form of appropriate models changing considerably across thresholds defining laminar, transitional, and turbulent conditions. For more about the fluid mechanics of HEFs, the reader is referred to detailed references such as Gualtieri and Mihailović (2013).

    A practical classification of HEFs considers the flow energetics discussed above but also considers the geomorphic features of river corridors that organize HEFs across scales ranging from individual boulders, sand ripples, logs, gravel bars, riffles, meanders, all the way up to the scale of valley widening and constrictions. These features and their associated HEFs vary in spatial and temporal scale across six orders of magnitude (ie, from millimeters to kilometers and seconds to decades). Fig. 8 illustrates broad regimes of geomorphic and biological features and the physical forcings that shape HEFs. Across many orders of magnitude, the spatial extent of HEFs scales roughly with river width and sediment permeability (Fig. 8). However, those factors tend to only account crudely for complex interactions between flow and geomorphic and biological roughness features. The objective of this section is to discuss the controls and interactions affecting HEFs, which are only broadly represented in the process domain diagrams shown in Fig. 8. As will be discussed later in this chapter, the relationships sometimes may be more usefully characterized using dimensionless measures of flow resistance such as channel friction factors or scaling laws that are specific to certain types of roughness features.

    Fig. 8 Fluvial, geomorphic and biological influences on hydrologic exchange flows. First order controls include river and valley width (A) and sediment permeability (B). (Part A of figure is from Boano, F., Harvey, J.W., Marion, A., Packman, A.I., Revelli, R., Ridolfi, L., Wörman, A., 2014. Hyporheic flow and transport processes: mechanisms, models, and biogeochemical implications. Rev. Geophys. 52, 603–679. http://dx.doi.org/10.1002/2012RG000417 . Part B of figure is from Huettel, M., Berg, P.P., Kostka, J.E., 2014. Benthic exchange and biogeochemical cycling in permeable sediments. Ann. Rev. Mar. Sci. 6, 23–51. http://dx.doi.org/10.1146/annurev-marine-051413-012706 for part B).

    Although the processes controlling HEFs are best understood at the scale of individual exchange flows, the consequences of HEFs, in terms of downstream water quality and ecology, are often more important to understand at the scale of large drainage basins or ecoregions. The disparity between the scale of processes and the cumulative effects creates a significant challenge for modeling, since confident predictions of future conditions are rarely made without both a good understanding of the small scale controlling processes, as well as their cumulative effects. There are few solid and well-demonstrated modeling approaches that operate across scales to combine small scale controlling processes and large-scale cumulative effects. Despite the difficulty, progress is being made, in part by combining field measurements, and also combining models that individually might be suited for a particular scale. Such multiscale investigations may reveal how many small-scale interactions add up to determine ecological outcomes throughout large basins.

    Overview of Modeling Approaches

    Modeling refers to any formal or informal application of concepts to simplify and help interpret data or information about a system. Hydrological models are often used for quantifying fluxes, residence times, or reactions rates. Other uses for models include exploring system sensitivities to change, and using observations and modeling of example systems to help predict behavior of similar unmeasured systems. In general, model selection depends on the specific scientific questions to be answered, the desire for transferability of results beyond a specific place and time, the appropriate degree of spatial and temporal averaging, and the amount and type of data that are already available or that are possible to obtain. Model choice is further affected by practicalities of time available, prior modeling skills, and previous experience with specific models; as well data needs and study budgets. Fig. 9 illustrates some common classes of models showing some familiar hydrologic transport models as examples.

    Fig. 9 Model complexity and type of understanding gained.

    Data-based statistical models examine relationships among variables that predict characteristics of transport and chemical reactions in river corridors. Results range from simple correlations and linear regression models all the way to multivariate statistical models with many possible uses spanning data exploration, hypothesis testing, and prediction. The lines distinguishing statistical and physically based models are sometimes blurred, as in scaling equations that are derived using empirical analysis, but with procedures that respect knowledge and intuition about the controlling physical factors.

    Physical process-mechanistic models are distinguished from data-based statistical models by obeying physical laws such as conservation of mass. Physically based models are useful to examine detailed interactions among hydrologic and chemical processes and sensitivities of outcomes. These models are solved using analytical or numerical solutions to governing equations for mass conservation, transport, storage, and reaction within a specified model domain. Boundary conditions at the edge of the modeled domain need to be specified and initial conditions also may need to be specified for transient models where conditions change over time.

    The most basic type of physical process-mechanistic models are mass balance models, which offer a practical means of quantifying exchange flows of water and solute mass over large areas. Often the mass balance is constructed around a control volume in surface water where most of the relevant water fluxes can be relatively easily measured. The difficult to measure fluxes (eg, groundwater fluxes) are often solved for by difference. Examples of the application of simple water mass balance models to characterize groundwater-surface water interactions are given by Winter (1981), Krabbenhoft et al. (1990), and Choi and Harvey (2000). Mass balance models are often extended to the analysis of solute reactions. Example applications of mass balance models to quantify in-stream and subsurface reactions may be found in Mulholland (1992), who examined nutrient uptake in a forest stream, Sheibley et al. (2014), who examined nutrient uptake in agricultural streams, and Kim et al. (1995), who examined biodegradation of toluene in a contaminated stream.

    The underlying physics of a mass balance model can be enhanced by recasting fluxes in terms of rate expressions that specify the physical controls on transport, storage, and reaction. For example, the physical conceptualization of a mass balance model can be enhanced by substituting appropriate rate laws (eg, Darcy’s law) for fluxes that depend on physical quantities, such as hydraulic head gradient and hydraulic conductivity. Physical process models may cautiously be used for prediction in a procedure known as forward modeling if parameter values are available from measurements or other reliable sources. Ideally, the model would first be validated by comparing simulation outcomes with available historical data, a step referred to as history matching. Models that perform inadequately may be calibrated by adjusting parameter values to better match outcomes, a step referred to as model verification. Once a model performs well, it potentially may be useful for predicting future outcomes by changing boundary or internal conditions to represent a change in land use or implementation of different

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