EPA/600/R-14/475F | January 2015 | epa.gov/research
United States
Environmental Protection
Agency
           Connectivity of Streams & Wetlands
           to Downstream Waters:
           A Review & Synthesis of the Scientific Evidence

                                                  I
                                    A        -      I
  Office of Research and Development
  NCEA (Washington DC, Cincinnati OH), NERL (Cincinnati OH, Las Vegas NV) and NHEERL (Corvallis OR)

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                                        EPA/600/R-14/475F
                                            January 2015
CONNECTIVITY OF STREAMS AND WETLANDS
        TO DOWNSTREAM WATERS:
     A REVIEW AND SYNTHESIS OFTHE
          SCIENTIFIC EVIDENCE
         Office of Research and Development
        U.S. Environmental Protection Agency
               Washington, DC

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Errata for Connectivity of Streams and Wetlands to Downstream Waters: A Review and
Synthesis of the Scientific Evidence (EPA/600/R-14/475F)

Page 2-12, the last four lines on the page have been revised to include text that was missing
(see bolded text).
Hyporheic exchange occurs when water moves from stream or river into alluvial deposits and then
returns to the channels (Figures 2-6B and 2-6C; Bencala, 2005; Leibowitz et al., 2008). Hyporheic
exchange allows for the mixing of surface water and ground water. It occurs during both high- and
low-flow periods, and typically has relatively horizontal flowpaths at scales of meters to tens of meters
(Bencala, 2005) and vertical flowpaths with depths ranging from centimeters to tens of meters (Stanford
and Ward, 1988; Woessner, 2000 and references therein).

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                                          DISCLAIMER

This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and

approved for publication. Mention of trade names or commercial products does not constitute

endorsement or recommendation for use.
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CONTENTS
PREFACE	xii
AUTHORS AND REVIEWERS	xiii
PHOTO CREDITS	xix
ACKNOWLEDGMENTS	xx
EXECUTIVE SUMMARY	ES-1
           BACKGROUND	ES-1
           SUMMARY OF MAJOR CONCLUSIONS	ES-2
           SUPPORT FOR MAJOR CONCLUSIONS	ES-6
           KEY FINDINGS FOR MAJOR CONCLUSIONS	ES-7
           CLOSING COMMENTS	ES-15
CHAPTER 1. INTRODUCTION	1-1
           1.1     Purpose	1-1
           1.2     Scientific Context	1-2
                   1.2.1   Concepts of Connectivity in Hydrology and Ecology	1-2
                   1.2.2   Connectivity Gradients and Descriptors	1-3
                   1.2.3   Cumulative Effects of Streams and Wetlands on Downstream Waters	1-10
                   1.2.4   Effects of Human Activities on Connectivity	1-11
           1.3     Report Approach	1-14
                   1.3.1   Selection and Screening of Scientific Materials	1-16
                   1.3.2   Report Structure	1-18
           1.4     Summary	1-18
CHAPTER 2. AN INTEGRATED SYSTEMS PERSPECTIVE ON INTERACTIONS OF WATERSHEDS, STREAMS,
   WETLANDS, AND DOWNSTREAM WATERS	2-1
           2.1     Introduction	2-1
           2.2     An Introduction to River Systems	2-2
                   2.2.1   River System Components	2-2
                   2.2.2   River System Hydrology	2-8
                   2.2.3   River Network  Expansion and Contraction	2-18
           2.3     Influence of Streams and Wetlands on Downstream Waters	2-22
                   2.3.1   Effects of Streams and Wetlands on Material Fluxes	2-22
                   2.3.2   Connectivity and Transport of Materials to and from Streams and Wetlands	2-26
                          2.3.2.1     Connectivity and Isolation	2-26
                          2.3.2.2     Spatial and Temporal Variability of Connectivity	2-29
           2.4     Factors Influencing Connectivity	2-30
                   2.4.1   Climate-Watershed Characteristics	2-31
                   2.4.2   Spatial Distribution Patterns	2-38
                   2.4.3   Biota	2-40
                   2.4.4   Human Activities and Alterations	2-44
                   2.4.5   Interactions Among Factors	2-47
                   2.4.6   Quantifying Connectivity	2-49
                          2.4.6.1     Hydrologic and Chemical Connectivity	2-49
                          2.4.6.2     Biological Connectivity	2-50
                          2.4.6.3     Summary	2-51
CHAPTER 3. STREAMS: PHYSICAL, CHEMICAL, AND BIOLOGICAL CONNECTIONS TO RIVERS	3-1
           3.1     Abstract	3-1
           3.2     Introduction	3-2
           3.3     Physical Connections	3-5
                   3.3.1   Water	3-5
                   3.3.2   Sediment	3-13

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                    3.3.3    Wood	3-17
                    3.3.4    Temperature (Heat Energy)	3-19
            3.4     Chemical Connections	3-21
                    3.4.1    Nutrients	3-23
                    3.4.2    Dissolved and Particulate Organic Matter	3-28
                    3.4.3    Ions	3-32
                    3.4.4    Contaminants and Pathogens	3-33
            3.5     Biological Connections	3-37
                    3.5.1    Invertebrates	3-38
                    3.5.2    Fishes	3-40
                    3.5.3    Genes	3-43
            3.6     Streams: Synthesis and Implications	3-45
CHAPTER 4. WETLANDS: PHYSICAL, CHEMICAL, AND BIOLOGICAL CONNECTIONS TO RIVERS	4-1
            4.1     Abstract	4-1
            4.2     Introduction	4-3
            4.3     Riparian/Floodplain Wetlands	4-3
                    4.3.1    Introduction	4-3
                    4.3.2    The Physical Influence of Riparian Areas on Streams	4-7
                            4.3.2.1      Hydrology	4-7
                            4.3.2.2      Geomorphology (Sediment-vegetation Interactions)	4-8
                            4.3.2.3      Temperature and Sunlight	4-9
                    4.3.3    The Chemical-nutrient Influence of Riparian Areas on Streams	4-10
                            4.3.3.1      Hyporheic/Soil Processing of Nutrients	4-11
                            4.3.3.2      Nitrogen	4-11
                            4.3.3.3      Phosphorus	4-12
                            4.3.3.4      Carbon and Allochthonous Inputs	4-13
                            4.3.3.5      Pesticides	4-14
                            4.3.3.6      Mercury	4-14
                    4.3.4    Biological Connections Between Riparian Areas and Streams	4-15
                            4.3.4.1      Vascular Plants and Phytoplankton	4-15
                            4.3.4.2      Vertebrates	4-17
                            4.3.4.3      Invertebrates	4-19
            4.4     Non-floodplain Wetlands	4-20
                    4.4.1    Introduction	4-20
                    4.4.2    The Physical Influence of Non-floodplain Wetlands on Streams	4-21
                            4.4.2.1      Surface-water Connections	4-21
                            4.4.2.2      Ground-water Connections	4-22
                            4.4.2.3      Effects of Non-floodplain Wetlands on Streamflow	4-24
                    4.4.3    Effects of Non-floodplain Wetlands on Water Quality	4-26
                            4.4.3.1      Non-floodplain Wetlands as Sources for Downstream Waters	4-27
                            4.4.3.2      Non-floodplain Wetlands as Sinks and Transformers for
                                        Downstream Waters	4-29
                    4.4.4    Biological Connections Between Non-floodplain Wetlands and Streams	4-30
                    4.4.5    Geographic Isolation of Non-floodplain Wetlands	4-35
            4.5     Wetlands: Synthesis and Implications	4-39
                    4.5.1    Riparian/Floodplain Wetlands	4-39
                    4.5.2    Non-floodplain Wetlands	4-39
CHAPTER 5. APPLICATIONS AND DISCUSSION: CONNECTIVITY CASE STUDIES	5-1
            5.1     Introduction	5-1
            5.2     Carolina and Delmarva Bays	5-2
                    5.2.1    Connectivity and Consequences on Downstream Waters	5-2
                    5.2.2    Effects of Human Alteration	5-3
            5.3     Oxbow Lakes	5-3
                    5.3.1    Connectivity and Consequences on Downstream Waters	5-3

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                    5.3.2    Effects of Human Alteration	5-4
            5.4     Prairie Potholes	5-4
                    5.4.1    Connectivity and Consequences on Downstream Waters	5-4
                    5.4.2    Effects of Human Alteration	5-5
            5.5     Prairie Streams	5-6
                    5.5.1    Connectivity and Consequences on Downstream Waters	5-6
                    5.5.2    Effects of Human Alteration	5-7
            5.6     Southwestern Intermittent and Ephemeral Streams	5-7
                    5.6.1    Connectivity and Consequences on Downstream Waters	5-7
                    5.6.2    Effects of Human Alteration	5-8
            5.7     Vernal Pools	5-8
                    5.7.1    Connectivity and Consequences on Downstream Waters	5-8
                    5.7.2    Effects of Human Alteration	5-9
            5.8     Synthesis	5-9
CHAPTER 6. CONCLUSIONS	6-1
            6.1     Major Conclusions and Key Findings	6-1
                    6.1.1    Conclusion 1: Streams	6-1
                            6.1.1.1      Conclusion 1, Key Findings	6-2
                    6.1.2    Conclusion 2: Riparian/Floodplain Wetlands and Open Waters	6-3
                            6.1.2.1      Conclusion 2, Key Findings	6-4
                    6.1.3    Conclusion 3: Non-floodplain Wetlands and Open Waters	6-5
                            6.1.3.1      Conclusion 3, Key Findings	6-6
                    6.1.4    Conclusion 4: Degrees and Determinants of Connectivity	6-8
                            6.1.4.1      Conclusion 4, Key Findings	6-9
                    6.1.5    Conclusion 5: Cumulative Effects	6-10
                            6.1.5.1      Conclusion 5, Key Findings	6-11
            6.2     Strength of Evidence for Conclusions and Data Gaps in the Available Literature	6-12
CHAPTER 7. REFERENCES	7-1
APPENDIX A. GLOSSARY	A-l
            References	A-15
APPENDIX B. CASE STUDIES	B-l
            B.I     Case Study: Carolina and Delmarva Bays	B-l
                    B.I.I    Abstract	B-l
                    B.1.2    Introduction	B-l
                            B.1.2.1      Definition and Geographic Extent	B-l
                            B.1.2.2      Geology	B-2
                            B.l.2.3      Hydrology	B-3
                            B.1.2.4      Water Chemistry	B-3
                            B.1.2.5      Biological Communities	B-4
                    B.I.3    Evidence of Connectivity	B-5
                            B.1.3.1      Physical Connections	B-5
                            B.l.3.2      Chemical Connections	B-6
                            B.l.3.3      Biological Connections	B-6
                    B.1.4    Carolina and Delmarva Bays: Synthesis  and Implications	B-7
            B.2     Case Study: Oxbow Lakes	B-8
                    B.2.1    Abstract	B-8
                    B.2.2    Introduction	B-8
                            B.2.2.1      Origin and Description	B-8
                    B.2.3    Evidence	B-9
                            B.2.3.1      Physical Connections	B-9
                            B.2.3.2      Chemical Connections	B-10
                            B.2.3.3      Biological Connections	B-ll
                    B.2.4    Oxbow Lakes: Synthesis and Implications	B-13

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            B.3     Case Study: Prairie Potholes	B-14
                    B.3.1   Abstract	B-14
                    B.3.2   Introduction	B-14
                            B.3.2.1     Hydrologic Dynamics	B-15
                            B.3.2.2     Chemical Functions	B-16
                            B.3.2.3     Ecological Characteristics	B-16
                    B.3.3   Evidence	B-17
                            B.3.3.1     Physical Connections	B-17
                            B.3.3.2     Chemical Connections	B-19
                            B.3.3.3     Biological Connections	B-20
                    B.3.4   Prairie Potholes: Synthesis and Implications	B-21
            B.4     Case Study: Prairie Streams	B-22
                    B.4.1   Abstract	B-22
                    B.4.2   Introduction	B-22
                            B.4.2.1     Geography and Climate	B-22
                            B.4.2.2     Hydrology and Geomorphology	B-24
                            B.4.2.3     Physicochemistry	B-25
                            B.4.2.4     Ecology	B-26
                            B.4.2.5     Human Alterations	B-27
                    B.4.3   Evidence	B-28
                            B.4.3.1     Physical Connections	B-28
                            B.4.3.2     Chemical Connections	B-31
                            B.4.3.3     Biological Connections	B-34
                    B.4.4   Prairie Streams: Synthesis and Implications	B-36
            B.5     Case Study: Southwestern Intermittent and Ephemeral Streams	B-37
                    B.5.1   Abstract	B-37
                    B.5.2   Introduction	B-38
                    B.5.3   Southwestern Rivers	B-39
                    B.5.4   San Pedro River	B-42
                            B.5.4.1     Basin Characteristics	B-42
                            B.5.4.2     Ephemeral Stream Connections and Their Influence on the
                                        San Pedro River	B-45
                    B.5.5   Other Southwestern Rivers	B-48
                            B.5.5.1     Physical Connections	B-48
                            B.5.5.2     Human Alterations	B-50
                            B.5.5.3     Biological Connections	B-55
                    B.5.6   Southwestern Intermittent and Ephemeral Streams: Synthesis and
                            Implications	B-59
            B.6     Case Study: Vernal Pools	B-60
                    B.6.1   Abstract	B-60
                    B.6.2   Introduction	B-60
                            B.6.2.1     Geography and Geology	B-60
                            B.6.2.2     Temporal Dynamics	B-61
                            B.6.2.3     Ecology	B-62
                    B.6.3   Evidence	B-62
                            B.6.3.1     Physical Connections	B-62
                            B.6.3.2     Biological Connections	B-64
                    B.6.4   Vernal  Pools: Synthesis and Implications	B-66
            References	B-67
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LIST OF TABLES
Table 1-1. Translating connectivity-related questions between policy and science	1-2
Table 1-2. Dimensions of watershed connectivity	1-4
Table 2-1. Functions by which streams and wetlands affect material and energy fluxes to downstream
            waters	2-25
Table 3-1. Examples of mechanisms by which streams are connected to and influence downstream
            waters, by functional type	3-47
Table 4-1. Examples of mechanisms by which riparian/floodplain wetlands and wetlands in non-
            floodplain settings influence downstream waters, by functional type	4-4
Table 4-2. Partial list of amphibian and reptile species known to use both streams and non-floodplain
            wetlands or other lentic waters	4-36
Table 4-3. Key conclusions on the effects of riparian/floodplain wetlands on rivers	4-40
Table 4-4. Key conclusions on the effects of non-floodplain wetlands on rivers	4-42
Table 6-1. Relative abundance of literature by functional category	6-15
Table 6-2. Relative abundance of literature by review topic area	6-16
Table B-l. California vernal pool inundation  and hydrologic connectivity	B-64
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LIST OF  FIGURES
Figure 1-1A. Hydrologicflowpaths	1-5
Figure 1-1B. Biological flowpaths	1-6
Figure 1-2. Temporal dynamics of hydrologic flowpaths	1-7
Figure 1-3. Effects of human alterations on watershed connectivity	1-12
Figure 1-4. The role of connectivity in maintaining the physical, chemical, and biological integrity of
            water	1-13
Figure 1-5. Waters and connections considered to be within scope for this report	1-15
Figure 1-6. Flow chart for screening and compiling literature	1-17
Figure 2-1. A generalized example of a river network within its watershed	2-3
Figure 2-2. Elements of a river system	2-5
Figure 2-3. Hypothetical cross-sections of (A) a headwater stream and (B) a large river within a river
            network	2-6
Figure 2-4. Water below the land surface occurs in either the unsaturated or the saturated zone	2-10
Figure 2-5. Cross-section showing major hydrologic flowpaths in a regional-scale stream-watershed
            system	2-11
Figure 2-6. Hyporheic zone flows	2-13
Figure 2-7. Hypothetical hydrographs illustrating maximum duration of flow (Dmax.q) for (A) perennial,
            (B) intermittent, and (C) ephemeral streams	2-15
Figure 2-8. (A) Hypothetical hydrograph showing stormflow and baseflow responses to a rainfall event.
            (B) Expansion and contraction of flowing water in a stream network following a rainfall
            event	2-16
Figure 2-9. Characteristics of U.S. streams by watershed, in terms of percent  of total stream length as
            (A) perennial, (B) intermittent, and (C) headwater streams	2-17
Figure 2-10. Extent and connectivity of streams with flowing water, wetlands, and other water bodies in
            (A) Spring Valley Creek, OR and (B) Spoon Creek, OR during dry summer (left) and wet
            winter (right) conditions	2-19
Figure 2-11. Stormflow moves downstream through the river network and interacts with lower stream
            reaches, floodplains, and alluvial aquifers	2-20
Figure 2-12. Landsat 5 satellite images of the Mississippi River along the borders of Tennessee,
            Kentucky, Missouri, and Arkansas on (A) May 12, 2006  and (B)  May 10, 2011	2-21
Figure 2-13. The direction and magnitude of interactions between surface water and ground water can
            dramatically change during large hydrologic events, including floods	2-23
Figure 2-14. Illustration of the sequential transformation of materials as they move through the river
            network, via either downstream transport with water flow (solid black arrows) or via aerial
            or terrestrial movements (dashed black arrows)	2-28
Figure 2-15. Map of annual runoff in contiguous United States showing locations of five example
            streams that illustrate daily runoff patterns and total annual runoff depths	2-32
Figure 2-16. Generalized hydrologic landscape forms	2-33
Figure 2-17. Major hydrologic flowpaths for hillslopes with combinations of permeable and
            impermeable soils and geologic formations	2-35
Figure 2-18. Types of hydrologic connections between non-floodplain wetlands and streams or rivers	2-37
Figure 2-19. Major types of basin shapes and network configurations	2-39
Figure 2-20. Examples of different landscapes showing interspersion of wetlands and streams or
            rivers	2-41
Figure 2-21. Comparison of percent wetland loss between (A) the 1780s and mid-1980s with (B) the
            distribution of artificially drained agricultural land in 1985	2-46
Figure 3-1. Longitudinal pattern of flow along (A) River Derwent and (B) River Trent, illustrating stepped
            increases in flow associated with tributary inflows	3-8
Figure 3-2. Time series of rainfall and streamflow observations in the Rio Puerco and Rio Grande,
            6-18 September 2003	3-9


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Figure 3-3. Airborne thermal infrared remotely sensed water temperature in the mainstem and at
            tributary confluences of the North Fork John Day River, OR, on 4 August 1998	3-22
Figure 3-4. (A) A dendritic network with multilevel hierarchical structure, and (B) a uninodal network
            with all headwater streams feeding directly into a river mainstem	3-44
Figure 5-1. Relative positioning of streams, riparian and floodplain waters, and non-floodplain waters
            along a gradient of connectivity	5-12
Figure B-l. Aerial photograph of Carolina bays within a region of the upper Coastal Plain of South
            Carolina	B-2
Figure B-2. Map of the United States showing physiographic subregions and major rivers of the Great
            Plains	B-23
Figure B-3. Map showing the location of Kings Creek and N01B, intermittent tributaries to the Kansas
            River	B-29
Figure B-4. Hydrographs (instantaneous and daily mean) showing propagation of the 13 May 1995
            (Julian date 133) flood downstream from headwater sites (N01B and Kings Creek) to the
            Kansas River at Wamego	B-30
Figure B-5. Upper: Geographic distribution of intermittent and ephemeral (red) and perennial (blue)
            streams in the Continental United States and two example watersheds in Arizona and
            Michigan/Ohio/Indiana from the National Hydrography Dataset (NHD) stream map	B-38
Figure B-6. 2003 calendar year hydrographs from (a) the White River near Fort Apache, AZ and (b) the
            San Pedro River near Tombstone, AZ	B-40
Figure B-7. San Pedro River basin map showing major physiographic features and current and
            historical perennial reaches	B-43
Figure B-8. Perennial (blue) and nonperennial (red) streams in the San Pedro Basin from the U.S.-
            Mexico border to its confluence with the Gila River based on USGS National Hydrography
            Dataset (NHD) stream map (http://nhd.usgs.gov/)	B-44
Figure B-9. Generalized east-west section and stratigraphic units in the middle San Pedro watershed	B-45
Figure B-10. Storm rainfall and downstream hydrographs with decreasing runoff volume and peak rate
            due to channel transmission losses as measured by in the USDA-ARS Walnut Gulch
            Experimental Watershed (WGEW) and the impact of this storm runoff on the San Pedro
            River in SE Arizona	B-47
Figure B-ll. Aerial photograph showing ephemeral tributaries to Cienega Creek, a perennial stream,
            flowing through the small community of Vail, southeast of Tucson, AZ	B-51
Figure B-12. Change in riparian vegetation along the Santa Cruz River, Tucson, AZ, as the result of
            water-level declines in the regional aquifer	B-55
Figure B-13. Aerial photograph showing dense corridor of vegetation lining ephemeral washes in
            southeastern Arizona	B-56
 LIST OF BOXES
Box 3-1. Urban Streams	3-3
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LIST OF ABBREVIATIONS AND ACRONYMS
CWA        Clean Water Act
DEM        digital elevation model
DOC        dissolved organic carbon
FROM       fine particulate organic matter
GW        groundwaterflowpath
HUC        Hydrologic Unit Code
NHD        National Hydrography Dataset
PPR        prairie pothole region
USDA-ARS    United States Department of Agriculture, Agricultural Research Services
U.S. ACE     United States Army Corps of Engineers
U.S. EPA     United States Environmental Protection Agency
USGS       United States Geological Survey
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LIST OF UNITS AND VARIABLES
A          drainage area
C          Celsius
c          scaling power constant
cm         centimeter
d          day
g          gram
ha         hectare
hr         hour
kg         kilogram
km         kilometer
L          liter
m         meter
mg         milligram
Mg         megagram
mm        millimeter
|jM         micromolar
N          metric normal temperature and pressure
ng         nanogram
Pg         petagram
Q          discharge
s          second
t          metric ton
TO         shear stress
V          velocity
yr         yea r
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This report was prepared by the National Center for Environmental Assessment, the National Health and
Environmental Effects Research Laboratory, and the National Exposure Research Laboratory, in the U.S.
Environmental Protection Agency's (U.S. EPA's) Office of Research and Development. It reviews and
evaluates evidence from peer-reviewed sources that were published or in press by December 2014.
Throughout this document, terms are used with their generally recognized scientific meaning. We have
provided definitions of technical terms in the Glossary (Appendix A). Two previous drafts prepared on 1
February 2011 and 12 July 2011 were reviewed by U.S. EPA and U.S. Army Corps of Engineers staff.
Additional comments were received from scientists in government, academic, nonprofit, and private
industry organizations listed in the Reviewers section who reviewed all or part of the 1 February 2011
preliminary draft. A draft prepared on 11 October 2011 was independently peer reviewed by a panel of
11 topic experts, listed in the Reviewers section, on 30 January 2012. An external review draft released
in September 2013  (600/R-11/098B) was reviewed by U.S. EPA staff and a panel of the U.S. EPA's
Science Advisory Board (SAB) that convened 16-18 December 2013 (SAB report number EPA-SAB-15-
001, available online at www.epa.gov/sabl. The 27 topic experts comprising the SAB panel are listed in
the Reviewers section. In addition, comments from the public were received through the docket or at
the SAB  panel meeting. Comments from these sources were considered and used to improve the clarity
and scientific rigor of the document.
Stream and Wetland Connectivity:
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                                     January 2015

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                            AUTHORS AND REVIEWERS
                                         AUTHORS
Laurie C. Alexander, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Washington, DC

Bradley Autrey, MS, JD
U.S. Environmental Protection Agency
Office of Research and Development, National Exposure Research Laboratory
Cincinnati, OH

Julie DeMeester, PhD
American Association for the Advancement of Science Fellow
U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Washington, DC

Ken M. Fritz, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Exposure Research Laboratory
Cincinnati, OH

Heather E. Golden, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Exposure Research Laboratory
Cincinnati, OH

David C. Goodrich, PhD
U.S. Department of Agriculture
Agricultural Research Service
Tucson, AZ

William G. Kepner, MS, MPA
U.S. Environmental Protection Agency
Office of Research and Development, National Exposure Research Laboratory,
Environmental Sciences Division
Las Vegas, NV
Stream and Wetland Connectivity:
A Review and Synthesis
XIII
                                     January 2015

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                                     AUTHORS (continued)
Charles R. Lane, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Exposure Research Laboratory
Cincinnati, OH

Stephen D. LeDuc, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Washington, DC

Scott G. Leibowitz, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Health and Environmental Effects Research
Laboratory
Corvallis, OR

Michael G. McManus, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Cincinnati, OH

Amina I. Pollard, PhD
U.S. Environmental Protection Agency
Office of Water, Office of Wetlands, Oceans, and Watersheds
Washington, DC

Hadas Raanan Kiperwas, PhD
Oak Ridge Institute for Science and Education Fellow, U.S. Environmental Protection Agency
Office of Water, Office of Wetlands, Oceans, and Watersheds
Washington, DC

Caroline E. Ridley, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Washington, DC

Kate Schofield, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Washington, DC
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A Review and Synthesis                                                                       3

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                                     AUTHORS (continued)
Melanie Vanderhoof, PhD
Oak Ridge Institute for Science and Education Fellow, U.S. Environmental Protection Agency
Office of Research and Development, National Center for Environmental Assessment
Washington, DC

Parker J. Wigington, PhD
U.S. Environmental Protection Agency
Office of Research and Development, National Health and Environmental Effects Research
Laboratory
Corvallis, OR

                                PEER CONSULTATION REVIEWERS
Robert T. Brooks, PhD
U.S. Department of Agriculture Forest Service, Amherst, MA

William H. Eldridge, PhD
Stroud Water Research Center, Avondale, PA

Keith B. Gido, PhD
Kansas State University, Manhattan, KS

Arthur J. Gold, PhD
University of Rhode Island, Kingston, RI

Tracie-Lynn Nadeau, PhD
U.S. Environmental Protection Agency, Portland, OR

Denis Newbold, PhD
Stroud Water Research Center, Avondale, PA

Michael J. Paul, PhD
TetraTech Inc., Owings Mills, MD

Donald Rosenberry, PhD
U.S. Geological Survey, Lakewood, CO

Doug Samson, PhD
The Nature Conservancy, Bethesda, MD

Rebecca Sharitz, PhD
Savannah River Ecology Laboratory, Aiken, GA

Kirk 0. Winemiller, PhD
Texas A&M University, College Station, TX

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                                EXTERNAL PEER REVIEW PANEL
David J. Cooper, PhD
Colorado State University, Fort Collins, CO

William G. Crumpton, PhD
Iowa State University, Ames, IA

Kenneth W. Cummins, PhD
Humboldt State University, Arcata, CA

Walter K. Dodds, PhD (Chair)
Kansas State University, Manhattan, KS

James W. La Baugh, PhD
U.S. Geological Survey, Reston, VA

Mark C. Rains, PhD
University of South Florida, Tampa, FL

John S. Richardson, PhD
University of British Columbia, Vancouver, BC

Joel W. Snodgrass, PhD
Towson University, Towson, MD

Arnold van der Valk, PhD
Iowa State University, Ames, IA

Mark S. Wipfli, PhD
U.S. Geological Survey, Fairbanks, AK

William R. Wise, PhD
University of Florida, Gainesville, FL
                U.S. ENVIRONMENTAL PROTECTION AGENCY SCIENCE ADVISORY BOARD
              PANEL FOR THE REVIEW OF THE EPA WATER BODY CONNECTIVITY REPORT
Amanda D. Rodewald, PhD (Chair)
Cornell University, Ithaca, NY

Allison Aldous, PhD
The Nature Conservancy, Portland, OR

Genevieve Ali, PhD
University of Manitoba, Winnipeg, MB, Canada
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                U.S. ENVIRONMENTAL PROTECTION AGENCY SCIENCE ADVISORY BOARD
          PANEL FOR THE REVIEW OF THE EPA WATER BODY CONNECTIVITY REPORT (continued)
J. David Allan, PhD
University of Michigan, Ann Arbor, MI

Lee Benda, PhD
Earth Systems Institute, Mt. Shasta, CA

Emily S. Bernhardt, PhD
Duke University, Durham, NC

Robert P. Brooks, PhD
Pennsylvania State University, University Park, PA

Kurt Fausch, PhD
Colorado State University, Fort Collins, CO

Siobhan Fennessy, PhD
Kenyon College, Gambler, OH

Michael Gooseff, PhD
Colorado State University, Fort Collins, CO

Judson Harvey, PhD
U.S. Geological Survey, Reston, VA

Charles Hawkins, PhD
Utah State University, Logan, UT

Lucinda B. Johnson, PhD
University of Minnesota Duluth, Duluth, MN

Michael Josselyn, PhD
Wetlands Research Associates, Inc., San Rafael, CA

LatifKalin, PhD
Auburn University, Auburn, AL

Kenneth Kolm, PhD
Hydrologic Systems Analysis, LLC, Golden, CO

Judith L. Meyer, PhD
University of Georgia, Lopez Island, WA
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                U.S. ENVIRONMENTAL PROTECTION AGENCY SCIENCE ADVISORY BOARD
         PANEL FOR THE REVIEW OF THE EPA WATER BODY CONNECTIVITY REPORT (continued)
Mark Murphy, PhD
Hassayampa Associates, Tucson, AZ

Duncan Patten, PhD
Arizona State University, Bozeman, MT

Mark Rains, PhD
University of South Florida, Tampa, FL

Ramesh Reddy, PhD
University of Florida, Gainesville, FL

Emma Rosi-Marshall, PhD
Gary Institute of Ecosystem Studies, Millbrook, NY

Jack Stanford, PhD
University of Montana, Poison, MT

Mazeika Sullivan, PhD
The Ohio State University, Columbus, OH

Jennifer Tank, PhD
University of Notre Dame, Notre Dame, IN

Maurice Valett, PhD
University of Montana, Missoula, MT

Ellen Wohl, PhD
Colorado State University, Fort Collins, CO
Stream and Wetland Connectivity:                                                           January 2015
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                                   PHOTO CREDITS
Front cover, Executive Summary, Chapter 5, and References
Back cover, Executive Summary, and References
Chapter 3
All other photos (U.S. EPA)
            Nambe Lake, New Mexico (L.C.
            Alexander, U.S. EPA)

            Children in Delaware inland wetland
            (Hennis H. Bartow, Delaware Center for
            the Inland Bays)

            Mayfly (Heptagenia culacanthd) (David
            H. Funk, Stroud Water Research Center)
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XIX
                                     January 2015

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                               ACKNOWLEDGMENTS
We gratefully acknowledge support provided by ICF International in Durham, NC and Tetra Tech, Inc. in
Owings Mills, MD for preparation and production of draft and final reports; Eastern Research Group, Inc.
in Lexington, MA for organizing and managing an independent peer review of a draft report; and Ms. Iris
Goodman, Dr. Thomas Armitage, and Dr. Angela Nugent at the U.S. Environmental Protection Agency,
Science Advisory Board (SAB) in Washington, DC for their service as Designated Federal Officers for the
SAB review of this report.
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                                    January 2015

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BACKGROUND
The objective of the Clean Water Act is to restore and maintain the chemical, physical, and biological
integrity of the nation's waters. The U.S. Environmental Protection Agency's (U.S. EPA's) Office of
Research and Development developed this report to inform rulemaking by the U.S. EPA and U.S. Army
Corps of Engineers (U.S. ACE) on the definition of "waters of the United States" under the Clean Water
Act (CWA). Its purpose is to summarize current scientific understanding about the connectivity and
mechanisms by which streams and wetlands, singly or in aggregate, affect the physical, chemical, and
biological integrity of downstream waters. The focus of the review is on surface and shallow subsurface
connections of small or temporary streams, nontidal wetlands, and certain open waters. Because this
report is a technical review of peer-reviewed scientific literature, it neither considers nor sets forth legal
standards for CWA jurisdiction, nor does it establish EPA policy.

The report is organized into six chapters. Chapter 1 outlines the purpose, scientific context, and
approach of the report. Chapter 2 describes the components of a river system and watershed; the types
of physical, chemical, and biological connections that link those components; the factors that influence
connectivity at various temporal and spatial scales; and methods for quantifying connectivity. Chapter 3
reviews literature on connectivity in stream networks in terms of physical, chemical, and biological
connections and their resulting effects on downstream waters. Chapter 4 reviews literature on the
connectivity and effects of nontidal wetlands and certain open waters on downstream waters. Chapter 5
applies concepts and evidence from previous chapters to six case studies from published literature on
Carolina and Delmarva bays, oxbow lakes, prairie potholes, prairie streams, southwestern streams, and
vernal pools. Chapter 6 summarizes key findings and conclusions, identifies data gaps, and briefly
discusses research approaches that could fill those gaps. A glossary of scientific terms used in the report
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and detailed case studies of selected systems (summarized in Chapter 5) are included in Appendix A and
Appendix B, respectively.


SUMMARY OF MAJOR CONCLUSIONS
Based on the review and synthesis of more than 1,200 publications from the peer reviewed scientific
literature, the evidence supports five major conclusions. Citations have been omitted from the text to
improve readability; please refer to individual chapters for supporting publications and additional
information.

       Conclusion 1: Streams
       The scientific literature unequivocally demonstrates that streams, individually or cumulatively,
       exert a strong influence on the integrity of downstream waters. All tributary streams, including
       perennial, intermittent, and ephemeral streams, are physically, chemically, and biologically
       connected to downstream rivers via channels and associated alluvial deposits where water and
       other materials are concentrated, mixed, transformed, and transported. Streams are the
       dominant source of water in most rivers, and the majority of tributaries are perennial,
       intermittent, or ephemeral headwater streams. Headwater streams also convey water into local
       storage compartments such as ponds, shallow aquifers, or stream banks, and into regional and
       alluvial aquifers; these local storage compartments are important sources of water for
       maintaining baseflow in rivers. In  addition to water, streams transport sediment, wood, organic
       matter, nutrients, chemical contaminants, and many of the organisms found in rivers. The
       literature provides robust evidence that streams are biologically connected to downstream
       waters by the dispersal and migration of aquatic and semiaquatic organisms, including fish,
       amphibians, plants, microorganisms, and invertebrates, that use both upstream and
       downstream habitats during one or more stages of their life cycles, or provide food resources to
       downstream communities. In addition to material transport and biological connectivity,
       ephemeral, intermittent, and perennial flows influence fundamental biogeochemical processes
       by connecting channels and shallow ground water with other landscape elements. Physical,
       chemical, and biological connections between streams and downstream waters interact via
       integrative processes such as nutrient spiraling, in which stream communities assimilate and
       chemically transform large quantities of nitrogen and other nutrients that otherwise would be
       transported directly downstream, increasing nutrient loads and associated impairments due to
       excess nutrients in downstream waters.

       Conclusion 2: Riparian/Floodplain Wetlands and Open Waters
       The literature clearly shows that wetlands and open waters in riparian areas and floodplains are
       physically, chemically, and biologically integrated with rivers via functions that improve
       downstream water quality, including the temporary storage and deposition of channel-forming
       sediment and woody debris, temporary storage of local ground water that supports baseflow in
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       rivers, and transformation and transport of stored organic matter. Riparian/floodplain wetlands
       and open waters improve water quality through the assimilation, transformation, or
       sequestration of pollutants, including excess nutrients and chemical contaminants such as
       pesticides and metals, that can degrade downstream water integrity. In addition to providing
       effective buffers to protect downstream waters from point source and nonpoint source
       pollution, these systems form integral components of river food webs, providing nursery habitat
       for breeding fish and amphibians, colonization opportunities for stream invertebrates, and
       maturation habitat for stream insects. Lateral expansion and contraction of the river in its
       floodplain result in an exchange of organic matter and organisms, including fish populations that
       are adapted to use floodplain habitats for feeding and spawning during high water, that are
       critical to river ecosystem function. Riparian/floodplain wetlands and open waters also affect
       the integrity of downstream waters by subsequently releasing (desynchronizing) floodwaters
       and retaining large volumes of stormwater, sediment, and contaminants in runoff that could
       otherwise negatively affect the condition or function of downstream waters.

       Conclusion 3: Non-floodplain Wetlands and Open Waters
       Wetlands and open waters in non-floodplain landscape settings (hereafter called "non-
       floodplain wetlands") provide numerous functions that benefit downstream water integrity.
       These functions include storage of floodwater; recharge of ground water that sustains river
       baseflow; retention and transformation of nutrients, metals, and pesticides; export of organisms
       or reproductive propagules to downstream waters; and habitats needed for stream species. This
       diverse group of wetlands (e.g., many prairie potholes, vernal pools, playa lakes) can be
       connected to downstream waters through surface-water, shallow subsurface-water, and
       ground-water flows and through biological and chemical connections.

       In general, connectivity of non-floodplain wetlands occurs along a gradient (Conclusion 4), and
       can be described in terms of the frequency, duration, magnitude, timing, and rate of change of
       water, material, and biotic fluxes to downstream waters. These descriptors are influenced by
       climate, geology, and terrain, which interact with factors such as the magnitudes of the various
       functions within wetlands (e.g., amount of water storage or carbon export) and their proximity
       to downstream waters to determine where wetlands occur along the connectivity gradient. At
       one end of this gradient, the functions of non-floodplain wetlands clearly affect the condition of
       downstream waters if a visible (e.g., channelized) surface-water or a regular shallow subsurface-
       water connection to the river network is present. For non-floodplain wetlands lacking a
       channelized surface or regular shallow subsurface connection (i.e., those at intermediate points
       along the gradient of connectivity), generalizations about their specific effects on downstream
       waters from the available literature are difficult because information on both function and
       connectivity is needed. Although there is ample evidence that non-floodplain wetlands provide
       hydrologic, chemical, and biological functions that affect material fluxes, to date, few scientific
       studies  explicitly addressing connections between non-floodplain wetlands and river networks
       have been published in the peer-reviewed literature. Even fewer publications specifically focus
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       on the frequency, duration, magnitude, timing, or rate of change of these connections. In
       addition, although areas that are closer to rivers and streams have a higher probability of being
       connected than areas farther away when conditions governing the type and quantity of flows—
       including soil infiltration rate, wetland storage capacity, hydraulic gradient, etc.—are similar,
       information to determine if this similarity holds is generally not provided in the studies we
       reviewed. Thus, current science does not support evaluations of the degree of connectivity for
       specific groups or classes of wetlands (e.g., prairie potholes or vernal pools). Evaluations of
       individual wetlands or groups of wetlands, however, could be possible through case-by-case
       analysis.

       Some effects of non-floodplain wetlands on downstream waters are due to their isolation, rather
       than their connectivity. Wetland "sink" functions that trap materials and prevent their export to
       downstream waters (e.g., sediment and entrained pollutant removal, water storage) result
       because of the wetland's ability to isolate material fluxes. To establish that such functions
       influence downstream waters, we also need to know that the wetland intercepts materials that
       otherwise would reach the downstream water. The literature we reviewed does provide limited
       examples of direct effects of wetland isolation on downstream waters, but not for classes of
       wetlands (e.g., vernal pools). Nevertheless, the literature we reviewed enables us to conclude
       that sink functions of non-floodplain wetlands, which result in part from their relative isolation,
       will affect a downstream water when these wetlands are situated between the downstream
       water and known point or nonpoint sources of pollution, and thus intersect flowpaths between
       the pollutant source and downstream waters.

       Conclusion 4: Degrees and Determinants of Connectivity
       Watersheds are integrated at multiple spatial and temporal scales by flows of surface water and
       ground water, transport and transformation of physical and chemical materials, and movements
       of organisms. Although all parts of a watershed are connected to some degree—by the
       hydrologic cycle or dispersal of organisms, for example—the degree and downstream effects of
       those connections vary spatially and temporally, and are determined by characteristics of the
       physical, chemical, and biological environments and by human activities.

       Stream and wetland connections have particularly important consequences for downstream
       water integrity. Most of the materials—broadly defined as any physical, chemical, or biological
       entity—in rivers, for example, originate from aquatic  ecosystems located upstream or elsewhere
       in the watershed. Longitudinal flows through ephemeral, intermittent, and perennial stream
       channels are much more efficient for transport of water, materials, and organisms than diffuse
       overland flows, and areas that concentrate water provide mechanisms for the storage and
       transformation, as well as transport, of materials.

       Connectivity of streams and wetlands to downstream waters occurs along a continuum that can
       be described in terms of the frequency, duration, magnitude, timing, and rate of change of water,
       material, and biotic fluxes to downstream waters. These terms, which we refer to collectively as
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       connectivity descriptors, characterize the range over which streams and wetlands vary and shift
       along the connectivity gradient in response to changes in natural and anthropogenic factors and,
       when considered in a watershed context, can be used to predict probable effects of different
       degrees of connectivity over time. The evidence unequivocally demonstrates that the stream
       channels and riparian/floodplain wetlands or open waters that together form river networks
       are clearly connected to downstream waters in ways that profoundly influence downstream
       water integrity. The connectivity and effects of non-floodplain wetlands and open waters are
       more variable and thus more difficult to address solely from evidence available in peer-
       reviewed studies.

       Variations in the degree of connectivity influence the range of functions provided by streams
       and wetlands, and are critical to the integrity and sustainability of downstream waters.
       Connections with low values of one or more descriptors (e.g., low-frequency, low-duration
       streamflows caused by flash floods) can have important downstream effects when considered in
       the context of other descriptors (e.g., large magnitude of water transfer). At the other end of the
       frequency range, high-frequency, low-magnitude vertical (surface-subsurface) and lateral flows
       contribute to aquatic biogeochemical processes, including nutrient and contaminant
       transformation and organic matter accumulation. The timing of an event can alter both
       connectivity and the magnitude of its downstream effect. For example, when soils become
       saturated by previous rainfall events, even low or moderate rainfall can cause streams or
       wetlands to overflow, transporting water and materials to downstream waters. Fish that use
       nonperennial or perennial headwater stream habitats to spawn or rear young, and invertebrates
       that move into seasonally inundated floodplain wetlands prior to emergence, have life cycles
       that are synchronized with the timing of flows, temperature thresholds, and food resource
       availability in those habitats.

       Conclusion 5: Cumulative Effects
       The incremental effects of individual streams and wetlands are cumulative across entire
       watersheds and therefore must be evaluated in context with other streams and wetlands.
       Downstream waters are the time-integrated result of all waters contributing to them. For
       example, the amount of water or biomass contributed by a specific ephemeral stream in a given
       year might be small, but the aggregate contribution of that stream over multiple years, or by all
       ephemeral streams draining that watershed in a given year or over multiple years, can have
       substantial consequences on the integrity of the downstream waters. Similarly, the downstream
       effect of a single event, such as pollutant discharge into a single stream  or wetland, might be
       negligible but the cumulative effect of multiple discharges could degrade the  integrity of
       downstream waters.

       In addition, when considering the effect of an individual stream or wetland, all contributions and
       functions of that stream or wetland should be evaluated cumulatively. For example, the same
       stream transports water, removes excess nutrients, mitigates flooding,  and provides refuge for

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       fish when conditions downstream are unfavorable; if any of these functions is ignored, the
       overall effect of that stream would be underestimated.


SUPPORT FOR MAJOR CONCLUSIONS
This report synthesizes a large body of scientific literature on the connectivity and mechanisms by
which streams, wetlands, and open waters, singly or in aggregate, affect the physical, chemical, and
biological integrity of downstream waters. The major conclusions reflect the strength of evidence
currently available in the peer-reviewed scientific literature for assessing the connectivity and
downstream effects of water bodies identified in Chapter 1 of this report.

The conclusions of this report were corroborated by two independent peer reviews by scientists
identified in the front matter of this report.

The term connectivity is defined in this report as the degree to which components of a watershed are
joined and interact by transport mechanisms that function across multiple spatial and temporal scales.
Connectivity is determined by the characteristics of both the physical landscape and the biota of the
specific system. Our review found strong evidence supporting the central roles of the physical, chemical,
and biological connectivity of streams, wetlands, and open waters—encompassing varying degrees of
both connection and isolation—in maintaining the structure and function of downstream waters,
including rivers, lakes, estuaries, and oceans. Our review also found strong evidence demonstrating the
various mechanisms by which material and biological linkages from streams, wetlands, and open waters
affect downstream waters, classified here into five functional categories (source, sink, refuge, lag, and
transformation; discussed below), and modify the timing of transport and the quantity and quality of
resources available to downstream ecosystems and communities. Thus, the currently available literature
provided a large body of evidence for assessing the types of connections and functions by which streams
and wetlands produce the  range of observed effects on the integrity of downstream waters.

We identified five categories of functions by which streams, wetlands, and open waters influence the
timing, quantity, and quality of resources available to downstream waters:

    •   Source: the net export of materials, such as water and food resources;

    •   Sink: the net removal or storage of materials, such as sediment and contaminants;

    •   Refuge: the protection of materials, especially organisms;

    •   Transformation: the transformation of materials, especially nutrients and chemical
       contaminants, into different physical or chemical forms; and

    •   Lag: the delayed or regulated release of materials, such as storm water.

These functions are not mutually exclusive; for example, the  same stream or wetland can be both a
source of organic matter and a sink for nitrogen. The presence or absence of these functions, which

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depend on the biota, hydrology, and environmental conditions in a watershed, can change over time; for
example, the same wetland can attenuate runoff during storm events and provide ground-water
recharge following storms. Further, some functions work in conjunction with others; a lag function can
include transformation of materials prior to their delayed release. Finally, effects on downstream waters
should consider both actual function and potential function. A potential function represents the capacity
of an ecosystem to perform that function under suitable conditions. For example, a wetland with high
capacity for denitrification is a potential sink for nitrogen, a nutrient that becomes a contaminant when
present in excessive concentrations. In the absence of nitrogen, this capacity represents the wetland's
potential function. If nitrogen enters the wetland (e.g., from fertilizer in runoff), it is removed from the
water; this removal represents the wetland's actual function. Both potential and actual functions play
critical roles in protecting and restoring downstream waters as environmental conditions change.

The evidence unequivocally demonstrates that the stream channels and riparian/floodplain wetlands or
open waters that together form river networks are clearly connected to downstream waters in ways
that profoundly influence downstream water integrity. The body of literature documenting connectivity
and downstream effects was most abundant for perennial and intermittent streams, and for
riparian/floodplain wetlands. Although less abundant, the evidence for connectivity and downstream
effects of ephemeral streams was strong and compelling, particularly in context with the large body of
evidence supporting the physical connectivity and cumulative effects of channelized flows that form and
maintain stream networks.

As stated in Conclusion 3, the connectivity and effects of wetlands and open waters that lack visible
surface connections to other water bodies are more difficult to address solely from evidence available in
the peer-reviewed literature. The limited evidence currently available shows that these systems have
important hydrologic, water-quality, and habitat functions that can affect downstream waters where
connections to them exist; the literature also provides limited examples of direct effects of non-
floodplain wetland isolation on downstream water integrity. Currently available peer-reviewed
literature, however, does not identify which types or classes of non-floodplain wetlands have or lack the
types of connections needed to convey the effects on downstream waters of functions, materials, or
biota provided by those wetlands.


KEY FINDINGS FOR MAJOR CONCLUSIONS
This section summarizes key findings for each of the five major conclusions, above and in Chapter 6 of
the report. Citations have been omitted from the text to improve readability; please refer to individual
chapters for supporting publications and additional information.

Conclusion 1, Streams: Key Findings
   •   Streams are hydrologically connected to downstream waters via channels that convey surface
       and subsurface water either year-round (i.e., perennial flow), weekly to seasonally (i.e.,
       intermittent flow), or only in direct response to precipitation (i.e., ephemeral flow). Streams are

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       the dominant source of water in most rivers, and the majority of tributaries are perennial,
       intermittent, or ephemeral headwater streams. For example, headwater streams, which are the
       smallest channels where streamflows begin, are the cumulative source of approximately 60% of
       the total mean annual flow to all northeastern U.S. streams and rivers.
    •  In addition to downstream transport, headwaters convey water into local storage compartments
       such as ponds, shallow aquifers, or stream banks, and into regional and alluvial aquifers. These
       local storage compartments are important sources of water for maintaining baseflow in rivers.
       Streamflow typically depends on the delayed (i.e., lagged) release of shallow ground water from
       local storage, especially during dry periods and in areas with shallow ground-water tables and
       pervious subsurfaces. For example, in the southwestern United States, short-term shallow
       ground-water storage in alluvial floodplain aquifers, with gradual release into stream channels,
       is a major source of annual flow in rivers.
    •  Infrequent, high-magnitude events are especially important for transmitting materials from
       headwater streams in most river networks. For example, headwater streams, including
       ephemeral and intermittent streams, shape river channels by accumulating and gradually or
       episodically releasing stored materials such as sediment and large woody debris. These
       materials help structure stream and river channels by slowing the flow of water through
       channels and providing substrate and habitat for aquatic organisms.
    •  There is strong evidence that headwater streams function as nitrogen sources (via export) and
       sinks (via uptake and transformation) for river networks. For example, one study estimated that
       rapid nutrient cycling in small streams with no agricultural  or urban impacts removed 20-40%
       of the nitrogen that otherwise would be delivered to downstream waters. Nutrients are
       necessary to support aquatic life, but excess nutrients lead to eutrophication and hypoxia, in
       which over-enrichment causes dissolved oxygen concentrations to fall below the  level necessary
       to sustain most aquatic animal life in the stream and streambed. Thus, the influence of streams
       on nutrient loads can have significant repercussions for hypoxia in downstream waters.
    •  Headwaters provide habitat that is critical for completion of one or more life-cycle stages of
       many aquatic and semiaquatic species capable of moving throughout river networks. Evidence
       is strong that headwaters provide habitat for complex life-cycle completion; refuge from
       predators, competitors, parasites, or adverse physical conditions in rivers (e.g., temperature or
       flow extremes, low dissolved oxygen, high sediment); and reservoirs of genetic- and species-
       level diversity. Use of headwater streams as habitat is especially critical for the many species
       that migrate between small streams and marine environments during their life cycles (e.g.,
       Pacific and Atlantic salmon, American eels, certain lamprey  species). The presence of these
       species within river networks provides robust evidence of biological connections between
       headwaters and larger rivers; because these organisms also transport nutrients and other
       materials as they migrate, their presence also provides  evidence of biologically mediated
       chemical connections. In prairie streams, many fishes swim upstream into tributaries to release
       eggs, which develop as they are transported downstream.
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    •  Human alterations affect the frequency, duration, magnitude, timing, and rate of change of
       connections between headwater streams, including ephemeral and intermittent streams, and
       downstream waters. Human activities and built structures (e.g., channelization, dams, ground-
       water withdrawals) can either enhance or fragment longitudinal connections between
       headwater streams and downstream waters, while also constraining lateral and vertical
       exchanges and tightly controlling the temporal dimension of connectivity. In many cases,
       research on human alterations has enhanced our understanding of the headwater stream-
       downstream water connections and their consequences. Recognition of these connections and
       effects has encouraged the development of more sustainable practices and infrastructure to
       reestablish and manage connections, and ultimately to protect and restore the integrity of
       downstream waters.

Conclusion 2, Riparian/Floodplain Wetlands and Open Waters:  Key Findings
    •  Riparian areas and floodplains connect upland and aquatic environments through both surface
       and subsurface hydrologic flowpaths. These areas are therefore uniquely situated in watersheds
       to receive and process waters that pass over densely vegetated areas and through subsurface
       zones before the waters reach streams and rivers. When pollutants reach a riparian or
       floodplain wetland, they can be sequestered in sediments, assimilated into wetland plants and
       animals, transformed into less harmful or mobile forms or compounds, or lost to the
       atmosphere. Wetland potential for biogeochemical transformations (e.g., denitrification) that
       can improve downstream water quality is influenced by local factors, including anoxic
       conditions and slow organic matter decomposition, shallow water tables, wetland plant
       communities, permeable soils, and complex  topography.
    •  Riparian/floodplain wetlands can reduce flood peaks by storing and desynchronizing
       floodwaters. They can also maintain river baseflows by recharging alluvial aquifers. Many
       studies have documented the ability of riparian/floodplain wetlands to reduce flood pulses by
       storing excess water from streams and rivers. One review of wetland studies reported that
       riparian wetlands reduced or delayed floods in 23 of 28 studies. For example, peak discharges
       between upstream and downstream gaging stations on the Cache River in Arkansas were
       reduced 10-20% primarily due to floodplain water storage.
    •  Riparian areas and floodplains store large amounts of sediment and organic matter from
       upstream and from upland areas. For example, riparian areas have been shown to remove
       80-90% of sediments leaving agricultural fields in North Carolina.
    •  Ecosystem function within a river system is  driven in part by biological connectivity that links
       diverse biological communities with the river system. Movements of organisms that connect
       aquatic habitats and their populations, even across different watersheds, are important for the
       survival of individuals, populations, and species, and for the functioning of the river ecosystem.
       For example, lateral expansion and contraction of the river in its floodplain result in an exchange
       of matter and organisms, including fish populations that are adapted to use floodplain habitats

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       for feeding and spawning during high water. Wetland and aquatic plants in floodplains can
       become important seed sources for the river network, especially if catastrophic flooding scours
       vegetation and seed banks in other parts of the channel. Many invertebrates exploit temporary
       hydrologic connections between rivers and floodplain wetland habitats, moving into these
       wetlands to feed, reproduce, or avoid harsh environmental conditions and then returning to the
       river network. Amphibians and aquatic reptiles commonly use both streams and
       riparian/floodplain wetlands to hunt, forage, overwinter, rest, or hide from predators. Birds can
       spatially integrate the watershed landscape through biological connectivity.

Conclusion 3, Non-floodplain Wetlands and Open Waters: Key Findings
    •  Water storage by wetlands well outside of riparian or floodplain areas can affect streamflow.
       Hydrologic models of prairie potholes in the Starkweather Coulee subbasin (North Dakota) that
       drains to Devils Lake  indicate that increasing the volume of pothole storage across the subbasin
       by approximately 60% caused simulated total annual streamflow to decrease 50% during a
       series of dry years and 20% during wet years.  Similar simulation studies of watersheds that feed
       the Red River of the North in North Dakota and Minnesota demonstrated qualitatively
       comparable results, suggesting that the ability of potholes to modulate streamflow could be
       widespread across eastern portions of the prairie pothole region. This work also indicates that
       reducing water storage capacity of wetlands by connecting formerly isolated potholes through
       ditching or drainage to the  Devils Lake and Red River basins could increase stormflow and
       contribute to downstream flooding. In many agricultural areas already crisscrossed by extensive
       drainage systems, total streamflow and baseflow are increased by directly connecting potholes
       to stream networks. The impacts of changing streamflow are numerous, including altered flow
       regime, stream geomorphology, habitat, and ecology. The presence or absence of an effect of
       prairie pothole water storage on streamflow depends on many factors, including patterns of
       precipitation, topography, and degree of human alteration. For example, in parts of the prairie
       pothole region with low precipitation, low stream density, and little human alteration,
       hydrologic connectivity between prairie potholes and streams or rivers is likely to be low.
    •  Non-floodplain wetlands act as sinks and transformers for various pollutants, especially
       nutrients, which at excess levels can adversely impact human and ecosystem health and pose  a
       serious pollution problem in the  United States. In one study, sewage waste waters were applied
       to forested wetlands in Florida for 4.5 years; more than 95% of the phosphorus, nitrate,
       ammonium, and total nitrogen were removed by the wetlands during the study period, and
       66-86% of the nitrate removed was attributed to the process of denitrification. In another
       study, sizeable phosphorus retention (0.3 to 8.0 mg soluble reactive P nr2  d-1) occurred in
       marshes that comprised only 7% of the lower Lake Okeechobee basin area in Florida. A non-
       floodplain bog in Massachusetts was reported to sequester nearly 80% of nitrogen inputs from
       various sources, including atmospheric deposition, and prairie pothole wetlands in the upper
       Midwest were found to remove >80% of the nitrate load via denitrification. A large prairie
       marsh was found to remove 86% of nitrate, 78% of ammonium, and 20% of phosphate through
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       assimilation and sedimentation, sorption, and other mechanisms. Together, these and other
       studies indicate that onsite nutrient removal by non-floodplain wetlands is substantial and
       geographically widespread. The effects of this removal on rivers are generally not reported in
       the literature.
       Non-floodplain wetlands provide unique and important habitats for many species, both common
       and rare. Some of these species require multiple types of waters to complete their full life cycles,
       including downstream waters. Abundant or highly mobile species play important roles in
       transferring energy and materials between non-floodplain wetlands and downstream waters.
       Biological connections are likely to occur between most non-floodplain wetlands and
       downstream waters through either direct or stepping stone movement of amphibians,
       invertebrates, reptiles, mammals, and seeds of aquatic plants, including colonization by invasive
       species. Many species in those groups that use both stream and wetland habitats are capable of
       dispersal distances equal to or greater than distances between many wetlands and river
       networks. Migratory birds can be an important vector of long-distance dispersal of plants and
       invertebrates between non-floodplain wetlands and the river network, although their influence
       has not been quantified. Whether those connections are of sufficient magnitude to impact
       downstream waters will either require estimation of the magnitude of material fluxes or
       evidence that these movements of organisms are required for the survival and persistence of
       biota that contribute to the integrity of downstream waters.
       Spatial proximity is one important determinant of the magnitude, frequency and duration of
       connections between wetlands and streams that will ultimately influence the fluxes of water,
       materials and biota between wetlands and downstream waters. However, proximity alone is not
       sufficient to determine connectivity, due to local variation in factors such as slope and
       permeability.
       The cumulative influence of many individual wetlands within watersheds can strongly affect the
       spatial scale, magnitude, frequency, and duration of hydrologic, biological and chemical fluxes or
       transfers of water and materials to downstream waters. Because of their aggregated influence,
       any evaluation of changes to individual wetlands should be considered in the context of past and
       predicted changes (e.g., from climate change) to other wetlands within the same watershed.
       Non-floodplain wetlands can be hydrologically connected directly to river networks through
       natural or constructed channels, nonchannelized surface flows, or subsurface flows, the latter of
       which can travel long distances to affect downstream waters. A wetland surrounded by uplands
       is defined as "geographically isolated." Our review found that, in some cases, wetland types such
       as vernal pools and coastal depressional wetlands are collectively—and incorrectly—referred to
       as geographically isolated. Technically, the term "geographically isolated" should be applied only
       to the particular wetlands within a type or class that are completely surrounded by uplands.
       Furthermore, "geographic isolation" should not be confused with functional isolation, because
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       geographically isolated wetlands can still have hydrologic, chemical, and biological connections
       to downstream waters.
    •  Non-floodplain wetlands occur along a gradient of hydrologic connectivity-isolation with
       respect to river networks, lakes, or marine/estuarine water bodies. This gradient includes, for
       example, wetlands that serve as origins for stream channels that have permanent surface-water
       connections to the river network; wetlands with outlets to stream channels that discharge to
       deep ground-water aquifers; geographically isolated wetlands that have local ground-water or
       occasional surface-water connections to downstream waters; and geographically isolated
       wetlands that have minimal hydrologic connection to other water bodies (but which could
       include surface and subsurface connections to other wetlands). This gradient can exist among
       wetlands of the same type or in the same geographic region.
    •  Caution should be used in interpreting connectivity for wetlands that have been designated as
       "geographically isolated" because (1) the term can be applied broadly to a heterogeneous group
       of wetlands, which can include wetlands that are not actually geographically isolated; (2)
       wetlands with permanent channels could be miscategorized as geographically isolated if the
       designation is based on maps or imagery with inadequate spatial resolution, obscured views,
       etc.; and (3) wetland complexes could have connections to downstream waters through stream
       channels even if individual wetlands within the complex are geographically isolated. For
       example, a recent study examined hydrologic connectivity in a complex of wetlands on the Texas
       Coastal Plain. The wetlands in this complex have been considered to be a type of geographically
       isolated wetland; however, collectively they are connected both geographically and
       hydrologically to downstream waters in the area: During an almost 4-year study period, nearly
       20% of the precipitation that fell on the wetland complex flowed out through an intermittent
       stream into downstream waters. Thus, wetland complexes could have connections to
       downstream waters through stream channels even when the individual wetland components
       are geographically isolated.

Conclusion 4, Degrees and Determinants of Connectivity: Key Findings
    •  The surface-water and ground-water flowpaths (hereafter, hydrologic flowpaths), along which
       water and materials are transported and transformed, determine variations in the degree of
       physical and chemical connectivity. These flowpaths are controlled  primarily by variations in
       climate, geology, and terrain within and among watersheds and over time. Climate, geology, and
       terrain are reflected locally in factors such as rainfall and snowfall intensity, soil infiltration
       rates, and the direction of ground-water flows. These local factors interact with the landscape
       positions of streams and wetlands relative to downstream waters, and with functions (such as
       the removal or transformation of pollutants) performed by those streams and wetlands to
       determine connectivity gradients.
    •  Gradients of biological connectivity (i.e., the active or passive movements of organisms through
       water or air and over land that connect populations) are determined primarily by species

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       assemblages, and by features of the landscape (e.g., climate, geology, terrain) that facilitate or
       impede the movement of organisms. The temporal and spatial scales at which biological
       pathways connect aquatic habitats depend on characteristics of both the landscape and species,
       and overland transport or movement can occur across watershed boundaries. Dispersal is
       essential for population persistence, maintenance of genetic diversity, and evolution of aquatic
       species. Consequently, dispersal strategies reflect aquatic species' responses and adaptations to
       biotic and abiotic environments, including spatial and temporal variation in resource availability
       and quality. Species' traits and behaviors encompass species-environment relationships over
       time, and provide an ecological and evolutionary context for evaluating biological connectivity
       in a particular watershed or group of watersheds.
    •  Pathways for chemical transport and transformation largely follow hydrologic flowpaths, but
       sometimes follow biological pathways (e.g., nutrient transport from wetlands to coastal waters
       by migrating waterfowl, upstream transport of marine-derived nutrients by spawning of
       anadromous fish, uptake and removal of nutrients by emerging stream insects).
    •  Human activities alter naturally occurring gradients of physical, chemical, and biological
       connectivity by modifying the frequency, duration, magnitude, timing, and rate of change of
       fluxes, exchanges, and transformations. For example, connectivity can be reduced by dams,
       levees, culverts, water withdrawals, and habitat destruction, and can be increased by effluent
       discharges, channelization, drainage ditches and tiles, and impervious surfaces.

Conclusion 5, Cumulative Effects: Key Findings
    •  Structurally and functionally, stream-channel networks and the watersheds they drain are
       fundamentally cumulative in how they are formed and maintained. Excess water from
       precipitation that is not evaporated, taken up by organisms, or stored in soils and geologic
       layers moves downgradient by gravity as overland flow or through channels carrying sediment,
       chemical constituents, and organisms. These channels concentrate surface-water flows and are
       more efficient than overland (i.e., diffuse) flows in transporting water and materials, and are
       reinforced over time by recurrent flows.
    •  Connectivity between streams and rivers provides opportunities for materials, including
       nutrients and chemical  contaminants,  to be transformed chemically as they are transported
       downstream. Although highly efficient at the transport of water and other physical materials,
       streams are dynamic ecosystems with permeable beds and banks that interact with other
       ecosystems above and below the surface. The exchange of materials between surface and
       subsurface areas involves a series of complex physical, chemical, and biological alterations that
       occur as materials move through different parts of the river system. The amount and  quality of
       such materials that eventually reach a river are determined by the aggregate effect of these
       sequential alterations that begin at the source waters, which can be at some distance  from the
       river. The opportunity for transformation of material (e.g., biological uptake, assimilation, or
       beneficial transformation) in intervening stream reaches increases with distance to the river.

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       Nutrient spiraling, the process by which nutrients entering headwater streams are transformed
       by various aquatic organisms and chemical reactions as they are transported downstream, is
       one example of an instream alteration that exhibits significant beneficial effects on downstream
       waters. Nutrients (in their inorganic form) that enter a headwater stream (e.g., via overland
       flow) are first removed from the water column by streambed algal and microbial populations.
       Fish or insects feeding on algae and microbes take  up some of those nutrients, which are
       subsequently released back into the stream via excretion and decomposition (i.e., in their
       organic form), and the cycle is repeated. In each phase of the cycling process—from dissolved
       inorganic nutrients in the water column, through microbial uptake, subsequent transformations
       through the food web, and back to dissolved nutrients in the water column—nutrients are
       subject to downstream transport. Stream and wetland capacities for nutrient cycling have
       important implications for the form and concentration of nutrients exported to downstream
       waters.
       Cumulative effects across a watershed must be considered when quantifying the frequency,
       duration, and magnitude of connectivity, to evaluate the downstream effects of streams and
       wetlands. For example, although the probability of a large-magnitude transfer of organisms
       from any given headwater stream in a given year might be low (i.e., a low-frequency connection
       when each stream is considered individually), headwater streams are the most abundant type of
       stream in most watersheds. Thus, the overall probability of a large-magnitude transfer of
       organisms is higher when considered for all headwater streams in a watershed—that is, a high-
       frequency connection is present when headwaters are considered cumulatively at the
       watershed scale, compared with probabilities of transport for streams individually. Similarly, a
       single pollutant discharge might be negligible but the cumulative effect of multiple discharges
       could degrade  the integrity of downstream waters. Riparian open waters (e.g., oxbow lakes),
       wetlands, and vegetated areas cumulatively can retain up to 90% of eroded clays, silts, and
       sands that otherwise would enter stream channels. The larger amounts of snowmelt and
       precipitation cumulatively held by many wetlands  can reduce the potential for flooding at
       downstream locations. For example, wetlands in the prairie pothole region cumulatively stored
       about 11-20% of the precipitation in one watershed.
       The combination of diverse habitat types and abundant food resources cumulatively makes
       floodplains important foraging, hunting, and breeding sites for fish, aquatic life stages of
       amphibians, and aquatic invertebrates. The scale of these cumulative effects can be extensive;
       for example, coastal ibises travel up to 40 km to obtain food from freshwater floodplain
       wetlands for nesting chicks, which cannot tolerate  salt levels in local food resources until they
       fledge.
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CLOSING COMMENTS
The structure and function of downstream waters highly depend on materials—broadly defined as any
physical, chemical, or biological entity—that originate outside of the downstream waters. Most of the
constituent materials in rivers, for example, originate from aquatic ecosystems located upstream in the
drainage network or elsewhere in the drainage basin, and are transported to the river through
flowpaths illustrated in the introduction to this report. Thus, the effects of streams, wetlands, and open
waters on rivers are determined by the presence of (1) physical, chemical, or biological pathways that
enable (or inhibit) the transport of materials and organisms to downstream waters; and (2) functions
within the streams, wetlands, and open waters that alter the quantity and quality of materials and
organisms transported along those pathways to downstream waters.

The strong hydrologic connectivity of river networks is apparent in the existence of stream channels
that form the physical structure of the network itself. Given the evidence reviewed in this report, it is
clear that streams and rivers are much more than a system of physical channels for efficiently conveying
water and other materials downstream. The presence of physical channels, however, is a compelling line
of evidence for surface-water connections from tributaries, or water bodies of other types, to
downstream waters. Physical channels are defined by continuous bed-and-bank structures, which can
include apparent disruptions (such as by bedrock outcrops, braided channels, flow-through wetlands)
associated with changes in the material and gradient over and through which water flows. The
continuation of bed and banks downgradient from  such disruptions is evidence of the surface
connection with the channel that is upgradient of the perceived disruption.

Although currently available peer-reviewed literature does not identify which types of non-floodplain
wetlands have or lack the types of connections needed to convey functional effects to downstream
waters, additional information (e.g., field assessments, analysis of existing or new data, reports from
local resource agencies) could be used in case-by-case analysis of non-floodplain wetlands. Importantly,
information from emerging research into the connectivity of non-floodplain wetlands, including studies
of the types identified in Section 4.5.2 of this report, could close some of the current data gaps in the
near future. Recent scientific advances in the fields of mapping, assessment, modeling, and landscape
classification indicate that increasing availability of high-resolution data sets, promising new
technologies for watershed-scale analyses, and methods for classifying landscape units by hydrologic
behavior can facilitate and improve the accuracy of connectivity assessments. Emerging research that
expands our ability to detect and monitor ecologically relevant connections at appropriate scales,
metrics to accurately measure effects on downstream integrity, and management practices that apply
what we already know about ecosystem function will contribute to our ability to identify waters of
national importance and maintain the long-term sustainability and resiliency of valued water resources.
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1.1   Purpose
The objective of the Clean Water Act is to restore and maintain the chemical, physical, and biological
integrity of the nation's waters. The U.S. Environmental Protection Agency's (U.S. EPA's) Office of
Research and Development developed this report to inform rulemaking by the U.S. EPA and U.S. ACE on
the definition of "waters of the United States" under the Clean Water Act (CWA). Its purpose is to
summarize current scientific understanding about the connectivity and mechanisms by which streams
and wetlands, singly or in aggregate, affect the physical, chemical, and biological integrity of
downstream waters. Because this report is a technical review of peer-reviewed scientific literature, it
does not consider or set forth legal standards for CWA jurisdiction. Rather, the report evaluates,
summarizes, and synthesizes the available peer-reviewed scientific literature to address three
questions:
    1.  What are the physical, chemical, and biological connections to and effects of ephemeral,
       intermittent, and perennial streams on downstream waters (e.g., rivers, lakes, reservoirs,
       estuaries)?
    2.  What are the physical, chemical, and biological connections to and effects of riparian or
       floodplain wetlands and open waters  (e.g., riverine wetlands, oxbow lakes) on downstream
       waters?
    3.  What are the physical, chemical, and biological connections to and effects of wetlands and open
       waters in non-floodplain settings (e.g., most prairie potholes, vernal pools) on downstream
       waters?

These questions were developed in collaboration with the U.S. EPA's Office of Water to translate
regulatory questions and terminology into more scientifically relevant questions and terms (Table 1-1).
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This report focuses on the physical, chemical, and biological connections (or lack thereof) by which
small or temporary streams, nontidal wetlands, and certain open waters can affect the integrity of
downstream waters.

In addition to a broad survey of literature responding to the three questions above, the U.S. EPA's Office
of Water asked the Office of Research and Development to create six case studies with more detailed
reviews of published literature on Carolina and Delmarva bays, oxbow lakes, prairie potholes, prairie
streams, southwestern streams, and vernal pools.
Table 1-1. Translating connectivity-related questions between policy and science. This table presents a
crosswalk of regulatory and scientific questions this report addresses. Policy questions use regulatory
terms (shown in quotation marks) that lack scientific definitions or are defined differently in scientific
usage. All terms used in this report reflect scientific definitions and usage.
Policy question
What tributaries have a "significant* nexus" to
"traditional navigable waters"?
What "adjacent" waters have a "significant* nexus" to
"traditional navigable waters"?
What categories of "other waters" have a "significant*
nexus" to "traditional navigable waters"?
Science question
What are the connections to and effects of ephemeral,
intermittent, and perennial streams on downstream
waters?
What are the connections to and effects of riparian or
floodplain wetlands and open waters on downstream
waters?
What are the connections to and effects of wetlands
and open waters in non-floodplain settings on
downstream waters?
* "Significant," as used here, is a policy determination informed by science; it does not refer to statistical significance.
1.2  Scientific Context

1.2.1   Concepts of Connectivity in Hydrology and Ecology
Streams, wetlands, and other surface waters interact with ground water and terrestrial environments
throughout the landscape, from the mountains to the oceans. Thus, an integrated perspective of the
landscape, described in this section, provides the appropriate scientific context for evaluating and
interpreting evidence about the physical, chemical, and biological connectivity of streams, wetlands, and
open waters to downstream waters.

Connectivity has long been a central tenet for the study of aquatic ecosystems. The River Continuum
Concept (Vannote et al., 1980) viewed the entire length of rivers, from source to mouth, as a complex
hydrologic gradient with predictable longitudinal patterns of ecological structure and function. The key
pattern is that downstream communities are organized, in large part, by upstream communities and
processes (Vannote et al., 1980; Battin et al., 2009). The Serial Discontinuity Concept (Ward and
Stanford, 1983) built on the River Continuum Concept to improve our understanding of how dams and
impoundments disrupt the longitudinal patterns of flowing waters with predictable downstream effects.
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The Spiraling Concept (Webster and Patten, 1979; Newbold et al., 1981; Elwood et al., 1983) described
how river network connectivity can be evaluated and quantified as materials cycle from dissolved forms
to transiently stored forms taken up by living organisms, then back to dissolved forms, as they are
transported downstream (Section 3.4.1). These three conceptual frameworks focused on the
longitudinal connections of river ecosystems, whereas the subsequent flood pulse concept (Junk et al.,
1989) examined the importance of lateral connectivity of river channels to floodplains, including
wetlands and open waters, through seasonal expansion and contraction of river networks. Ward (1989)
summarized the importance of connectivity to lotic ecosystems along four dimensions: longitudinal,
lateral, vertical (surface-subsurface), and temporal connections; he concluded that running water
ecosystems are open systems that are highly interactive with both contiguous habitats and other
ecosystems in the surrounding landscape. As these conceptual frameworks illustrate, scientists have
long recognized the hydrologic connectivity that the physical structure of river networks represents.

More recently, scientists have incorporated this connected network structure into conceptual
frameworks describing ecological patterns in river ecosystems and the processes linking them to other
watershed components, including wetlands and open waters (Power and Dietrich, 2002; Benda et al.,
2004; Nadeau and Rains, 2007; Rodriguez-Iturbe et al., 2009). The Network Dynamic Hypothesis (Benda
et al., 2004) is a physically based framework for predicting patterns of habitat heterogeneity observed
along a river, based on dynamics that generate potential biological "hotspots" at tributary confluences. It
essentially reexamines earlier, linearly driven frameworks given the patchy and stochastic nature of
lotic ecosystems (e.g., Resh etal., 1988; Townsend, 1989; Rice etal., 2001), and  thus reflects a more
realistic river network perspective. Bunn and Arthington (2002) identified natural flow variability and
associated lateral and longitudinal connectivity of stream channels and floodplains as two principal
mechanisms linking hydrology to aquatic biodiversity of riverine species (also Leigh et al., 2010). In
addition, application of metapopulation theory and population genetic theory to natural populations has
greatly improved our understanding of the role of dispersal and migration in the demographic
persistence, community assembly, and evolution of aquatic species (Hastings and Harrison, 1994;
Moilanen and Hanski, 1998; Hanski, 1999; Pannell and Charlesworth, 2000;  Pagan, 2002; Bohonak and
Jenkins, 2003; Waples, 2010; Fronhofer et al., 2012). Sheaves (2009) emphasized the key ecological
connections—which include process-based connections that maintain habitat function (e.g., nutrient
dynamics, trophic function) and movements of individual organisms—throughout a complex of
interlinked freshwater, tidal wetland, and estuarine habitats as critical for the persistence of aquatic
species, populations, and communities over the full range of time scales.

1.2.2   Connectivity Gradients and Descriptors
The landscape and flowpath perspectives illustrated in Figure 1-1 draw heavily from the connectivity
frameworks described in Section 1.2.1. These perspectives are essential to understanding connections
from streams, wetlands, and open waters that affect the integrity of downstream waters. Connectivity is
defined here as the degree to which components of a watershed are joined and interact by transport
mechanisms that function across multiple spatial and temporal scales (Section 2.3.2.1). The primary
transport mechanisms considered in this report are surface-water and shallow  ground-water flows,
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Table 1-2. Dimensions of watershed connectivity.
     Dimension
               Examples and flowpaths in Figure 1-1 or Figure 1-2
Longitudinal
Streamflow and downstream transport of materials, organisms (1-1A); hyporheic flow
(1-1A); ground-water flow through local and larger scale aquifers (1-1A), aquatic or
overland movement of organisms in or along stream channels (1-1B); biogeochemical
transport and transformation (1-1B) (Alexander etal., 2007; Freeman etal., 2007)
Lateral
Overbank flow and transport from channels into banks, floodplains, and riparian areas
(1-1A); spillage and transport from wetlands and open waters into streams (1-1A);
overland flow and interflow (1-1A); ground-water recharge from streams and wetlands
(1-1A); bank storage (1-1A); transport or movement of organisms between streams and
wetlands or open waters (1-1B) (Ward, 1989; Stanford and Ward, 1993)
Vertical
Surface-subsurface exchange of water, materials, organisms (1-lAand 1-1B); ground-
water recharge from streams and wetlands (1-1A); atmospheric losses (1-1A) (Amoros
and Bornette, 2002; Banks etal., 2011)
Temporal
Variable source area (1-2); seasonal cycles of wetland inundation and outflow to
streams (1-1A); migration or diapause of aquatic organisms (1-1B) (Hewlett and
Hibbert, 1967; Bohonak and Jenkins, 2003; Zedler, 2003)
transport and transformation of physical and chemical materials, and movements of aquatic and
semiaquatic organisms, all of which connect watersheds in four dimensions (Table 1-2). Figure 1-1
illustrates the continuous hydrologic flowpaths (Figure 1-1A) and biological pathways (Figure 1-1B)
that connect watershed components spatially; Figure 1-2 illustrates the temporal dynamics of
hydrologic flowpaths (Sections 2.2.3 and 2.3.2.2).

Although all parts of a watershed are connected to some degree—by the hydrologic cycle or dispersal of
organisms, for example—the degree of connectivity among aquatic components varies along a
continuum from highly connected to highly isolated. This continuum can be described in terms of the
frequency, duration, magnitude, timing, and rate of change (Poff et al., 2007) of physical and
chemical fluxes to and biological exchanges with downstream waters. These terms, which we refer to
collectively as connectivity descriptors, characterize the range over which streams and wetlands vary
and shift along the connectivity gradient in response to changes in natural and anthropogenic factors
and, when considered in a watershed context, can be used to predict probable effects of different
degrees of connectivity over time. These and similar descriptors are used in hydrology and disturbance
ecology to characterize the variability and alteration of natural flow regimes (Resh et al., 1988; Poff,
1992; Poff etal., 1997; Lake, 2000; Leibowitz etal., 2008). For  example, in hydrology, magnitude is the
amount of water moving past a fixed location per unit time, frequency is how often a particular flow
magnitude occurs, duration  is a measure of how long a particular flow magnitude persists, and rate of
change is how quickly one type of flow changes to another. Because the presence of water determines
hydrologic connectivity, these descriptors also can be used to describe the timing and magnitude of
hydrologic connections. Further, they can describe other types of connections. The number of
individuals immigrating or emigrating during a dispersal event, for example, could be used to determine
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        Figure 1-1A. Hydrologic f lowpaths. Arrows are representative of surface-water and ground-water flows occurring throughout the watershed.

        Subsurface flows are shown within the cross section, and by faded arrows outside the cross section.
1-3
§  ffl
If
n
ro
o
                                                                                                                         Stream and wet/and recharge of

                                                                                                                         local and regional aquifers
        Key
              - Perennial stream


            .... Ephemeral  stream


                Intermittent stream


                Precipitation
                            Unsaturatedzone


                            Saturated zone


                            Local aquifer and hyporheic zone


                            Confining layer
Atmospheric losses

(e.g., evapotranspiration, volatilization, denitrification)


Wetland (dry period)


Open water (dry period)


Expansion and overbank flow into floodplain and overflow of

wetlands and open-waters during wetter periods
     Water table level
V

     Ground-water flow through local and larger scale aquifers


     Overland and interflow


     Streamflow and transport of materials, organisms


     Overbank flow and transport or spillage of materials, organisms


     Bank storage


     Hyporheic flow and surface-subsurface exchange of water, materials, organisms

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       Figure 1-1B. Biological flowpaths. Arrows are representative of biological pathways occurring throughout the watershed. This figure also

       includes representative biogeochemical pathways occurring in streams and floodplains.
1-3
§  ffl
If
n
(/>  o
       Key
            — Perennial stream


            •••- Ephemeral stream


            -  Intermittent stream


               Wetland (dry period)


               Open water (dry period)
Unsaturatedzone


Saturated zone


Local aquifer and hyporheic zone


Confining layer
               Expansion and overbank flow into floodplain and overflow of

               wetlands and open-waters during wetter periods
Water table level
Aquatic transport or movement


Overland transport or movement (aerial or terrestrial)


Surface-subsurface exchange of water, materials, organisms


Biochemical transformation and transport (e.g., nutrient spiraling)

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Figure 1-2. Temporal dynamics of hydrologic flowpaths. (A) A riverscape at peak hydrologic expression.
(B) The same riverscape in a dry period. Intermittent and ephemeral streams, and some wetlands, are dry.
 Key
         Perennial stream
Unsaturated zone

Saturated zone

Local aquifer and
hyporheiczone

Confining layer
 Onoint Ephemeral stream

 ^"^Y Intermittent stream

       -  Precipitation

 „.	^ Atmospheric losses
         (e.g., evapotranspiration,
         volatilization, denitrification)

         Wetland (dry period)

         Open water (dry period)
         Expansion and overbankflow intofloodplain and over-
         flow of wetlands and open-waters during wetter periods

         Dry wetland
Water table level

Ground-water flow through local and larger
scale aquifers

Overland and interflow
                             Streamflow and transport of
                             materials, organisms
                             Overbank flow and transport or spillage
                             of materials, organisms

                             Bank storage

                             Hyporheicflow and surface-subsurface
                             exchange of water, materials, organisms
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              1-7
                              January 2015

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the magnitude of the event; the probability, length, and predictability of similar events could be
expressed in terms of their frequency, duration, and timing; and fluctuations in dispersal could be
described as the rate of change through time (e.g., across seasons or years).

Stream and wetland connections have particularly important consequences for downstream water
integrity. Longitudinal flows through ephemeral, intermittent, and perennial stream channels
(Figure 1-1A, blue lines and arrows) are much more efficient for transport of water, materials, and
organisms than diffuse overland flows and interflows (Figure 1-1A, green arrows). Over time, stream
transport path ways are reinforced by recurrent flows that maintain channel form. Areas that
concentrate water also provide mechanisms for storage, transformation, and transport of materials.
Differences in flow frequency, duration, magnitude, timing, and rate of change (e.g., rapid flow in
mountain streams, slow flow through glacial ice or bedrock, intermittent flow in seasonal streams,
ephemeral flow in arid rivers) create conditions needed for a range of ecosystem functions that affect
downstream waters. Such functions include short- and long-term storage of water and sediment,
transformation or sequestration of contaminants, recycling of excess nutrients, provision of habitat for
aquatic and semiaquatic species, recharge of river baseflow, and provision of drinking water for humans
and wildlife. For example, areas that are prone to wetting and drying cycles in response to seasonal
conditions (e.g., stream and wetland perimeters shown in Figure 1-1A) are "hotspots" for chemical
transformations (Vidon etal., 2010).

Ultimately, differences in the frequency, duration, magnitude, timing, and rate of change of physical,
chemical, and biological connections describe different positions along the connectivity gradient and
produce different types of downstream effects. For example, highly connected stream channels convey
water and channel-forming sediment to rivers, whereas highly isolated wetlands can reduce flooding
and store excess sediment. Connections with low values of one or more descriptors (e.g., low-frequency,
short-duration flooding) can have important downstream effects when values for other descriptors are
high (e.g., large-magnitude downstream transfer of floodwaters, sediment, large woody debris, and
organisms). At the other end of the frequency gradient, high-frequency, low-magnitude vertical and
lateral flows (Table 1-2) contribute to aquatic biogeochemical processes, including nutrient and
contaminant transformation and organic matter accumulation (e.g., Brunke and Gonser, 1997; Karwan
and Saiers, 2012; Lawrence et al., 2013).

In addition, timing is a key connectivity descriptor that can influence downstream waters. For example,
when soils are saturated by previous rainfall events, even low or moderate rainfall can cause streams or
wetlands to overflow, transporting water and materials to downstream waters. The same wetland or
wetland type can attenuate floods or generate  floods, depending on hydrologic conditions (Acreman and
Holden, 2013). Predictable events also can profoundly influence the effects of connections. Wetlands and
river networks expand and contract in response to seasonal and decadal cycles and longer term changes
in environmental conditions. In wet conditions (Figure 1-2A), streams and rivers expand longitudinally
into headwaters and laterally into floodplains or riparian areas, wetlands inundate and connect via
surface water and ground water to other wetlands and the stream network, the water table rises, and
local aquifers are recharged. In dry conditions (Figure 1-2B), the river network is limited to perennial
Stream and Wetland Connectivity:                                                             January 2015
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streams, wetlands dry down, and the water table level lowers. Seasonal flooding and drying events over
an annual cycle are formative processes of physical, chemical, and biological attributes of streams in the
western United States (Gasith and Resh, 1999). Large seasonal waterfowl migrations can move
nutrients, plants (seeds), and invertebrates between wetlands and downgradient waters (Figuerola and
Green, 2002; Green and Figuerola, 2005; Frisch et al., 2007). Fish that use nonperennial or perennial
headwater stream habitats to spawn or rear young, and invertebrates that move into seasonally
inundated floodplain wetlands prior to emergence, have life cycles that are synchronized with the timing
of flows and flood pulses, temperature thresholds, and food resource availability in those habitats (Junk
et al., 1989; Falke et al., 2010).

The surface-water and ground-water flowpaths along which water and materials are transported and
transformed (Sections 2.2.2, 3.3, 3.4, 4.3.2, 4.3.3, 4.4.2, and 4.4.3; Figure 1-1A) determine variations in
the degrees of physical and chemical connectivity. These flowpaths are controlled primarily by variation
in climate, geology, and terrain within and among watersheds and over time. These factors have been
used to group watersheds into hydrologic landscapes units that, although not necessarily spatially
contiguous, are predicted to exhibit similar hydrologic function (Wolock et al., 2004; Wigington et al.,
2013). Climate, geology, and terrain are reflected locally in factors such as rain and snowfall intensity,
soil infiltration rates, and the direction of ground-water flows. These local factors interact with stream
and wetland function and landscape position to influence degrees of connectivity through time and
across space. When considered together with these local factors, hydrologic landscapes could provide a
regional context for evaluating the physical and chemical connectivity of streams and wetlands in a
particular watershed or group of watersheds (Section 2.4.1).

Gradients of biological connectivity (i.e., the active or passive movements of organisms through water
and air and over land that connect populations of aquatic species; Sections 3.5, 4.3.4, and 4.4.4; Figure
1-1B) are determined primarily by species assemblages and by landscape features, including the factors
discussed above, that facilitate or impede the movement of organisms. Organisms move  across the
landscape to colonize new habitats, avoid inbreeding, escape predation or competition, locate mates,
and acquire resources needed to survive and reproduce. The temporal and spatial  scales at which
biological pathways connect aquatic habitats depend on characteristics of both the landscape and
species, and overland transport or movement can occur across watershed boundaries. Dispersal is
essential at higher levels of biological organization for population persistence, maintenance of genetic
diversity, and evolution of aquatic species (Labbe and Fausch, 2000; Pagan, 2002; Malmqvist, 2002;
Bohonak and Jenkins, 2003; Armsworth and Roughgarden, 2005). Consequently, dispersal strategies
reflect aquatic species' responses and adaptations to biotic and abiotic environments, including spatial
and temporal variation in resource availability and quality (e.g., Clobert et al., 2009). Dispersal-related
traits and behaviors (e.g., habitat specialization, dispersal mode, behavioral response to  environmental
cues) therefore encompass species-environment relationships over time and provide an ecological and
evolutionary context for evaluating biological connectivity in a particular watershed or group of
watersheds.
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Pathways for chemical transport and transformation largely follow hydrologic flowpaths (Figure 1-1A),
but sometimes follow biological pathways (e.g., nutrient transport from wetlands to coastal waters by
migrating waterfowl, upstream transport of marine-derived nutrients by anadromous fish, uptake and
removal of nutrients by emerging stream insects; Figure 1-1B). The transport and transformation of
nutrients (e.g., sequential transformations, Section 2.3.2.1; and nutrient spiraling in streams, Section
3.4.1) and  other chemicals associated with water integrate physical, chemical, and biological
connectivity of streams and wetlands to downstream waters (Figure 1-1B).

1.2.3   Cumulative Effects of Streams and Wetlands on Downstream
         Waters
Stream and wetland connectivity to downstream waters, and the resulting effects on downstream water
integrity, must be considered cumulatively. First, when considering the effect of an individual stream or
wetland, including the cumulative effect of all the contributions and functions that a stream or wetland
provides is essential. For example, the same stream transports water, removes excess nutrients,
mitigates flooding, and provides refuge for fish when conditions downstream are unfavorable; ignoring
any of these functions would underestimate the overall effect of that stream.

Secondly, stream channel networks and the watersheds they drain are fundamentally cumulative in how
they are formed and maintained. Excess precipitation that is not evaporated, taken up by organisms, or
stored in soils and geologic layers moves downgradient as overland flow or through channels, which
concentrate flows and carry sediment, chemical constituents, and organisms (Sections 3.3, 3.4, and 3.5).
As flows from numerous headwater channels combine in larger channels, the volume and effects of
those flows accumulate as they move through the river network. As a result, the incremental
contributions of individual streams and wetlands accumulate in the downstream waters. Important
cumulative effects are exemplified by ephemeral flows in arid  landscapes, which are key sources of
baseflow for downgradient waters (Sections  5.6 andB.5; Schlesinger and Jones, 1984; Baillie etal., 2007;
Izbicki, 2007), and by the high rates of denitrification in headwater streams (Section 3.4.1). The amount
of nutrients removed by any one stream over multiple years or by all headwater streams in a watershed
in a given year can have substantial consequences for downstream waters (Alexander et al., 2007;
Alexander et al., 2009; Bb'hlke et al., 2009; Helton et al., 2011). Similar cumulative effects on
downstream waters have been documented for other material contributions from headwater streams
(Chapter 3). For example, although the probability of a large-magnitude transfer of organisms from any
given headwater stream in a given year might be low (i.e., a low-frequency connection when each stream
is considered individually), headwater streams are the most abundant type of stream in most
watersheds (Section 3.2). Thus, the  overall probability of a large-magnitude transfer of organisms is
higher when considered for all headwater streams in a watershed—that is, there is a high-frequency
connection when considered cumulatively at the watershed scale, compared with probabilities of
transport for streams individually. Similarly, a single pollutant discharge might be negligible but the
cumulative effect of multiple discharges could degrade the integrity of downstream waters.
Stream and Wetland Connectivity:                                                           January 2015
A Review and Synthesis                                                                       3

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Evaluating cumulative contributions over time is critical in streams and wetlands with variable degrees
of connectivity. For example, denitrification in a single headwater stream in any given year might not
affect downstream waters; over multiple years, however, this effect could accumulate. Western vernal
pools provide another example of cumulative effects over time. These pools typically occur as complexes
in which the hydrology and ecology are tightly coupled with the local and regional geological processes
that formed them (Section B.6). When seasonal precipitation exceeds wetland storage capacity and
wetlands overflow into the river network and generate stream discharge, the vernal pool basins, swales,
and seasonal streams function as a single surface-water and shallow ground-water system connected to
the river network.

1.2.4   Effects of Human Activities on Connectivity
Human activities alter naturally occurring gradients of physical, chemical, and biological connectivity by
modifying the frequency, duration, magnitude, timing, and rate of change effluxes, exchanges, and
transformations. For example, all dimensions of connectivity (Table 1-2) can be reduced by dams and
levees (Ward and Stanford, 1983; Ligon et al., 1995; Collier et al., 1996; Wohl, 2005; Franklin et al.,
2009), water withdrawals (Haag and Pfeiffer, 2012), and habitat destruction. Alternatively, connectivity
can be increased by point source discharges (Brooks et al., 2006); channelization, drainage ditches, and
tiles (Randall et al., 1997; Min et al., 2010); and storm drains and impervious surfaces (Booth, 1990; Paul
and Meyer, 2001; Elmore and Kaushal, 2008; Walsh etal., 2012). The effects of human activities on
connectivity are often complex. For example, a levee will decrease connectivity between a river channel
and its floodplain at the levee site, but might increase connectivity of the channel and floodplain farther
downstream, due to increased flow. Similarly, drainage ditches that increase hydrologic connectivity
between isolated aquatic systems also can decrease biological connectivity through habitat loss  and
fragmentation.

Human activities modify the natural biological processes, material fluxes, and energy fluxes that link
watershed components, resulting in a suite of stressors with measurable effects on downstream
ecosystems. Some of these activities are illustrated in a hypothetical watershed (Figure 1-3). In
Figure 1-3 (A), buried and ditched streams have eliminated aquatic habitat, increased downstream
export of runoff and contaminants, and eliminated stream functions that could benefit downstream
water quality. Figure  1-3 (B) shows a dam and reservoir that have constrained natural river expansion
and contraction cycles by increasing water storage, trapping sediment, and regulating the volume and
timing of river discharge. Dams and reservoirs also block upstream movement of migrating fish  and
other organisms, alter riparian areas, and impair riparian and floodplain wetland functions. In Figure
1-3 (C), levees and channelization have disconnected the river from its floodplain; decreased exchange
of water, materials, and biota between the channel bed and hyporheic zone; and eliminated stream and
wetland habitats. In addition, levees decrease the volume of river discharge at the levee site, but
increase discharge downstream of the levee site. In Figure 1-3 (D), urban stormwater drainage has
increased export of runoff and contaminants from impervious surface areas, altered stream
temperature, and impaired instream habitats. In Figure 1-3 (E), drained and ditched wetlands have
impaired wetland habitat and functions; increased downstream export of excess nutrients and
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A Review and Synthesis                                                                        3

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      Figure 1-3. Effects of human alterations on watershed connectivity. See Section 1.2.4 for description of alterations illustrated in A-G.
f
I 3
  a
~ s
<2. O
(/) o
       Key


       	Perennial stream


       ••••	• Ephemeral stream
Unsaturatedzone


Saturated zone
' - i Effluent (
^^^ Ditch
Wetland


A
B

Si Confining layer
Buried and ditched streams
Dam and reservoir

c
D
E

Levees and channelization
Urban stormwater drainage
Drained and ditched wetlands

F
G


Ground-water withdrawal
Effluent dominated stream


ro
o

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 Figure 1-4. The role of connectivity in maintaining the physical, chemical, and biological integrity of
 water. Climate, landscape, and species' traits (Influencing Factors) interact to form Connections
 (hydrologic, chemical, and biological) that control the frequency, duration, magnitude, timing, and rate
 of change of material and energy fluxes, and biological dynamics (Processes) linking watershed
 components. The Functions by which these connections affect downstream waters modify the timing
 of transport and the quantity and quality of resources available to downstream communities.
 Biomonitoring programs have developed structural metrics for assessing physical habitat, water
 quality, and biological assemblages as indicators of the physical, chemical, and biological integrity of
 downstream waters (Assessment Endpoints and Metrics).
                                             FUNCTIONS
      CLIMATE FACTORS
       • Annual watersurplus
       • Seasonality
       • Rainfall intensity
       • Temperature

      LANDSCAPE FACTORS
       • Topography
       • Landform
       • Soil type
       • Aquifer permeability
       • Spatial distribution

      SPECIES' TRAITS
       • Life cycle
       • Dispersal capability
       • Dispersal cues
       • Dispersal behavior

      HUMAN ACTIVITIES
     INFLUENCING FACTORS -»   CONNECTIONS -»
                         PHYSICAL & CHEMICAL
                             INTEGRITY
                         • Habitatquality
                         • Waterquality
                         • Toxicity

                         BIOLOGICAL INTEGRITY
                         • Community structure
                         • Indicatorspecies
                         • Functional groups
                         • Population attributes

                         ECOSYSTEM INTEGRITY,
                        SUSTAINABILITY, RESILIENCY
                                            PROCESSES ->
                                                          EFFECTS
                                                                            ASSESSMENT
                                                                        ENDPOINTS & METRICS
other contaminants; and decreased recharge of local and regional aquifers. In Figure 1-3 (F), ground-
water withdrawal has lowered the water table, disconnecting surface water and ground water, thereby
causing local streams and wetlands to dry. Finally, in Figure 1-3 (G), pollutant discharges into effluent-
dominated streams have altered the volume and timing of streamflow, and increased the export of
contaminants into streams. Because watersheds typically experience multiple covarying stressors,
determining the cause of a specific downstream effect can be difficult. Relating observed effects to
probable causes requires not only reliable measures of candidate stressors and observed effects, but
also a clear understanding of the intermediate processes that link them mechanistically (U.S. EPA, 2010;
Farraretal., 2014).

Multiple indicators and measures have been proposed for detecting and quantifying changes in
connectivity associated with human activities (With etal., 1997; Tischendorf and Fahrig, 2000; Moilanen
and Nieminen, 2002; Calabrese and Pagan, 2004; Martin and Soranno, 2006; Fullerton et al., 2010;
Hermoso etal., 2012). Impairments that result from structural alteration of landscape attributes (e.g.,
dam construction, channel incision, loss of overland dispersal corridors) are relatively easier to detect
and quantify than impairments of functional processes (e.g., altered nutrient dynamics, reduced gene
Stream and Wetland Connectivity:
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January 2015

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flow), but both have important consequences for the short- and long-term integrity of freshwater
ecosystems. Palmer and Febria (2012) proposed that ecosystem impairment can be better identified and
diagnosed by a combination of structural and functional metrics than by either type alone. Because
connectivity can be defined in both structural and functional terms and is an integral component of
aquatic ecosystem integrity, this approach is more appropriate for detecting and assessing effects of
altered connectivity. To this end, systematic approaches that are rooted in landscape analysis and which
incorporate hydroecological dynamics present in streams and wetland complexes (Section 2.4.6) are
likely to provide useful information for inferring when and where altered connectivity is a cause of
impairment to water resources.


1.3  Report Approach
In this report, we focus entirely on peer-reviewed, publicly accessible sources of information about
surface-water and ground-water (particularly shallow ground-water) connections and interactions from
streams, wetlands, and open waters that influence the function and condition of downstream surface
waters (Figure 1-5). Information about connections among water bodies of the same type (e.g., wetland-
to-wetland or headwater stream-to-headwater stream connections) and connections from terrestrial
systems to downstream waters are considered out of scope (Figure 1-5).

The topical scope of this report was chosen to consider waters that often fall under the purview of the
CWA. As a scientific review, however, this report does not consider or make judgments regarding legal
standards for CWA jurisdiction. Our review of subsurface flows emphasizes shallow (local) ground
water, because flows in this category have the greatest interchange with surface waters  (Winter et al.,
1998) although relevant surface-subsurface exchanges occur at depths ranging from centimeters to tens
of meters, depending on geographic location, stream channel geometry, and other factors (Woessner,
2000). As with any literature review, readers should refer to the cited publications for quantitative
information, such as flow distance, depth, duration, timing, and magnitude, about specific surface-water
and ground-water connections, and for other details about the systems and studies discussed in this
report.

To identify connections and effects of streams, wetlands, and other water bodies on downstream waters,
we used two types of evidence from peer-reviewed, published literature:  (1) direct evidence that
demonstrated a connection or effect (e.g., observed transport of materials or movement of organisms
from streams or wetlands to downstream waters)  and (2) indirect evidence that suggested a connection
or effect (e.g., presence of environmental factors known to influence connectivity, a gradient of
impairment associated with cumulative loss of streams or wetlands). In some cases, an individual line of
evidence demonstrated connections along the entire river network (e.g., from headwaters to large
rivers). In most cases, multiple sources of evidence were gathered and conclusions drawn via logical
inference—for example, when one body of evidence shows that headwater streams are connected to
downstream segments, another body of evidence shows those downstream segments are linked to other
Stream and Wetland Connectivity:                                                            January 2015
A Review and Synthesis                                                                       3

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       Figure 1-5. Waters and connections considered to be within scope for this report.
fl
I 3
If
n
                                                                                                                Chapter 3: Transport and transformation of water,
                                                                                                                materials, and biota from ephemeral, intermittent, and
                                                                                                                perennial streams
              Chapters: Movement of biota between
                 tributaries and downstream waters
        Key
                          Chapter4: Non-floodplain
                         wetlands and open-waters
                            with outlets to streams
                                                          Chapters 3 and 4: Lateral
                                                               exchange of water,
                                                              materials, and biota
                                                                between waters in
                                                          channels andf/oodp/ains
                                                                                                                           Chapter 4: Non-floodplain
                                                                                                                           wetland and open-water fill-
                                                                                                                           and-spill into streams


                                                                                                                                                     Chapter 4: Overland
                                                                                                                                                     movement of biota from
                                                                                                                                                     wetlands to streams
                                                                             Chapter 3: Longitudinal hydrologic
                                                                                flowpaths: surface and shallow
                                                                                       subsurface streamflow
             —- Perennial stream

             "•• Ephemeral stream

              ~  Intermittent stream

                 Wetland (dry period)

                 Open-water (dry period)
        Unsaturatedzone

^^^,  Saturated zone

^_  ^,  Local aquifer and hyporheic zone

'ffl-y!*  Confining layer
                                                                                                   Chapter 3: Vertical exchange of water,
                                                                                                   materials, biota between surface and
                                                                                                   shallow subsurface waters
                 Expansion and overbank flow into floodplain and overflow of
                 wetlands and open-waters during wetter periods
      Aquatic transport or movement of organisms

      Overland transport or movement of organisms (aerial or terrestrial)

      Overbank flow and transport or spillage of materials, organisms

^    Bank storage

t  ^  Hyporheic flow and surface-subsurface exchange of water, materials, organisms
°
ui

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segments farther downstream, and so on. This approach, which borrows from weight-of-evidence
approaches in causal analysis (Suter et al., 2002; Suter and Cormier, 2011), is an effective way to
synthesize the diversity of evidence needed to address questions at larger spatial and longer temporal
scales than are often considered in individual scientific studies.

1.3.1  Selection and Screening of Scientific Materials
We searched the scientific literature for information on the types of waters, connections, and
downstream effects identified in the report objectives and scope (Section 1.1; Figure 1-5). We conducted
keyword searches using terms inclusive of the types of waters, connections, and downstream effects of
interest (e.g., [wetland* AND [river* OR stream*] AND [connect* OR isolat*]]). Because simple keyword
searches would have omitted relevant publications, we also searched for literature on related topics.
Topics included conceptual frameworks of watershed and landscape connectivity; hydrologic flowpaths
among watershed components; biogeochemical transformation and cycling in streams and wetlands;
natural or artificial tracers of difficult-to-observe flows (e.g., ground-water flow, gene flow); chemical
and biological processes associated with aquatic habitat fragmentation and spatial isolation; and climate
or landscape factors that influence connectivity or isolation. We also reviewed citations provided by
peer-review panels and in public comments on drafts of the report. We then screened those results and
selected the  most relevant publications for review and synthesis in this report, based on the criteria in
Figure 1-6.

We used science citation databases and search engines available through Web of Science™ and Google
Scholar™ to search primary (original research) and secondary (review) literature. These searches
included examination of references citing or cited in relevant publications obtained through specific
searches.

Because the  breadth and depth of topics covered in this report made an exhaustive literature review
impractical, we emphasized highly influential papers on relevant topics, review papers that summarized
multiple studies in narrative form, meta-analyses that used statistical methods to combine results from
multiple independent studies into a single evaluation of evidence, and superseding editions or versions
of published research. Publications that did not provide new information, an alternative perspective or
interpretation of evidence, or a technical improvement (e.g.,  improved accuracy or better study design)
were not summarized in the report to avoid redundancy and excessive length and detail.

We summarized the relevant literature in narrative form and organized each chapter into lines of
evidence pertaining to different types of connections (physical, chemical, biological) for different types
of systems (streams, riparian/floodplain wetlands, non-floodplain wetlands). Lines of evidence were
evaluated for strength, consistency, mechanistic plausibility, and relevance to the endpoints identified in
the report objectives. Finally, conclusions for each of the report's three questions were derived from the
key findings, and placed in context with concepts and evidence provided in each chapter.

Cited in this  report are 1,353 references. Most were published in refereed scientific journals (86%), as
scientific reports by federal agencies that follow peer-review guidelines of the Office of Management and
Stream and Wetland Connectivity:                                                            January 2015
A Review and Synthesis                                                                         3

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 Figure 1-6. Flow chart for screening and compiling literature.
                                 1. Search literature on streams,
                               wetlands, and open waters; review
                              citations provided by peer reviewers
                                     and public comments.
                                  2. For each publication under
                                         consideration:
                                           3.  Does it
                                       contain scientific
                                information about  the physical,
                              chemical, or biological connectivity of
                              streams, wetlands, or open waters to
                             larger downstream waters (e.g., rivers,
                                     lakes, coastal waters)?
                                         4. Has it been
                                       peer reviewed* or
                                       verified for quality
                                          assurance?
                                     5. Does it present new
                                information on a relevant topic,
                              alternative interpretations of existing
                             information, or technical improvements
                                  to studies already reviewed?
                                6. Add to compiled literature for
                                       further evaluation.
 * Peer review is the formal evaluation of scientific information by independent experts who were not involved in the work but
 have equivalent scientific and technical expertise. Its purpose is to ensure that materials accepted for publication have been
 critically reviewed and revised as needed to meet the documented standards of scientific integrity and qualityfor specific
 journals or organizations. All reports published by the U.S. EPA Office of Research and Development meet or exceed peer-review
 requirements established by the Office of Management and Budget (OMB, 2004).
Stream and Wetland Connectivity:
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January 2015

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Budget (4%), or scientific books (~9%). The remaining citations refer to photographs, maps, non-federal
reports, or websites (<1%) that provide supplemental information.

1.3.2   Report Structure
The report is organized into six chapters. Chapter 1 outlines the purpose, scientific context, and
approach of the report. Chapter 2 describes the components of a river system and watershed; the types
of physical, chemical, and biological connections that link those components; the factors that influence
connectivity at various temporal and spatial scales; and methods for quantifying connectivity. Chapter 3
reviews literature on connectivity in stream networks in terms of physical, chemical, and biological
connections and their resulting effects on downstream waters. Chapter 4 reviews literature on the
connectivity and effects of nontidal wetlands and certain open waters on downstream waters. Chapter 5
applies concepts and evidence from previous chapters to the case studies detailed in Appendix B.
Chapter 6 presents the five major conclusions of this report, with a summary of key findings from the
literature synthesized  to develop these conclusions. It also discusses the relative abundance of literature
on topics reviewed in this report, and briefly discusses emerging research that can close some current
data gaps identified in  the report. A glossary of scientific terms used in the report and detailed case
studies of selected systems (summarized in Chapter 5) are included in Appendix A and Appendix B,
respectively.
1.4  Summary
This report evaluates, summarizes, and synthesizes available peer-reviewed scientific literature on the
connectivity and mechanisms by which streams, wetlands, and open waters, singly or in aggregate,
affect the physical, chemical, and biological integrity of downstream waters.

Connectivity has long been a central tenet for the study of aquatic ecosystems. Watersheds are
integrated at multiple spatial and temporal scales by flows of surface water and ground water, transport
and transformation of physical and chemical materials, and movements of organisms. Although all parts
of a watershed are connected, the degrees and downstream effects of those connections vary; the effects
also are influenced by characteristics of the physical environment, the biological environment, and by
human activities in the watershed.

Variation in the degree of connectivity is critical to the integrity and sustainability of downstream
waters, and can be described in terms of the frequency, duration, magnitude, timing, and rate of change
effluxes to and biological exchanges with downstream waters. These descriptors characterize the range
over which streams and wetlands vary and shift along connectivity  gradients and the probable effects of
different types (hydrologic, chemical, biological) and degrees of connectivity over time. Gradients of
physical, chemical, and biological connectivity are controlled primarily by variation in climate, geology,
terrain, aquatic organisms, and human activities within and among  watersheds, and over time.

Ultimately, differences in the frequency, duration, magnitude, timing, and rate of change of physical,
chemical, and biological connections describe different positions along the connectivity gradient and
Stream and Wetland Connectivity:                                                             January 2015
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produce different types of downstream effects. Connections with low values of one or more descriptors
(e.g., low-frequency, short-duration floods) can have important downstream effects when values for
other descriptors are high (e.g., large-magnitude transfers of floodwaters, sediment, large woody debris,
and organisms downstream). Atthe other end of the frequency gradient, the effects of high-frequency,
low-magnitude vertical and lateral flows strongly contribute to biogeochemical functions, including
nutrient and contaminant transformation and organic matter accumulation.

Stream channel networks and the watersheds they drain are fundamentally cumulative in how they are
formed and maintained. The downstream consequences (e.g., the amount and quality of materials that
eventually reach  a river) are determined by the aggregate effect of contributions and sequential
alterations that begin at the source waters and function along continuous flowpaths to the watershed
outlet. Cumulative effects across a watershed must therefore be considered when quantifying the
frequency, duration, and magnitude of connectivity, to evaluate the downstream effects of streams,
wetlands, and open waters.
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2.1  Introduction
A river is the time-integrated result of all waters contributing to it, and connectivity is the property that
spatially integrates the individual components of the watershed. In discussions of connectivity, the
watershed scale is the appropriate context for interpreting technical evidence about individual
watershed components (Newbold et al., 1982b; Stanford and Ward, 1993; Bunn and Arthington, 2002;
Power and Dietrich, 2002; Benda et al., 2004; Naiman et al., 2005; Nadeau and Rains, 2007; Rodriguez-
Iturbe et al., 2009). Such interpretation requires that freshwater resources be viewed within a
landscape—or systems—context (Baron et al., 2002). Addressing the questions asked in this report
(Section 1.1), therefore, requires an integrated systems perspective that considers both the components
contributing to the river and the connections between those components and the river. This chapter
describes this integrated systems perspective. Section 2.2 outlines the basic hydrologic foundation of
river systems. Section 2.3 provides  a general overview of how streams and wetlands affect downstream
waters, focusing on functions within streams and wetlands and how they are connected to downstream
waters. Finally, Section 2.4 examines key factors that affect connectivity between streams and wetlands
and rivers. Although we focus our discussion here on interactions between streams, wetlands, and
rivers, similar exchanges of water, influenced by many of the same factors, also occur between rivers,
lakes, estuaries, and marine waters.
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2.2  An Introduction to  River Systems

2.2.1   River System Components
In this report, the term river refers to a relatively large volume of flowing water within a visible
channel, including subsurface water moving in the same direction as the surface water and lateral flows
exchanged with associated floodplain and riparian areas (Naiman and Bilby, 1998). Channels are
natural or constructed passageways or depressions of perceptible linear extent that convey water and
associated materials downgradient. They are defined by the presence of continuous bed and bank
structures, or uninterrupted (but permeable) bottom and lateral boundaries. Although bed and bank
structures might in places appear to be disrupted (e.g., bedrock outcrops, braided channels, flow-
through wetlands), the continuation of the bed and bank downgradient from such disruptions is
evidence of the surface connection with the channel that is upgradientof the perceived disruption. Such
disruptions are associated with changes in the gradient and in the material over and through which the
water flows. If a disruption in the bed and bank structure prevented connection, the area downgradient
would lack a bed and bank, be colonized with terrestrial vegetation, and be indiscernible from the
nearby land. The concentrated longitudinal movement of water and sediment through these channels
lowers local elevation, prevents soil development, selectively transports and stores sediment, and
hampers the colonization and persistence of terrestrial vegetation. Streams are defined in a similar
manner as rivers: a relatively small volume of flowing water within a visible channel, including
subsurface water moving in the same direction as the surface water and lateral flows exchanged with
associated floodplain and riparian areas (Naiman and Bilby, 1998).

A river network is a hierarchical, interconnected population of channels that drains surface and
subsurface water (Sections 2.2.2 and 2.2.3) from a watershed to a river and includes the river itself.
Watershed boundaries traditionally are defined topographically, such as by ridges, but ground-water
sources and losses can occur outside of topographic boundaries (Winter et al., 2003). These channels
can convey water year-round, weekly to seasonally, or only in direct response to rainfall and snowmelt
(Frissell etal., 1986;  Benda etal., 2004). The smallest of these channels, where streamflows begin, are
considered headwater streams. Headwater streams are first- to third-order streams (Vannote et al.,
1980; Meyer and Wallace, 2001; Gomi etal., 2002; Fritz etal., 2006b; Nadeau and Rains, 2007), where
stream order is a classification system based on the position of the stream in the river network (Figure
2-1; Strahler, 1957).  The point at which stream or river channels intersect within a river network is
called a confluence (Figure 2-1). The confluence of two streams with the same order results in an
increase of stream order (i.e., two first-order streams join to form a second-order stream, two second-
order streams join to form a third-order stream, and so on); when streams of different order join, the
order of the larger stream is retained.

One weakness of classification based on stream order is that it disregards the contributions of lower
order streams where they join a higher order stream. Link magnitude, an alternative method for
classifying streams, resolves this issue. Link magnitude is the sum of all source streams draining into a
given stream segment (Scheidegger, 1965; Shreve, 1967). Therefore, unlike stream order, the link

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 Figure 2-1. A generalized example of a river network within its watershed. Blue lines illustrate the
 river network, within the light green area of its watershed. Numbers represent Strahler stream order,
 with streams increasing in order when two streams of equal order join. Blue squares indicate channel
 heads, and orange dots depict confluences.
magnitude of a segment accounts for all contributing lower order streams regardless of their position in
river networks. For some properties, link magnitude might better reflect the aggregate upstream
contributions to downstream waters.

Mock (1971) presented a classification of the streams comprising stream or river networks. He
designated first-order streams that intersect other first-order streams as sources. We refer to these as
terminal source streams. Mock defined first-order streams that flow into higher order streams as
tributary sources, and we refer to this class of streams as lateral source streams (Figure 2-1).

Terminal and lateral source streams typically originate at channel heads (Dietrich and Dunne,  1993),
which occur where surface-water runoff is sufficient to erode a definable channel. The channel head
denotes the upstream extent of a stream's continuous bed and bank structure (Figure 2-1). Channel
heads are relatively dynamic zones in river networks, as their position can advance upslope by overland
or subsurface flow-driven erosion,  or retreat downslope by colluvial infilling. Source streams also can
originate at seeps or springs and associated wetlands.
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When two streams join at a confluence, the smaller stream (i.e., that with the smaller drainage area or
lower mean annual discharge) is called a tributary of the larger stream, which is referred to as the
mainstem. A basic way of classifying tributary contributions to a mainstem is the symmetry ratio,
which describes the size of a tributary relative to the mainstem at their confluence, in terms of their
respective discharges, drainage areas,  or channel widths (Roy and Woldenberg, 1986; Rhoads, 1987;
Benda,2008).

Surface-water hydrologic connectivity within river network channels occurs, in part, through the
unidirectional movement of water from channels at higher elevations to ones at lower elevations—that
is, hydrologic connectivity exists because water flows downhill. In essence, the river network represents
the aboveground flow route and associated subsurface-water interactions, transporting water, energy,
and materials from the surrounding watershed to downstream rivers, lakes, estuaries, and oceans (the
River Continuum Concept; Vannote et  al., 1980).

A river system (Figure 2-2) consists of a river network and its entire watershed. It includes all
connected or isolated surface-water bodies (e.g., lakes and wetlands), any ground-water flow systems
connecting the drainage basin with the river network and surface-water bodies, and terrestrial
ecosystems (Stanford and Ward, 1993; Naiman et al., 2005).

Streamflow and the quantity and character of sediment—interacting with watershed geology, terrain,
soils and vegetation—shape morphological changes in the stream channel that occur from river network
headwaters to lower rivers (Montgomery, 1999; Church, 2002). Headwater streams are typically
erosion zones in which sediment from the base of adjoining hillslopes moves directly into stream
channels and is transported downstream. As stream channels increase in size and decrease in slope, a
mixture of erosion and deposition processes usually is at work. At some point in the lower portions of
river networks, sediment deposition becomes the dominant process and floodplains form. Floodplains
are level areas bordering stream or river channels that are formed by sediment deposition from those
channels under present climatic conditions (Figure 2-3). These natural  geomorphic features are
inundated during moderate to high water events (Leopold, 1994; Osterkamp, 2008).  Floodplain and
associated river channel forms (e.g., meandering, braided, anastomosing) are determined by interacting
fluvial factors, including sediment size and supply, channel gradient, and streamflow (Church, 2002,
2006). Terraces are historical floodplains, formed under different climatic conditions, that are no longer
connected to the  river or stream channel that formed them (Figure 2-3).

Both riparian areas and floodplains are important components of river  systems (Figure 2-3). Riparian
areas are transition zones between terrestrial and aquatic ecosystems that are distinguished by
gradients in biophysical conditions, ecological processes, and biota. They are areas through which
surface and subsurface hydrology connect water bodies with their adjoining uplands, and they include
those portions of terrestrial ecosystems that significantly influence exchanges of energy and matter with
aquatic ecosystems (National Research Council, 2002). Riparian areas often have high biodiversity
(Naiman et al., 2005). They occur near lakes and estuarine-marine shorelines and along river networks,
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 Figure 2-2. Elements of a river system. These elements include: the drainage basin (light green area),
 river network (rivers and streams), and other water bodies (riparian/floodplain wetlands, lakes, and
 wetlands in non-floodplain settings). Note that the non-floodplain wetland that lacks a stream outlet
 also would be considered  "geographically isolated" sensu Tiner (2003b).
                                                                    Drainage boundary
                                                                    Floodplain boundary
                                                                    River
                                                                    Perennial stream
                                                             	Intermittent stream
                                                             ——•-  Ephemeral stream
                                                                    Wetland with
                                                                    surface outlet
                                                                    Riparian wetland
                                                                    Geographically
                                                                    isolated wetland
where their width can vary from narrow bands along headwater streams (Figure 2-3A) to broad zones
that encompass the floodplains of large rivers (Figure 2-3B).

Floodplains are also considered riparian areas, but not all riparian areas have floodplains. All rivers and
streams within river networks have riparian areas, but small streams in constrained valleys are less
likely to have floodplains than larger streams and rivers in unconstrained valleys (Figures 2-2 and 2-3).
The Federal Emergency Management Agency defines the area that will be inundated by the flood event
having a 1% chance of being equaled or exceeded in any given year as the "Special Flood Hazard Area,"
also referred to as the "100-year floodplain" (https://www.fema.gov/floodplain-management/flood-
zones). The 100-year  floodplain can but need not coincide with the geomorphic floodplain. Like riparian
areas, wetlands are transitional areas between terrestrial and aquatic ecosystems. According to
Cowardin etal. (1979), an area is classified as a wetland if it has one or more of the following three
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 Figure 2-3. Hypothetical cross-sections of (A) a headwater stream and (B) a large river within a river
 network. The headwater stream in (A) is a constrained reach with a narrow riparian area and no
 floodplain; the river in (B) has both a riparian area and a floodplain with the same spatial extent.
 Examples of other common natural floodplain features are shown in (B). The lateral extent of riparian
 areas varies depending on the criteria used for delineation.
            A. Headwater Stream with Riparian Area and Minimal
               or No Floodplain
            B. River with Riparian Area and Floodplain
                         I	Floodplain and riparian area
             Terrace
attributes: (1) the area supports predominantly hydrophytes (i.e., water-loving plants) at least
periodically; (2) the land has substrate that is predominantly undrained hydric soil; or (3) the land has
nonsoil substrate that is saturated with water or covered by shallow water at some time during the
growing season of each year. Note that the Cowardin etal. (1979) definition requires only one of these
characteristics, in contrast to the federal regulatory definition, which requires all three (33 Code of
Federal Regulations 328.3(b); see also USAGE, 1987). Thus, as used in this report, a wetland need not
meet the federal regulatory definition. Wetlands include areas such as swamps, bogs, fens, marshes,
ponds, and pools (Mitsch et al., 2009).

Many classification systems have been developed for wetlands (Mitsch and Gosselink, 2007). These
classifications can focus on vegetation, hydrology, hydrogeomorphic characteristics, or other factors
(Cowardin etal., 1979; Brinson, 1993; Tiner, 2003a; Comer etal., 2005). Because this report focuses on
downstream connectivity (Section 1.3), we consider two landscape settings in which wetlands occur
based on directionality of hydrologic flows. Directionality of flow also is included as a component of
hydrodynamic setting in the hydrogeomorphic approach (Brinson, 1993; Smith etal., 1995) and as an
element of water flowpath in an enhancement of National Wetlands Inventory data (Tiner, 2011). This
emphasis on directionality of flow is necessary because hydrologic connectivity plays a dominant role in
determining the types of effects wetlands have on downstream waters (Section 2.3.2).
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A non-floodplain wetland setting is a landscape setting where the potential exists for unidirectional,
lateral hydrologic flows from wetlands to the river network through surface water or ground water.
Such a setting would include upgradient areas such as hillslopes or upland areas outside of the
floodplain. Any wetland setting where water could only flow from the wetland toward a river network
would be considered a non-floodplain setting, regardless of the magnitude and duration of flows and of
travel times. In this document, we therefore refer to wetlands that occur in these settings as non-
floodplain wetlands.

A riparian or floodplain wetland setting is a landscape setting (e.g., floodplains, most riparian areas,
lake and estuarine fringes) that is subject to bidirectional, lateral hydrologic flows. Wetlands in
riparian/floodplain settings can have some of the same types of hydrologic connections as those in non-
floodplain settings. In addition, wetlands in these settings also have bidirectional flows. For example,
wetlands within a riparian area are connected to the river network through lateral movement of water
between the channel and riparian area (e.g., through overbank flooding, hyporheic flow). Given our
interest in addressing the effects of wetlands on downstream waters (Section 1.1), we have focused in
particular on the subset of these wetlands that occur in riparian areas with and without floodplains
(collectively referred to hereafter as riparian/floodplain wetlands); we generally do not address
wetlands at lake and estuarine fringes. Riparian wetlands are portions of riparian areas that meet the
Cowardin etal. (1979) three-attribute wetland criteria (i.e., having wetland hydrology, hydrophytic
vegetation, or hydric soils); floodplain wetlands are portions of the floodplain that meet these same
criteria.

Our use of landscape setting to define riparian/floodplain wetlands and non-floodplain wetlands is
similar to the use of landscape position by Tiner (2011) to supplement the Cowardin etal. (1979)
classification. Our use of riparian/floodplain wetland setting is generally consistent with Tiner's
estuarine, lotic, and lentic landscape positions, whereas our non-floodplain setting is similar to his
terrene category (Tiner, 2011). One important difference is that Tiner (2011) would consider a wetland
to be terrene if it were located along a river but not subject to frequent overflow. Given that even
infrequent flooding can have profound effects on wetland development and function, we would consider
such a wetland to be in a riparian/floodplain setting.

The terms "riparian/floodplain" and "non-floodplain" are meant to describe the landscape setting in
which wetlands occur and do not refer to wetland type or class. Many wetland types occur in both
settings. For example, a palustrine emergent wetland (Cowardin et al., 1979) could be located outside a
floodplain, or it could be located within a floodplain and subject to bidirectional flows. A wetland that is
classified as  depressional in the hydrogeomorphic approach could have any combination of inlets and
outlets or none at all (Smith et al., 1995). The setting for such a wetland would be riparian/floodplain if
it had both an input  and output channel because water from the stream flows into and affects the
wetland. A depressional wetland with a surface outlet and no inlet or with no outlets and inlets,
however, would be considered non-floodplain because water could flow downgradient only from the
wetland to the river  network, and not from a stream to the wetland. Similarly, a riverine wetland (Smith
etal., 1995) that is the origin for a stream would be considered non-floodplain if it had no input channel,
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even though it occurs in a riparian area. In most cases, however, riverine wetlands would be considered
riparian/floodplain. Thus, directionality of hydrologic flow is a function of landscape setting and cannot
necessarily be determined from wetland class.

A major consequence of the two different landscape settings is that waterborne materials can be
transported only from the wetland to the river network for a non-floodplain wetland, whereas
waterborne materials can be transported from the wetland to the river network and from the river
network to the wetland for a riparian/floodplain wetland. In the latter case, there is a mutual,
interacting effect on the structure and function of both the wetland and river network. In contrast, a
non-floodplain wetland can affect a river through the transport of waterborne material, but the opposite
is not true. Note that we limit our use of riparian/floodplain and non-floodplain landscape settings to
describe the direction of hydrologic flow; the terms cannot be used to describe directionality of
geochemical or biological flows. For example, mobile organisms can move from a stream to a non-
floodplain wetland (e.g., Subalusky et al., 2009a; Subalusky et al., 2009b). In Alaska, transport of live
salmon or their carcasses from streams to riparian areas by brown bears (Ursus arctos) account for
more than 20% of riparian nitrogen budgets (Helfield and Naiman, 2006). Although this example is in a
riparian/floodplain setting, it shows how geochemical fluxes can be decoupled from hydrologic flows.

Both non-floodplain and riparian/floodplain wetlands can include geographically isolated wetlands,
or wetlands completely surrounded by uplands (Tiner, 2003b). These wetlands have no apparent
surface-water outlets, but can hydrologically connect to downstream waters through spillage or ground
water. We define an upland as any area not meeting the Cowardin et al. (1979) three-attribute wetland
criteria, meaning that uplands can occur in both terrestrial and riparian areas. Thus, a wetland that is
located on a floodplain but is surrounded by upland would be considered a geographically isolated,
riparian/floodplain wetland that is subject to periodic inundation from the river network. Although the
term "geographically isolated" could be misconstrued as implying functional isolation, the term has been
defined in the peer-reviewed literature to refer specifically to wetlands surrounded by uplands.
Furthermore, the literature explicitly notes that geographic isolation does not imply functional isolation
(Leibowitz, 2003; Tiner, 2003b). Discussion of geographically isolated wetlands is essential because
hydrologic connectivity (an element of connectivity, which is the focus of this  document) is generally
difficult to characterize for these wetlands. The difficulty arises because hydrologic monitoring or
additional information and analyses would be necessary to determine whether surface or subsurface
hydrologic connections occur for such wetlands.

2.2.2   River System Hydrology
River system hydrology is controlled by hierarchical factors that result in a broad continuum of
belowground and aboveground hydrologic flowpaths connecting river basins  and river networks
(Winter, 2001; Wolocketal., 2004; Devito etal., 2005; Poole etal., 2006; Wagener et al., 2007; Poole,
2010; Bencala etal., 2011; Jencso and McGlynn, 2011). At the broadest scale, regional climate interacts
with river-basin terrain and geology to shape inherent hydrologic infrastructure that bounds the nature
of basin hydrologic flowpaths. Different climate-basin combinations form identifiable hydrologic

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landscape units with distinct hydrologic characteristics (Winter, 2001; Wigington et al., 2013). Buttle
(2006) posited three first-order controls of watershed streamflow generated under specific
hydroclimatic conditions: (1) the ability of different landscape elements to generate runoff by surface or
subsurface lateral flow of water; (2) the degree of hydrologic linkage among landscapes by which
surface and subsurface runoff can reach river networks; and (3) the capacity of the river network itself
to convey runoff downstream to the river-basin outlet. River and stream waters are influenced by not
only basin-scale or larger ground-water systems, but also local-scale, vertical and lateral hydrologic
exchanges between water in channels and sediments beneath and contiguous with river network
channels (Ward, 1989; Woessner, 2000; Malard etal., 2002; Bencala, 2011). The magnitude and
importance of river-system hydrologic flowpaths at all spatial scales can radically change over time at
hourly to yearly temporal scales (Junk et al., 1989; Ward, 1989; Malard et al., 1999; Poole et al., 2006).

Because interactions between ground waters and surface waters are essential processes in rivers,
knowledge of basic ground-water hydrology is necessary to understand the interactions between
surface and subsurface water and their relationship to connectivity within river systems. Subsurface
water occurs in two principal zones: the unsaturated zone and the saturated zone (Figure 2-4; Winter et
al., 1998). In the unsaturated zone, the spaces between soil, gravel, and other particles contain both air
and water. In the saturated zone, these spaces are completely filled with water. Ground water refers to
any water that occurs and flows (saturated ground-water flow) in the saturated zone beneath a
watershed surface (Winter et al., 1998). Rapid flow (interflow) of water can occur through large pore
spaces in the unsaturated zone (Beven and Germann, 1982).

Traditionally, geologic formations in which ground water occurs are divided into two major categories:
(1) aquifers, which are saturated geologic units capable of transmitting significant amounts of water
under ordinary hydraulic gradients; and (2) aquicludes, which are saturated geologic units that are not
capable of transmitting significant quantities of water (aquicludes are also referred to as confining
layers or confining units; Freeze and Cherry, 1979). Water flow in an aquifer can take various forms:
Water can flow in small voids and pores between the aquifer strata (porous media aquifers), in large
voids (karst), or in fractures and cracks within the aquifer formation (fractured flow aquifers). Flow
differs in its characteristics between the various aquifer types mentioned, yet follows the same basic
rule, by which flow occurs from regions of high hydraulic pressure to regions of lower hydraulic
pressure, down the pressure gradient (Jones and Mulholland, 2000).

There are two main types of aquifers (Freeze and Cherry, 1979). Unconfined aquifers are underlain by
a confining unit but remain open to the  atmosphere at their top and exchange gases with the
environment. The upper saturated horizon in unconfined aquifers is known as the water table (Figure
2-4). Complex geologic conditions can lead to more complex distributions of saturated and unsaturated
zones. Discontinuous saturated lenses creating perched water tables can occur where low
permeability layers (e.g., clay) are present in the midst of highly permeable materials such as sand
(Freeze, 1971). Confined aquifers are bounded by an underlying confining unit and an overlying
confining unit and typically lack a direct connection with current surface and atmospheric conditions
(Figure 2-5). Water in confined aquifers is often pressurized, and, consequently, water levels in wells
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 Figure 2-4. Water below the land surface occurs in either the unsaturated or the saturated zone.
 The upper surface of the saturated zone is the water table. Ground water and ground-water flow occur
 in the saturated zone. If a surface-water body is connected to the ground-water system, the water
 table intersects the water body at or near the surface of its shoreline. Modified from Winter et al.
 (1998).
               Unsaturated zone
              -T	Water table
                                                                      Surf ace water
                                 turated zone (around wat
penetrating confined aquifers occur at elevations above the upper confining unit The surface of the
water levels in wells penetrating a confined aquifer is called the potentiometric surface. Confined
aquifers typically occur deeper below the land surface than unconfined aquifers and generally have less
frequent influence on surface waters than unconfined aquifers.

Traditionally, aquifers were identified based solely on their ability to support wells for water
production, but in recent years hydrologists studying ground water-surface water interactions have
recognized the need for a broader definition that recognizes the importance of low-flow geologic
formations to aquatic ecosystems. Payne and Woessner (2010) highlighted the importance of aquifers
with varying flow rates on streams and proposed a classification of aquifer flow systems that ranged
from high flow to low flow, with low flow aquifers having limited ground-water discharge potential
except for small streams and wetlands. Winter et al. (1998) simply defined aquifers as the permeable
materials (e.g., soil, rock) through which ground water flows. In this report, we have adopted the Winter
et al. (1998) aquifer definition. Unless  otherwise noted, our discussion of ground water and aquifers is
limited to unconfined systems.

Ground-water recharge areas occur where water from land surfaces or surface-water bodies infiltrates
and moves  into saturated zones. Discharge areas occur where water flows from saturated zones into a
river network, other water bodies, or onto land surfaces. A gaining stream (or wetland; also referred
to as a discharge wetland) within a river network receives inflow of ground water. In this situation, the
water table elevation near the  stream (or wetland) must be higher than the elevation of the stream
water surface. In a losing stream (or wetland; i.e., recharge wetland), water flows from the stream
(wetland) to ground water. In this situation, the water table elevation near the stream or wetland is
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 Figure 2-5. Cross-section showing major hydrologic f lowpaths in a regional-scale stream-watershed
 system. USF = unsaturated flow, GW = ground-water flowpath (saturated flow); GW1, GW2, and
 GW3 = ground-water flowpaths of varying depth and length. GW1 represents local ground water and
 GW3 represents regional ground water. GWCF = ground-water flowpath in confined aquifer.
                                        Precipitation
                                             GW3

                                             Confining layer/formation
lower than the stream or wetland water surface. Conditions that determine whether streams and
wetlands are gaining or losing can change over short periods of time and over short distances within
river networks and river basins (Winter et al., 1998; Harrington et al., 2002; Wilson and Guan, 2004;
Goes and Pool, 2005; Scanlon etal., 2006; Vivoni etal., 2006; Larned etal., 2008). Overall, however, the
volume and sustainability of streamflow within river networks typically depend on contributions from
ground water (Winter, 2007), especially in areas with  shallow ground-water tables and pervious
subsurfaces (de Vries, 1995; Kish et al., 2010).

Ground-water flow systems within river basins can be complex, of varying sizes and depths, and overlie
one another (Toth, 1963; Winter etal., 1998; Haitjema and Mitchell-Bruker, 2005). Although in reality
there is a continuum of flowpath lengths that occur within river basins (Bencala et al., 2011), they are
commonly grouped into three categories (Figure 2-5). In local ground-water flow systems (also
referred to as shallow ground-water flow systems), ground water flows from the highest elevations of
water tables (water table highs) to nearby lowlands or surface waters (Winter and LaBaugh, 2003).
Local ground-water flow is the most dynamic of ground-water flow systems, having the greatest
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interchange with surface waters. If the depth-to-width ratios of aquifers are sufficiently large, regional
flow systems (deepest ground-water flowpaths) also might be present. Regional ground water (also
referred to as deep ground water) originates from precipitation in distant upland recharge areas and
moves long distances, through deep regional-scale aquifers, to river networks (Figure 2-5). The contact
times between ground water and subsurface materials are longer for these deep and long flow systems
than for local systems. Eventually, deep regional flow systems also discharge to surface waters in the
lower portions of river networks where they influence surface-water conditions. An intermediate
ground-water flow system is one in which ground water flows from a water table high to a lowland that
is not immediately adjoining the water table high. Intermediate ground-water flow systems are
representative of the wide range of flowpath lengths and depths that occur between local and regional
ground-water systems.

Other hydrologic flowpaths are also significant in determining the characteristics of river systems. The
most obvious is the downstream water movement within stream or river channels, or open-channel
flow. River water in stream and river channels can reach riparian areas and floodplains via overbank
flow (Figure 2-6A), which occurs when floodwaters  flow over stream and river channels (Mertes, 1997).
Overland flow is the portion of streamflow derived from net precipitation that flows over the land
surface to the nearest stream channel with (Figure 2-6A; Hewlett, 1982). Overland flow can be
generated by several mechanisms. Infiltration-excess overland flow occurs when the rainfall rates
exceed the infiltration rates of land surfaces (Horton, 1945). Saturation-excess overland flow occurs
when precipitation inputs cause water tables to rise to land surfaces so that precipitation inputs to the
land surfaces cannot infiltrate and flow overland (Dunne and Black, 1970). Return flow occurs when
water infiltrates, percolates through the unsaturated zones, enters saturated zones, and then returns to
and flows over watershed surfaces, commonly at hillslope-floodplain transitions (Dunne and Black,
1970).

Alluvium (Figure 2-3B) comprises deposits of clay, silt, sand, gravel, or other particulate materials that
running water has deposited in a streambed, on a floodplain, on a delta, or in a fan at the base of a
mountain. These deposits occur near active river systems but also can be found in buried river valleys—
the remnants of relict river systems (Lloyd and Lyke, 1995). In this report, we are concerned primarily
with alluvium deposited along active river networks. Commonly, alluvium is highly permeable, creating
an environment conducive to ground-water flow. Alluvial ground water (typically a mixture of river
water and local, intermediate, and regional ground water) moves through the alluvium. Together, the
alluvium  and alluvial ground water comprise alluvial aquifers. Alluvial aquifers are closely associated
with floodplains and have high levels of hyporheic exchange (Stanford and Ward, 1993; Amoros and
Bornette, 2002; Poole et al., 2006). Hyporheic exchange occurs when water moves from stream or river
It occurs  during both high- and low-flow periods, and typically has relatively horizontal flowpaths at
scales of meters to tens of meters (Bencala, 2005) and vertical flowpaths with depths ranging from
centimeters to  tens of meters (Stanford and Ward, 1988; Woessner, 2000 and references therein).
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 Figure 2-6. Hyporheic zone flows. (A) Common hydrologic flowpaths by which water flows between
 watersheds and river networks. (B) and (C) The three-dimensional process of hyporheic flow, or the
 movement of water from a river or stream to nearby alluvium and then back to the river or stream.
 Modified from Winter et al. (1998).
              A. Common River-Floodplain Hydrologic Flowpaths

                                                             Riparian
                              1 - overland flow     4 - regional ground water
                              2-overbankflow     5-hyporheic flow
                              3 - local ground water 6 - wetland overflow
              B. Hyporheic Zone Cross-Section
                Water
                table
                                 ground-water flow
             hyporheic flow
              C. Hyporheic Zone Longitudinal Profile
                                 ground-water flow
             hyporheic flow
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Riparian areas and floodplains can have a diverse array of hydrologic inputs and outputs, which, in turn
influence riparian/floodplain wetlands. Riparian areas and floodplains receive water from precipitation;
overland flow from upland areas; local, intermediate, regional ground water; and hyporheic flows
(Figure 2-6A; National Research Council, 2002; Richardson etal., 2005; Vidon etal., 2010). Water
flowing over the land surface in many situations can infiltrate soils in riparian areas. If low permeability
subsoils or impervious clay layers are present, water contact with the plant root zone is increased and
materials in the water are subject to ecological functions such as denitrification before it reaches the
stream channel (Section 4.3.2; National Research Council, 2002; Naiman et al., 2005; Vidon et al., 2010).

The relative importance of the continuum of hydrologic flowpaths among river systems varies, creating
streams and rivers with different flow duration (or hydrologic permanence) classes (Figures 2-2 and
2-7). Perennial streams or stream reaches (Figure 2-7A) typically flow year-round. They are
maintained by local or regional ground-water discharge or streamflow from higher in the stream or
river network. Intermittent streams or stream reaches (Figure 2-7B) flow continuously at certain
times of the year (e.g., during certain seasons such as spring snowmelt); drying occurs when the water
table falls below the channel bed elevation. Ephemeral streams or stream reaches (Figure 2-7C) flow
briefly (typically hours to days) during and immediately following precipitation; these channels are
above the water table at all times. Streams in these flow duration classes often transition longitudinally,
from ephemeral to intermittent to perennial, as drainage area increases and elevation decreases along
river networks. Many headwater streams, however, originate from permanent springs and flow into
intermittent downstream reaches. At low flows, intermittent streams can contain dry segments
alternating with flowing segments. Transitions between flow duration classes can coincide with
confluences or with geomorphic discontinuities within the network (May and Lee,  2004; Hunter et al.,
2005). Variation of streamflow within river systems occurs in response to hydrologic events resulting
from rainfall or snowmelt. Stormflow is  streamflow that occurs in direct response to rainfall or
snowmelt (Figure  2-8A), which might stem from multiple ground-water and surface-water sources
(Dunne and Leopold, 1978). Baseflow is streamflow originating from ground-water discharge or
seepage (locally or from higher in the river network), which sustains water flow through the channel
between hydrologic events (Figure 2-8A). Perennial streams have baseflow year-round; intermittent
streams have baseflow seasonally; ephemeral streams have no baseflow. All three stream types convey
stormflow. Thus, perennial streams are more common in areas receiving high precipitation, whereas
intermittent and ephemeral streams are  more common in the more arid portions of the United States
(Figure 2-9; NHD,  2008). The distribution of headwater streams (perennial, intermittent, or ephemeral)
as a proportion of total stream length is similar across geographic regions and climates (Figure 2-9C).

Similar to streams, the occurrence and persistence of riparian/floodplain wetland and non-floodplain
wetland hydrologic connections with river networks, via surface water (both channelized and
nonchannelized) or ground water, can be continuous, seasonal, or ephemeral, depending on the overall
hydrologic conditions in the watershed. For example, a non-floodplain wetland might have a direct
ground-water connection with a river network during wet conditions but an indirect regional ground-
water connection  (via ground-water recharge) under dry conditions. Geographically isolated wetlands
can be hydrologically connected to the river network via nonchannelized surface flow (e.g., swales or
overland flow) or ground water.
Stream and Wetland Connectivity:                                                             January 2015
A Review and Synthesis                                                                        3

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 Figure 2-7. Hypothetical hydrographs illustrating maximum duration of flow (Dmax.q) for (A)
 perennial, (B) intermittent, and (C) ephemeral streams. Source: Reprinted from Non-navigable
 streams and adjacent wetlands: Addressing science needs following the Supreme Court's Rapanos
 decision, (2008) by Leibowitz et al. with permission of Ecological Society of America.
                       TO

                       to
                      CM


                       0)
                       0)
                       (5

                       u
                                         •D«,., = 365 days -
                             B
                                    H
                          Oct
Jan
 Apr
Time
July
Oct
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                                      January 2015

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 Figure 2-8. (A) Hypothetical hydrograph showing stormflow and baseflow responses to a rainfall
 event. (B) Expansion and contraction of flowing water in a stream network following a rainfall
 event. Panel B Source: Reprinted from Subsurface stormflows in the highly permeable forested
 watersheds of southwestern British Columbia, (1988) by Cheng et al. with permission of Elsevier.
                                        Time (days)
            .5
   B.

0.5-


0.4-


0.3-
            £
            3
           £  0.2-
            ra
            i
           £  o.i-
           1/1
                         i
                         11
                       i
                      12
         13
October 1973
 i
14
 \
15
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                              2-16
                                           January 2015

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 Figure 2-9. Characteristics of U.S. streams by watershed, in terms of percent of total stream length
 as (A) perennial, (B) intermittent, and (C) headwater streams. Data from the National Hydrography
 Dataset (NHD) Reach Address Database (RAD) v2.0 at 1:100,000 scale using 8-digit HUG (Hydrologic
 Unit Code) watersheds. Here, "intermittent" includes streams having intermittent or ephemeral flow.
 Note that NHD data generally do not capture streams <1.6 km (1 mile) in length, and  ranges of color
 categories are not consistent across maps.
                                                                     Perennial Stream Length
                                                                       as a Percentage of
                                                                      Total Stream Length

                                                                       % Perennial Stream
                                                                            1-15
                                                                            16-35
                                                                            36-58
                                                                            59-81
                                                                            82-100
                                                                            State Boundary
       B.
                                                                    Intermittent Stream Length
                                                                       as a Percentage of
                                                                      Total Stream Length

                                                                       % Intermittent Stream
                                                                       I    10
                                                                       I    I 1-16
                                                                       I    I 17-38
                                                                       I    I 39-60
                                                                       I    161-81
                                                                       BB 82-100
                                                                       I    I State Boundary
                                                                    Headwater Stream Length
                                                                       as a Percentage of
                                                                      Total Stream Length

                                                                       % Headwater Stream
                                                                           10
                                                                           I 1-19
                                                                           I 20-36
                                                                           I 37-48
                                                                       BB 49-57
                                                                       BB 58-100
                                                                       I    I State Boundary
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2.2.3   River Network Expansion and Contraction
The portions of river networks with flowing water expand and contract longitudinally (in an upstream-
downstream direction) and laterally (in a stream channel-floodplain direction) in response to seasonal
environmental conditions and precipitation events (Hewlett and Hibbert, 1967; Gregory and Walling,
1968; Dunne and Black, 1970; Day, 1978; Junketal., 1989; Hunter etal., 2005; Wigington etal., 2005;
Rains et al., 2006; Rains et al., 2008). The longitudinal expansion of channels with flowing water in
response to major precipitation events represents a transient increase in the extent of headwater
streams. Figure 2-10 shows the expansion of the flowing portion of two stream networks in western
Oregon between dry, summer and wet, winter seasons. Intermittent and perennial streams flow during
wet seasons, whereas ephemeral streams flow only in response to rainfall or snowmelt. During dry
periods, flowing portions of river networks are limited to perennial streams; these perennial portions of
the river network can be discontinuous (Stanley et al., 1997; Hunter et al., 2005; Larned et al., 2010) or
interspersed with intermittently flowing stream reaches.

The dominant sources of water to a stream can shift during river network expansion and contraction
(Malard etal., 1999; McGlynn and McDonnell, 2003; McGlynn  etal., 2004; Malard etal., 2006). Rainfall
and snowmelt cause a river network to expand in two ways. First, local aquifers expand and water
moves into dry channels, which increases the total length of the wet channel (Winter et al., 1998); the
resulting intermittent streams will contain water during the entire wet season. Second, stoonflow can
cause water to enter ephemeral and intermittent streams (Figure 2-8). The larger the rainfall or
snowmelt event, the greater the number of ephemeral streams and total length of flowing channels that
occur within the river network. Ephemeral flows cease within days after rainfall or snowmelt ends
(Figure 2-8B), causing the length of wet channels to decrease and river networks to contract. The
flowing portion of river networks further shrinks as the spatial extent of aquifers with ground water in
contact with streams contract and intermittent streams  dry. In many river systems across the United
States, stoonflow comprises a major portion of annual streamflow (Hewlett et al., 1977; Miller et al.,
1988; Turton et al., 1992; Goodrich et al., 1997; Vivoni et al., 2006). In these systems, intermittent and
ephemeral streams are major sources of river water (Section B.5). When rainfall or snowmelt induces
stormflow in headwater streams  or other portions of the river network, water flows downgradient
through the network to its lower  reaches. As water moves downstream through a river network, the
hydrograph for a typical event broadens with a lower peak (Figure 2-11). This broadening of the
hydrograph shape (Figure 2-11A) results from transient storage of water in river network channels and
nearby alluvial aquifers (Fernald etal., 2001).

Floodplains and riparian areas can be locations with significant ground-water recharge and discharge
(National Research Council, 2002; Naiman etal., 2005). During very large hydrologic events, aggregate
flows from headwaters and other tributary streams can  result in overbank flooding in river reaches with
floodplains; this occurrence represents lateral expansion (Figure 2-12) of the river network (Mertes,
1997). Water from overbank flows can recharge alluvial aquifers, supply water to floodplain wetlands,
surficially connect floodplain wetlands to rivers, and shape the geomorphic features of the floodplain
Stream and Wetland Connectivity:                                                            January 2015
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 Figure 2-10. Extent and connectivity of streams with flowing water, wetlands, and other water
 bodies in (A) Spring Valley Creek, OR and (B) Spoon Creek, OR during dry summer (left) and wet
 winter (right) conditions. Source: Reprinted from Stream network expansion: A riparian water quality
 factor, (2005) by Wigington et al. with permission of John Wiley & Sons.
      A. Spring Valley Creek
                                  Summer
                                   Winter
                                                                               0    1    2
                                                                               Kilometers
      B. Spoon Creek
                                  Summer
                                   Winter

                                                                               Kilometers
              Perennial stream
        	Intermittent stream
              Ephemeral stream
              Surface field drainage
Swale
Road ditch
Ephemeral water bodies (depressions)
(Wolman and Miller, 1960; Hammersmark et al., 2008). Depending on the nature of the hydraulic
gradients, ground water within floodplain alluvium can move both parallel and perpendicularly to
streams or rivers (National Research Council, 2002) and enter river networks at various discharge
points. Bidirectional exchanges of water between ground water and river networks, including hyporheic
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 Figure 2-11. Stormflow moves downstream through the river network and interacts with lower
 stream reaches, f loodplains, and alluvial aquifers. (A) Hydrographs for three nested rivers in the
 Potomac River watershed (drainage area Potomac > Shenandoah > South). (B) Hydrographs for the
 same three rivers with streamflow normalized by drainage area. Source: Reprinted from Elements of
 physical hydrology, (1998) by Hornberger et al., with permission of Johns Hopkins University Press.
          5000
                A.
 4000-

 3000-

 2000-
r
 1000-

    0
                                                      Potomac
                                       4
                                         I
                                         6
8
10
12
                           2468
                             Time (days from April 13,1987)
                                                               10
                      12
flow, can occur under a wide range of streamflows, from flood flows to low flows (National Research
Council, 2002; Naiman etal., 2005; Vivoni etal., 2006).

The hydrologic connections with river networks fundamentally differ for riparian/floodplain wetlands
and non-floodplain wetlands. Riparian/floodplain wetlands can have bidirectional, lateral hydrologic
connections to the river network, either through overbank flooding (i.e., lateral expansion of the
network) or hyporheic flow, in addition to unidirectional flows from upland and ground-water sources
(Figure 2-6A). In contrast, hydrologic connections between non-floodplain wetlands and river networks
originate via surface-water spillage or ground-water flow when water inputs exceed evapotranspiration
and available storage. Although wetlands that serve as origins for streams are riparian, we group them
with non-floodplain wetlands because they also have unidirectional flow through their outlet streams. In
both cases, the degree of hydrologic connectivity between riparian/floodplain and non-floodplain
wetlands and the river network varies with lateral expansion and subsequent contraction.
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 Figure 2-12. Landsat 5 satellite images of the Mississippi River along the borders of Tennessee,
 Kentucky, Missouri, and Arkansas on (A) May 12, 2006 and (B) May 10, 2011. Images courtesy of
 U.S. Geological Survey/National Aeronautics Space Administration.
One factor affecting the lateral distance that overbank flow spreads is preexisting moisture conditions
on the floodplain (Mertes, 1997; Naiman et al., 2005). River overbank flow that enters a dry floodplain
will spread and then infiltrate the soil (Naiman et al., 2005). If inflows from streams, rainfall, or ground
water have water tables elevated to the floodplain surface, water entering the riparian area from
overbank flow cannot infiltrate soils. The result is standing water on the floodplain and subsequent
movement of water to lower elevations of the floodplain. This water can alter the geomorphology of the
floodplain (Hupp and Osterkamp, 1996), be biogeochemically transformed (Section 4.3.2; Naiman et al.,
2005), be lost by evaporation, or be transpired by vegetation (Meyboom, 1964). As the river and
floodplain water table elevations decrease, surface water on the floodplain can flow back into the river,
infiltrate floodplain soils, or evapotranspire.

Many studies have documented the fact that riparian/floodplain wetlands can attenuate flood pulses of
streams and rivers by storing excess water from streams and rivers. Bullock and Acreman (2003)
reviewed wetland studies and reported that wetlands reduced or delayed floods in 23 of 28 studies. For
example, Walton et al. (1996) found that peak discharges between upstream and downstream gaging
stations on the Cache River in Arkansas were reduced 10-20% primarily due to floodplain water
storage. Locations within floodplains and riparian areas with higher elevations likely provide flood
storage less frequently than lower elevation areas.

The interactions of high flows with floodplains and associated alluvial aquifers of river networks are
important determinants of hydrologic and biogeochemical conditions of rivers (Ward, 1989; Stanford
and Ward, 1993; Boulton etal., 1998; Burkart et al., 1999; Malard etal., 1999; Amoros and Bornette,
2002; Malard etal., 2006;  Poole, 2010). Bencala (1993; 2011) noted that streams and rivers are not
pipes: They interact with the alluvium and geologic materials adjoining and under channels. In streams
or river reaches constrained by topography, significant floodplain and near-channel alluvial aquifer
Stream and Wetland Connectivity:                                                             January 2015
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interactions are limited (Figure 2-3A). In reaches with floodplains, however, stormflow commonly
supplies water to alluvial aquifers during high-flow periods through the process of bank storage
(Figure 2-13; Whiting and Pomeranets, 1997; Winter et al., 1998; Chen and Chen, 2003). As streamflow
decreases after hydrologic events, the water stored in these alluvial aquifers can serve as another source
of baseflowin rivers (Figure 2-13C).

In summary, the extent of wetted channels is dynamic because interactions between surface water in the
channel and alluvial ground water, via hyporheic exchange, determine open-channel flow. The flowing
portion of river networks expands and contracts in two primary dimensions: (1) longitudinally, as
intermittent and ephemeral streams wet up and dry; and (2) laterally, as floodplains and associated
alluvial aquifers gain (via overbank flooding, bank storage, and hyporheic exchange) and lose (via
draining of alluvial aquifers and evapotranspiration) water. Vertical ground-water exchanges between
streams and rivers and underlying alluvium are also key connections, and variations in these vertical
exchanges contribute to the expansion and contraction of the portions of river networks with open-
channel flow. Numerous studies have documented expansion and contraction of river systems (e.g.,
Gregory and Walling, 1968); the temporal and spatial pattern of this expansion and contraction varies in
response to many factors, including interannual and long-term dry cycles, climatic conditions, and
watershed characteristics (Cayan and Peterson, 1989; Fleming et al., 2007).


2.3  Influence of Streams and Wetlands on Downstream
       Waters
The previous section provided background on river system hydrology. In this section, we present a
general overview of how streams and wetlands affect downstream waters, focusing on functions within
streams and wetlands and their connectivity to rivers.

The structure and function of rivers are highly dependent on the constituent materials stored in and
transported through them. Most of these materials, broadly defined here as any physical, chemical, or
biological entity, including water, heat energy, sediment, wood, organic matter, nutrients, chemical
contaminants, and organisms, originate outside of the river: They originate from either the upstream
river network or other components of the river system, and then are transported to the river by water
movement or other mechanisms. Thus, the fundamental way in which streams and wetlands affect river
structure and function is by altering fluxes of materials to the river. This alteration of material fluxes
depends on two key factors: (1) functions within streams and wetlands that affect material fluxes, and
(2) connectivity (or isolation) between streams and wetlands and rivers that allows (or prevents)
transport of materials between the systems.

2.3.1   Effects of Streams and Wetlands on Material Fluxes
Streams and wetlands affect the amounts and types of materials that are or are not delivered to
downstream waters, ultimately contributing to the structure and function of those waters. Leibowitz  et
al. (2008) identify three functions, or general mechanisms of action, by which streams and wetlands

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 Figure 2-13. The direction and magnitude of interactions between surface water and ground water
 can dramatically change during large hydrologic events, including floods. (A) In a hypothetical
 stream-floodplain cross-section, ground water flows from the alluvial aquifer to the stream before a
 major hydrologic event. (B) During the bank-full hydrologic event, surface water moves from the
 stream and becomes ground water in the alluvial aquifer. (C) After recession of the event, ground
 water that was stored in the alluvial aquifer during the hydrologic event flows back to the stream. This
 process is called bank storage, which can sustain baseflow in streams and rivers after the hydrologic
 event has ended. Modified from Winter et al. (1998).
HUnsaturated
zone
• Saturated
zone
^ Elevation of
water in stream
	 ^ Groundwater
flow
                A.
influence material fluxes into downstream waters: source, sink, and refuge. We have expanded on this
framework to include two additional functions: lag and transformation. These five functions
(summarized in Table 2-1) provide a framework for understanding how physical, chemical, and
biological connections between streams and wetlands and downstream waters influence river systems.
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These five functions (Table 2-1) are neither static nor mutually exclusive, and often the distinctions
between them are not sharp. A stream or wetland can provide different functions at the same time.
These functions can vary with the material considered (e.g., acting as a source of organic matter and a
sink for nitrogen) and can change over time (e.g., acting as a water sink when evapotranspiration is high
and a water source when evapotranspiration is low). The magnitude of a given function also is likely to
vary temporally: For example, streams generally are greater sources of organic matter and
contaminants during high flows.

Leibowitz et al. (2008) explicitly focused on functions that benefit downstream waters, but these
functions also can have negative effects—for example, when streams and wetlands serve as sources of
chemical contamination (Sections 3.4.4, 4.3.3.5, 4.3.3.6; Table 2-1). In fact, benefits need not be linear
with respect to concentration; a beneficial material could be harmful at higher concentrations due to
nonlinear and threshold effects. For example, nitrogen can be beneficial at lower concentrations but can
reduce water quality at higher concentrations. Although here we focus primarily on the effects of
streams and wetlands on downstream waters, these same functions can describe effects of downstream
waters on streams and wetlands (e.g., downstream rivers can serve as sources of colonists for upstream
tributaries).

Because many of these functions depend on import of materials and energy into streams and wetlands,
distinguishing between actual function and potential function is instructive. For example, a wetland with
appropriate conditions (e.g., a reducing environment and denitrifying bacteria) is a potential sink for
nitrogen (Sections 4.3.3.2 and 4.4.3.2): If nitrogen is imported into the wetland, the wetland can remove
it by denitrification. The wetland will not serve this function, however, if nitrogen is not imported. Thus,
even if a stream or wetland does not currently serve a function, it has the potential to provide that
function under appropriate conditions (e.g., when material imports or environmental conditions
change). Although potential functions do not actively affect downstream waters,  they can be
instrumental in protecting those waters from future impacts. Ignoring potential function also can lead to
the paradox that degraded streams and wetlands (e.g., those receiving nonpoint-source nitrogen inputs)
receive more protection than less degraded systems (Leibowitz etal., 2008).

Three factors influence the effect that material and energy fluxes from streams and wetlands have on
downstream waters: (1) proportion of the material originating from (or reduced by) streams and
wetlands relative to the importance of other system components, such as the river itself; (2) residence
time of the material in the downstream water; and (3) relative importance of the material. In many
cases, the  effects on downstream waters need to be considered in aggregate. For  example, the
contribution of material by a particular stream or wetland (e.g., a specific ephemeral stream) might be
small, but the aggregate contribution by an entire class of streams or wetlands (e.g., all ephemeral
streams in the river network) might be substantial. Integrating contributions over time also might be
necessary, taking into account the frequency, duration, and timing of material export and delivery.
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1-3
  a
" 3
<2. O
(/) o
energy imports to and exports from a stream or wetland, in terms of mass or energy; arrow widths represent relative material mass or energy
and differences in arrow shades represent timing (lag) or composition (transformation) changes. Imports to streams and wetlands can come
from upland terrestrial areas, other streams and wetlands, or from the river itself. Arrows are meant to be illustrative, and do not necessarily
represent upstream/downstream relationships. For example, materials and energy can move downstream, upstream, or laterally into streams
and wetlands. Examples of commonly exchanged materials and energy include water, heat energy, nutrients, contaminants, sediment,
participate organic matter, organisms, and reproductive propagules; note that exchange of materials and energy between streams and wetlands
and downstream systems can result in positive or negative effects on downstream waters.
          Function
                                    Definition
                              Examples
                         Net increase in a material or energy flux
                         (exports > imports)
                                                               Streams: invertebrate production (Wipfli and Gregovich, 2002)
                                                               Wetlands', phytoplankton production from floodplain (Schemel etal., 2004;
                                                               Lehman eta I., 2008)
                         Net decrease in a material or energy flux
                         (exports < imports)
                                                               Streams: upstream fish populations that are not sustainable without net
                                                               immigration from downstream areas (Woodford and Mclntosh, 2010)
                                                               Wetlands', sediment deposition, denitrification (Johnston, 1991)
ro
to
en
                    Avoidance of a nearby sink function, thereby
                    preventing a net decrease in material or energy
                    flux (exports = imports)
Streams: headwaters as summer coldwater refuges (Curry et al., 1997)
Wetlands', riparian wetlands as aquatic refuges in dryland rivers (Leigh etal.
2010)
              River
                         Temporary storage and subsequent release of
                         materials or energy without affecting
                         cumulative flux (exports = imports); delivery is
                         delayed and can be prolonged
                                                               Streams: delay of downstream peak flows due to bank storage (Burt, 1997);
                                                               temporary heat storage within the alluvial aquifer (Arrigoni etal., 2008)
                                                               Wetlands', flood attenuation (Bullock and Acreman, 2003)
              River
                    Conversion of a material or energy into a
                    different form; the amount of the base material
                    or energy is unchanged (base exports = base
                    imports), but its composition (e.g., mass of the
                    different forms) can vary
                                                                    Streams: conversion of coarse to fine pa rticulate organic matter (Wallace etal.,
                                                                    1995)
                                                                    Wetlands', mercury methylation (Galloway and Branfireun, 2004; Selvendiran et
                                                                    a I., 2008)
ro
o

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Considering the cumulative material fluxes that originate from a specific stream or wetland, rather than
the individual materials separately, is essential in understanding the effects of material fluxes on
downstream waters (Section 1.2.3).

In general, the more frequently a material is delivered to a river, the greater its effect. The effect of an
infrequently supplied material, however, can be large if the material has a long residence time in the
river (Leibowitz et al., 2008). For example, woody debris might be exported to downstream waters
infrequently but it can persist in downstream channels. In addition, some materials are more important
in defining the structure and function of a river. Using the same example, woody debris can have a large
effect on river structure and function because it affects water flow, sediment and organic matter
transport, and habitat (Harmon et al., 1986; Gurnell et al., 1995). Another example is salmon migrating
to a river: They can serve as a keystone species to regulate other populations and as a source of marine-
derived nutrients (Schindler et al., 2005).

2.3.2   Connectivity and Transport of Materials to and from Streams and
         Wetlands

2.3.2.1   Connectivity and Isolation
The functions discussed above represent general mechanisms by which streams and wetlands influence
downstream waters. For these altered material and energy fluxes to affect a river, however, transport
mechanisms that deliver (or could deliver) these materials to the river are necessary. Connectivity
describes the degree to which components of a system are connected and interact through various
transport mechanisms; connectivity is determined by the characteristics of both the physical landscape
and the biota of the specific system. This definition is related to, but is distinct from, definitions of
connectivity based on the actual flow of materials between system components (e.g., Pringle, 2001).
That connectivity among river-system components, including streams and wetlands, plays a significant
role in the structure and function of these systems is not a new concept. In fact, much of the theory
developed to explain how these systems work focuses on connectivity and linkages between system
components (e.g., Section 1.2; Vannote etal., 1980; Newbold etal., 1982a; Newbold etal., 1982b; Junk et
al., 1989; Ward, 1989; Benda etal., 2004; Thorp etal., 2006).

In addition to its central role in defining river systems (Section 2.2.1), water movement through the
river system (Figure 2-6) is the primary mechanism providing physical connectivity both within river
networks and between those networks and the surrounding landscape (Fullerton et al., 2010).
Hydrologic connectivity results from the flow of water, which provides a "hydraulic highway" (Fausch et
al., 2002) along which physical, chemical, and biological materials  associated with the water are
transported (e.g., sediment, woody debris, contaminants, organisms).

Ecosystem function within a river system is driven by interactions between the river system's physical
environment and the diverse biological communities living within it (Wiens, 2002; Schroder, 2006).
Thus, river system structure and function also depend on biological connectivity among the system's
populations of aquatic and semiaquatic organisms. Biological connectivity refers to the movement of
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organisms, including transport of reproductive materials (e.g., seeds, eggs, genes) and dormant stages,
through river systems. These movements link aquatic habitats and populations in different locations
through several processes important for the survival of individuals, populations, and species (Sections
3.5, 4.3.4, and 4.4.4). Movements include dispersal, or movement away from an existing population or
parent organism; migration, or long-distance movements occurring seasonally; localized movement
over an organism's home range to find food, mates, or refuge from predators or adverse conditions; and
movement to different habitats to complete life-cycle requirements. At the population and species levels,
dispersal and migration contribute to persistence at local and regional scales via colonization of new
habitats (e.g., Hecnar and McLoskey, 1996; Tronstad etal., 2007); location of mates and breeding
habitats (Semlitsch, 2008); rescue of small populations threatened with local extinction (Brown and
Kodric-Brown, 1977); and maintenance of genetic diversity (e.g., Waples, 2010). These movements can
result from passive transport by water, wind, or other organisms (e.g., birds, terrestrial mammals);
active movement with or against water flow (e.g., upstream fish migration); or active movement over
land (for organisms capable of terrestrial dispersal) or through the air (for birds or insects capable of
flight; Figure 1-1B). Thus, biological connectivity can occur within aquatic ecosystems or across
ecosystem or watershed boundaries, and it can be multidirectional. For example, organisms can move
downstream from perennial, intermittent, and ephemeral headwaters to rivers; upstream from
estuaries to rivers to headwaters; and laterally between floodplain wetlands, geographically isolated
wetlands, rivers, lakes, or other water bodies. Significant biological connectivity can also exist between
aquatic and terrestrial habitats (Nakano  et al., 1999; Gibbons, 2003; Baxter et al., 2004), but our focus is
on connections among components of aquatic systems (Section 1.3).

As noted in Section 2.2.3, streams and rivers are not pipes (Bencala, 1993; Bencala et al., 2011); they
provide opportunities for water to interact with internal components (e.g., alluvium, organisms)
through the five functions by which streams and wetlands alter material fluxes (Table 2-1). Connectivity
between streams and wetlands provides opportunities for material and energy fluxes to be altered
sequentially by multiple streams and wetlands as the materials are transported downstream. The
aggregate effect of these sequential fluxes determines the proportion of material that ultimately reaches
the river. The form of the exported material can change as it moves down the river network (Figure 2-
14), however, making quantitative assessments of the importance of individual stream and wetland
resources within the entire river system  difficult. For example, organic matter can be exported from
headwater streams and consumed by downstream macroinvertebrates (Figure 2-14). Those
invertebrates can drift farther downstream and be eaten by juvenile fish that eventually move into the
mainstem of the river, where they continue to feed and grow.

The assessment of stream and wetland influence on rivers also is complicated by the cumulative time lag
resulting from these sequential transformations and transportations. For example, removal of nutrients
by streambed algal and microbial populations, subsequent feeding by fish and insects, and release by
excretion or decomposition delays the export of nutrients downstream (Figure 2-14).
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 Figure 2-14. Illustration of the sequential transformation of materials as they move through the
 river network, via either downstream transport with water flow (solid black arrows) or via aerial or
 terrestrial movements (dashed black arrows). Here, an ephemeral headwater stream exports organic
 matter (at left) and an intermittent headwater stream exports ammonium, which is incorporated into
 algal biomass (at right). Macroinvertebrates consume these basal food resources and transform them
 reaches.
The opposite of connectivity is isolation, or the degree to which transport mechanisms (i.e., pathways
between system components) are lacking; isolation acts to reduce material fluxes between system
components. Although here we primarily focus on the benefits that connectivity can have on
downstream systems, isolation also can have important positive effects on the condition and function of
downstream waters. For example, waterborne contaminants that enter a wetland cannot be transported
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to a river if the wetland is hydrologically isolated from the river, except by nonhydrologic pathways.
Increased isolation can decrease the spread of pathogens (Hess, 1996) and invasive species (e.g.,
Bodamer and Bossenbroek, 2008), and increase the rate of local adaptation (e.g., Fraser et al., 2011).
Thus, both connectivity and isolation should be considered when examining material fluxes from
streams and wetlands, and biological interactions should be viewed in light of the natural balance
between these two factors.

When assessing the effects of connectivity or isolation and the five general functions (sources, sinks,
refuges, lags, and transformations; Table 2-1) on downstream waters, dimensions of time and space
must be considered. Water or organisms transported from distant headwater streams or wetlands
generally will take longer to travel to a larger river than materials transported from streams or wetlands
near the river (Section 2.4.2). This can introduce a lag between the time the function occurs and the time
the material arrives at the river. In addition, the distribution of streams and wetlands can be a function
of their distance from the mainstem channel. For example, in a classic dendritic network, there is an
inverse geometric relationship between number of streams and stream order. In such a case, the
aggregate level of function could be greater for terminal source streams, compared to higher order or
lateral source streams. This is one reason why watersheds of terminal source streams often provide the
greatest proportion of water for major rivers. Connectivity, however, results from many interacting
factors (Section 2.4.5). For example, the relationship between stream number and order can vary with
the shape of the watershed and the configuration of the network (Section 2.4.2). Thus, caution must be
exercised when generalizing about these spatial and temporal relationships. Spatial and temporal
variability of connectivity is discussed below, and the factors influencing them are considered in
Section 2.4.

2.3.2.2    Spatial and Temporal Variability of Connectivity
Connectivity is not a fixed characteristic of a system, but varies over space and time (Ward, 1989;
Leibowitz, 2003; Leibowitz and Vining, 2003). Variability in hydrologic connectivity results primarily
from the longitudinal (Figures 2-8 and 2-10) and lateral (Figure 2-12) expansion and contraction of the
river network and transient connection with other components of the river system (Section 2.2.3). The
variability of connectivity can be described in terms of frequency, duration, magnitude, timing, and rate
of change (Section 1.2.2).

The expansion and contraction of river networks affect the extent, magnitude, timing, and type of
hydrologic connectivity. For example, intermittent and ephemeral streams (Figure 2-7)  flow only during
wetter seasons (Section 2.4) or during and immediately following precipitation events. Thus, the spatial
extent of connectivity between streams and wetlands and rivers increases greatly during these high-
flow events because intermittent and ephemeral streams are estimated to account for 59% of the total
length of streams in the contiguous United States (Nadeau and Rains, 2007). Changes in the spatial
extent of connectivity due to expansion and contraction are even more pronounced in the arid and
semiarid Southwest, where more than 80% of all streams are intermittent or ephemeral (Figures 2-9B
Stream and Wetland Connectivity:                                                             January 2015
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and B-5; Levicketal., 2008). Expansion and contraction also affect the magnitude of connectivity
because larger flows provide greater potential for material transport (e.g., Section 3.3.2).

Besides affecting the spatial extent and magnitude of hydrologic connectivity, expansion and contraction
of the stream network also affect the duration and timing of flow in different portions of the network.
Perennial streams have year-round connectivity with a downstream river, whereas intermittent streams
have seasonal connectivity. The temporal characteristics of connectivity for ephemeral streams depend
on the duration and timing of storm events (Figure B-10). Similarly, connectivity between wetlands and
downstream waters can range from permanent to seasonal to episodic.

The expansion and contraction of river systems also affect the type of connectivity. For example, during
wet periods when input from precipitation can exceed evapotranspiration and available storage, non-
floodplain wetlands could have connectivity with other wetlands or streams through surface spillage
(Leibowitz and Vining, 2003; Rains et al., 2008). When spillage ceases due to drier conditions,
hydrologic connectivity could only occur through ground water (Rains et al., 2006; Rains et al., 2008).

When the flow of water mediates dispersal, migration, and other forms of biotic movement, biological
and hydrologic connectivity can be tightly coupled. For example, seasonal flooding of
riparian/floodplain wetlands creates temporary habitat that fish, aquatic insects, and other organisms
use (Junk et al., 1989; Smock, 1994; Tockner et al., 2000; Robinson et al., 2002; Tronstad et al., 2007).
Factors other than hydrologic dynamics also can affect the temporal and spatial dynamics of biological
connectivity. Such factors include movement associated with seasonal habitat use (Moll, 1990;
Lamoureux and Madison, 1999) and shifts in habitat use due to life-history changes (Huryn and Gibbs,
1999; Gibbons et al., 2006; Subalusky et al., 2009a), quality or quantity of food resources (Smock, 1994),
presence or absence of favorable dispersal conditions (Schalk and Luhring, 2010), physical differences
in aquatic habitat structure (Grant et al., 2007), or the number and sizes of nearby populations (Gamble
et al., 2007). For a specific river system with a given spatial configuration, variability in biological
connectivity also occurs due to variation in the dispersal distance of organisms and reproductive
propagules (Section 2.4.4; Semlitsch and Bodie, 2003).

Finally, just as  connectivity from temporary or seasonal wetting of channels can  affect downstream
waters, temporary or seasonal drying also can affect river networks. Riverbeds or streambeds that
temporarily dry up are used by aquatic organisms that are specially adapted to wet and dry conditions,
and can serve as egg and seed banks for several organisms, including aquatic invertebrates and plants
(Steward et al., 2012). These temporary dry areas also can affect nutrient dynamics due to reduced
microbial activity, increased oxygen availability, and inputs of terrestrial sources of organic matter and
nutrients (Steward etal., 2012).
2.4  Factors Influencing Connectivity
Numerous factors affect physical, chemical, and biological connectivity within river systems. These
factors operate at multiple spatial and temporal scales, and interact with each other in complex ways to

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determine where components of a system fall on the connectivity-isolation gradient at a given time. In
this section, we focus on four key factors—climate-watershed characteristics, spatial distribution
patterns, biota, human activities and alterations. These are by no means the only factors influencing
connectivity, but they illustrate how many different variables shape physical, chemical, and biological
connectivity. We also examine how interactions among different factors influence connectivity, using as
an example wetlands in the prairie pothole region.

2.4.1  Climate-Watershed Characteristics
The movement and storage of water in watersheds varies with climatic, geologic, physiographic, and
edaphic characteristics of river systems (Winter, 2001; Wigington etal., 2013). Atthe largest spatial
scale, climate determines the amount, timing, and duration of water available to watersheds and river
basins. Key characteristics of water  availability that influence connectivity include annual water surplus
(precipitation minus evapotranspiration), timing (seasonality) of water surplus during the year that is
heavily influenced by precipitation timing and form (e.g., rain, snow), and rainfall intensity.

Annual runoff generally reflects water surplus and varies widely across the United States (Figure 2-15).
Seasonality of water surplus during the year determines when and for how long runoff and ground-
water recharge occur. Precipitation  and water surplus in the eastern United States is less seasonal than
in the West (Finkelstein and Truppi, 1991). The Southwest experiences summer monsoonal rains
(Section B.5), whereas the West Coast and Pacific Northwest receive most precipitation during the
winter season  (Wigington et al., 2013). Throughout the West, winter precipitation in the mountains
occurs as snowfall, where it accumulates in seasonal snowpack and is released during the spring and
summer melt seasons to sustain streamflow during late spring and summer months (Brooks et al.,
2012). The flowing portions of river networks tend to have their maximum extent during seasons with
the highest water surplus (Section 2.2.3; Figure 2-10), when conditions for flooding are most likely.
Typically, the occurrence of ephemeral and intermittent streams is greatest in watersheds with low
annual runoff and high water surplus seasonality but also is influenced by watershed geologic and
edaphic features (Gleeson et al., 2011).

Rainfall intensity can affect hydrologic connectivity in localities where watershed surfaces have low
infiltration capacities relative to rainfall intensities. Infiltration-excess overland flow occurs when
rainfall intensity exceeds watershed surface infiltration, and it can be an important mechanism in
providing water to wetlands and river networks (Goodrich et al., 1997; Levick et al., 2008). Overland
flow is common at low elevations in the Southwest, due to the presence of desert soils with low
infiltration capacities combined with relatively high rainfall intensities (Section B.5). The Pacific
North west has low rainfall intensities, whereas many locations in the Mid-Atlantic, Southeast, and Great
Plains have higher rainfall intensities. The prevalence of impermeable surfaces in urban areas can
generate overland flow in virtually any setting (Booth et al., 2002).

River system topography and landscape form can profoundly influence river network drainage patterns,
distribution of wetlands, and ground-water and surface-water flowpaths. Winter (2001) described six
generalized hydrologic landscape forms (Figure 2-16) common throughout the United States. Mountain
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I 3
Figure 2-15. Map of annual runoff in contiguous United States showing locations of five example streams that illustrate daily runoff patterns
and total annual runoff depths. (A) Rapidan River, VA; (B) Noyo River, CA; (C) Crystal River, CO; (D) San Pedro River, AZ; and (E) Metolius River,
OR. All data are from http://waterdata.usgs.gov/usa/nwis/sw (downloaded June 27, 2011). Runoff can be conceived as the difference between
precipitation and evapotranspiration at the watershed scale. The varied runoff patterns in the five rivers result from divergent climate, geology,
and topography.
<£. O
(/) o
                         <25.4mm
                        i 25.4 254mm
                        1254-508mtn
                        I -508mm
                                                                              C. Crystal River, CO |2009 annual runoff = 679 mm)
                                                                         100.00
                                                                         : 10.00
                                                                         ;  1.00
                                                                           0.10
                                                                           0.01
                                                                              c*
                                                                             •<   <   <
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(JO
ro
          A. Rapidan River, VA |2005 annual runoff = 450 mm|
          100.00
          •  10.00
          '.  1.00
                 0.10
                 0.01
                       f  9"  Jf
                   *   *i   <
                                                                              D. San Pedro River, AZ [2005 annual runoff = 9 mm]
                                                                              100.00
                                                                               10.00
                                                                           0.10
                                                                           0.01
                                                                                                 	
                                                                              .«-   A   O
                                                                                 *°  oa
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           B. Noyo River, CA |2006 annual runoff = 1338 runoff]
           100.00
          I  10.00
          \  1.00
          !  0.10
          I
          :  0.01
                                                                              E. Metolius River, OR |2008 annual runoff = 1744 mm|
                                                                              100.00
                                                                               10.00
                                                                            t   1.00
                                                                            c   0.10
                                                                            3
                                                                            tt   0.01
                                                                                              /
                                                                                             S;   ^?   (
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                                                                                            <   <   •>.

-------
 Figure 2-16. Generalized hydrologic landscape forms. (A) Mountain Valley: narrow uplands and
 lowlands separated by large steep valley sides; (B) Playa: large broad lowland separated from narrow
 uplands by steeper valley sides (playas and basins of interior drainage); (C) Plateau and High Plains:
 small narrow lowlands separated from broad uplands by steeper valley sides; (D) Riverine Valley:
 small fundamental landscape units nested inside broader fundamental landscape unit; (E) Coastal
 Terrain: small fundamental landscape units nested inside broader fundamental landscape unit
 (coastal plain with terraces and scarps); and (F) Hummocky Terrain: small fundamental landscape
 units superimposed randomly on larger fundamental landscape unit. A fundamental hydrologic
 landscape unit is defined by land-surface form, geology, and climate. Modified from Winter (2001).
   A. Mountain Valley
         IUnsaturated
         zone
I Saturated       Surface
zone           water
                                                             Ground-water
                                                             flow
                                Water
                                table
                                               B. Playa
   C. Plateau and High Plains
   D. Riverine Valley
   E. Coastal Terrain
   F. Hummocky Terrain
Valleys (Figure 2-16A) and Plateaus and High Plains (Figure 2-16C) have constrained valleys through
which streams and rivers flow. The Mountain Valleys form has proportionally long, steep sides with
narrow to nonexistent floodplains resulting in the rapid movement of water downslope. In contrast,
Riverine Valleys (Figure 2-16D) have extensive floodplains that promote strong surface-water,
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hyporheic water, and alluvial ground-water connections between wetlands and rivers. Small changes in
water table elevations can influence the water levels and hydrologic connectivity of wetlands over
extensive areas in this landscape form (Figure 2-16D). Local ground-water flowpaths are especially
important in Hummocky Terrain (Figure 2-16F). Constrained valleys, such as the Mountain Valley
landform (Figure 2-16A), have limited opportunities for the development of floodplains and alluvial
aquifers, whereas unconstrained valleys, such as the Riverine Valley landform (Figure 2-16D), provide
opportunities for the establishment of floodplains. Some river basins can be contained within a single
hydrologic landscape form, but larger river basins commonly comprise complexes of hydrologic
landscape forms. For example, the James River in Virginia, which flows from mountains through the
Piedmont to the Coastal Plain, is an example of a Mountain Valley-High Plateaus and Plains-Coastal
Terrain-Riverine Valley complex.

Floodplain hydrologic connectivity to rivers and streams occurs primarily through overbank flooding,
shallow ground-water flow, and hyporheic flow (Section 2.2). Water-table depth can influence
connectivity across a range of hydrologic landscape forms, but especially in floodplains. Rivers and
wetlands can shift from losing reaches (or recharge wetlands) during dry conditions to gaining reaches
(or discharge wetlands) during wet conditions. Wet, high water-table conditions influence both ground-
water and surface-water connectivity. When water tables are near the watershed surface, they create
conditions in which swales and small stream channels fill with water and flow to nearby water bodies
(Wigington et al., 2003; Wigington et al., 2005). Nanson and Croke (1992) noted that a complex
interaction of fluvial processes forms floodplains, but their character and evolution are essentially a
product of stream power (the rate of energy dissipation against the bed and banks of a river or stream)
and sediment characteristics. They proposed three floodplain classes based on the stream power-
sediment characteristic paradigm: (1) high-energy noncohesive, (2) medium-energy noncohesive, and
(3) low-energy cohesive. The energy term describes stream power during floodplain formation, and the
cohesiveness term depicts the nature of material deposited in the floodplain. The cohesiveness term is
also related to  the hydraulic properties of alluvial aquifers. Alluvium for Class 1 and 2 floodplains tends
to have higher hydraulic conductivity, or a higher rate at which water moves through a saturated,
permeable soil or rock layer, than Class 3 floodplains. The higher the hydraulic conductivity of an
alluvial aquifer, the greater the exchange rate between the alluvial aquifer and river waters (Whiting
and Pomeranets, 1997). In addition, hyporheic and alluvial aquifer exchanges are more responsive to
seasonal discharge changes in floodplains with complex topography (Poole et al., 2006).

Within hydrologic landscape forms, soil and geologic formation permeabilities are important
determinants of hydrologic flowpaths (Figure 2-17). Permeable soils promote infiltration that results in
ground-water hydrologic flowpaths (Figures 2-17A and 2-17B), whereas the presence of impermeable
soils with low infiltration capacities is conducive to overland flow (Figures 2-17C and 2-17D). In
situations in which ground-water outflows from watersheds or landscapes dominate, the fate of water
depends in part on the permeability of deeper geologic strata. The presence of an aquiclude near the
watershed surface leads to shallow subsurface flows through soil or geologic materials (Figure 2-17A).
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 Figure 2-17. Major hydrologic flowpaths for hillslopes with combinations of permeable and
 impermeable soils and geologic formations. (A) Permeable soil and impermeable underlying
 geologic formation; (B) permeable soil and permeable underlying geologic formation; (C)
 impermeable soil and  impermeable underlying geologic formation; and (D) impermeable soil and
 permeable underlying  geologic formation. Width of arrow indicates relative magnitude of flow. Note
 that pavement can be  another source of impermeable surfaces and subsequent overland flow in
 anthropogenically influenced settings.
     Precipitation
  A.
     Pre
cipitati
              on
                                            Precipitation
Precipitation
1 Permeable soil
• Permeable geologic
formation

8sl3 Impermeable soil

ggSl Impermeable geologic
^^ formation

> Ground-water
recharge
Overland
. / fl«w

Local
. ground-water
W flow
These local ground-water flowpaths connect portions of watersheds to nearby wetlands or streams
(Figure 2-3). Alternatively, if a deep permeable geologic material (an aquifer) is present, water is likely
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to move farther downward within watersheds and recharge deeper aquifers (Figure 2-17B). The
permeability of soils and geologic formations both can influence the range of hydrologic connectivity
between non-floodplain wetlands and river networks. For example, a wetland that is the origin of a
stream can have a permanent or temporary surface-water connection with downstream waters through
a channelized outlet (Figure 2-18A); a wetland can be connected to downstream waters by transient
surface-water flows through swales (Figure 2-18B) or by shallow ground-water flows (Figure 2-18C); or
a wetland can be hydrologically isolated from downstream waters (Figure 2-18D) because it recharges a
deep ground-water aquifer that does not feed surface waters, or it is located in a basin where
evapotranspiration is the dominant form of water loss.

The importance of climate-watershed interactions in determining the amount and seasonality of water
surpluses, the timing and duration of streamflow, and thus the timing and extent of hydrologic
connectivity, is illustrated by annual hydrographs for five rivers in different regions of the United States
(Figure 2-15).

The hydrograph for the Rapidan River in Virginia (Figure 2-15A) illustrates the uniform annual
precipitation pattern of the East (with small variations due to increased evapotranspiration in the
summer months) interacting with a steep Blue Ridge Mountain watershed comprising metamorphic
bedrock with alluvial and colluvial fill in the lower riparian areas (Castro and Hornberger, 1991).
Hydrologic events driven by rainfall can occur anytime during the year, but are especially common in
winter and spring months; these events result in expansion of the river network as ephemeral streams
flow. Baseflow sustains perennial flow over a large part of the network.

Located in a region of steep slopes and impermeable bedrock (Mayer and Naman, 2011), the Noyo River
watershed in California (Figure 2-15B) has highly seasonal water surplus because rainfall occurs
primarily from November through May and the impermeable bedrock prevents precipitation water  from
moving to deep ground water. Consequently, runoff timing is similar to precipitation temporal patterns.
Total runoff for the basin is high, and baseflow levels are high during the winter and low during the  dry
summer season. These low baseflow periods create conditions favorable for intermittent flows in
streams with significant channel alluvium (Wigington et al., 2006).

The Crystal River of Colorado (Figure 2-15C) drains a glaciated landscape in the upper portion of the
Gunnison River in the Colorado Rocky Mountains. It has protracted high flow during the spring that is
controlled by the accumulation and melting of snow in the basin's higher elevations during the winter
and subsequent melting during spring and summer. This streamflow pattern also promotes the
occurrence of intermittently flowing streams due to large water surplus differences between the high-
flow and low-flow periods.

Total runoff in the San Pedro River, Arizona is low (Figure 2-15D), and short, intense rainstorms during
the summer monsoons commonly drive hydrologic events (Levick et al., 2008). Because a major
proportion of water reaching the San Pedro River originates as overland flow to ephemeral streams that
ultimately flow to the mainstem river, baseflow is limited (Section B-5). In other San Pedro River
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 Figure 2-18. Types of hydrologic connections between non-floodplain wetlands and streams or
 rivers. (A) A wetland connected to a river by surface flow through a headwater stream channel. (B) A
 wetland connected to a river by surface flow through a nonchannelized swale. Such a wetland would
 be considered geographically isolated if the swale did not meet the Cowardin et al. (1979)
 three-attribute wetland criteria. (C) A geographically isolated wetland connected to a river by ground-
 water flow (flowpath can be local, intermediate, or regional). (D) A geographically isolated wetland
 that is hydrologically isolated from a river. Note that in A-C, flows connecting the wetland and river
 may be perennial, intermittent, or ephemeral.
       A.
    B.



                                                D.


                          Wetland with
                          surface outlet
                          Geographically
                          isolated wetland
      	Headwater stream
      ^^™ Stream/river
      - - • • Ground-water flow
      LX~'J Swale
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mainstem reaches, ground-water flow from regional and alluvial aquifers supports baseflow (Dickinson
et al., 2010). Like the Crystal River, the Metolius River in Oregon (Figure 2-15E) also has snowpack in its
higher elevations, but geologic conditions in the watershed alter the climate signal. Meltwaters in the
Metolius River flow through long flowpaths in porous bedrock to springs in or near the river (James et
al., 2000; Gannett et al., 2001). Although intermittent and ephemeral streams occur in the Metolius
basin, most streams are spring-fed and perennial.

2.4.2   Spatial Distribution Patterns
Climate and watershed characteristics directly affect spatial and temporal patterns of connectivity
between streams and wetlands and rivers by influencing the timing and extent of river network
expansion and contraction. They also influence the spatial distribution of water bodies within a
watershed (e.g., Tihansky, 1999), and in particular, the spatial relationship between those water bodies
and the river.

Hydrologic  connectivity between streams and rivers can be a function of the distance between the two
water bodies (Bracken and Croke, 2007; Peterson etal., 2007). If channels functioned as pipes, this
would not be the case, and any water and its constituent materials exported from a stream eventually
would reach the river. Because streams and rivers are not pipes (Section 2.2.3; Bencala, 1993), water
can be lost from the channel through evapotranspiration and bank storage and diluted through
downstream inputs. Thus, material from a headwater stream that flowed directly into the river would be
subject to less transformation or dilution. On the other hand, the greater the distance a material travels
between a particular stream reach and the river, the greater the opportunity for that material to be
altered (e.g., taken up, transformed, or assimilated) in intervening stream reaches; this alteration could
reduce the material's direct effect on the river, but it could also allow for beneficial transformations. For
example, organic matter exported from a headwater stream located high in a drainage network might
never reach the river in its original form, instead becoming reworked and incorporated into the food
web (Figure 2-14). Similarly, higher order streams generally are located closer to rivers and, therefore,
can have higher connectivity than upstream reaches of lower order. Note that although an individual
low-order stream can have less connectivity than a high-order stream, a river network has many more
low-order streams, which can represent a large portion of the watershed (Section 3.2); thus, the
magnitude of the cumulative effect of these low-order streams can be significant.

The relationship between streams and the river network is a function of basin shape and network
configuration. Elongated basins tend to  have trellis networks where relatively small streams join a
larger mainstem (Figure 2-19A); compact basins tend to have dendritic networks with tree-like
branching, where streams gradually increase in size before joining the mainstem (Figure 2-19B). This
network configuration describes the incremental accumulation of drainage area along rivers, and
therefore provides information about the relative contributions of streams to downstream waters.
Streams in a trellis network are more likely to connect directly to a mainstem, compared with a
dendritic network. The relationship between basin shape, network configuration, and connectivity,
however, is complex. A mainstem in a trellis network also is more likely to have a lower stream order

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 Figure 2-19. Major types of basin shapes and network configurations. (A) A rectangular basin with
 trellis network, and (B) a compact basin with a dendritic network.
             A.
than one in a dendritic network. For example, the lowest reach in the trellis network in Figure 2-19A is a
third-order stream, while that of the dendritic network (Figure 2-19B) is a fourth-order stream.

Distance also affects connectivity between non-floodplain and riparian/floodplain wetlands and
downstream waters. Riverine wetlands that serve as origins for lateral source streams that connect
directly to a mainstem river have a more direct connection to that river than wetlands that serve as
origins for terminal source streams high in a drainage network. This also applies to riparian/floodplain
wetlands that have direct surface-water connections to streams or rivers. If geographically isolated non-
floodplain wetlands have surface-water outputs (e.g., depressions that experience surface-water spillage
or ground-water seeps; Figure 2-18B), the probability that surface water will infiltrate or be lost
through evapotranspiration increases with distance. For non-floodplain wetlands connected through
ground-water flows, less distant areas are generally connected through shallower flowpaths
(Figure 2-5), assuming similar soil and geologic properties. These shallower ground-water flows have
the greatest interchange with surface waters (Section 2.2.2) and travel between points in the  shortest
amount of time. Although elevation is the primary factor determining areas that are inundated through
overbank flooding, connectivity with the river generally will be higher for riparian/floodplain wetlands
located near the river's edge compared with riparian/floodplain wetlands occurring near the floodplain
edge.

Distance from the river network also influences biological connectivity among streams and wetlands.
For example, mortality of an organism due to predators and natural hazards generally increases with
the distance it has to travel to reach the river network. The likelihood that organisms or propagules
traveling randomly or by diffusive mechanisms such as wind will arrive  at the river network generally
decreases as distance increases.
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The distribution of distances between wetlands and river networks depends on both the drainage
density of the river network (the total length of stream channels per unit area) and the density of
wetlands. Climate and watershed characteristics influence these spatial patterns, which can vary widely.
For example, a subset of fens in New York State was located closer to each other, on average, than a
subset of Carolina bays at the Savannah River Site: The proportion of wetlands located at distances of 0-
100,100-500, and >500 m was 27, 39, and 35%, respectively, for the fens and 12, 44, and 44% for the
Carolina bays, respectively (Bedford and Godwin, 2003; Sharitz, 2003). When interpreting such
distributions, however, other factors that affect connectivity (e.g.,  differences in soils or slope) should be
considered.

Figure 2-20 compares the spatial  distribution of wetlands and streams to the river network in six
different landscape settings. The figure shows landscape settings ranging from no nearby streams and
dense small wetlands (Figure 2-20A), to a few nearby streams with high wetland density (Figures 2-20B
and 2-20C), to less spatially uniform wetlands (Figure 2-20D), to areas with higher drainage densities
and riparian (Figure 2-20E) or larger, more extensive (Figure 2-20F) wetlands. The maps in Figure 2-20
are single examples of these various settings, so they might not be representative. They are useful,
however, for illustrating the degree to which landscape setting can affect the interspersion—and thus
average distance—between wetlands and the river network, and the large variability that can result. In
settings having many wetlands and relatively low drainage density (Figures 2-20B, 2-20C, and 2-20D),
the distances between individual  wetlands and the stream can vary greatly. In contrast, the distances in
areas having a higher drainage density (Figure 2-20E and 2-20F) are shorter and vary less. All factors
being equal, wetlands closer to the stream network will have greater hydrologic and biological
connectivity than wetlands located farther from the same network.

2.4.3  Biota
Biological connectivity results from the interaction of physical characteristics of the
environment—especially those facilitating or restricting dispersal—and species' traits or behaviors, such
as life-cycle requirements, dispersal ability, or responses to environmental cues (Section 1.2.2). Thus,
the types of biota within a river system are integral in determining the river system's connectivity, and
landscape features or species traits that necessitate or facilitate movement of organisms tend to
increase biological connectivity among water bodies.

Diadromous fauna (e.g., Pacific and Atlantic salmon, certain freshwater shrimps and snails, American
eels), which  require both freshwater and marine habitats over their life cycles and therefore migrate
along river networks, provide one of the clearest illustrations of biological connectivity. Many of these
taxa are either obligate or facultative users of headwater streams  (Erman and Hawthorne, 1976;
Wigington et al., 2006), meaning that they either require (obligate) or  can take advantage of (facultative)
these habitats; these taxa thereby create a biological connection along the entire length of the river
network. For example, many Pacific salmon species spawn in headwater streams, where their young
grow for a year or more before migrating downstream, living their adult life stages in the ocean, and
then migrating back upstream to spawn. Many taxa also can exploit temporary hydrologic connections

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 Figure 2-20. Examples of different landscapes showing interspersion of wetlands and streams or
 rivers. (A) Prairie potholes within the Missouri Coteau in North Dakota; (B) prairie potholes within the
 Drift Prairie in North Dakota; (C) playas in Texas; (D) vernal pools in California; (E) bottomland
 hardwood wetlands in Illinois; and (F) Carolina bays in North Carolina. Note all maps are at the same
 scale. Wetlands smaller than the minimum mapping unit (currently 0.4 ha) might not appear on
 maps. Source: National Wetlands Inventory Wetlands Mapper
 (http://www.fws.gov/wetlands/Data/Mapper.html).
           A. Prairie potholes (Missouri Coteau)
                                    ••->»!
                                  '    *
                                                                '
           U. Prairie potholes (Drift Prairie)
                                I
                                ^Wfe-JT^^X'l
                  •^'^j&is^V
                  , v. ' * *W ._•_»•'•   •»,

            "*^V-'.>?:1^?^«
           |>... ;^^^
           5' ,».,-•: V
-------
 Figure 2-20. Examples of different landscapes showing interspersion of wetlands and streams or
 rivers (continued).
        C. Playa
        D. Vernal pools
               Wetlands
                                                               Riparian
d] Freshwater Emergent          CZ1 Estuarine and Marine  CZI Riverine       Herbaceous
^•Freshwater Forested/Shrub      d] Freshwater Pond      CD Other      CZI Forested/Shrub
• Estuarine and Marine Deepwater  • Lake
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 Figure 2-20. Examples of different landscapes showing interspersion of wetlands and streams or
 rivers (continued).
            E. Bottomland hardwood wetlands
                                                ••'..«
                                                w
                                     ,
                -.-W'   :,v';> •••:*&<'     :
                •           •j                   •
                                                •
                     • .""••a.irv   • .>  •
              :&.  •     •:»•  .-••••     *-I
                                                              V-, ' '  - AV •  • /•
                                                                             '
             F. Carolina bay$
                  Wetlands                                           Riparian
                  EH Freshwater Emergent        CU Estuarine and Marine  •Riverine   I   Herbaceous
                  ^•Freshwater Forested/Shrub    I	] Freshwater Pond    L	J Other    I	) Forested/Shrub
                  ^B Estuarine and Marine Deepwater ^B Lake
between rivers and floodplain wetland habitats caused by flood pulses (Section 1.2.1; Junk et al., 1989;

Tockner et al., 2000), moving into these wetlands to feed, reproduce, or avoid harsh environmental

conditions and then returning to the river network (Copp, 1989; Smock, 1994; Richardson et al., 2005).
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Biological connectivity does not solely depend on diadromy, however, as many nondiadromous
organisms are capable of significant movement within river networks (Section 1.2.2). For example,
organisms such as pelagic-spawning fish and mussels release eggs or larvae that disperse downstream
with water flow (e.g., Platania and Altenbach, 1998; Schwalb et al., 2010); many fish swim significant
distances both upstream and downstream (e.g., Gorman, 1986; Hitt and Angermeier, 2008); and many
aquatic macroinvertebrates move or drift downstream (e.g., Elliott, 1971; Miiller, 1982; Brittain and
Eikeland, 1988; Elliott, 2003). Taxa capable of movement over land, via either passive transport (e.g.,
wind dispersal or attachment to animals capable of terrestrial dispersal) or active movement (e.g.,
terrestrial dispersal or aerial dispersal of winged adult stages), can establish biotic linkages between
river networks and wetlands, as well as linkages  across neighboring river systems (Hughes et al., 2009).

The fundamental influence that biological connectivity has on species distributions can last long after a
system is disconnected. In a global analysis of freshwater fish diversity, Bias et al. (2014) found that
paleoconnected drainage basins (basins that had hydrologic connections during the most recent glacial
maximum) currently have greater species richness and lower endemism and beta diversity than
paleodisconnected basins. This study indicates that hydrologic connectivity, by allowing dispersal of
aquatic organisms, can have a long-lasting legacy effect on the geographic distribution of species.

The examples discussed above illustrate how environmental characteristics provide the  physical
structure through which biological connectivity occurs, as mediated by biological traits and behavior.
The physical structure of the environment is not  static, however, and also can be altered by biological
behavior. The beaver (Castor canadensis) is a keystone species that builds dams that can alter
connectivity in several ways. Most obviously, beaver dams reduce hydrologic connectivity by
impounding streams and modifying conditions above the dam from lotic to lentic. The area impounded
by beaver dams can be large: In the Kabetogama  Peninsula of Minnesota, impounded area accounted for
up to 13% of the landscape, with an average pond area of about 4 ha (Johnston and Naiman, 1990a, b).
In a review of the effects of beaver on stream ecosystems, Collen and Gibson (2001) noted that, although
the hydrologic effects of a single beaver dam can  be small, the impact of a series of dams on streams can
be significant; for example, up to 30% of the water in an Oregon catchment was impounded by beaver
dams. Such dams can directly affect material transport (e.g., the ability of the stream to carry sediment is
reduced) and alter biogeochemical characteristics (Naiman et al., 1994; Collen and Gibson, 2001).
Beaver dams also can affect biological connectivity, for example, by obstructing upstream migration, and
cause changes in fish distributions (Collen and Gibson, 2001).

2.4.4   Human Activities and Alterations
Human activities frequently alter connectivity between headwater streams, riparian/floodplain
wetlands, non-floodplain wetlands, and downgradient river networks (Sections 1.2.4, 3.2, 4.3, and 4.4).
In doing so, they alter the transfer and movement of materials and energy between river system
components. In fact, the individual or cumulative effects of headwater streams and wetlands on river
networks often become discernible only following human-mediated changes in degree of connectivity.
These human-mediated changes  can increase or decrease hydrologic and biological connectivity (or,

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alternatively, decrease or increase hydrologic and biological isolation). For example, activities and
alterations such as dams, levees, water abstraction, piping, channelization, and burial can reduce
hydrologic connectivity between streams and wetlands and rivers, whereas activities and alterations
such as wetland drainage, irrigation, impervious surfaces, interbasin transfers, and channelization can
increase hydrologic connections. Biological connectivity can be affected similarly: For example, dams
and impoundments might impede biotic movement, whereas nonnative species introductions artificially
increase biotic movement. Further complicating the issue is that a given activity or alteration might
simultaneously increase and decrease connectivity, depending on which part of the river network is
considered. For example, channelization and levee construction reduce lateral expansion of the river
network (thereby reducing hydrologic connections with floodplains), but might increase this
connectivity downstream due to increased frequency and magnitude of high flows.

To illustrate, we describe two notable alterations that affect river system connectivity: dams (and their
associated impoundments) and wetland drainage. The United States has more than 80,000 dams, over
6,000 of which exceed 15 m in height (USAGE, 2009). Numerous studies have shown that dams impede
biotic movements, reduce biological connectivity between upstream and downstream locations (e.g.,
Greathouse et al., 2006; Hall et al., 2011), and form a discontinuity in the normal stream-order-related
progression in stream ecosystem structure and function (Stanford and Ward, 1984). Dams, however, can
have the opposite effect with respect to natural lakes: increasing their biological connectivity with
respect to invasive species by adding impoundments that decrease average distances between lakes and
serving as stepping stone habitat (Johnson et al., 2008). Upstream of large dams, riparian areas are
permanently inundated, increasing lateral hydrologic connectivity. Downstream, dams decrease peak
stream volumes during the normal high-runoff seasons, while increasing minimum flows during normal
low-flow seasons—an overall dampening of stream-flow variability (Poff etal., 2007). Because many
riverine organisms are adapted (via life history, behavioral, and morphological characteristics) to the
seasonality of natural flow regimes, dampening flow variability can have deleterious effects on species
persistence where dams have been built (Lytle and Poff, 2004). This reduction in high flows also
decreases the connectivity of riparian wetlands with the stream by reducing the potential for overbank
lateral flow. Reducing overbank lateral flow can affect downstream water quality, because overbank
flow deposits sediment and nutrients that otherwise remain entrained in the river (Hupp et al., 2009).

The greatest human impact on riparian/floodplain wetlands and non-floodplain wetlands has been
through wetland drainage (Figure 2-21), primarily for agricultural purposes. Estimates show that, in the
conterminous United States, states have lost more than half their original wetlands, with some losing
more than 90%; wetland surface areas also have declined significantly (Dahl, 1990).

Drainage causes a direct loss of function and connectivity in cases where wetland characteristics are
completely lost. In the Des Moines lobe of the prairie pothole region, where more than 90% of the
wetlands have been drained, a disproportionate loss of smaller and larger wetlands has
occurred. Accompanying this loss have been significant decreases in perimeter-area ratios—which are
associated with greater biogeochemical processing and ground-water recharge rates—and increased
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 Figure 2-21. Comparison of percent wetland loss between (A) the 1780s and mid-1980s with (B)
 the distribution of artificially drained agricultural land in 1985. One dot equals 8100 ha. From Blann
 et al. (2009), as modified from Dahl (1990).
       A. Percent of Wetlands Lost, 1780s-1980s
            CH Less than 50
            CH 50-95 (16 States)
            CD More than 95 (6 States)
                             The
                             Everglades
       B. Artificially Drained Agricultural Land, 1985 (1 dot = 8100 ha)
mean distances between wetlands, which reduces biological connectivity (Van Meter and Basu, In
press). Wetland drainage also increases hydrologic connectivity between the landscape—including
drained areas that retain wetland characteristics—and downstream waters. Effects of this enhanced
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hydrologic connectivity include (1) reduced water storage and more rapid conveyance of water to the
network, with subsequent increases in total runoff, baseflows, stormflows, and flooding risk (Wiskow
and van der Ploeg, 2003; Blann etal., 2009); (2) increased delivery of sediment and pollutants to
downstream waters; and (3) increased transport of water-dispersing organisms (Babbitt and Tanner,
2000; Baber et al., 2002; Mulhouse and Galatowitsch, 2003). Biological connectivity, however, also can
decrease with drainage and ditching, as average distances between wetlands increase and limit the
ability of organisms to disperse between systems aerially or terrestrially (Leibowitz, 2003). Ground-
water withdrawal can have an effect similar to drainage on some wetlands, which can affect wetland
connectivity by reducing the number of wetlands. Of particular concern in the arid Southwest is that
ground-water withdrawal can decrease regional and local water tables, reducing or altogether
eliminating ground-water-dependent wetlands (Patten etal., 2008). Ground-water withdrawal,
however, also can increase connectivity in areas where that ground water is applied or consumed.

Particularly noteworthy is that restoration of hydrologic connectivity, especially in systems with
widespread human alterations, also might adversely affect downstream waters (Jackson and Pringle,
2010). For example, dam removal can result in the downstream transport of previously sequestered
pollutants (Jackson and Pringle, 2010); dam releases to restore flows, without simultaneous restoration
of sediment supplies, can result in downstream channel degradation (Germanoski and Ritter, 1988;
Schmidt and Wilcock, 2008). Hammersmark et al. (2008) used a modeling study to show how the
restoration of incised stream channels can improve connectivity between streams and floodplains and
thus restore predisturbance hydrology (i.e., increased floodplain water storage, reduced peak
stoonflow, and reduced baseflow).

2.4.5   Interactions Among Factors
Interactions among the factors discussed above can be complex. Here we provide an example of
temporary surface-water connections between wetlands in the prairie pothole region (PPR) to illustrate
these complex interactions (Leibowitz and Vining, 2003). Further details on wetlands in the PPR are
provided in Sections 5.4 and B.3.

During high-water conditions in 1995, a temporary surface-water connection was observed between
two geographically isolated prairie potholes in the region's Drift Prairie. Based on a spatial analysis
during similarly wet conditions in 1996, 28% of the wetlands in a 40 km2  area containing the sites had a
temporary surface-water connection to at least one other wetland, including a complex (defined in the
study as a group of wetlands interconnected through temporary surface-water connections) of 14
wetlands.

In considering these  findings, Leibowitz and Vining (2003) suggested that precipitation and local relief
are the primary factors controlling the spatial distribution of these temporary surface connections.
Precipitation is the ultimate source of water that fills these wetlands, whereas relief controls how much
the water level in a wetland must rise before spillage occurs (water level is also influenced by
evapotranspiration and ground water, but ground-water dynamics are difficult to predict for individual
wetlands). Relief also controls mixing—which could occur in flatter areas when the boundaries of
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expanding wetlands overlap—by determining the change in surface area per change in water level. Thus,
for a given level of precipitation, the number of surface connections occurring between wetlands should
be inversely proportional to local relief. Within the PPR, precipitation generally decreases from east to
west, while relief generally increases. The easternmost physiographic region in the PPR is the Red River
Valley, a relatively flat ancient lakebed (Lake Agassiz) having deep deposits of silt and clay. Water can
pond easily on these deposits, producing shallow wetlands and integrated drainage (i.e., the presence of
stream networks). The Missouri Coteau, which forms the western boundary of the PPR,  consists of dead-
ice glacial moraine. This area has hummocky terrain, and local relief can be as great as 15-45 m in
steeper areas (Winter et al., 1998). As a result, the Coteau has deeper wetlands and little to no integrated
drainage. The Drift Prairie, located between the Red River Valley and the Missouri Coteau, is an
undulating plain formed on ground moraine. Relief, wetland depth, and the level of integrated drainage
in the Drift Prairie are intermediate in comparison with the other two regions.

Leibowitz and Vining (2003) hypothesized that the combined effect of these patterns in precipitation
and relief should produce a strong east-west gradient across the PPR in the occurrence of intermittent
surface-water connections. Both the absolute number of connections and complex size (the number of
wetlands contained in a complex) should be highest in the Red River Valley. Given the relative flatness of
this area, mixing should be the more common mechanism for temporary connections. The number of
temporary connections and complex size should be lower in the Drift Prairie, and spillage might
dominate in this hillier terrain. In the Missouri Coteau, where relief is greatest, the occurrence of these
temporary connections should be rare and limited to small complex sizes. Human impacts, however,
could affect these trends (Section 2.4.4).

Beyond these regional trends in relief and precipitation, local variation in the occurrence of intermittent
surface-water connections should be influenced strongly by ground-water dynamics. The ground-water
hydrology of prairie potholes has been well investigated at several sites  (e.g., Winter et al., 1998; Winter
and Rosenberry, 1998). The specific ground-water interactions—and hence the effects of ground-water
movement on spillage or mixing, however, are unknown for most prairie potholes. All else being equal,
ground-water discharge wetlands should receive more water, and so should have a higher probability of
spillage, than ground-water recharge wetlands because recharge should reduce the amount of water
available for spillage.

A major factor influencing the temporal distribution of intermittent connections within  the PPR is wet-
dry cycles. Climatic changes that have occurred throughout the Holocene drive these cycles. Evidence,
for example, exists for 20-, 22-, 50-, 100-, and 200-year climatic cycles (Ashworth, 1999). Wetland
hydrology responds dramatically to these wet-dry cycles as ground-water levels and precipitation
patterns fluctuate. In 1996, the average monthly Palmer Hydrological Drought Index for central North
Dakota was 4.02 (88th percentile), compared with a median of 1.00 for annually calculated monthly
averages between 1895 and 2001. Moisture levels of this magnitude—and consequently the degree of
connectivity observed (Leibowitz and Vining, 2003)—would be expected to occur during wetter portions
of wet-dry cycles.
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2.4.6   Quantifying Connectivity
As previously discussed, watershed connectivity is a dynamic and scalable quantity that occurs along a
gradient from highly connected to highly isolated (Ward, 1989; Euliss etal., 2004). Connectivity can be
quantified using structural metrics of physical landscape features (e.g., watershed topography, the
spatial arrangement of habitat patches), or functional metrics of system dynamics, which integrate
information about processes and interactions that influence hydrologic flows or biological dispersal.
Selection of specific metrics for quantifying connectivity depends on the purpose of the assessment, the
environmental context (e.g., humid versus arid), type of connection (e.g., hydrologic, chemical,
biological), spatial and temporal scale of interest, and available data (Calabrese and Pagan, 2004;
Lexartza-Artza and Wainwright, 2009).

2.4.6.1    Hydrologic and Chemical Connectivity
In hydrology, connectivity research has aimed to understand how and when water volume inputs (e.g.,
precipitation minus water loss through infiltration, evaporation and transpiration) and moisture
thresholds trigger surface and subsurface flow, thereby influencing streamflows in a given watershed
(Western etal., 2001; Ali and Roy, 2010; Bracken etal., 2013). Because movement of water is the
primary mechanism by which chemical substances are transported downstream, quantifying chemical
connectivity is closely related to quantifying hydrologic connectivity (Michalzik et al., 2001; Borselli et
al., 2008). Hydrologic connectivity research has focused on relating patterns of soil moisture following
precipitation events to stream discharge (Western etal., 2001; James and Roulet, 2007; Ali and Roy,
2010) or measuring flow-process connectivity at the hillslope scale (Knudby and Carrera, 2005; Reaney,
2008; Smith et al., 2010). Although this research provides a critical understanding of how water moves
through a watershed, it is only indirectly related to connectivity between small streams and rivers, or
between wetlands and streams. Metrics for quantifying hydrologic connections between upstream and
downstream waters have started to be explored through research characterizing the hydrologic
permanence of streams (Fritz etal., 2008; Fritz etal., 2009) or mapping temporal variation in surface
connections between wetlands and streams using field (McDonough et al., 2015) or remotely sensed
data (Sass and Creed, 2008; Lang et al., 2012; Huang et al., 2014). More commonly, research efforts have
focused on data collection methods that could inform measurement of connectivity (e.g., deriving
relationships between connectivity and topography or water quality; hydrologic tracers; geostatistical
modeling; and watershed, ground-water, or coupled surface water-ground water modeling).

Structural indices derived from topography can be used to predict patterns of watershed wetness.
Examples include the Topographic Wetness Index (Quinn et al., 1995), which is quantified using the
upslope contributing area and local slope, as well as quasi-dynamic indices that calculate the effective
contributing area (variable source area) in a watershed (e.g., Barling et al., 1994; Tarboton, 1997;
Creed and Beall, 2009). These indices could be used to predict the location of hydrologic flowpaths and
areas of a watershed that might be efficient exporters of nutrients, sediment, or pollutants following
heavy rainfall or snowmelt periods (Creed and Beall, 2009; Lane etal., 2009). In flatter landscapes, a
more dynamic contributing area model is typically required (Shaw et al., 2013). One example is the  fill-

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and-spill model in which the watershed contributing area expands when wetland storage reaches
capacity (fill) and wetlands overflow (spill) onto the land surface and into other surface-water bodies
(Tromp-van Meerveld and McDonnell, 2006; Shaw etal., 2013; McCauley and Anteau, 2014). Other
researchers have quantified basin-scale hydrologic connectivity as the ratio of flowing stream reaches
connected to the outlet to the total potentially flowing stream reaches (Phillips etal., 2011; Spence and
Phillips, 2015), or as transport potential in a given direction quantified by a directional connectivity
index (Larsen et al., 2012). Similar to this, the volume-to-breakthrough concept quantifies connectivity
as actual runoff relative to water inputs, where connectivity decreases with increased infiltration,
depression storage, slope length, barriers, or other factors (Bracken and Croke, 2007).

Several other lines of research are contributing to a general understanding of connectivity between
water features. Water quality indicators have been used to identify connectivity between wetlands and
streams (Johnston et al., 1990; Leibowitz and Vining, 2003). Tracer experiments using 15N, bromide, salt
solutions, fluorescing particles, or other conservative compounds have been conducted that can inform
flowpaths in aquatic systems (Mulholland et al., 2004; Bencala et al., 2011; O'Brien et al., 2012).
Modeling and measuring the mass transfer efficiency of a watershed using a parameter such as the
sediment delivery ratio, which describes and predicts the relationship between erosion and sediment
yield in a watershed, can indicate the degree of connectivity within a watershed (Atkinson, 1995; Hooke,
2003; Bracken and Croke, 2007). Geostatistical approaches are being developed to consider how
connectivity would be quantified within a branched stream network (Pagan, 2002; Ganio et al., 2005;
Peterson et al., 2007). In addition, numerous mechanistic modeling and simulation tools can be modified
and applied to investigate connectivity dynamics from geographically isolated wetland systems (Golden
et al., 2014) and headwaters (e.g., TOPMODEL; Beven and Kirkby, 1979) to downstream  surface-water
systems.

Although the research community has not reached a consensus regarding the best methods or metrics to
quantify or predict hydrologic or chemical connectivity (Lexartza-Artza and Wainwright, 2009; Ali and
Roy, 2010; Bracken et al., 2013), future efforts to quantify connectivity using the descriptors discussed
in Chapter 1 (frequency, magnitude, duration, timing, and rate of change) or other connectivity metrics
will help to further refine and quantify the lines of research summarized above.

2.4.6.2    Biological Connectivity
In the quantification of biological connectivity, species traits (e.g., dispersal mode, habitat requirements,
behavior) also must be considered (Calabrese and Pagan, 2004). Structural connectivity  can be
quantified from the physical landscape (e.g., the size, shape, and arrangement of habitat patches)
assuming that the spatial configuration of habitats reflects species' ability to move between them.
Functional connectivity directly incorporates information about species' movement obtained from field
studies or from models to inform  estimates of connectivity (Calabrese and Pagan, 2004; Wainwright et
al.,2011).

Indices based on graph theory calculate connectivity using a graph to represent the landscape as a
network of nodes (e.g., habitat patches) connected by edges (pathways of movement; Urban and Keitt,
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2001). Such connectivity indices include the Minimum Spanning Tree (Urban and Keitt, 2001),
Correlation Length (Keitt et al., 1997; Rae et al., 2007), the Integral Index of Connectivity (Pascual-Hortal
and Saura, 2006), and the Probability of Connectivity (Saura and Pascual-Hortal, 2007). Graph-theory
approaches can be used to assess structural or functional connectivity at multiple spatial scales (Eros et
al., 2012). Specific information about habitats and focal species is incorporated by applying node
weights (e.g., habitat area or quality, population abundance), edge weights (e.g., Euclidean distance,
landscape resistance), or edge characteristics (e.g., direction of movement; Galpern et al., 2011). Indices
derived from such graphs seek to characterize connectivity in terms of habitat (e.g., total connected
habitat area), dispersal pathways (e.g., relative abundance of individuals using a pathway, path
redundancy or vulnerability), or both (Rayfield et al., 2010). The Integral Index of Connectivity, for
instance, incorporates patch area, the topological distance between patches and the proportion of
connected patches (Pascual-Hortal and Saura, 2006), and has been successfully used to quantify
connectivity within a river network at varying spatial scales for otters (Van Looy et al., 2013).

The dendritic nature of stream networks also can be explicitly integrated when considering the
biological connectivity for obligate aquatic species, such as fish. The branching structure of a dendritic
network (Figure 2-19B), which has a single pathway (the stream channel) between habitat patches (e.g.,
stream reaches), influences individual movement and population distribution and abundance, and thus
the impact of disturbances and fragmentation on connectivity (Pagan, 2002; Grantetal., 2007); this can
be reflected in graph-theoretic connectivity indices (Malvadkar et al.,  2015). An example of a dendritic
metric is the Dendritic Connectivity Index, which uses the number of barriers (e.g., culverts) and the
passability of these barriers to quantify the probability that fish can move between two points in a river
network (Cote etal., 2009).

2.4.6.3    Summary
This section briefly reviews the growing body of research into testable indices and metrics that
represent hydrologic and biological connectivity of functional importance to downstream waters. Data
availability is a critical issue, as the information content that connectivity indices provide often is related
directly to their data requirements (Calabrese and Pagan, 2004; Bergsten and Zetterberg, 2013).
Additionally, the many proposed connectivity indices and approaches discussed in the literature suggest
that different metrics are needed to quantify different types of connectivity across diverse
environments, scales, and ecosystem functionalities (Rayfield et al., 2010; Galpern et al., 2011; Bracken
et al., 2013). With further development and refinement, the  utilization of connectivity indices can
provide graphical, quantitative assessments of connectivity.
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3.1  Abstract
The physical structure of a river network inherently demonstrates cumulative connectivity
(Section 1.2.3) between all streams and their downstream rivers. Substantial evidence supports
physical, chemical, and biological connections from headwater streams—including those with
ephemeral, intermittent, and perennial flows—to waters immediately downstream through transport of
water and associated materials, movement of organisms and their products, and bidirectional
geomorphic adjustments. Among the most compelling evidence for the effects of headwater streams on
rivers is as sources of water, nitrogen, organic carbon, and sediment (clean and contaminated); as
transformers of and sinks for nitrogen, carbon, and contaminants; and as providers of essential habitat
for migratory animals such as anadromous salmon. Headwater streams as a class provide substantial
quantities of water to larger water bodies. For example, first-order streams cumulatively contribute
approximately 60% of the total mean annual flow to all northeastern U.S. streams and rivers. Infrequent,
high-magnitude events are especially important for transmitting materials from headwater streams in
most river networks. The strongest lines of evidence supporting the effects of headwater streams are
from watersheds where headwater streams drain a unique portion of the basin (e.g., hydrology, geology,
human alteration). Investigation of connections among river network components continues to be an
active area of scientific research, with progress occurring in the development of river  network models
and connectivity metrics for quantifying connections and their downstream effects. Physical, chemical,
and biological connections between headwater streams and downstream waters are fundamental to the
structure and function of river networks, and additional empirical data and further breakthroughs that
quantify linkages across large spatiotemporal scales will continue to enhance our understanding of river
network complexity.
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3.2  Introduction
In this chapter, we describe the state of knowledge of stream connectivity and its effects on the physical,
chemical, and biological condition of downstream waters. Although we recognize that streams also are
important sources of water and other materials to nearby terrestrial systems and deep ground-water
systems via lateral and vertical connections (e.g., Gray, 1993; Shentsis and Rosenthal, 2003; Walters et
al., 2008), we focus here on longitudinal surface-water connections between streams and rivers, and on
shallow subsurface-water interactions integral to surface-water connections and downstream water
condition. The evidence primarily focuses on the connections between headwater streams and
downstream waters, but we draw some evidence from connections of larger streams to rivers,
reservoirs, lakes, and coastal waters. We consider the peer-reviewed evidence for connectivity and its
consequent effects on downstream rivers in terms of physical (Section 3.3), chemical (Section 3.4), and
biological (Section 3.5) connections between upstream and downstream habitats. Although we
recognize that many linkages between streams and downstream waters cross physical, chemical, and
biological boundaries, we have chosen this format for ease of presentation. In each section we  also
consider how human alteration of streams affects their connectivity and resulting effects on
downstream rivers (Sections 1.2.4 and 2.4.4). In some cases, connectivity and its effects on downstream
waters become more discernable with human alteration (e.g., Chin and Gregory, 2001; Wigmosta and
Perkins, 2001); however, when human alterations are widespread and relatively uniform (e.g., Blann et
al., 2009) attributing downstream effects to particular tributaries or parts of the river network can be
more complex. Coupled human-natural systems are an area of active research (Box 3-1). Section 3.6
closes this general section with a discussion on stream-river connections by synthesizing evidence in
terms of the conceptual framework (Chapter 2) and viewing streams in a connectivity gradient context
(Section 1.2.2). In addition, two case studies on specific types of stream systems are in Appendix B:
prairie streams (Section B.4) and southwestern intermittent and ephemeral streams (Section B.5).

Streams range greatly in size in terms of both drainage area and discharge. In general, their abundance
is inversely related to their size. First-order streams typically are most abundant, although individually
they have the smallest drainage areas and shortest average stream lengths (Horton,  1945; Schumm,
1956; Ijjasz-Vasquez etal., 1993). When considering drainage area and stream length of headwater
streams together, however, they can represent most of the river watershed and network. Thus, despite
their small individual size, these headwater streams cumulatively can have a large influence on
downstream waters  (Section 1.2.3).

Some headwater streams lack channel connections to large downstream water bodies because they
drain closed or endorheic basins. Endorheic basins have no surface outflows to oceans, but terminate as
inland lakes, seas, playas, or pans (Shaw and Bryant, 2011). Although endorheic streams are common in
some areas (Section  B.5), endorheic basins represent only approximately 2% of the North American
continent (Vorb'smarty et al., 2000) and generate 0.15% (9 of 5,892 km3 yr1)  of its annual discharge
(Fekete etal., 2002).
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                                      Box 3-1. Urban Streams
Urban development alters the structure and function of stream ecosystems in numerous ways (Paul and
Meyer, 2001; Walsh et al., 2005). Although the specific symptoms of what Walsh etal. (2005) referred to as
the "urban stream syndrome" depend on numerous factors, including the location, density, type, and age of
urban development,  common patterns have emerged. For example,  urban streams typically experience
increased stormflows (from direct runoff to channels), flashier hydrographs, altered baseflows, increased
nutrient and contaminant concentrations, and decreased organic matter retention. Many of these attributes
are related to changes in connectivity—that is, alteration  of the longitudinal, lateral, and vertical connections
between the landscape, headwater streams, and downstream waters.
Connectivity and consequences on downstream waters. One pervasive effect of urban development is the
alteration of hydrologic connectivity along river networks. The frequency, duration, magnitude, timing, and rate
of change of both stormflows and baseflows are altered via multiple pathways. The highly connected,
engineered network  of impervious surfaces, pipes, and storm drains increases the volume and rapidity of
stormwater runoff into urban streams,  resulting in increased frequency, magnitude, and rate of change of
stormflows within the river network. This quick delivery of stormwater runoff to streams also means that
stormflows tend to recede quickly, shorteningstormflow  duration. Because impervious surfaces reduce
infiltration and watershed storage of water, urban development also can reduce baseflow magnitudes.
Together, these patterns result in the typical flashy hydrographs of urban streams and altered hydrologic
connections throughout urban river networks.  Higher stormflow magnitudes and frequencies also can scour
sediments from urban channels, which, in combination with engineered channel straightening, can cause
urban channels to enlarge via incision and expansion. Direct
wastewater discharges to urban streams (e.g., from wastewater
treatment plants, industrial facilities, or combined sewer
overflows) and water withdrawals for municipal and  industrial uses
also can affect the frequency, duration, and magnitude of
hydrologic connections in urban streams. Vertical hydrologic
connections can be augmented by leaky subsurface sewer and
water pipes, or diminished by reduced  infiltration due to  increased
impervious surface area and channel incision, straightening,
hardening, and simplification.
Stream  burial, or the diversion of streams into pipes, culverts,  and
other conveyances, is common in urban watersheds, and provides
another illustration of how urban development alters connections.
For example, more than 60% of all streams in  Baltimore  City,
particularly small headwater streams, have been buried (Elmore
and Kaushal, 2008). As a result, most  lateral and longitudinal
connections along urban river networks have been replaced by
urban infrastructure, resulting in greatly expanded headwater
drainage areas (Kaushal and Belt, 2012).
These changes in hydrologic connectivity have significant
consequences for downstream waters  in urban areas. Between
rain events, urban landscapes accumulate materials such as organic material, nutrients, and contaminants,
which then are delivered quickly to urban streams with surface runoff. As natural stream channels are
converted to simplified engineered structures, they lose their ability to retain and transform these materials,
resulting in  reduced  storage and lagtime before transport to downstream waters (Nedeau etal., 2003; Carey
and Migliaccio, 2009; Kaushal and Belt, 2012).
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                               Box 3-1. Urban Streams (continued)

Longitudinal connectivity in urban streams also influences the
movement and distribution of organisms in these systems.
Urban stream habitats frequently become fragmented and
homogenized, as connectivity is disrupted  by road crossings,
channel incision, and other impacts associated with urban
development. Habitat homogenization reduces complexity,
which limits the availability of habitats needed throughout
species' life cycles (for reproduction, rearing, refuge from
disturbance and predation). Fragmentation can result in
reduced movement of mobile organisms, most notably fish,
through the river network (Perkin and Gido, 2012). Urban
streams also can benefit, however, from connectivity with
intact, upstream habitats. For example, Waits etal. (2008)
found that immigration from less disturbed upstream areas
serving as source habitats maintained central stoneroller
populations in an urban stream.
Connectivity and restoration of urban streams. Because so
many of the adverse effects associated with urban
development are related to changes in lateral, longitudinal,
and vertical connections along urban riverscapes, restoration
of these systems often involves re-establishing connections
that existed before urbanization. For example, detention ponds
and green infrastructure (rain gardens, bioswales, permeable
pavements, green roofs) are designed to slow stormwater runoff into urban streams, thereby increasing
retention  and processing of water, nutrients, sediment, and contaminants. Ultimately, the slowing of
stormwater runoff can re-establish lateral and longitudinal connections as retention and transformation
pathways, rather than the primarily export  pathway these connections traditionally served in urban river
networks.
The contribution of headwater streams to river networks in terms of stream number, length, or drainage
area over large geographic regions has been difficult to determine, even with advances in remote
sensing and geographic information systems. The small size of headwater streams makes distinguishing
them from surrounding areas and overlying tree canopies difficult in most regions (Gilvear and Bryant,
2003). Numerous studies have shown that existing U.S. hydrographic databases and topographic maps
underestimate the extent of headwater streams (Morisawa, 1957; Gregory, 1976; Hansen, 2001; Heine
etal., 2004; Stoddard etal., 2005; Roy etal., 2009). Therefore, most streams portrayed on databases and
maps as first-order streams are, when ground-truthed, second- or third-order streams. For example,
more than 80% of mapped (l:25,000-scale topographic maps) stream terminuses in a Massachusetts
watershed underestimated the upstream extent of the channels (Brooks and Colburn, 2011). On
average, these unmapped upstream segments were nearly 0.5 km in length, and 40% had one or more
upstream tributaries (Brooks and Colburn, 2011). Even with this widely known underestimation by
databases and maps, first-order streams recognized in the U.S. Geological Survey (USGS) medium-
resolution (l:100,000-scale) National Hydrography Dataset (NHD) represent 53% (2,900,000 km) of
total stream length (Nadeau and Rains, 2007). Moreover, approximately 50% of these first-order
streams were classified as not having year-round flow (i.e., nonperennial; Section 2.2.2; Nadeau and
Rains, 2007). Southwestern and prairie streams are predominantly ephemeral and intermittent
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(Sections 5.5, 5.6, B.4, and B.5). Thus, despite the shortcomings of existing national maps and
hydrographic databases, it is still clear that headwater streams—including ephemeral and intermittent
streams—represent a large fraction of river networks in the United States. Combining their
overwhelming extent with their high biogeochemical activity (Section 3.4) means that headwater
streams, including ephemeral and intermittent channels, have a large cumulative or aggregate effect on
the river network (Benstead and Leigh, 2012).

In the following sections, we consider longitudinal connectivity between streams and downstream
waters in terms of the physical, chemical, and biological connections between them.
3.3  Physical Connections
Physical connections result from the transport of nonliving materials that do not chemically change (or
change slowly) enroute from streams to downstream rivers. In this section, we discuss factors
controlling water, temperature (heat energy), sediment, and wood in streams; how these materials are
transported downstream; and evidence that these connections affect the condition of downstream
rivers.

3.3.1   Water
The recurrent, concentrated surface flow of water from surface runoff and ground water develops and
maintains river networks, and water is the primary medium carrying other materials from streams to
rivers (Section 2.3). The temporal dynamics of flow (its frequency, duration, magnitude, timing, and rate
of change) within and among river networks vary in space and time and influence the physical, chemical,
and biological connectivity between streams and downstream waters (Sections 2.2.2, 2.2.3, and 2.3.2.2).
Thus, the physical connection of water flow through river networks largely forms the foundation for
chemical and biological connections and where along the dynamic connectivity gradient streams are
positioned (Section 1.2.2).

Most rivers receive the majority of their water from tributaries rather than from direct precipitation on
or ground-water input to river segments (Winter, 2007; Bukaveckas, 2009). Alexander etal. (2007)
modeled flow through river networks  in the northeastern United States and estimated that first-order
streams (designated on the l:100,000-scale NHD river network) provide approximately 70% of the
mean annual water volume in second-order streams and about 55% and 40% of the mean water volume
in fourth- and higher order rivers, respectively. Overall, first-order streams cumulatively contribute
about 60% of the total volume of mean annual flow to all northeastern streams (Alexander et al., 2007).

Headwater stream contributions to downstream baseflow vary among river networks, based on several
large-scale factors (Section 2.4). For example,  headwater streams that have stronger connections to
ground water or that consistently receive more precipitation relative to downstream reaches have a
larger effect on downstream river baseflows. Hydrologic data from 11 nested gages distributed
throughout a watershed (176 km2) in the Catskill Mountains, NY were used to assess the extent of

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spatial correlation in baseflow discharge (Shaman et al., 2004). Baseflow discharge in smaller streams
(i.e., with watersheds <8 km2) was more weakly correlated with mainstem discharge than discharge in
larger streams; the authors concluded that this pattern reflected greater contributions by deep ground
water as drainage area increased (Shaman et al., 2004). Using geochemical tracers and hydrologic data
from 32 nested stations in a watershed (1,849 km2) of the River Dee in Scotland, Tetzlaff and Soulsby
(2008) determined that streams draining the upper 54% of the watershed contributed 71% of baseflow.
However, the upper watershed received only 58% of the total annual precipitation, indicating that long
residence time ground-water flowpaths from the headwater watersheds were also important in
maintaining downstream baseflows (Tetzlaff and Soulsby, 2008). In contrast, headwater streams
(0.11-3.5 km2) making up 33% of the total area in a northern Sweden watershed (78 km2) contributed
only 18% of the summer baseflow at the basin outlet (Temnerud et al., 2007). The specific discharge
contribution (L s-1 knv2) for headwater streams, however, varied by an order of magnitude (~0.5-8.0),
reflecting the heterogeneity (i.e., mires, lakes, forest) of the study watershed (Temnerud et al., 2007).
Jencso etal. (2009) monitored 24 transects with a total of 84 wells along lower hillslopes, toe-slope, and
riparian areas in a northern Rocky Mountains watershed (22.8 km2) and found that the duration of
connectivity from hillslopes to streams was positively correlated (r2 = 0.95) with the duration of higher
than normal downgradient watershed streamflow. This finding demonstrates the strong link between
downstream flow conditions and the connectivity of ephemeral and intermittent streamflow from
nearby hillslopes, and that the cumulative downstream effect of the hydrologic connections between the
hillslope and stream channel is time varying. Hydrologic connections to downstream rivers are often
complex, involving longitudinal, lateral, and vertical exchanges that vary over space and time. This
means that the flowpath by which headwater streams contribute to downstream waters will vary
according to climatic, topographic, and geologic context.

We can also infer the importance of headwater streams from variation in river hydrologic responses
over space. Discharge increases with drainage area, and the general assumption, particularly for mesic
environments, is that drainage area can be used as  a proxy for discharge. The relationship can be written
as Q = kAc, where Q is  discharge (m3 s'1), k is a constant representing hydrologic factors such as
antecedent moisture and precipitation, A is drainage area (km2), and c is the scaling power constant.
This scaling power reflects how the rate of discharge increases with drainage area, and can be useful for
qualitatively assessing headwater contributions to  downstream discharge. Where c « 1, discharge is
generated proportionally with increasing drainage area. Where c < 1, upstream portions of the
watershed (where headwater streams tend to be most abundant) generate more discharge per unit area
than downstream portions, suggesting that rivers with c < 1 derive a higher proportion of their flow
from headwater streams. Where c> 1, downstream portions generate more discharge per area than
upstream reaches, suggesting that rivers with c> 1 might store more water per unit area in upstream vs.
downstream areas. Alternatively, urbanization in the lower portions of the watershed can lead to a
similar relationship (Galster et al., 2006). Data from multiple  USGS gages along large, unregulated rivers
showed that mean and peak annual discharge do not always increase proportionally with drainage area
(Galster, 2007, 2009). Of the 40 rivers examined, only 16 had linear peak annual discharge-area
relationships (c« 1) throughout their period of record (Galster, 2009). Eleven rivers had relationships
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where c < 1, three rivers had relationships where c> 1, and ten showed changes in the relationship over
their period of record.

Despite variability in area-discharge relationships, most mesic watersheds have a value of c between 0.8
and 1 (Galster, 2007), suggesting that drainage area can be used to roughly estimate the proportion of
flow that arises from headwater streams. For example, Alexander et al. (2007) found that the
watersheds of first-order streams cumulatively accounted for 57% of the total drainage area and 55% of
the total annual river flow of the New England states. In more xeric arid and semiarid watersheds where
the ground-water table can be below the stream  channel and thunderstorms of limited spatial extent
dominate runoff, however, c is generally < 1. For instance, in the highly instrumented Walnut Gulch
Experimental Watershed (operated by the U.S. Department of Agriculture, Agricultural Research
Services [USDA-ARS]) in southeastern Arizona, discharge becomes more nonlinear (c decreases) with
increasing watershed area, and  a critical transition threshold area occurs roughly within 37-60 ha
(Goodrich etal., 1997). The primary causes of increasingly nonlinear response are (1) the increasing
role of ephemeral channel infiltration losses to the subsurface, unconsolidated alluvium, and (2) the
continual decline of fractional storm area coverage as watershed area increases. Caruso and Haynes
(2011) reported that first-order watersheds made up 61% of total drainage area of the Upper Colorado
River basin. In this case, the first-order streams produced a lower proportion (41%) of the total annual
river flow than suggested by their total drainage area, in part because 84% of the streams were
intermittent. Both studies used the l:100,000-scale NHD, in which first-order watersheds generally
correspond to second-order watersheds at the 1:24,000 scale (Alexander etal., 2007). These results,
representing two very different parts of the United States, strongly suggest that headwater streams,
even where seasonally dry, cumulatively generate a  large fraction of the nation's stream and river flows.

The propagation of stormflow through river networks provides clear evidence of hydrologic
connectivity between headwater streams and rivers, particularly when an intense storm occurs over
only the headwater portions of a river network. In these cases, the hydrograph peaks sharply in the
headwater streams, indicating a quick response to precipitation (Figures 2-8 and 2-11). Timing of the
storm and onset of the peak are increasingly delayed with increasing distance down the network (Figure
2-11;  see below for further discussion of hydrologic  dispersion). Typically, discharge magnitude
increases as stormflow accumulates incrementally over the river network (Allan, 1995). The
contribution of tributaries to rivers during widespread floods manifests as stepped increases in
discharge immediately below confluences, as water flows accumulate through a river network
(Figure 3-1).

Such propagation was recorded following a monsoonal storm event through an arid network of
ephemeral channels in the Rio Grande, NM (Figure 3-2). The high-intensity storm dropped
approximately 18-25% of annual rainfall on the  stream's approximately 16,000 km2 drainage area over
a 2-day period. Discharge recorded at two gages  on the stream and three gages on the Rio Grande
downstream of the  confluence illustrated lag (residence) time and peak hydrograph broadening at least
127 km downstream (Vivoni etal., 2006).  Stormflow contributions from the ephemeral stream
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 Figure 3-1. Longitudinal pattern of flow along (A) River Derwent and (B) River Trent, illustrating
 stepped increases in flow associated with tributary inflows. Small arrows indicate location of
 tributary confluences along the mainstem; bold arrow in (B) indicates the confluence of the two rivers.
 Source: Reprinted from Fluvial Forms and Processes: A New Perspective, (1998) by Knighton with
 permission of Routledge.
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                            0  10   20   30  40  50   60  70  80   90  100  110
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 Figure 3-2. Time series of rainfall and streamflow observations in the Rio Puerco and Rio Grande,
 6-18 September 2003. Source: Reprinted from Analysis of a monsoon flood event in an ephemeral
 tributary and its downstream hydrologic effects, (2006) by Vivoni et al. with permission of John Wiley
 &Sons.
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                                              Mean Radar
                                                Rainfall
                                              Rio Puerco at
                                                Bernardo
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                                                              Rto Grande at
                                                               San Acacia
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These areas, which mix with the main channel flows at relatively slow rates, are collectively part of the
stream's transient storage. As streamflow decreases after a storm, water that was temporarily stored in
the banks, the floodplain, and other off-channel habitats flows back into the channel and supports
stream baseflow (Sections 2.2.3 and 4.3.2.1; Whiting and Pomeranets, 1997; Chen and Chen, 2003;
Baillie etal., 2007). Hydrodynamic dispersion is also readily apparent when flow resumes in ephemeral
channels. The velocity at the front of flow moving down the dry channel is much slower than upgradient
of the front because of higher turbulence and infiltration losses at the front Flow in these situations,
piles up at the front and is reflected as rapid rises in the hydrographs (Figures B-6 and B-10).

Hyporheic flowpaths have been characterized for a variety of situations that affect streambed
topography and impede flow across a range of spatial scales (e.g., gravel bars, channel meanders, pool-
riffle sequences, and large woody debris; Buffington and Tonina, 2009; Stonedahl et al., 2010; Sawyer et
al., 2011) and in varying flow conditions that shift streambed topography (Harvey et al., 2012). The
residence time that water spends in the subsurface alluvium before upwelling into streams—that is, the
hyporheic residence time—is defined locally by the pressure head, alluvial volume, hydraulic
conductivity, bed stability, and near-bed turbulence. For example, because  90% of the stream length in
mountainous drainage basins is composed of steep channels with associated bed-form sequencing and
limited alluvial volumes, most hyporheic exchange in these systems is expected to be rapid,  shallow, and
occur over small spatial scales (Buffington and Tonina, 2009). Slower, deeper, and longer hyporheic
flowpaths occur in streams in unconfined valleys, with moderate hydraulic gradients and extensive
alluvial volumes. In streams  of both regions, hydrologic connections exist between shallow ground-
water sources and stream channels, but the characteristics of these connections differ. These differences
in hydrologic residence time are important, given that residence time reduces downstream flooding,
controls various biogeochemical processes, and influences the distribution of stream organisms
(Sections 3.4 and 3.5).

Geomorphologic dispersion is the cumulative effect of different travel distances over the larger spatial
scale of entire river networks (Rodriguez-Iturbe and Valdes, 1979; Gupta etal., 1980; Rinaldo etal.,
1991; Snell and Sivapalan, 1994). Not all points along the river network (or even headwater streams)
are equidistant from the network outlet, so water simultaneously entering different parts of the network
will not simultaneously arrive at the outlet.

Geomorphologic dispersion assumes water flowing through the network moves at a constant velocity or
has varying resistance to downgradient transport. Within river networks, however, water velocity and
related hydrodynamics change over space and time (e.g., channel slope and dimensions are  not uniform
across all pathways through the river network; Saco and Kumar, 2002; Paik and Kumar, 2004).
Kinematic dispersion  is the cumulative effect of spatially variable water velocity as it moves through
river networks (Saco and Kumar, 2002). The physical configuration and variable channel form of
streams within a river network, which influence components of hydrologic dispersion at varying scales,
are the primary controls dispersing flow from streams to rivers over time and thereby cumulatively
mediate the arrival time of stormwater pulses in rivers following rainstorms (Saco and Kumar, 2008).
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Another factor that influences hydrologic response is channel transmission loss, or the loss of surface-
flow volume due to infiltration into unconsolidated alluvium (Section 2.2). Transmission is another
process by which streams, particularly in arid and semiarid regions, can slow or divert from the
longitudinal flow of water to downstream rivers and thus minimize downstream flooding. Channel
transmission losses are readily apparent from a series of hydrographs recorded in the USDA-ARS
Walnut Gulch Experimental Watershed (Figure B-10). These hydrographs are the result of several high-
intensity thunderstorms in the upper and lower portions of the watershed. As little or no lateral
overland or tributary inflow occurs between the two upstream flumes, the decrease in both peak runoff
rate and runoff volume is the result of channel transmission losses and dispersion only. As illustrated in
this figure, however, even though runoff transmission losses are large there is sufficient runoff to
increase flow in the San Pedro River at the downstream Tombstone USGS gaging station. Over relatively
short time frames, infiltration or seepage through channel bed and banks typically dominates
transmission losses, although evapotranspiration losses can be significant in stream reaches with
prolonged surface flows (Hamilton et al., 2005; Costelloe et al., 2007). In many arid areas, precipitation
and the potential for runoff are highest in mountainous regions, where small, ephemeral streams are
most abundant (Section B.5). Because streams represent the topographic low points in watersheds that
collect and concentrate surface water, they tend to have more water available for infiltration, be more
permeable (have coarser sediment) than upland soils, have fewer plants, have higher antecedent
moisture, and be closer to shallow ground water—all of which are factors that increase the potential for
infiltration. In fact, evidence is mounting that ground-water recharge in hot arid and semiarid areas will
occur only where water is concentrated and focused, such as in channels, depressions, or areas of high
infiltration (e.g., karst;  Brahana and Hollyday, 1988; Hughes and Sami, 1992; Sharma and Murthy, 1995;
Scanlon etal., 1997; Scott etal., 2000; Constantz etal., 2002; Goes and Pool, 2005). Infiltrated
precipitation in upland portions of alluvial drainage basins rarely reaches the ground-water table as
recharge due to high potential evapotranspiration, the adaptation of xeric plants to use available soil
moisture efficiently, and upward temperature gradients that transport water vapor upward in thick
vadose zones. Relative to their cumulative surface area, an  inordinate amount of ground-water recharge
occurs in headwater ephemeral and intermittent channels  within arid drainage basins (Osterkamp et al.,
1994; Goodrich etal., 2004).

Channel bed and bank  permeability also governs the degree to which infiltration is an important
pathway between streams and ground-water aquifers. Fine bed and bank sediments slow infiltration. In
many semiarid and arid streams, bed sediments become finer in the downstream direction because flow
competence declines (Dunkerley, 1992), suggesting that lateral and vertical hydrologic connections
might be especially important in headwater streams. Sand  and gravel mining in ephemeral and
intermittent channels and other human alterations that increase fine sediment loading and deposition
can further slow percolation (Bull and Scott, 1974). Because fine sediments can concentrate in channels
following moderate flows, higher flows that scour fine sediments or submerge more permeable
floodplains have higher infiltration rates (Lange, 2005). In  the Walnut Gulch Experimental Watershed,
cumulative transmission losses over 54 km of channel resulted in a 57% decrease in flow volume
associated with a storm (Renard and Keppel,  1966). Infiltration losses accounted for up to half the flow
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volume along three ephemeral channels in the southwestern United States (Constantz et al., 2002).
Chemical and isotopic tracers have confirmed that ephemeral streams are cumulatively important areas
for floodwaters to recharge ground-water aquifers in desert regions (Tang et al., 2001). Although
transmission losses represent disruptions of surface connectivity between streams and downstream
waters, such losses indicate vertical hydrologic connections that reduce downstream flooding and
recharge the ground-water aquifers that eventually contribute to flow in downstream waters (Izbicki,
2007).

Human alterations designed to control the spatial and temporal distribution of water have affected the
longitudinal, lateral, vertical, and temporal dimensions of hydrologic connectivity in river networks.
Structures such as dams, weirs, levees, culverts, and pipes alter longitudinal transport, restrict lateral
expansion, and alter vertical exchange (e.g., Gregory, 2006; Hester and Doyle, 2008; Park et al., 2008).
Surface-water and ground-water abstraction and diversion can cause tributary segments to dry, thereby
severing longitudinal and vertical connectivity and reducing or eliminating lateral connectivity during
low-flow periods (e.g., Colvin and Moffitt, 2009; Scanlon et al., 2012). Human alterations that increase
fine sediment deposition or microbial biofilm in streambeds also can hamper vertical exchange (Battin
and Sengschmitt, 1999; Rehg et al., 2005), causing conditions that can  become chronic without periodic
floods to flush out deposited sediments and biofilms (Box 3-1).

Human alterations also can affect the temporal dynamics of hydrologic connectivity in river networks. In
a predominantly rural river network in central Illinois, the total dispersion of the flow was controlled
primarily by geomorphological (~60%) and kinematic dispersion (~35%; Saco and Kumar, 2002). In
contrast, hydrodynamic dispersion cumulatively contributed to 72-86% of the total dispersion in highly
urbanized watersheds in the Chicago metropolitan area (Cantone and  Schmidt, 2011). The rapid
hydrologic travel times associated with impervious surface runoff and rapid flow through the sewer and
storm drain networks contributed to the predominant influence of hydrodynamic dispersion (Cantone
and Schmidt, 2011).

Interbasin water transfer also affects the temporal and spatial dynamics of flow in human-dominated
river networks (Meador, 1996). Water is fundamental to human societies for drinking, food production,
industry, waste transport and processing, recreation, and aesthetics. Engineered infrastructure moves
water (and associated waste products) where and when it is needed (or removes it from where it is
unwanted). Many streams in human-dominated watersheds, particularly streams that historically have
ephemeral and intermittent flows, receive a significant proportion of their baseflow from municipal and
industrial waste water effluent discharges (Box 3-1). Streams that would be dry in the absence of these
discharges are called effluent-dependent streams, whereas those that receive most, but not all, of their
flow from effluent are called effluent-dominated streams (Brooks etal., 2006). About 25% of permitted
effluent discharges in the United  States enter streams with mean annual flows incapable of diluting
effluents by more than 10-fold. This percentage of permitted effluent discharges entering streams
incapable of diluting effluents by more than 10-fold increases to  60% when low-flow discharge is
considered (Brooks et al., 2006).  Streams draining human-dominated areas also can derive baseflow
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from ground water recharged by over-irrigation and leaky infrastructure (Lerner, 1986; Roach et al.,
2008; Townsend-Small et al., 2013).

Ultimately, these alterations can increase the frequency, duration, magnitude, and predictability of
baseflows when tributaries might otherwise contain little or no water. Because dry periods in
intermittent and ephemeral streams contribute to the key transformation, lag, and refuge functions
these systems perform (Sections 3.4 and 3.5), loss of these dry periods has consequences for
downstream waters. In addition, when water is stored or imported for human use, it is essentially being
"borrowed" from another period or location, which then must contend with reduced water availability.
Without careful water management and reuse (e.g., Bischel et al., 2013), any benefits of baseflow
augmentation can be overshadowed by potential risks, such as increased contaminant and pathogen
exposures (Section 3.4.4) and increased success of introduced species (Jackson and Pringle, 2010).

3.3.2   Sediment
Sediment carried with water flow from streams to downstream waters is critical for maintaining the
river network. Fluvial sediments scour channels, deposit to form channel features, and influence  channel
hydrodynamics (Church, 2006). Although sediment is essential to river systems, excess sediment can
impair ecological integrity by filling interstitial spaces, reducing channel capacity, blocking sunlight
transmission through the water column, and increasing contaminant and nutrient concentrations (Wood
andArmitage, 1997).

Sediment in headwater streams originates from nearby hillslopes and enters these streams via overland
flow, bank erosion (Grimshaw and Lewin, 1980), and infrequent disturbances such as landslides  and
debris flows (e.g., Benda and Dunne, 1987; Swanson etal., 1998; Eaton etal., 2003). Sediment
transported within river networks can be divided into two major categories: suspended and bedload.
Suspended sediment is fine sediment (clay, silt, fine sand) that requires slow velocities and little
turbulence to remain entrained in the water column; bedload sediment is coarser particles that slide,
roll, and bounce along the streambed during faster, more turbulent flows (Church, 2006; Wilcock et al.,
2009).

The dynamic balance between sediment supply and transport capacity (Lane, 1955; Bull, 1991; Trimble,
2010)—with the variables of sediment flux and sediment grain size on one side, and discharge and
channel slope on the other—is a principal paradigm of fluvial geomorphology. If one of these variables
changes, a compensatory change occurs in at least one of the other variables. For example, if discharge
increases, a lower channel slope is needed to transport the same amount of similarly sized sediment;
alternatively, less discharge or lower channel  slope is needed to move a load of fine sediment than the
same load of coarse sediment. Associated with this balance is the relationship between channel
geometry (width and depth) and discharge (Leopold and Maddock, 1953), and adjustments to maintain
a dynamic balance also can include changes in channel dimensions.

The sediment supply-transport capacity balance is particularly relevant to geomorphologic connectivity
in river networks, because these variables typically differ as one moves from headwater streams to

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downstream rivers (Ferguson etal., 2006; Ferguson and Hoey, 2008). For example, slope and grain size
typically decrease, whereas discharge and channel size typically increase, in downstream reaches
(Church, 2002). Thus, streams cumulatively and aggregatively affect rivers in part by changing sediment
supply or transport capacity locally at confluences over time. Relatively small, local contributions in
sediment and discharge from a tributary stream might elicit no detectable change or only a short-lived
spike in downstream sediment characteristics, discharge, or channel geometry. In contrast, tributary
streams making large relative contributions at mainstem confluences elicit strong, stepped changes in
mainstem characteristics. Because headwater streams can make large contributions during infrequent
disturbances (e.g., floods, debris flows), the influence of headwater streams on downstream waters can
vary significantly over time, and even headwater streams can have long-lasting effects on rivers.

Human alterations can exert considerable influence on the structure and  distribution of a watershed's
river network, thereby affecting sediment-based connections between headwater streams and
downstream waters. For example, road building in steep forested areas in the U.S. Pacific Northwest can
cause soil erosion, create concentrated discharge, and increase stream channel network lengths, all of
which affect the spatial distribution, intensity, and timing of erosional processes and cumulative
sediment delivery to downstream waters (Montgomery, 1994; Wemple et al., 1996; Wemple et al.,
2001).

Dams also modify sediment dynamics within river networks. Sediment concentrations and suspended
loads can be reduced for hundreds of kilometers downstream of dams, as is especially apparent in the
semiarid and arid western U.S. river networks (Williams and Wolman, 1984). The disruption of
downstream sediment supply by dams alters the balance between sediment supply and transport
capacity (Williams and Wolman, 1984; Kondolf,  1997). Water released from dams lacks sediment load
and thus has excess energy. This energy often downcuts channels downstream of dams, causing channel
incision and streambed coarsening as finer gravels and sands are transported downstream over time
(Williams and Wolman, 1984; Kondolf, 1997). The elimination of floods enables the encroachment of
terrestrial vegetation, resulting in channel narrowing and the conversion of complex, multithreaded
channels into simple, single-thread channels.

Other human activities also can affect sediment dynamics. Gravel and sand mining locally removes bed
sediment and lowers streambed elevation, creating a steep gradient change. Erosion of the streambed
can occur both  upstream and downstream of the mine. The steep gradient change increases stream
power locally, which increases sediment demand and causes the streambed to erode in the upstream
direction via headcutting, which often extends far up into tributary channels (e.g., Florsheim et al., 2001;
Rinaldi et al., 2005; Rieke-Zapp and Nichols, 2011). Erosion in the downstream direction occurs because
most of the sediment being carried by water is deposited in the mining pit, leaving the water that passes
over the pit with excess energy that subsequently leads to downstream channel downcutting (Bull and
Scott, 1974; Kondolf, 1997). These examples show that the dynamic balance between sediment supply
and transport capacity represents a fundamental longitudinal connection along the river network that
must be considered to determine the potential repercussions of human alterations.
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Streams transport and store sediment. Headwater streams tend to have low competence to transport
sediment during baseflow (Gooderham etal., 2007), but they have structures (boulders, woody debris)
that entrain and store colluvial sediments between infrequent disturbances (e.g., stoonflows) that are
the dominant means for downstream sediment transport (e.g., Gomi and Sidle, 2003). Because of their
abundance and distribution, headwater streams can have a substantial cumulative effect on downstream
waters via sediment storage and transport. Poor soil conservation, drainage of wetlands, deforestation,
and tributary channelization associated with the development of agricultural land has long been
recognized as being detrimental to downstream waters via their connections with headwater streams
(Person et al., 1936). To stem further degradation, government agencies encouraged and funded various
soil conservation practices and the construction of small impoundments on headwater streams to trap
sediment and provide stable water supplies for livestock, irrigation, and recreation (Person et al., 1936;
Renwick et al., 2005). Although most such ponds are small (<1 ha or 2.5 acre) and represent only ~20%
of the total impounded area (or 0.4% of the total watershed area), they can cumulatively have a
significant effect. For example, Smith and Kraft (2005) estimated that the approximately 2.3 million
ponds distributed primarily on headwater streams of the Mississippi River network cumulatively
captured 25-50% of the eroded soil from the landscape.

Ephemeral desert streams are another example of sediment connections between headwater streams
and downstream waters. These ephemeral streams can exhibit high sediment export efficiency by
having higher bedload per unit stream power than that of forested perennial streams (Laronne and
Reid, 1993). Despite infrequent flows of short duration, flood waves (bores) in ephemeral desert
streams can carry substantial amounts of sediment downstream (Hassan, 1990). The transport distance
associated with these floods, however, often is insufficient to link them directly to perennial rivers. For
example, a reach-scale study in the Walnut Gulch Experimental Watershed in Arizona estimated sand
transport distances of only 401 and 734 m in nine floods over two consecutive years (Powell et al.,
2007). Over longer times spans the episodic nature of flow in ephemeral and intermittent channels
transfers sediment in a stepwise manner, depositing sediment some distance downstream and then
moving it farther downstream by subsequent events. The frequency, timing, and predictability of stream
runoff and therefore sediment transport vary widely with significant seasonal, annual, and interannual
variations that depend on elevation, climate, channel substrate, geology and the presence of shallow
ground water. Over longer time spans, however, sediment will continue to move downstream and affect
downstream waters (Brooks and  Lemon, 2007).

Despite increasing bank erosion rates with increasing channel size and discharge, sediment yield from
watersheds typically decreases with increasing drainage area, due to increased sediment deposition
within channels and on nearby floodplains (Walling, 1983). This storage of sediment contributes to the
temporal attenuation or lag in the sediment delivery to downstream waters; it also illustrates that
headwater streams  are important sediment sources for maintaining channels and floodplains.

Streams also can store substantial amounts of sediment that are released only during rare export events.
A series of experimental sediment introductions into steep, ephemeral, second-order streams in
southwestern Washington showed that between 30 and 45% of the added sediment (ranging from clay
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to coarse sand) was exported to the mainstem 95-125 m downstream, during stormflows of 66-69% of
bank full discharge (Duncan et al., 1987). Virtually all the added fine clay particles were exported from
the ephemeral streams to the mainstem, presumably because this fraction remained suspended at even
moderate flows (Duncan etal., 1987). Headwater streams within an Oregon Coastal Range watershed
(2.5 km2 area) stored 23% of total stored sediment within the watershed's river and valley network,
compared with only 9% storage within the mainstem channel (May and Gresswell, 2003). Trimble
(1999) constructed a long-term sediment budget for the Coon Creek watershed (360 km2), a Wisconsin
stream in the Mississippi River drainage, over periods coinciding with major land-use changes. When
agricultural practices caused major soil erosion (1853-1938), streams acted as net sources of sediment
(42 x 103 Mgyr-1); after erosion control, streambank stabilization, and revegetation (1975-1993),
streams became net sediment sinks (9 x 103 Mgyr-1) (Trimble, 1999).

Several studies identify abrupt changes in sediment size and channel morphology that coincide with
stream confluences having sufficiently high symmetry ratios (Knighton, 1980; Rhoads, 1987; Rice and
Church, 1998; Rice et al., 2001). Reviews of tributary confluence data have identified that symmetry
ratios ranging from 0.2 to 0.7 are needed to create a discernible sediment or channel morphology
discontinuity along a mainstem (Rhoads, 1987; Benda, 2008). Suspended particulate matter (inorganic +
organic) and bed particle size were measured above and below eight confluences on the Acheron River
in Australia to determine stream contributions (Wallis et al., 2008; Wallis et al., 2009). Suspended
particulate matter downstream of confluences approximated the sum of mainstem and stream exports
during high flows, but stream contributions were negligible during low flows (Wallis et al., 2009). Four
of the eight confluences showed expected changes in bed particle size below confluences with streams,
but bed particle sizes were similar in the mainstem and stream for the remaining confluences  (Wallis et
al., 2008).

Streams, through their connections to rivers at confluences, can disrupt longitudinal trends in discharge
of water and sediment in rivers (Best, 1988; Benda etal., 2004; Ribeiro etal., 2012). For example, dams
often remove much of the sediment from transport, whereas most streams naturally are sediment
sources. The objective of a study on the Agigawa River in Japan was to examine contrasting disruptions
associated with a dam (sediment removal) and a stream confluence (sediment discharge) downstream
of the dam (Katano et al., 2009). Stream sediment contributions to the river reversed many of the dam-
related changes to downstream waters, including restoration of turbidity levels and the proportion of
sand and gravel substrate in the river bed (Katano et al., 2009). Other upstream land uses can  also have
an effect on downstream sediment transport. Numerous modeling studies have shown how land use can
affect sediment export from headwater streams to downstream waters. For example, Howarth et al.
(1991) used the Generalized Watershed Loading Function model in the Hudson River estuary  and its
associated watershed and demonstrated that urban, suburban, and agricultural land uses in headwater
watersheds produced the highest proportion of downstream sediment and organic carbon delivery to
the estuary. More recently, Wilson and Weng (2011) applied the Soil and Water Assessment Tool in the
Des Plaines River watershed in Illinois to simulate the cumulative effects of headwater streams on
downstream total suspended solids concentrations. Their calibrated model projected that expansion of

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medium- and high-density residential development in place of low-density residential development in
headwater subwatersheds would decrease downstream total suspended solid concentrations.

3.3.3   Wood
Large woody debris (typically considered >10 cm diameter and >1 m long) has a strong influence on
hydrodynamics, sediment transport and storage, and channel morphology (e.g., Harmon et al., 1986;
Nakamura and Swanson, 1993; Abbe and Montgomery, 1996; Naiman and Decamps, 1997; Montgomery
et al., 2003). Woody debris dissipates energy, traps moving material, and forms habitat for aquatic
plants and animals (Anderson and Sedell,  1979; Harmon etal., 1986; Abbe and Montgomery, 1996;
Naiman and Decamps, 1997; Gurnell et al., 2002). In-channel wood can redirect water movements,
create pools, and slow water movement through a channel (Nakamura and Swanson, 1993; Abbe and
Montgomery, 1996; Naiman and Decamps, 1997). Wood recruitment to forested streams occurs because
of chronic tree mortality; episodic disturbances such as fire, debris flows, landslides, and windthrow;
and bank erosion. The steeper topography associated with hillslopes along many headwater streams
increases the likelihood that trees will fall toward the channel (Sobota et al., 2006), relative to streams in
flatter terrain. Environmental setting, including valley slope, influences the supply of wood to streams
and therefore the degree of connectivity between streams and downstream waters.

Wood tends to accumulate in, rather than be exported from, most forested headwater streams, due to
their low discharge and relatively narrow channel widths (Keller and Swanson, 1979;  Bilby and Ward,
1989; Gurnell, 2003). For example, wood was determined to have entered the channel more than 60
years earlier in a North Carolina headwater stream (Wallace et al., 2001); in some Pacific Northwest
streams, wood entered the channel more than a century earlier (Swanson and Bachmann, 1976; Keller
et al., 1981). Because of the large occurrence of wood and small size of streams, wood  has a stronger
influence on hydrologic and geomorphic processes in headwater streams than in most larger rivers
(Bilby and Bisson, 1998).

Large, infrequent disturbance events are the primary drivers for wood movement from headwater
streams (Benda and Cundy, 1990; Benda et al., 2005; Bigelow et al., 2007). Reeves et al. (2003)
determined that 65% of the wood pieces and 46% of the wood volume in a fourth-order  stream in
Oregon's Coastal Range were delivered downstream from headwater streams by debris flows, rather
than originating from the riparian zone next to the fourth-order channel. Using data from 131 reservoirs
in Japan, investigators identified a curvilinear relationship between watershed area and  large woody
debris export (Seo et al., 2008); wood export per unit area increased with stream size  for headwater
streams (6-20 km2), peaked at intermediate-sized streams (20-100 km2), and then decreased with
stream size for large streams (100-2,370 km2). The amount of wood in low-gradient midwestern
streams was determined to be supply limited mainly because human alteration both depletes large
wood sources and results in altered hydrology and channel structure enhancing downstream transport
of small wood (Johnson etal., 2006). Topography and topology also govern wood delivery from
headwater streams. Downstream segments draining steep, finely dendritic networks receive a greater
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proportion of wood from headwater streams than networks that are low gradient and weakly dissected
(Benda and Cundy, 1990; Reeves etal., 2003).

Additional evidence on wood-mediated connections along the river network comes from studies of
wood upstream and downstream of tributary confluences. Several studies have assessed the
distribution of wood associated with confluences. Wood volumes were measured upstream and
downstream of 13 confluences (symmetry ratios ranged from 0.05 to 0.49) in the Cascade Range of
western Washington (Kiffney et al., 2006). Wood volumes tended to peak at or immediately downstream
of stream confluences (Kiffney et al., 2006), suggesting that streams are either important sources of
wood to mainstems or alter channel form to enhance wood storage at confluences. Elevated wood
density, however, was not associated with confluences of eight streams to the Acheron River in Australia
(Wallis etal., 2009). The authors concluded that the study streams had insufficient capacity to transport
wood to the mainstem, because streams had similar slope to the mainstem but lower discharges (Wallis
etal., 2009).

Large wood can shorten sediment transport distances and debris flow runout by entrainment
(Lancaster et al., 2003). Woody debris in 13 Coastal Range streams in Oregon had accumulation rates
ranging from 0.003 to 0.03 m3 nr1  yr-1, largely based on time since the last debris flow (May and
Gresswell, 2003). The volume of instream wood was strongly related to the volume of sediment stored.
On average, 73% of stream sediment, prone to debris flow transport, was stored behind instream wood
(May and Gresswell, 2003). Unlike  most human-built dams, natural logjams and beaver dams are
temporary structures that do not completely restrict transport of water, sediment, and biology across all
discharge levels. Although natural wood accumulations act to restrict longitudinal connectivity by
slowing the downstream transport, these features enhance lateral and vertical connectivity with the
floodplain andhyporheic zone, respectively (Burchsted etal., 2010; Sawyer etal., 2011). The importance
of wood in decreasing longitudinal connectivity, while enhancing lateral connectivity, temporary
storage, and habitat diversity has been documented not only locally at unit and reach spatial scales (1-
100m stream length) but along entire networks where valley confinement is an important predictor for
wood storage (Wohl and Beckman, 2014). Past and ongoing human activities (timber harvest, beaver
trapping, road building along streams, placer mining, log floating, desnagging) have so completely
removed in-channel wood and availability of near-channel old-growth wood recruitment, that retention
of new wood in channels is unlikely (Wohl and Beckman, 2014). Wood (and associated sediment)
movement from headwater streams to downstream segments occurs through infrequent, high-
magnitude events (e.g., debris flows, fire). Once in larger streams, wood and sediment can be stored in
alluvial fans and floodplains between stormflows that trigger additional downstream movement
through the network (Benda et al.,  2005). Because of the long distances and infrequent triggers
associated with wood transport from most headwater streams to rivers, the relevant periods for
governing transport aggregate over decades to centuries (Benda et al., 1998). Wood entering headwater
streams can affect the downstream transport of water and materials in headwater streams, but also can
be transported downstream from headwater streams where it is important habitat for aquatic life, a
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source of dissolved and particulate organic matter, and influential in controlling hydrodynamics and
channel morphology of rivers.

3.3.4  Temperature (Heat Energy)
Connections between streams and downstream waters can affect heat transfer, and thus water
temperature, throughout river networks (Knispel and Castella, 2003; Rice etal., 2008). Heat is thermal
energy transferred across a boundary, whereas temperature is the amount of thermal energy per unit
volume (Coutant, 1999; Poole and Berman, 2001). Therefore, the amount of heat and the size of the
water body (i.e., volume, discharge) are fundamental controls of water temperature. Because water
temperature is such a fundamental property that drives physical (e.g., viscosity and density of water),
biological (e.g., organism behavior and physiology), and biogeochemical (e.g., nutrient assimilation and
mineralization) characteristics of stream ecosystems, it can cumulatively have significant indirect effects
on downstream waters via its effects on other forms of connectivity. This influence can occur over even
relatively small spatial scales or patches (Sections 3.4 and 4.5; Allan, 1995). For example, water
temperature strongly regulates stream ecosystem respiration, which then drives nutrient uptake
(Section 3.4.1; Demars et al., 2011). Warmer temperatures exacerbates eutrophication problems such as
fish kills, and heat stress can interact with chemicals synergistically or antagonistically making them
more or less toxic to organisms, respectively (e.g., Holmstrup et al., 2010).

The total net heat exchange for a stream has several components, including heat flux from solar
radiation, evaporation, convection with air, conduction with the  streambed sediments, and advection
with direct inputs from precipitation, ground water, tributaries, and effluents (Webb, 1996; Coutant,
1999). Given these diverse thermal energy fluxes, numerous direct and indirect factors can change
stream temperature. For instance, riparian vegetation directly affects stream temperature by insulation
(shading incoming solar radiation and trapping air, reducing wind; Moore et al., 2005) and indirectly
affects stream temperature via its influence on channel morphology (e.g., Trimble, 1997) and degree of
hyporheic exchange through input of woody debris (e.g., Sawyer et al., 2012). Channel morphology can
directly influence stream temperature by affecting bank shading and altering channel width-to-depth
ratio, and indirectly influence stream temperature by affecting hyporheic exchange. Hyporheic exchange
influences stream temperature via buffering (reducing the diel temperature range) and lagging
(offsetting daily temperature patterns relative to surface-water patterns) effects, due to the extended
alluvial flowpath and by the advection or conduction of thermal energy or both (Arrigoni et al., 2008).

Over coarse spatial scales, a nonlinear increase in mean daily water temperature typically occurs from
headwater streams to large rivers (Caissie, 2006). A unimodal trend occurs in daily variation (i.e., daily
maximum-minimum) of water temperature, as stable ground-water temperatures (in headwater
streams) and greater depth and volume of water (in large rivers) buffer water temperatures from the
daily changes typical in intermediate-sized streams (Caissie, 2006). The steep increase in water
temperature immediately downstream of headwater streams is associated with more rapid flux of heat
into headwater streams, as  shallow water contacts the surrounding air  and receives direct radiation
(Caissie, 2006). This longitudinal pattern, however, does not hold for all river networks: Some river

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networks receive substantial deep ground-water contributions at lower reaches or advective inputs
from tributaries along the mainstem. Channel network configurations can influence the length,
dominant aspect relative to the sun, and distribution of tributaries, which influence the thermal
heterogeneity along a stream that might be associated with inflowing surface and hyporheic water.
Callahan etal. (2015) illustrated how topographic, geomorphic, riparian, and hyporheic exchange can
interact to influence stream temperature in the Kenai Peninsula, AK. Ground-water inputs played
important moderating roles in determining stream temperatures in both low-gradient versus steep
headwater streams, despite these streams having different channel morphologies, draining contrasting
topographies, and having different riparian canopies (Callahan et al., 2015). Although low-gradient
headwater streams had fewer channel margin seeps and lower hyporheic exchange than the steep
headwater streams, the subsurface-water temperature entering the low-gradient streams was lower
during summer than that entering the steep streams (Callahan et al., 2015).

Although many studies have determined that several direct and indirect factors can alter stream
temperature, including those listed above, these effects typically have been documented to carry for only
short distances downstream. This is in part because most studies measuring stream temperature
changes are conducted over reach or subreach scales (<100 m) and because stream-water temperature
equilibrates rapidly (~4 hr) to immediate surrounding conditions (e.g., Zwieniecki  and Newton, 1999;
Rutherford et al., 2004; Hester et al., 2009). Some studies, however, do provide evidence of thermal
connections along river networks. The empirical evidence supporting thermal connections between
headwater streams and downstream waters includes studies that have gauged the spatial relationship of
water temperature  over river networks and studies that have detected discontinuities in river
temperature associated with stream confluences. Geospatial analyses are used to assess the degree of
spatial dependence of a variable across a river network, and are particularly well suited for studying
connectivity within these systems. Studies of this type have shown that upstream water temperature is
significantly related to downstream water temperature, even over relatively long distances. For
example, water temperature data collected at 72 locations throughout a Catskill Mountain, NY
watershed were used to predict daily mean summer water temperatures spatially throughout
approximately 160  km of channel (Gardner and Sullivan, 2004). Results showed that water
temperatures at points along the  river network separated by up to nearly 20 km were related. Johnson
et al. (2010) similarly used geostatistical analyses to determine the influence  of headwater streams on
downstream physicochemistry, including water temperature. Water temperature within the eastern
Kentucky watershed was correlated across the river network over an average distance of approximately
5 km (Johnson etal., 2010).

Studies that have detected discontinuities in river temperature associated with stream confluences also
provide evidence of thermal connections along river networks. Ebersole etal. (2003)  identified and
characterized cold patches along a river network in northeastern Oregon that largely had summer water
temperatures exceeding the tolerance limit of native salmonids. Floodplain springbrook streams were
among the cold patches identified and were determined to contribute the coldest water to the river
network (Ebersole etal., 2003). A subsequent study in northeastern Oregon determined that tributary

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confluences typically provided coldwater (>3 °C colder than mainstem temperatures) patches during the
summer (Ebersole et al., 2015). In addition, 39% of these tributary confluences were with streams that
contributed cold hyporheic water even when they lacked surface water—that is, they were ephemeral
and intermittent streams that were significantly connected to downstream waters even when the
streambed surfaces were dry (Ebersole et al., 2015). Unexpectedly, factors such as tributary size, flow
presence, and flowpath length were not important in predicting whether a tributary's confluence would
be a cold patch. Rather, the probability of a confluence's being a cold patch was largely explained by
amount of available water at the end of the snowmelt season (Ebersole etal., 2015).

Thermal infrared sensors are a recent remote-sensing tool that can provide snapshots of thermal
heterogeneity along river corridors (Torgersen et al., 2001; Torgersen et al., 2008; Cristea and Burges,
2009). Thermal maps and plots of longitudinal profiles overlaid by stream locations show that
confluences coincide with distinct peaks and troughs in river temperature (Figure 3-3). The effects of
streams were discernible when temperature differences of streams and the mainstem exceeded 1 °C and
streams had large symmetry ratios  (Cristea and Burges, 2009). In most cases, the effect of the stream on
river-water temperature was minor relative to longitudinal changes over the course of the river
(Torgersen et al., 2001; Cristea and Burges, 2009). Despite having a relatively minor effect on
temperature over the length of entire rivers, however, streams provide persistent coldwater habitats
that are less susceptible to meteorological variation than other classes of thermal refuges and therefore
are particularly important for aquatic life (Section 3.5.2; Dugdale et al., 2013).

Although headwater stream temperatures are highly responsive to local conditions, they still can have a
cumulative effect on downstream waters. The fact that large-scale alteration of headwater streams has
been documented to affect downstream water temperature illustrates this point. For example,
reductions in baseflow (ground-water inputs) resulting from increased surface runoff from impervious
surfaces (Leopold, 1968) and reduced hyporheic exchange through the engineered piping, straightening,
and hardening of streambeds contribute to increased average and maximum summer water
temperatures and decreased average and minimum winter temperatures in downstream waters. The
combination of riparian vegetation removal, increased urban runoff, and storm sewer inputs results in
larger temperature swings associated with increased channel width-to-depth ratios and thus air-water
surface area available for radiant, evaporative, and convective fluxes (LeBlanc etal., 1997).


3.4  Chemical Connections
Chemical connections are linkages between headwater and other tributary streams and their
downstream waters based on the transport of chemical elements and compounds (e.g., nutrients,
dissolved and particulate organic matter, ions, and contaminants). Chemical connectivity between
streams and rivers involves the transformation, removal, and transport  of these substances throughout
the river network; these processes, in turn, influence water quality, sediment deposition, nutrient
availability, and biotic functions in rivers.
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 Figure 3-3. Airborne thermal infrared remotely sensed water temperature in the mainstem and at
 tributary confluences of the North Fork John Day River, OR, on 4 August 1998. Line indicates
 mainstem, black dots indicate tributary confluences, and dashed vertical lines indicate location of
 tributary confluences along the mainstem. Reprinted with permission from Torgersen et al. (2008).
                  26  -i
                  24  -
              L,  22
               a;

               ro  20
               L.
               0)
               D-
               I  1B
               O
                  16  -
                  14  -
                              10    20     30    40     50    60
                                    Distance downstream (km)
                        70
80
Because water flow is the primary mechanism for downstream transport of chemical substances,
chemical connectivity is closely related to hydrologic connectivity (Sections 2.2 and 3.3.1). The
movement of water across and through landscapes and into river networks integrates potential solute
sources and sinks throughout the watershed. Thus, solute concentrations are an integration of upstream
mixing processes and transport processes in the stream channel. In simplest terms, streams generally
operate in two modes: a high-discharge throughput mode in which solutes and particles entering the
stream channel are quickly transported downstream, and a low-discharge processing mode whereby
solutes and particles are processed or stored near where they entered the river network (Meyer and
Likens, 1979).

Factors that affect hydrologic connectivity (including precipitation patterns and human alterations)
modify these upstream-downstream chemical linkages. For example, the spatial and temporal variability
of rainfall affects chemical connectivity between streams and rivers. Many headwater streams receive
pulsed inputs of water, sediment, organic matter, and other materials during rain events. Periodic flows
in ephemeral or intermittent streams can have a strong influence on biogeochemistry by connecting the
channel to other landscape elements (Valett et al., 2005), and this episodic connection can transmit
substantial amounts of material into downstream rivers (Nadeau and Rains, 2007).

The alternation of dry and flowing periods largely drives the temporal dynamics of chemical
connections between ephemeral and intermittent streams and downstream waters. The frequency,
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duration, magnitude, timing, and rate of change of flow further account for the variable connectivity
observed within and across river networks over space and time (Section 1.2.2). Materials accumulate on
and within dry streambeds where they are temporarily stored and can undergo transformations (Acuna
etal., 2005; Fritz etal., 2006a; Ademollo etal., 2011; Arce etal., 2014). Transmission losses, tributary
confluences, various channel forms, and retention structures also can contribute to the spatial
distribution of materials and processes in dry streambeds (Marcus, 1987; Graf etal., 1991; Reneau etal.,
2004; Taylor and Little, 2013). The onset of flows in ephemeral and intermittent stream channels,
particularly those following long dry periods and initiated by floods (i.e., first flushes), are important in
transporting and transforming large amounts of unique materials for long distances downstream, which
then can have significant effects (e.g., Obermann etal., 2009; Hladyz etal., 2011; David etal., 2012).
Human alteration of channel characteristics (e.g., channel shape and depth) and organic matter inputs
also affect the ability of streams to temporarily store and cycle materials before transport to
downstream waters.

Biogeochemical transformations control the mobility of different chemicals by altering chemical
properties, such as form (e.g., dissolved, colloidal, gravitoidal), bioavailability, and toxicity. Thus,
transformation is a key process influencing the downstream transport and attenuation of chemicals.
Physicochemical (e.g., pH, redox potential, chelator concentration, light, hydrologic residence time) and
biological (e.g., extracellular enzymes, physiology, lipid content) conditions control the location, rate,
and timing of chemical transformations in streams and downstream rivers. For example, the
introduction of stream restoration structures (e.g., small log dams) can affect the spatial distribution of
oxic and anoxic  zones in streambeds and thus biogeochemical cycling and reaction rates for instream
biogeochemical processes throughout the river network (Lautz and Fanelli, 2008). These types of
human alterations, in turn, affect the form of chemical substances and the timing of their transport
downstream (Box 3-1). Data from the Baltimore  Ecosystem Study Long-Term Ecological Research site
suggest that increased hydrologic connectivity from urban infrastructure (e.g., pipes, storm drains,
ditches) in headwaters increases the frequencies of occurrence and transport rates of nutrients, carbon,
and metals to downstream surface waters (Kaushal and Belt, 2012). Urbanization  can cause complex
downstream responses, however, and sometimes creates longer travel times (i.e., reduced downstream
connections). For example, aging infrastructure can leak water and pollutants into ground water rather
than transporting these materials directly downstream.

3.4.1   Nutrients
Studies have documented nutrient-based  chemical connections along river networks. Alexander et al.
(2007) investigated  how stream size affected nitrogen transport in a northeastern U.S. river network.
First-order headwater streams contributed approximately 65% of the nitrogen mass in second-order
streams, and approximately 40% of that mass in fourth-order and higher order streams (Alexander et
al., 2007). Alexander et al. (2000) conducted a study of major regional watersheds of the Mississippi
River basin, which showed that instream nitrogen loss was inversely related to mean stream depth. This
finding most likely resulted from the reduced occurrence of denitrification and settling of particulate
nitrogen in deeper channels, due to reduced contact and exchange between stream water and benthic
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sediments (Alexander etal., 2000). Bb'hlke etal. (2009) used laboratory-, local-, and reach-scale studies
to describe the effect of seasonal and event-based variation of instream properties (e.g., stream depth,
flow rates, temperature) on denitrification rates in headwater streams, which can cause interannual
variations in rates of nitrate export to downstream waters. A dynamic transport model using a one-
dimensional version of the advection-dispersion equation was developed to estimate progressive
instream nitrate removal from first- to fourth-order streams (Alexander etal., 2009). Model simulations
indicated that denitrification rate constants in headwater tributaries varied strongly by season, based on
biogeochemical and hydrologic factors. This in turn had a cumulative effect on downstream nitrate
export (Alexander et al., 2009). These studies highlight how stream size affects nitrogen-based chemical
connections, with headwater streams within the network affecting downstream water quality.

Phosphorus-based chemical connections also have been documented. Doyle et al. (2003) modeled the
relative influence of hydrogeomorphic and uptake processes on longitudinal phosphorus retention
through a river network of first- through sixth-order streams. The model revealed greater variation in
uptake relative to hydrogeomorphic processes, and the authors concluded that uptake processes
influence downstream variation in phosphorus retention at the watershed scale more than
hydrogeomorphology.

Research on hydrologic control and seasonality of nutrient export from streams in the Mississippi River
basin similarly provides evidence of downstream connectivity (Section B.4.3.2.1). Export of dissolved
reactive phosphorus from second-  and fourth-order streams in agricultural watersheds occurred  mainly
during high-discharge conditions, with discharges equal to and greater than the 90th percentile
exporting 84% of the dissolved reactive phosphorus, primarily during January and June (Royer et al.,
2006). Similar patterns have been documented in total phosphorus concentrations of first- through
fourth-order streams from another Mississippi River basin (Bayless et al., 2003). In another study,
researchers modeled riverine dissolved reactive phosphorus yield of 73 watersheds within the
Mississippi River basin during the January to June period, as a function of nutrient sources and
precipitation (Jacobson et al., 2011). Riverine dissolved reactive phosphorus yield was positively related
to fertilizer phosphorus inputs, human sources of phosphorus (e.g., sewage effluent), and precipitation,
which generates surface runoff that moves fertilizer applied to the landscape into streams and rivers
that then transport it downstream  (Jacobson et al., 2011). These studies demonstrate the connections
and processes by which nutrients exported  from streams in the Mississippi River basin contribute to
anoxia in the Gulf of Mexico (Rabalais etal.,  2002).

Other environmental and biological processes also can affect nutrient-based chemical connections. The
underlying geology of the Mokelumne River in California's central Sierra Nevada Mountains affected the
spatial and temporal variability in chemical connections. Holloway et al. (1998) examined water quality
in that watershed to identify primary sources of nitrate entering downstream reservoirs. They
conducted a paired watershed comparison with two ephemeral streams in nearby watersheds that were
underlain with different rock types (diorite  vs. biotite schist) but had similar land-use, vegetation,
topography, and watershed area. Many samples from the diorite watershed had nitrate concentrations
below detection limits (<4  uM), with  a median concentration of 3.3 uM; concentrations were not
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strongly associated with the start or end of the high precipitation period. In the biotite schist watershed,
maximum stream concentrations of nitrate (>300 uM) occurred at the start of the high precipitation
period, and concentrations decreased over time. A nearby perennial stream, also in a biotite schist
watershed, displayed this same temporal trend, with highest nitrate concentrations at the beginning of
the rainy season and decreasing concentrations during the spring. Holloway et al. (1998) concluded that
biotite schist streams contributed a disproportionately large amount of total nitrate to downstream
reservoirs, despite draining only a small area of the entire watershed.

In another study, nitrate concentrations were measured at 50 sites across the West Fork watershed of
the Gallatin River in southwestern Montana's northern Rocky Mountains under different hydrologic
conditions and across two seasons, growing and dormant (Gardner and McGlynn, 2009). Streams ranged
from first-order mountain streams to fourth-order streams near the West Fork-Gallatin River
confluence. In the dormant season, the distance over which nitrate concentrations were  spatially
correlated ranged from 3.2 to 5.5 km. In the growing season, this range decreased to 1.9  to 2.7 km. This
seasonal difference likely resulted from greater biological uptake and use of nitrate during the growing
season, which then limited its downstream transport; during the dormant season, downstream
transport increased, resulting in greater spatial dependence in nitrate concentrations (Gardner and
McGlynn, 2009).

Seasonal variability in chemical connectivity also was observed in Arizona's San Pedro River. Differences
in dissolved organic nitrogen concentration were detected among three  segments of the river during the
dry season, but stream water was well mixed, the system was hydrologically connected,  and no
differences in dissolved organic nitrogen concentration were detected during the wet season (Brooks
and Lemon, 2007). These seasonal differences occur because nitrogen accumulates locally atvarying
levels during drier periods but is mixed and transported downstream during large, infrequent storm
events, making nitrogen concentrations more longitudinally uniform (Fisher et al., 2001).

Peterson et al.  (2001) examined chemical connectivity by studying similar network components across
different types of river networks. After measuring nitrogen export from  12 headwater streams
distributed throughout the contiguous United States, Alaska, and Puerto Rico, they found that uptake
and transformation of inorganic nitrogen were most rapid in the smallest headwater streams (Peterson
etal., 2001). Given the prevalence of headwater streams on the landscape (Section 3.2) and their
hydrologic connectivity to other river network components (Sections 2.2 and 3.3.1), headwater stream
nitrogen processing can improve water quality in downstream waters. Many other studies also highlight
the importance of nitrogen processing in headwater streams (e.g., Hill et al., 1998; Hill and Lymburner,
1998; Triska etal., 2007). Mulholland et al. (2008) measured in situ rates of nitrate removal by
denitrification in 72 streams across different biomes and used those rates to model how headwater and
larger streams in a river network respond to simulated nitrate loading increases. At low loading rates,
the biotic removal of dissolved nitrogen from water is high and occurs primarily in headwater streams,
which reduces loading to larger streams and rivers downstream. At moderate loading rates, the ability
of headwater streams to remove  nitrogen is reduced, but larger streams can remove the excess nitrogen.
At high loading rates, removal by headwater streams and larger streams in the river network is
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ineffective, resulting in high nitrogen export to rivers (Mulholland et al., 2008). Similar results were
obtained by Wollheim et al. (2008) in the Ipswich River, MA.

Helton etal. (2011) conducted simulation experiments that illustrated the effects of connectivity in the
Ispwich River (MA) and Flat Creek (WY) networks, via the use of river-network models of nitrate
dynamics. The nitrate models underpredicted nitrogen removal in many reaches, which was attributed
to connections between the river channels and neighboring wetlands that were not characterized by the
model and that functioned as nitrogen sinks (Section 4.3.3.2). By not representing the fine-scale
variability in nitrogen uptake in river-network models and assuming that nitrogen uptake decreases
with depth along a river network, simulations can potentially misrepresent the export of nitrogen from
headwater streams to downstream waters (Darracq and Destouni, 2005, 2007). The potential for this
misrepresentation, however, depends on the spatial scale of the study and the specific characteristics of
the river network.

The influences of headwater and other tributary streams on nutrient concentrations in larger
downstream waters, as detailed in the numerous examples above, reflect the combined processes of
nutrient cycling and downstream transport that occur throughout river networks, albeit most
intensively in headwater streams. The concept of nutrient spiraling provides an approach to quantifying
these cycling and transport processes and a relatively simple framework for understanding their
implications. As nutrients cycle through various forms or ecosystem compartments, being consumed
and regenerated for reuse, they complete a "cycle" only after having been displaced some distance
downstream, which stretches the cycle into a helix or "spiral" (Webster and Patten, 1979). The stretch of
the spiral, or the openness between its loops, is primarily determined by flow, whereas the diameter of
the loops is mainly determined by biological activity (Cummins et al., 2006). Nutrients such as dissolved
phosphorus and nitrogen, which enter the stream via ground-water or overland flow, are removed from
the water column by algae and microbial organisms. These nutrients are then consumed by organisms at
higher trophic levels, transported farther downstream as suspended particles, or returned to the
dissolved pool through cell death and lysis. Nutrients flowing through the food web also are regenerated
to the dissolved pool via excretion and microbial decomposition. Nutrients in the dissolved, particulate,
and living tissue phases of the cycling process are subject to downstream transport, such that each
phase transition moves some distance downstream. The average downstream distance associated with
one complete cycle—from a dissolved inorganic form in the water column, through microbial uptake,
subsequent transformations through the food web, and back to a dissolved available form—is termed the
"spiraling length."

Although measurement of total spiraling length requires detailed study of tracer dynamics through
multiple compartments of the stream ecosystem, Newbold et al. (1981; 1983a) have shown that it can be
approximated by "uptake length" or the distance traveled in the water column before algal and
microbial assimilation occurs. Uptake lengths for phosphorus and nitrogen can be estimated precisely
only from tracer additions of radioactive or stable isotopes, but they can be roughly estimated from
experimental additions that briefly raise the concentration of the natural form of the nutrient Ensign
and Doyle (2006) compiled results of 404 measurements of uptake length of phosphate, ammonium, and
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nitrate in streams and rivers ranging from first- to fifth-order. For a given stream order, they estimated
the number of cycles that each nutrient had undergone as the ratio of median uptake length to the
average length of stream for that stream order (from Leopold et al., 1964). They found that the three
nutrient forms cycle between roughly 8 (nitrate) and 40 (ammonium) times within the length  of a first-
order stream, and between roughly 8 and 90 times within the respective lengths of first- to fourth-order
streams.

Withers and Jarvie (2008) also compared phosphorus uptake lengths among different streams. Shorter
uptake lengths are indicative of more rapid phosphorus cycling and greater efficiency of phosphorus
retention. The shortest uptake lengths (2-580 m) were in first-order streams that drained "pristine"
watersheds. Uptake lengths were longer (26-3,460 m) in second- to fourth-order streams that drained
agricultural watersheds, and longest (4,140-367,000 m) in fifth-order rivers that drained a mixture of
urban and agricultural land use (Withers and Jarvie, 2008).

These studies highlight the high nutrient-processing potential of headwater streams. This potential
results from their low water volume-to-bed sediment area ratio, which enhances conditions for key
nutrient uptake processes (e.g., adsorption, precipitation, assimilation) not only at the water-bed
interface but within the streambed sediments (Withers and Jarvie, 2008). Downstream ecosystems
depend on processes that occur in headwater streams. Given that roughly half the water reaching larger
tributaries and rivers originates from headwater streams (Section 3.3.1), the results of Ensign  and  Doyle
(2006) make clear that phosphorus and nitrogen arrive at downstream waters having already been
cycled many times in headwater and smaller tributaries. This cycling is, fundamentally, a complex of
ecosystem processes that intensively uses nutrients and then regenerates them for delivery to
downstream waters much in their original form. Because nutrients undergo transformations across
various forms (e.g., dissolved, particulate, inorganic, or in living organisms) while being transported
downstream (i.e., spiraling), explicitly identifying their exact origin in the network can be difficult.

Although headwater nutrient cycling, or spiraling, functions largely to deliver regenerated nutrients
downstream, headwater stream processes measurably alter the delivery of nutrients to downstream
waters in many ways. For example, if cycling has been seriously impaired such that nutrient
regeneration is inhibited or nutrients are generated in biologically unavailable or toxic forms, the
downstream effects could be large. Nutrients taken up as readily available inorganic forms can be
released back to the water column as organic forms (Mulholland et al., 1988) that are less available for
biotic uptake (Seitzinger etal., 2002). Similarly, nutrients incorporated into particles are not entirely
regenerated (Merriam et al., 2002; Hall et al., 2009), but rather accumulate and contribute to
longitudinally increasing particulate loads (Whiles and Dodds, 2002). The amount of phosphorus and
nitrogen delivered downstream by headwater streams cycles seasonally due to the accumulation of
nutrients in temporarily growing streambed biomass (Mulholland and Hill, 1997; Mulholland et al.,
2004). Such variations affect downstream productivity (Mulholland et al., 1995) and help explain the
seasonality in the spatial correlations of nutrient concentrations described above.
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Microbially mediated transformations affect the forms of nitrogen transported from headwater streams
to downstream waters, and these transformations can influence—and be influenced by—human
alterations of the landscape. Nitrification, or the transformation of ammonium to nitrate, occurs
naturally in undisturbed headwater streams (e.g., Bernhardt et al., 2002) but increases sharply in
response to ammonium inputs (e.g., Newbold et al., 1983b), thereby reducing potential ammonium
toxicity from pollutant inputs (Chapra, 1996). Denitrification, which removes nitrate from stream-water
through transformation to atmospheric nitrogen, is also widespread among headwater streams, as
demonstrated by stable isotope tracer additions to 72 streams in the conterminous United States and
Puerto Rico (Mulholland etal., 2008). Mulholland etal. (2008) estimated that headwater streams
(<100 L s"1, about third order or less) free from agricultural or urban impacts reduce downstream
delivery of nitrogen by 20-40%. Alexander etal. (2007) and Wollheim et al. (2008), using earlier and
less extensive measurements of denitrification rates, estimated nitrogen removal of 8 and 16% by
stream networks of first to third order and first to fifth order, respectively. In headwater agricultural
streams, denitrification in stream sediments might not be effective at removing nitrate from stream
water because of altered hydrology. In watersheds with tile drains and channelized headwaters, stream
nitrate concentration is positively correlated with stream discharge, suggesting that these altered
streams are in throughput mode, whereby nitrate inputs are rapidly transported downstream with little
retention or processing (Royer et al., 2004).

Small tributaries also affect the downstream delivery of nutrients through abiotic processes. Meyer and
Likens (1979) showed that phosphorus concentrations in a forested first-order New Hampshire stream
were reduced by sorption to stream sediments. A much stronger  sorption of phosphorus by stream
sediments was observed by Simmons (2010) in first- to third-order West Virginia streams impacted  by
acid mine drainage, where phosphorus sorbed  to metal hydroxide precipitates introduced by mine
drainage. These examples further illustrate the potential for headwater streams to absorb nutrient
impacts to the benefit of downstream waters.

3.4.2   Dissolved and Particulate Organic Matter
Headwater streams supply downstream waters with dissolved and particulate organic carbon, which
support biological activity throughout the river network. Organic carbon enters headwater streams
from the surrounding landscape, including wetlands (Section 4.3.3.4 and 4.4.3.1), in the form of
terrestrial leaf litter and other seasonal inputs, dissolved organic carbon (DOC) in subsurface and
surface runoff, and fine particulate organic matter (including eroded soil) in surface runoff. Headwater
reaches also export organic carbon produced within the stream by photosynthesis, both as DOC (Kaplan
and Bott, 1982)  and suspended particles (Marker and Gunn, 1977; Lamberti and Resh, 1987).

Agren etal. (2007) determined that headwater streams exported the largest amount of terrestrial DOC
on a per unit basis in the Krycklan watershed in Sweden. The amount of organic matter exported from
headwater streams to downstream waters varies with multiple factors, including surrounding land use.
For example, Schelker et al. (2014) developed a mixing-model approach and quantified that forest
harvesting at areal proportions of 11% and 23-25% of a northern Sweden watershed induced stepped

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increases in DOC delivery, due to disturbance of shallow forest soils and subsequent transport from
headwaters to downstream locations. Similarly, a 20% increase in downstream DOC concentrations was
predicted folio wing forest harvesting in the headwater areas of the H.J. Andrews Long Term Ecological
Research site, using the VELMA (Visualizing Ecosystems for Land Management Assessments) model
(Abdelnour etal., 2013). In southeast Arizona, Meixner etal. (2007) found that DOC consistently
doubled to tripled in the San Pedro River during storm events from a flush of terrestrial organic matter
and nutrients. This is comparable to the flush response observed by others (Fisher et al., 1982; Brooks et
al., 2007) during monsoon precipitation events in the southwestern United States. These examples
further demonstrate connectivity of headwater streams and their cumulative effects on downstream
water quality.

Fisher and Likens  (1973) followed the fate of these inputs in a forested headwater stream in New
Hampshire. They concluded that 34% of inputs were mineralized through respiration by consumers and
microbes within the headwater stream, which represented the "ecosystem efficiency" of the reach. The
remaining 66%  was exported downstream and constituted, as Fisher and Likens (1973) observed, "...
inputs to the next stream section where they are assimilated, or passed on (throughput) or both." Other
studies have reported similar amounts of export. Webster and Meyer (1997) compiled organic matter
budgets from 13 North American first- and second-order streams. The median ecosystem efficiency was
31%, implying a median export of 69% of organic matter inputs. A large body of literature has
demonstrated that headwater streams modify and export organic carbon that significantly affects
ecosystem processes throughout the river network.

Vannote et al. (1980) recognized that exported carbon was not simply the unutilized fraction but was
also greatly modified in character. A basic tenet of their River Continuum Concept is that longitudinal
variations in the structure of stream ecosystems reflect, in part, the cumulative effects of upstream
organic matter processing. Much or most of the organic carbon exported from headwater streams has
been altered either physically or chemically by ecosystem processes within the headwater reaches. Leaf
litter contributes an average of 50% of the organic matter inputs to forested headwater streams
(Benfield, 1997), but leaves and leaf fragments (>1  mm) accountfor only 2% or less of organic matter
exports (Naiman and Sedell, 1979; Wallace etal., 1982; Minshall etal., 1983). The conversion of whole
leaves to fine particles (<1 mm) involves physical abrasion, microbial decomposition, and invertebrate
feeding and egestion (Kaushik and Hynes, 1971; Cummins et al., 1973; Petersen and Cummins, 1974).
The rate of that  conversion is affected by whether the leaves are in an aerobic environment, such as
riffles, or an anaerobic environment, such as depositional pools (Cummins et al., 1980). Feeding
activities of aquatic invertebrates called "shredders" break down leaves that have entered streams
(Cummins and Klug, 1979; Cummins etal., 1989). Invertebrate activity is particularly important, as
demonstrated by large reductions of fine particle export following experimental removal of
invertebrates from a headwater stream (Cuffney et al., 1990; Wallace et al., 1991). Strong invertebrate
influence on fine particle export also has been inferred from analysis of seasonal (Webster, 1983) and
daily (Richardson  et al., 2009) variations.
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Downstream organisms consume organic carbon exported from headwater streams, supporting
metabolism throughout the river network. In part, this results from direct consumption of detrital
organic matter (Wallace et al., 1997; Hall et al., 2000), but much of the metabolic consumption of organic
matter in streams occurs via microbial decomposition (Fisher and Likens, 1973). The microbes
themselves are then consumed by other organisms (Hall and Meyer, 1998; Augspurger et al., 2008),
whose energy in turn supports the food web through what is known as the "microbial loop" (Meyer,
1994). In addition to transformations associated with microbial and invertebrate activity, organic
matter in streams can be transformed through other processes such as immersion (Corti et al., 2011)
and abrasion (Paul etal., 2006); photodegradation also can be important in ephemeral and intermittent
streams where leaves accumulate in dry channels exposed to sunlight (Dieter et al., 2011; Fellman et al.,
2013).

The organic carbon turnover length, derived from the nutrient spiraling concept (Section 3.4.1; Newbold
et al., 1982b), is a measure of the downstream fate of exported carbon. Carbon turnover length is the
ratio of the downstream flux of organic carbon to ecosystem respiration per length of stream. It
approximates the average distance that organic carbon would travel before being consumed and
mineralized by aquatic organisms. Carbon turnover length for first-order streams is on the order of 1 to
10 km (Newbold et al., 1982b; Minshall et al., 1983), suggesting that organic carbon exported from
headwater streams is likely to be used primarily in the somewhat larger streams to which they are
direct tributaries (i.e., second- or third-order streams). The carbon turnover length, however, actually
represents a weighted average of widely varying turnover lengths associated with the diverse array of
particulate and dissolved forms of organic carbon in stream and river ecosystems (Newbold, 1992).
Turnover lengths of specific organic carbon forms can be estimated if their rates of downstream
transport and mineralization (or assimilation) are known. For example, Webster et al. (1999) estimated
a turnover length of 108 m for whole leaves in a North Carolina second-order stream, but a much longer
turnover length of 40 km for fine (<1 mm) organic particles. Newbold et al. (2005) obtained similar
estimates of 38 and 59 km for the turnover lengths of two different size fractions of fine organic
particles in a second-order Idaho stream. Kaplan et al. (2008) concluded that DOC in a third-order
southeastern Pennsylvania stream consisted of a rapidly assimilated "labile" fraction with a turnover
length of 240 m, a more slowly assimilated "semilabile" fraction with a turnover length of 4,500 m, and  a
"refractory" fraction with immeasurably slow assimilation, implying an indefinitely long turnover length
sufficient to carry the carbon to coastal waters.

Because turnover length increases with stream size, organic carbon that travels to a larger order stream
is likely to travel farther than its original turnover length predicts (Minshall et al., 1983; Webster and
Meyer, 1997). For example, the organic carbon turnover length of the Salmon River, ID increased from
3.7 km in a second-order headwater stream to 1,200 km in the eighth-order reach, about 600 km
downstream (Minshall et al., 1992). In a modeling study, Webster (2007) estimated that turnover length
increased from several hundred meters in the headwater streams to greater than 100 km in a large
downstream river. This progression of increasing turnover length from headwater streams to
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increasingly larger streams and rivers implies that organic carbon exported from headwaters supports
metabolism throughout the river network.

Although turnover length reflects the spatial scale over which upstream exports of organic carbon are
likely to support downstream metabolism, it does not provide direct evidence for or quantify the actual
use of organic carbon in downstream reaches. Studies of transport and mass balance throughout the
river network provide such evidence. Shih et al. (2010) applied the SPARROW (SPAtially Referenced
Regressions On Watershed attributes) model to organic carbon data from 1,125 monitoring sites
throughout the conterminous United States. They estimated that all river reaches (large and small)
delivered an annual average of 72 kg C ha-1 of incremental drainage area, whereas the river systems as a
whole exported 30 kg C ha-1. Thus, 58% of carbon inputs were respired within the river networks, while
the rest (42%) were transported downstream. Shih et al. (2010) did not specify the proportion of inputs
originating from headwater streams, but using their results (with certain assumptions), we can estimate
the amount of organic carbon in river networks that originates from headwater streams. We begin with
the proportion of carbon originating from allochthonous sources as 0.78 (Shih etal., 2010). If we assume
that the proportion of headwater streams in a drainage area is 0.50 (Section 3.2; Alexander etal., 2007;
Caruso and Haynes, 2011), headwater streams then provide 0.39 (= 0.78 x 0.50) of the total organic
carbon supply, with the input from the larger downstream network being 0.61  (i.e., 61%) of the carbon
supply. Using the ecosystem efficiency for headwater streams of 31% (Webster and Meyer, 1997), the
proportion of carbon originating from headwater streams that is delivered downstream is 0.39 x (1 -
0.31) = 0.27. The proportion of carbon exported from headwater streams (0.27), plus the proportion of
carbon input directly to the downstream network (0.61), equals the total carbon input to the
downstream network (0.88). Thus, 31% (= 0.27/0.88 x 100) of the total carbon supplied to downstream
reaches originates from headwater streams.

Most terrestrial organic matter that enters headwater streams is transported downstream (Gomi et al.,
2002; MacDonald and Coe, 2007), typically as fine particulate or dissolved organic matter (Bilby and
Likens, 1980; Naiman, 1982; Wallace et al., 1995; Kiffney et al., 2000). These headwater streams also can
export significant amounts of autochthonous organic matter via the downstream transport of benthic
algae (Swanson and Bachmann, 1976). Both allochthonous and autochthonous organic matter can be
transported significant distances downstream (Webster et al., 1999), especially during high flows
(Bormann and Likens, 1979; Naiman, 1982; Wallace etal., 1995). The importance of discharge in
determining organic matter transport dynamics highlights the interdependence of physical and
biological connections within the river network. For example, Wallace et al. (1995) examined coarse
particulate organic matter export in three headwater streams in North  Carolina and found that 63-77%
of export over a 9-year period occurred during the 20 largest floods. This finding suggests that
headwater streams (including ephemeral and intermittent streams) can provide temporary storage for
organic matter (Gomi et al., 2002), which is then transported downstream during storms or snowmelt.
Exports also can vary seasonally, increasing in autumn and winter when deciduous trees drop their
leaves (Wipfli et al., 2007) and in the spring when flowers and catkins are shed.
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The amount of organic matter exported from headwater streams can be large, and often depends on
factors such as discharge, abiotic retention mechanisms within the channel (Bilby and Likens, 1980),
biological communities (Cuffney et al., 1990), and the quality and quantity of riparian vegetation in
headwater watersheds (Wipfli and Musslewhite, 2004). For example, Wipfli and Gregovich (2002) found
that organic matter export ranged from <1 to 286 g of detritus (dead organic matter) per stream per day
in 52 coastal headwater streams in Alaska. When debris dams were removed from a New Hampshire
headwater stream, export of fine particulate organic carbon increased by 632% (Bilby and Likens,
1980). The longitudinal discontinuities created by logjams and beaver dams slow the downstream
transport of organic matter, enabling instream organisms to process the carbon and slowly leak material
downstream (Wohl and Beckman, 2014). The strong links among organic matter storage, processing,
and downstream transport in ephemeral streams of the southwestern United States can be seen in the
distribution of organic matter of varying quality and mobility over periods with varying rainfall
intensities (Norton et al., 2007). Arroyos or ephemeral channels in northeastern New Mexico are
important in transporting and transforming organic matter that enhances the fertility of agricultural
areas along downstream alluvial fans. More frequent but low-intensity rainfall was important in driving
biochemical transformations that altered organic matter mobility and quality, which was subsequently
transported downstream by larger storms (Norton et al., 2007). Traditional farming practices in the
region relied on the temporary storage, transformation, and transport of organic matter from ephemeral
streams (Norton et al., 2007; Sandor et al., 2007).

Although organic matter clearly is exported from headwater streams, effects on downstream organisms,
and the distance over which these effects propagate are difficult to quantify (Wipfli et al., 2007). Many
downstream organisms rely on organic matter and its associated microbes for food, but demonstrating
where in the river network such material originates presents a challenge. Similarly, the conversion of
organic matter to other forms (e.g., invertebrate or fish biomass via consumption), each with its own
transport dynamics, makes tracking sources of downstream  contributions difficult. Given the prevalence
of headwater streams in both the landscape and the river network (Leopold et al., 1964), and their
primacy in organic matter collection and processing, a  logical conclusion is that headwater streams
exert a strong influence on downstream organic matter dynamics. Benstead and Leigh (2012) estimated
that headwater streams, including intermittent and ephemeral channels, result in a global carbon efflux
of 1.6 Pg C yr1, making the overall contributions of rivers and streams about equivalent to all inland
lakes and wetlands combined. In addition, headwater streams also serve as a source of colonists for
downstream habitats (Section 3.5). For example, headwater  springs can provide algae a winter refuge
from freezing, then serve as a source of propagules for downstream reaches upon spring thaws (Huryn
etal.,2005).

3.4.3   Ions
Measurements of ions and conductivity from nested study designs provide additional evidence for
connectivity by various transport mechanisms. Rose (2007)  collected data at 52 sampling stations in
Georgia's Chattahoochee River basin, which includes the heavily urbanized region of Atlanta, over a
2-year period. The study sought to characterize baseflow hydrochemistry across  a rural-to-urban land-
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use gradient. A plot of the major ion (sodium, bicarbonate alkalinity, chloride, and sulfate)
concentrations versus downstream river distance showed distinct peaks relative to baseflow
measurements, with elevated concentrations persisting downstream.

In a study of mined and unmined streams in the Buckhorn Creek basin in Kentucky, water
measurements taken at several locations within the same tributary had similar conductivity values
(Johnson et al., 2010). As expected, confluences disrupted this spatial similarity along the river network.
Conductivity values along the mainstem decreased at confluences with unmined streams and increased
at confluences with mined streams, demonstrating that headwater streams were transporting ions
downstream and affecting downstream conductivity. This spatial pattern in conductivity was consistent
between spring and summer surveys of the river network.

In a study in Sweden, measurements of pH from the outlets of seven watersheds were statistically
related to headwater pH measurements in those watersheds (Temnerud et al., 2010). As pH at outlets
increased under low-flow conditions, so did median pH of the headwater streams. This study illustrates
the connectivity between the headwater components of the river network and the outlets of the
watersheds and the cumulative effects of headwater streams to downstream waters.

3.4.4   Contaminants and Pathogens
The movement of contaminants—that is, substances that adversely affect organisms when present at
sufficient concentrations—and waterborne pathogens provides another line  of evidence for chemical
connectivity between tributaries and the river network. Existing information typically has been derived
from either empirical experiments that release tracer substances into  streams to monitor movement
along a longitudinal gradient or the use of modeled projections and characterization  of contaminants.
Studies also have examined trace metal data  collected at multiple sites throughout a specific watershed,
relative to a point source or a complex mixture of point-source inflows (e.g., active mining areas,
wastewater treatment plant discharges). These studies provide a way to understand sediment transport
in streams and rivers and to determine how metals are spatially and temporally dispersed in the
watershed (Rowan etal., 1995).

The degree of surface-water and ground-water mixing or exchange in  the hyporheic zone influences the
transport and uptake of trace metals. In a 7 km perennial stream segment contaminated by copper
mining in Arizona, 20% of the dissolved manganese load was removed by microbial activity that was
likely stimulated by the physicochemical conditions and increased residence time (compared with
surface channel residence  time) associated with hyporheic exchange (Harvey and Fuller, 1998). That
oxidation of manganese enhanced the uptake of other trace metals and thereby decreased cobalt, nickel,
and zinc loads 12-68% over the 7 km reach (Fuller and Harvey, 2000). Modeling the contributions of
hyporheic exchange on contaminant dynamics over entire river networks requires further research.

Another example of chemical connections along the river network is how inputs of water associated
with natural gas (coalbed methane) extraction and hardrock mining can influence trace element and
dissolved solute concentrations in perennial  rivers. Patz etal. (2006) examined trace elements and other

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water quality parameters in ephemeral streams resulting from coalbed methane extraction activities
that are connected to the perennial Powder River, WY. Iron, manganese, arsenic, fluoride, dissolved
oxygen, pH, and turbidity differed across sample locations, demonstrating connectivity between
wellhead discharge and ephemeral streams. The contribution of ephemeral streams was detected in the
Powder River, where pH was consistently elevated downstream of the confluence with a high-pH stream
(Patzetal., 2006).

In a broader study, Wang et al. (2007) used retrospective USGS data (1946-2002) to investigate spatial
patterns in major cation and anion concentrations related to coalbed methane development in the
Powder River basin (33,785 km2) in Wyoming and Montana. The study indicated that coalbed methane
development could have detrimental effects on the Powder River, especially in terms of sodium
adsorption ratio (sodicity). Although the authors indicated connectivity and adverse effects in stream
quality with increased sodium and stream sodicity, data also revealed inconsistent patterns associated
with complex spatial variability within the drainage basin due to the geographic distribution of the
coalbed methane wells.

The spatial extent of metal transport has been demonstrated in the upper Arkansas River of Colorado,
where the headwaters have been affected by past mining activities (Kimball et al., 1995). Bed sediments
sampled from the headwaters to approximately 250 km downstream showed an inverse relationship
between sediment cadmium, lead, and zinc concentrations and downstream distance. That same spatial
distribution pattern in bed sediment metal concentrations was observed from headwater streams to the
downstream Clark Fork River in Montana, which has been impacted by mining and smelting activities in
its headwaters  (Axtmann and  Luoma, 1991). Based on regression models, bed sediment metal
concentrations from river sites were inversely related to downstream distance, and predictions from
those models indicated that sediments with metals originating from headwater mining and smelting
areas were reaching Lake Pend Oreille, more than 550 km downstream. Hornberger et al. (2009) used a
19-year data set from the Clark Fork River, with sites from the headwater streams to 190 km
downstream, and found that bed sediment copper concentrations at downstream sites were positively
correlated with concentrations at upstream sites.

Lewis and Burraychak (1979) examined the downstream transport of heavy metals from ephemeral and
intermittent streams to a downstream perennial stream, due to the impacts of active and abandoned
copper mines. Water chemistry in Pinto  Creek was monitored biweekly for 2 years at four stations, one
above and three below a point discharge associated with the Pinto Valley Mine in east-central Arizona
(Lewis and Burraychak, 1979). Surveys offish, aquatic macroinvertebrates, and vegetation were
conducted during the same period at 13  sampling stations along the total stream length. Contaminants
from the Pinto Valley Mine entered Pinto Creek via accidental discharge of waste from tailings ponds
(Lewis, 1977). Monitoring revealed that mine wastes comprised up to 90% of total flow in Pinto Creek,
and that most chemical parameters increased in concentration below the discharge point, then
decreased progressively downstream (Lewis and Burraychak, 1979). Increases in sulfate, conductivity,
and total hardness between above-mine and below-mine locations were most apparent, although
increases in heavy metals and suspended solids were considered most detrimental to organisms.
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Suspended solids settled in and buried intermittent channels, which contained up to 50 cm of mine-
waste sediment; these sediments were present all the way to the stream terminus. Increased heavy
metal concentrations in the food web and sediments also were detected below the discharge point
(Lewis and Burraychak, 1979).

Lampkin and Sommerfeld (1986) similarly showed that intermittent streams can contribute highly
mineralized, acidic waters to a downstream perennial reach, in a study that characterized acid mine
drainage impacts on water and sediment chemistry (particularly major cations, silica, sulfate, selected
heavy metals, and acidity) in Lynx Creek, a small intermittent stream in east-central Arizona. Six
stations, two above and four below an abandoned copper mine, were monitored (water and sediment
samples) monthly for 1 year. Specific conductance, pH, and dissolved ion concentrations varied with
proximity to the mining complex. Concentrations of most constituents were higher near the mine and
progressively decreased downstream toward the terminus of Lynx Creek, due to precipitation and
dilution by headwater streams. All heavy metal and sulfate concentrations were higher at the immediate
discharge location versus the above-mine stations; sulfate concentrations downstream of mine-drainage
inputs also significantly differed from the rest of the creek. Sediments throughout the creek were high in
metals, suggesting downstream transport of contaminated sediments. Acid-mine  drainage from the
mine had a major but mostly localized impact on Lynx Creek.

As discussed in previous sections, headwater streams are connected to downstream waters through the
transport of chemicals but also through transformation processes. Boreal river networks, in which
headwater streams are sources of DOC and pH increases downstream, provide these transformations.
Iron exported from the acidic headwater tributaries  is bound to DOC (mobile form). As pH increases,
iron-rich ground water enters the channel, and iron transforms to iron (oxy) hydroxides that aggregate
and precipitate out of solution (Neubauer etal., 2013). These iron (oxy) hydroxides can function as
carriers of toxic metals and metalloids  (e.g., arsenic), thereby removing them from solution and
temporarily storing them in and along the river network  (Neubauer et al., 2013).

Several studies also have projected the cumulative effect of headwater systems on downstream mercury
concentrations and loads in response to land use, climate, and atmospheric deposition. The Water
Quality Analysis Simulation Program and the Bioaccumulation and Aquatic System Simulator models
were used to predict changes in water, sediment, and fish-tissue mercury concentrations across water
bodies with varying upstream headwater drainage areas  (Knightes et al., 2009). Simulations predicted
that watersheds with high headwater drainage densities would exhibit longer lag times for mercury
delivery downstream compared to those with low headwater drainage densities.  This work suggests
that headwater streams can serve a mercury storage function, and that temporally varying connectivity
contributes to the transport of mercury from headwater streams to downstream waters.

The cumulative effects of land-cover change on total and methylmercury fluxes from a North Carolina
headwater watershed to the Cape Fear River were simulated using the  Grid Based Mercury Model
(Golden and Knightes, 2011). The simulations estimated a 95% increase in total mercury fluxes from the
landscape to downstream waters in response to new suburbanization and a 7% decrease in total and

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methylmercury export in response to reforestation. Predicted changes in total mercury fluxes from the
landscape to the downstream assessment point resulted primarily from changes in landscape land
cover, rather than changes in connections within the river network.

The effects of climate change on total mercury export from headwater tributaries draining a Coastal
Plain watershed (79 km2) in South Carolina were simulated using multiple watershed models (Golden et
al., 2014). Results indicated increased total mercury export under the high-precipitation scenario and
decreased total mercury export under the low-precipitation scenario, showing that precipitation, and
thus hydrologic connections, drive mercury transport from headwater streams to downstream waters.

Contaminants are commonly transported from tributaries to downstream rivers bound to sediments.
Using isotopic fingerprinting, Gehrke et al. (2011) identified different tributaries as contributing to
downstream mercury contamination of surface sediments in San Francisco Bay. Historic gold mining in
the tributary watersheds of the San Joaquin and Sacramento Rivers contributed to contaminated
mercury sediments in the northern part of San Francisco Bay, whereas wastes from mercury mine
operations were delivered to the southern part of the bay via the Guadalupe River (Gehrke et al., 2011).

Studies of radionuclide (e.g., plutonium, thorium, uranium) distribution, transport, and storage provide
convincing evidence for long-distance chemical connections in river networks. Although the natural
occurrence of radionuclides  is extremely rare, their production, use, and release for military and energy
applications have been monitored for more than 50 years. Like metals, radionuclides adsorb readily to
fine sediment; thus, the fate  and transport of radionuclides in sediment generally mirrors that of fine
sediment. From 1942 to 1952, plutonium dissolved in acid was discharged untreated into several
intermittent headwater streams that flow into the Rio Grande at the Los Alamos National Laboratory,
NM (Graf, 1994; Reneau et al., 2004). These intermittent headwaters drain into Los Alamos Canyon
(152 km2 drainage area), which joins the Rio Grande approximately 160 km upriver from Albuquerque.
Also during this time, nuclear weapons testing occurred west of the upper Rio Grande near Socorro, NM
(Trinity blast site) and in Nevada. The San Juan Mountains in the northwestern portion of the upper Rio
Grande basin (farther upstream from the site where Los Alamos Canyon enters the Rio Grande) is the
first mountain range greater than 300 m in elevation east of these test locations. The mountains
therefore have higher plutonium concentrations than the latitudinal and global averages because of
their geographic proximity to the test sites. The mountain areas are steep with thin soils, so plutonium
from testing fallout was readily transported to headwater streams in the upper Rio Grande basin via
erosion  and subsequent overland movement. The distribution of plutonium within the Rio Grande
illustrates how headwater streams transport and store  contaminated sediment that has entered the
basin through both fallout and direct discharge. Although Los Alamos Canyon represented only 0.4% of
the drainage area at its confluence with the Rio Grande, its mean annual bedload contribution of
plutonium was almost seven times that of the mainstem (Graf, 1994). Much of this contribution occurred
sporadically during intense storms that were out of phase with flooding on the upper Rio Grande. Total
estimated contributions of plutonium to the Rio Grande are approximately 90% from fallout to the
landscape and 10% from direct effluent at Los Alamos National Laboratory (Graf, 1994). Based on
plutonium budget calculations, only about 10% of the plutonium directly discharged into Los Alamos
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Canyon and less than 2% of the fallout over the upper Rio Grande basin have been exported to the Rio
Grande. Much of the plutonium is adsorbed to sediment and soil that has either not yet been transported
to the river network or is stored on floodplains or in tributary channels (Graf, 1994). Approximately
50% of the plutonium that entered the Rio Grande from 1948 to 1985 is stored in the river and its
floodplain; the remaining amount is stored in a downriver reservoir. Similar export of radionuclides
through a river network has been traced following the Fukushima Dai-ichi Nuclear Power Plant accident
in Japan (Chartin etal., 2013). The highest levels of radionuclide falloutwere in areas drained by
headwater tributaries. Isotopic analysis of sediment-bound radionuclides collected from throughout the
river network over time documented the downstream transfer of contaminated sediment during a
succession of summer typhoons and spring snowmelt (Chartin etal., 2013).

Waterborne pathogens (bacteria, viruses, protozoa) are another class of contaminants of concern
because of the associated risks to human health and well-being. The principal origins of waterborne
pathogens to downstream waters are as point and diffuse sources from livestock and municipal wastes
via tributaries (Ferguson et al., 2003). Rainfall events and waterborne disease outbreaks in the United
States are strongly correlated, pointing to hydrologic connectivity through tributaries and stormwater
drains as  a key link in transporting pathogens downstream, where they can overwhelm treatment plants
and eventually contaminate drinking water sources (Curriero et al., 2001). Ephemeral and intermittent
tributaries also transport waterborne pathogens downstream from livestock and human waste (e.g.,
Parker etal., 2010; Wilkes etal., 2013). Moist sediments in and near ephemeral and intermittent
streams can act as temporary pathogen reservoirs (Chase et al., 2012). Survival of fecal indicator
bacteria in dry sediments of an intermittent stream was high and remained constant over 1 month, but
declined to unculturable levels after 51 days at 20 °C and 163 days at 5 °C (Chahinian et al., 2012). As for
contaminants, various physicochemical (e.g., discharge, nutrient concentrations, temperature, humic
acids) and biological (predation, competition) conditions in tributaries can mediate the transport or
inactivation of pathogens (Ferguson et al., 2003).
3.5  Biological Connections
Biological connections are linkages throughout the river network, from headwater streams (including
those with intermittent and ephemeral flow) to their downstream waters, that are mediated by living
organisms or their products (e.g., seeds, exudates, or excreta; Lamberti and Resh, 1987).

Because biological connections often result from passive transport of organisms or their products with
water flow, biological connectivity often depends on hydrologic connectivity (Section 3.3.1). Many living
organisms, however, also can actively move with or against water flow; others disperse actively or
passively over land by walking, flying, drifting, or "hitchhiking." All of these organism-mediated
connections form the basis of biological connectivity between headwater streams and downstream
waters.

Biological connections between upstream and downstream reaches can affect downstream waters via
multiple pathways or functions. For organisms capable of significant upstream movement, headwater
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streams, including ephemeral and intermittent streams, can increase both the amount and quality of
habitat available to those organisms. Many organisms require different habitats for different resources
(e.g., food, spawning habitat, overwintering habitat), and thus move throughout the river network—
both longitudinally and laterally—over their life cycles (Schlosser, 1991; Fausch et al., 2002). For
example, headwater streams can provide refuge habitat under adverse conditions, enabling organisms
to persist and recolonize downstream areas once adverse conditions have abated (Meyer and Wallace,
2001; Meyer etal., 2004; Huryn etal., 2005). Headwater streams also provide food resources to
downstream waters: as Progar and Moldenke (2002) state, "...headwater streams are the vertex for a
network of trophic arteries flowing from the forest upland to the ocean."

In this section, we consider longitudinal biological connections in terms of both the aquatic organisms—
specifically invertebrates and fishes—that move along river networks and their consequent effects on
downstream waters (see Section 3.4.2 for discussion of particulate organic matter dynamics and Section
3.4.4 for discussion of waterborne pathogens). We then discuss the importance of organism movement
throughout the river network for genetic connectivity in a separate section. We also recognize the many
important biological connections between river networks and terrestrial systems (Lamberti and Resh,
1987), but as discussed in Chapter 1, these connections are outside the scope of this document. Lateral
biological connections between the river network and riparian and floodplain habitats are considered in
Chapter 4.

3.5.1   Invertebrates
Headwater streams provide habitat for diverse and abundant stream invertebrates (Meyer et al., 2007)
and serve as collection areas for terrestrial and riparian invertebrates that fall into them (Edwards and
Huryn, 1995; Kawaguchi and Nakano, 2001). These aquatic and terrestrial invertebrates can be
transported downstream with water flow and ultimately serve as food resources for downstream
organisms. Many fish feed on drifting insects (Nakano and Murakami, 2001; Wipfli and Gregovich,
2002), and these organisms can also settle out of the water column and become part of the local benthic
invertebrate assemblage in downstream waters. Drift, however, has been shown to increase
invertebrate mortality significantly (Wilzbach and Cummins, 1989), suggesting that most drifting
organisms are exported downstream in the suspended detrital load (Section 3.4.2).

The downstream drift of stream invertebrates (Miiller, 1982; Brittain and Eikeland, 1988) and the
contribution of terrestrial and riparian invertebrates to overall drift (Edwards and Huryn, 1995;
Kawaguchi and Nakano, 2001; Eberle and Stanford, 2010) have been well documented. For example,
drift estimates in 52 small coastal streams in Alaska ranged from 5 to 6,000 individuals per stream per
day (Wipfli and Gregovich, 2002). This export of invertebrates can be especially high in intermittent and
ephemeral streams, as terrestrial invertebrates accumulate in these channels during dry periods and are
then transported downstream upon channel rewetting (Corti and Datry, 2012; Rosado et al., 2015). The
amount of invertebrate drift often is closely related to stream discharge (e.g., Harvey et al., 2006), as
well as diel invertebrate behavioral patterns that are independent of flow (Rader, 1997). To compensate
for loss of individuals to downstream drift, invertebrate populations in headwater streams are

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maintained and replenished through a combination of high productivity and upstream dispersal
(Hershey et al., 1993; Humphries and Ruxton, 2002). This dispersal creates downstream to upstream
biological connections along the river network; for organisms capable of directed movement over long
distances (e.g., winged adult forms of aquatic invertebrate larvae), these connections can occur over
significant network distances.

Given this evidence, that headwater streams are biologically connected to downstream waters via the
active and passive export of invertebrates is clear, and the cumulative export of invertebrates from
numerous headwater streams to downstream waters can be substantial. As with organic matter,
however, assessing the effect of headwater invertebrate production and export on downstream waters
is difficult, given that these resources enter downstream waters at multiple points and times throughout
the river network. Nevertheless, some studies have documented the importance of drifting invertebrates
for downstream organisms. Wipfli and Gregovich (2002) estimated that drifting insects and detritus (i.e.,
particulate organic matter; Section 3.4.2) from fishless headwater streams in Alaska supported between
100 and 2,000 young-of-year salmonids per km in a large, salmon-bearing stream. This estimate of
headwater importance in systems where juvenile salmonids move into headwater streams to feed and
grow is likely conservative (Section 3.5.2). Other studies have shown increased fish growth with
increased invertebrate drift (Wilzbach et al., 1986; Nielsen, 1992; Rosenfeld and Raeburn, 2009),
indicating that drift does provide a valuable food resource, especially when food is limiting (Boss and
Richardson, 2002).

Headwater streams also serve as habitat for invertebrates. Many invertebrate species are well adapted
to seasonal or episodic periods of drying (Feminella, 1996; Williams, 1996; Bogan and Lytle, 2007) or
freezing temperatures (Banks, 2007) and can be found throughout a range of stream sizes (e.g., Hall et
al., 2001b) and flow regimes (intermittent and perennial, e.g., Feminella, 1996). Intermittent streams
also can provide refuge from adverse biotic conditions. For example, Meyer et al. (2004) found that
native amphipods can persist in intermittent reaches but are replaced by nonnative amphipods in
perennial reaches. After disturbance, these upstream habitats can provide colonists to downstream
reaches. This phenomenon can be especially important in intermittent streams, where permanent
upstream pools can serve as refuges during drying. For example, Fritz and Dodds (2002, 2004)
examined invertebrate assemblages before and after drying in intermittent prairie streams and found
that initial recovery of invertebrate richness, richness of invertebrate drift, and richness of aerially
colonizing insects were negatively related to distance from upstream perennial water. Dry stream
channels also can facilitate dispersal of aquatic invertebrates by serving as dispersal corridors for
terrestrial adult forms (Bogan and Boersma, 2012; Steward etal., 2012).

Headwater stream invertebrates also provide critical functional roles in maintaining physical and
chemical connectivity to downstream waters (Covich et al., 1999). Invertebrates accelerate the
breakdown of coarse particulate organic matter (e.g., leaves) to more mobile fine and dissolved forms
(Section 3.4.2; Wallace and Webster, 1996); promote algal productivity and microbial activity (and
nutrient uptake) by biofilm grazing (Feminella and Hawkins, 1995); and temporarily store and transfer
sediments, nutrients, and contaminants through their trophic and physical activity (e.g., via
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bioconsolidation and bioturbation; Pringle et al., 1993; Walters et al., 2008; Statzner, 2012). The
contribution of invertebrates in controlling sediment mobilization can be substantial. For example,
Statzner (2012) estimated that the discharge necessary to move approximately 0.4 kg of sediments-1 in
the Colorado River would increase by an order of magnitude in response to bioconsolidation by net-
spinning caddisflies and would decrease by an order of magnitude in response to bioturbation by
crayfish.

Diverse and abundant invertebrate assemblages also inhabit the hyporheic zone of river networks
(Stanford and Ward, 1988; Boulton, 2000). Hyporheic assemblages are composed of invertebrate
species that inhabit shallow subsurface sediments within streambeds to various degrees. Some taxa
spend their entire lives in the hyporheic zone (Boulton, 2000). Other taxa spend only part of their life
cycles, typically their earliest larval stages or periods of disturbances, in the hyporheic zone, and others
spend their entire aquatic stages in the hyporheic zone then migrate out for their aerial adult stages
(Boulton, 2000). These hyporheic assemblages make similar contributions to physical and chemical
connectivity with downstream waters as benthic invertebrates do, while also enhancing hyporheic
exchange (Section 3.3.1) through movements and migration within the hyporheic zone (Boulton, 2000).

3.5.2  Fishes
Although some fish species maintain resident headwater populations, many species move into and out
of headwater streams at some point in their life cycles (Ebersole etal., 2006; Meyer etal., 2007). Some
fish species occur only in headwater streams, contributing to regional aquatic biodiversity (e.g., Paller,
1994). As with invertebrates, however, certain fish species can be found throughout a range of stream
sizes (Freeman et al., 2007) and flow durations (Schlosser, 1987; Labbe and Fausch, 2000), and the fish
species found in headwater streams often are a subset of species found in downstream habitats
(Horwitz, 1978). Use of headwater streams as habitat is especially evident for the many diadromous
species that migrate between headwater streams and marine environments during their life cycles (e.g.,
Pacific and Atlantic salmon, American eels, certain lamprey species), and the presence of these species
within river networks provides robust evidence of biological connections between headwater streams
and larger rivers.

Through their activities, migratory fish can be important in modifying habitat, and transforming and
transporting materials (e.g., Taylor etal., 2006; Hassan etal., 2008). Return migration of diadromous
fishes provides a feedback loop in which marine-derived nutrients are transported upstream to
headwater streams, for subsequent processing and export (Section 3.4.1). This example illustrates how
biological connections also can create chemical connections throughout the river network. Migratory
fish also can bioaccumulate and transport contaminants long distances between headwater streams and
downstream waters (e.g., Krummel etal., 2003; Morrissey et al., 2011). Fish also can act as transport
vectors of other organisms (e.g., seeds, pathogens, glochidia), moving other organisms against flow or
extending their dispersal distances (e.g., Chick et al., 2003; Senderovich et al., 2010; Schwalb et al.,
2013). Even nonmigratory taxa can travel substantial distances within river networks throughout their
life cycles (Gorman, 1986; Sheldon, 1988; Hitt and Angermeier, 2008). As a result, the distribution and

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movement of fish throughout river networks can be highly variable, both spatially and temporally
(Schlosser, 1991; Labbe and Fausch, 2000; Fausch et al., 2002).

The importance of connectivity in structuring fish  assemblages provides further evidence of biological
connections along river networks. Fish assemblages among connected streams tend to be more similar,
in that assemblages in reaches located closer together tend to have more species in common than
assemblages in distantly separated reaches (Matthews and Robinson, 1998; Hitt et al., 2003; Grenouillet
et al., 2004). Measures of river network structure also can explain fish assemblage structure, with
studies showing that metrics such as link magnitude (the sum of all first-order streams draining into a
given stream segment) and confluence link (the number of confluences downstream of a given stream
segment) are significant predictors offish assemblages (e.g., Osborne and Wiley, 1992; Smith and Kraft,
2005).

The importance of biological connections along river networks is often highlighted by human alterations
that affect these connections. For example, fish assemblages within highly connected river networks
were more homogeneous, whereas fragmentation by road crossings resulted in greater dissimilarity of
fish assemblages between upstream and downstream habitats (Perkin and Gido, 2012). Many studies
have documented statistically significant associations between impoundment of prairie streams and loss
of native fishes (e.g., Winston et al., 1991; Luttrell et al., 1999; Schrank et al., 2001; Falke and Gido, 2006;
Matthews and Marsh-Matthews, 2007), and fragmentation of river networks has been consistently
related to local extinction of salmonid populations (Morita and Yamamoto, 2002; Letcher et al., 2007).

For certain taxa, headwater streams—including intermittent and ephemeral streams— provide critical
habitat for specific portions of their life cycles. Many fish, both salmonids and nonsalmonids, spawn in
headwater streams, including those with intermittent flow (Erman and Hawthorne, 1976; Schrank and
Rahel, 2004; Ebersole etal., 2006; Wigington etal., 2006; Colvin etal., 2009). Kanno etal. (2014)  found
that many brook trout moved between mainstem and tributary habitats over their life cycles. Because
reproductive success varied across these habitats, this movement resulted in substantial gene
movement into tributary habitats (Section 3.5.3).

After spawning, fish using headwater streams return downstream for feeding and overwintering. For
example, Bonneville cutthroat trout moved from less than 1 km to more than 80 km downstream
postspawning, typically within 30 days (Schrank and Rahel, 2004). Many salmonids also grow in
headwater streams (Brown and Hartman, 1988; Curry et al., 1997; Bramblett et al., 2002). In some
cases, these headwater streams, including intermittent streams, can provide higher quality habitat for
juvenile fish, as evidenced by increased growth, size, and overwinter survival in these habitats (Ebersole
etal., 2006; Ebersole etal., 2009), perhaps due to warmer temperatures and higher prey and lower
predator densities (Limm and Marchetti, 2009).

In prairie streams (Section B.4), the importance of hydrologic connectivity for biological connectivity is
especially evident, as many fishes broadcast spawn, or release eggs into the water column, which then
develop as they are transported downstream (Cross and Moss, 1987; Fausch and Bestgen, 1997).
Platania and Altenbach (1998) estimated that unimpeded eggs could travel as far as 144 km before
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hatching, and another 216 km as developing protolarvae (i.e., the swim-up stage), illustrating that
downstream transport of these drifting organisms can be extensive. Adult fish then migrate upstream
prior to egg release (Fausch and Bestgen, 1997). Thus, these fishes require hydrologic connectivity to
maintain both upstream and downstream populations (Fausch and Bestgen, 1997).

When abiotic or biotic conditions farther downstream in the river network are adverse, upstream
reaches can provide refuge habitat for downstream fishes. Examples of adverse abiotic conditions
include temperature (Curry et al., 1997; Cairns et al., 2005) and flow (Pires et al., 1999; Wigington et al.,
2006) extremes, low dissolved oxygen concentrations (Bradford et al., 2001), and high sediment levels
(Scrivener et al., 1994). Examples of adverse biotic conditions include the presence of predators,
parasites, and competitors (Fraser et al., 1995; Cairns et al., 2005; Woodford and Mclntosh, 2010).

Because headwater streams often depend on ground-water inputs, temperatures in these ecosystems
tend to be warmer in winter (when ground water is warmer than ambient temperatures) and colder in
summer (when ground water is colder than ambient temperatures), relative to reaches farther
downstream (Section 3.3.4; Power etal., 1999). Thus, these headwater streams can provide organisms
with both warmwater and coldwater refuges at different times of the year (Curry et al., 1997; Baxter and
Hauer, 2000; Labbe and Fausch, 2000; Bradford etal., 2001), again highlighting the spatial and temporal
variability of these fish-based biological connections. In some cases, loss of coolwater refuges can
facilitate invasion by species more tolerant of warmwater conditions (Karr et al., 1985).

Headwater streams also can provide refuge from flow extremes. Fish can move into headwater streams,
including intermittent streams, to avoid high flows downstream (Wigington et al., 2006); fish also can
move downstream during peak flows (Sedell et al., 1990), highlighting the bidirectionality of biological
connections within these systems. Low flows can cause adverse conditions for organisms, as well, and
residual pools that are often fed by hyporheic flow can enable organisms to survive dry periods within
intermittent streams (Pires et al., 1999; May and Lee, 2004; Wigington et al., 2006).

Biotic conditions within the river network—that is, the taxa found in the system—also can create an
adverse environment, as the presence of invasive species or other predators and competitors can
negatively affect native taxa. In some cases, headwater streams can provide these taxa refuge from other
species and enable populations to persist. For example, Fraser et al. (1995) found that prey fish moved
downstream when piscivores (fish-eating fish) were excluded, but moved upstream into headwater
streams when they were present. The role of headwater streams as refuges from adverse biotic
conditions can be closely related to where along the connectivity-isolation continuum these habitats fall,
with isolation allowing for persistence of native populations (Letcher et al., 2007). Physical barriers
(which reduce connectivity and increase isolation) have been used to protect headwater streams from
invasion (Middleton and Liittschwager, 1994; Freeman et al., 2007); similarly, most genetically pure
cutthroat trout populations are confined to small, high-elevation streams that are naturally or
anthropogenicallyisolated (Cook etal., 2010).

When adverse conditions have abated and these organisms move back down the river network, they can
serve as colonists of downstream reaches (Meyer and Wallace, 2001). For example, Hanfling and
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Weetman (2006) examined the genetic structure of river sculpin and found that upstream populations
were emigration biased (i.e., predominant movements were out of these reaches), whereas downstream
populations were immigration biased (i.e., predominant movements were into these reaches).

3.5.3   Genes
Genetic connectivity results from biotic dispersal and subsequent reproduction and gene flow, or the
transfer of genetic material within and among spatially subdivided populations. Populations connected
by gene flow have a larger breeding population size, making them less prone to inbreeding and more
likely to retain genetic diversity or variation—a basic requirement for adaptation to environmental
change (Lande and Shannon, 1996). Genetic connectivity exists at multiple spatial and temporal scales. It
can extend beyond a single river watershed (Hughes etal., 2009; Anderson etal., 2010), and in
diapausing organisms, can provide a direct link between distant generations (dispersal through time;
Bohonak and Jenkins, 2003).

Although physical barriers  can protect headwater habitats and populations by isolating them from
colonization by and hybridization with invasive species (Section 2.3.2.1), isolation also can have serious
adverse effects on native species via reductions in genetic connectivity. For example, Hanfling and
Weetman (2006) found that artificial weirs  intensified natural patterns of limited headwater
immigration, such that headwater (above-barrier) sculpin populations diverged genetically from
downstream (below-barrier) populations and lost significant amounts of genetic diversity. This pattern
of strong genetic divergence accompanied by loss of headwater genetic diversity above natural and
artificial barriers has been documented in multiple fish species and regions (Yamamoto et al., 2004;
Wofford et al., 2005; Deiner et al., 2007; Guy et al., 2008; Gomez-Uchida et al., 2009; Whiteley et al.,
2010). Loss of headwater-river genetic connectivity might be exerting selection pressure against
migrant forms in fish with life cycles requiring movement along the entire river corridor (Morita and
Yamamoto, 2002). Ultimately, tradeoffs exist between the risks associated with headwater-river genetic
connectivity (e.g., hybridization with nonnative species and hatchery fish) and those associated with
genetic isolation (e.g., reduced reproductive fitness, increased risk of local extinction, deterioration of
overall genetic variation, and selection against migratory traits; Fausch et al., 2009).

In general, genetic connectivity decreases with increasing spatial distance (Wright, 1943). Genetic
connectivity in river networks is also strongly influenced by the hierarchical structure of a river network
(Section 2.4.2), the direction of dispersal (upstream, downstream, or both), dispersal modes and
pathways used (e.g., swimming, flying), and species' life histories (Hudy et al., 2010).

Computer simulation approaches examine the spatial and temporal processes of genetic connectivity for
realistic behaviors and life histories of species inhabiting complex, dynamic landscapes and riverscapes
(Epperson et al., 2010). For example, Morrissey and de Kerckhove (2009) demonstrated that
downstream-biased dispersal in dendritic river networks (which by definition have more tributaries
than mainstems) can promote higher levels of genetic diversity than other geographical habitat
structures. Under these conditions, low-dispersing headwater stream populations can act as reservoirs
of unique genetic alleles (units of genetic variation) that occasionally flow into and mix with highly
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dispersing downstream populations. Although the number of headwater streams (i.e., potentially unique
genetic reservoirs) is important in maintaining genetic diversity, networks with more complex
hierarchical structures (Figure 3-4) are more efficient at maintaining genetic diversity than networks in
which all tributaries flow directly into the mainstem (Morrissey and de Kerckhove, 2009). In another
simulation, Chaput-Bardy et al. (2009) demonstrated that out-of-network gene flow (e.g., terrestrial
dispersal by insects or amphibians) or very high levels of within-network gene flow (e.g., fish that move
and reproduce throughout the network) can counteract the effects of network structure; thus, individual
species behavior can profoundly affect observed genetic patterns.
 Figure 3-4. (A) A dendritic network with multilevel hierarchical structure, and (B) a uninodal
 network with all headwater streams feeding directly into a river mainstem. Source: Reprinted from
 The maintenance of genetic variation due to asymmetric gene flow in dendritic metapopulations,
 (2009) by Morrissey and de Kerckhove with permission of The Univ of Chicago Press.
Most empirical evidence for the role of headwater streams in maintaining genetic connectivity and
diversity comes from studies of economically important fish species, but correlations of river network
structure or landscape alteration with genetic patterns have been reported for other species. Consistent
with the model of Morrissey and de Kerckhove (2009), Per and Hroudova (2008) found higher genetic
diversity in downstream populations of yellow pond-lily (Nuphar luted), which disperses over long
distances via water-mediated dispersal of detached rhizomes. Frequent dispersal and high gene flow
among headwater and downstream populations of the giant Idaho salamander (Dicamptodon aterrimus;
Mullen et al., 2010) are expected to contribute to genetic diversity of upstream and downstream
populations.

Headwater populations contribute to the maintenance of genetic diversity even in animals capable of
overland dispersal. In a field study of the common stream mayfly Ephemerella invaria, which emerges
into streamside forests to mate and disperse, Alexander et al. (2011) found that regional genetic
diversity was strongly correlated with tree cover in first-order (headwater) stream watersheds.
Observed loss of genetic diversity in this species could be related to degradation of stream habitats,
degradation of out-of-network dispersal path ways, or both (Chaput-Bardy et al., 2009; Grant etal., 2010;
Alexander etal., 2011).
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In summary, genetic connectivity in river systems reflects the breeding potential of a metapopulation.
The maintenance of genetic diversity is directly related to genetic connectivity, and thus is critical to a
species' regional persistence. Genetic connectivity is influenced by the landscape, riverscape, and
biology of the organisms involved; spatially subdivided stream and river populations can maintain
genetic diversity, provided they remain connected by at least low levels of gene flow (Waples, 2010).


3.6  Streams: Synthesis and Implications
Despite widespread human alterations, rivers are not simple conduits draining watersheds. A river,
including the water and material it carries and the organisms living in it, represents the cumulative
longitudinal, lateral, and vertical connections of its network of channels integrated over time (Section
1.2.3). Although we recognize that streams also exchange water and other materials with nearby
terrestrial and deep ground-water systems via lateral and vertical connections, this chapter focused on
longitudinal surface-water connections between streams and rivers, as well as shallow subsurface-water
interactions integral to surface-water connections and downstream water condition.

A substantial body of evidence unequivocally demonstrates connectivity between streams and
downstream rivers via both structural and functional connectivity (as defined in  Wainwright et al.,
2011).  Streams are structurally connected to rivers through the network of continuous channels (beds
and banks)  that make these systems physically contiguous, and the very existence of a continuous bed
and bank structure provides strong geomorphologic evidence for connectivity (Section 2.2.1). A stream
must be linked to a larger, downstream water body by a channel for the two to have a surface-water
(hydrologic) connection. Although some streams lack a channel connection to larger water bodies (i.e.,
small endorheic basins), they are the exception. Streams that link larger water bodies through networks
of continuous bed and bank are the rule. The network structure reflects the aggregate and cumulative
nature  of the connections between distant headwater streams and the downstream river.

Although not comprehensive or equally studied among all stream types, the existing science indicates
that connectivity with downstream waters varies among streams and over time. This variation in
connectivity to downstream waters can be described as a connectivity gradient, ranging from highly
connected to highly isolated (Section 1.2.2). A stream's position on the gradient is influenced not only by
distance to  downstream waters but also by the frequency, magnitude, duration, timing, and rate of
change effluxes to downstream waters. Connectivity is dynamic: It changes with immediate, seasonal,
and interannual or interdecadal (e.g., climate oscillations) conditions that affect the availability and
distribution of water, materials, and biota. Because connectivity is dynamic, a complete understanding
of a stream's connections and consequences to downstream waters should aggregate connections over
relatively long time scales (multiple years to decades; Section 1.2.3). Although distance between streams
and downstream waters vary, other factors such as intervening resistance, relative size or chemical load,
and species assemblage also influence the degree of connectivity with and level of consequence on
downstream waters. Despite being distant from downstream waters, headwater  streams make up the
majority of stream channels in most river networks and cumulatively supply most of the water in rivers.

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Streams are functionally connected to rivers by the movement of water and other materials through this
network of channels (Table 3-1). The longitudinal, vertical, and lateral connections within river
networks are inextricably tied. Even losing-stream reaches that at times lack sufficient flow for
hydrologic connection can still influence downstream waters by functioning as sinks for water and
materials carried by water. The river network and its flow of materials represent the integration of its
streams' cumulative contributions to downstream waters. Existing evidence indicates that headwater
streams (including intermittent and ephemeral streams) transform, store, and export significant
amounts of material (e.g., water, organic matter, organisms) to downstream waters. The most
compelling evidence linking headwater streams to downstream habitats supports source, sink (or lag),
and transformation functions (Section 2.3.1; Table 2-1). For example, studies that involved sampling
throughout river networks have documented headwater streams as sources of water (via floods and
baseflow) to rivers (Section 3.3.1). Nitrogen and carbon transported from headwater streams
cumulatively contribute to nitrogen and carbon levels in downstream rivers, and headwater streams can
function as nitrogen and carbon sinks for river networks (Sections 3.4.1 and 3.4.2). Studies documenting
the fate and transport of contaminants through headwater streams to downstream waters also
represent clear lines of evidence for headwater streams as sources and sinks (Section 3.4.4). Many
organisms, such as anadromous salmon, have complex life cycles that involve migration through the
river network, from headwater streams to downstream rivers and oceans, over the course of their lives
(Section 3.5). In fact, the importance of headwater streams (including intermittent and ephemeral
streams) in the life cycles of many organisms capable of moving throughout river networks provides
strong evidence for connectivity among these systems.

Most of the evidence relevant to issues of connectivity between headwater streams and large rivers is
based on data collected either in the upper (i.e., from headwater streams to intermediate tributaries) or
lower (i.e., from large tributaries to mainstem rivers) portions  of the river network. Although few
studies have explicitly examined the movement of materials along entire river networks, the exchange of
materials among closely located stream reaches—which numerous studies have documented, for a
variety of materials—can be extended over large spatial scales.
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Table 3-1. Examples of mechanisms by which streams are connected to and influence downstream
waters, by functional type. See relevant section and appendix numbers in parentheses for greater detail.
Note that the distinction between types of functions is not always clear. For example, denitrification can
be considered a sink or transformation function. Bold letters represent the primary type of connection (B
= biological; C = chemical; and P = physical).
                                           Source Function
    Streams supply water downstream through baseflow and floods that influence discharge and habitat (3.3.1,
    B.4.2.5, B.4.3.1.1, B.5.3, B.5.4.2, B.5.5.1). P
    Streams supply downstream waters with sediment (3.3.2, 3.4.4, B.4.3.1.3, B.5.3, B.5.4.2). P
    Streams supply downstream waters with nutrients and other ions (3.4.1, 3.4.3, B. 4.3.2.1, B.5.4.2). C
    Streams can transport to downstream waters contaminants and pathogens that adversely affect organisms
    and human health (3.4.4, B.4.3.1.3).  C
    Streams supply dissolved and particulate organic matter that can fuel heterotrophy in downstream waters
    and influence physicochemical conditions (3.3.3, 3.4.2, B.4.3.2.2, B.5.4.2). C
    Organisms actively and passively move between streams and downstream waters, carrying with them
    nutrients, contaminants,  pathogens, and other organisms (3.5, B.4.2.4, B.4.3.3). B
    Organisms can enhance the supply of materials to downstream waters (3.5.1, 3.5.2). B
                                            Sink Function
    Streams can divert surf ace flow from downstream waters via infiltration into underlying alluvium and
    evapotranspiration to the atmosphere (3.3.1, B.5.3, B.5.4.2, B.5.5.1). P
    Streams can divert nitrate from downstream waters via denitrification (3.4.1, B.4.3.2.1). C
    Streams can prevent sediment and associated contaminants from being transported to downstream waters
    through deposition on floodplains (3.3.2, 3.4.4, B.5.3). C
                                           Refuge Function
    Streams can afford protection from temperature extremes, drying, predators, and competition with
    nonnative species for organisms that inhabit downstream waters (3.5, B.4.3.3). B
                                       Transformation Function
    Streams can mediate the form and mobility of nutrients before they enter downstream waters via nutrient
    spiraling (3.4.1, B.4.3.2.1). C
    Streams can mediate the form and mobility of organic matter before they enter downstream waters via
    carbon spiraling (3.4.2, B.4.3.2.2). C
    Streams can mediate the form and mobility of contaminants before they enter downstream waters via
    hyporheic exchange or exposure to other physicochemical gradients that lead to biogeochemical
    transformations (3.4.4). C
    Organisms can mediate the transformation of materials through their trophic and physical activities (3.4.1,
    3.4.2,3.5.1,3.5.2, B.4.3.2.2). B
                                            Lag Function
    Streams can delay water from arriving at downstream waters through local and network structures, thus
    reducingflood magnitudes, but increasing baseflows in downstream waters (3.3.1, 3.3.3, B.4.3.1.1, B.5.3,
    B.5.4.2). P
    Streams can delay sediment from arriving at downstream waters through local and network structures
    (3.3.2, 3.3.3, 3.4.4, B.5.3). P
    Streams can delay nutrients from arriving at downstream waters through local and network structures and
    biological uptake (3.4.1, B.4.2.4, B.4.3.2.1). C
    Streams can delay organic matter from arriving at downstream waters through local and network structures
    and biological uptake (3.3.3, 3.4.2, B.4.3.2.2). C
    Streams can delay contaminants from arriving at downstream waters through local and network structures
    and exchanges that enhance mineralization and precipitation or adsorption to sediment, or both (3.4.4). C
    Organisms can delay nutrients, organic matter, and contaminants from arriving at downstream waters
    through consumption, assimilation, and bioconsolidation (3.4.1, 3.4.2, 3.5.1, 3.5.2, B.4.3.2.2). B
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                CHAPTER 4. WETLANDS: PHYSICAL, CHEMICAL,
                   AND BIOLOGICAL CONNECTIONS TO RIVERS
4.1  Abstract
Wetlands are transitional ecosystems that occur between terrestrial and aquatic systems. They are
inundated or saturated by water at a frequency and duration sufficient to support hydrophytic
vegetation and development of hydric soils. The effects of wetlands on rivers and other downstream
waters depend on functions within the wetlands and connectivity between wetlands and downstream
waters. Riparian/floodplain wetlands can be hydrologically connected to streams and rivers through
unidirectional flows (i.e., from wetlands to rivers and streams, but not vice versa) of surface water and
ground water from upgradient areas (e.g., hillslopes and nearby uplands). In addition,
riparian/floodplain wetlands have bidirectional connections to streams and rivers (i.e., from wetlands to
streams and rivers and vice versa) through lateral movement of surface and ground water between the
channel and riparian/floodplain areas. Connections between riparian/floodplain wetlands and streams
or rivers occur over a gradient of connectivity, for example, they can be permanent, can occur frequently
(e.g., if the wetland is located within the mean high-water mark), or can occur infrequently (e.g., if the
wetland occurs near the edge of the floodplain; Sections 1.2.2 and 2.4.2). Even riparian/floodplain
wetlands that rarely flood can have important, long-lasting effects on streams and rivers.
Riparian/floodplain wetlands can reduce flood peaks by storing floodwaters, store large amounts of
sediment and nutrients from upland areas, influence stream geomorphology by providing woody debris
and sediment, and regulate stream temperature. Riparian/floodplain wetlands also are sources of food
for stream and river invertebrates and serve as rearing habitat for fish.

Wetlands in non-floodplain landscape settings lack bidirectional hydrologic connections with  channels
(i.e., water flows from the wetland to the channel but not from the channel to the wetland). These
settings, however, have the potential for unidirectional hydrologic flows from wetlands to the river
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network through surface water or ground water. Non-floodplain wetlands can attenuate floods through
depressional storage and can recharge ground water and thereby contribute to baseflow. These
wetlands can affect nutrient delivery and improve water quality by functioning as sources (e.g., of
dissolved organic carbon) and as sinks for nutrients (e.g., nitrogen), metals, and pesticides. Non-
floodplain wetlands also can provide habitat or serve as sources of colonists for biological communities
in downstream waters, through movement of amphibians, reptiles, birds, and mammals. The extent to
which non-floodplain wetlands perform these functions depends on their hydrologic and biological
connectivity with downstream waters. Non-floodplain wetlands also occur on a hydrologic gradient,
from wetlands having permanent connections with perennial channels, to geographically isolated
wetlands having ground-water or occasional surface-water connections, to highly isolated wetlands
having minimal hydrologic connection to the river network (but which could include surface and
subsurface connections to other wetlands; Section 4.4.2). Non-floodplain wetlands that are connected to
the river network through a channel (i.e., wetlands that serve as stream origins) will have an effect on
downstream waters, regardless of whether the outflow is permanent, intermittent, or ephemeral. For
non-floodplain wetlands that do not connect to the river network through a stream channel  (i.e.,
geographically isolated wetlands and wetlands that spill into losing streams that are completely
disconnected from the river network), the type and degree of connectivity with downstream waters will
vary with position in the watershed and over time.

This literature review is unable to provide evaluations of connectivity for specific groups or  classes of
wetlands (e.g., prairie potholes or vernal pools). Evaluations of individual wetlands or groups of
wetlands, however, could be possible through case-by-case analysis. We can conclude the following:
    1.  A non-floodplain wetland having a surface-water outflow to a stream network (e.g., a wetland
       that serves as a stream origin) is connected to the stream network and has an influence on
       downstream waters.
    2.  Many non-floodplain wetlands interact with ground water, which can travel long distances and
       affect downstream waters.
    3.  Even when wetlands lack a hydrologic connection to other water bodies, they can influence
       downstream water through water and material storage and mitigation of peak flows (flood
       reduction and flood attenuation). Sink functions of non-floodplain wetlands will have effects on
       a downstream water when these wetlands are situated between the downstream water and
       known point or nonpoint sources of pollution, thereby intersecting the flowpath between
       pollutant source and downstream water. More generally, wetland sink functions are likely to  be
       greatest when the wetland is located downgradient from pollutant sources and upgradient from
       a stream or river.
    4.  Within a watershed or wetland landscape setting, wetlands and open waters that are closer to
       rivers and streams will have a higher probability of being connected than more distant areas,
       assuming that conditions governing type and quantity of flows (e.g., slope, soil, and aquifer
       permeability) are similar.

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    5.  Caution should be used in interpreting connectivity for wetlands that have been designated as
       "geographically isolated."


4.2  Introduction
This chapter provides detailed information, based on a review of the pertinent peer-reviewed literature,
on how wetlands connect to and influence streams and rivers. In particular, we address two questions
(Section 1.1): (1) What are the connections to and effects of riparian/floodplain wetlands and open
waters (e.g., oxbow lakes) on downstream waters? (2) What are the connections to and effects of non-
floodplain wetlands and open waters on downstream waters?

In Chapter 1, we provided the scientific context for concepts and gradients of connectivity in hydrology
and ecology (Section 1.2). In Chapter 2, we provided definitions for wetlands, gave a rationale for
distinguishing between wetlands in riparian/floodplain and non-floodplain settings, and discussed
general hydrologic and biological mechanisms by which wetlands can connect to and affect streams and
rivers. Given that streams and rivers are the endpoints of interest, we limit our discussion of
riparian/floodplain wetlands to those occurring in riparian and floodplain settings. Below, we provide a
detailed review of the contributions of riparian/floodplain wetlands (Section 4.3) and non-floodplain
wetlands (Section 4.4) to rivers, followed by conclusions concerning these wetlands and their effects on
rivers (Section 4.5). Examples of some of the functions discussed in these two sections are found in
Table 4-1. In addition, four case studies on specific types of wetlands  or lentic waters representing
different landscape settings and geographic regions are in Appendix B: Carolina and Delmarva bays
(Section B.I), oxbow lakes (Section B.2), prairie potholes (Section B.3), and vernal pools (Section B.6).

Much of the literature that we evaluate in this chapter does not specify the type or size of the stream or
river (or other water body) to which the wetland(s) are connected or which they influence. If available,
we note this information (e.g., whether riparian areas were located in floodplains or along portions of
river networks without floodplains), but often we can discuss only generic connections to streams,
rivers, or downstream waters. Given that rivers are connected to all upstream components of the river
network, including streams (Chapter 2), and the functional relationships between streams and rivers
(Chapter 3), however, we consider any evidence of connectivity with  a stream (other than endorheic
streams; Sections 3.2 and B.5.5.1) to be evidence  of connectivity with the river and other downstream
waters.


4.3  Riparian/Floodplain Wetlands

4.3.1   Introduction
This section focuses on the connections and influence of riparian/floodplain wetlands on downstream
waters. As previously defined in Section 2.2.1, riparian/floodplain wetlands are locations within riparian
areas and floodplains (Figures 1-1A, 2-2, and 2-3), respectively, that meet the Cowardin et al. (1979)

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Table 4-1. Examples of mechanisms by which riparian/floodplain wetlands and wetlands in non-
floodplain settings influence downstream waters, by functional type. See relevant section and appendix
numbers in parentheses for more detail. Note that the distinction between types of functions is not
always clear, for example, denitrification could be considered a sink or transformation function.
                                           Source Function
   Riparian/floodplain wetlands and non-floodplain wetlands connected to the stream network by channelized
   flow—ranging from ephemeral to permanent—are sources of downstream water (4.3.2.1, 4.4.2.1, B.I.2.3,
   B.2.3.1, B.3.3.1, B.6.3.1).
   Wetlands that serve as origins for streams (e.g., seeps) can be sources of ground-water discharge,
   contributing to stream baseflow (4.4.2.3).
   Non-floodplain wetlands lacking a channel outlet can be sources of water via overland flow to the stream
   network if wetland storage capacity is exceeded (4.4.2.1, B.3.3.1, B.6.3.1.1). They can  also provide water
   via subsurface drains ("tile drains") or surface ditches (4.4.2.1, B.I.3.1, B.3.3.1).
   Riparian/floodplain wetlands and non-floodplain wetlands can be sources of nutrients and sediments to
   downstream waters (4.3.2.2, 4.3.3, 4.4.3.1, B.l.3.2, B.3.3.2).
   Riparian areas are a source of allochthonous inputs, the primary energy input into the food webs of small,
   forested streams (4.3.3.4). They also are sources of woody debris that can affect stream morphology and
   flow regime, and provide habitat for aquatic organisms (4.3.2.2).
   Riparian areas and non-floodplain wetlands can be sources of dissolved organic matter that aquatic food
   webs use, with additional potential effects on pH and mercury concentrations of downstream waters
   (4.3.3.4, 4.3.3.6, 4.4.3.1).
   Riparian/floodplain wetlands and non-floodplain wetlands can be sources of organisms, including plants,
   invertebrates, amphibians, reptiles, and fish, to downstream waters transported via passive or active
   dispersal (4.3.4, 4.4.4, B.2.3.3, B.3.3.3, B.6.3.2).
   Riparian/floodplain wetlands can provide feeding habitat for riverine organisms, such as fish, during periods
   of overbank flow (4.3.4.2, B.2.3.3).
                                            Sink Function
   Riparian/floodplain wetlands and non-floodplain wetlands can be sinks for water by intercepting overland or
   subsurface flow, if available water storage capacity of the wetlands is not exceeded, which can reduce or
   attenuate flow to downstream waters and flooding (4.3.2.1, 4.4.2.3, B.3.3.1).
   Riparian areas and non-floodplain wetlands can be sinks for sediment and chemical contaminants, such as
   pesticides, metals,  mercury, and excess nutrients carried by overland or subsurface flow, potentially
   reducing loading to downstream waters (4.3.2.2, 4.3.3, 4.4.3.2).
   Riparian areas can  be sinks for water, sediment, pesticides, and nutrients from overbank flow events,
   reducing or attenuating downstream peak flows and  materials entrained in the water column (4.3.2.1,
   4.3.2.2, 4.3.3, B.2.3.2). They can also be sinks for seeds and plant fragments deposited via overbank flow
   (4.3.4.1).
   Riparian/floodplain wetlands and non-floodplain wetlands can be sinks for nitrogen by converting oxidized
   forms of nitrogen to molecular nitrogen through denitrification, which is then  lost to the atmosphere
   (4.3.3.2, 4.4.3.2).
                                           Refuge Function
   Riparian/floodplain wetlands and non-floodplain wetlands can provide refuge for fish, aquatic insects, or
   other lotic organisms from predators or other environmental stressors, facilitating individual or population
   survival (4.3.4, 4.4.4).
   Riparian/floodplain wetlands and non-floodplain wetlands can provide refuge during certain life stages for
   lotic organisms. For example, they are breeding sites for frogs and other amphibians that reside in streams
   as adults (4.4.4, B.I.3.3, B.6.3.2; Table 4-2); non-floodplain wetlands are additionally nesting and nursery
   sites for American alligators that otherwise primarily reside in streams (4.4.4).
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Table 4-1. Examples of mechanisms by which riparian/floodplain wetlands and wetlands in non-
flood plain settings influence downstream waters, by functional type. See relevant section and
appendix numbers in parentheses for greater detail. Note that the distinction between types of
functions, is not always clear, for example, denitrification could be considered a sink or transformation
function (continued).
                                     Transformation Function
   Microbial communities in riparian/floodplain wetlands and non-floodplain wetlands can transform
   elemental mercury to methylmercury before it enters a stream. Methylmercury is a particularly toxic and
   mobile form that bioaccumulates in aquatic food webs (4.3.3.6, 4.4.3.1).
   Riparian/floodplain wetlands and non-floodplain wetlands can transform nitrate to molecular nitrogen
   through denitrification (4.3.3.2, 4.4.3.2).
                                          Lag Function
   Riparian/floodplain wetlands can temporarily store water following overbank flow, which then can move
   back to the stream over time as baseflow (4.3.2.1).
   Non-floodplain wetlands can contribute to ground-water recharge under low water table conditions, which
   ultimately contributes to baseflow (4.4.2.3,  B.3.3.1).
   Non-floodplain wetlands can increase the time for stream discharge to rise and fall in response to a
   precipitation event due to wetland storage capacity (4.4.2.3).
definition of having wetland hydrology, hydrophytic vegetation, or hydric soils. The terms "riparian
wetland" and "floodplain wetland" frequently describe the same geographic area. Because riparian areas
and floodplains also contain upland areas, some riparian/floodplain wetlands are geographically
isolated (i.e., completely surrounded by upland).

Although ample literature is available on riparian/floodplain wetlands—especially bottomland
hardwood and swamp wetlands—most papers on riparian areas and floodplains do not specify whether
the area is a wetland. This lack of specification occurs because riparian areas and floodplains also are
studied by stream ecologists and hydrologists who might not focus on whether their study site meets
the Cowardin et al. (1979) definition of a wetland. This situation creates a dilemma, because limiting our
literature review to papers that explicitly describe the area as a wetland would exclude a major portion
of this body of literature and greatly restrict our discussion of wetland science. Alternatively, if we
include papers that do not explicitly classify the area as a wetland, we could mistakenly incorporate
results that are relevant only to upland riparian areas. Our response to this dilemma was to survey the
floodplain and riparian literature broadly and include any results and conclusions that we judged
pertinent to riparian/floodplain wetlands. This judgment was based, in part, on: (1) the processes
described in the integrated systems perspective on interactions of watersheds, streams, wetlands and
downstream waters (Sections 2.2.2 and 2.2.3); (2) whether the information applies to all riparian areas,
regardless of whether they are wetlands or  uplands  (e.g., all riparian areas are subject to periodic
overbank flooding); and (3) an understanding of the specific processes. For example, riparian studies of
denitrification are likely to be either in a wetland or  applicable to riparian/floodplain wetlands, because
the alternating oxidation/reduction conditions required  for denitrification are present in wetlands.
Therefore, in our assessment of evidence regarding the connectivity and effects of riparian areas and
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floodplains, we have concluded that the processes and functions discussed occur in water bodies within
those areas.

As addressed in Chapter 2, much of the theory developed to explain how river systems function has
focused on linkages between system components (Vannote et al., 1980; Newbold et al., 1982a; Newbold
et al., 1982b; Junk et al., 1989; Ward, 1989; Power et al., 1995a; Power et al., 1995b; Huggenberger et al.,
1998; Ward, 1998; Fausch etal., 2002; Ward etal., 2002b; Wiens, 2002; Benda etal., 2004; Thorp etal.,
2006; Humphries et al., 2015). The integral connectivity between rivers and their floodplains and
riparian areas is a central tenet of stream hydrology and ecology, as is the  substantial influence that this
bidirectional exchange has on the physical form, hydrology, chemistry, and biology of the river system
(Junk et al., 1989; Abbott et al., 2000; Tockner et al., 2000; Woessner, 2000; Amoros and Bornette, 2002;
Ward et al., 2002a; King et al., 2003; Naiman et al., 2005; Church, 2006; Kondolf et al., 2006; Poole et al.,
2006; Poole, 2010; Tockner et al., 2010; Vidon et al., 2010; Helton et al., 2011; Mclaughlin et al., 2011;
Humphries et al., 2015). For example, the flood pulse concept, which Junk  et al. (1989) first articulated
and Tockner et al. (2000) extended, is a fundamental paradigm in river ecology, depicting the lateral
expansion and contraction of the river in its floodplain and the resulting exchange of matter and
organisms.

The influence of riparian/floodplain wetlands on downstream waters is especially notable because of
the potential magnitude and spatial extent of their interactions with rivers and their locations within
river networks. Although floodplains can form in modest size streams (Hughes and Lewin, 1982), they
typically form in the lower portion of river networks (Montgomery, 1999; Church, 2002, 2006), where
they can provide transient storage and subsequent release of river water and materials (Stanford and
Ward, 1993; Squillace, 1996; Mertes, 1997; Winter etal., 1998; Tockner etal., 2000; Fernald etal., 2001;
Amoros and Bornette, 2002; Malard etal., 2002; Claxton etal., 2003; Davis etal., 2011). Floodplain
patterns and river channel complexity are determined by sediment supply and character, river valley
slope, stream power, woody debris, and vegetation (Montgomery, 1999; Church, 2002; Coulthard, 2005;
Church, 2006; Osterkamp and Hupp, 2010; Sear etal., 2010; Collins etal., 2012). Circumstances
conducive to the formation of complex, rapidly changing channel forms (e.g., anastomosing, braided,
meandering) and the deposition of coarse sediment create conditions optimal for river-floodplain
interactions (Nanson and Croke, 1992; Mertes etal., 1995; Fernald etal., 2001; Fernald etal., 2006;
Poole et al., 2006; Whited et al., 2007).

Wetlands that occur in floodplains are referred to as riverine wetlands within the hydrogeomorphic
classification system (Smith et al., 1995). Although floodplain wetlands can occur as marshes (Villar et
al., 2001; Lee etal., 2005) or scrub-shrub wetlands (Chipps etal., 2006), these areas are known for
supporting forested wetlands. Mitsch and Gosselink (2007) classify floodplain forested wetlands as
freshwater swamps—for example, cypress-tupelo swamps (Taxodium distichum and Nyssa aquatica,
respectively) and white cedar swamps [Chamaecyparis thyoides)—if water is available throughout most
of the growing season, or as riparian ecosystems if the floodplain receives seasonal pulses of flooding.
Examples of the latter are bottomland hardwoods in the Southeast—for example, sycamore-sweetgum
(Platanus occidentalis and Liquidambar styraciflua, respectively) and cypress-tupelo forests—or
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cottonwood-willow (Populus spp. and Salix spp., respectively) and alder (Alnus spp.) riparian
communities in the Southwest (Mitsch and Gosselink, 2007).

This section provides further details on the connections between riparian/floodplain wetlands and
streams and rivers, and the resulting effects. Below, we examine the physical (Section 4.3.2), chemical
(Section 4.3.3), and biological (Section 4.3.4) effects of riparian/floodplain wetlands on rivers and other
downstream waters.

4.3.2   The Physical Influence of Riparian Areas on Streams

4.3.2.1    Hydrology
Riparian areas within and outside of floodplains are an important part of the overall riverine landscape
(Ward, 1998). Riparian areas are also connected to streams and rivers by a diverse set of hydrologic
inputs and outputs (Figure 2-6A; Junk etal., 1989; Winter and Rosenberry, 1998; Benke etal., 2000;
Tockner et al., 2000; Bunn et al., 2006). These inputs and outputs are described in Section 2.2 and have
been reviewed by various authors (National Research Council, 2002; Naiman etal., 2005; Vidon etal.,
2010).

Many studies document that riparian floodplains help attenuate flood pulses in streams and rivers by
capturing water from overbank flow and by storing excess water from streams (Mertes et al., 1995;
Poole et al., 2006; Rassam et al., 2006). Bullock and Acreman (2003) reviewed the wetland literature
and reported thatfloodplain wetlands reduced or delayed floods  in 23 of 28 studies. Walton etal. (1996)
found that peak discharges between upstream and downstream water gages on the Cache River in
Arkansas were reduced 10-20%, primarily due to floodplain water storage. Gamble et al. (2007)
reported that 12 floodplain wetlands in Ohio stored an average of 3,654 m3 ha-1 of water. The authors
developed equations relating volume to area and depth for more  than 650 regional wetlands and
reported that these systems could store approximately 1-2% of the daily flow of larger streams and
approximately 40% of the daily flow of small streams. As streamflow decreases after hydrologic events,
the water temporarily stored in riparian/floodplain areas can flow back into the channel, supporting
stream baseflow (Whiting and Pomeranets, 1997; Chen and Chen, 2003). Although not all
riparian/floodplain wetlands store the same amount of water, nearly all of them have the potential to
perform this function.

The potential for  hydrologic connectivity between riparian/floodplain wetlands and rivers and streams
is high during periods of overbank flow and during periods of lower streamflow. Hyporheic exchange
occurs when water moves from river or stream channels into riparian or floodplain alluvial deposits and
back to the channels, and it occurs during flooded and non-flooded conditions (Sjodin et al., 2001;
Gooseff etal., 2008; Bencala, 2011) and on scales ranging from meters to kilometers (Stanford and
Ward, 1988; Bencala, 1993, 2005). Complex floodplains typically are environments with high levels of
hyporheic exchange (Woessner, 2000; Poole etal., 2006; Poole, 2010).
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Vegetation in riparian/floodplain wetlands can influence hyporheic and river water through
transpiration. Phreatophytes (plants that obtain their water from the saturated zone) can intercept
ground-water and overland flow before it enters a stream and decrease streamflow by directly taking up
stream water through their roots. For example, Meyboom (1964) studied two streams in the prairie
region of the United States to understand the effect of floodplain vegetation on streamflow fluctuations.
When the two streams decreased in flow, the floodplain vegetation accounted for 20% and 100% of this
reduction (Meyboom, 1964).

4.3.2.2    Geomorphology (Sediment-vegetation Interactions)
A bidirectional relationship exists between fluvial geomorphology and riparian and floodplain
vegetation (Corenblit et al., 2007). Distributions of vegetation communities often are shaped by river
flow dynamics and associated erosional and deposition processes, but the communities also exert
controls on geomorphic processes and riverine landforms.

Riparian/floodplain wetlands are key depositional environments for sediment that overland flow
carries from erosion of nearby uplands (Boto and Patrick, 1979; Whigham et al., 1988). Riparian areas
retain portions of this sediment before it enters the stream, especially if the overland flow enters the
riparian area as sheetflow runoff rather than as channelized flow, due to the greater volume of water
exposed to riparian-wetland soils and vegetation surfaces (Dabney et al., 1995; Meyer et al., 1995;
Naiman and Decamps,  1997; National Research Council, 2002; Naiman et al., 2005). Riparian open
waters (e.g., oxbow lakes; Section B.2) and wetlands are effective at retaining eroded clays, silts, and
sands that otherwise would enter stream channels (Cooper et al., 1987; Heimann and Roell, 2000).
Riparian areas were shown to remove 80-90% of sediments leaving agricultural fields in North Carolina
(Cooper et al., 1987; Daniels and Gilliam, 1996; Naiman and Decamps, 1997). Grassy riparian areas alone
can trap more than 50% of sediments from uplands when overland water flows are less than 5 cm deep
(Dillaha et al., 1989; Magette et al., 1989; Naiman and Decamps, 1997). Thus, riparian areas can buffer
stream channels against excessive sediment input.

Riparian areas and floodplains can be both  sinks and sources for sediments in streams. When streams
flood their banks, increased surface contact and friction decrease the flow velocity. The slower moving
water has a diminished capacity for keeping material in the water column in suspension, which causes
the sediments to deposit (Church, 2002, 2006). Heavy particles  such as sand are the first to be removed,
whereas finer,  lighter particles such as clays and silts take longer to deposit. In southeastern Coastal
Plain systems, sediment deposition rates from the stream to the floodplain are high because of frequent
overbank flow and relatively high sediment loads of the rivers (Hupp, 2000).

Conversely, riparian areas and floodplains can also be a source of sediment to the stream, particularly
through streambank erosion. Although streambank erosion is a natural process, it can be accelerated
through vegetational changes because root tensile strength of riparian vegetation reinforces the soil
(Naiman and Decamps, 1997; Burt et al., 2002). Streambanks that are devoid of vegetation are often
highly susceptible to channel widening (Hupp et al., 1995; Naiman and Decamps, 1997). In a study of
748 bends in four southern British Columbia streams, for example, Beeson and Doyle (1995) reported
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that bank erosion was 30 times more prevalent on nonvegetated versus vegetated banks. In a
comparison of row-crop agricultural, grazing, and forested riparian areas in central Iowa, the forested
areas exhibited significantly reduced streambank erosion rates (Zaimes et al., 2004). Certain riparian
wetland vegetation types, such as black willow (Salix nigrd), maintain bank integrity and decrease
erosion so well that they are used in river restoration and bank stabilization projects (Pezeshki et al.,
2007).

Riparian vegetation also influences stream and river geomorphology through inputs of woody debris or
logs, which in turn shape stream channels (Brummer et al., 2006; Sear et al., 2010; Collins et al., 2012).
Woody debris can enter streams through tree mortality, bank undercutting, windthrow, wildfire, floods,
landslides, and debris flows (Gurnell et al., 2002; Reeves etal., 2003). Gurnell etal. (2002) reported that
the amount of woody debris deposited into streams can range from 12 to 40 t knr1 yr-1, depending on
the type of stream and nearby vegetation. As discussed in Section 3.3.3, woody debris can alter stream
channels, trap sediments, and form new aquatic habitat (Anderson and Sedell, 1979; Harmon et al.,
1986; Nakamura and Swanson, 1993; Abbe and Montgomery, 1996; Naiman and Decamps, 1997;
Gurnell etal., 2002).

4.3.2.3    Temperature and Sunlight
Riparian areas can modify stream temperatures and the amount of light available for photosynthesis in
stream and river environments through stream shading, particularly in forested settings (Barton et al.,
1985; Gregory et al., 1991; Blann et al., 2002). Dense, overhanging vegetation greatly reduces the
intensity of light, whereas open canopies allow light to penetrate (Gregory et al., 1991). This radiant
energy, or lack thereof, strongly influences stream temperature (Barton et al., 1985; Gregory et al., 1991;
Blann etal., 2002). The maximum temperature of a stream in Oregon, for example, was 7 °C higher in a
reach where the riparian vegetation was removed compared to its temperature when it was forested.
Fifteen years of regrowth in the harvested area was required for the stream temperature to return to
preharvest levels (Johnson and Jones, 2000).

By affecting stream temperatures, shading by riparian vegetation can alter fish growth, activity, and
mortality, while also influencing their prey species (Beschta et al., 1987). Higher temperatures, for
example, can lead to greater stream invertebrate biomass (Beschta et al., 1987). The net temperature
effect on fish growth, however, depends on the balance between food availability and higher metabolic
rates (Beschta et al., 1987). Riparian vegetation enhancement can be used by managers to promote fish
habitat for certain desired species. Blann etal. (2002) investigated the degree to which different types of
riparian vegetation could increase shade, reduce stream temperatures, and promote habitat for brook
trout (Salvelinus fontinalis) in Minnesota. The researchers concluded that both forested and herbaceous
riparian vegetation shaded the stream and buffered stream temperature, and could aid in creating
appropriate coldwater trout habitat (Blann et al., 2002).

Shading of the stream by riparian vegetation also directly influences the instream net primary
productivity of aquatic plants and other photosynthetic organisms, such as algae, by altering light
availability (Gregory et al., 1991). Net primary production is greatest in open reaches and is significantly
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less in reaches that are forested and shaded (Gregory et al., 1991). For example, Gregory et al. (1991)
reported that net primary productivity in open streams in Oregon averaged 210 mg carbon (C) nr2 d-1,
whereas forested reaches of streams with deciduous vegetation averaged 58 mg C nr2 d-1. Reduced net
primary production leads to lower densities of herbivores in streams (Hawkins and Sedell, 1981;
Gregory et al., 1991). Shading can limit stream productivity (Hill and Knight, 1988; Gregory et al., 1991),
but it can also be beneficial by reducing excessive algal production in nutrient-enriched waters. Algae
can lead to excessive biological oxygen demand and turbidity and can decrease water quality in
downstream systems (Volkmar and Dahlgren, 2006).

In addition to shading by riparian vegetation, riparian areas and floodplains can influence stream and
river water temperature through hyporheic exchange (Brosofske et al., 1997; Naiman and  Decamps,
1997; Poole and Berman, 2001; Naiman et al., 2005). Hyporheic cooling of stream and river water
during warm summer periods has been observed in a wide range of settings, including large gravel bed
rivers in Oregon (Fernald etal., 2006; Burkholder etal., 2008; Seedangetal., 2008), an alpine stream in
the mountains of Colorado (Constantz, 1998), a boreal river in Sweden (Nyberg et al., 2008), and small
streams in Illinois (Peterson and Sickbert, 2006) and northern California (Loheide and Gorelick, 2006).
Important to note, however, is that hyporheic exchange can warm streams (Valett et al., 1990). Arscott
etal. (2001) found that hyporheic and other thermal regulating processes can lead to large thermal
heterogeneity of water bodies associated with complex floodplains. Hester and Gooseff (2010) argue
that, for streams impacted by human activities, restoration of hyporheic zones is essential  for the
recovery of stream functions and ecosystem services.

4.3.3   The Chemical-nutrient  Influence of Riparian Areas on Streams
Riparian areas in and outside of floodplains are instrumental in controlling the biogeochemistry of
riverine systems through (1) overbank flooding (flood pulse); (2) internal biogeochemical processes;
and (3) hyporheic exchange (Junk et al., 1989; Thurman et al., 1991; Heiler et al., 1995; Tockner et al.,
2000; Adair etal., 2004; Noe and Hupp, 2005; Valett etal., 2005; Noe and Hupp, 2007; Helton etal.,
2011; Powers etal., 2012; Bennett et al., 2015). All three mechanisms help shape nitrogen, carbon,
phosphorus, and pesticide cycling with the riverine environment.

Wetlands have been described as depositional areas in an eroding landscape (Brittain and Eikeland,
1988). Pollutants and materials relevant to discussions on water quality—such as nutrients, pesticides,
and metals—enter wetlands (e.g., Tiner, 2003c; Comer etal., 2005) through flowpaths that include  dry
and wet (e.g., rain, snow) atmospheric deposition; point sources such as outfalls, pipes, and ditches; and
nonpoint sources, such as runoff from agricultural and urban fields and lawns, drift spray,  and diffuse
near-surface water inputs (Nixon and Lee, 1986; Whigham and Jordan, 2003; Whitmire and Hamilton,
2008). For riparian/floodplain wetlands, transport from upstream reaches or through the  hyporheic
zone (Figure 2-6) is another important source of these substances. Such materials can then be
sequestered via sorption  (adsorption and absorption) or sedimentation processes, assimilated into the
flora and fauna, transformed into other compounds, or lost to the atmosphere through transformational
processes (Nixon and Lee, 1986; Johnston, 1991; Mitsch and Gosselink, 2007). These processes include

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conversion between particulate and dissolved forms of compounds via biologically mediated
degradation (e.g., Barlocher et al., 1978) and reduction-oxidation (redox) reactions (Nixon and Lee,
1986; Reddy and DeLaune, 2008). Redox reactions are essential to microbial respiration and are critical
to both defining wetland systems and understanding transformational processes that microbes mediate
(Boon, 2006; Reddy and DeLaune, 2008).

4.3.3.1    Hyporheic/Soil Processing of Nutrients
Riparian areas connect upland and aquatic environments through both surface and subsurface
hydrologic flowpaths (Figure 2-6; Naiman et al., 2005). Riparian areas act as buffers that are among the
most effective tools for mitigating nonpoint source pollution (Knight et al., 2010). These areas are
uniquely situated in watersheds to receive and process waters that pass through the root zone before
reaching streams (Gregory et al., 1991). These processes do not affect deep ground-water hydrologic
flowpaths (Figure 2-5) that enter a river or stream below the active riparian root zone. The focus of this
section, however, is on surface and shallow subsurface flows; we do not address deep ground-water
flowpaths here.

Riparian areas can significantly influence nutrients and other exports from watersheds (Gregory et al.,
1991) and can be considered areas of major nutrient transformation as subsurface waters move through
them (Dahm et al., 1998). Riparian areas remove nutrients such as nitrogen and phosphorus from water
as it flows from uplands to streams (Lowrance etal., 1997; Dosskey, 2001; Mayer etal., 2007). For
instance, Johnston (1993) reported that a floodplain wetland retained, 15.2,13.7, and 14.2% of the
solids, total nitrogen, and total phosphorus fluxes, respectively, from the watershed. The degree to
which a riparian area serves as either a source or a sink for nitrogen, phosphorus,  organic matter,
pesticides, and mercury is controlled largely by the substance's concentration in riparian soils (Gregory
et al., 1991), soil redox conditions, and hydrology (Vidon et al., 2010). For example, riparian plant
communities can release seasonal pulses of dissolved leachates derived from stream litter (Fisher and
Likens, 1973). Riparian areas are therefore central to watershed water quality management (Burt, 1997;
Lowrance et al., 1997).

4.3.3.2    Nitrogen
Riparian areas can remove dissolved nitrogen (N) in subsurface flowpaths that would otherwise flow
into streams (Vidon et al., 2010). Removal occurs via plant uptake and microbial transformations (i.e.,
assimilative uptake, assimilatory nitrate reduction to ammonium, and dissimilatory nitrate reduction to
ammonium or nitrogen gases such as dinitrogen, nitric oxide, and nitrous oxide via denitrification). One
study demonstrated that intact riparian and hyporheic zones are critical in decreasing the amount of
dissolved inorganic nitrogen that moves from headwaters to larger, downstream waters (Triska et al.,
2007). Vidon et al. (2010) showed that riparian areas remove more than half the nitrogen from surface
and shallow subsurface water transporting ammonium and nitrate through the rhizosphere (Vidon et
al., 2010). Leaching from nitrogen-fixing plants (e.g., red alder, Alnus rubrd) in riparian systems,
however, also can be a major source of nitrogen to  stream systems (Compton et al., 2003).
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Denitrification potential in surface and shallow subsurface flows is not homogeneous across the riparian
area, increasing markedly in the presence of organic carbon or anoxic conditions that create
denitrification "hot spots" (McClain et al., 2003; Orr et al., 2014). Therefore, for riparian areas to
appreciably increase nitrogen removal, flowpaths that convey nitrate-rich water into such
denitrification "hot spots" must be present (Vidon etal., 2010).

The highest denitrification potentials occur in floodplain systems where high organic matter levels,
denitrifying microbes, and saturated soil conditions are present (Vidon et al., 2010). Rates of
denitrification are greater in riparian soils nearer to streams (Gregory et al., 1991). Johnston (1993)
reported nitrate removal along a floodplain gradient of 6.6 g per 100-m distance from the stream. High
soil moisture and deposited organic matter enhance microbial activity, thereby tending to increase
denitrification (Reddy and DeLaune, 2008).

As subsurface flow passes through riparian areas, vegetative demand for dissolved nutrients also can
reduce nutrient loads (Vidon et al., 2010). More than three-quarters of the dissolved nitrate (NOs')
transported from agricultural fields to a Maryland river (Vidon et al., 2010) was removed by riparian
forests. Nitrogen was removed at a rate of 45 kg N ha-1 yr-1 as subsurface flow moved from agricultural
fields through riparian zones to nearby streams (Peterjohn and Correll, 1984). In the coastal plains of
Georgia, riparian forests retained more than 65% of the nitrogen and 30% of the phosphorus
contributed from nearby agriculture (Vidon et al., 2010). In southern Pennsylvania, a forested riparian
area had a subsurface nitrate budget with an average removal of 90 kg NOs-ha-1 yr-1, which was 26% of
the total nitrate input (Newbold et al., 2010).

4.3.3.3    Phosphorus
The movement and uptake of phosphorus in riparian areas are a function of phosphorus sources,
hydrology, and biogeochemistry (Vidon et al., 2010), with  interactions between ground water and
surface waters driving the biogeochemical processes (Hoffmann et al., 2009). Phosphorus loss and
retention in riparian areas are related to the flowpath of the water through the riparian area to the
stream (e.g., overland flow of water from nearby agricultural fields, river-water inundation of floodplain
riparian areas). Flowpath dictates the confluence and interaction of phosphorus with minerals that drive
biogeochemical cycling of phosphorus in riparian areas (Hoffmann et al., 2009). The physical processes
of sedimentation and plant uptake are active in these flowpaths and can account for particulate
phosphorus retention rates as high as 128 kg P ha-1 yr-1 and 15 kg P ha-1 yr-1, respectively (Hoffmann et
al., 2009).  Retention of dissolved phosphorus in riparian areas is more modest, with values less than 0.5
kg P ha-1 yr-1 often reported. Studies show, however, significantly higher numbers for the release of
dissolved phosphorus: up to 8 kg P ha-1 yr-1 (Hoffmann et al., 2009).

Although riparian soils  generally serve as sources of phosphorus when soils are anoxic or when mineral
dissolution releases phosphorus (Baldwin and Mitchell, 2000; Chacon et al., 2008), riparian areas are
phosphorus sinks in oxic soils (Carlyle and Hill, 2001). Portions of riparian areas where agricultural
sediments are deposited are phosphorus sources to streams if the phosphorus is desorbed and leached
but can be sinks by adsorbing dissolved phosphorus if sediment phosphorus concentrations are low
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(Dillaha and Inamdar, 1997; Sharpley and Rekolainen, 1997). Riparian areas also serve as phosphorus
sinks when upland surface runoff travels through the riparian area or when fine-grained sediment
containing phosphorus is deposited overbank onto the riparian area (Dillaha and Inamdar, 1997). These
sediments, however, can become sources of phosphorus if they are later saturated with water and iron
and manganese are reductively dissolved during anoxic conditions, thus causing them to desorb
phosphorus (Reddy and DeLaune, 2008).

4.3.3.4    Carbon and Allochthonous Inputs
Both production and consumption of organic and inorganic carbon occur in riparian areas. In areas with
reducing conditions, microbes generally oxidize organic carbon and reduce available electron acceptors,
releasing carbon dioxide gas and making the soils more alkaline (Vidon et al., 2010). This process can
result in chemical gradients in which electron acceptor concentrations decrease and alkalinity increases
along subsurface flowpaths (Burns, 1996; Cirmo et al., 2000; Bailey Boomer and Bedford, 2008).
Riparian areas, especially those in low-lying flatlands, tend to have low subsurface flow velocities
resulting in anoxic conditions, shallow water tables, and slow organic matter decomposition, as is often
seen in riparian wetlands. This is why riparian areas are active areas for biogeochemical
transformations (Vidon etal., 2010).

Allochthonous inputs from riparian areas to streams are critical to aquatic food webs, particularly in
headwater catchments (reviewed in Tank et al., 2010). Allochthonous inputs are terrestrial organic
materials that enter the stream through vegetation litter (i.e., woody debris, leaves,  and partially
decomposed plant parts), erosion, and hydrologic flows (Wetzel, 1992). In small forested watersheds,
overhanging trees provide organic matter inputs, while simultaneously reducing photosynthesis by
auto trophic organisms (Vannote et al., 1980). This dual effect makes allochthonous  inputs the primary
source of energy flow into the food webs of these streams. For example, in a New Hampshire stream the
surrounding forest supplied more than 98% of the organic matter (Gregory et al., 1991). Organic matter
inputs are important because they affect food availability to aquatic organisms by releasing organic
carbon and nitrogen into streams (Wetzel and Manny, 1972; Mulholland and Hill, 1997). For example, in
a small headwater stream near Louisville, KY, macroinvertebrate communities, which are critical food
sources for fish (Wallace and Webster, 1996), relied almost exclusively on leaf inputs (Minshall, 1967).
Excluding litter from the riparian area changed the food web structure of a North Carolina stream
(Wallace et al., 1997) and decreased its dissolved organic carbon concentrations and loadings (Meyer et
al., 1998). In addition to the impacts of total inputs, the composition and timing of allochthonous inputs,
largely determined by riparian plant species composition, also can influence instream decomposition
and aquatic invertebrates  (Cummins et al., 1989; Swan and Palmer, 2006).

Downstream, much less of the stream is directly influenced by streamside vegetation, due to larger
stream widths and consequently greater distances from the banks. This decreases the relative
importance of allochthonous inputs while concomitantly increasing the importance of instream
photosynthesis (Vannote et al., 1980). The macroinvertebrate community responds to this shift in input
types. For example, macroinvertebrate shredders that use large inputs, such as leaves, become less

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prevalent as streams increase in size. Besides changing longitudinally with stream size, riparian
allochthonous inputs also can vary seasonally, with a large pulse occurring in deciduous forests during
autumn leaf fall.

4.3.3.5    Pesticides
The roots in riparian areas can be important in removing pesticides from shallow subsurface flow,
because the labile organic matter and organic residues that accumulate near roots can increase
microbial biomass and activity (Vidon etal., 2010). Pesticides and their metabolites can be mineralized
and adsorbed where surface area contact is high and contact time with roots is sufficient (Krutz et al.,
2006). A study of the pesticides alachlor and atrazine in a riparian area notes the importance of plant
uptake in the fate of these pesticides, and suggests that vegetated buffer zones help protect water
supplies (Paterson and Schnoor, 1992). Studies examining specific pesticides—for example, isoproturon
(Benoit et al., 1999), metolachlor (Staddon et al., 2001), and atrazine (Mudd et al., 1995)-found that the
presence of vegetation, associated root zones, and accumulated organic matter increased the removal of
those pesticides (Vidon et al., 2010). Pesticide-degrading microbial populations increase after repeated
chemical applications (Gonod etal., 2006), suggesting that riparian areas can become better at
degrading pesticides that enter these zones (Vidon etal., 2010). In addition, microbial biomass has been
shown to be positively correlated with the loss of the herbicides 2,4-D (2,4-dichlorophenoxyacetic acid)
and dicamba, suggesting a relationship between the amount of microbial biomass in the soil and the
capacity of an ecosystem to degrade pesticides (Voos and Groffman, 1996).

4.3.3.6    Mercury
Mercury enters the global atmosphere primarily through waste incineration and coal combustion. It can
directly enter wetland systems or can be deposited on terrestrial areas and then transported into
riparian areas and wetlands via rainfall and runoff (St. Louis et al., 1994). Riparian soils and wetlands
are important both for mercury mobilization (Mierle and Ingram, 1991;  Driscoll et al., 1995) and the
production of methylmercury, a particularly toxic and mobile form of the element. Mercury methylation
occurs in the presence of anoxic, saturated soils high in organic matter, mercury-methylating microbes,
and mercury from either atmospheric deposition or soils (St. Louis et al., 1996). The redox conditions
found in the presence of a fluctuating water table are thought to be a strong driver of mercury
methylation (Heyes etal., 2000; Branfireun and Roulet, 2002; Branfireun, 2004). Export of mercury and
methylmercury can expose organisms in downstream aquatic ecosystems to potential toxicity
(Thurman, 1985; Driscoll et al., 1995). Mercury bioaccumulates in fish, and consumption offish is the
main human pathway for exposure to mercury (Rypel et al., 2008).

The source-sink dynamics of riparian areas with respect to mercury are  complex. Because soils
accumulate mercury, they buffer aquatic ecosystems against the full impact of this pollutant (Aastrup et
al., 1991). Because some of this mercury and methylmercury moves from soils to surface waters,
however, riparian areas might also be a source of the mercury that ends up in the aquatic food web.
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4.3.4   Biological Connections Between Riparian Areas and Streams
The dynamic nature of river systems is most apparent in riparian areas and floodplains, where a shifting
landscape mosaic supports diverse communities of aquatic, amphibious, and terrestrial plant and animal
species adapted to periodic or episodic inundation of riparian areas and floodplains (Power et al.,
1995a; Power et al., 1995b; Galat et al., 1998; Robinson et al., 2002; Toth and van der Valk, 2012;
Rooney et al., 2013; Granado and Henry, 2014). In unregulated rivers, floodplain inundation greatly
increases the area and diversity of aquatic habitats (Junketal., 1989; Tockner etal., 2000; Brooks and
Serfass, 2013). It also enables rapid cycling of nutrients imported from river channels (Section 4.3.3.2),
resulting in high primary productivity of plants and algae (Junk et al., 1989; Tockner et al., 1999). The
combination of diverse habitat types and abundant food resources makes floodplains important
foraging, hunting, and breeding sites for fish (Copp, 1989; Bestgen et al., 2000; Schramm and Eggleton,
2006; Sullivan and Watzin, 2009; Alford and Walker, 2013; Magana, 2013), aquatic life stages of
amphibians (Richardson etal., 2005), and aquatic  invertebrates (Smocketal., 1992; Smock, 1994). Many
of these organisms have growth stages or reproductive cycles timed to coincide with seasonal
hydrologic connectivity between rivers and floodplains. Thus, lateral fluctuations in hydrologic
connectivity can increase overall levels of species productivity and biodiversity in river systems (Junk et
al., 1989) and can be integral to the viability of many riverine species (Bunn and Arthington, 2002).
Here, we review examples of adaptation to and exploitation of riparian habitats by aquatic species of
plants, fish, mammals, and invertebrates.

4.3.4.1    Vascular Plants and Phytoplankton
Channels and riparian/floodplain wetlands provide habitat for aquatic vegetation, emergent vegetation,
and phytoplankton. When seeds, plant fragments,  or whole organisms move back and forth between
riparian/floodplain wetlands and the river network (via water, wind, or animal dispersal), these areas
become biologically connected. Species can disperse via overbank flow between channels and
riparian/floodplain wetlands (e.g., Schneider and Sharitz, 1988; Middleton, 2000; Nilsson et al.,  2010).
Seeds from vegetation within the channel or that have been mobilized from upstream
riparian/floodplain wetlands can be deposited on  bordering or downstream riparian areas and
floodplains (Nilsson et al., 2010), much like sediment and in many cases with sediment (Gurnell, 2007;
Gurnell et al., 2008). For example, in the southwestern United States, soil seed banks of wetland plants
can be established or replenished in floodplains when those areas are connected to a stream channel by
overbank flow (Boudell and Stromberg, 2008). In another example, 41% of plant species for which the
seeds were deposited on riparian areas during winter flood flow in two United Kingdom rivers were
wetland or aquatic plants (Gurnell et al., 2008). Overland flow or flooding also can dislodge viable plant
fragments in riparian/floodplain wetlands, which then are transported down the river network.
Fragments of seep monkeyflower [Mimulusguttatus) are easily dislodged by the relatively high  flow
velocities along the riparian-channel interface, and fragments can survive and reestablish downstream
at rates exceeding 90% (Truscott et al., 2006).
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Floodplains can function as sinks for seeds and plant fragments. For example, in a forested floodplain
wetland in Illinois, many bald cypress (Taxodium distichuni) seeds dispersed by the river network were
deposited but did not germinate (Middleton, 2000). Alternatively, establishment and reproduction of
refuge floodplain populations can become important wetland seed sources for the river network,
especially if catastrophic flooding scours vegetation and seed banks that can exist on streambeds
(Gurnelletal., 2008).

Hydrologic connectivity between channels and riparian/floodplain wetlands can significantly enhance
riparian vegetation diversity (Jansson et al., 2005) and determine floodplain wetland community
structure (Boschilia et al., 2008). For nonnative species, however, connectivity can facilitate invasion,
resulting in changes in riparian vegetation community structure. In an intermittent stream in Illinois,
tubers of the nonnative Chinese yam (Dioscorea oppositifolid) were dispersed via stormflow and
overbank flow and became established along a narrow upstream riparian area and wider channel and
floodplain more than 1 km downstream; the presence of the nonnative plant significantly reduced native
plant cover (Thomas et al., 2006). Vegetation community composition, in turn, can affect the function of
riparian areas as nutrient sources or sinks to the river network (Sections 4.3.3.2 and 4.3.3.3). Invasion
by nonnative riparian plants also can result in altered stream invertebrate diversity, among other effects
(Lecerfetal., 2007).

Seeds of aquatic and riparian plants also can be actively dispersed by animals that consume them. For
example, seeds of the aquatic emergent bur-reed [Sparganium emersum) were ingested and viably
excreted by common carp [Cyprinus carpid) (Pollux et al., 2007), which elsewhere have been observed
using channel and floodplain wetland habitat (King et al., 2003). Riparian floodplain and wetland
vegetation can also disperse and exchange seeds via terrestrial animal vectors and the wind. Animals
that travel overland can also disperse ingested seeds or seeds adhering to fur, feathers, or limbs
between riparian/floodplain wetlands and the river network (see Sections 4.3.4.2, 4.4.4, and B.3.3.3 for
discussions of animal movement). Many macrophyte species have evolved for dispersal by wind,
including some of the most invasive in North America, cattail and reed canary grass (Barrat-Segretain,
1996; Soons, 2006 and references therein). Given the proximity of riparian/floodplain wetlands and the
river network itself, dispersal of pollen and seeds between these habitats could be quite frequent. For
example, seeds of some 20 species found in floodplain wetlands in bald cypress swamps in Illinois were
caught in aerial seed traps, and dispersal of three species averaged more than 100 seeds nr2 yr-1
(Middleton, 2000).

Phytoplankton also move via water between floodplain wetlands and the river network. A river with
overbank flow can homogenize the phytoplankton communities in floodplain wetlands separated by
more than 5 km (Angeler et  al., 2010), and phytoplankton communities in river networks can be
bolstered by high-productivity conditions in temporarily connected floodplain wetlands. For example, a
portion of flow from California's Sacramento River is seasonally diverted from the main channel into the
Yolo Bypass, a nearby 240 km2 floodplain. From January to June 2003,14 and 31% of total diatom and
total green algae biomass, respectively, was produced in the floodplain (Lehman et al., 2008). This
considerable contribution of carbon to the aquatic food web, which ultimately supports downstream
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fisheries, resulted from the high net primary productivity of the floodplain. This observation is
particularly noteworthy because the median flow through the floodplain during the period of
measurement (23m s~l] was just 3% of the median flow through the main channel. Considered
collectively, these studies indicate riparian/floodplain wetlands can be both sources and sinks for
phytoplankton and water-, animal-, and wind-dispersed vascular plants with respect to the river
network.

4.3.4.2    Vertebrates
Animals, including many fish and mammals, move between riparian/floodplain wetlands and the river
network. The evidence is strong and abundant that fish can move between the main river channel and
riparian/floodplain wetlands when the channel and wetlands are hydrologically connected, even when,
in some cases, the connection is seasonal or temporary. Such wetlands provide refuge, feeding, and
rearing habitat for many fish species and augment recruitment to the river network (Boltz and Stauffer,
1989); examples include fish taxa in forested floodplain wetlands of the southeastern and southwestern
United States and salmonids of the northwestern United States such as coho salmon (Oncorhynchus
kisutch) and Chinook salmon [Oncorhynchus tshawytschd) (e.g., Wharton et al., 1982; Matheney and
Rabeni, 1995; Pease etal., 2006; Henning et al., 2007; Jeffres etal., 2008). In one section of the mainstem
Rio Grande in New  Mexico, more than 90% of the larval and juvenile fish of six captured species were
from riparian areas with zero water velocity (backwaters, former side channels, and isolated pools;
Pease etal., 2006).  Oxbow lakes are also important habitats for fish feeding and  rearing. Based on a 5-
year study of fish in oxbow lakes, Shoup and Wahl (2009) concluded that the entire floodplain should be
considered a single functioning unit that supports the overall biological integrity of a river (Section B.2).
The use of riparian/floodplain wetlands by fish depends on many factors intrinsic to the particular river
system (e.g., periodicity and duration of floodplain inundation) and the characteristics of the resident or
migratory fish community (King et al., 2003).

Fish also move between lacustrine wetlands (wetlands associated with lakes) and large  lakes when
hydrologic connections exist. Fish communities in the Great Lakes and their surrounding wetlands
become more homogeneous when surface connections between the wetlands and lake are present. Fish
use these wetlands for refuge from predators and as rearing habitat (Jude and Pappas, 1992). Miyazono
et al. (2010), studying floodplain lakes in the Yazoo River Basin, found that conditions that included
decreases in habitat connectivity, wetland buffers, and certain water quality parameters led to the
increased dominance of environmentally tolerant fish in those lakes. Fish assemblages in riparian
wetlands along the  semiarid region of the Murray River, Australia showed a large decline in diversity
when those wetlands were disconnected from the river through hydrologic modifications. This trend
was reversed after  a managed inundation treatment restored connections between the wetlands and the
river (Vilizzi et al., 2013). River-dwelling mammals also move between rivers and riparian/floodplain
wetlands, including river otters, which have been observed using wetlands extensively as latrines
(Newman and Griffin, 1994). In addition, both river otters and beavers have a strong preference for
riparian areas that  are pond- and lake-dominated (Swimley et al., 1999). Thus, movement of animals,
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especially fish, connects riparian/floodplain wetlands to the river network and supplies streams and
rivers with a source of biological materials.

In addition to acting as sources, sinks, and refuges for individual species of organisms,
riparian/floodplain wetlands can improve the overall health of biological communities. For example, a
positive relationship between wetland cover and an index of biological integrity for fish communities in
rivers was observed in 23 sites in several small catchments of the River Raisin in Michigan (Roth et al.,
1996).

Besides providing a form of biological connectivity that can link riparian/floodplain wetlands and
downstream waters, vertebrates in riparian areas can affect stream characteristics and influence various
forms of connectivity. Perhaps the most familiar example of this is the beaver (Castor canadensis).
Although beaver damming would be expected to reduce hydrologic connectivity through impoundment,
their influence can be more complex. For example, Westbrook et al. (2006) found that beaver dams in
the Colorado River affected depth, extent, and duration of inundation resulting from a 10-year flood
event. In addition, beaver dams attenuated declines in water tables during drier summer periods in 25%
of their 58 ha study area. They concluded that the main hydrologic effects occurred downstream,
however, rather than near the dam (Westbrook et al., 2006). The hydraulic head generated by the dam
raised the water level above the banks, resulting in lateral and downstream spreading of flows during
high- and low-flow periods; these effects extended over hundreds of meters. For example, mottled soils
occurred throughout the study area, suggesting that the dams caused waterlogged soils for extended
periods. Increased overbank flooding increases hydrologic connectivity between riparian areas and
streams. In contrast, when no dams were present, flooding was limited to the area immediately near the
stream channel. Beaver dams also can affect stream biogeochemistry. For example, beaver dams modify
nutrient cycling and decomposition dynamics and can affect downstream transport of materials
(Naiman et al., 1988; Naiman et al., 1994). For example, beaver-dam wetlands can serve as a source of
methylmercury (Roy etal., 2009). Beaver dams also can affect fish species, such as coho salmon  (Pollock
etal.,2004).

Vertebrates also can indirectly affect hydrologic connectivity through cascading effects on riparian plant
communities. Beschta and Ripple (2012) provide evidence from analyses at three western National
Parks for a trophic cascade model where large predators can affect the morphology of river channels
through intermediate effects on ungulate browsers and riparian plant community structure. For
example, extirpation of wolves (Canis lupus) at Yellowstone National Park by the mid-192 Os led  to an
increase in elk [Cervus canadensis] numbers. This increase caused suppression and mortality of riparian
willow (Salix spp.) communities, ultimately resulting in changes to stream morphology such as bank
erosion, decreased sinuosity, increased active channel width, and increased amount of unvegetated
alluvium (Beschta and Ripple, 2012). Based on results from the three National Parks and other sites,
Beschta and Ripple (2012) concluded that the removal of apex predators due to extirpation increased
ungulate herbivory, which altered riparian plant communities, thereby increasing bank erosion  that led
to either widening of the active  channel or channel incision. These channel alterations, in turn, reduced
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the frequency of overbank flows, which decreases hydrologic connectivity between the riparian area
and downstream waters.

4.3.4.3    Invertebrates
Stream macroinvertebrates (e.g., insects, crayfish, mollusks) and microinvertebrates (e.g., cladocerans,
copepods, rotifers, gastropods) colonize nutrient-rich riparian areas and floodplains in large numbers
during seasonal or episodic immersion by rivers and streams (Junk et al., 1989; Ilg et al., 2008).
Macroinvertebrates and microinvertebrates (also called zooplankton) are the intermediate link between
primary producers (e.g., algae), detrital pools (e.g., leaf litter), and predators (e.g., fish, amphibians) in
river food webs (Malmqvist, 2002; Woodward and Hildrew, 2002; Stead et al., 2005; Woodford and
Mclntosh, 2010). The distribution of invertebrate populations in dynamic river systems is governed by
the location of resources required for different needs and life stages, and invertebrates actively
dispersing to find and exploit resources wherever they become available (Malmqvist, 2002). As with
vascular plants, hydrologic connectivity between channels and riparian/floodplain wetlands can
significantly influence macroinvertebrate community structure in riparian areas (Paillex et al., 2009;
Yetter, 2013). For example, the species diversity and abundance of macroinvertebrates in the wetlands
of a river delta have been found to  be positively correlated with a gradient of connectivity (Dou et al.,
2015).

Invertebrates have evolved two basic strategies to exploit habitats near streams and rivers: (1) rapid
colonization of flooded areas and short life cycles that complete before floodplains dry again, or (2) use
of aquatic refuges or dormant life stages to persist in permanent waters, the hyporheic zone, or
floodplain soils between inundations (Tronstad etal., 2007). To evaluate the relative importance of each
strategy in the same river system, Jenkins and Boulton (2003) compared the abundance and species
composition of microinvertebrates emerging from floodplain sediments to those transported by
floodwater from instream habitats at reach and watershed scales. Initially, most colonizers of newly
flooded riparian habitats came from distant upstream reaches of the river network, washed
downstream by floodwaters. After a few days, however, species hatching from eggs diapausing in soils
greatly increased the diversity and size of the river/floodplain community. This study illustrates two
important points about biological connectivity of river/riparian habitats:
    1.  Stream invertebrate communities comprise species adapted to different stresses in their
       environment (in this case,  resilient species adapted to high flows and resistant species adapted
       to desiccation).
    2.  Floods that periodically connect different parts of the river network generate potential for gene
       flow across time and space by mixing individuals from different locations (e.g.,
       upstream/downstream, channel/floodplain) and different years (e.g., eggs that might have
       diapaused for tens or even hundreds of years).

The findings by Jenkins and Boulton (2003), that resting egg banks in riparian soils are important to the
persistence of aquatic species and the composition of river communities, were validated in a separate

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study by Frisch and Threlkeld (2005), who compared flood-pulse colonization in a field study with
laboratory hatching of copepod microcrustaceans from egg banks of inundated soils in Mississippi. The
laboratory samples showed that, in the absence of hydrologic connections, egg banks were sufficient for
persistence of copepod populations; the field samples showed that when hydrologic connections were
present, water dispersal and hatching from dormant stages were both important colonization pathways
for copepods. In a perched floodplain in Missouri, Fisher and Willis (2000) showed that flood-pulsed
movement of water and organisms between river channels and floodplains was bidirectional.
Adaptations by stream-dwelling invertebrates to variable moisture conditions, and rapid two-way
dispersal to exploit temporary or seasonal hydrologic connections, are strong evidence of long-term
biological connectivity between rivers and riparian areas.

Invertebrates that disperse by aerial means also take advantage of flooded riparian habitats. Tronstad et
al. (2007) investigated aerial colonization of floodplains by insects during multiple flood pulses having
different inundation periods in an unregulated river in Alabama's Coastal Plain. At least 41 genera in 21
families across 7 orders of flight-capable insects colonized floating trays placed in floodplain waters in
June, August, November, and April. Insect densities varied across the period and reached a maximum in
August of about 80,000 individuals nr2, most of which were seeking mates or oviposition sites rather
than foraging or hunting. High densities (21,291 individuals nr2) of passively dispersing (e.g., via wind
or animal vectors) microcrustaceans also were observed. Vanschoenwinkel etal. (2009) erected 9
windsocks (sampling devices for aerially dispersing organisms) near temporary rock pools for 1 month,
during which 850 viable dormant eggs, larvae, and adults from 17 invertebrate taxa were collected.
Results from these studies illustrate that aerial dispersal of multiple taxonomic orders and phyla is a
significant source of stream invertebrate colonists in newly inundated floodplain habitats.


4.4  Non-floodplain  Wetlands

4.4.1   Introduction
This section focuses on the connections and influence of non-floodplain wetlands (defined in Section
2.2.1) on downstream waters. Brinson (1993), in his hydrogeomorphic classification system,
categorized wetlands according to four geomorphic settings. This system subsequently was expanded to
the following seven classes by Smith et al. (1995): riverine, depressional, slope, mineral soil flats,
organic soil flats, estuarine fringe, and lacustrine fringe. Non-floodplain wetlands consist of certain
depressional, slope, and flats wetlands (although some  of these wetlands can occur in riparian and
floodplain wetland settings; Section 2.2.1). Depressional wetlands, as their name suggests, occur in
topographic depressions and might or might not have a surface water inlet or outlet. Common types of
depressional wetlands include kettles, potholes, vernal pools, playa lakes, and Carolina bays (Brinson,
1993). Slope wetlands (also known as seeps) are located in breaks of slopes and are sites of ground-
water discharge (Hall et al., 2001a; O'Driscoll and DeWalle, 2010). Slope wetlands include fens, which
typically are ground-water driven and have diffuse outputs (Brinson, 1993; Bedford and  Godwin, 2003).
Mineral soil flats commonly occur on interfluves, relic lake bottoms, or large floodplain terraces.

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Precipitation dominates the water sources in mineral soil flats, with little ground-water input. Wet pine
flatwoods and large playas are examples of this wetland type. Non-floodplain wetlands also include
organic soil flats. These contain extensive peatlands, or peatbogs, where the accumulation of partially
decayed organic matter dominates (Mitsch and Gosselink, 2007). Precipitation also generally dominates
the water inputs to bogs, which can connect to downstream waters via a channel outlet or diffuse
overland flow (Brinson, 1993). Bogs are generally more acidic than fens (Bedford and Godwin, 2003).
Depressional, slope, or flats wetlands also can serve as stream origins (Figure 2-18A).

Below, we examine the physical (Section 4.4.2), water quality (Section 4.4.3), and biological (Section
4.4.4) effects of non-floodplain wetlands on rivers and other downstream waters. We then briefly
consider the issue of geographic isolation in non-floodplain wetlands (Section 4.4.5).

4.4.2  The Physical Influence of Non-floodplain Wetlands on Streams
Section 2.4.1 provided a general description of how non-floodplain wetlands can connect to downstream
waters via surface and ground-water flow (Figure 2-18). In this section, we provide further details on
these connections and discuss how such connections affect streamflow.

4.4.2.1    Surface-water Connections
Non-floodplain wetlands can be connected by perennial surface flows to river networks. For example,
seeps are likely to have perennial connections to streams that provide important sources of baseflow,
particularly during summer (Morley et al., 2011). In a study in Maine, seeps were found to provide 40-
80% of stream water during baseflow periods (Morley et al., 2011). In other cases, surface connections
between non-floodplain wetlands and streams can be intermittent or ephemeral. Rains et al. (2008) and
Rains et al. (2006) showed that California vernal pools, situated on both clay and hardpan soils,
connected with streams through channels containing transient water flow (Section B.6). The series of
vernal pools on the clay soils were filled with water for 200 days of the year, and water spilled from
these wetlands through swales and channels for 60% of those days (Rains et al., 2008). McDonough et al.
(2015) found that forested Delmarvabays had seasonally intermittent surface water connections to
streams; these connections occurred during periods of low evapotranspiration and high  water tables,
that is, from mid-fall to late-spring. In contrast, surface-water connectivity of restored and prior
converted (wetlands converted to agriculture before 1985) bays was ephemeral, that is,  it occurred in
response to rainfall. The cumulative  duration of connections to perennial streams was greater and had
fewer transitions between connected and disconnected states for forested bays than for  restored and
prior converted bays (McDonough et al., 2015). Drainage of wetlands via ditching also can produce
surface water outflows from depressional wetlands directly to streams  (Section 2.4.4); ditches, however,
also can introduce nutrients and ions into  downstream waters (Brunet and Westbrook, 2012).

Even non-floodplain wetlands that are considered to be geographically isolated (i.e., completely
surrounded by uplands), can have surface-water outflows that connect them to other water bodies
(Figure 2-18B). Tiner (2003b) identifies vernal pools as 1 of 10 types of geographically isolated
wetlands. Yet, as just discussed, the studies by Rains et al. (2008) and Rains et al. (2006) indicate that

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vernal pools can be connected to stream networks by channels. As another example, a recent study of
depressional wetlands in the Texas Gulf Coast area showed that, although classified as geographically
isolated, these wetlands are actually connected to nearby waterways via intermittent streams (Wilcox et
al., 2011). During a study period of almost 4 years, nearly 20% of the precipitation that fell on a wetland
complex flowed as surface runoff through the stream to a nearby water body, the Armand Bayou
(Wilcox et al., 2011). Non-floodplain wetlands also can have temporary hydrologic connections to each
other. Such connections can occur through the expansion and contraction of surface water that occur
between wet and dry periods (e.g., Figure 2 in Niemuth etal., 2010) and through fill and spill of surface
waters. One consequence of fill-and-spill behavior is that the contributing area of such a wetland is
dynamic and has a nonlinear relationship to potential storage area (Shaw et al., 2012; Shaw et al., 2013).
In the intermontane West, evidence suggests that depressional wetlands can connect to one another via
temporary overland or shallow ground-water flows (Cook and Hauer, 2007). In the prairie pothole
region, temporary overland connectivity between potholes has been observed in wet years. In 1996,
during heavy spring rains, an estimated 28% of the wetlands in the study area had surface-water
connections to at least one other wetland (Leibowitz and Vining, 2003). Le and Kumar (2014) analyzed
topographic depressions in five study areas across the United States and found that hydrologic
connectivity—as determined by nearest neighbor distances—followed a universal power law
distribution. One implication of this distribution is that, although most depressions are connected over
short distances, a few are connected by long distances, which could cause rapid increases in hydrologic
connectivity as the system wets up (Le and Kumar, 2014). However, the distribution can be altered
through wetland drainage (Van Meter and Basu, In press). Although some of these studies focused  on
wetland-to-wetland connections, the findings illustrate (1) the potential for geographically isolated
wetlands to exhibit temporary surface water connections with other water bodies, and (2) that
interacting wetland complexes might best be understood as a functional unit (Section 4.4.5).

4.4.2.2    Ground-water Connections
In addition to surface-water connections, ground-water flow can connect non-floodplain wetlands  with
other water bodies, potentially over great distances (Figures 2-5 and 2-18C). Many studies have shown
that non-floodplain wetlands can connect to ground water, either receiving ground-water discharge
(flow of ground water to the wetland), contributing to ground-water recharge (flow of water from  the
wetland to the ground water), or both (e.g., Lide et al., 1995; Devito et al., 1996; Matheney and Gerla,
1996; Rosenberry and Winter, 1997; Pyzoha etal., 2008). For example, a 1989 study of four North
Dakota prairie pothole wetlands by Arndtand Richardson (1989) clearly demonstrated ground-water
connections as one wetland recharged ground water, one was a flow-through wetland, and one was a
discharge system. Hunt et al. (2006) found that benthic invertebrate communities were correlated with
amounts of ground-water discharge to stream-wetland complexes in northern Wisconsin. Using stable
hydrogen and oxygen isotopes in water, Matheney and Gerla (1996) concluded that, although most of
the water in a depressional prairie wetland came from precipitation, ground-water connections
accounted for the high salinity of the wetland soil. The high salinity is indicative of net ground-water
discharge to the wetland (Brinson, 1993). Min et al. (2010) reported that 38% of rainfall that entered

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four historically geographically isolated wetlands in Florida was recharged to ground water. A literature
survey by Bullock and Acreman (2003) found 69 studies making reference to ground-water recharge
from wetlands; of these, 32 studies observed ground-water recharge from a wetland, whereas 18 studies
did not

Ground-water flow-through wetlands are sites of both ground-water discharge and recharge, in essence
a surface expression of the ground-water system (Richardson et al., 1992; Kehew et al., 1998; Ferone
and Devito, 2004). In these wetlands, ground-water discharge generally flows into the wetland on one
side or area, and flows back into the ground water on the other side or area of the wetland. This dynamic
has been shown in many locations, including prairie potholes (Richardson et al., 1992), wetlands in
glacially formed landscapes in southwest Michigan (Kehew et al., 1998), Alaskan ponds (Rains, 2011),
Florida cypress dome systems (Sun et al., 1995), and small Wisconsin lakes (Born et al., 1979). The lakes
and wetlands of the Nebraska Sand Hills are also predominantly flow-through and an expression of a
large regional ground-water system (Winter, 1999). The flow-through wetland influences the chemistry
of the transiting, shallow ground water. Kehew et al. (1998) found a wetland of this type diluted
nitrogen concentrations in the ground  water of an agricultural watershed.

Whether a wetland recharges ground water, is a site of ground-water discharge, or both, is determined
by topography, geology, soil features, and seasonal position of the water table relative to the wetland.
Shedlock et al. (1993), for example, concluded that ground water discharged into a bog along Lake
Michigan through a breach in the sediments underlying the wetland. In  dry periods when water tables
are low, water tends to move from wetlands into the ground water, while in wetter periods with higher
water tables, water can flow in the opposite direction from shallow ground water into the wetlands
(Phillips and Shedlock, 1993; Pyzoha etal., 2008; Mclaughlin etal., 2014). Lide etal. (1995) observed
both ground-water flow into and from  a Carolina bay wetland, with discharge to the wetland when the
water table was high and recharge to the ground water when the water table was low. Sun et al. (1995)
observed similar phenomena in a Florida cypress dome. This exchange and temporary storage of water
represents a lag function that can make wetlands particularly important for ground-water recharge
during dry periods. Rosenberry and Winter (1997) indicated that ground-water discharge to a wetland
often alternates with flow from the wetland to ground water, and the direction  of flow is controlled by
the balance of recent precipitation with current evapotranspiration demands.

The magnitude and transit time of ground-water flow from a wetland to other surface waters depends
on the intervening distance and the properties of the rock or unconsolidated sediments between the
water bodies (i.e., the hydraulic conductivity of the material). In some carbonate or volcanic rocks, for
example, ground water can flow relatively freely through large openings; while in unconsolidated
material—such as gravel, sand, silt, or clay—the spaces between particles determine the time required
for water to flow a given distance (Winter et al., 2003). In porous material, such as gravel, water can
travel a distance of a kilometer in a few days; in fine-textured materials, such as silt or clay, hundreds to
thousands of years might be required for a single parcel of water to travel the same distance (Winter
and LaBaugh, 2003).
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In agricultural regions, the transit time of subsurface flows can be decreased substantially by artificial
subsurface drainage pipes, known as tile drains (Section 2.4.4; Schiller et al., 2012). Wetlands in these
areas are sometimes fitted with inlets that connect directly to tile drains, quickly moving temporarily
ponded water through the subsurface and to outlets that discharge directly to ditches or streams
(Tomer etal., 2010).

In summary, non-floodplain wetlands can have a range of hydrologic connectivity with other waters
(Figure 2-18). Non-floodplain wetlands can be connected by permanent, intermittent, or ephemeral
surface flows through swales or channels, or be connected to other water bodies via shallow or deep
ground-water flows. Conversely, a wetland can be isolated hydrologically if it lacks surface water and
ground-water connections entirely and evapotranspiration is the dominant form of water loss. A
wetland also can be hydrologically isolated from streams and rivers if it recharges a ground-water
aquifer that does not feed surface waters. Wetlands that lack surface connectivity in a particular season
or year can be connected, nevertheless, in wetter seasons or years. A wetland that serves as the origin of
a stream will have a permanent or temporary surface water connection with a stream network through
a stream channel, unless the wetland feeds an endorheic stream (Sections 3.2 and B.5.5.1).

4.4.2.3    Effects  of Non-floodplain  Wetlands on Streamflow
Non-floodplain wetlands can affect streamflow by altering baseflow or stormflow (Section 2.2.2; Figure
2-8) through several mechanisms, including surface storage and ground-water recharge. Depressional
wetlands effectively store water because the aboveground portion of the wetland contains a largely
empty volume for water storage, in contrast to belowground water storage where only part of the
volume is available for water storage, for example, due to soil particles (i.e., the specific yield; Johnson,
1967; McLaughlin etal., 2014). Large-scale studies have shown that wetlands, by storing water, reduce
peak streamflows, and thus, downstream flooding. Hubbard and Linder (1986), for example, calculated
the water retention capacity of more than 200 closed depressional prairie potholes in northeastern
South Dakota. They observed that a large amount of snowmelt and precipitation could be cumulatively
held by many small wetlands, reducing the potential for flooding at downstream locations. Similarly, a
USGS study in the prairie pothole region  found that wetlands—including both depressional and
nondepressional types—stored about 11-20% of the precipitation thatfell in a given watershed, and
that storage could be increased by wetland restoration (Gleason et al., 2007). Vining (2002) concluded
that wetland storage in the Starkweather Coulee subbasin of North Dakota likely resulted in decreased
streamflow. Rovansek et al. (1996) found snowmelt to be the most important source of water for
wetlands and ponds in the Alaskan Arctic Coastal Plain, and that these wetlands and ponds functioned as
surface storage, thereby removing water from the snowmelt floods.  However, Ford and Bedford (1987)
note that in permafrost-dominated areas of Alaska, wetland soils tend to be frozen during snowmelt
events, resulting in a significant proportion of these floodwaters running directly to streams, thus
rendering these wetlands unimportant in streamflow regulation. Likewise, Rouletand Woo (1986)
found that wetlands in the Continuous Permafrost Region of Canada tended to be unimportant for either
long-term water storage or streamflow regulation.
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Regression equations developed to predict peak flows during flooding events generally use lake and
wetland storage areas as variables. Using this approach for Wisconsin watersheds, Novitzki (1979)
estimated that peak flood flows were only 20% as large in watersheds with 40% lake and wetland area
relative to watersheds without lakes or wetlands. Johnston et al. (1990) found that small losses of
wetlands in watersheds with <10% wetlands could have major effects on flood flow in basins around
Minneapolis, Minnesota. Wang et al. (2010) modeled the influence of wetlands on hydrologic processes
in Manitoba and Minnesota and found that the loss of 10-20% of the wetlands in the study basins would
increase peak discharge by 40%. Similarly, Yang et al. (2010) calculated restoration of 600 ha of
wetlands in a 25,139 ha watershed would decrease peak stream discharge by 23%. Peak streamflows
were shown to be negatively correlated with lake and wetland storage in Minnesota (Jacques and
Lorenz, 1988), although a later study found peak flows to be correlated with lake storage only and not
wetland storage (Lorenz etal., 2010).

The ability of wetlands to reduce flooding via storage varies with topography, wetland type, antecedent
moisture conditions, and available water storage capacity. Using stable hydrogen and oxygen isotopes of
water, McEachern etal.  (2006) found that snowmelt in boreal forests was discharged rapidly in a sloped
watershed. In contrast, in a lowland watershed, much of the snowmelt was stored by wetlands,
particularly by bogs with stream channel outlets. In  northern Canada, stream runoff was positively
correlated with slope and the presence of channel fens, but negatively correlated with lowland
depressional bogs (Quinton et al., 2003). In a Light Detection and Ranging (LiDAR)-based assessment of
depressional wetlands in Florida, Lane and D'Amico (2010) found an average potential wetland water
storage capacity of  1,619 m3 ha"1, with values ranging from 1,283 m3 ha-1 for palustrine  scrub-shrub
wetlands to 2,906 m3 ha-1 for palustrine aquatic-bed wetlands. A literature review found that four out of
four studies that examined  surface  water depressions having no direct connectivity to a  river system
concluded that those wetlands reduced or delayed flooding (Bullock and Acreman, 2003). Findings were
more varied for slope wetlands with direct connectivity to a river: 26 of 62 studies found reduced
flooding, while 27 of the 62 studies concluded that those wetlands increased flooding.

In addition to wetland type, antecedent moisture conditions and available storage capacity also
influence wetland water retention.  The wetlands noted above, that serve as stream origins, likely
increased flood peaks under saturated conditions, with low additional wetland water storage capacity
(due to spring rains or snowmelt, for example), and  thus conveyed any additional precipitation rapidly
downstream (Bullock and Acreman, 2003). Similarly, Branfireun and Roulet (1998) concluded that prior
saturation of upland areas immediately surrounding a wetland produced increased stoonflows. This
might mean that wetlands have less attenuating effect on larger floods because floods commonly occur
during saturated conditions.

Besides affecting peak flows and downstream flooding, non-floodplain wetlands can alter baseflow or
stormflows during dry periods. Ground-water discharge wetlands that are connected to  streams, such as
fens or seeps, are important sources of baseflow (Morley et al., 2011). Moreover, wetlands can be focal
points for ground-water recharge and thus might contribute to baseflow. Rains (2011), for example,
found that perched and flow-through ponds in southwestern Alaska were sites of net ground-water
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recharge. Given the high prevalence of ponds on the landscape (Rains, 2011), these wetland types
cumulatively could substantially affect stream baseflow via ground-water inputs.

Other wetlands, however, might actually reduce flows during dry periods. Bullock and Acreman (2003)
concluded that this was the case in two-thirds of the studies they surveyed. Antecedent moisture
conditions and available wetland storage could partially explain this finding, in combination with
relatively high evaporation rates from wetland-dominated landscapes (Bullock and Acreman, 2003).
One study cited in their review (Boelter and Verry, 1977) noted that two storms of nearly equal volume
and intensity produced different runoff responses from the same peatland. One storm occurring in the
spring at a time of already high water tables led to runoff. The other, in midsummer at a time of low
water tables, increased the water depth in the peatland but did not exceed the wetland's water storage
capacity, precluding runoff. This mechanism has been observed in simulations of prairie pothole
hydrology, in which wetlands reduced streamflow until storage capacity was exceeded (Haan and
Johnson, 1968). Thus, wetlands can function as a sink in dry periods if storage capacity is not exceeded
and evaporation rates surpass ground-water recharge. Where storage capacity is exceeded during storm
events in otherwise dry periods, watersheds containing extensive wetlands can require more time for
water discharge to rise and fall in response to storm events (Lindsay et al., 2004). This finding suggests
that watersheds with wetlands take longer to fill and exceed water-holding capacity than watersheds
without wetlands and so, in this case, they provide a lag function by releasing water downstream more
slowly.

Non-floodplain wetlands also can reduce the variability of baseflow through landscape hydrologic
capacitance (McLaughlin etal., 2014). McLaughlin etal. (2014) simulated the effects of geographically
isolated wetlands on the variation in baseflow and found that the magnitude of this effect increased with
total wetland area. Holding area constant and increasing the number of wetlands (while decreasing their
size) also increased this capacitance. The effect of these wetlands on baseflow was the result of
differences in specific yield (the change in output or input depth  from evaporation or rain per change in
water level) between wetlands and uplands, which causes flow reversals between them (McLaughlin
and Cohen, 2013; McLaughlin et al., 2014). Specifically, water flows from upland areas to wetlands
(wetland discharge) during wet periods and from wetlands to uplands (wetland recharge) during dry
periods, thereby buffering water tables and baseflow.

4.4.3   Effects of Non-floodplain Wetlands on Water Quality
Non-floodplain wetlands can affect water quality of rivers and other aquatic systems through processes
that can be generalized as source and sink functions, often mediated by transformational processes (see
Section 4.3.3 for details on specific mechanisms). In some cases, non-floodplain wetlands directly modify
the water quality in downstream waters through their relative lack of surface water connections; this
modification is accomplished by removal, sequestration, or transformation of pollutants such as
nitrogen, phosphorus, and metals through processes described by Ewel and Odum  (1984), Mitsch et al.
(1995), Reddy and DeLaune (2008), and Kadlec and Wallace (2009), among others. Although non-
floodplain wetlands can lack surface water connections to downstream waters, surface and near-surface

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hydrologic connections to downstream waters do occur in many non-floodplain systems (Section 4.4.2;
Figure 2-18; Sun etal., 1995; Whigham and Jordan, 2003; Wilcox etal., 2011), providing pathways for
materials transformed in non-floodplain wetlands (such as methylmercury or degraded organic matter)
to reach and affect other aquatic systems.

Below we show that non-floodplain wetlands are areas where extensive microbially mediated processes
occur that can affect downstream waters. In Section 4.4.3.1, we describe how non-floodplain wetlands
are sources for dissolved organic matter and entrained elements like carbon, nitrogen, and phosphorus,
which are important components of food webs in downstream waters. Dissolved organic matter is also
shown to be important in regulating whole-lake acidity and buffering capacity. Mercury is another
material affected by microbial processing in non-floodplain wetlands; mercury can be transported along
with dissolved organic matter to downstream waters, where it can become incorporated into the food
web with potentially deleterious effects. In Section 4.4.3.2, we discuss how non-floodplain wetlands
serve as sinks by sequestering or transforming materials, thereby affecting the chemical, physical, or
biological condition of downstream waters. Nitrogen, nitrate, ammonium, and phosphorus compounds
are shown to be removed or assimilated—often at high rates—in non-floodplain wetlands. Pesticides,
metals, and other potential pollutants also can be sequestered or assimilated in non-floodplain wetlands.

4.4.3.1    Non-floodplain Wetlands as Sources for Downstream Waters
Like all wetlands, non-floodplain wetlands contain diverse microbial populations that have adapted to
hydrologic,  physical, and chemical extremes (Reddy and DeLaune, 2008). Microbial populations abound
in wetland systems; for example, Boon (1991) reported that Australian wetlands contained 100 times
more microbes in the  water column than nearby rivers,  with up to 157 x 109 cells Ir1. Functions that
occur in non-floodplain wetlands can affect streams, rivers, and lakes when compounds that are
transformed in wetland environments move to downstream waters through overland flow or shallow
ground water (Section 4.4.2; Winter et al., 2003). Two processes that occur in non-floodplain wetlands
(and in riparian/floodplain wetlands) are useful to illustrate the influence of non-floodplain wetlands on
downstream waters: the methylation and transport of the bioaccumulating pollutant mercury, and the
breakdown and transport of organic compounds to receiving waters.

Freshwater wetlands/peatlands are areas of active methylmercury (MeHg) production (Grigal, 2002).
Ullrich et al. (2001) noted that methylmercury production was linked to low pH, low salinity, and
presence of decomposable organic matter in reducing environments. Sulfate-reducing bacteria are
primarily responsible for biological mercury methylation and thrive in the reduced conditions at
wetland aerobic/anaerobic boundaries (Benoit et al., 1999); the addition of sulfate (e.g., through
atmospheric acid deposition) increases the formation of methylmercury in peatlands (Branfireun et al.,
1999). Once formed through microbial (or other) processes, mercury and methylmercury export is
controlled by the export of organic matter, such as dissolved organic compounds and humic and fulvic
acids (Linqvist et al., 1991; Mierle  and Ingram, 1991; Driscoll etal., 1995). Methylmercury can be
translocated in watersheds having non-floodplain wetlands by entrainment with organic matter exports.
It also can move through near-surface and surface flows from non-floodplain peatlands to downstream

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waters. For example, Branfireun et al. (1996) reported 58% of MeHg-laden peat porewater leaving a
headwater catchment study area occurred during stormflow, 41% during baseflow, and 1% transported
via ground water. St. Louis et al. (1994) found that boreal forest catchments in Minnesota with non-
floodplain wetlands reduced total mercury concentrations, but had yields of methylmercury from
wetlands that were 26-79 times higher than upland areas. This yielded 1.84-5.55 mg MeHg ha-1 yr-1 to
streams in the Great Lakes basin, where mercury could be incorporated into lake-wide food webs.
Hurley et al. (1995) contrasted MeHg yields from different land use groups in Wisconsin and found that
wetland/forest sites were higher than agricultural/forested and agricultural-only sites. Similarly,
Porvari and Verta (2003) found that bioaccumulating methylmercury export from non-floodplain
peatlands to downstream waters ranged from 0.03 to 3.8 ng MeHg Ir1, and that catchments with greater
wetland abundances had greater methylmercury export.

Export of dissolved organic matter can have negative effects on downstream waters because
contaminants, such as methylmercury and other trace metals, can be adsorbed to it (Thurman, 1985;
Driscoll et al., 1995). Dissolved organic matter, however, is also an important source of energy for
downstream aquatic communities (Hobbie and Wetzel, 1992; Reddy and DeLaune, 2008). Wetlands are
the principal source of dissolved organic compounds to downstream waters in forested ecosystems
(Mulholland and Kuenzler, 1979; Urban et al., 1989; Eckhardt and Moore, 1990; Koprivnjak and Moore,
1992; Kortelainen, 1993; Clair etal., 1994; Hope etal., 1994; Dillon and Molot, 1997; Gergel etal., 1999).
Over prolonged periods, reductions in dissolved organic carbon (DOC) export (e.g., through wetland
conversion or degradation or alterations in hydrology) decrease the ability of downstream waters to
support primary productivity, due to reduced export of entrained carbon, nitrogen, sulfur, and
phosphorus (Hedin etal., 1995; Nuff and Asner, 2001). Changes in DOC export also affect the pH and
buffering capacity of downstream aquatic systems (Eshelman and Hemond, 1985) and their exposure to
damaging UV-B  rays (Schindler and Curtis, 1997). Boreal forest basins composed of non-floodplain
wetlands in central Ontario were found to export between 11.4 and 31.5 kg C ha-1 yr-1 to downstream
waters (Creed etal., 2003). Furthermore, near-surface lateral transport of DOC explained 88% of the
variation in basin DOC export to lake systems where it directly affected pH and buffering capacity. Other
studies have similarly shown a relationship between the proportion of wetlands in a watershed and the
average annual concentration of DOC in the receiving streams of that area, and other areas of the boreal
forest/Precambrian Shield (Urban et al., 1989; Eckhardt and Moore, 1990; Koprivnjak and Moore, 1992;
Detenbeck et al., 1993; Clair et al., 1994; Hope et al., 1994; Dillon and Molot, 1997; Johnston et al., 2008).

The export of dissolved organic compounds from non-floodplain wetlands also can affect the acidity of
downstream waters. Gorham et al. (1986) addressed watershed factors associated with lake and forest
acidification in Nova Scotia, Canada. In addition to atmospheric deposition of acid precipitates, they
found that the ratio of non-floodplain muskeg peatlands to lakes was significantly correlated with lake
acidification, as  muskeg wetland-dominated watersheds exported high-molecular-weight organic acids
via either overland or shallow ground-water flow. Further linking non-floodplain wetlands to lakes,
Gorham et al.  (1986) reported that even small amounts of humic DOC can greatly affect lake water pH;
the pH of waters with a dissolved organic carbon value of 4.5 mg DOC L-1 (the log-normal mean) was

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100 times more acidic than waters with a dissolved organic carbon of <1 mg DOC Ir1 (the minimum
concentration).

4.4.3.2    Non-floodplain Wetlands as Sinks and Transformers for Downstream Waters
The wetland literature is replete with examples of wetlands improving water quality through
assimilation, transformation, or sequestration of nutrients and other pollutants (e.g., Ewel and Odum,
1984; Nixon and Lee, 1986; Johnston, 1991; Detenbeck et al., 1993; Mitsch and Gosselink, 2007; Reddy
and DeLaune, 2008; Kadlec and Wallace, 2009). These functions act on the large pool of pollutants that
are available through nonpoint sources. Non-floodplain wetland processes that affect pollutant
attenuation include denitrification, ammonia volatilization, and microbial and plant biomass
assimilation (Reddy and DeLaune, 2008). Other pollutants in wetland systems can be retained through
sedimentation, sorption and precipitation reactions, biological uptake, and long-term storage in plant
detritus (Reddy et al., 1999; Reddy and DeLaune, 2008).

Non-floodplain wetlands act as sinks and transformers for various pollutants. For example, high levels of
human sewage were applied to a forested non-floodplain wetland site for 4.5 years (Ewel and Odum,
1984 and chapters therein). More than 95% of the phosphorus (P), nitrate, ammonium, and total
nitrogen (N) were removed by the wetland during the study period (Dierberg and Brezonik, 1984), and
66-86% of the nitrate removed was attributed to the process of denitrification. In another example,
phosphorus retention in non-floodplain marshes of the lower Lake Okeechobee basin ranged from 0.3 to
8.0 mg soluble reactive P nr2 d-1 (Dunne etal., 2006). This retention represents a sizeable amount of
phosphorus removal, because only about 7% of the watershed comprised non-floodplain marsh.
Similarly, wetlands in the Lake Okeechobee, Florida basin were found to have greater storage of total
phosphorus than the uplands in which they were bedded, 236 kg ha-1 vs. 114 kg ha-1 (Cheesman et al.,
2010). These findings were echoed by Dunne etal. (2007), who reported that more phosphorus was
stored in wetland plant biomass and soil than in corresponding upland compartments, with wetland
surface soils (0-10 cm) representing the largest phosphorus reservoir (>87%) and soil organic matter
accounting for >69% of the soil total phosphorus variability. They further suggest that restoring 5-20%
of the geographical isolated wetland area in priority basins draining to Lake Okeechobee, Florida, could
increase phosphorus storage in geographical isolated wetlands by up to 13 kg P ha-1, mostly through
increased soil organic matter with its concomitant phosphorus in wetland soils (Dunne et al., 2007).
Marton et al. (2014) found that mean phosphorus sorption was approximately two to three  times
greater in natural depressional wetlands than in restored wetlands and agricultural fields (297,114, and
86 mg P kg soil-1, respectively). Marton et al. (2014) also found that depressional wetlands sorbed twice
as much phosphorus as riparian systems. Craft and Casey (2000) reported similar accretion rates in
depression and floodplain wetlands of Georgia for sediment, organic carbon, and nitrogen, and
significantly highly floodplain storage of phosphorus. Cohen et al. (2007) found that riparian wetlands
had higher phosphorus-sorption capacities than non-riverine wetlands. Non-floodplain wetland flats
studied in Maryland and Delaware had microbially mediated denitrification enzyme activity (an
indicator of potential denitrification) rates of 0.06-0.76 mgN kg-1 d-1 (Jordan etal., 2007). Because flats
comprise greater than 70% of the wetland area in the basin, this value indicates a significant
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denitrification capacity. Marton et al. (2014) found that depressional wetlands denitrified at twice the
rate upland systems did, 12.3 ± 4.5 ng N g-1 hr1 versus 5.3 ± 1.7 ng N g-1 hr1. Craft and Chiang (2002)
determined that wetland soils stored a disproportionately large share of nitrogen, compared with
upland soils, in spite of uniform soil organic matter across the landscape. A non-floodplain bog in
Massachusetts was reported to sequester nearly 80% of the system's various nitrogen inputs, including
precipitation that had a range of 1.2-1.9 mg N Ir1 (Hemond, 1983). Prairie pothole wetlands in the
upper Midwest removed >80% of the nitrate load via denitrification (Moraghan, 1993). A large non-
floodplain prairie marsh removed 86% of nitrate, 78% of ammonium, and 20% of phosphate through
assimilation and sedimentation, sorption, and other mechanisms (Davis et al., 1981). Geographically
isolated, non-floodplain wetland systems in Michigan were found to remove nitrate-nitrogen (NOs-N)
and sulfate (S042-) at rates of 0.04-0.55 mgN03-N Ir1 ha-1 and 0.06-0.30 mgS042- L-1 ha-1. These rates
are significant, considering that nitrate-nitrogen pollution of ground water in Michigan was reported to
average 0.50 mgN03-N L-1 (Whitmire and Hamilton, 2008). Bhadha etal. (2011) found that infiltration
to the ground accounted for 14% of phosphorus loss from two historically isolated wetlands in a Florida
study area, suggesting that near-surface flow gradients are important to landscape-level phosphorus
dynamics. Together, these studies indicate that sink removal of nutrients by non-floodplain wetlands is
significant and geographically widespread.

Other pollutants and compounds can be mitigated by non-floodplain wetland sink and transformation
processes. For example, microbial methanogenesis completely removed the pesticide atrazine from a
mountainous bog in North Carolina (Kao et al., 2002). The environmental contaminants cobalt (Co) and
nickel (Ni) can be phytoremediated by wetland plants common in forested non-floodplain wetlands of
the Southeast; plant concentrations were found to range from 1 to  530 mg Co kg-1 and up to 250 mg
Ni kg-1 (Brooks et al., 1977). A bog in Massachusetts that Hemond (1980) extensively studied acted as a
sink and annually stored 54 mg magnesium nr2, 3 6 mg potassium nr2, and 46 mg lead nr2; the bog also
provided acid-rain buffering for downstream waters. Based on the literature, Boon (2006)  concluded
that wetland microbial communities can mediate processes that degrade diesel fuel and other
hydrocarbons, pesticides, heavy metals and metalloids, and chlorinated solvents that can pollute ground
water.

4.4.4   Biological Connections  Between  Non-floodplain Wetlands and
         Streams
Many of the same factors that affect movement of organisms between riparian/floodplain wetlands and
the river network (Section 4.3.4)  govern movement of organisms between non-floodplain wetlands and
the river network. Non-floodplain wetlands, however, are generally farther from stream channels than
riparian/floodplain wetlands, which reduces hydrologic connectivity. The distance, number, and variety
of heterogeneous landscape patches (including barriers) over which organisms must disperse also can
be greater. Organisms have evolved numerous complex dispersal strategies to overcome non-floodplain
flows, reduced hydrologic connectivity, and increased geographic distance between habitats and
spatially subdivided populations. Passive transport (e.g., wind dispersal, "hitchhiking" on other animals)
and active movement (e.g., walking, crawling, flying) are common modes of dispersal that can establish
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connectivity in the absence of hydrologic flows. Such dispersal events are often sporadic and
asymmetric in non-floodplain wetland landscapes, making them more difficult to observe than surface
water flows. Their effects on community structure and diversity—including metapopulation effects of
wetland-to-wetland connectivity—have been well documented (e.g., Wellborn et al., 1996; Snodgrass et
al., 2000; Julian et al., 2013), especially for amphibians. Other effects, such as water quality and
population or species persistence, are not well understood. Below we review the various dispersal
mechanisms that operate in non-floodplain wetland landscapes.

Despite being sessile, plants have evolved many adaptations that facilitate dispersal. Considerable
attention has been given to waterborne dispersal of aquatic and emergent macrophytes (Nilsson et al.,
2010), which can play a role in non-floodplain wetlands that are periodically connected hydrologically
to river networks. In addition, significant numbers of such plants can be dispersed as seeds or pollen by
wind (Soons, 2006). Wind dispersal enables colonization of geographically isolated non-floodplain
wetlands such as prairie potholes (Galatowitsch and van der Valk, 1996). Given that geographically
isolated wetlands are surrounded by uplands, using wind as a vector carries the relatively high risk that
propagules of obligate wetland plants will land in unsuitable habitat. Plants have developed colonization
strategies to compensate for such risks. For example, Soons and Heil (2002) showed that producing
large numbers of seeds increased colonization success of short- and long-distance dispersing grassland
forbs; results from this and other studies are being applied to models of wetland dispersal and
colonization (e.g., Soons, 2006). Viable seeds or vegetative plant parts also can travel great distances
within the guts of or externally attached to migratory birds (Murkin and Caldwell, 2000; Amezaga et al.,
2002; Figuerola and Green, 2002), which move between non-floodplain wetlands and river networks,
depending on temporally dynamic habitat availability (Murkin and Caldwell, 2000; Haukos et al., 2006
and references therein).

Identifying specific source and recipient populations for any organism over these distances can be
challenging, but especially for plants having passively mobile life stages that cannot be precisely tracked.
Determining whether wetlands function as sources to or recipients of plant propagules from river
networks is especially difficult. Genetic similarity between populations can provide general evidence of
connectivity between non-floodplain wetlands and the river network. Sawgrass (Cladium jamaicense)
populations in Everglades wetlands showed low population genetic divergence at distances greater than
100 km; wind pollination and water dispersal of propagules through flooding likely keeps channel and
wetland populations genetically similar (Ivey and Richards, 2001). Another approach that can provide
evidence for dispersal is community-level surveying, which takes into account local determinants of
community composition and structure. Controlling for local conditions like rainfall and soil type, a study
in Connecticut (Capers et al., 2010) found that bodies of water—from small isolated wetlands to large
lakes—that were located closer together had more similar plant communities. This finding suggests
biological connectivity between proximal lakes and wetlands.

Recent evidence suggests that invertebrate hitchhiking on birds and mammals is more common than
previously thought (Figuerola and Green, 2002; Figuerola etal., 2005). Allen (2007) trapped
zooplankton dispersing from a pond in Illinois and found that animals wider than 3 cm were the primary
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vector of reproductive adult zooplankton forms. These results suggest that animals moving among
water bodies can be an important factor in structuring non-floodplain wetland invertebrate
metapopulations. Frisch et al. (2007) found that diapausing invertebrate eggs that dispersed by
hitchhiking on birds had higher incidences of hatchingin January (59.4%) than in November (11.5%).
These invertebrates included nematodes, zooplankton (i.e., rotifers, ostracods, copepods), and insects
(i.e., crane flies, nonbiting midges, hemipterans). This study indicates that winter migrations of aquatic
birds can be an important mechanism for spring colonization of habitats separated by hundreds or even
thousands of kilometers. Studies have thus shown that migratory birds can passively connect viable
plant matter, macroinvertebrates, and zooplankton from disparate habitats across the landscape, with
likely—although unresolved—impacts on food web dynamics (Polls etal., 1997).

The scientific literature has many examples of migratory birds—especially migratory waterfowl,
including cranes, geese, ducks, and shorebirds—actively moving between and using the different
available resources of estuarine, riverine, and riparian systems and non-floodplain wetlands. For
example, wood ducks (Aixsponsd) are found throughout freshwater deciduous forests of North America.
Preferred breeding sites include river floodplains, remote ponds, and woodland pools that receive
snowmelt and spring rain, the latter particularly indicative of non-floodplain wetland use (Haramis,
1990). Below we provide several examples of this type of biological connectivity that can connect non-
floodplain wetlands to each other and to other aquatic systems.

Approximately 80% of the entire North American population of redhead ducks (Aythya americand)
winters along coastal Texas and northern Mexico (Weller, 1964). Woodin (1994) identified more than
20,000 redheads using both estuarine systems and freshwater wetlands, reporting that the estuarine
systems were exclusively used for feeding, while freshwater coastal pond wetlands were used  almost
exclusively for drinking water and courting (Mitchell et al., 1992). The coastal ponds redheads used
were seasonal basins, which frequently dried completely (Ballard etal., 2010). Ballard etal. (2010)
further noted that although the ponds were densely distributed in coastal Texas (up to 4.8 coastal basins
per km2), water availability varied year-to-year. As a result, during dry years redheads would use
available coastal ponds up to 8.1 km from the estuarine forging areas, while in wetter years closer ponds
would be used (likely to minimize energy expended through flying). Similarly, Adair et al. (1996)
reported that lesser scaup [Aythya affinis) and redheads avoided salt stress and metabolically expensive
osmoregulation through salt-gland excretory functions by feeding in estuaries; drinking, preening, and
resting in coastal basins; and then returning to estuaries. Grey teals (Anasgibberifronsgracilis) in
Australia that feed in  saline areas similarly required freshwater to osmoregulate (Lavery, 1972). Mallard
ducks (Anas platyrhynchos) transiting Iowa during spring migration used seasonally flooded farmed
basins in agricultural fields (also known as sheetwater wetlands; LaGrange and Dinsmore, 1989) for
feeding and roosted in more permanent emergent wetlands at night. In the study, these shallow
sheetwater wetlands provided 19,530 mallard use-days during the daytime compared with 103 use-
days for the emergent wetlands.

Nebraska's Rainwater Basin historically had more than 11,000 playas, shallow wind-formed wetland
depressions, although human activities over the past 100 years have resulted in the loss of 90% of the
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number and approximately 88% of the area (Webb et al., 2010; Uden et al., 2014). Nevertheless, the
remaining basins are critical to dependent migratory waterfowl, with 7-10 million waterfowl using the
approximately 16,000 km2 area, including "virtually all of the 600,000 midcontinental greater white-
fronted geese (Anser albifrons), 500,000 Canada geese (Branta Canadensis), 50% of midcontinent
mallards (Anas platyrhynchos], and 30% of continental northern pintails (Anas acutd)" (Webb et al.,
2010, p. 109), 38 shorebird species, and the endangered whooping crane (Grus americand). In a 3-year
spring migration study of 36-40 playas, Webb et al. (2010) identified 72 migratory species and more
than 1.6 million birds actively using these playa basins. The abundance of all wetland bird taxa was
related to wetland area within 5-10 km of the study playas, although diving duck abundance (e.g.,
redhead, canvasback, lesser scaup) was specifically related to riparian area within 5 km, likely due to the
presence of open water within these systems (Webb et al., 2010; see their Table 1 for a complete list of
taxa found).

Many additional studies have identified Nebraska as an important staging and stopover area for
numerous species, perhaps due to its location on the Central Flyway. For example, almost the entire
population of midcontinent sandhill cranes (Grus canadensis] uses the Central Platte River Valley. Avian
researchers reported that cranes roost along both the current and former Platte River channel (Krapu et
al., 1984) and forage in grasslands on semipermanent (unconsolidated mud bottom) and temporary
palustrine wetlands (Folk and Tacha, 1990) and on frequently inundated soils—especially those within
4.8 km of roost sites (Anteau etal., 2011). Pearse etal. (2010) noted that after feeding in cornfields,
sandhill cranes roosted along the Central Platte River Valley in pastures with ponds. These pond
systems are likely either playas, as noted above, or palustrine wetlands often surrounded by croplands
(Austin and Richert, 2005). Austin and Richert (2005) further stated that the  endangered whooping
crane was noted as roosting, feeding, and resting in both riverine and palustrine wetlands of the Great
Plains. Vrtiska and S.Sullivan (2009) found that lesser snow geese (Chen caerulescens] and Ross's geese
(Chen rossii), which numbered up to 7.3 million in 2001 during peak migration, used wetland habitats in
both the Rainwater Basin and Central Platte River Valley, depending on the availability of suitable (e.g.,
inundated) habitat.

Blanchong et al. (2006) found that this concentrated use of the Rainwater Basin by migratory lesser
snow geese resulted in greater contact between individuals, contributing to the spread ofPastruella
multocida, the bacterium that causes avian cholera. The loss of wetlands within the basin has resulted in
higher concentrations of migratory birds within the remaining wetlands, which has led to higher risks of
outbreaks of infectious diseases (Blanchong et al., 2006).

The U.S. Fish and Wildlife Service's Subcommittee on Rocky Mountain Greater Sandhill Cranes (SRMGSC,
2007) reviewed the literature  on habitat use for the migratory population of Rocky Mountain sandhill
cranes. This population, one of five in North America, migrates from wintering areas in Arizona, New
Mexico, and central Mexico to breeding areas in Canada, Montana, Idaho, Wyoming, Utah, and Colorado.
SRMGSC (2007) reported that this population of sandhill cranes overwintered in multiple riverine,
riparian, and non-floodplain habitats, including playas in New Mexico and southeastern Arizona. Areas
used in the breeding range include non-floodplain wetlands, such as northern boreal forest bogs, and
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other habitat types (e.g., large marsh complexes, smaller, scattered marshes, intermittent streams,
beaver ponds, subirrigated wet meadows along riparian zones; SRMGSC, 2007).

Shorebirds also use multiple habitat types during their North American migration. Skagen and Knopf
(1993) concluded that dispersion and opportunism, rather than concentration and predictability,
characterize movements of shorebirds in the Great Plains.  For example, Haig et al. (1998) noted that
large population declines of the endangered migratory piping plover (Charadrius melodus) along the
Missouri River were not actually declines, but a result of the birds moving to the Missouri Coteau (a 7.3
million ha region of the Upper Midwest and Canada replete with closed-basin prairie potholes; Phillips
et al., 2005), due to increased flooding along the Missouri. Farmer and Parent (1997) monitored pectoral
sandpipers [Calidris melanotus) migrating through non-floodplain sheetwater wetlands in Missouri and
small depressional wetlands of the Rainwater Basin in Nebraska and found that habitat connectivity
affected shorebird movements. Habitat patch density affected movements such that pectoral sandpipers
often perceived groups of wetlands as functionally connected and actively exploited the best feeding
habitat within that wetland complex. As the landscape became disconnected, however, the monitored
species altered their movement behavior, minimizing energy expenditure (Farmer and Parent, 1997).

Other taxa have been reported as linking downstream systems and non-floodplain wetlands. Fish tend
to disperse between non-floodplain wetlands and the river network during periodic surficial hydrologic
connections  or when humans create surface-water connections via ditching (Snodgrass et al., 1996;
Langston and Kent, 1997; Zimmer et al., 2001; Baber et al., 2002; Hanson et al., 2005; Herwig et al.,
2010). Mammals that can disperse overland can also contribute to connectivity. Although muskrat
territories are usually restricted (Shanks and Arthur, 1952), dispersal between suitable river and non-
floodplain wetland habitat over longer distances that is seasonal, climate-induced, and density-
dependent has been observed (Serfass etal., 1999; Clark, 2000 and references therein). Spinola etal.
(2008) tracked translocated river otters (Lontra canadensis) in New York and found that, after release,
most otters inhabited a mosaic of isolated aquatic habitats distributed throughout the agriculture-
dominated landscape. As noted above for waterfowl, mammals (including muskrats) also can act as
transport vectors for hitchhiking organisms like algae (Roscher, 1967).

Numerous flight-capable insects, including mayflies, caddisflies, diving beetles, backswimmers, whirligig
beetles, water striders, water boatmen, scavenger beetles,  crane flies, and nonbiting midges, use both
streams and non-floodplain wetlands (Williams, 1996). Aerial dispersal enables such insects to move
outside the stream network to seek suitable habitat for overwintering, refuge from adverse conditions,
hunting, foraging, or breeding (Williams, 1996; Bohonak and Jenkins, 2003).

Amphibians  and reptiles also move between streams or rivers and non-floodplain wetlands to satisfy
part of their  life-history requirements (Table 4-2). For example, Subalusky et al. (2009a) and Subalusky
et al. (2 009b) reported movement of adult female alligators (Alligator mississippiensis) from creeks to
shallow, seasonal limesink wetlands for nesting and use of the wetlands as nurseries for juveniles.
Subadults then shift to habitats within the river network by moving overland to the creek (Subalusky et
al., 2009a; Subalusky et al., 2009b). Lamoureuxand Madison (1999) used radio tracking to follow

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movements of green frogs (Rana clamitans) for 9 months in New York. Green frogs, which breed in
wetlands and then move into terrestrial habitats, are susceptible to freezing temperatures. In late
autumn, the frogs moved from upland habitats near breeding ponds to rapidly flowing streams and
seeps to overwinter. Boreal toads (Bufo boreas boreas} disperse long distances (>1 km) in streams
through home ranges (Adams etal., 2005). Knutson etal. (1999) found that the strongest land-use
predictor of anuran richness was urban land use. They speculated that, in addition to urban landscapes
being detrimental to anuran habitat quality, their tendency to fragment (i.e., disconnect) anuran habitats
is also a factor in the decline of these assemblages. In northwestern Ohio and southern Michigan
wetland complexes, the abundance of northern watersnakes [Nerodia sipedon sipedori) was positively
correlated with wetland size and wetland connectivity, defined by the authors as a wetland's distance to
other wetlands (Attum et al., 2007). The American toad [Anaxyrus [=Bufo] americanus) and eastern newt
[Notophthalmus viridescens) are widespread habitat generalists that move among streams and wetlands
to take advantage of both habitats, feed on aquatic invertebrate prey, and avoid predators (Table 4-2;
Babbitt et al., 2003; Green, 2005; Hunsinger and Lannoo, 2005; Petranka and Holbrook, 2006).

4.4.5   Geographic Isolation of Non-floodplain Wetlands
In defining non-floodplain wetlands (Section 2.2.1), we noted that this category could include wetlands
that are geographically isolated and those that are not. Further, we noted (Section 2.4.1) that certain
types of wetlands can be found with or without an outlet and can occur along a gradient of hydrologic
connectivity. This gradient can include non-floodplain wetlands that have permanent hydrologic
connections to the river network through perennial channels; wetlands that have losing streams that are
completely disconnected from the river network as output channels; geographically isolated wetlands
that have ground-water or occasional surface-water connections; and geographically isolated wetlands
that have minimal hydrologic connection to the river network (but which could include surface and
subsurface connections to other wetlands). The existence of this gradient (Section 1.2.2) can make
determining the degree to which particular non-floodplain wetlands are connected to or isolated from
downstream waters difficult.

A related issue is that spatial scale must be considered when determining geographic isolation. Tiner
(2003c) provided examples of how a wetland that was not isolated at a local scale could be
geographically isolated at a larger scale. Conversely, individual wetlands that are geographically isolated
could be connected to downstream waters when considered as a complex (a group of interacting
wetlands). This concept is demonstrated by Wilcox etal. (2011), who examined a depressional wetland
complex on the Texas Coastal Plain. Although the wetlands are hydrologically connected to each other
by shallow swales, they might be geographically isolated, because swales often are considered upland. In
fact, Tiner (2003c) classifies these Coastal Plain wetlands as geographically isolated. At the scale of the
wetland complex, however, the wetlands are connected to a nearby waterway via an intermittent
stream. During an almost 4-year study, nearly 20% of the precipitation that fell on the wetland complex
flowed as surface runoff through the channel to a nearby waterway, the Armand Bayou (Wilcox et al.,
2011). Although these wetlands might be geographically isolated at the local scale, the wetland
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^H Table 4-2. Partial list of amphibian and reptile species known to use both streams and non-floodplain wetlands or other lentic waters.
Stream and Wetland Connect
A Review and Synthesis
1
f-
w
O
Common Name
Green frog
Leopa rd frog
Bullfrog
Columbia spotted frog
Southern leopard frog
Pacific chorus frog
American toad
Fowler's toad
Two-toed amphiuma
Greater siren
Eastern newt
Scientific Name
Rana clamitans
Rana pipiens
Rana catesbeiana
Rana luteventris
Rana sphenocephala
Pseudacris regilla
Anaxyrus [=Bufo]
americanus
Anaxyrus [=Bufo] fowleri
Amphiuma means
Siren lacertina
Notophthalmus viridescens
Habitat Use
Breeds in wetlands and pools; overwinters in streams (Lamoureux and Madison, 1999)
Breeds in wetlands and pools; overwinters in streams (Rorabaugh, 2005)
Uses seasonal pools as complementary nonbreeding habitat (Gahl et al., 2009)
Breeds in streams and wetlands; overwinters in streams (Pilliod etal., 2002)
Breeds in shallow pools and wetlands; adults inhabit many shallow freshwater habitats, including
temporary pools, cypress ponds, ponds, lakes, ditches, streams, river edges, floodplain pools, and
slightly brackish coastal wetlands (Butterfield, 2005)
Breeds in wetlands, ponds, temporary pools, streams, lakes, rivers, and other aquatic habitats
(Rorabaugh and Lannoo, 2005)
Breeds in lakes, ponds, streams, ephemeral wetlands, prairie potholes, ditches, and floodplain
pools (Green, 2005)
Breeds in ponds, temporary pools, streams, ditches, lake shores, and shallows of rivers (Green,
2005)
Adults inhabit a wide variety of aquatic environments, including ponds, lakes, ephemeral
wetlands, wet prairies, streams, and ditches (Gibbons and Semlitsch, 1991; Johnson and Owen,
2005)
Breeds in shallow pools and streams, adults live in lakes, streams, ponds, and wetlands (Gibbons
and Semlitsch, 1991; Hendricks, 2005)
Breeds in permanent and semipermanent pools, ponds, wetlands, and low-flow areas of streams;
adults live in pools, ponds, streams, and wetlands (Hunsinger and Lannoo, 2005; Timm et al.,
2007)
to
o

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£=?
sam and Wetland Connectivity:
eview and Synthesis

(continued).
Common Name
Yellow-bellied
watersnake
Copper-bellied
watersnake
Spotted turtle
Blanding's turtle
Painted turtle
Snapping turtle
American alligator
Scientific Name
Nerodia erythrogaster
flavigaster
Nerodia erythrogaster
neglecta
Clemmys guttata
Emydoidea blandingii
Chrysemys picta
Chelydra serpentina
Alligator mississippiensis
^^^^^^1
Habitat Use
Hunts in temporary pools and wetlands (Roe etal., 2004; Mitchell etal., 2007)
Hunts in temporary pools and wetlands (Roe etal., 2004; Mitchell etal., 2007)
Uses temporary wetlands for foraging, mating, basking, and aestivating (Joyal et al.,
Uses temporary wetlands for foraging, mating, basking, and aestivating (Joyal et al.,
2001)
2001)
Uses temporary wetlands for basking and foraging (Mitchell etal., 2007)
Uses temporary wetlands for basking and foraging (Mitchell etal., 2007)
Juveniles use seasonal wetlands as nurseries, subadults move back to river networks (Subalusky
etal., 2009a; Subalusky etal., 2009b)
to
o

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complex serves as the source of water for a headwater stream, and therefore, the complex is not
geographically isolated at a larger scale.

Besides the spatial scale of the wetland unit, assessments of non-floodplain wetland to stream
connectivity can be affected by the resolution and source of the spatial data that are used. For example,
higher connectivity was found in the Tuckahoe Creek watershed in Maryland, when wetland
connectivity was evaluated for streams determined from LiDAR compared to streams from both the
High Resolution National Hydrography Dataset (NHD) and NHD Plus (Lang et al., 2012). Yang and Chu
(2013) found that Digital Elevation Model (DEM) resolution also affected connectivity assessments, with
finer OEMs having a higher number of connected areas and less total connected area than coarser DEMs.

Given this discussion, caution should be used in interpreting connectivity for wetlands that have been
designated as "geographically isolated," because (1) the term can be broadly applied to a heterogeneous
group of wetlands that can include wetlands that are not actually geographically isolated, (2) wetlands
with permanent channels could be miscategorized as geographically isolated if the designation is based
on maps or imagery with inadequate spatial resolution (e.g., Lang et al., 2012), obscured views, etc., and
(3) wetland complexes could have connections to downstream waters through stream channels even if
individual wetlands within the complex are geographically isolated. The term "geographically isolated"
should be applied only to groups of wetlands if all those wetlands are, in fact, known to be
geographically isolated. Further, even geographically isolated wetlands can be connected to other
wetlands and downstream waters through ground-water connections, occasional spillage, or biological
connections. Thus, the term "geographically isolated" should not be used to infer lack of hydrologic,
chemical, or biological connectivity.

Finally, precisely this isolation is responsible for many of the functions that geographically isolated
wetlands provide to downstream waters. In particular, many of the sink and lag functions of these
wetlands result from their relative isolation from the river network. This relative isolation, combined
with the wetlands' storage capacity, enables them to store water and reduce peak streamflows and
downstream flooding (Novitzki, 1979; Hubbard and Linder, 1986; Vining, 2002; Bullock and Acreman,
2003; McEachern etal., 2006; Gleason etal., 2007). For example, depressional wetlands in Florida had
an average potential wetland water  storage capacity of 1,619 m3 ha-1 (Lane and D'Amico, 2010). These
same sink and lag functions will also act on any materials associated with stored water, such as
sediments and pollutants. Increased isolation also  can decrease the spread of pathogens (e.g., Hess,
1996) and invasive species (e.g., Bodamer and Bossenbroek, 2008) and increase the rate of local
adaptation (e.g., Fraser et al., 2011).
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4.5  Wetlands:  Synthesis  and Implications

4.5.1   Riparian/Floodplain Wetlands
Based on our review of the literature, riparian/floodplain wetlands are highly connected to streams and
rivers through surface water, shallow ground water, and biological connectivity. The effects of wetlands
on streams and rivers are a function of the magnitude of floodwaters, the geomorphic structure of the
floodplain, and the proximity of the channel. Although a gradient occurs in the frequency of connectivity
within the floodplain (Section 1.2.2), even riparian/floodplain wetlands that rarely flood can be
important because of long-lasting effects on streams and rivers. In fact, most of the major changes in
sediment load and river-channel structure—for example, movement of rivers through meander belts
and creation of oxbow lakes—that are critical to maintaining the health of the river result from large
floods that provide infrequent connections with more distant riparian/floodplain wetlands. Areas that
surface water infrequently floods also can be connected to the river more regularly through ground
water and the organisms. Key conclusions from our literature review on riparian/floodplain wetlands
are summarized in Table  4-3.

4.5.2   Non-floodplain Wetlands
Non-floodplain wetlands  consist of depressional, slope, and flats wetlands that lack surface water inlets.
Non-floodplain wetlands  can include regional wetland types such as prairie potholes, playa lakes, vernal
pools, and Carolina bays.  Hydrologic flows through these wetlands are predominantly unidirectional, in
contrast to bidirectional flows that occur in riparian/floodplain wetlands.

The literature we examined on non-floodplain wetlands indicates that these systems have important
hydrologic, water-quality, and habitat functions that affect downstream waters and rivers provided a
connection exists between the wetland and downstream water (Table 4-4). The challenge is to identify
which non-floodplain wetlands have such a connection. Addressing this issue is difficult, because most
wetland studies do not investigate wetland effects on downstream waters or, if they do, they rarely
address connectivity explicitly.

Based on what is known about how water flows across the landscape (Chapter 2), hydrologists and
ecologists would generally agree that all non-floodplain wetlands are interconnected to some degree
and are connected with stream networks, which is why the water-cycle environment is referred to as
the hydrosphere. Hydrologists and ecologists also generally agree that some areas are more connected
or have a greater influence than others. The purpose of this review is to determine, based on the peer-
reviewed literature, the degree of connectivity and associated effects between different non-floodplain
wetlands and downstream waters.

Non-floodplain wetlands  occur along the gradient discussed in Chapter 1, and can be described in terms
of the frequency, duration, magnitude, timing, and rate of change of water, material, and biotic fluxes to
downstream waters. With respect to hydrologic connectivity, this gradient includes wetlands that have
permanent hydrologic connections to the river network through perennial channels; wetlands that have

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Table 4-3. Key conclusions on the effects of riparian/floodplain wetlands on rivers.
                                  Physical Connectivity and Function
   Riparian areas are highly connected to streams, so much so that considering the riparian influence on
   streams is essential to understanding their structure and function.
   Riparian connectivity ranges from longitudinal flow and exchange in mountainous headwater streams to
   increasing lateral flow and exchange in  river valleys and coastal terrain.
   Water storage by riparian areas, especially wetlands and lentic water bodies (such as oxbow lakes) that lack
   surface channel  connections to stream  networks, attenuate downstream flood pulses.
   Heterogeneous riparian areas that include wetlands and open waters remove large amounts of sediment
   and nutrients from upland areas before they can enter the stream network.
   Riparian areas influence stream geomorphology during periodic flooding by releasing stored sediments.
   Forested riparian areas provide woody debris that helps shape stream morphology.
   Riparian vegetation shades the stream and influences and regulates stream temperature and stream net
   primary productivity.
   Ground water that flows through riparian areas and into the stream helps  moderate stream temperatures.
                                 Chemical Connectivity and Function
   Riparian areas, acting as buffers, are critical to protecting stream-water quality.
   The structure of the riparian area (e.g., vegetation, wetlands, redox potential) influences its ability to
   increase water quality before it reaches the stream.
   The near-stream portion of a riparian area is often more important in protecting stream-water quality than is
   the near-field (near uplands) portion.
   Allochthonous inputs generally are most important to food webs in small headwater streams, especially in
   forested areas. As rivers become larger, primary production  becomes increasingly important.
   Some of the best-documented functions of oxbow lakes are  as sinks for nutrients from upland runoff that
   might otherwise flow into rivers.
                                 Biological Connectivity and Function
   Many types of organisms move between riparian/floodplain wetlands and the river network; those
   transported by water often move in response to flooding and those transported by other mechanisms (e.g.,
   wind) move in response to seasonal cues or life-history stage requirements.
   Riparian/floodplain wetlands and oxbow lakes can be sources or sinks of organisms; one of the most
   important source functions is to provide rearing habitat for fish.
   Riparian/floodplain wetlands provide food sources for stream and river invertebrates.
   Many riparian/floodplain wetlands and  open waters (e.g., oxbow lakes) are used by fish and other
   organisms from the stream or river during flood ing.
output channels but are isolated from the river network; geographically isolated wetlands (i.e., wetlands
completely surrounded by uplands) that have local or regional ground-water or occasional surface-
water connections; and geographically isolated wetlands that have minimal hydrologic connection to the
river network (but which could include surface and subsurface connections to other wetlands).

Based on our literature review and basic hydrologic principles, we conclude thatnon-floodplain
wetlands that are connected to the river network through surface water will have an influence on
downstream waters, regardless of whether the outflow is permanent, intermittent, or ephemeral. Such
non-floodplain wetlands include wetlands that are the origins of streams or are connected downstream
to the river network through ditches. They also would include geographically isolated wetlands that are
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connected downstream to the river network through upland swales. Further, although the literature
review did not address other non-floodplain water bodies to the same extent as wetlands, our overall
conclusions also apply to these water bodies (e.g., ponds and lakes that lack surface water inlets)
because the same principles govern hydrologic connectivity between these water bodies and
downstream waters (Chapter 2).

Non-floodplain wetlands that do not connect to the river network through surface water include
wetlands that spill into losing streams that are completely disconnected from the river network; that is,
the wetland exports water through an output channel but the water is completely lost before it reaches
the river network due to evapotranspiration or loss to ground water. Also included are geographically
isolated wetlands that either do not spill, or spill into an upland swale that does not enter the river
network. Although such wetlands lack surface-water connections to streams and rivers, they can be
connected through local, intermediate, or regional ground-water flows or through biological movement.
Connectivity between these wetlands and downstream waters will vary within a watershed as a function
of local factors (e.g., position, topography, and soil characteristics; Sections 2.4.1 and 2.4.2), some of
which are identified and discussed in this section. Connectivity also will vary over time, as the river
network and water table expand and contract in response to local climate.

It is difficult to generalize about the specific downstream effects of non-floodplain wetlands that lack
surface water connections to downstream waters. In Chapter 2 we note  that the influence of wetlands
and streams on downstream waters depends on two factors: (1) functions that affect material fluxes and
(2) connectivity (or isolation) that allows (or prevents) transport of materials between the  systems
(Section 2.3). The literature we reviewed and summarized provides ample evidence that non-floodplain
wetlands provide hydrological, chemical, and biological functions that affect material fluxes. Thus, these
wetlands could affect downstream waters if they are connected to (or isolated from) the river network
in such a way that it allows (or prevents) transport of materials to downstream waters. However, the
more than 200 peer-reviewed references on non-floodplain wetlands we reviewed infrequently
evaluated connections between non-floodplain wetlands and river networks and rarely examined the
frequency, duration, magnitude, timing, and rate of change of these connections. Even if it is known from
an article that the study site is located near a downstream water, connectivity cannot be established
without specific information on frequency and magnitude of precipitation events, soil infiltration rate,
wetland storage capacity, hydraulic gradients, etc.—information that is only rarely available in
publications. Thus, the literature provided no evaluations of connectivity for specific groups or classes of
wetlands (e.g., prairie potholes or vernal pools). This lack of information applies to groups of these
wetlands within a particular watershed and to comparisons between different types of regional
wetlands. For example, our review did not reveal whether connectivity between vernal pools and
downstream waters is greater than connectivity between prairie potholes and downstream waters. We
emphasize that this does not mean these wetlands do or do not have connectivity with downstream
waters: It simply means the literature we reviewed does not enable us to distinguish connectivity of
these wetland types from each other. Literature that was not included in our review, such as reports
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Table 4-4. Key conclusions on the effects of non-floodplain wetlands on rivers.
                                  Physical Connectivity and Function
   The connections of non-floodplain wetlands with downstream waters exist along a spectrum from isolated
   depressional wetlands, to those connected through ground water, to those connected via intermittent or
   permanent surface flows.
   The degree to which outputs (or connections) are dominated by surface water vs. ground water is controlled
   in part by soil permeability: Permeable soils favor ground-water outputs, while impermeable soils result in
   surface water outputs. Other factors, such as topographic setting, also can play a role.
   Ground-water recharge is common in  non-floodplain wetlands and can be a particularly important source of
   water to aquifers during dry periods.
   Ground-water networks extend from the local to the intermediate and regional scales, and provide a
   mechanism by which non-floodplain wetlands can influence other water bodies over various periods.
   Even when non-floodplain wetlands lack a connection to other water bodies, they can influence downstream
   water through water storage and mitigation of peak flows (flood reduction and attenuation).
                                  Chemical Connectivity and Function
   Insofar as they often act as buffers between sources of pollution and riparian areas, non-floodplain
   wetlands are a "first line of defense" in protecting streams from polluted waters.
   Non-floodplain wetlands affect nutrient delivery and water quality.
   Non-floodplain wetlands are a principal source for dissolved organic carbon (which supports primary
   productivity) to some downstream waters; the area of a basin with non-floodplain wetlands is directly
   correlated to the contribution of that basin to dissolved organic carbon in downstream waters.
   Non-floodplain wetlands are sources of mercury: Microbial processes in non-floodplain wetlands methylate
   mercury, which can be translocated through near-surface and surface flows to downstream waters where it
   can bioaccumulate.
   Non-floodplain wetlands are sinks for sediment, nutrients (including phosphorus, nitrate, and ammonium),
   metals (e.g., nickel and cobalt), and pesticides (e.g., atrazine).
   Non-floodplain wetlands can remove, retain, or transform many of the nutrient inputs to which they are
   exposed.
                                  Biological Connectivity and Function
   Natural periodic and permanent human-engineered surface-water connections can connect biological
   communities in non-floodplain wetlands and the river network; in addition, wind dispersal and overland
   movement connect these types of water bodies with frequency decreasing as a function of distance,
   landscape barriers, or both.
   Migratory birds are vectors of plants and invertebrates between non-floodplain wetlands and the river
   network, although their influence has not been quantified fully.
   Non-floodplain wetlands promote biological interactions that can be critical to the life-history requirements
   of some stream species.
   Overland ("fill-and-spill") hydrologic connections can support biological connections. For example, stream
   fish found in wetlands that periodically dry down indicate presence of surf ace flows sufficient for
   colonization.
from local resource agencies, could allow the connectivity of these wetlands to be evaluated further, as
could analysis of existing or new data or field evaluation.

Further complicating our evaluation is that some of the effects that wetlands have on downstream
waters are due to their isolation, rather than their connectivity. Wetland functions that trap materials
and prevent their export to downstream waters (e.g., sediment and entrained pollutant removal, water
storage) result because of the wetland's ability to isolate material fluxes. As above, to establish that a
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wetland influences a downstream water through its isolation, it would have to be known that the
wetland intercepted materials that would otherwise reach the downstream water, and this information
is typically not provided in publications. The literature we reviewed does provide limited examples of
the direct effects of such isolation on downstream waters for some specific wetlands, but not for classes
of wetlands (e.g., vernal pools). However, the literature we reviewed allows us to conclude that sink
functions of non-floodplain wetlands, which result in part from their relative isolation, will have effects
on a downstream water when these wetlands are situated between the downstream water and known
point or nonpoint sources of pollution, and thus intersect the flowpath between pollutant source and
downstream water. For example, in cases where agricultural land use is a known contributor of
sediment to downstream waters, the presence of depressional wetlands along the flowpath between the
agricultural land and downstream water will result in reduced sediment loading to the downstream
water. These effects would also be realized from sink functions that do not result from the wetland's
isolation perse, but are emergent wetland properties (e.g., biogeochemical reactivity based on anoxic
conditions). Using the same example, if the agricultural land use is a known contributor of nitrogen to
downstream waters, depressional wetlands occurring along the flowpath will result in reduced nitrogen
loading to the downstream water. In such settings, wetland loss or increased connectivity (e.g., due to
ditching or tiling) is likely to reduce  the effects of such functions on downstream waters (although
functions that depend on connectivity could be increased).

To provide more specific evaluations of the connectivity of non-floodplain wetlands to downstream
waters, studies are needed that: (1) further develop and validate methods for assessing wetland and
watershed connectivity; (2) apply such methods to different classes of non-floodplain wetlands,
especially those that lack channelized surface-water or regular shallow subsurface-water connections;
(3) evaluate the frequency, duration, magnitude, timing, and rate of change of water, material, and biotic
fluxes to downstream waters; and (4) consider aggregate functions and connectivity of wetland
complexes (groups of closely located and interacting wetlands). Such studies are needed throughout the
country to cover the breadth  of wetlands in non-floodplain settings satisfactorily (e.g., across areas with
different climate, geology, and terrain).

Despite these limitations, we  can make some conclusions:
   1.  A non-floodplain wetland having a surface-water outflow to a stream network (e.g., a wetland
       that serves as a stream origin) is connected  to the stream network and has an influence on
       downstream waters.
   2.  Many non-floodplain wetlands interact with ground water, which can travel long distances and
       affect downstream waters.
   3.  Even when wetlands  lack a hydrologic connection to other water bodies, they can influence
       downstream water through  water and material storage and mitigation of peak flows (flood
       reduction and flood attenuation). Sink functions of non-floodplain wetlands will have effects on
       a downstream water  when these wetlands are situated between the downstream water and
       known point or nonpoint sources of pollution, thereby intersecting the flowpath between

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       pollutant source and downstream water. More generally, wetland sink functions are likely to be
       greatest when the wetland is located downgradient from pollutant sources and upgradient from
       a stream or river.
    4.  Non-floodplain wetlands provide unique and important habitats for many species, both common
       and rare. Some of these species require multiple types of waters to complete their full life cycles,
       including downstream waters. Abundant or highly mobile species play important roles in
       transferring energy and materials between non-floodplain wetlands and downstream waters.
    5.  Biological connections are likely to occur between most non-floodplain wetlands and
       downstream waters through either direct or stepping stone movement of amphibians,
       invertebrates, reptiles, mammals, and seeds of aquatic plants, including colonization by invasive
       species. Many species in those groups that use both stream and wetland habitats are capable of
       dispersal distances equal to or greater than distances between many wetlands and river
       networks. Migratory birds can be an important vector of long-distance dispersal of plants and
       invertebrates between non-floodplain wetlands  and the river network, although their influence
       has not been quantified. Whether those connections are of sufficient magnitude to impact
       downstream waters will either require estimation of the magnitude of material fluxes or
       evidence that these movements of organisms are required for the survival and persistence of
       biota that contribute to the integrity of downstream waters.
    6.  Spatial proximity is one important determinant of the magnitude, frequency and duration of
       connections between wetlands and streams that will ultimately influence the fluxes of water,
       materials and biota between wetlands and downstream waters.  However, proximity alone is
       not sufficient to determine connectivity, due to local variation in factors such as slope and
       permeability.
    7.  The cumulative influence of many individual wetlands within watersheds can strongly affect the
       spatial scale, magnitude, frequency, and duration of hydrologic, biological and chemical fluxes or
       transfers of water and materials to downstream waters. Because of their aggregated influence,
       any evaluation of changes to individual wetlands should be considered in the context of past and
       predicted changes (e.g., from climate change) to  other wetlands within the same watershed
    8.  Caution should be used in interpreting connectivity for wetlands that have been designated as
       "geographically isolated" because
       a.  the term can be applied broadly to a heterogeneous group of wetlands, which can include
           wetlands that are not actually geographically isolated (e.g., some vernal pools are not
           geographically isolated because they have output channels;
       b.  wetlands with permanent channels could be miscategorized as  geographically isolated if the
           designation is based on maps or imagery with inadequate spatial resolution, obscured
           views, etc.; and
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       c.   wetland complexes could have connections to downstream waters through stream channels
           even if individual wetlands within the complex are geographically isolated.

       Thus, the term "geographically isolated" should be applied only to groups of wetlands if all those
       wetlands are, in fact, known to be geographically isolated, something that we cannot determine
       based on this literature review. As previously noted, additional information that was not
       included in our literature review (e.g., reports from local resource agencies, analysis of existing
       or new data, field evaluations) could allow some wetlands that are truly geographically isolated
       to be distinguished from some of those that are not. Further, even geographically isolated
       wetlands can be connected to other wetlands and downstream waters through ground-water
       connections, occasional spillage, or biological connections. Thus, the term "geographically
       isolated" should not be used to infer lack of hydrologic, chemical, or biological  connectivity. Key
       conclusions from our literature review on non-floodplain wetlands are summarized in
       Table 4-4.
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    CHAPTER
                 J: CONNECTIVITY CASE
                                         STUDIES
5.1  Introduction
Chapters 3 and 4 of this report review evidence from the literature for the physical, chemical, and
biological connections of three broad categories of waters—streams, riparian/floodplain wetlands, and
non-floodplain wetlands—to, and their resulting effects on, downstream waters. In addition to the three
questions in Table 1-1, the EPA's Office of Water asked us to provide detailed information on six specific
water body types: Carolina and Delmarva bays, oxbow lakes, prairie potholes, prairie streams,
southwestern streams, and vernal pools (Appendix B).

In this chapter, we summarize the results of the six case studies, applying the concepts in Chapters 1 and
2 to the detailed evidence in Appendix B, for each habitat. The full body of evidence and supporting
citations, which we omitted here to improve readability, are provided in Appendix B. We summarize
evidence from the individual case studies in terms of (1) the descriptors of connectivity (i.e., the
frequency, duration, magnitude, timing, rate of change effluxes to and biological exchanges with
downstream waters; Section 1.2.2); (2) the consequences of different systems and degrees of
connectivity on downstream waters (Sections 1.2.3 and 2.3); (3) and the effects of typical human
alterations (Sections 1.2.4 and 2.4.4). We then use the information from these case studies and from
Chapters 3 and 4 to illustrate, hypothetically, where streams, riparian/floodplain wetlands, and non-
floodplain wetlands are positioned along a connectivity gradient, highlighting the primary lines of
evidence that support that positioning.
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5.2  Carolina and Delmarva Bays
Carolina bays are elliptical, ponded, depressional wetlands that occur along the Atlantic Coastal Plain
from northern Florida to New Jersey, although they are most abundant in North Carolina and South
Carolina (Section B.I). Carolina bays that are geographically specific to the Delmarva Peninsula are often
referred to as Delmarva bays. Carolina and Delmarva bays range in size from less than 1 ha to greater
than 3,600 ha and are densely concentrated in many areas. In the 1950s, roughly 500,000 bays existed,
although the number today is markedly less due to human modification of the landscape. Bays primarily
gain water from direct precipitation on their surfaces (with some water deriving from inlet channels,
surface runoff, shallow ground water, and natural springs) and lose water through evapotranspiration.
As a result, these relatively permanent bays experience fluctuating water levels. Their extensive
distribution and wet-dry cycles promote and support a diverse biota.

5.2.1   Connectivity and Consequences on Downstream Waters
Some Carolina and Delmarva bays connect to each other and some connect to downstream waters.
Delmarva bays inundate seasonally and connect hydrologically to other bays and to stream networks via
intermittent stream channels. Studies also document shallow ground-water connections, via both nearly
continuous shallow ground-water recharge and periodic shallow ground-water discharge.

When they occur, hydrologic connections  are likely to result in effects on downstream waters. Carolina
and Delmarva bays can reduce the amount of nitrate transported between surface-water systems and
ground water via denitrification, which is  promoted by the periodicity of wetting and drying that occurs
in bays, and dilution. Seasonal connections of Delmarva bays to stream networks export accumulated
organic matter from wetlands into tributaries of Chesapeake Bay. Hydrologic connections also export
methylmercury from these systems (see below).

Although the current published evidence for biological connections is limited and primarily indirect, the
potential for movement of organisms between bays and other water bodies is high. These bays provide
valuable habitat and food web support for numerous plant and animal species. Fish presence in bays
known to dry out periodically indirectly demonstrates that these bays must be connected to other
waters. Amphibians and reptiles use bays extensively for breeding and for rearing young. In bays that
lack fish, the absence of predators allows abundant amphibian populations to thrive, particularly those
with aquatic larval stages. These animals can then disperse many meters across the landscape and
colonize downstream waters. Bays also foster abundant aquatic insects, and their emergence can have
consequences for nearby waters. Many species documented  in Carolina and Delmarva bays are known
to live in pond, wetland, and stream environments. As a result, species emerging from bays can become
important food sources for organisms in nearby streams after aerial or terrestrial dispersal. Cumulative
emergence from thousands of small bays across the landscape could create a significant food source for
downstream waters.
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5.2.2   Effects of Human Alteration
Human alteration of Carolina and Delmarva bays has affected their physical, chemical, and biological
connections to, and effects on, downstream waters. Agriculture, logging, and other human activities have
altered the vast majority of Carolina and Delmarva bays, affecting the frequency, duration, magnitude,
and timing of hydrologic connections between bays and other waters. Agricultural practices have greatly
reduced the number of bays over the past several decades. Channelization and ditching of bays for
agriculture is common. Draining bays for agricultural use disrupts or alters numerous wetland
functions: sediment and chemical storage and transformation, biological habitat and sources, and
organic matter export. Because the ditches commonly connect the surface water of bays that drain
agricultural fields to stream networks that drain into downstream water bodies, they serve as
conveyances for nutrients, sediment, and contaminants—thereby increasing physical, chemical, and
biological connections between bays and the downstream systems. The consequences of this increased
connectivity for downstream waters can be especially important in terms of nutrient and contaminant
transport. In addition to runoff from farmed fields, periodic drying and flooding of shallow Carolina and
Delmarva bays promote the bacteria-mediated methylation of mercury. Subsequent transport of
bioavailable methylmercury through ditches can pose a contamination risk to fish and piscivorous birds
inhabiting downstream water bodies.


5.3  Oxbow Lakes
Oxbow lakes are natural features of floodplains, originating from curves (meanders) in the river that
become cut off from the active river channel (Section B.2). They are located in flat, unconstrained
floodplains of river systems.

5.3.1   Connectivity and Consequences on Downstream Waters
The evidence for physical, chemical, and biological connectivity of oxbow lakes to downstream waters is
considerable. Because of their location within river floodplains, many oxbows are connected seasonally
or episodically to downstream waters during natural flood events via surface and shallow subsurface
flows. The frequency, duration, magnitude, and timing of these hydrologic connections depend on river
stage, lake geomorphology, and relative position along and distance from the river network. Despite this
spatial and temporal variability, oxbow lakes collectively are likely to influence downstream waters.

The frequency, magnitude, and duration of physical connection between oxbow lakes and the river
channel have important consequences on the river network. Physical surface connections facilitate
biological and chemical exchange between oxbow lakes and rivers. Oxbow lakes function as sinks,
because they intercept and store nutrients and other materials from upland runoff that otherwise would
flow directly into the river network. In these  cases, the lack of a permanent connection between an
oxbow lake and a river helps to preserve the  chemical integrity of the river network.

When oxbow lakes are connected, the biological material produced within them can subsidize riverine
food webs by passive or active transport from the lake to downstream waters. Oxbow lakes are
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important areas of biological productivity on floodplains. Periodic surface-water connections between
rivers and oxbow lakes facilitate the movement offish, allowing riverine fish to exploit these productive
floodplain water bodies before they move back to the river. In this way, connectivity between oxbow
lakes and rivers supports the biological integrity of the river network.

5.3.2   Effects of Human Alteration
Human alterations of the natural flow regime in rivers can influence connectivity between oxbow lakes
and the active river channel. In some cases, permanent channels are constructed between oxbows and
the river channel and connectivity is increased; in other cases, such as the creation of dikes or levees,
connectivity is reduced between oxbows and the altered area of the river network. Practices that alter
the natural flow regime of the river (e.g., dams) or inhibit periodic flooding of oxbow lakes (e.g., levees)
affect movement of water and sediment and the use of oxbow lakes by riverine fish. When cut off from
periodic inundation by the river channel, water in oxbow lakes can evaporate. Over time, these lakes can
dry up, be colonized by terrestrial vegetation, and eventually become dry land.


5.4  Prairie Potholes
The prairie pothole region, located in northern-central North America, is named for the abundant,
glacially formed wetlands that occur throughout the region, typically as depressions lacking natural
outlets (Section B.3). The prairie pothole region covers approximately 777,000 km2, a vast area that
varies in climate, terrain, geology, land use, and human alteration. These variations result in a gradient
of connectivity to and effects on downstream waters across the potholes themselves. For instance, the
three major physiographic areas within the prairie pothole region (Red River Valley, Drift Prairie, and
Missouri Coteau) vary in precipitation, distribution, and density of potholes and streams connecting
potholes to downstream waters. Potholes exhibit a wide range of hydrologic permanence, from holding
permanent standing water to wetting only in years with high precipitation. Differences in the frequency,
duration, and timing of pothole inundation across the region influence wetland function and the
diversity and structure of their biological communities.

5.4.1   Connectivity and Consequences on Downstream Waters
Individual prairie potholes span the continuum of isolation from and connection to the river network
and other water bodies. In addition to differences among individual potholes, interactions between
regional factors (e.g., precipitation) and local factors (e.g., landscape relief) can result in spatial patterns
of connectivity across the landscape (Sections 2.4.5 and B.3.2.1) that have consequences for the
downstream connectivity and effects of prairie potholes. Considered collectively, unaltered prairie
pothole systems have infrequent direct surface-water connections to downstream waters. Evidence of
the consequences of these connections on downstream waters is variable. Some studies document
measurable effects of water storage capacity of potholes on flood attenuation and maintenance of
stream baseflow, whereas other studies show no effect of pothole water storage on streamflows. These
differences in observed effects might be explained, in part, by the spatial variation observed within the
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prairie pothole region. Potholes can connect to downstream waters via ground-water flows when both
are within a continuous zone of a shallow local aquifer. In areas with restricted surface-water and
ground-water interactions, the magnitude of effects from such connections will be small.

The chemical connectivity of prairie potholes is largely mediated by their hydrologic connectivity. As
depressions on the landscape, potholes tend to accumulate nutrients, sediment, and pesticides that can
be chemically transformed and decrease potential effects on downstream waters (e.g., denitrification
frequently occurs in saturated pothole sediments). Although chemical sink (storage) functions and
periodic source functions of potholes have been documented in the literature, their overall influence on
lakes and river networks has been difficult to quantify. This difficulty exists in part because altered and
unaltered potholes co-occur in watersheds with different land use and management practices, and many
different parts of this complex landscape can affect the integrity of downstream waters. Thus, prairie
potholes can have substantial hydrologic and chemical consequences on downstream water levels and
flows, but this type of connectivity and its downstream effects are difficult to predict, demonstrate, and
quantify.

Although direct evidence is sparse, indirect evidence suggests that prairie potholes are highly
biologically connected. Prairie pothole systems have biological connections to downstream waters via
annual bird migrations—especially for migratory waterfowl such as cranes, geese, ducks, and
shorebirds, which actively move between and use multiple aquatic habitats, including prairie pothole
systems. For instance, the prairie pothole region has been identified as an area of global and regional
importance for migratory birds, and at least 15 duck species use prairie pothole wetlands. Mammals and
many species of amphibians also use potholes. Plants and invertebrates disperse to and from prairie
potholes via "hitchhiking" on waterfowl. That potholes lack an endemic aquatic and  semiaquatic flora
and fauna indicates that communities in potholes are biologically well connected with other aquatic
ecosystems, but evidence for effects of biological connections  on downstream waters is limited.

5.4.2  Effects of Human Alteration
Human alterations of the landscape affect the connectivity of prairie potholes. Land use in an upland
that drains to a wetland can alter the amount of runoff that wetland receives. Much of Upper Midwest
cropland is artificially drained to increase agricultural productivity. Filling potholes  and lowering the
regional water table through agriculture tile drainage have increased the isolation of remaining potholes
by decreasing the density of depressions containing water. In some areas, extensive surface draining
and ditching has directly and dramatically increased connectivity between pothole basins and the river
network. Ditches create surface-water outlets from potholes, connecting potholes to streams and rivers;
drains and underground pipes fitted at the bottoms of potholes often  discharge to open ditches or
streams. This increased hydrologic and chemical connectivity decreases water retention time, thereby
reducing storage and biogeochemical processing of nutrients, sediments, and pesticides. The cumulative
influence of human alterations on connectivity between potholes and downstream waters has not been
systematically studied or reported across the entire prairie pothole region.
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5.5  Prairie Streams
Prairie streams drain temperate grasslands in the Great Plains physiographic region of the central
United States and Canada (Section B.4). Eventually, these streams drain into the Mississippi River or
flow directly into the Gulf of Mexico or the Hudson Bay. Climate in the Great Plains region ranges from
semiarid to moist subhumid and intra- and interannual variation in precipitation and
evapotranspiration is high. This variation is reflected in the hydrology of prairie streams, which include
ephemeral, intermittent, and perennial streamflows. Row cropping and livestock agriculture are the
dominant land uses in the region, resulting in the withdrawal of water from stream channels and
regional aquifers and its storage in reservoirs to support agriculture.

5.5.1  Connectivity and Consequences on Downstream Waters
Prairie streams typically are connected to downstream waters. Like other types of streams, prairie
streams present strong fluvial geomorphic evidence for connectivity to downstream waters, in that they
have continuous channels (bed and banks) that make them physically contiguous with downstream
waters. Prairie river networks are dendritic and generally have a high drainage density, so they are
particularly efficient at transferring water and materials to downstream waters. Their pool-riffle
morphology, high sinuosity, and seasonal drying, however, also enhance material storage and
transformation. The timing of connections between prairie streams and downstream waters is seasonal
and therefore relatively predictable. For example, high-magnitude floods tend to occur in late fall into
later spring, although they also occur at other times during the year (Section B.4.2.1); this observation
indicates that the magnitude of connections to downstream also varies seasonally.

The frequent and predictable connections between prairie streams and downstream waters have
multiple physical, chemical, and biological consequences for downstream waters. Dissolved solids,
sediment, and nutrients are exported from the prairie river network to downstream waters. Ultimately,
the expansion of the hypoxic zone in the Gulf of Mexico is a downstream consequence of cumulative
nutrient loading to the Mississippi River network. Relative to small streams and large rivers draining the
moist eastern parts of the Mississippi River basin, small to midsized prairie streams deliver less than
25-50% of their nutrient load to the Gulf of Mexico. Nonetheless, given the large number and spatial
extent of headwater prairie streams connected to the Mississippi River, their cumulative effect likely
contributes substantially to downstream nutrient loading.

Organisms inhabiting prairie streams have adapted to their variable hydrologic regimes  and harsh
physicochemical conditions via evolutionary strategies that include rapid growth, high dispersal ability,
resistant life stages, fractional reproduction, and life cycles timed to avoid predictably harsh periods.
Alterations in the frequency, duration,  magnitude, and timing of flows—and thus hydrologic
connectivity—are  associated with the extinction or extirpation of species in downstream systems.
Moreover, many fish species (e.g., Arkansas River shiner, speckled chub, flathead chub) in prairie river
networks require sufficient unfragmented (i.e., connected) channel length with adequate discharge to
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keep their nonadhesive, semibuoyant eggs in suspension for incubation and early development. When
these conditions are not met, the biological integrity of downstream waters is impaired.

5.5.2   Effects of Human Alteration
Human alteration of prairie river networks has affected the physical, chemical, and biological
connectivity to and their consequences for downstream waters. Impoundments and water removal,
through both surface flow diversions and pumping of ground-water aquifers, are common in this region.
These activities have reduced flood magnitude and variability, altered timing, and increased
predictability of flows to downstream waters. As a result, physical, chemical, and biological connections
to downstream waters have been altered. In addition to the altered land uses and application of
nutrients and pesticides for agriculture, human alteration of the river network itself, through
channelization, levee construction, desnagging, dredging, and ditching, has enhanced longitudinal
connectivity while reducing lateral and vertical connectivity with the floodplain and hyporheic zone,
respectively. Pumping from streams and ground water has caused historically perennial river segments
to regularly dry during summer months. Changes to the prairie's grazing (from bison to cattle) and
burning regimes increase nutrient and suspended sediment loading to downstream waters. Introduced
species have extirpated endemic species and altered food web structure and processes in prairie
streams, thereby affecting the biological integrity of downstream waters.


5.6  Southwestern  Intermittent and  Ephemeral Streams
Southwestern streams are predominantly ephemeral and intermittent (nonperennial) systems located
in the southwestern United States (Section B.5). Based on the National Hydrography Dataset, 94%, 89%,
88%, and 79% of the streams in Arizona, Nevada, New Mexico, and Utah, respectively, are nonperennial.
Mostof these streams connect to downstream waters, although 66% and 20% of the drainage basins in
Nevada and New Mexico, respectively, are closed and drain into playas (dry lakes). Southwestern
streams generally are steep and can be divided into two main types: (1) mountainous streams that drain
higher portions of basins and receive higher rates of precipitation, often as snow, compared to lower
elevations; and (2) streams located in valley or plateau regions that generally flow in response to high-
intensity thunderstorms. Headwater streams are common in both types of southwestern streams.

5.6.1   Connectivity and Consequences on Downstream Waters
Nonperennial southwestern streams, excluding those that drain into playas, are periodically connected
to downstream waters by low-duration, high-magnitude flows. In contrast to streams in humid regions
where discharge is typically supplemented by ground water as drainage area increases, many
southwestern streams lose streamflow to channel transmission losses as runoff travels downstream
(Figure B-10). Connection of runoff and associated materials in ephemeral and intermittent streams to
downstream waters is therefore a function of distance, the relative magnitude of the runoff event, and
transmission losses.
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Spatial and temporal variation in frequency, duration, and timing of southwestern stream runoff is
largely explained by elevation, climate, channel substrate, geology, and the presence of shallow ground
water. In nonconstraining substrate, southwestern rivers are dendritic and their watersheds tend to
have a high drainage density. When high flows are present, southwestern streams are efficient at
transferring water, sediment, and nutrients to downstream reaches. Due to the episodic nature of flow
in ephemeral and intermittent channels, sediment and organic matter can be deposited some distance
downstream, and then moved farther downstream by subsequent precipitation events. Over time,
sediment and organic matter continue to move downstream and affect downstream waters.

The southwestern streams case study (Section B.5) describes the substantial connection and important
consequences of runoff, nutrients, and particulate matter originating from ephemeral tributaries on the
integrity and sustainability of downstream perennial streams. Channel transmission losses can be an
important source of ground-water recharge that sustains downstream perennial stream and riparian
systems. For example, isotopic studies indicate that runoff from ephemeral tributaries like Walnut
Gulch, Arizona supplies roughly half the San Pedro River's baseflow through shallow alluvial aquifer
recharge.

5.6.2   Effects of Human Alteration
Human alterations to southwestern river networks affect the physical, chemical, and biological
connectivity to downstream waters. Impoundments trap water, sediment, and particulate nutrients and
result in downstream impacts on channel morphology and aquatic function. Diversion of water for
consumptive uses can decrease downstream baseflows but typically does not affect the magnitude of
peak flows. Excessive ground-water pumping can lower ground-water tables, thereby diminishing or
eliminating baseflows. Urbanization increases runoff volume and flow velocity, resulting in more erosive
energy that can cause bank erosion, streambed downcutting, and reduced infiltration to ground water.


5.7  Vernal  Pools
Vernal pools are shallow, rain-fed, fishless pools situated on bedrock or low-permeability soils
(Section B.6). Vernal pools inundate seasonally and lack continuous surface-water connections to
downstream water bodies. Although they can occur in other parts of the United States, this case study
focuses on pools in the western states and the glaciated areas of northeastern states. Western vernal
pools typically occur in open grasslands; most northern vernal pools are detrital and are fully contained
within forest ecosystems. When inundation occurs, vernal pools can fill and overflow through swales or
intermittent streams, which connect them to downstream waters.

5.7.1   Connectivity and Consequences on  Downstream Waters
Direct surface connection of vernal pools to downstream waters is infrequent. The duration and
magnitude of such connections are highly variable and depend on the climate, terrain, and geology of the
region and on the location of the vernal pool in the watershed. Vernal pools generally are clustered,

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forming wetland complexes. Pools located at the downgradient end of a complex can receive surface
water through stepping-stone spillage in addition to precipitation, and generally are inundated longer
than upper pools. Because they experience greater inundation and are likely to be located nearer to
streams, these downgradient pools are also more likely to be directly connected to streams. Temporary
storage of heavy rainfall and snowmelt in individually small vernal pool systems (pools plus soils) can
attenuate flooding, provide a reservoir for nearby vegetation during the spring growth period, and
increase nutrient availability.

The timing of seasonal inundation and lack of permanent surface connections make vernal pools
important biological refuges, which has consequences on the biological health of downstream waters.
Vernal pools are highly productive ecosystems that have evolved in a "balance between isolation and
connectedness" (Zedler, 2003; page 597). Because they are connected to other aquatic habitats through
dispersal, they provide rich reservoirs of genetic and species diversity. Food webs in vernal pools
include highly fecund amphibians and insects that convert detrital organic matter into biomass, which is
then exported to aquatic ecosystems in other parts of the watershed. Northern vernal pools can provide
alternative breeding habitat, refuge from predators or environmental stressors, hunting or foraging
habitat, or stepping-stone corridors for dispersal and migration.

5.7.2  Effects of Human Alteration
Vernal pools have been drained and converted to other land uses (e.g., agriculture, logging, urban
development). These activities have increased fragmentation of habitats for amphibians, plants, and
invertebrates, and had similar effects on the frequency, duration, magnitude, and timing of inundations,
surface-water outflows, and shallow subsurface-water connections to downstream waters as those
described in Section 5.2.1 (Carolina and Delmarva bays).
5.8  Synthesis
These case study summaries highlight the key connections between specific water body types and
downstream waters. The case study evidence provides further support that the structure and function of
downstream waters highly depend on constituent materials and organisms contributed by and
transported through water bodies located throughout the watershed. In addition, the studies support
that variation in the types and degrees of connectivity determines the range of downstream effects.

These case study summaries illustrate two key points. First, each type of water body addressed here
demonstrates variability in connectivity to and effects on downstream waters. Oxbow lakes, for
example, are more or less connected to the main river channel based largely on their relative position in
the landscape: Systems close to the river channel are highly connected and those farther away are
connected less often or the impact on the river takes longer to be realized. Evidence presented in the
prairie pothole case study also demonstrates variation in connectivity patterns across the region and
shows the consequences of this variability on downstream rivers and lakes. The prairie streams case
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study discusses functions and varying degrees of connectivity of streams and their cumulative effects on
downstream waters.

Second, the effects of human alteration on the connectivity to and effects on downstream waters depend
on the type of water body. Human alteration of different types of streams and wetlands can be complex,
either increasing or decreasing connectivity and subsequent effects on downstream waters. For
example, evidence shows that ditches in the prairie pothole region increase hydrologic connectivity, and
connectivity of oxbow lakes near active river channels can be reduced if that portion of the river is
leveed. Coupled human-natural systems are an area of active research and new information about the
effects of human activities on connectivity and water integrity is emerging in the peer-reviewed
literature.

Positioning the specific water body types  in the case studies (Appendix B) along a gradient of
connectivity and effect proved to be premature for several reasons. First, the amount of documented
evidence (i.e., number of published studies) varied among the water body types. In some instances, a
large body of evidence exists  and in others, only a few studies exist, limiting sound comparisons. Second,
variation in connectivity consistently was reported to be high within some water body types, creating
substantial overlap in ranges of connectivity among those water body types. In addition to a need for
more  studies documenting connectivity in less studied regions, a more refined classification using the
descriptors of connectivity described in Chapter 1 (or others) and their controls (e.g., climate, geology,
and terrain) within wetland landscape settings are required.

Based on the evidence presented in Chapters 3 and 4, ordering the three broad categories of water
bodies considered in this report—streams, floodplain wetlands, and non-floodplain wetlands—along a
connectivity gradient (Figure 5-1) is possible. Of these three water body types, streams are, in general,
more  connected to and have better-documented effects on downstream waters than either wetland
category. Floodplain wetlands, in turn, tend to be more connected to downstream waters, and have
better-documented downstream effects, than non-floodplain wetlands. This ordering must be
recognized as a broad generalization, and considerable overlap can occur among the types, given the
spatial and temporal variability in connectivity documented in these habitats (Figure 5-1). Nevertheless,
several key lines of evidence support this hypothesized ordering of water body types along the gradient.
    1.  Streams are connected to rivers by a continuous channel, which is a physical reflection of
       surface connectivity.  Formation of a channel indicates that connectivity, in terms of its combined
       descriptors (frequency, duration, magnitude, timing) is sufficiently strong (or "effective") and
       outweighs terrestrialization processes (e.g., revegetation, wind-mediated  processes, soil
       formation processes).
    2.  Within-channel flows are more efficient for moving water, sediment, pollutants, and other
       materials than overland flow; for  some aquatic organisms, channels are the only possible
       transport routes. Channels are places where excess water and materials from the landscape are
       concentrated as they are transmitted downstream. Recurrent flow of sufficient magnitude over a
       given area of landscape selects routes with least resistance, which develop into branched

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       channel networks with a repeating, cumulative pattern of smaller channels that join at
       confluences to form larger channels.
    3.  The continuous channels connecting streams to rivers also represent areas of relatively high
       shallow subsurface connectivity (shallow ground-water recharge and upwelling). Channels are
       typically more permeable than surrounding soils, lack dense terrestrial vegetation (and thus
       have lower uptake and evapotranspiration loss), and are topographic low points closer to
       concentrated shallow ground water.
    4.  Floodplain wetlands and open waters are connected to rivers by historical and recurrent surface
       connectivity. Riparian/floodplain wetlands are maintained by the recurrent inundation and
       deposition of materials from streams and rivers during the peak and recession of flood flows.
    5.  Riparian/floodplain wetlands and open waters are close to river networks and thus more likely
       to have strong connectivity with the downstream water than more distant wetlands, when all
       other conditions are similar.
    6.  Non-floodplain wetlands are positioned outside the floodplain, and so are not subject to direct
       flooding from the river or stream. Any hydrologic connections to the river system are therefore
       unidirectional (from wetland to downstream water and not vice-versa). They are also likely to
       be more distant from the network, increasing the flowpath lengths and travel time to the
       network.
    7.  Because of their large numbers, headwater streams and associated wetlands cumulatively
       represent a large portion of the landscape interface with a downstream water. These areas
       provide functions that enhance both exchanges with and buffering of the downstream water,
       making them critical to mediating the recognized relationship between the integrity of
       downstream waters and the land use and stressor loadings from the surrounding landscape.
    8.  Connectivity to downstream waters is reflected in the distribution of aquatic organisms and
       their dependence on particular aquatic habitats across different stages  of their life cycles. For
       example, the recurrent presence of completely aquatic organisms (i.e., organisms that lack
       terrestrial life stages, overland dispersal, stages resistant to drying) in streams and wetlands
       that periodically dry provides indirect evidence for surface-water connections. Because many
       aquatic species can move and disperse overland, aquatic habitats can be highly connected
       biologically in the absence of hydrologic connectivity.
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 Figure 5-1. Relative positioning of streams, riparian and floodplain waters, and non-floodplain
 waters along a gradient of connectivity. Ellipses are used to illustrate the degree of expected overlap
 among water-body types based on the range of variation documented in the reviewed literature.
                   Non-floodplain
                   waters
Riparian &      streams
Floodplain waters
                               Connection to downstream waters
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This chapter presents the five major conclusions of this report, with a summary of key findings from the
literature synthesized to develop these conclusions. It also discusses the relative abundance of literature
on topics reviewed in this report. Finally, it briefly discusses emerging research that can close some
current data gaps and help further clarify the role of connectivity in maintaining the integrity of
downstream waters.

Citations have been omitted from the text of the conclusions and key findings to improve readability;
please refer to individual chapters for supporting publications and additional information.
6.1  Major  Conclusions and Key Findings
Based on our review and synthesis of the literature, we developed five major conclusions, which are
presented in this section with a summary of key findings for each conclusion.

6.1.1   Conclusion 1: Streams
The scientific literature unequivocally demonstrates that streams, individually or cumulatively, exert a
strong influence on the integrity of downstream waters. All tributary streams, including perennial,
intermittent, and ephemeral streams, are physically, chemically, and biologically connected to
downstream rivers via channels and associated alluvial deposits where water and other materials are
concentrated, mixed, transformed, and transported. Streams are the dominant source of water in most
rivers, and the majority of tributaries are perennial, intermittent, or ephemeral headwater streams.
Headwater streams also convey water into local storage compartments such as ponds, shallow aquifers,
or stream banks, and into regional and alluvial aquifers; these local  storage compartments are important
sources of water for maintaining baseflow in rivers. In addition to water, streams transport sediment,
wood, organic matter, nutrients, chemical contaminants, and many of the organisms found in rivers. The
literature provides robust evidence that streams are biologically connected to downstream waters by
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the dispersal and migration of aquatic and semiaquatic organisms, including fish, amphibians, plants,
microorganisms, and invertebrates, that use both upstream and downstream habitats during one or
more stages of their life cycles, or provide food resources to downstream communities. In addition to
material transport and biological connectivity, ephemeral, intermittent, and perennial flows influence
fundamental biogeochemical processes by connecting channels and shallow ground water with other
landscape elements. Physical, chemical, and biological connections between streams and downstream
waters interact via integrative processes such as nutrient spiraling, in which stream communities
assimilate and chemically transform large quantities of nitrogen and other nutrients that otherwise
would be transported directly downstream, increasing nutrient loads and associated impairments due
to excess nutrients in downstream waters.

6.1.1.1    Conclusion 1, Key Findings
   •  Streams are hydrologically connected to downstream waters via channels that convey surface
       and subsurface water either year-round (i.e., perennial flow), weekly to seasonally (i.e.,
       intermittent flow), or only in direct response to precipitation (i.e., ephemeral flow). Streams are
       the dominant source of water in most rivers, and the majority of tributaries are perennial,
       intermittent, or ephemeral headwater streams. For example, headwater streams, which are the
       smallest channels where streamflows begin, are the cumulative source of approximately 60% of
       the total mean annual flow to all northeastern U.S. streams and rivers.
   •  In addition to downstream transport, headwaters convey water into local storage compartments
       such as ponds, shallow aquifers, or stream banks, and into regional and alluvial aquifers. These
       local storage compartments are important sources of water for maintaining baseflow in rivers.
       Streamflow typically depends on the delayed  (i.e., lagged) release of shallow ground water from
       local storage, especially during dry periods and in areas with shallow ground-water tables and
       pervious subsurfaces. For example, in the southwestern United States, short-term shallow
       ground-water storage in alluvial floodplain aquifers, with gradual release into stream  channels,
       is a major source of annual flow in rivers.
   •  Infrequent, high-magnitude events are especially important for transmitting materials from
       headwater streams in most river networks. For example, headwater streams, including
       ephemeral and intermittent streams, shape river channels by accumulating and gradually or
       episodically releasing stored materials such as sediment and large woody debris. These
       materials help  structure stream and river channels by slowing the flow of water through
       channels and providing substrate and habitat for aquatic organisms.
   •  There is strong evidence that headwater streams function as nitrogen sources (via export) and
       sinks (via  uptake and transformation) for river networks. For example, one study estimated that
       rapid nutrient cycling in small streams with no agricultural or urban impacts removed 20-40%
       of the nitrogen that otherwise would be delivered to downstream waters. Nutrients are
       necessary to support aquatic life, but excess nutrients lead to eutrophication and hypoxia, in
       which over-enrichment causes dissolved oxygen concentrations  to fall below the level necessary

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       to sustain most aquatic animal life in the stream and streambed. Thus, the influence of streams
       on nutrient loads can have significant repercussions for hypoxia in downstream waters.
    •  Headwaters provide habitat that is critical for completion of one or more life-cycle stages of
       many aquatic and semiaquatic species capable of moving throughout river networks. Evidence
       is strong that headwaters provide habitat for complex life-cycle completion; refuge from
       predators, competitors, parasites, or adverse physical conditions in rivers (e.g., temperature or
       flow extremes, low dissolved oxygen, high sediment); and reservoirs of genetic- and species-
       level diversity. Use of headwater streams as habitat is especially critical for the many species
       that migrate between small streams and marine environments during their life cycles (e.g.,
       Pacific and Atlantic salmon, American eels, certain lamprey species). The presence of these
       species within river networks provides robust evidence of biological connections between
       headwaters and larger rivers; because these organisms also transport nutrients and other
       materials as they migrate, their presence also provides evidence of biologically mediated
       chemical connections. In prairie streams, many fishes swim upstream into tributaries to release
       eggs, which develop as they are transported downstream.
    •  Human alterations affect the frequency, duration, magnitude, timing, and rate of change of
       connections between headwater streams, including ephemeral and intermittent streams, and
       downstream waters. Human activities and built structures (e.g., channelization, dams, ground-
       water withdrawals) can either enhance or fragment longitudinal connections between
       headwater streams and downstream waters, while also constraining lateral and vertical
       exchanges and tightly controlling the temporal dimension of connectivity. In many cases,
       research on human alterations has enhanced our understanding of the headwater stream-
       downstream water connections and their consequences. Recognition of these connections and
       effects has encouraged the development of more sustainable practices and infrastructure to
       reestablish and manage connections, and ultimately to protect and restore the  integrity of
       downstream waters.

6.1.2   Conclusion 2: Riparian/Floodplain Wetlands and Open Waters
The literature clearly shows that wetlands and open waters in riparian areas and floodplains are
physically, chemically, and biologically integrated with rivers via functions that improve downstream
water quality, including the temporary storage and deposition of channel-forming sediment and woody
debris, temporary storage of local ground water that supports baseflow in rivers, and transformation
and transport of stored organic matter. Riparian/floodplain wetlands and open waters improve water
quality through the assimilation, transformation, or sequestration of pollutants, including excess
nutrients and chemical contaminants such as pesticides and metals, that can degrade downstream water
integrity. In addition to providing effective buffers to protect downstream waters from point source and
nonpoint source pollution, these  systems form integral components of river food webs, providing
nursery habitat for breeding fish and amphibians, colonization opportunities for stream invertebrates,
and maturation habitat for stream insects. Lateral expansion and contraction of the river in its

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floodplain result in an exchange of organic matter and organisms, including fish populations that are
adapted to use floodplain habitats for feeding and spawning during high water, that are critical to river
ecosystem function. Riparian/floodplain wetlands and open waters also affect the integrity of
downstream waters by subsequently releasing (desynchronizing) floodwaters and retaining large
volumes of stormwater, sediment, and contaminants in runoff that could otherwise negatively affect the
condition or function of downstream waters.

6.1.2.1    Conclusion 2, Key Findings
    •  Riparian areas and floodplains connect upland and aquatic environments through both surface
       and subsurface hydrologic flowpaths. These areas are therefore uniquely situated in watersheds
       to receive and process waters that pass over densely vegetated areas and through subsurface
       zones before the waters reach streams and rivers. When pollutants reach a riparian or
       floodplain wetland, they can be sequestered in sediments, assimilated into wetland plants and
       animals, transformed into less harmful or mobile forms or compounds, or lost to the
       atmosphere. Wetland potential for biogeochemical transformations (e.g., denitrification) that
       can improve downstream water quality is influenced by local factors, including anoxic
       conditions and slow organic matter decomposition, shallow water tables, wetland plant
       communities, permeable soils, and complex topography.
    •  Riparian/floodplain wetlands can reduce flood peaks by storing and desynchronizing
       floodwaters. They can also maintain river baseflows by recharging alluvial aquifers. Many
       studies have documented the ability of riparian/floodplain wetlands to reduce flood pulses by
       storing excess water from streams and rivers. One review of wetland studies reported that
       riparian wetlands reduced or delayed floods in 23 of 28 studies. For example, peak discharges
       between upstream and downstream gaging stations on the Cache River in Arkansas were
       reduced 10-20% primarily due to floodplain water storage.
    •  Riparian areas and floodplains store large amounts of sediment and organic matter from
       upstream and from upland areas. For example, riparian areas have been shown to remove
       80-90% of sediments leaving agricultural fields in North Carolina.
    •  Ecosystem function within a river system is driven in part by biological connectivity that links
       diverse biological communities with the river system. Movements of organisms that connect
       aquatic habitats and their populations, even across different watersheds, are important for the
       survival of individuals, populations, and species, and for the functioning of the river ecosystem.
       For example, lateral expansion and contraction of the river in its floodplain result in  an exchange
       of matter and organisms, including fish populations that are adapted to use floodplain habitats
       for feeding and spawning during high water. Wetland and aquatic plants in floodplains can
       become important seed sources for the river network, especially if catastrophic flooding scours
       vegetation and seed banks in other parts of the channel. Many invertebrates exploit temporary
       hydrologic connections between rivers and floodplain wetland habitats, moving into these
       wetlands to feed, reproduce, or avoid harsh environmental conditions and then returning to the

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       river network. Amphibians and aquatic reptiles commonly use both streams and
       riparian/floodplain wetlands to hunt, forage, overwinter, rest, or hide from predators. Birds can
       spatially integrate the watershed landscape through biological connectivity.

6.1.3   Conclusion 3: Non-floodplain Wetlands and Open Waters
Wetlands and open waters in non-floodplain landscape settings (hereafter called "non-floodplain
wetlands") provide numerous functions that benefit downstream water integrity. These functions
include storage of floodwater; recharge of ground water that sustains river baseflow; retention and
transformation of nutrients, metals, and pesticides; export of organisms or reproductive propagules to
downstream waters; and habitats needed for stream species. This diverse group of wetlands (e.g., many
prairie potholes, vernal pools, playa lakes) can be connected to downstream waters through surface-
water, shallow subsurface-water, and ground-water flows and through biological and chemical
connections.

In general, connectivity of non-floodplain wetlands occurs along a gradient (Conclusion 4), and can be
described in terms of the frequency, duration, magnitude, timing, and rate of change of water, material,
and biotic fluxes to downstream waters. These descriptors are influenced by climate, geology, and
terrain, which interact with factors such as the magnitudes of the various functions within wetlands
(e.g., amount of water storage or carbon export) and their proximity to downstream waters to
determine where wetlands occur along the connectivity gradient. At one end of this gradient, the
functions of non-floodplain wetlands clearly affect the condition of downstream waters if a visible (e.g.,
channelized) surface-water or a regular shallow subsurface-water connection to the river network is
present. For non-floodplain wetlands lacking a channelized surface or regular shallow subsurface
connection (i.e., those at intermediate points along the gradient of connectivity), generalizations about
their specific effects on downstream waters from the available literature are difficult because
information on both function and connectivity is needed. Although there is ample evidence that non-
floodplain wetlands provide hydrologic, chemical, and biological functions that affect material fluxes, to
date, few scientific studies explicitly addressing connections between non-floodplain wetlands and river
networks have been published in the peer-reviewed literature. Even fewer publications specifically
focus on the frequency, duration, magnitude, timing, or rate of change of these connections. In addition,
although areas that are closer to rivers and streams have a higher probability of being connected than
areas farther away when conditions governing the type and quantity of flows—including soil infiltration
rate, wetland storage capacity, hydraulic gradient, etc.—are similar, information to determine if this
similarity holds is generally not provided in the studies we reviewed. Thus, current science does not
support evaluations of the degree of connectivity for specific groups or classes of wetlands (e.g., prairie
potholes or vernal pools). Evaluations of individual wetlands or groups of wetlands, however, could be
possible through case-by-case analysis.

Some effects of non-floodplain wetlands on downstream waters are due to their isolation, rather than
their connectivity. Wetland sink functions that trap materials and prevent their export to downstream
waters (e.g., sediment and entrained pollutant removal, water storage) result because of the wetland's

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ability to isolate material fluxes. To establish that such functions influence downstream waters, we also
need to know that the wetland intercepts materials that otherwise would reach the downstream water.
The literature we reviewed does provide limited examples of direct effects of wetland isolation on
downstream waters, but not for classes of wetlands (e.g., vernal pools). Nevertheless, the literature we
reviewed enables us to conclude that sink functions of non-floodplain wetlands, which result in part
from their relative isolation, will affect a downstream water when these wetlands are situated between
the downstream water and known point or nonpoint sources of pollution, and thus intersect flowpaths
between the pollutant source and downstream waters.

6.1.3.1    Conclusion 3, Key Findings
    •  Water storage by wetlands well outside of riparian or floodplain areas can affect streamflow.
       Hydrologic models of prairie potholes in the Starkweather Coulee subbasin (North Dakota) that
       drains to Devils Lake indicate that increasing the volume of pothole storage across the subbasin
       by approximately 60% caused simulated total annual streamflow to decrease 50% during a
       series of dry years and 20% during wet years.  Similar simulation studies of watersheds that feed
       the Red River of the North in North Dakota and Minnesota demonstrated qualitatively
       comparable results, suggesting that the ability of potholes to modulate streamflow could be
       widespread across eastern portions of the prairie pothole region. This work also indicates that
       reducing water storage capacity of wetlands by connecting formerly isolated potholes through
       ditching or drainage to the Devils Lake and Red River basins could increase stormflow and
       contribute to downstream flooding. In many agricultural areas already crisscrossed by extensive
       drainage systems, total streamflow and baseflow are increased by directly connecting potholes
       to stream networks. The impacts of changing streamflow are numerous, including altered flow
       regime, stream geomorphology, habitat,  and ecology. The presence or absence of an effect of
       prairie pothole water storage on streamflow depends on many factors, including patterns of
       precipitation, topography, and degree of human alteration. For example, in parts of the prairie
       pothole region with low precipitation, low stream density, and little human alteration,
       hydrologic connectivity between prairie  potholes and streams or rivers is likely to be low.
    •  Non-floodplain wetlands act as sinks and transformers for various pollutants, especially
       nutrients, which at excess levels can adversely impact human and ecosystem health and pose a
       serious pollution problem in the United States. In one study, sewage waste waters were applied
       to forested wetlands in Florida for 4.5 years; more than 95% of the phosphorus, nitrate,
       ammonium, and total nitrogen were removed by the wetlands during the study period, and
       66-86% of the nitrate removed was attributed to the process of denitrification. In another
       study, sizeable phosphorus retention (0.3 to 8.0 mg soluble reactive P nr2  d-1) occurred in
       marshes that comprised only 7% of the lower Lake Okeechobee basin area in Florida. A non-
       floodplain bog in Massachusetts was reported to sequester nearly 80% of nitrogen inputs from
       various sources, including atmospheric deposition, and prairie pothole wetlands in the upper
       Midwest were found to remove >80% of the nitrate load via denitrification. A large prairie
       marsh was found to remove 86% of nitrate, 78% of ammonium, and 20% of phosphate through

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       assimilation and sedimentation, sorption, and other mechanisms. Together, these and other
       studies indicate that onsite nutrient removal by non-floodplain wetlands is substantial and
       geographically widespread. The effects of this removal on rivers are generally not reported in
       the literature.
    •  Non-floodplain wetlands provide unique and important habitats for many species, both common
       and rare. Some of these species require multiple types of waters to complete their full life cycles,
       including downstream waters. Abundant or highly mobile species play important roles in
       transferring energy and materials between non-floodplain wetlands and downstream waters.
    •  Biological connections are likely to occur between most non-floodplain wetlands and
       downstream waters through either direct or stepping stone movement of amphibians,
       invertebrates, reptiles, mammals, and seeds of aquatic plants, including colonization by invasive
       species. Many species in those groups that use both stream and wetland habitats are capable of
       dispersal distances equal to or greater than distances between many wetlands and river
       networks. Migratory birds can be an important vector of long-distance dispersal of plants and
       invertebrates between non-floodplain wetlands and the river network, although their influence
       has not been quantified. Whether those connections are of sufficient magnitude to impact
       downstream waters will either require estimation of the magnitude of material fluxes or
       evidence that these movements of organisms are required for the survival and persistence of
       biota that contribute to the integrity of downstream waters.
    •  Spatial proximity is one important determinant of the magnitude, frequency, and duration of
       connections between wetlands and streams that will ultimately influence the fluxes  of water,
       materials, and biota between wetlands and downstream waters. However, proximity alone is
       not sufficient to determine connectivity, due to local variation in factors such as slope and
       permeability.
    •  The cumulative influence of many individual wetlands within watersheds can strongly affect the
       spatial scale, magnitude, frequency, and duration of hydrologic, biological, and chemical fluxes
       or transfers of water and materials to downstream waters. Because of their aggregated
       influence, any evaluation of changes to individual wetlands should be considered in  the context
       of past and predicted changes (e.g., from climate change)  to other wetlands within the same
       watershed.
    •  Non-floodplain wetlands can be hydrologically connected directly to river networks through
       natural or constructed channels, nonchannelized surface  flows, or subsurface flows, the latter of
       which can travel long distances to affect downstream waters. A wetland surrounded by uplands
       is defined as "geographically isolated." Our review found  that, in some cases, wetland types such
       as vernal pools and coastal depressional wetlands are collectively—and incorrectly—referred to
       as geographically isolated. Technically, the term "geographically isolated" should be applied only
       to the particular wetlands within a type or class that are completely surrounded by uplands.
       Furthermore, "geographic isolation" should not be confused with functional isolation, because

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       geographically isolated wetlands can still have hydrologic, chemical, and biological connections
       to downstream waters.
    •  Non-floodplain wetlands occur along a gradient of hydrologic connectivity-isolation with
       respect to river networks, lakes, or marine/estuarine water bodies. This gradient includes, for
       example, wetlands that serve as origins for stream channels that have permanent surface-water
       connections to the river network; wetlands with outlets to stream channels that discharge to
       deep ground-water aquifers; geographically isolated wetlands that have local ground-water or
       occasional surface-water connections to downstream waters; and geographically isolated
       wetlands that have minimal hydrologic connection to other water bodies (but which could
       include surface and subsurface connections to other wetlands). This gradient can exist among
       wetlands of the same type or in the same geographic region.
    •  Caution should be used in interpreting connectivity for wetlands that have been designated as
       "geographically isolated" because (1) the term can be applied broadly to a heterogeneous group
       of wetlands, which can include wetlands that are not actually geographically isolated; (2)
       wetlands with permanent channels could be miscategorized as geographically isolated if the
       designation is based on maps or imagery with inadequate spatial resolution, obscured views,
       etc.; and (3) wetland complexes could have connections to downstream waters through stream
       channels even if individual wetlands within the complex are geographically isolated. For
       example, a recent study examined hydrologic connectivity in a complex of wetlands on the Texas
       Coastal Plain. The wetlands in this complex have been considered to be a type of geographically
       isolated wetland. Collectively, however, they are connected both geographically and
       hydrologically to downstream waters in the area: During an almost 4-year study period, nearly
       20% of the precipitation that fell on the wetland complex flowed out through an intermittent
       stream into downstream waters. Thus, wetland complexes could have connections to
       downstream waters through stream channels even when the individual wetland components
       are geographically isolated.

6.1.4   Conclusion 4: Degrees and Determinants of Connectivity
Watersheds are integrated at multiple spatial and temporal scales by flows of surface water and ground
water, transport and transformation of physical and chemical materials, and movements of organisms.
Although all parts of a watershed are connected to some degree—by the hydrologic cycle or dispersal of
organisms, for example—the degree and downstream effects of those connections vary spatially and
temporally, and are determined by characteristics of the physical, chemical, and biological environments
and by human activities.

Stream and wetland connections have particularly important consequences for downstream water
integrity. Most of the materials—broadly defined as any physical, chemical, or biological entity—in
rivers, for example, originate from aquatic ecosystems located upstream or elsewhere in the watershed.
Longitudinal flows through ephemeral, intermittent, and perennial stream channels are much more
efficient for transport of water, materials, and organisms than diffuse overland flows, and areas that
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concentrate water provide mechanisms for the storage and transformation, as well as transport, of
materials.

Connectivity of streams and wetlands to downstream waters occurs along a continuum that can be
described in terms of the frequency, duration, magnitude, timing, and rate of change of water, material,
and biotic fluxes to downstream waters. These terms, which we refer to collectively as connectivity
descriptors, characterize the range over which streams and wetlands vary and shift along the
connectivity gradient in response to changes in natural and anthropogenic factors and, when considered
in a watershed context, can be used to predict probable effects of different degrees of connectivity over
time. The evidence unequivocally demonstrates that the stream channels and riparian/floodplain
wetlands or open waters that together form river networks are clearly connected to downstream waters
in ways that profoundly influence downstream water integrity. The connectivity and effects of non-
floodplain wetlands and open waters are more variable and thus more difficult to address solely from
evidence available in peer-reviewed studies.

Variations in the degree of connectivity influence the range of functions provided by streams and
wetlands, and are critical to the integrity and sustainability of downstream waters. Connections with
low values of one or more descriptors (e.g., low-frequency, low-duration streamflows caused by flash
floods) can  have important downstream effects when considered in the context of other descriptors
(e.g., large magnitude of water transfer). At the other end of the frequency range, high-frequency, low-
magnitude vertical (surface-subsurface) and lateral flows contribute to aquatic biogeochemical
processes, including nutrient and contaminant transformation and organic matter accumulation. The
timing of an event can alter both connectivity and the magnitude of its downstream effect. For example,
when soils become saturated by previous rainfall events, even low or moderate  rainfall can cause
streams or wetlands to overflow, transporting water and materials to downstream waters. Fish that use
nonperennial or perennial headwater stream habitats to spawn or rear young, and invertebrates that
move into seasonally inundated floodplain wetlands prior to emergence, have life cycles that are
synchronized with the timing of flows, temperature thresholds, and food resource availability in those
habitats.

6.1.4.1    Conclusion 4, Key Findings
    •  The surface-water and ground-water flowpaths (hereafter, hydrologic flowpaths), along which
       water and materials are transported and transformed, determine variations in the degree of
       physical and chemical connectivity. These flowpaths are controlled primarily by variations in
       climate, geology, and terrain within and among watersheds and over time. Climate, geology, and
       terrain are reflected locally in factors such as rainfall and snowfall intensity, soil infiltration
       rates, and the direction of ground-water flows. These local factors interact with the landscape
       positions of streams and wetlands relative to downstream waters, and with functions (such  as
       the removal or transformation of pollutants) performed by those streams and wetlands to
       determine connectivity gradients.
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    •  Gradients of biological connectivity (i.e., the active or passive movements of organisms through
       water or air and over land that connect populations) are determined primarily by species
       assemblages, and by features of the landscape (e.g., climate, geology, terrain) that facilitate or
       impede the movement of organisms. The temporal and spatial scales at which biological
       pathways connect aquatic habitats depend on characteristics of both the landscape and species,
       and overland transport or movement can occur across watershed boundaries. Dispersal is
       essential for population persistence, maintenance of genetic diversity, and evolution of aquatic
       species. Consequently, dispersal strategies reflect aquatic species' responses and adaptations to
       biotic and abiotic environments, including spatial and temporal variation in resource availability
       and quality. Species' traits and behaviors encompass species-environment relationships over
       time, and provide an ecological and evolutionary context for evaluating biological connectivity
       in a particular watershed or group of watersheds.
    •  Pathways for chemical transport and transformation largely follow hydrologic flowpaths, but
       sometimes  follow biological pathways (e.g., nutrient transport from wetlands to coastal waters
       by migrating waterfowl, upstream transport of marine-derived nutrients by spawning of
       anadromous fish, uptake and removal  of nutrients by emerging stream insects).
    •  Human activities alter naturally occurring gradients of physical, chemical, and biological
       connectivity by modifying the frequency, duration, magnitude, timing, and rate of change of
       fluxes, exchanges, and transformations. For example, connectivity can be reduced by dams,
       levees, culverts, water withdrawals, and habitat destruction, and can be increased by effluent
       discharges, channelization, drainage ditches and tiles, and impervious surfaces.

6.1.5   Conclusion 5:  Cumulative  Effects
The incremental effects of individual streams and wetlands are cumulative across entire watersheds and
therefore must be evaluated in context with other streams and wetlands. Downstream waters are the
time-integrated result of all waters contributing to them. For example, the amount of water or biomass
contributed by a specific ephemeral stream in  a given year might be small, but the aggregate
contribution of that stream over multiple years, or by all ephemeral streams draining that watershed in
a given year or over multiple years, can have substantial consequences on the integrity of the
downstream waters. Similarly, the downstream effect of a single event, such as pollutant discharge into
a single stream or wetland, might be negligible but the cumulative effect of multiple discharges could
degrade the integrity of downstream waters.

In addition, when considering the effect of an individual stream or wetland, all contributions and
functions of that stream or wetland should be  evaluated cumulatively. For example, the same stream
transports water, removes excess nutrients, mitigates flooding, and provides refuge for fish when
conditions downstream are unfavorable; if any of these functions is ignored, the overall effect of that
stream would be underestimated.
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6.1.5.1    Conclusion 5, Key Findings
    •  Structurally and functionally, stream-channel networks and the watersheds they drain are
       fundamentally cumulative in how they are formed and maintained. Excess water from
       precipitation that is not evaporated, taken up by organisms, or stored in soils and geologic
       layers moves downgradient by gravity as overland flow or through channels carrying sediment,
       chemical constituents, and organisms. These channels concentrate surface-water flows and are
       more efficient than overland (i.e., diffuse) flows in transporting water and materials, and are
       reinforced over time by recurrent flows.
    •  Connectivity between streams and rivers provides opportunities for materials, including
       nutrients and chemical contaminants, to be transformed chemically as they are transported
       downstream. Although highly efficient at the transport of water and other physical materials,
       streams are dynamic ecosystems with permeable beds and banks that interact with other
       ecosystems above and below the surface. The exchange of materials between surface and
       subsurface areas involves a series of complex physical, chemical, and biological alterations that
       occur as materials move through different parts of the river system. The amount and quality of
       such materials that eventually reach a river are determined by the aggregate effect of these
       sequential alterations that begin at the source waters, which can be at some distance from the
       river. The opportunity for transformation of material (e.g., biological uptake, assimilation, or
       beneficial transformation) in intervening stream reaches increases with distance to the river.
       Nutrient spiraling, the process by which nutrients entering headwater streams are transformed
       by various aquatic organisms and chemical reactions as they are transported downstream, is
       one example of an instream  alteration that exhibits significant beneficial effects on downstream
       waters. Nutrients (in their inorganic form) that enter a headwater stream (e.g., via overland
       flow) are first removed from the water column by streambed algal and microbial populations.
       Fish or insects  feeding on algae and microbes take up some of those nutrients, which are
       subsequently released back  into the stream via excretion and decomposition (i.e., in their
       organic form),  and the cycle  is repeated. In each phase of the cycling process—from dissolved
       inorganic nutrients in the water column, through microbial uptake, subsequent transformations
       through the food web, and back to dissolved nutrients in the water column—nutrients are
       subject to downstream transport. Stream and wetland capacities for nutrient cycling have
       important implications for the form and concentration of nutrients exported to downstream
       waters.
    •  Cumulative effects across a watershed must be considered when quantifying the frequency,
       duration, and magnitude of connectivity, to evaluate the downstream effects of streams and
       wetlands. For example, although the probability of a large-magnitude transfer of organisms
       from any given headwater stream in a given year might be low (i.e., a low-frequency connection
       when each stream is considered individually), headwater streams are the most abundant type of
       stream in most watersheds.  Thus, the overall probability of a large-magnitude transfer of
       organisms is higher when considered for all headwater streams in a watershed—that is, a high-
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       frequency connection is present when headwaters are considered cumulatively at the
       watershed scale, compared with probabilities of transport for streams individually. Similarly, a
       single pollutant discharge might be negligible but the cumulative effect of multiple discharges
       could degrade the integrity of downstream waters. Riparian open waters (e.g., oxbow lakes),
       wetlands, and vegetated areas cumulatively can retain up to 90% of eroded clays, silts, and
       sands that otherwise would enter stream channels. The larger amounts of snowmelt and
       precipitation cumulatively held by many wetlands can reduce the potential for flooding at
       downstream locations. For example, wetlands in the prairie pothole region cumulatively stored
       about 11-20% of the precipitation in one watershed.
    •  The combination of diverse habitat types and abundant food resources cumulatively makes
       floodplains important foraging, hunting, and breeding sites for fish, aquatic life stages of
       amphibians, and aquatic invertebrates. The scale of these cumulative effects can be extensive;
       for example, coastal ibises travel up to 40 km to obtain food from freshwater floodplain
       wetlands for nesting chicks, which cannot tolerate salt levels in local food resources until they
       fledge.


6.2  Strength  of Evidence for Conclusions  and Data Gaps in
       the Available Literature
This report synthesizes a large body of scientific evidence to address the questions in Table 1-1 of this
report. The major conclusions (Section 6.1) reflect the strength of evidence currently available in the
peer-reviewed scientific literature for assessing the connectivity and downstream effects of water
bodies identified in Table 1-1.

The conclusions of this report were corroborated by two independent peer reviews by scientists
identified in the front matter of this report.

The term connectivity is defined in this report as the degree to which components of a watershed are
joined and interact by transport mechanisms that function across multiple spatial and temporal scales
(Sections 1.2.2 and 2.3.2.1). Our review found strong evidence supporting the central roles of the
physical, chemical, and biological connectivity of streams, wetlands, and open waters—encompassing
varying degrees of both connection and isolation—in maintaining the structure and function of
downstream waters, including rivers, lakes, estuaries, and oceans. Our review also found strong
evidence demonstrating the various mechanisms by which material and biological linkages from
streams, wetlands, and open waters affect downstream waters, classified here into five functional
categories (source, sink, refuge, lag, and transformation), modify the timing of transport and the
quantity and quality of resources available to downstream ecosystems and communities. Thus, the
currently available literature provided a large body of evidence for assessing the connections and
functions by which streams and wetlands produce the range of observed effects on the integrity of
downstream waters.
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The body of literature on functions provided by streams and riparian/floodplain wetlands was abundant
in all five categories (Table 6-1). The body of literature on functions of non-floodplain wetlands was
abundant in two categories (sink and transformation) and moderate in the other three categories
(source, refuge, and lag; Table 6-1). The evidence unequivocally demonstrates that the stream channels
and wetlands or open waters that together form river networks are clearly connected to downstream
waters in ways that profoundly influence downstream water integrity. The body of literature
documenting connectivity and downstream effects was most abundant for perennial and intermittent
streams, and for riparian/floodplain wetlands (Table 6-2). Although less abundant, the available
evidence for connectivity and downstream effects of ephemeral streams was strong and compelling,
particularly in context with the large body of evidence supporting the physical connectivity and
cumulative effects of channelized flows that form and maintain stream networks.

As stated in Conclusion 3 (Section 6.1.3), the connectivity and effects of wetlands and open waters that
are not structurally linked to other waters by stream channels and their lateral extensions into riparian
areas and floodplains are more difficult to address solely from evidence available in  peer-reviewed
studies. One limitation was the relatively small number of published, peer-reviewed studies examining
the relationships of non-floodplain wetlands to downstream waters (Table 6-2). The literature on non-
floodplain wetlands that is available shows that these systems have important hydrologic, water-quality,
and habitat functions that can affect downstream waters where connections to them exist; the literature
also provides limited examples of direct effects of non-floodplain wetland isolation on downstream
water integrity. Currently available peer-reviewed literature, however, does not identify which types of
non-floodplain wetlands have or lack the types of connections needed to convey the effects on
downstream waters of functions, materials, or biota provided by those wetlands. These limitations of the
literature, considered in context with comments from the Science Advisory Board on an external review
draft of this report (U.S. EPA, 2014), are reflected in the lower strength of evidence expressed in the
conclusions (Section 6.1.3).

Additional information from other sources not included in this report (e.g., field assessments, analysis of
existing or new data, reports from local resource agencies) could be used in case-by-case analysis of
non-floodplain wetlands. Importantly, information from emerging research into the  connectivity of non-
floodplain wetlands, including studies of the types identified in Section 4.5.2 of this report, could close
some of the current data gaps in the near future. Recent scientific advances in the fields of mapping (e.g.,
Heine etal., 2004; Tiner, 2011; Langetal., 2012), assessment (e.g., McGlynn and McDonnell, 2003;
Gergel, 2005; McGuire etal., 2005; Ver Hoef etal., 2006; Leibowitz etal., 2008; Moreno-Mateos etal.,
2008; Lane and D'Amico, 2010; Ver Hoef and Peterson, 2010; Shook and Pomeroy, 2011; Powers etal.,
2012; McDonough et al., 2015), modeling (e.g., Golden et al., 2013; Mclaughlin et al., 2014), and
landscape classification (e.g., Wigington et al., 2013) indicate that increasing availability of high-
resolution data  sets, promising new technologies for watershed-scale analyses, and methods for
classifying landscape units by hydrologic behavior can facilitate and improve the accuracy of
connectivity assessments. Emerging research that expands our ability to detect and monitor ecologically
relevant connections at appropriate scales, metrics to accurately measure effects on downstream

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A Review and Synthesis                                                                         3

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integrity, and management practices that apply what we already know about ecosystem function, will
contribute to our ability to identify waters of national importance and maintain the long-term
sustainability and resiliency of valued water resources.
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A Review and Synthesis                                                                           3

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1-3
§ ffl
     body of literature documented in the report, in the evidence for source, sink, refuge, lag, and transformation functions of streams and wetlands
     and their associated effects on downstream waters. A small dot (•) indicates relatively lower confidence, a medium dot (•) indicates relatively
     intermediate confidence, and a large dot (^)) indicates a relatively high level of confidence. The dot size does not necessarily correspond with
     many references. The dot size also does not correspond with the level of confidence in particular conclusions.
  a
Type of water body
Streams
Riparian/floodplain wetlands
Non-floodplain wetlands
Function
Source
O
o
o
Sink (Storage)
O
o
o
Refuge
O
o
o
Lag
O
o
o
Transformation
O
o
o
Uncertainty discussion
(Section)
3.6
4.5.1
4.5.2
to
o

-------
1-3
  a
" 3
<2. O
(/) o
Table 6-2. Relative abundance of literature by review topic area. The table shows the relative size of the body of literature documented in the
report that addresses the physical, chemical, or biological connectivity to and effects on downstream waters. A small dot (•) indicates a relatively
smaller body of literature, a medium dot (•) indicates a relatively intermediate body of literature, and a large dot (^)) indicates a relatively
large body of literature. The dot size does not necessarily correspond with the number of associated citations in this report because some
     level of confidence in particular conclusions.

Topic


Streams



Riparian/
Floodplain
Wetlands



Non-
floodplain
wetlands



Question


What are the physical, chemical,
and biological connections to and
effects of ephemeral, intermittent,
and perennial streams on
downstream waters?

What are the physical, chemical,
and biological connections to and
effects of riparian orfloodplain
wetlands and open waters (e.g.,
riverine wetlands, oxbow lakes) on
downstream waters?
What are the physical, chemical,
and biological connections to and
effects of wetlands and open
waters in non-floodplain settings
(e.g., most prairie potholes, vernal
pools) on downstream waters?



ephemeral
intermittent

perennial









Biological


Connection
O
o

o

o




o



Effect
o
O

o

o




o


Chemical


Connection
O
o

o

o




o



Effect
O
O

O

o




o


Physical


Connection
O
o

o

o




o



Effect
O
O

O

o




o


to
o

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                                APPENDIX A. GLOSSARY
Absorption—A reversible process that occurs when molecules in one state or phase penetrate those of
another phase.

Adsorption—Adhesion of molecules to a surface, either physically or chemically. Physical adsorption
occurs when the surface tension of a solid causes molecules to be held at its surface; this process can be
reversible, depending on environmental conditions. Chemical adsorption occurs when chemicals bond
at the surface of a solid, and is not readily reversible.

Allochthonous—Describing organic material that originates from outside of streams, rivers, wetlands,
or lakes (e.g., terrestrial plant litter, soil).

Alluvial Aquifer—An aquifer with geologic materials deposited by a stream or river (alluvium) that
retains a hydraulic connection with the depositing stream.

Alluvial Deposits—See Alluvium.

Alluvial Ground Water—Ground water occurring in an alluvial aquifer.

Alluvium—Deposits of clay, silt, sand, gravel, or other particulate materials that have been deposited by
a stream or other body of running water in a streambed, on a flood plain, on a delta, or at the base of a
mountain. See Colluvium.

Anastomosing Channel—A multithreaded stream or river channel in which the channels
(distributaries) branch and rejoin farther downstream; distributary channels are separated by stable
islands (usually vegetated) that are large relative to the size of the channels.

Anoxic Conditions—Without detectable dissolved oxygen; anaerobic. See Hypoxia.

Aquatic Ecosystem—Any aquatic environment, including all of the environment's  living and nonliving
constituents and the interactions among them.

Aquifer—A geologic formation (e.g., soil, rock, alluvium) with permeable materials partially or fully
saturated with ground water  that yields ground water to a well, spring, or stream.

Artificial Drainage—Use of constructed channels or subsurface structures to drain an area by
increasing the rate of flow of water from the area.

Assimilatory Processes—The incorporation or transformation of simple compounds into more
complex compounds.

Autochthonous—Describing organic matter that originates from production within streams, rivers,
wetlands, or lakes (e.g., periphyton, macrophytes, phytoplankton).
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Bank Storage—Storage of water that flows from a stream to an alluvial aquifer during a flood or period
of high streamflow. The volume of water is stored and released after the high-water event over days to
months. The volume of water stored and the timing of release depends on the hydraulic properties of
the alluvial aquifer.

Baseflow—Sustained flow of a stream (or river) in the absence of stormflow (direct runoff). Natural
baseflow is sustained by ground-water discharge in the stream network. Baseflow also can be sustained
by human sources (e.g., irrigation recharges to ground water).

Basin—See Drainage Basin.

Bedrock—Solid rock underlying loose deposits such as  soil or alluvium.

Bog—A peat-accumulating wetland that is generally nutrient poor.

Braided Channel—A multithreaded channel in which the channels (distributaries) branch and rejoin
farther downstream and the channels are separated by  mobile, transient bars (poorly vegetated) that
are small relative to the size of the channels.

Carolina Bays—Elliptical, ponded, depressional wetlands that range along the Atlantic Coastal  Plain
from northern Florida to New Jersey. See Delmarva Bays.

Catchment—The area drained by a stream, river, or other water body; typically defined by the
topographic divides between one water body and another. Synonymous with Watershed and Drainage
Basin.

Channel—A natural or constructed passageway or depression of perceptible linear extent that conveys
water and associated material downgradient.

Channelization—A type of artificial drainage in which complex channels are straightened to increase
the rate of water flow from an area.

Channelized Flow—Flow that occurs in a natural or artificial channel.

Colluvium—A layer of unconsolidated soils, sediment and rock fragments deposited by surface runoff
and gravitational processes; colluvium generally occurs as a blanket of poorly sorted sediment and rock
fragments on the lower parts of hillslopes underlain by  bedrock. See Alluvium.

Condition—General health or quality of an ecosystem, typically assessed using one or more indicators.

Confined Aquifer—An aquifer bounded above and below by confining units of distinctly lower
permeability than that of the aquifer itself.

Confluence—The point at which two stream channels intersect to form a single channel.

Connectivity—The degree to which components of a  river system are joined, or connected, by various
transport mechanisms; connectivity is determined by the characteristics of both the physical landscape
and the biota of the specific system.
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Connectivity Descriptors (for streams and wetlands)—The frequency, duration, magnitude, timing,
and rate of change effluxes to and biological exchanges with downstream waters.

Contributing Area—Location within a watershed/river network that serves as a source of stream flow
or material flux.

Contaminants—Any material that might be harmful to humans or other organisms when released to the
environment.

Deep Ground Water—Ground-water flow systems having the deepest and longest flowpaths; also
referred to as regional ground-water flow systems, they can occur beneath local and intermediate
ground-water flow systems. See Local Ground Water, Regional Ground Water.

Delmarva Bays—Carolina bays that are geographically specific to the Delmarva Peninsula. These
wetlands frequently have the same elliptical shape and orientation as Carolina bays. See Carolina Bays.

Dendritic Stream Network—A stream network pattern of branching tributaries (see Figure 2-19B).

Depressional Wetland—A wetland occupying a topographic low point that allows the accumulation of
surface water. Depressional wetlands can have any combination of inlets and outlets or lack them
completely. Examples include kettles, prairie potholes, and Carolina bays. This category also includes
slope wetlands (wetlands associated with surface discharge of ground water or saturated overflow with
no channel formation).

Diadromous—Migratory between fresh and salt waters.

Direct Runoff—Runoff that occurs in direct response to precipitation. See Stormflow.

Discharge—The volume of water (surface water or ground water) that passes a given location over a
given period of time; the rate of runoff. Often expressed as ft3 s~l or m3 s~l.

Discontinuous Flow—Refers to stream and river reaches that have flow in one part of the reach but not
another part of the reach. See Reach.

Dispersal—Movement from natal breeding sites to new breeding sites.

Drainage Area—The spatial extent of a drainage basin. Typically expressed in mi2 or km2.

Drainage Basin—The area drained by a stream, river, or other water body; typically defined by the
topographic divides between one water body and another. Synonymous with Catchment one? Watershed.

Drainage Density—The total length of stream channels per unit drainage area (e.g., per mi2 or km2).

Drainage Network—See River Network.

Egg Bank—Viable dormant eggs that accumulate in soil or in sediments under water. See Seed bank.

Endorheic Basins—A closed drainage basin with no outflows to other water bodies.
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Endorheic Stream—A stream or river reach that experiences a net loss of water to a ground-water
system. See Losing Stream or Wetland.

Ephemeral Stream—A stream or river that flows briefly in direct response to precipitation; these
channels are always above the water table.

Eutrophication—Natural or artificial enrichment of a water body by nutrients, typically phosphates and
nitrates. If enrichment leads to impairment (e.g., toxic algal blooms), eutrophication is a form of
pollution.

Evapotranspiration—The combined loss of water to the atmosphere due to evaporation and
transpiration losses. Transpiration is the loss of water vapor to air by plants.

Fen—A peat-accumulating wetland characterized by mineral-rich water inputs.

Flood—The occurrence of stream or river flow of such magnitude that it overtops the natural or artificial
banks in a reach of the stream or river; where a floodplain exists, a flood is any flow that spreads over or
inundates the floodplain. Floods also can result from rising stages in lakes and other water bodies.

Flood (100-year)—Flood level  (stage or discharge) with a 1% probability of being equaled or exceeded
in a given year.

Flood Flows—Discharge or flow of sufficient (or greater) magnitude to cause a flood.

Flood Stage—The stage at which streams or rivers overtop their natural or artificial banks.

Floodwater—Water associated with a flood event.

Floodplain—A level area bordering  a stream or river channel that was built by sediment deposition
from the stream or river under present climatic conditions and is inundated during moderate to high
flow events. Floodplains formed under historic  or prehistoric climatic conditions can be abandoned by
rivers and form terraces.

Floodplain Wetland—Portions of floodplains that meet the Cowardin etal. (1979) three-attribute
definition of a wetland (i.e., having wetland hydrology, hydrophytic vegetation, or hydric soils). See
Wetland.

Flow—Water movement above ground or below ground.

Flow Duration Class—A classification that assigns streamflow duration to ephemeral, intermittent, or
perennial classes.

Flow Regime—Descriptor of flow types in a temporal or magnitude sense (i.e., slow-flow regime, low-
flow regime)

Flowpath—See Hydrologic Flowpath.
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Fluvial—Refers to or pertains to streams; e.g., stream processes (fluvial processes), fluvial landforms,
such as fluvial islands and bars, and biota living in and near stream channels.

Flux—Flow of materials between system components per unit time.

Gaining Stream or Wetland—A wetland or a stream or river reach that experiences a net gain of water
from ground water  (see Figure 2-5). In this situation, the water table elevation near the stream or
wetland is higher than the stream or wetland water surface. Conditions conducive to losing or gaining
streams and wetlands can change over short distances within river networks and river basins. See
Losing Stream or Wetland.

Geographically Isolated Wetland—A wetland that is completely surrounded by uplands; for example,
hydrophytic plant communities surrounded by terrestrial plant communities or undrained hydric soils
surrounded by nonhydric soils. This term often is mistakenly understood to mean hydrologically
isolated. Geographically isolated wetlands vary in their degree of hydrologic and biotic connectivity.

Ground Water—Any water that occurs and flows in the saturated zone. See Saturated Zone.

Ground-water Discharge —The flow of ground water to surface waters; discharge areas occur where
the water tables intersect land surfaces. See Seep, Spring

Ground-water Discharge Wetland—A  wetland that receives ground-water discharge.

Ground-water Flow—Flow of water in the subsurface saturated zone.

Ground-water Flow-through Wetland—A wetland that has both ground-water inputs and outputs.
Ground water enters the wetland through the upgradient direction and exits the wetland downgradient.

Ground-water Recharge—The process by which ground water is replenished; a recharge area occurs
where precipitation or surface water infiltrates and is transmitted downward to the saturated zone
(aquifer). See Infiltration, Percolation, Transmission.

Ground-water Recharge Wetland—A wetland that recharges ground water.

Ground-water Reservoir—A saturated body of ground water having loosely definable spatial limits.

Ground-water System—Reference to the ground water and geologic materials comprising the saturated
zone; the ground-water system, as a whole, is a three-dimensional flow field.

Ground water-Surface water Interactions—Movement of water between surface-water bodies and
ground-water systems. Flows can occur in either direction.

Ground-water Withdrawal—Pumping  of water from aquifers for human uses.

Habitat—Environment (place and conditions) in which organisms reside.

Headwater—Areas from which water originates within a river or stream network. This term typically
refers to stream channels but can also describe wetlands or open waters, such as ponds.

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Headwater Stream—Headwater streams are first- to third-order streams. Headwater streams can be
ephemeral, intermittent, or perennial. See Stream Order, Flow Duration Class.

Hillslope—A sloping segment of land surface.

Hydraulic Conductivity—A measure of the permeability of a porous medium. For a given hydraulic
gradient, water moves more rapidly through media with high hydraulic conductivity than low hydraulic
conductivity.

Hydraulic Gradient—Slope of the water table. See Water Table.

Hydraulic Head—The height above a standard datum of the surface of a column of water that can be
supported by the static pressure at a given point; for a well, the hydraulic head is the height of the water
level in the well compared to a datum elevation.

Hydraulics—The physics of water in its liquid state.

Hydric—An area, environment, or habitat that is generally very wet with plenty of moisture. See Mesic,
Xeric.

Hydrograph—A graph of stream or river discharge over time. Stage or water table elevation also can be
plotted.

Hydrologic Event—An increase in streamflow resulting from precipitation or snowmelt.

Hydrologic Flowpath—The pathway that water follows as it moves over the watershed surface or
through the subsurface environment.

Hydrology—The study of the properties, distribution, and effects of water as a liquid, solid, and gas on
Earth's surface, in the soils and underlying rocks, and in the atmosphere.

Hydrologic Landscape—A landscape with a combination of geology, soils, topography, and climate that
has characteristic influences on surface water and ground water.

Hydrologic Permanence—The frequency and duration of streamflow in channels or the frequency and
duration of standing water in wetlands.

Hyporheic Flow—Water from a stream or river channel that enters subsurface materials of the
streambed and bank and then returns to the stream or river.

Hyporheic Exchange—Water and solutes exchanged between a surface channel and the shallow
subsurface. See Hyporheic Flow.

Hyporheic Zone—The area adjacent to and beneath  a stream or river in which hyporheic flow occurs.
The dimensions of the hyporheic zone are controlled by the distribution and characteristics of alluvium
and hydraulic gradients between streams and local ground water.
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Hypoxia—The condition in which dissolved oxygen is below the level necessary to sustain most animal
life. See Anoxic Conditions.

Infiltration—The downward entry of water from the land surface into the subsurface.

Infiltration Capacity—The maximum rate at which infiltration can occur at a given location.

Interfluve—The area of higher terrain between adjacent stream valleys.

Intermediate Ground Water—Ground-water flow systems representative of the wide range of
flowpath lengths and depths that occur between local and regional ground-water systems.

Intermittent—This term also can be applied to other surface-water bodies and ground-water flow or
level. See Intermittent Stream.

Intermittent Stream—A stream or portion of a stream that flows continuously only at certain times of
year; for example, when it receives water from a spring, ground-water source, or a surface source such
as melting snow. At low flow, dry segments alternating with flowing segments can be present.

Inundation—To cover dry land with floodwaters.

Isolation—Condition defined by reduced or nonexistent transport mechanisms between system
components.

Isotopic Tracer—See Stable  Isotope Tracer.

Lag Function—Any function within a stream or wetland that provides temporary storage and
subsequent release of materials without affecting cumulative flux (exports = imports); delivery is
delayed and can be prolonged.

Lateral Source Stream—A first-order stream that flows into a higher order stream.

Lentic—Of, relating to, or living in still water. See Lotic.

Levee (Artificial)—An engineered structure built next to a stream or river from various materials to
prevent flooding of surrounding areas. The levee raises the elevation of the channel height to convey
greater discharge of water without flooding.

Levee (Natural)—A broad, low ridge or embankment of coarse silt and sand that is deposited by a
stream on its floodplain and  along either bank of its channel. Natural levees are formed by reduced
velocity of flood flows as they spill onto floodplain surfaces and can no longer transport the coarse
fraction of the suspended sediment load.

Local Ground Water—Ground water with a local flow system. Water that recharges at a high point in
the water table that discharges to a nearby lowland. Local ground-water flow is the most dynamic and
shallowest of ground-water flow systems. Therefore, it has the greatest interchange with surface water.
Local flow systems can be underlain by intermediate and regional flow systems. Water in these deeper
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flow systems have longer flowpaths and longer contact time with subsurface materials. Deeper flow
systems also eventually discharge to surface waters and influence their condition.

Losing Stream or Wetland—A stream, wetland, or river reach that experiences a net loss of water to a
ground-water system (see Figure 2-5). In this situation, the water table elevation near the stream or
wetland is lower than the stream or wetland water surface. Conditions conducive to losing or gaining
streams and wetlands can change over short distances within river networks and river basins. See
Gaining Stream or Wetland.

Lotic—Of, relating to, or living in moving water. See Lentic.

Mainstem—Term used to distinguish the larger (in terms of discharge) of two intersecting channels in a
river network.

Materials—Any physical, chemical, or biological entity, including but not limited to water, heat energy,
sediment, wood, organic matter, nutrients, chemical contaminants, and organisms.

Meltwater—Liquid water that results from the melting of snow, snowpacks, ice, or glaciers.

Mesic—An area, environment, or habitat with a moderate amount of moisture. See Hydric, Xeric.

Migration—Long-distance movements undertaken by organisms on a seasonal basis.

Non-floodplain Wetland—An area outside of the floodplain that meets the Cowardin et al. (1979)
three-attribute definition of a wetland (i.e., having wetland hydrology, hydrophytic vegetation, or hydric
soils). For the purposes of this report, riparian wetlands that occur outside of the floodplain are not
included as non-floodplain wetlands, since these wetlands are subject to bidirectional, lateral hydrologic
flows. See Floodplain, Wetland.

Nutrients (In Aquatic Systems)—Elemental forms of nitrogen, phosphorus, and trace elements,
including sulfur, potassium, calcium, and magnesium, that are essential for the growth of organisms but
can be contaminants when present in high concentrations.

Nutrient Spiraling—Longitudinal cycles ("spirals") of nutrient uptake and release along the stream or
river continuum. The spirals are created as aquatic organisms consume, transform, and regenerate
nutrients, altering the rates of nutrient transport to downstream waters.

Open-channel Flow—Water flowing within natural or artificial channels.

Open Waters—Nontidal lentic water bodies such as lakes and oxbow lakes that are frequently small or
shallow.

Overbank Flow—Streamflow that overtops a stream or river channel.

Overland Flow—The portion of streamflow derived from net precipitation that fails to infiltrate the land
surface at any point and runs over the surface to the nearest stream channel.
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Oxbow Lakes—Water bodies that originate from the cutoff meanders of rivers; such lakes are common
in floodplains of large rivers.

Peatland—A wetland that accumulates partially decayed organic matter. Fens and bogs are common
examples.

Perched Ground Water—Unconfined ground water separated from an underlying body of ground
water by an unsaturated zone; perched ground water is supported by a perching layer (bed) for which
the permeability is so low that water percolating downward to the underlying unsaturated zone is
restricted.

Perching Water Tables—See Perched Ground Water.

Percolation—The downward movement of water through soil or rock formations.

Perennial— See Perennial Stream. This term can be applied to other surface-water bodies and to
ground-water flow or level.

Perennial Stream—A stream or portion of a stream that flows year-round and is maintained by local,
intermediate, or regional ground-water discharge or flow from higher in the river network.

Permanent Waters—Water bodies that contain water year-round; perennial waters.

Permeability—Property of a porous medium that enables it to transmit fluids under a hydraulic
gradient. For a given hydraulic gradient, water will move more rapidly through high permeability
materials than low permeability materials.

Phreatophyte—Plants that use water from the saturated zone.

Potential Evapotranspiration—The amount of water that would be lost to the atmosphere over a given
area through evaporation and transpiration, assuming no limits on the water supply. See
Evapotranspiration.

Potentiometric Surface—The surface representing the level to which ground water will rise in a well
penetrating a confined aquifer.

Prairie Potholes—Complex of glacially formed wetlands, usually lacking natural outlets, found in the
central United States and Canada.

Precipitation—Water that condenses in the atmosphere and falls to a land surface. Common types
include rain, snow, hail, and sleet.

Precipitation Intensity—The rate at which precipitation occurs; generally refers to rainfall intensity.

Primary Production—The fixation of inorganic carbon into organic carbon (e.g., plant and algae
biomass) through the process of photosynthesis. Primary production is the first level of the food web,
and provides most of the autochthonous carbon produced in ecosystems. The rate of fixation is referred
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to as gross primary productivity (GPP) or net primary productivity (NPP), where NPP is equal to GPP
minus respiration. See Respiration, Secondary Production.

Propagule—Any part of an organism that can give rise to a new individual organism. Seeds, eggs, and
spores are propagules.

Reach—A length of stream channel with relatively uniform discharge, depth, area, and slope.

Recession [of Flow)—Decrease in flow following a hydrologic event.

Recharge Area—An area in which water infiltrates the surface and reaches the zone of saturation.

Refuge Function—The protective function of a stream or wetland that allows an organism (or material)
to avoid mortality (or loss) in a nearby sink area, thereby preventing the net decrease in material flux
that otherwise would have occurred (exports = imports). This term typically refers to organisms but can
be used for nonliving materials. See Sink Function.

Regional Ground Water—Ground water with a deep, regional-scale flow system; also referred to as
deep ground water. These flow systems can occur beneath local and intermediate ground-water flow
systems. See Local Ground Water, Deep Ground Water.

Respiration—The chemical process by which organisms break down organic matter and produce
energy for growth, movement, and other biological processes. Aerobic respiration uses oxygen and
produces carbon dioxide.

Return Flow—Water that infiltrates into a land surface and moves to the saturated zone and then
returns to the land surface (or displaces water that returns to the soil surface).

Riparian Areas—Transition areas or zones between terrestrial and aquatic ecosystems that are
distinguished by gradients in biophysical conditions, ecological processes, and organisms. They are
areas through which surface hydrology and subsurface hydrology connect water bodies with their
uplands. They include those portions of terrestrial ecosystems that significantly influence exchanges of
energy and matter with aquatic ecosystems. Riparian areas are adjacent to perennial, intermittent, and
ephemeral streams, lakes, and estuarine-marine shorelines. See Upland.

Riparian Wetland—Portions of riparian areas that meet the Cowardin etal. (1979) three-attribute
definition of a wetland (i.e., having wetland hydrology, hydrophytic vegetation, hydric soils). See
Wetland.

River—A relatively large volume of flowing water within a visible channel, including subsurface water
moving in the same direction as the surface water, and lateral flows exchanged with associated
floodplain and riparian areas. See Stream.

River Network—A hierarchical, interconnected population of channels or swales that drain water to a
river. Flow through these channels can be perennial, intermittent, or ephemeral.
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River Network Expansion/Contraction—The extent of flowing water in a river network increases
during wet seasons and large precipitation events and decreases during dry periods. See Variable Source
Area.

River System—A river and its entire drainage basin, including its river network, associated riparian
areas, floodplains, alluvial aquifers, regional aquifers, connected water bodies, geographically isolated
water, and terrestrial ecosystems.

Runoff—The part of precipitation, snowmelt, or other flow contributions (e.g., irrigation water) that
appears in surface streams at the outlet of a drainage basin; it can originate from both above land
surface (e.g., overland flow) and below land surface sources (e.g., ground water). Units of runoff are
depth of water (similar to precipitation units, e.g., mm). This measurement is the depth of water if it
were spread across the entire drainage basin. Can also be expressed as a volume of water (i.e., m3, feet3,
acre-ft).

Saturated Zone—The zone below the land surface where the voids in soil and geologic material are
completely filled with water. Water in the saturated zone is referred to as ground water. The upper
surface of the saturated zone is referred to as the water table. See Ground Water, Unsaturated Zone,
Water Table.

Saturation Overland Flow—Water that falls onto a saturated land surface and moves overland to the
nearest stream or river.

Seasonality—Refers to the seasonal distribution of water surplus of a river system. See Water Surplus.

Secondary Production—The generation of biomass of consumer organisms that feed on organic
material from primary producers (algae, microbes, aquatic and terrestrial plants), and biomass of
predators that feed on consumer organisms. See Primary Production.

Seed Bank—Viable dormant seeds that accumulate in soil or in sediments under water. See Egg bank.

Seep—A small area where water slowly flows from the subsurface to the surface. A seep can also refer to
a wetland formed by a seep; such a wetland is referred to as a ground-water slope wetland.

Seepage—Water that flows from a seep.

Shallow Ground Water—Ground water with shallow hydrologic flowpaths. See Local Ground Water.

Sink Function—Any function within a stream or wetland that causes a net decrease in material flux
(imports exceed exports).

Snowpack—Accumulation of snow during the winter season; an important source of water for streams
and rivers in the western United States.

Snowmelt—The complete or partial melting and release of liquid water from seasonal snowpacks.

Solute—A substance that is dissolved in water.

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Source Area—The originating location of water or other materials that move through a river system.

Source Function—Any function within a stream or wetland that causes a net increase in material flux
(exports exceed imports).

Spillage—Overflow of water from a depressional wetland to a swale or channel.

Spring—A surface-water body formed when the side of a hill, a valley bottom, or other excavation
intersects a flowing body of ground water at or below the local water table.

Stable Isotope Tracer—Certain elements such as oxygen, hydrogen, carbon, and nitrogen have multiple
isotopes that occur in nature that do not undergo radioactive decay. These isotopes can be used to track
the source and movement of water and other substances.

Stage—The elevation of the top of a water surface.

Stream—A relatively small volume of flowing water within a visible channel, including subsurface water
moving in the same direction as the surface water, and lateral flows exchanged with associated
floodplain and riparian areas. See River.

Stream Burial—The process of incorporating streams—particularly headwaters—into storm sewer
systems, usually by routing through underground pipes.

Stream Power—A measure of the erosive capacity of flowing water in stream channels or the rate of
energy dissipation against the stream bed or banks per unit of channel length that has the mathematical
form: ooa = pgQS where ooa is the stream power, p is the density of water (1000 kg/m3), g is acceleration
due to gravity (9.8 m/s2), Q is discharge (m3/s), and Sis the channel slope.

Stream Network—See River Network. A stream network is the same as river network, but typically
refers to a smaller spatial scale.

Stream Reach—See Reach.

Storm—A precipitation event that produces an increase in streamflow.

Stormflow—The part of flow through a channel that occurs in direct response to precipitation; it
includes surface and subsurface sources of flow. See Direct  Runoff.

Stream Order (Strahler)—A method for stream classification based on relative position within a river
network, when streams lacking upstream tributaries (i.e., headwater streams) are first-order streams
and the junction of two streams of the same order results in an increase in stream order (i.e., two first-
order streams join to form a second-order stream, two second-order streams join to form a third-order
stream, and so on). When streams of different order join, the order of the larger stream is retained.
Stream-order classifications can differ, depending on the map scale used to determine order.

Streamflow—Flow of water through a stream or river channel. See Discharge.

Subsurface Water—All water that occurs below the land surface.
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Surface Runoff—See Overland Flow.

Surface Water—Water that occurs on Earth's surface (e.g., springs, streams, rivers, lakes, wetlands,
estuaries, oceans).

Surface-water Bodies—Types of water bodies that comprise surface water. See Surface Water.

Swale—A nonchannelized, shallow trough-like depression that carries water mainly during rainstorms
or snowmelt. A swale might or might not be considered a wetland depending on whether it meets the
Cowardin et al. (1979) three-attribute wetland criteria. See Wetland.

Symmetry Ratio—The size ratio of a minor tributary (T2) to a major tributary (71) at a confluence.
Discharge (Q2/Q1), drainage area [A2/A1], or channel width [W2/W1] can be used to characterize the
ratio of tributary size.

Terminal Source Stream—A first-order stream that intersects another first-order stream.

Terrace—An historic or prehistoric floodplain that has been abandoned by its river and is not currently
in the active floodplain. See Floodplain.

Terrene Wetlands—"Wetlands surrounded or nearly so by uplands and lacking a channelized outlet
stream; a stream may enter or exit this type of wetland but it does not flow through it as a channel;
includes a variety of wetlands and natural and human-made ponds" (Tiner, 2011).

Tracer—A substance that can be used to track the source and movement of water and other substances.

Transformation Function—Any function within a stream or wetland that converts a material into a
different form; the amount of the base material is unchanged (base exports equal base imports), but the
mass of the different forms can vary.

Transmission Loss—The loss of runoff water by infiltration into stream and river channel beds as water
moves downstream; this process is common in arid and semiarid environments.

Transport Mechanism—Any physical mechanism, such as moving water, wind, or movement of
organisms, which can transport materials or energy. As used in this report, the term specifically refers to
physical mechanisms that move  material or energy between streams or wetlands and downstream
waters.

Tributary—A stream or river that flows into a higher order stream or river.

Turnover Length—The ratio of the downstream flux of organic carbon to ecosystem respiration per
length of stream. It approximates the average distance that organic carbon is expected to travel before it
is consumed and mineralized by aquatic organisms.

Unconfined Aquifer—An aquifer that has a water table; the aquifer is not bounded by lower
permeability layers. See Confined Aquifer.
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Unsaturated Zone— Also referred to as the vadose zone. The zone between land surface and the water
table within which the moisture content is less than saturation and pressure is less than atmospheric.
Soil pore spaces also typically contain air or other gases. See Saturated Zone.

Uplands—(1) Higher elevation lands surrounding streams and their floodplains. (2) Within the wetland
literature, specifically refers to any area that is not a water body and does not meet the Cowardin et al.
(1979)-attribute wetland definition. See Wetland.

Uptake Length (for dissolved nitrogen in streams)—The distance traveled in the water column
before algal and microbial assimilation  occurs.

Valley—A depression of the earth's surface that drains water between two upland areas.
Variable Source Area—Neither stormflow nor baseflow is uniformly  produced from the entire surface
or subsurface area of a basin. Instead, the flow of water in a stream at  any given moment is influenced by
dynamic, expanding or shrinking source areas, normally representing only a few percent of the total
basin areas. The source area is highly variable during stormflow. During large rainfall or snowmelt
events, the flowing portions of the river network, and associated source areas, expand. As the event
ends, the network and source areas contract.
Vernal Pool—Shallow seasonal wetlands that generally accumulate water during colder, wetter months
and gradually dry down during warmer, dryer months.
Water Balance—The accounting of the  volume of water that enters, leaves, and is stored in a hydrologic
unit, area, or arbitrarily defined control volume, typically a drainage basin or aquifer, during a specified
period of time.
Water Body—Any sizable accumulation of water on the land surface, including streams, rivers, lakes,
and wetlands.
Water Surplus—Water that is available for streamflow or recharge of ground water; precipitation
minus evapotranspiration.
Water Table—The top of the zone of saturation of an unconfined aquifer.
Watershed—The area drained by a stream, river, or other water body; typically defined by the
topographic divides between one water body and another. Synonymous with Catchment and Drainage
Basin.
Wet Channel—Channel with flowing or standing water.
Wetland—An area that generally exhibits at least one of the following three attributes (Cowardin et al.,
1979): (1) is inundated or saturated at a frequency sufficient to support, at least periodically, plants
adapted to a wet environment; (2) contains undrained hydric soil; or (3) contains nonsoil saturated by
shallow water for part of the growing season.
Wetland Storage—The capacity of a wetland to detain or retain water from various sources.
Xeric—An area, environment, or habitat that is generally dry with very little moisture. See Hydric, Mesic.
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References
Cowardin, L. M., V. Carter, F. C. Golet, and E. T. LaRoe. 1979. Classification of wetlands and deepwater
    habitats of the United States. U.S. Department of the Interior, U.S. Fish and Wildlife Service, Office of
    Biological Services, Washington, DC.
Tiner, R. W. 2011. Dichotomous keys and mapping codes for wetland landscape position, landform,
    water flow path, and waterbody type descriptors: Version 2.0. U.S. Fish and Wildlife Service,
    National Wetlands Inventory Program, Northeast Region, Hadley, MA.
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                            APPENDIX B. CASE STUDIES
B.I  Case Study: Carolina and  Delmarva Bays

B.1.1   Abstract
Carolina and Delmarva bays are ponded depressional wetlands that occur along the Atlantic Coastal
Plain from northern Florida to New Jersey. Most bays receive water through precipitation, lose water
through evapotranspiration, and lack natural surface outlets. Both mineral-based and peat-based bays
have shown connections to shallow ground water. Bays typically are near each other or near permanent
waters, providing the potential for surface-water connections in large rain events via overland flow. Fish
are reported in bays that are known to dry out, indirectly demonstrating surficial connections.
Amphibians and reptiles use bays extensively for breeding and for rearing young. These animals can
disperse many meters on the landscape and can colonize, or serve as a food source to, downstream
waters. Similarly, bays foster abundant insects that can become part of the downstream food web.
Humans have ditched and channelized a high percentage of bays, creating new surface connections to
other waters and allowing transfer of nutrients, sediment, and methylmercury.

B.1.2   Introduction
B.1.2.1   Definition and Geographic Extent
Carolina bays are elliptical, ponded, depressional wetlands that occur along the Atlantic Coastal Plain
from northern Florida to New Jersey (Prouty, 1952; Williams, 1996; Hunsinger and Lannoo, 2005). They
have been called "geographically isolated" wetlands (i.e., wetlands surrounded by uplands; Tiner, 2003),
and range from permanently inundated to frequently dry (Sharitz, 2003). Carolina bays range in size
from greater than 3,600 ha to less than 1 ha and are most abundant in North Carolina and South
Carolina (Sharitz and Gibbons, 1982; Sharitz, 2003). Carolina bays that are geographically specific to the
Delmarva Peninsula are often referred to as Delmarva bays. Delmarva bays frequently have the same
elliptical shape and orientation as other Carolina bays (Stolt and Rabenhorst, 1987a), yet some lack the
shape or rim (Sharitz, 2003).

The number of Carolina bays was estimated at 500,000 in the 1950s (Prouty, 1952), but only
10,000-20,000 remained by the early 1990s (Richardson and Gibbons, 1993). Carolina and Delmarva
bays have been ditched and drained for agricultural purposes (Figure B-l; Sharitz, 2003). A study of
2,651 Carolina bays in South Carolina found that 97% of bays larger than 0.8 ha had been disturbed by
agriculture or logging (Bennett and Nelson, 1991). The northern Delmarva Peninsula has an estimated
1,500-2,500 Delmarva bays remaining (Stolt and Rabenhorst, 1987a). The number of Carolina and
Delmarva bays is likely an underestimation, because many are too small to be readily mapped. The
National Wetlands Inventory maps have mapping units of 0.4-1.2 ha, but the Department of Energy's
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Figure B-l. Aerial photograph of Carolina bays within a region of the upper Coastal Plain of South
Carolina. (A) Infrared image showing the pattern of intact and disturbed Carolina bays within a region of
the upper Coastal Plain of South Carolina (scale: 1 cm = 1.5 km), and (B) the same image with bays (or
former bays that have been disturbed by agriculture) outlined. Reprinted with permission from Sharitz
(2003).
Savannah River Site on the upper Coastal Plain of South Carolina has 371 known Carolina bays with 46%
having an area of 1.2 ha or less (Sharitz, 2003).

B.l.2.2    Geology
The origin of Carolina and Delmarva bays is unknown, but has been attributed to meteorite impacts,
substrate dissolution, and historic modification of shallow ponds through the action of waves generated
by winds (Johnson, 1942; Savage, 1982; Ross, 1987; Stoltand Rabenhorst, 1987a; Grant etal., 1998).
The soils of Carolina and Delmarva bays range from mineral to organic depending on the position in the
landscape, hydrologic conditions, vegetation, and disturbance (Stolt and Rabenhorst, 1987b; Sharitz,
2003). Most bays have alternating layers of sand or silt with impervious clay (Bliley and Pettry, 1979).
The organic horizons in bays can range from 1 to 200 cm, with bays near the coast more likely to have
the thicker peat deposits (Newman and Schalles, 1990). Despite variation in soil content, water often
quickly infiltrates these soils before reaching an impervious clay layer (Sharitz, 2003).
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B.1.2.3    Hydrology
Carolina and Delmarva bays gain water primarily from precipitation and lose water by
evapotranspiration (Sharitz, 2003). Thus, these systems respond to seasonal rainfall, snowmelt, and
temperature. The water levels of Carolina and Delmarva bays therefore fluctuate. The water level in a
bay can change from 1-2 m above the soil surface to more than 1 m below the surface (Knight et al.,
1989; Schalles and Shure, 1989; Lide et al., 1995; Sharitz, 2003). Bays often are wetter in winter and
early spring, when evapotranspiration rates are low, and tend to dry down in summer when
evapotranspiration rates are high. Recent work by Lang et al. (2012) using highly accurate LiDAR-
derived stream maps has shown that the proportion of wetlands intersected by stream channels (and
thus not geographically isolated) is higher than previously thought.

In an analysis of the Tuckahoe Creek watershed in the Delmarva Peninsula, the High Resolution NHD
and NHD Plus were found to underestimate the number of wetlands intersected by natural stream
channels by 13% and 27%, respectively (Lang et al., 2012). Other hydrologic inputs to bays include
artesian wells (Wells and Boyce, 1953), shallow ground water (Phillips and Shedlock, 1993; Lide et al.,
1995; Caldwell etal., 2007b), inlet channels (Sharitz, 2003), and some surface runoff during periods of
high rainfall. Some bays, particularly those along the coast, can be flooded by high tides and thus are
connected to coastal waters  (Bliley and Pettry, 1979; Sharitz, 2003).

Despite the prevalence of clay substrates below many of these bays, some studies have found that bays
exchange shallow ground water with the surroundings (Phillips et  al., 1993; Lide et al., 1995; Sun et al.,
2006; Caldwell etal., 2007a; Pyzoha etal., 2008). Some Carolina bays have natural outlet channels
(Sharitz, 2003), and many have human-created outlet channels  (i.e., ditches) typically resulting in
connections to other bays or small streams (Sharitz, 2003).

B.1.2.4    Water Chemistry
Water chemistry of Carolina and Delmarva bays is affected by their position on the landscape,
weathering of underlying mineral substrate, accrual and decomposition of organic matter, and the
degree to which surface runoff, precipitation, and ground water influence their hydrology (Sharitz,
2003). In general, precipitation-fed wetlands are typically acidic and low in nutrients (Whigham and
Jordan, 2003).

Newman and Schalles (1990) reported variable water chemistry in a study of 49 Carolina bays in North
Carolina and South Carolina that spanned two transects from inland to the coast. All 49 bays were acidic
(median pH = 4.6) and were classified as soft waters (median calcium = 1.69 mg Ca2+ L-1). DOC
represented 38% of the water anions (median DOC = 17.2 mg L-1).  Bays with thick peat layers tended to
be low in nutrients, whereas bays with thin peat layers had water quality characteristics similar to local
ground water (Newman and Schalles, 1990). Phillips and Shedlock (1993) also associated bay water
chemistry with shallow ground water; their study found similarities in water chemistry between upland
ground water and the margins of three Delmarva bays. The few studies of nutrient cycling within bays
indicate some have the proper wetting and drying cycles to promote denitrification.
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Several studies have shown that Carolina bays have the proper hydrology, organic matter content, and
pH for the methylation of mercury (Snodgrass et al., 2000b; Brant et al., 2002). Mercury pollution enters
water bodies from atmospheric deposition, typically in the ionic form of Hg2+. Bacteria can convert Hg2+
to methylmercury, the bioavailable form of mercury that can accumulate in fish, birds, and other
organisms. Periodic drying and flooding of Carolina bays, especially shallow ones, promotes mercury
methylation and release (Snodgrass et al., 2000b). Mercury levels did not reach acute doses but posed a
chronic risk to fish (Snodgrass etal., 2000b) and birds that feed on these fish (Brant etal., 2002).

B.I.2.5    Biological Communities
The wetting and drying cycles of Carolina and Delmarva bays promote a diverse biota, including the
presence of numerous rare and endemic species (Sutter and Krai, 1994; Edwards and Weakley, 2001;
Sharitz, 2003). Eleven types of vegetation communities have been described in regional surveys of
Carolina bays, including species-rich herbaceous communities and cypress ponds (Bennett and Nelson,
1991; Weakley and Schafale, 1991). A seed bank study at the Savannah River Site in South Carolina
reported higher diversity than any other reported freshwater wetland habitat (Kirkman and Sharitz,
1994). Researchers estimate that more than one-third of rare plant species in the Southeast occur in
nonalluvial wetlands, including Carolina bays (Sutter and Krai, 1994; Sharitz, 2003).

Carolina and Delmarva bays are highly valuable for providing habitat and food web support for
invertebrates and vertebrates (Sharitz, 2003). For example, a Savannah River Site study of zooplankton
found 44 species of cladocerans and 7 species of copepods (Mahoney et al., 1990). Another invertebrate
study showed that a  1.5-ha Carolina bay contained 115 taxa of aquatic and semiaquatic insects from 29
families and 7 orders; more than 11,600 and 8,400 insects emerged from the bay in 1992 and 1993,
respectively (Leeper and Taylor, 1998).

Approximately 10-21% of sampled Carolina and Delmarva bays had fish populations (Gibbons and
Semlitsch, 1991; Snodgrass etal., 2000a; Sharitz, 2003). The absence of predatory fish in many bays
enables abundant amphibian populations to thrive, especially those that have aquatic larval stages
(Sharitz and Gibbons, 1982; Sharitz, 2003). For example, one study sampled two 1-ha bays over the
course of a year and captured more than 72,000 amphibians, including 9 salamander and 16 frog species
(Sharitz and Gibbons, 1982). The Savannah River Site supports 34 species of amphibians, 16 of which
depend entirely on seasonal wetlands for breeding (Gibbons and Semlitsch, 1991). Several of these
amphibians are  endangered or threatened, including the flatwoods salamander (Ambystoma
cingulatuni) and the gopher frog (Rana capita) (Sharitz, 2003).

Sharitz and Gibbons (1982) reported 6 turtle species, 9 lizard species, 19 snake species, and 13 small
mammal  species in bays. American alligators [Alligator mississippiensis) are indigenous to southern
Carolina bays (Sharitz and Gibbons, 1982). Endangered wood storks [Mycteria americand) nest in
Carolina bays, and birds such as egrets, coots, wood ducks, and other migratory waterfowl also use
Carolina and Delmarva bays (Sharitz and Gibbons, 1982).
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B.1.3   Evidence of Connectivity
B. 1.3.1    Physical Connections
Research is ongoing on the hydrologic connectivity of Carolina and Delmarva bays to surrounding areas
via ground-water flows and intermittent surface flows. A few studies have found ground-water
connections or indirect evidence of surface-water connections.

A study by Lide et al. (1995) found a ground-water connection to a Carolina bay. The study examined a
7-ha Carolina bay on the Savannah River Site typical of other bays in western South Carolina with
loamy-sand substrate and an underlying clay layer (Lide et al., 1995). The 2-year study examined data
from 38 piezometers, borehole logs, pond-stage records, and weather data. They concluded that the
Carolina bay was not a perched wetland, but a surface expression of the water table. Although
fluctuation of pond stage was largely controlled by precipitation and evapotranspiration, nearly
continuous shallow ground-water recharge was present and shallow ground-water discharge occurred
periodically.

Phillips and Shedlock (1993) studied three Delmarva bays and also concluded that the bays were
connected to local ground water. They studied water table levels and chemistry in transects that ran
from uplands through the Delmarva bays. Local ground water strongly influenced the height of the
water table in the Delmarva bays. The ground water also was attributed to maintaining a low pH,
contributing dissolved aluminum and lowering bicarbonate in the Delmarva bay (Phillips et al., 1993).

Another Carolina bay study in western South Carolina also found evidence for ground-water
connectivity (Pyzoha et al., 2008). The more than 13-year study examined piezometer and bay water
levels monthly in an 8-ha bay with sandy-loam substrate and an underlying clay layer. Researchers
concluded that surface-water and ground-water connections were important to bay hydrology and the
bay was not an isolated system. Sun et al. (2006) incorporated climate, vegetation, and soil information
to model  the hydrology of this bay, which confirmed that the bay was receiving ground-water discharge
and recharging ground water to lower topographic areas.

Caldwell  et al. (2007b) also used a model to understand the hydrology of three Carolina bays in North
Carolina and inferred ground-water connections. All three bays were larger than 100 ha,  and their
hydrology had not been altered by artificial drainage. Soil types were mineral on the perimeter to mostly
organic in the center. The team modeled bay hydrology using climate, vegetation, soils, and hydrology
data. They estimated that 10% of water  inputs to the bays were surface runoff. Ground-water inflow was
the source of 3-26% of water volume into the perimeter of the bays, and  ground-water outflow volume
(2-21%) was frequentin the center of the bays (Caldwell etal., 2007b).

In addition to ground water, several studies infer Carolina and Delmarva  bays are connected to other
water bodies through surface-water connections. For example, a study of Carolina bays in Virginia
revealed  that several of the largest bays were at sea level and bordered the Chesapeake Bay (Bliley and
Pettry, 1979). Tidal marshes have encroached and entered these  Carolina bays, reflecting a direct link
between  the Carolina bays and the estuarine environment.

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Researchers have used geographic information system methods to determine the nearest river or
tributary to Carolina bays (Sharitz, 2003). A geographic information system analysis at the Savannah
River Site of 371 Carolina bays showed that 8% were within 50 m of a stream or tributary and 12%
were within 100 m (mapping units with a minimum resolution of 0.22 ha; Sharitz, 2003). The same
methods showed that 12% of the 2,170 Delmarva bays in Maryland were within 50 m and 19% were
within 100 m of streams (mapping units with a minimum resolution of 0.40 ha; Sharitz, 2003). During
large storms, the bays located closest to the river network can exhibit hydrologic connections via
overland flow or shallow ground-water flow.

Perhaps the strongest evidence that Carolina bays are connected hydrologically to streams or estuaries
is that many of these bays are ditched, creating a conveyance for surface water. These ditches commonly
connect the surface water of bays to other bays that are lower on the landscape, and ultimately, to
streams (Sharitz, 2003).

B.I.3.2    Chemical Connections
Few peer-reviewed papers examine chemical connections between Carolina and Delmarva bays and
other waters. One, by Phillips et al. (1993),  examined ground water in the Delmarva Peninsula and found
that the amount of nitrate in ground water  decreased with the presence of forested depressional bays.
The authors speculated that the nitrate reduction was due to denitrification in the wetlands. These
systems do  have the appropriate wetting and drying hydrology to promote denitrification, which could
reduce the amount of nitrate in both ground water and surface waters (Groffman et al., 1992).

Carolina and Delmarva bays are frequently connected chemically to downstream waters through
ditches. If the bays are sediment and nutrient sinks due to their surficial isolation, ditch connections
would make them sources for these materials. For example, Bennett and Nelson (1991) reported that
71% of 2,600 bays were disturbed by agriculture. Whereas the bays might have been a nutrient sink for
excess fertilizer that was in surface runoff, these nutrients now could pass through the bays and into the
ditches, reaching downstream locations. Additionally, the conditions in Carolina bays have been shown
to promote  mercury methylation (Snodgrass etal., 2000b). If these bays connect to downstream waters
via ditches,  some bioavailable mercury would be expected to move to other waters.

B.I.3.3    Biological Connections
Carolina and Delmarva bays are "hotspots" for regional biological diversity and animal use (Sharitz,
2003), which indicates a high potential for movement between bays and other water bodies. The current
published evidence for biological connections between bays and other waters is, however, limited or
indirect.

The presence offish in Carolina and Delmarva bays indirectly demonstrates that these bays are
connected to other waters. For example, fish were found in 21% of 63 Carolina bays on the Savannah
River Site, many of which dry out during parts of the year; fish likely colonized these bays through
intermittent or permanent surface hydrologic connections (Snodgrass et al., 1996). One Carolina bay in
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North Carolina, Mattamuskeet Bay, has been colonized by both freshwater and estuarine fishes through
four canals connecting the bay to Pamlico Sound (Rulifson and Wall, 2006).

Insect emergence from bays can affect nearby waters. Leeper and Taylor (1998) studied insects in a
1.5-ha Carolina bay and recorded 115 taxa representing 29 families. Of the 39 genera of the family
Chironomidae represented, 16 are known to live in both pond and stream environments (Hudson et al.,
1990; Leeper and Taylor, 1998). Although Leeper and Taylor (1998) did not directly document
movement, these species can hatch in Carolina bays and then become important food sources for fish in
nearby streams after adult emergence and aerial dispersal. The total number of chironomids emerging
from the aforementioned Carolina bay was moderate compared to other wetlands, but cumulative
emergence from thousands of bays across the landscape would create a significant food source for
organisms, including fishes, in other nearby waters.

Carolina and Delmarva bays are immensely productive amphibian breeding habitats, and are critical for
persistence of pond-breeding amphibian populations that can move to other water bodies (Sharitz and
Gibbons, 1982). Gibbons etal. (2006) documented more than 360,000 juvenile amphibians from 24
species, emigrating from one Carolina bay during a single breeding season. More than 95% of the
biomass (about 1,330 kg) came from juveniles of the southern leopard frog [Rana sphenocephald), which
is known to use both stream and wetland habitats (Table 4-2). Given the finding that 12-19% of
Carolina and Delmarva bays were within 100 m of a tributary (Sharitz, 2003), amphibians emigrating
from these bays could transfer extremely high levels of energy and organic matter into rivers and
streams. About 90% of Carolina bays located in the Savannah River Site have a tributary or river within
1,600 m (Sharitz, 2003).

B.1.4   Carolina and Delmarva Bays: Synthesis and Implications
The key findings of this case study are as follows:
    •  Both peat-based and mineral-based bays have been shown to have shallow ground-water inputs
       and outputs.
    •  Some Delmarva bays have surface-water connections to the Chesapeake Bay, and the many bays
       near  each other and near permanent waters can be connected during high-precipitation events.
    •  Human channeling and ditching of the bays are widespread and create surface connections to
       other waters.
    •  Fish are found in bays that periodically dry out, indirectly showing that a hydrologic connection
       occurred at some time.
    •  Dispersive amphibians and reptiles use bays for breeding or rearing young.
    •  The abundant insects in bays could become part of the food web for downstream fish.

Although generally supporting the existence of or potential for connectivity between Carolina and
Delmarva bays and regional rivers or estuaries, the preponderance of evidence found in the literature

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we reviewed for this case study is indirect. Furthermore, evidence from this literature review that these
connections influence the physical, chemical, and biological conditions and functions of rivers or
estuaries is circumstantial. Therefore, the literature that we reviewed does not provide sufficient
information to evaluate fully the influence of Carolina and Delmarva bays on rivers and estuaries at this
time.

B.2  Case Study: Oxbow Lakes

B.2.1   Abstract
Oxbow lakes are water bodies that originate from the meanders of rivers that become cut off. They are
common in the floodplains of large rivers around the world. In the following case study, we provide
evidence from the peer-reviewed literature to support two conclusions: (1) oxbow lakes periodically
connect to the active river channel, and (2) the connection between oxbow lakes and the active river
channel provides for several ecological effects on the river ecosystem.

B.2.2   Introduction
B.2.2.1   Origin and  Description
Oxbow lakes and ponds (hereafter referred to as oxbow lakes) originate from river meanders that are
cutoff from the active river channel. In floodplain rivers, natural erosion of the outer banks of curves in
the active river channel leads to increased meandering over time. As these meanders grow, the active
channel can come into contact with itself and cutoff the curved segment of the river; this cutoff channel
becomes an oxbow lake within the floodplain.

Oxbow lakes are dynamic ecosystems. Young oxbow lakes are located near the active river channel and
tend to have steep banks. As oxbow lakes are subjected to flooding over time and begin to fill with
sediment, they can become shallower and eventually develop terrestrial characteristics. Continued
movement and meandering of unconstrained, shallow river channels can leave some oxbow lakes at
considerable distances from the active river channel (Winemiller et al., 2000). Owing to the dynamic
physical processes that create and promote succession in oxbow lakes, among-lake variation in the
character and connectivity of individual oxbow lakes within a floodplain often is large.

Oxbow lakes are an integral element in alluvial floodplain valleys of meandering rivers around the world
(Winemiller et al., 2000; Glinska-Lewczuk, 2009). Studies of these ecosystems have been conducted in
river floodplains in Australia (Crook and Gillanders, 2006), Europe (Hein et al., 2003), North America
(Winemiller etal., 2000; Zeugetal., 2005), and South America (da Silva etal., 2010). Due to the common
origin, characteristics of, and interactions between oxbow lakes and rivers, evidence from around the
world is presented here.
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B.2.3   Evidence
Oxbow lakes commonly connect with the active river channel. The most evident connections are direct
physical linkages, in which water movement between the active river channel and oxbow lakes is
traceable. Although these physical connections are intrinsically important, they also facilitate the
movement and exchange of chemical and biological material between the river and lake ecosystems.

B.2.3.1    Physical Connections
Physical connections between the active river channel and oxbow lakes can be through water movement
as overland surface flow, subsurface flow from river infiltration, and subsurface flow from hillslope
aquifers (Amoros and Bornette, 2002). In some cases, natural or constructed stream channels are
present between the river and the oxbow lake. For the purpose of this report, oxbow lakes with this type
of permanent physical connection are a priori considered an integrated part of the river network.
Evidence presented here is largely for oxbow lakes that lack permanent physical connections to the
river network; therefore, we focus on overland flow events (i.e., temporary connections occurring
during high river stages and floods) and shallow ground-water flow as the dominant surface
connections between ecosystems.

Regional- and local-scale climate and hydrogeologic patterns are important for understanding the
dynamics of physical connectivity between oxbow lakes and active river channels. Regional  differences
influence the predictability of hydrologic connectivity between rivers and oxbow lakes. In temperate
rivers (e.g., Brazos River, TX), surface flow connections between the river channel and oxbow lakes are
likely to occur at irregular intervals, in response to flow magnitude and lake geomorphology
(Humphries et al., 1999; Zeug and Winemiller, 2008). Tropical rivers, in contrast, are likely to have more
regular inundation patterns associated with seasonal flooding (Junk et al., 1989; da Silva et al., 2010).
The predictability of subsurface connections also can vary regionally. An isotope tracer analysis of lakes
in the Old Crow Flats, Yukon Territory, Canada, indicated that oxbow lakes receive much of their water
input from shallow ground-water flow during the relatively short thaw season (Turner etal., 2010). The
regularity of connectivity has important implications for  the exchange of chemical and biological
material between oxbow lakes and the river (Junk et al., 1989; Humphries et al., 1999).

Local landscape characteristics and position of water bodies in the floodplain influence the relative
contribution of surface-water and subsurface-water movement between individual lakes and the active
river channel, as a study of oxbow lakes on the Loire and Allier Rivers, France, demonstrates. Water in
two oxbow lakes had different geochemical signatures, suggesting a difference between when river
water was introduced to the lakes (Negrel et al., 2003). The younger oxbow lake was more connected to
the surface network due to its closer proximity to the river channel and a small stream connection, while
an older oxbow lake, which was more distant from the river channel, was more dependent on
subsurface flow (Negrel etal., 2003).

In addition to these spatial differences, temporal differences can occur in the short-term dynamics of
hydrologic connectivity. Amoros and Bornette (2002) describe a system of pulsing connectivity, where

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the direction of water exchange between floodplain water bodies, including oxbow lakes, and a river is
related to river stage. At low water stage, floodplain water bodies might receive water from a hillslope
aquifer, and water from the oxbow lake likely drains through the alluvium toward the river. In contrast,
when a river has a high water stage, water is more likely to seep through the alluvium from the river to
the oxbow lake. Finally, inundation would result in surface-water connectivity, where river water moves
overland to the oxbow lake. This pattern of pulsing connectivity is influenced by the local topography
and the characteristics of the floodplain alluvium (Amoros and Bornette, 2002) and is an illustration of
the expansion and contraction concepts described in the framework (Section 2.2.3; Figure 1-2).

Physical connectivity between oxbow lakes and the river network has direct consequences on the
hydrologic dynamics of that river network. Oxbow lakes provide flood protection. Like other floodplain
water bodies, they retain water. This retention lowers water velocity and can reduce the height of
floodwater over nearby terrestrial landscapes (Winemiller et al., 2000). In addition to storing
floodwaters, oxbows trap sediment as the velocity of floodwaters declines during the process of
retention, allowing sediment to settle out of suspension.

Human alterations of natural flow patterns in rivers can influence connectivity between oxbow lakes
and the active river channel. On one hand, connectivity can be enhanced. Channels between oxbow lakes
and the river channel often are constructed for their benefits to biological productivity (Glinska-
Lewczuk, 2009). On the other hand, isolation might be enhanced. An analysis of sediment cores in two
small oxbow lakes in the Vistula River valley, Poland, showed changes in sedimentation rate and grain
size following flood dike construction along the river (Galbarczyk-Gasiorowska etal., 2009). These
changes in sedimentation can alter the balance of subsurface connections. The  absence of channel
migration since the 1980s has restricted flooding to areas close to the main channel of the Ebro River,
Spain. The effects of this diminished river-floodplain interaction (e.g., erosive floods) left two of three
oxbow lakes examined relatively isolated from the river channel, with a thick layer of fine sediment and
thus little connection to subsurface flows (Cabezas et al., 2009).

B.2.3.2    Chemical Connections
The dynamics of hydrologic connectivity are important for understanding the chemical character of
oxbow lakes. Flooding of the river facilitates exchange of chemicals between the river water and the
water in oxbow lakes. In some cases, these surface-water exchanges reset the chemical environment in
oxbow lakes (e.g., periodic floods introducing well-aerated water to oxbow lakes in Poland; Obolewski et
al., 2009). The chemical effects of flooding are not limited to changes in the water column. For example,
the isolation of oxbow lakes from the active river channel corresponded with changes in sediment
chemistry, and ultimately, an acceleration of eutrophication (Galbarczyk-Gasiorowska etal., 2009).

Subsurface connections also influence oxbow lake chemistry in important ways. For example, an
assessment of oxbow lakes on the River Lyna, Poland indicated that nutrient concentrations in oxbow
lakes likely were influenced by a combination of river water from surface connections, ground-water
seepage from the alluvial aquifer, infiltration from hillslope runoff, and inlake nutrient processing
(Glinska-Lewczuk, 2009). In some cases, these other connection types can play a more important role in

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oxbow lake chemistry than periodic surface connections created during flood events. An examination of
sediment chemistry in floodplain water bodies on the River Havel, Germany showed little effect of
flooding on sediment chemistry (particulate organic matter, carbon, nitrogen, phosphorus, and iron) in
oxbow lakes (Knosche, 2006). As is the case with physical connectivity, the relative importance of
surface and subsurface connectivity depends on local characteristics of the floodplain ecosystem.

Alterations of natural flood dynamics affect the exchange of chemical materials between the river and
oxbow lakes. Total organic carbon accretion and total nitrogen accretion in river floodplains are
important ecosystem functions of floodplain water bodies, like oxbow lakes, that might improve water
quality in rivers (Mitsch, 1992). An analysis of sediment, carbon, and nitrogen accretion in oxbow lakes
on the River Ebro, Spain showed lower recent accumulation (1963-2007) compared to the past
(1927-1963; Cabezas etal., 2009). In this example, the reduced accumulation of carbon and nitrogen
concentrations in oxbow lake sediment was related to reduced size and frequency of flood events in this
floodplain ecosystem (Cabezas etal., 2009).

Importantly, oxbow lakes reduce pollution loading to the river network. Oxbow lakes can intercept
nutrients from upland runoff, leaving them in the oxbow lake rather than in the river (Glinska-Lewczuk,
2009). A similar process of physical interception is observed in riparian wetlands, where wetland
ecosystems have been considered habitats that might control nonpoint-source  pollution of nutrients
(Mitsch, 1992), sediment (Brix, 1994), or pesticides (Gregoire et al., 2009) to rivers. In addition to being
areas of deposition, high mineralization rates in oxbow lakes suggest that these lakes can process and
remove some nutrients in terrestrial runoff before the runoff reaches the river  channel (Winemiller et
al.,2000).

B.2.3.3    Biological  Connections
Hydrologic connectivity influences the biological character of oxbow lakes and  facilitates exchange of
biological material between oxbow lakes and the active river channel. Evidence also suggests a
temporally dynamic relationship between biological assemblages of river and oxbow lake ecosystems.

Oxbow lakes represent important areas of relatively high biological productivity in the floodplain
landscape. Oxbow lakes can be a source of plankton to the active river channel  (Hein et al., 2003). In
contrast to terrestrial sources of carbon that often dominate the water column  of rivers, plankton is
more labile and easier to assimilate into aquatic food webs (Thorp and Belong,  2002; Bunn et al., 2003).

The connectivity relationship has added complexity for plankton, because oxbow lakes need to be
periodically isolated from the river to establish populations of these organisms. Intermediate residence
times (i.e., the amount of time a water molecule spends in a lake) of between 10 and 27 days in oxbow
lakes along the River Danube resulted in the highest carbon flow between phytoplankton and
zooplankton (Keckeis et al., 2003). Likewise, the time since inundation is an important factor influencing
the composition of zooplankton communities. Recently inundated floodplain water bodies are
dominated by rapid-colonizing rotifers, and then become dominated by cladocerans as the time since
inundation increases  (Baranyi et al., 2002). In this study, total zooplankton biomass, crustacean

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biomass, and the number of crustacean species were positively related to time since inundation. These
results indicate a relationship between the time since inundation and plankton assemblages, and
suggest that this relationship exists because colonization and reproduction within an oxbow lake
requires time without disturbance.

Although short periods of isolation are necessary for the development of within-oxbow productivity,
periodic connections are important for plankton exchange between oxbow lakes and the active river
channel. Exchange can occur from the river to the oxbow lake (e.g., juvenile riverine fish might feed in
floodplain water bodies; Baranyi et al., 2002) or from the oxbow lake to the river (e.g., phytoplankton;
Hein et al., 2003). These periodic connections between floodplain water bodies and the corresponding
export of labile phytoplankton from floodplain water bodies to rivers contribute to the food sources of
biological assemblages in nearby rivers (Thorp and Belong, 2002; Bunn etal., 2003; Keckeis etal., 2003).

Connectivity between oxbow lakes in the floodplain and the active river channel is important for
maintaining mollusk populations in oxbow lakes. A comparison of three  oxbow lakes with different
levels of connectivity (lotic, semilotic, and isolated) showed the highest level of mollusk diversity in the
semilotic lake (eight vs. four taxa in each of the other lakes) on the Lyna River, Poland (Obolewski et al.,
2009). In this example, the occurrence of taxa was associated with physiochemical characteristics
(oxygen, temperature, and phosphorus) of oxbow lakes. These findings support the  idea that the degree
of oxbow lake-river connectivity influences the abundance and composition of mollusk communities in
floodplain water bodies, and these communities support the diversity of mollusk taxa throughout the
river system (Reckendorfer etal., 2006).

Physical connectivity between oxbow lakes and the active river channel influences the composition of
benthic macroinvertebrate communities in oxbow lakes. For example, hydrologic connection explained
28% of the variability in benthic invertebrate communities among sites in the active river channel,
constructed oxbow lakes, and natural oxbow lakes  of the Middle Ebro River, Spain (Gallardo et al.,
2008). Macroinvertebrate richness and abundance increased with hydrologic connectivity (i.e., floods
and flow pulses) between oxbow lakes and the river channel, and a diversity metric (Shannon index)
peaked at intermediate levels of connectivity (Gallardo etal., 2008).

Oxbow lakes have food resources and habitat that often support abundant fish populations (Winemiller
et al., 2000; Zeug et al., 2005; Zeug and Winemiller, 2008;  Zeug et al., 2009). A comparison offish
biomass in oxbow lakes and a river channel showed that fish biomass in oxbow lakes was three times
the biomass caught in rivers. Average catch per unit effort in oxbow lakes was 364.3 g per 10-m seine
haul and 5,318 gnr1 ha-1 of gillnet sampling, versus 138.1 gper 10-m seine haul and 495 gnr1 ha-1 of
gillnet sampling in the river (Winemiller et al., 2000). Additional studies by this research group have
found similar patterns for juvenile fish (Zeug and Winemiller, 2008).

Periodic surface-water connections between the river and oxbow lakes facilitate the movement offish
from the river to oxbow lakes, where riverine fish can exploit these relatively productive floodplain
water bodies before  moving back to the river. Dietary data provide evidence  that oxbow lakes are
important spawning and nursery habitats for gizzard shad in the Brazos River, TX (Zeug et al., 2009).
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Isotope analysis showed that gizzard shad in oxbow lakes had different isotopic signatures based on
habitat type: oxbow, river, and an oxbow-river mix (Zeug et al., 2009). Although oxbow lakes clearly
provided habitat for both juvenile and adult shad, the authors did not observe oxbow-specific isotopic
signatures in shad in the river channel (Zeug et al., 2009). In addition, an analysis of otolith chemical
signatures by Crook and Gillanders (2006) indicates that floodplain lakes were an important source of
carp recruitment to the Murray-Darling River, where floodplain lakes were estimated to be the source of
98% of the young-of-year carp for areas 140 km downstream of the floodplain lakes. In a third example,
floodplain water bodies, with their diverse and productive habitats, were considered nurseries for
drifting larvae of migratory fish (Meschiatti et al., 2000). Half the migratory fish species from the Mogi-
Guacu River, Brazil also were observed as juveniles in oxbow lakes along the river (24 of the 46
migratory riverine species were observed in 2 oxbow lakes), and most of the migratory fish observed in
oxbow lakes were juveniles, rather than larvae  or reproductively mature age classes (Meschiatti et al.,
2000).  This age structure suggests that the oxbow lakes were not the site of reproduction, but were
important habitats for juvenile fish.

Individual fish species have specific habitat and reproductive requirements and use floodplain habitats
in different ways, giving the dynamic hydrologic connectivity of oxbow lakes and the river network
added significance. For example, owing to variable flow in the Rio Grande, NM, recruitment success
varies between years of high (Junk et al., 1989) and low flow (Humphries et al., 1999), which contributes
to overall fish diversity in the Rio Grande (Pease et al., 2006). Likewise, in a 5-year study offish in
floodplain lakes, Shoup  and Wahl (2009) discuss how individual oxbow lakes had different conditions
and thus varied in suitability for different fish species. In their study, interannual variability was present
in oxbow lake hydrology (lake-river connectivity ranged from 0 to more than 21 weeks per year) and
water chemistry, and in associated differences in fish assemblages (Shoup and Wahl, 2009). Because of
the complex relationships observed in their  study, Shoup and Wahl  (2009) concluded that the entire
floodplain should be considered a single functioning unit that supports the overall biological integrity of
a river.

B.2.4  Oxbow  Lakes: Synthesis and Implications
The key findings of this case study are as follows:
    •   Evidence indicates the presence of physical, chemical, and biological connections between
       oxbow lakes and the river channel. The specific local and regional characteristics of both the
       oxbow lakes and the river influence  these connections.
    •   Some of the best-documented observed functions of oxbow lakes are as sources or sinks for
       water, sinks for nutrients from upland runoff that might otherwise flow into rivers, and sources
       of food and refuges for riverine organisms.
    •   Human alteration of these connections  can be detrimental to the dynamics that balance
       connectivity and exchange between oxbow lakes and the active river channel. Practices that
       alter the natural flow regime of the river (e.g., river regulation) or inhibit periodic flooding of

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       oxbow lakes (e.g., levees) affect movement of water and sediment, the use of oxbow lakes by
       riverine fish, and the regional biological diversity of floodplain water bodies.
    •  Interannual variability in oxbow lake hydrology, water chemistry, and fish assemblages
       demonstrate complex relationships between rivers and floodplain open waters and river
       systems, in which the water bodies in floodplains function as single unit supporting the overall
       biological integrity of the river.

Although the incidence of observed connectivity between oxbow lakes and river networks varies
according to spatial, temporal, physical, and biological factors, most of the evidence examined indicates
that oxbow lakes are important determinants of the physical, chemical, and biological condition and
function of rivers.

B.3  Case Study: Prairie Potholes

B.3.1  Abstract
Prairie potholes are a complex of glacially formed wetlands, usually occurring in depressions that lack
permanent natural outlets, that are found in the central United States and Canada. The vast area they
occupy is variable in many aspects, including climatically, topographically, geologically, and in terms of
land use and alteration, which imparts variation on the potholes themselves. Potholes demonstrate a
wide range of hydrologic permanence, from holding permanent standing water to wetting only in years
with high precipitation, which in turn influences the diversity and structure of their biological
communities. Owing in large part to their spatial and temporal variability, individual prairie potholes
span the entire continuum of connectivity to and isolation from the river network and other bodies of
water. Potholes generally accumulate and retain water effectively due to the low permeability of their
underlying soil, which can modulate flow characteristics of nearby streams and rivers. Potholes also can
accumulate chemicals in overland flow, thereby reducing chemical loading to other bodies of water.
When potholes are artificially connected to streams and lakes through drainage, isolation is eliminated
and they become sources of water and chemicals.  Potholes also support a community of highly mobile
organisms, from plants to invertebrates to birds, that travel among potholes and that can biologically
connect the entire complex to the river network.

B.3.2  Introduction
Prairie potholes are a complex of wetlands and water bodies that cover more than 700,000 km2 of the
north-central United States and southern Canada, in an area referred to as the prairie pothole region
(PPR; Kantrud et al., 1989). Formed by the retreat of Pleistocene glaciers, potholes are shallow
depressions underlain by low-permeability, clay-rich glacial tills that allow for the collection and
temporary retention of water. Prairie potholes range widely from more than 200 ha to less than 0.5 ha
in surface area with an average of 1 ha or less (Cowardin et al., 1981; Kahara et al., 2009). Their density
across the landscape varies from region to region, from roughly 5 potholes knr2 in the eastern part of
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the region to up to 90 knr2 in the western part as a result of several factors, including patterns of glacial
movement, topography, and climate (van der Valk and Pederson, 2003; Kahara et al., 2009).

By the 1980s, more than 50% of potholes in the region were filled, drained, or ditched, with much higher
percentages lost in agriculturally intensive regions like Iowa (Figure 2-21; Dahl, 1990). Conservation of
remaining potholes and restoration of others have been prompted by various means, including the
"Swampbuster" provision of the 1985 Food Security Act and the Wetland Reserve Program
(administered by the U.S. Department of Agriculture National Resource Conservation Service since
1990).

B.3.2.1    Hydrologic Dynamics
Prairie potholes are hydrologically dynamic and heterogeneous, varying both spatially and temporally
(Euliss et al., 2004). Water inflows consist largely of precipitation in the form of spring snowmelt runoff
or summer rain falling directly into the depressions (Carroll et al., 2005). Some potholes also receive
ground-water discharge (Winter and Rosenberry, 1998). Evapotranspiration accounts for most of the
water outflow in most potholes (Carroll etal., 2005; van der Kamp and Hayashi, 2009).  In some
situations, water can leave the basin as overland flow (known as "fill-and-spill") and shallow or regional
ground-water recharge. Potholes with ground-water flow-through or with directional reversal of
ground-water flow (discharge under some conditions and recharge under others) also have been
identified (Rosenberry and Winter, 1997).

Prairie potholes experience seasonal cycles in water level. Potholes fill in the spring, typically reaching
maximum water volume as melting snow, unable to infiltrate frozen upland soils, runs overland into
topographically low places on the landscape. Water levels decline through the summer, although they
can be maintained or increase due to summer rains (Winter and Rosenberry, 1995). Hydrologic
permanence of these systems varies among prairie potholes in response to precipitation, pothole depth,
underlying soil permeability, and position in relation to the water table. Temporary potholes have
intermittent standing water only in periods of high precipitation. Seasonal potholes collect water in
spring, but typically dry by mid-summer each year. Semipermanent potholes usually maintain standing
water throughout the year and occasionally dry in years with low precipitation. Permanent potholes
have standing water year-round and maintain standing water from year to year. Importantly, loss of
temporary and seasonal potholes has occurred at higher rates than loss of permanent pothole wetlands,
because shallower, less permanent basins are easier to drain (Miller et al., 2009).

Spatial variation in precipitation affects interannual variation in water level and hydrologic permanence.
The east-west gradient across much of the PPR delivers more than 800 mm of average precipitation to
northwestern Iowa each year and less than 500 mm of average precipitation to most of North Dakota.
These dynamics also depend on 20- to 200-year, large-scale climate cycles, including periodic flood and
drought conditions (Ashworth, 1999; Leibowitz and Vining, 2003). Annual average climate and longer
climate cycles profoundly affect individual pothole dynamics and the interactions both among potholes
and between potholes and broader landscape features (Winter and Rosenberry, 1998; Johnson et al.,
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2004). Hydrologic dynamics can have major effects on the diversity and abundance of organisms (Euliss
and Mushet, 2004).

In addition, topography at multiple scales, soil characteristics, and underlying geology influence pothole
dynamics and interactions. Three major physiographic regions comprise the PPR from east to west: the
Red River Valley, Drift Prairie, and Missouri Coteau. The Red River Valley was formerly a vast lake filled
with glacial melt, and today consists of the relatively topographically flat, clay-rich till surrounding the
Red River of the North. The Drift Prairie is higher in elevation than the Red River Valley, and consists of
rolling, hummocky terrain formed by glacial deposits. The Missouri Coteau has the highest elevation of
the region and relatively steep relief due to thick glacial debris deposits (Kantrud et al., 1989). More
restricted local landform zones, various till plains in the Des Moines Lobe in Iowa and the Prairie Coteau
in eastern South Dakota for example, also influence hydrologic characteristics of potholes (Miller etal.,
2009).

B.3.2.2    Chemical Functions
The chemical composition of prairie potholes is determined largely by the degree of connectivity with
ground water and the position of the wetland with respect to local and regional ground-water systems.
Seasonal wetlands located high in the landscape tend to be less saline than the wetlands situated low in
the landscape. This simplistic view is made more complex, however, by watershed characteristics,
concentration of solutes by evapotranspiration, variability in ground-water and surface-water residence
times, changing wetland volumes, and climatic variability. For example, LaBaugh et al. (1996)
documented substantial interannual changes in dominant ionic species in response to climatic
variability. These changes persisted beyond the climatic inputs, indicating that antecedent moisture
conditions also influence wetland response to a changing climate.

Nutrient (including carbon, nitrogen, and phosphorus) cycling in prairie potholes likely depends on
fluctuating water levels, wet-dry cycles, and resulting effects of vegetation cycling. Potholes tend to be
nitrogen-limited environments, with the notable exception of potholes located on agricultural land that
tend to receive runoff high in nitrate (Crumpton and Goldsborough, 1998). Denitrification that takes
place in the anaerobic zone of these and other wetlands can make them effective nitrogen sinks (van der
Valk, 2006).

B.3.2.3    Ecological Characteristics
The high spatial and temporal abiotic heterogeneity, both within an individual pothole and between
potholes across the region, creates a variety of ecological niches and contributes to high biodiversity in
these habitats. In response to hydrologic cycles, a semipermanent pothole can have up to four distinct,
concentric zones of vegetation, ranging from floating aquatic plants to upland plants. Depending on the
timing within annual or between interannual wet-dry cycles, a given pothole can have all zones or just
one zone. A pothole also could be in the process of developing zones (regenerative phase)  or losing
zones (degenerative phase). Invasive species like reed canarygrass [Phalaris arundinacea) and cattail
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(Typha angustifolia and T, xglaucd) have established in streams and wetlands across the region,
disrupting natural pothole vegetation communities.

Perhaps the best-known and most well-studied attribute of prairie potholes is their role as productive
feeding and nesting habitat for waterfowl. Of the 34 species of duck that breed in North America, 12 are
common in the region, which contributes up to 80% of the continent's waterfowl game (Batt et al.,
1989). In addition, a diverse assemblage of microorganisms, invertebrates, amphibians, reptiles, and
sometimes fish, obligately or facultatively use potholes to feed or reproduce. For example, 44 different
invertebrate taxa, including nematodes, mollusks, and arthropods, were collected in Iowa potholes
(Hentges and Stewart, 2010).

B.3.3  Evidence
B.3.3.1    Physical Connections
Because prairie potholes are small wetlands that form in depressions often lacking permanent outlets,
they have been described as hydrologically isolated from each other and from other waters.  In some
instances, this generalization has proved true but in others, it is false.

One of the most noted hydrologic functions of potholes is water storage. Because most of the water
outflow in potholes is via evapotranspiration, potholes can become water sinks, preventing flow to other
waters in their river or terminal lake basins. Several studies have quantified the large water storage
capacity of prairie pothole complexes. A conservative estimate puts the amount of precipitation that can
be retained in prairie potholes on land enrolled in the federal Conservation Reserve Program and
Wetland Reserve Program atmore than 555 million m3 (Gleason et al., 2008). In various subbasins
across the PPR, including those that feed Devils Lake and the Red River of the North, both of which have
a long history of flooding,  potholes have consistently been estimated to hold tens of millions of cubic
meters of water (Hubbard and Linder, 1986; Vining, 2002; Gleason et al., 2007).

Water storage by prairie potholes can affect streamflow. Simulations of the Starkweather Coulee
subbasin that drains to Devils Lake indicate that streamflow declines substantially with increased
wetland storage capacity.  Increasing the volume of pothole storage across the subbasin by
approximately 60% caused simulated total annual streamflow to decrease by 50% during a series of dry
years and by 20% during wet years. The weaker effect of potholes on streamflow during wet years is
likely due to high soil moisture conditions and maintenance of high water levels within potholes across
years, which causes a greater proportion of runoff to reach streams relative to dry years  (Vining, 2002).
Similar simulation studies of watersheds in the Red River basin (one in North Dakota and one in
Minnesota) produced qualitatively comparable results, suggesting that the ability of potholes to
modulate streamflow can be widespread across the PPR (Vining, 2004). This work also indicates that
reducing water storage capacity of wetlands by connecting formerly isolated potholes through ditching
or drainage to the Devils Lake and Red River basins could increase stormflow and contribute to
downstream flooding. In many agricultural areas already crisscrossed by extensive surface and
subsurface drainage systems (Figure 2-21), total streamflow and baseflow are increased by directly

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connecting potholes to stream networks (Blann etal., 2009). The ensuing impacts of changing
streamflow are numerous, including effects on stream geomorphology, habitat alteration, and ecological
effects (reviewed in Blann et al., 2009).

Studies in some regions show a lack of association between pothole water storage and aspects of
streamflow. For instance, modeling of an Iowa watershed indicated that total pothole outflow and total
maximum pothole volume do not affect streamflow characteristics (Du et al., 2005). At the Minnesota
watershed within the Red River basin discussed previously, simulated annual and daily streamflow
decreased with increased pothole water storage capacity but peak streamflow was not reduced during a
simulated flooding event, possibly due to an overwhelmed capacity of wetlands and upland soils to
retain additional water (Vining, 2004). In yet another Minnesota watershed, wetland water storage
provided no explanatory power in estimating peak streamflows for small streams (Lorenz et al., 2010).

The presence or absence of an effect of pothole water storage on streamflow depends on many factors,
including patterns of precipitation, topography, and degree of human alteration. For instance, in parts  of
the PPR with low precipitation, low stream density, and little human alteration, the extreme hydrologic
isolation of potholes likely results in few effects on larger waters. Neither a comprehensive examination
of the downstream effects nor  a systematic characterization of potholes for the factors that determine
those effects has been conducted.

Surface-water isolation is common for many prairie potholes under average precipitation conditions,
but intense precipitation events or high cumulative precipitation over one or more seasons can result in
temporary hydrologic connectivity via overland flow. These "fill-and-spill" events between potholes
have been witnessed and measured in the Missouri Coteau and in the Drift Prairie zones of the PPR in
North Dakota (Winter and Rosenberry, 1998; Leibowitz and Vining, 2003), and inferred using digital
aerial photography (Kahara et al., 2009). All else being equal, a wetter climate such as that experienced
in the southeastern part of the PPR should promote hydrologic connectivity (Johnson et al., 2005). Local
topography can enhance or diminish the likelihood and frequency of temporary surface-water
connections. Authors have reasoned that the relatively wet and topographically low Red River Valley
zone of the PPR should display greater surface-water connectivity of potholes than either the Drift
Prairie or Missouri Coteau zones. Furthermore, they suggest that stream density will influence the
chance that pothole spillage connects to the larger river network. Thus, potholes in the Missouri Coteau,
with its limited network of streams, should be more hydrologically isolated than potholes in the Red
River Valley or Drift Prairie (Leibowitz and Vining, 2003).

Individual potholes range from isolated to highly connected to other potholes via shallow local and
deeper regional ground-water flows. A high water table and soil pocketed with root pores or fractures
from wet-dry cycles promote water movement between wetlands via shallow ground-water aquifers. In
these cases, water moves most often from topographically high, recharge wetlands to low, discharge
wetlands (van der Kamp and Hayashi, 2009), although a single wetland can shift from recharge to
discharge in years where the water table is high (Carroll et al., 2005). Other wetlands shift multiple
times from recharge to discharge conditions during a single year, which can either facilitate or prevent

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ground-water connections to nearby wetlands (Rosenberry and Winter, 1997). Potholes can connect to
the river network via ground water if both are located within the zone of shallow local aquifer flows.
One study in North Dakota described prairie wetlands and lakes as water sources to the topographically
low James River via shallow ground-water flow (Swanson et al., 1988). Broader, regional movement of
ground water is restricted by very low permeability clay-rich tills that can keep deep ground-water
recharge to only millimeters per year on average over a drainage basin (van der Kamp and Hayashi,
1998).

Human alterations of the landscape have had an impact on the connectivity of prairie potholes. Presence
or absence of a crop on the upland near a wetland can alter the degree to which the wetland receives
overland flow from the upland and the removal of water via transpiration that otherwise would
recharge ground water (Hayashi etal., 1998).  Up to 30% of cropland in the Upper Midwest is artificially
drained to increase agricultural productivity (Pavelis, 1987). Filling potholes and lowering the water
table through use of field tiling for agriculture has likely increased isolation of remaining potholes by
decreasing the density of depressions containing water. Extensive surface draining and ditching,
however, have directly and dramatically increased connectivity between pothole basins and surface
waters of the river network, converting these  systems from precipitation sinks to water sources (Blann
et al., 2009). Ditches create new surface-water outlets from potholes, allowing collected water to flow
into streams and rivers; drains fitted at the bottom of potholes connected to shallow subsurface pipes
often discharge to open ditches or streams (Ginting et al., 2000).

B.3.3.2    Chemical Connections
The chemical connectivity of prairie potholes is largely mediated by their hydrologic connectivity.
Hydrologically isolated potholes tend also to be isolated chemically. Unaltered potholes with no outlet
can accumulate nutrients, sediment, and other chemical compounds as they collect runoff (Crumpton
and Goldsborough, 1998; Donald et al., 1999). Such accumulations have measurable effects on the water
quality of potholes and the resident organisms (Gleason etal., 2003). Presence of these materials in
potholes is influenced by inflow, itself a function of precipitation and surrounding land use. Potholes
surrounded by tilled fields with higher precipitation, for example, tend to accumulate nutrients,
sediment, and pesticides (Gleason et al., 2008). Additionally, potholes within agricultural areas that have
not been drained or ditched are hypothesized to be nitrogen sinks, transforming nitrate in the
agricultural runoff they receive to nitrous oxide or nitrogen gas. Denitrification can transform up to 80%
of nitrate that runs off into potholes (Crumpton and Goldsborough, 1998 and references therein).

On the other hand, potholes that periodically are connected hydrologically to other bodies of water via
overland flow can transfer chemicals, such as dissolved ions  (Leibowitz and Vining, 2003). Potholes
modified by ditching or drainage also have increased hydrologic connectivity and, therefore, chemical
connectivity to other water bodies (Whigham and Jordan, 2003). Wetlands drained for agriculture can
contribute nitrogen, phosphorus, sediment, pesticides,  and herbicides to the waters into which they
drain (reviewed in Blann et al., 2009). For example, two wetlands in southwestern  Minnesota fitted with
surface drains that connected to subsurface tiles emptying into the Watonwan River (a tributary of the

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A Review and Synthesis                                                                         3

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Minnesota River) were found to be sources of total solids and total phosphorus to the river during
periods of high runoff (Ginting et al., 2000).

Although the chemical sink and periodic chemical source functions of potholes have been documented in
the literature, the overall influence of these functions on larger waters and river networks have been
difficult to quantify. This inability is partly because altered and unaltered potholes are embedded in a
matrix of land use and land management types, and many different parts of this complex landscape
affect downstream water quality and ecological communities (Blann et al., 2009). The most fruitful
future approach might be to model drainage basin sediment, nutrient, and pesticide transport under
various climatic conditions, using pothole characteristics and functions as independent, explanatory
variables (Gleason et al., 2008).

B.3.3.3    Biological  Connections
Dispersal capabilities of organisms residing in potholes and features of the landscapes they must
traverse help determine the strength of biological connectivity. Although some research has focused on
internal seed and egg bank dynamics (van der Valk and Davis, 1978; Gleason et al., 2004), increasing
evidence  suggests that potholes are not biologically isolated. In fact, the observation that potholes lack
an endemic aquatic and semiaquatic flora or fauna suggests that, at least over evolutionary time,
potholes have been well connected biologically to communities in other ecosystems (van der Valk and
Pederson, 2003).

Organisms can move into and out of potholes via wind, water, or land, by either self-propelling or
hitchhiking on other mobile organisms. Many species of wetland plants and insects are dispersed on the
wind (Keiper et al., 2002; Soons, 2006), including cattail (Typha spp.) seeds, which can disperse over
huge areas (more than 80 ha; van Digglen, 2006) and have been found to colonize, quickly and passively,
previously drained, restored potholes (Galatowitsch and van der Valk, 1996). Plants and invertebrates
also can travel by becoming attached to or consumed and excreted by waterfowl (Amezaga et al., 2002).
Seeds of up to half a dozen common pothole plants can be consumed and excreted by ducks in a viable
state; because migrating waterfowl fly such long distances, the maximum dispersal distance of these
hitchhiking plants is estimated to be 1,400 km (Mueller and van der Valk, 2002). Additionally, fast and
efficient recolonization of species in restored potholes, inc