EPA/600/R-14/475F | January 2015 | epa.gov/research

Office of Research and Development

NCEA (Washington DC, Cincinnati OH), NERL (Cincinnati OH, Las Vegas NV) and NHEERL (Corvallis OR) 

Connectivity of Streams & Wetlands 

to Downstream Waters:

A Review & Synthesis of the Scientific Evidence
EPA/600/R-14/475F

January 2015 

CONNECTIVITY OF STREAMS AND WETLANDS

TO DOWNSTREAM WATERS: 

A REVIEW AND SYNTHESIS OF THE 

SCIENTIFIC EVIDENCE

Office of Research and Development

U.S. Environmental Protection Agency

Washington, DC
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).
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.

Stream and Wetland Connectivity:

A Review and Synthesis ii January 2015
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

Stream and Wetland Connectivity:

A Review and Synthesis iii January 2015
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

Stream and Wetland Connectivity:

A Review and Synthesis iv January 2015
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-1

References ............................................................................................................................................... A-15

APPENDIX B. CASE STUDIES ........................................................................................................................................... B-1

B.1 Case Study: Carolina and Delmarva Bays................................................................................ B-1

B.1.1 Abstract ................................................................................................................................ B-1

B.1.2 Introduction ......................................................................................................................... B-1

B.1.2.1 Definition and Geographic Extent ............................................................ B-1

B.1.2.2 Geology ......................................................................................................... B-2

B.1.2.3 Hydrology ..................................................................................................... B-3

B.1.2.4 Water Chemistry ......................................................................................... B-3

B.1.2.5 Biological Communities ............................................................................. B-4

B.1.3 Evidence of Connectivity ................................................................................................... B-5

B.1.3.1 Physical Connections ................................................................................. B-5

B.1.3.2 Chemical Connections ............................................................................... B-6

B.1.3.3 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-11

B.2.4 Oxbow Lakes: Synthesis and Implications ................................................................... B-13

Stream and Wetland Connectivity:

A Review and Synthesis v January 2015
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

Stream and Wetland Connectivity:

A Review and Synthesis vi January 2015
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 nonfloodplain 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-1. California vernal pool inundation and hydrologic connectivity. ..................................................................... B-64

 

Stream and Wetland Connectivity:

A Review and Synthesis vii January 2015
LIST OF FIGURES 

Figure 1-1A. Hydrologic flowpaths. ......................................................................................................................................... 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

Stream and Wetland Connectivity:

A Review and Synthesis viii January 2015
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-1. 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-11. 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

Stream and Wetland Connectivity:

A Review and Synthesis ix January 2015
LIST OF ABBREVIATIONS AND ACRONYMS 

CWA Clean Water Act

DEM digital elevation model

DOC dissolved organic carbon

FPOM fine particulate organic matter

GW groundwater flowpath

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

Stream and Wetland Connectivity:

A Review and Synthesis x January 2015
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

μM micromolar

N metric normal temperature and pressure

ng nanogram 

Pg petagram

Q discharge

s second

t metric ton

τo shear stress

V velocity

yr year

Stream and Wetland Connectivity:

A Review and Synthesis xi January 2015
PREFACE

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/sab). 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:

A Review and Synthesis xii January 2015
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
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

Stream and Wetland Connectivity:

A Review and Synthesis xiv January 2015
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 O. Winemiller, PhD

Texas A&M University, College Station, TX 

Stream and Wetland Connectivity:

A Review and Synthesis xv January 2015
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

Stream and Wetland Connectivity:

A Review and Synthesis xvi January 2015
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, Gambier, 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

Latif Kalin, PhD 

Auburn University, Auburn, AL

Kenneth Kolm, PhD 

Hydrologic Systems Analysis, LLC, Golden, CO

Judith L. Meyer, PhD 

University of Georgia, Lopez Island, WA

Stream and Wetland Connectivity:

A Review and Synthesis xvii January 2015
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

Cary Institute of Ecosystem Studies, Millbrook, NY

Jack Stanford, PhD 

University of Montana, Polson, 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:

A Review and Synthesis xviii January 2015
PHOTO CREDITS

Front cover, Executive Summary, Chapter 5, and References Nambe Lake, New Mexico (L.C. 

Alexander, U.S. EPA)

Back cover, Executive Summary, and References Children in Delaware inland wetland 

(Hennis H. Bartow, Delaware Center for 

the Inland Bays)

Chapter 3 Mayfly (Heptagenia culacantha) (David 

H. Funk, Stroud Water Research Center)

All other photos (U.S. EPA)

Stream and Wetland Connectivity:

A Review and Synthesis xix January 2015
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.

Stream and Wetland Connectivity:

A Review and Synthesis xx January 2015
EXECUTIVE SUMMARY

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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-1 January 2015
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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-2 January 2015
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 “nonfloodplain 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 subsurfacewater 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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-3 January 2015
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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-4 January 2015
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 peerreviewed 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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-5 January 2015
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 stormwater.

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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-6 January 2015
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 nonfloodplain 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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-7 January 2015
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 specieslevel 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. 

Stream and Wetland Connectivity:

A Review and Synthesis ES-8 January 2015
 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, groundwater 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 streamdownstream 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 

Stream and Wetland Connectivity:

A Review and Synthesis ES-9 January 2015
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 wastewaters 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 m−2 d−1) occurred in 

marshes that comprised only 7% of the lower Lake Okeechobee basin area in Florida. A nonfloodplain 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 highfrequency 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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CHAPTER 1. INTRODUCTION

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 Science question

What tributaries have a “significant* nexus” to 

“traditional navigable waters”?

What are the connections to and effects of ephemeral, 

intermittent, and perennial streams on downstream 

waters?

What “adjacent” waters have a “significant* nexus” to 

“traditional navigable waters”?

What are the connections to and effects of riparian or 

floodplain wetlands and open waters on downstream 

waters?

What categories of “other waters” have a “significant* 

nexus” to “traditional navigable 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 et al., 1988; Townsend, 1989; Rice et al., 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; Fagan, 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 et al., 2007; Freeman et al., 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 (1-1A and 1-1B); groundwater recharge from streams and wetlands (1-1A); atmospheric losses (1-1A) (Amoros 

and Bornette, 2002; Banks et al., 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 et al., 1997; Lake, 2000; Leibowitz et al., 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 flowpaths. 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. 
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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. 
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.

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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 pathways 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 et al., 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:

A Review and Synthesis 1-8 January 2015
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; Fagan, 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. 

Stream and Wetland Connectivity:

A Review and Synthesis 1-9 January 2015
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 and B.5; Schlesinger and Jones, 1984; Baillie et al., 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; Böhlke 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:

A Review and Synthesis 1-10 January 2015
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 of fluxes, 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 et al., 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

Stream and Wetland Connectivity:

A Review and Synthesis 1-11 January 2015
A Review and Synthesis

Stream and Wetland Connectivity:

1-12 January 2015

Figure 1-3. Effects of human alterations on watershed connectivity. See Section 1.2.4 for description of alterations illustrated in A-G.
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).

other contaminants; and decreased recharge of local and regional aquifers. In Figure 1-3 (F), groundwater 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 effluentdominated 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; 

Farrar et al., 2014). 

Multiple indicators and measures have been proposed for detecting and quantifying changes in 

connectivity associated with human activities (With et al., 1997; Tischendorf and Fahrig, 2000; Moilanen 

and Nieminen, 2002; Calabrese and Fagan, 2004; Martin and Soranno, 2006; Fullerton et al., 2010; 

Hermoso et al., 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 

PHYSICAL & CHEMICAL 

INTEGRITY

• Habitat quality

• Water quality

• Toxicity

BIOLOGICAL INTEGRITY 

• Community structure

• Indicator species 

• Functional groups 

• Population attributes 

ECOSYSTEM INTEGRITY, 

SUSTAINABILITY, RESILIENCY

CLIMATE FACTORS

• Annual water surplus

• 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  PROCESSES  EFFECTS 

BIOLOGICAL 

CONNECTIVITY 

HYDROLOGIC 

CONNECTIVITY

CHEMICAL 

CONNECTIVITY

MATERIAL FLUX

ENERGY FLUX

EVOLUTIONARY 

DYNAMICS

COMMUNITY 

DYNAMICS

POPULATION 

DYNAMICS

ASSESSMENT

ENDPOINTS & METRICS

FUNCTIONS 

Stream and Wetland Connectivity:

A Review and Synthesis 1-13 January 2015
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., wetlandto-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:

A Review and Synthesis 1-14 January 2015
A Review and Synthesis

Stream and Wetland Connectivity:

1-15 January 2015

Figure 1-5. Waters and connections considered to be within scope for this report. 
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 ScienceTM and Google 

ScholarTM 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:

A Review and Synthesis 1-16 January 2015
Figure 1-6. Flow chart for screening and compiling literature. 

* 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 quality for 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). 

1. Search literature on streams, 

wetlands, and open waters; review 

citations provided by peer reviewers 

and public comments.

2. For each publication under 

consideration:

5. Does it present new 

information on a relevant topic, 

alternative interpretations of existing 

information, or technical improvements 

to studies already reviewed? 

4. Has it been

peer reviewed* or 

verified for quality 

assurance? 

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)?

(Figure 1-5)

6. Add to compiled literature for 

further evaluation.

Stop

Stop

Stop

No

Yes

No

Yes

No

Yes

Stream and Wetland Connectivity:

A Review and Synthesis 1-17 January 2015
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 

of fluxes 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:

A Review and Synthesis 1-18 January 2015
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). At the 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.

Stream and Wetland Connectivity:

A Review and Synthesis 1-19 January 2015
CHAPTER 2. AN INTEGRATED SYSTEMS PERSPECTIVE ON INTERACTIONS 

OF WATERSHEDS, STREAMS, WETLANDS, AND DOWNSTREAM WATERS

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; RodriguezIturbe 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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-1 January 2015
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, flowthrough wetlands), the continuation of the bed and bank downgradient from such disruptions is 

evidence of the surface connection with the channel that is upgradient of 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 et al., 1986; Benda et al., 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 et al., 2002; Fritz et al., 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 secondorder 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-2 January 2015
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.

Terminal streams

Lateral stream

Stream and Wetland Connectivity:

A Review and Synthesis 2-3 January 2015
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, 

Stream and Wetland Connectivity:

A Review and Synthesis 2-4 January 2015
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). 

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/floodzones). 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 et al. (1979), an area is classified as a wetland if it has one or more of the following three 

Stream and Wetland Connectivity:

A Review and Synthesis 2-5 January 2015
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.

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 et al. (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 USACE, 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 et al., 1979; Brinson, 1993; Tiner, 2003a; Comer et al., 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 et al., 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). 

Stream and Wetland Connectivity:

A Review and Synthesis 2-6 January 2015
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 nonfloodplain 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 nonfloodplain 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 et al. (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 et al. (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 

et al., 1995) that is the origin for a stream would be considered non-floodplain if it had no input channel, 

Stream and Wetland Connectivity:

A Review and Synthesis 2-7 January 2015
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 nonfloodplain 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; Wolock et al., 2004; Devito et al., 2005; Poole et al., 2006; Wagener et al., 2007; Poole, 

2010; Bencala et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-8 January 2015
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 et al., 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

Stream and Wetland Connectivity:

A Review and Synthesis 2-9 January 2015
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). 

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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-10 January 2015
Figure 2-5. Cross-section showing major hydrologic flowpaths 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.

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; 

Coes and Pool, 2005; Scanlon et al., 2006; Vivoni et al., 2006; Larned et al., 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 (Tóth, 1963; Winter et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-11 January 2015
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). 

Stream and Wetland Connectivity:

A Review and Synthesis 2-12 January 2015
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). 

Stream and Wetland Connectivity:

A Review and Synthesis 2-13 January 2015
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 et al., 2005; Vidon et al., 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 groundwater 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:

A Review and Synthesis 2-14 January 2015
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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-15 January 2015
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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-16 January 2015
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 HUC (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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-17 January 2015
2.2.3 River Network Expansion and Contraction 

The portions of river networks with flowing water expand and contract longitudinally (in an upstreamdownstream 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; Junk et al., 1989; Hunter et al., 2005; Wigington et al., 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 et al., 1999; McGlynn and McDonnell, 2003; McGlynn et al., 2004; Malard et al., 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, stormflow 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, stormflow 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 et al., 2001). 

Floodplains and riparian areas can be locations with significant ground-water recharge and discharge 

(National Research Council, 2002; Naiman et al., 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:

A Review and Synthesis 2-18 January 2015
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. 

(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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-19 January 2015
Figure 2-11. Stormflow moves downstream through the river network and interacts with lower 

stream reaches, floodplains, 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.

flow, can occur under a wide range of streamflows, from flood flows to low flows (National Research 

Council, 2002; Naiman et al., 2005; Vivoni et al., 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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-20 January 2015
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 et al., 1998; Burkart et al., 1999; Malard et al., 1999; Amoros and Bornette, 

2002; Malard et al., 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 

A B

Stream and Wetland Connectivity:

A Review and Synthesis 2-21 January 2015
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 baseflow in 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 openchannel 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

Stream and Wetland Connectivity:

A Review and Synthesis 2-22 January 2015
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). 

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. 

Stream and Wetland Connectivity:

A Review and Synthesis 2-23 January 2015
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 et al., 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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-24 January 2015
Table 2-1. Functions by which streams and wetlands affect material and energy fluxes to downstream waters. Arrows indicate material and 

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, 

particulate 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 et al., 2004; 

Lehman et al., 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 McIntosh, 2010) 

Wetlands: sediment deposition, denitrification (Johnston, 1991) 

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 et al., 

2010) 

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 et al., 2008) 

Wetlands: flood attenuation (Bullock and Acreman, 2003) 

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 particulate organic matter (Wallace et al., 

1995) 

Wetlands: mercury methylation (Galloway and Branfireun, 2004; Selvendiran et 

al., 2008) 

A Review and SynthesisStream and Wetland Connectivity:

2-25 January 2015
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 marinederived 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 et al., 1980; Newbold et al., 1982a; Newbold et al., 1982b; Junk et 

al., 1989; Ward, 1989; Benda et al., 2004; Thorp et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-26 January 2015
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 et al., 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). 

Stream and Wetland Connectivity:

A Review and Synthesis 2-27 January 2015
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 

into biomass, which in turn is eaten and transformed into fish biomass in both local and downstream 

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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-28 January 2015
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 highflow 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:

A Review and Synthesis 2-29 January 2015
and B-5; Levick et al., 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, nonfloodplain 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-30 January 2015
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 et al., 2013). At the 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 groundwater 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 

Northwest 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-31 January 2015
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.

A Review and SynthesisStream and Wetland Connectivity:

2-32 January 2015
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). 

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, 

Stream and Wetland Connectivity:

A Review and Synthesis 2-33 January 2015
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 groundwater 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 powersediment 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). 

Stream and Wetland Connectivity:

A Review and Synthesis 2-34 January 2015
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.

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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-35 January 2015
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 highflow 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-36 January 2015
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 groundwater 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.

Stream and Wetland Connectivity:

A Review and Synthesis 2-37 January 2015
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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-38 January 2015
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.

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 nonfloodplain 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.

A. B.

Stream and Wetland Connectivity:

A Review and Synthesis 2-39 January 2015
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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-40 January 2015
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).

Stream and Wetland Connectivity:

A Review and Synthesis 2-41 January 2015
Figure 2−20. Examples of different landscapes showing interspersion of wetlands and streams or 

rivers (continued).

Stream and Wetland Connectivity:

A Review and Synthesis 2-42 January 2015
Figure 2−20. Examples of different landscapes showing interspersion of wetlands and streams or 

rivers (continued).

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). 

Stream and Wetland Connectivity:

A Review and Synthesis 2-43 January 2015
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; Müller, 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, Dias 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, 

Stream and Wetland Connectivity:

A Review and Synthesis 2-44 January 2015
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 (USACE, 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 2-45 January 2015
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). 

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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A Review and Synthesis 2-46 January 2015
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 et al., 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). Groundwater 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 et al., 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 

stormflow, 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 deadice 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 wetdry 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 et al., 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 Fagan, 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 et al., 2001; Ali and Roy, 2010; Bracken et al., 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 et al., 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 et al., 2008; Fritz et al., 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 et al., 2009). In flatter landscapes, a 

more dynamic contributing area model is typically required (Shaw et al., 2013). One example is the fillStream and Wetland Connectivity:

A Review and Synthesis 2-49 January 2015
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 et al., 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 et al., 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 (Fagan, 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 Fagan, 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 Fagan, 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 (Fagan, 2002; Grant et al., 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 et al., 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 Fagan, 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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CHAPTER 3. STREAMS: PHYSICAL, CHEMICAL, AND

BIOLOGICAL CONNECTIONS TO RIVERS 

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 et al., 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 (Vörösmarty et al., 2000) and generate 0.15% (9 of 5,892 km3 yr-1) of its annual discharge 

(Fekete et al., 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 et al. (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, shortening stormflow 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 lag time before transport to downstream waters (Nedeau et al., 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 et al. (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 

et al., 2004; Stoddard et al., 2005; Roy et al., 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 (1:25,000-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) mediumresolution (1:100,000-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 et al. (2007)

modeled flow through river networks in the northeastern United States and estimated that first-order 

streams (designated on the 1:100,000-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 km-2) 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 et al. (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 et al., 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 1:100,000-scale NHD, in which first-order watersheds generally 

correspond to second-order watersheds at the 1:24,000 scale (Alexander et al., 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 Río 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 Río Grande 

downstream of the confluence illustrated lag (residence) time and peak hydrograph broadening at least 

127 km downstream (Vivoni et al., 2006). Stormflow contributions from the ephemeral stream 

Stream and Wetland Connectivity:

A Review and Synthesis 3-7 January 2015
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.

accounted for 76% of flow at the Río Grande, even though these channels were considered to have a 

flood return interval of 1.11 to 1.84 years across the USGS gages in the network (Vivoni et al., 2006). 

How water flows through the streams in river networks shapes hydrologic responses (time to peak flow, 

peak-flow magnitude, and recession of peak flow) in downstream rivers (also see Sections 2.2, 4.3.2.1, 

and B.2 for discussion of hydrologic exchange between main channels and floodplains and associated 

water bodies). A key effect streams in a network structure have on hydrologic responses is dispersion, 

or the spreading of water output from a drainage basin over time. Hydrologic dispersion is the combined 

effect of several mechanisms operating across different spatial scales that influence the travel time (or 

residence time) and volume of water reaching a river network outlet (Saco and Kumar, 2002). 

The components of hydrologic dispersion most relevant to river networks include hydrodynamic 

dispersion, geomorphologic dispersion, and kinematic dispersion. At the scale of individual channels 

within the network, hydrodynamic dispersion represents storage, turbulence, and shear stress 

processes that make portions of a channel’s water volume move downstream faster than others, rather 

than as a single, discrete pulse. Hydrodynamic dispersion, which can be visualized by placing a volume 

Stream and Wetland Connectivity:

A Review and Synthesis 3-8 January 2015
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.

of dye tracer in an upstream location and watching how the dye disperses longitudinally as it moves 

downstream, takes into account water flowing into and out of recirculating eddies at channel margins, 

off-channel sloughs, the streambed, and nearby bank sediments (see hyporheic exchange, Section 2.2.2).

Stream and Wetland Connectivity:

A Review and Synthesis 3-9 January 2015
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 et al., 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, poolriffle 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 groundwater 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 (Rodríguez-Iturbe and Valdes, 1979; Gupta et al., 1980; Rinaldo et al., 

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). 

Stream and Wetland Connectivity:

A Review and Synthesis 3-10 January 2015
Another factor that influences hydrologic response is channel transmission loss, or the loss of surfaceflow 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 highintensity 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 et al., 1997; Scott et al., 2000; Constantz et al., 2002; Coes 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 3-11 January 2015
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 wastewater 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 3-12 January 2015
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 

and Armitage, 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 et al., 1998; Eaton et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 3-13 January 2015
downstream rivers (Ferguson et al., 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.

Stream and Wetland Connectivity:

A Review and Synthesis 3-14 January 2015
Streams transport and store sediment. Headwater streams tend to have low competence to transport 

sediment during baseflow (Gooderham et al., 2007), but they have structures (boulders, woody debris) 

that entrain and store colluvial sediments between infrequent disturbances (e.g., stormflows) 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 

Stream and Wetland Connectivity:

A Review and Synthesis 3-15 January 2015
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 et al., 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 × 103 Mg yr−1); after erosion control, streambank stabilization, and revegetation (1975–1993), 

streams became net sediment sinks (9 × 103 Mg yr−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 et al., 2004; Ribeiro et al., 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 damrelated 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 

Stream and Wetland Connectivity:

A Review and Synthesis 3-16 January 2015
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 et al., 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 et al., 2006). Topography and topology also govern wood delivery from 

headwater streams. Downstream segments draining steep, finely dendritic networks receive a greater 

Stream and Wetland Connectivity:

A Review and Synthesis 3-17 January 2015
proportion of wood from headwater streams than networks that are low gradient and weakly dissected 

(Benda and Cundy, 1990; Reeves et al., 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 et al., 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 

et al., 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 m−1 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 and hyporheic zone, respectively (Burchsted et al., 2010; Sawyer et al., 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–

100 m 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, highmagnitude 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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A Review and Synthesis 3-18 January 2015
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 et al., 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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A Review and Synthesis 3-19 January 2015
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 et al. (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 et al., 2010). 

Studies that have detected discontinuities in river temperature associated with stream confluences also 

provide evidence of thermal connections along river networks. Ebersole et al. (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 et al., 2003). A subsequent study in northeastern Oregon determined that tributary 

Stream and Wetland Connectivity:

A Review and Synthesis 3-20 January 2015
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 et al., 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 et al., 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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A Review and Synthesis 3-21 January 2015
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). 

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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A Review and Synthesis 3-22 January 2015
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 (Acuña 

et al., 2005; Fritz et al., 2006a; Ademollo et al., 2011; Arce et al., 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 et al., 1991; Reneau et al., 

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 et al., 2009; Hladyz et al., 2011; David et al., 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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A Review and Synthesis 3-23 January 2015
sediments (Alexander et al., 2000). Böhlke et al. (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 onedimensional version of the advection-dispersion equation was developed to estimate progressive 

instream nitrate removal from first- to fourth-order streams (Alexander et al., 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 et al., 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 μM), with a median concentration of 3.3 μM; concentrations were not 

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A Review and Synthesis 3-24 January 2015
strongly associated with the start or end of the high precipitation period. In the biotite schist watershed, 

maximum stream concentrations of nitrate (>300 μM) 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 at varying 

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 

et al., 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 et al., 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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A Review and Synthesis 3-25 January 2015
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 et al. (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 firstorder 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 et al., 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 et al., 2008). Mulholland et al. (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 et al. (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). 

Ågren et al. (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 following 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 et al., 2013). In southeast Arizona, Meixner et al. (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) account for only 2% or less of organic matter 

exports (Naiman and Sedell, 1979; Wallace et al., 1982; Minshall et al., 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 et al., 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 et al., 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 

Stream and Wetland Connectivity:

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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 et al., 2010). If we assume 

that the proportion of headwater streams in a drainage area is 0.50 (Section 3.2; Alexander et al., 2007; 

Caruso and Haynes, 2011), headwater streams then provide 0.39 (= 0.78 × 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 × (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 × 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 et al., 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 yr-1, 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 

et al., 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 landStream and Wetland Connectivity:

A Review and Synthesis 3-32 January 2015
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 et al., 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 et al. (2006) examined trace elements and other 

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A Review and Synthesis 3-33 January 2015
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 

(Patz et al., 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 of fish, 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 minewaste 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 et al., 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 

Stream and Wetland Connectivity:

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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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A Review and Synthesis 3-36 January 2015
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 et al., 2013). The highest levels of radionuclide fallout were 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 et al., 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 et al., 2010; Wilkes et al., 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 et al., 2004; Huryn et al., 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 (Müller, 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 (Danks, 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 et al., 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 sediment s-1 in 

the Colorado River would increase by an order of magnitude in response to bioconsolidation by netspinning 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 et al., 2006; Meyer et al., 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 et al., 2006; Hassan et al., 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., Krümmel et al., 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 of fish 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 et al., 2006; Wigington et al., 2006; Colvin et al., 2009). Kanno et al. (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 

et al., 2006; Ebersole et al., 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 McIntosh, 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 et al., 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 et al., 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 

anthropogenically isolated (Cook et al., 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 et al., 2009; Anderson et al., 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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A Review and Synthesis 3-43 January 2015
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), Fer and Hroudova (2008) found higher genetic 

diversity in downstream populations of yellow pond-lily (Nuphar lutea), 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 pathways, or both (Chaput-Bardy et al., 2009; Grant et al., 2010; 

Alexander et al., 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 of fluxes 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 surface 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 

reducing flood 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-1 January 2015
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. Nonfloodplain 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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A Review and Synthesis 4-2 January 2015
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 nonfloodplain 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.1), 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)

Stream and Wetland Connectivity:

A Review and Synthesis 4-3 January 2015
Table 4-1. Examples of mechanisms by which riparian/floodplain wetlands and wetlands in nonfloodplain 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.1.2.3, 

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.1.3.1, 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.1.3.2, 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.1.3.3, 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 nonfloodplain 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-5 January 2015
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 et al., 2002; Ward et al., 2002b; Wiens, 2002; Benda et al., 2004; Thorp et al., 

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 et al., 1998; Tockner et al., 2000; Fernald et al., 2001; 

Amoros and Bornette, 2002; Malard et al., 2002; Claxton et al., 2003; Davis et al., 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 et al., 2010; Collins et al., 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 et al., 1995; Fernald et al., 2001; Fernald et al., 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 et al., 2005) or scrub-shrub wetlands (Chipps et al., 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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A Review and Synthesis 4-6 January 2015
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 et al., 1989; Winter and Rosenberry, 1998; Benke et al., 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 et al., 2005; Vidon et al., 

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 that floodplain wetlands reduced or delayed floods in 23 of 28 studies. Walton et al. (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 et al., 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 et al., 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 nigra), 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 et al., 2003). Gurnell et al. (2002) reported that 

the amount of woody debris deposited into streams can range from 12 to 40 t km−1 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 et al., 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 et al., 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 et al. (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) m−2 d−1, 

whereas forested reaches of streams with deciduous vegetation averaged 58 mg C m−2 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 et al., 2006; Burkholder et al., 2008; Seedang et al., 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 

et al. (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 et al., 2004; Noe and Hupp, 2005; Valett et al., 2005; Noe and Hupp, 2007; Helton et al., 

2011; Powers et al., 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-10 January 2015
conversion between particulate and dissolved forms of compounds via biologically mediated 

degradation (e.g., Bärlocher 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 et al., 1997; Dosskey, 2001; Mayer et al., 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 rubra) 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 et al., 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 (NO3−) 

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 NO3− 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 et al., 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 

autotrophic 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 et al., 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 et al., 2006), suggesting that riparian areas can become better at 

degrading pesticides that enter these zones (Vidon et al., 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 et al., 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 of fish 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 (Junk et al., 1989; Tockner et al., 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 et al., 2005), and aquatic invertebrates (Smock et al., 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 (Mimulus guttatus) 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 distichum) 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 

(Gurnell et al., 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 oppositifolia) 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 

(Lecerf et al., 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 carpio) (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 m−2 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 (23 m s−1) 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 tshawytscha) (e.g., Wharton et al., 1982; Matheney and 

Rabeni, 1995; Pease et al., 2006; Henning et al., 2007; Jeffres et al., 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 et al., 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 et al., 2009). Beaver dams also can affect fish species, such as coho salmon (Pollock 

et al., 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-1920s 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 

McIntosh, 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 et al., 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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A Review and Synthesis 4-19 January 2015
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 m−2, most of which were seeking mates or oviposition sites rather 

than foraging or hunting. High densities (21,291 individuals m−2) of passively dispersing (e.g., via wind 

or animal vectors) microcrustaceans also were observed. Vanschoenwinkel et al. (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 groundwater 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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A Review and Synthesis 4-20 January 2015
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 peat bogs, 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 Delmarva bays 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-21 January 2015
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 et al., 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 et al., 2008). For example, a 1989 study of four North 

Dakota prairie pothole wetlands by Arndt and 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-22 January 2015
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 et al., 2008; McLaughlin et al., 2014). Lide et al. (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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A Review and Synthesis 4-23 January 2015
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 et al., 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 et al., 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 that fell 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, Roulet and 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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A Review and Synthesis 4-24 January 2015
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 et al., 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 et al. (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 stormflows. 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-25 January 2015
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 et al., 2014). McLaughlin et al. (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 nonfloodplain wetlands can lack surface water connections to downstream waters, surface and near-surface 

Stream and Wetland Connectivity:

A Review and Synthesis 4-26 January 2015
hydrologic connections to downstream waters do occur in many non-floodplain systems (Section 4.4.2; 

Figure 2-18; Sun et al., 1995; Whigham and Jordan, 2003; Wilcox et al., 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 × 109 cells L−1. 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 et al., 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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A Review and Synthesis 4-27 January 2015
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 nonfloodplain 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 L−1, 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 et al., 1994; Hope et al., 1994; Dillon and Molot, 1997; Gergel et al., 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 et al., 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-28 January 2015
100 times more acidic than waters with a dissolved organic carbon of <1 mg DOC L−1 (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 m−2 d−1 (Dunne et al., 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 et al. (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 mg N kg−1 d−1 (Jordan et al., 2007). Because flats 

comprise greater than 70% of the wetland area in the basin, this value indicates a significant 

Stream and Wetland Connectivity:

A Review and Synthesis 4-29 January 2015
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 hr-1 versus 5.3 ± 1.7 ng N g-1 hr-1. 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 L−1 (Hemond, 1983). Prairie pothole wetlands in the 

upper Midwest removed >80% of the nitrate load via denitrification (Moraghan, 1993). A large nonfloodplain 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 (NO3-N) 

and sulfate (SO42−) at rates of 0.04−0.55 mg NO3-N L−1 ha−1 and 0.06−0.30 mg SO42− L−1 ha−1. These rates 

are significant, considering that nitrate-nitrogen pollution of ground water in Michigan was reported to 

average 0.50 mg NO3-N L−1 (Whitmire and Hamilton, 2008). Bhadha et al. (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 m−2, 36 mg potassium m−2, and 46 mg lead m−2; 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 

Stream and Wetland Connectivity:

A Review and Synthesis 4-30 January 2015
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 et al., 2005). Allen (2007) trapped 

zooplankton dispersing from a pond in Illinois and found that animals wider than 3 cm were the primary 

Stream and Wetland Connectivity:

A Review and Synthesis 4-31 January 2015
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 hatching in 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 (Polis et al., 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 (Aix sponsa) 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 nonfloodplain wetlands to each other and to other aquatic systems.

Approximately 80% of the entire North American population of redhead ducks (Aythya americana) 

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 et al., 2010). Ballard et al. (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 (Anas gibberifrons gracilis) 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 usedays 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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A Review and Synthesis 4-32 January 2015
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 whitefronted geese (Anser albifrons), 500,000 Canada geese (Branta Canadensis), 50% of midcontinent 

mallards (Anas platyrhynchos), and 30% of continental northern pintails (Anas acuta)” (Webb et al., 

2010, p. 109), 38 shorebird species, and the endangered whooping crane (Grus americana). 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 et al., 2011). Pearse et al. (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 of Pastruella 

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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A Review and Synthesis 4-33 January 2015
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 nonfloodplain wetland habitat over longer distances that is seasonal, climate-induced, and densitydependent has been observed (Serfass et al., 1999; Clark, 2000 and references therein). Spinola et al. 

(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 agriculturedominated 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. (2009b) 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). Lamoureux and 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 et al., 2005). Knutson et al. (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 sipedon) 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 et al. (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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Table 4-2. Partial list of amphibian and reptile species known to use both streams and non-floodplain wetlands or other lentic waters. 

Common Name Scientific Name Habitat Use

Green frog Rana clamitans Breeds in wetlands and pools; overwinters in streams (Lamoureux and Madison, 1999)

Leopard frog Rana pipiens Breeds in wetlands and pools; overwinters in streams (Rorabaugh, 2005)

Bullfrog Rana catesbeiana Uses seasonal pools as complementary nonbreeding habitat (Gahl et al., 2009)

Columbia spotted frog Rana luteventris Breeds in streams and wetlands; overwinters in streams (Pilliod et al., 2002)

Southern leopard frog Rana sphenocephala 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) 

Pacific chorus frog Pseudacris regilla Breeds in wetlands, ponds, temporary pools, streams, lakes, rivers, and other aquatic habitats 

(Rorabaugh and Lannoo, 2005) 

American toad Anaxyrus [=Bufo] 

americanus

Breeds in lakes, ponds, streams, ephemeral wetlands, prairie potholes, ditches, and floodplain 

pools (Green, 2005) 

Fowler’s toad Anaxyrus [=Bufo] fowleri Breeds in ponds, temporary pools, streams, ditches, lake shores, and shallows of rivers (Green, 

2005) 

Two-toed amphiuma Amphiuma means 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) 

Greater siren Siren lacertina Breeds in shallow pools and streams, adults live in lakes, streams, ponds, and wetlands (Gibbons 

and Semlitsch, 1991; Hendricks, 2005) 

Eastern newt Notophthalmus viridescens 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) 
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Table 4-2. Partial list of amphibian and reptile species known to use both streams and non-floodplain wetlands or other lentic waters

(continued).

Common Name Scientific Name Habitat Use

Yellow-bellied 

watersnake 

Nerodia erythrogaster 

flavigaster

Hunts in temporary pools and wetlands (Roe et al., 2004; Mitchell et al., 2007)

Copper-bellied 

watersnake 

Nerodia erythrogaster 

neglecta

Hunts in temporary pools and wetlands (Roe et al., 2004; Mitchell et al., 2007)

Spotted turtle Clemmys guttata Uses temporary wetlands for foraging, mating, basking, and aestivating (Joyal et al., 2001)

Blanding’s turtle Emydoidea blandingii Uses temporary wetlands for foraging, mating, basking, and aestivating (Joyal et al., 2001)

Painted turtle Chrysemys picta Uses temporary wetlands for basking and foraging (Mitchell et al., 2007)

Snapping turtle Chelydra serpentina Uses temporary wetlands for basking and foraging (Mitchell et al., 2007) 

American alligator Alligator mississippiensis Juveniles use seasonal wetlands as nurseries, subadults move back to river networks (Subalusky 

et al., 2009a; Subalusky et al., 2009b) 
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 DEMs 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 et al., 2006; Gleason et al., 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 peerreviewed 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 flooding.

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 surfacewater 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 that non-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 surface 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 per se, 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 5. APPLICATIONS AND DISCUSSION: 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 of fluxes 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 nonfloodplain 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.1). 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 of fish, 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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A Review and Synthesis 5-5 January 2015
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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A Review and Synthesis 5-6 January 2015
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. 

Most of 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 highintensity 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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A Review and Synthesis 5-7 January 2015
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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A Review and Synthesis 5-8 January 2015
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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A Review and Synthesis 5-9 January 2015
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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A Review and Synthesis 5-10 January 2015
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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A Review and Synthesis 5-11 January 2015
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.

Connection to downstream waters

Riparian & Streams

Floodplain waters

Non-floodplain 

waters

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A Review and Synthesis 5-12 January 2015
CHAPTER 6. CONCLUSIONS

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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A Review and Synthesis 6-1 January 2015
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 specieslevel 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, groundwater 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 streamdownstream 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 surfacewater, 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 nonfloodplain 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 

Stream and Wetland Connectivity:

A Review and Synthesis 6-5 January 2015
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 wastewaters 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 m−2 d−1) occurred in 

marshes that comprised only 7% of the lower Lake Okeechobee basin area in Florida. A nonfloodplain 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 

Stream and Wetland Connectivity:

A Review and Synthesis 6-6 January 2015
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 

Stream and Wetland Connectivity:

A Review and Synthesis 6-7 January 2015
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 

Stream and Wetland Connectivity:

A Review and Synthesis 6-8 January 2015
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 nonfloodplain 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, lowmagnitude 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. 

Stream and Wetland Connectivity:

A Review and Synthesis 6-9 January 2015
 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.

Stream and Wetland Connectivity:

A Review and Synthesis 6-10 January 2015
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 highStream and Wetland Connectivity:

A Review and Synthesis 6-11 January 2015
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. 

Stream and Wetland Connectivity:

A Review and Synthesis 6-12 January 2015
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 nonfloodplain 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 nonfloodplain 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 et al., 2004; Tiner, 2011; Lang et al., 2012), assessment (e.g., McGlynn and McDonnell, 2003; 

Gergel, 2005; McGuire et al., 2005; Ver Hoef et al., 2006; Leibowitz et al., 2008; Moreno-Mateos et al., 

2008; Lane and D'Amico, 2010; Ver Hoef and Peterson, 2010; Shook and Pomeroy, 2011; Powers et al., 

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 highresolution 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 

Stream and Wetland Connectivity:

A Review and Synthesis 6-13 January 2015
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.

Stream and Wetland Connectivity:

A Review and Synthesis 6-14 January 2015
A Review and Synthesis

Stream and Wetland Connectivity:

6-15 January 2015

Table 6-1. Relative abundance of literature by functional category. The table shows our confidence, which is based on the relative size of the 

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 

the number of associated citations in this report because some citations are review articles or meta-analyses, which summarize information for 

many references. The dot size also does not correspond with the level of confidence in particular conclusions.

Type of water body 

Function Uncertainty discussion 

(Section) Source Sink (Storage) Refuge Lag Transformation

Streams 3.6

Riparian/floodplain wetlands 4.5.1

Non-floodplain wetlands 4.5.2
A Review and Synthesis

Stream and Wetland Connectivity:

6-16 January 2015

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 

citations are review articles or meta-analyses, which summarize information from many references. The dot size also does not correspond with 

level of confidence in particular conclusions.

Topic Question

Biological Chemical Physical

Connection Effect Connection Effect Connection Effect

Streams

What are the physical, chemical, 

and biological connections to and 

effects of ephemeral, intermittent, 

and perennial streams on 

downstream waters?

ephemeral

intermittent

perennial

Riparian/ 

Floodplain 

Wetlands

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?

Nonfloodplain 

wetlands

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?
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Woodford, D. J., and A. R. McIntosh. 2010. Evidence of source-sink metapopulations in a vulnerable 

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Woodin, M. 1994. Use of saltwater and freshwater habitats by wintering redheads in southern Texas. 

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Woodward, G. U. Y., and A. G. Hildrew. 2002. Food web structure in riverine landscapes. Freshwater 

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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 of fluxes 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−1 or m3 s−1. 

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 and 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 et al. (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, lowflow 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 et al. (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: ωa = ρgQS where ωa is the stream power, ρ is the density of water (1000 kg/m3), g is acceleration 

due to gravity (9.8 m/s2), Q is discharge (m3/s), and S is 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 firstorder 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 (T1) 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.

Stream and Wetland Connectivity:

A Review and Synthesis A-15 January 2015
APPENDIX B. CASE STUDIES

B.1 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-1; 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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A Review and Synthesis B-1 January 2015
Figure B-1. 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.1.2.2 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; Stolt and Rabenhorst, 1987a; Grant et al., 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 LiDARderived 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 et al., 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 et al., 2007a; Pyzoha et al., 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 et al., 2000b) and birds that feed on these fish (Brant et al., 2002). 

B.1.2.5 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 Kral, 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 Kral, 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 et al., 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 

cingulatum) and the gopher frog (Rana capito) (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 americana) 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 frequent in the center of the bays (Caldwell et al., 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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A Review and Synthesis B-5 January 2015
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.1.3.2 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 et al., 2000b). If these bays connect to downstream waters 

via ditches, some bioavailable mercury would be expected to move to other waters. 

B.1.3.3 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 of fish 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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A Review and Synthesis B-6 January 2015
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 et al. (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 sphenocephala), 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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A Review and Synthesis B-7 January 2015
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 

cut off 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 cut off 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 et al., 2000; Zeug et al., 2005), and South America (da Silva et al., 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 et al., 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 et al., 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 (GlinskaLewczuk, 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 et al., 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 et al., 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 et al., 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 et al., 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 Delong, 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 Delong, 2002; Bunn et al., 2003; Keckeis et al., 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 et al., 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 et al., 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 of fish 

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 g m−1 ha−1 of gillnet sampling, versus 138.1 g per 10-m seine haul and 495 g m−1 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 of fish 

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 MogiGuaçu 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 of fish 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 km−2 in the eastern part of 

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the region to up to 90 km−2 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 et al., 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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A Review and Synthesis B-15 January 2015
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 et al., 

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. x glauca) 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 at more 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 et al., 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 et al., 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 et al., 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 

Stream and Wetland Connectivity:

A Review and Synthesis B-19 January 2015
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, including floating aquatics and emergent 

perennials, is likely facilitated by waterfowl movement (Aronson and Galatowitsch, 2008). Waterfowl 

often move between wetlands during the breeding season in search of food and cover, and some species 

also use habitats within the river network as wetlands dry or freeze (Pattenden and Boag, 1989; Murkin 

and Caldwell, 2000). Water also can provide a means for biologically connecting potholes. Fish and other 

organisms or parts of organisms that can be suspended in water (e.g., floating insect larvae or seeds) 

have been hypothesized to move between potholes during spillage events (Zimmer et al., 2001; van der 

Valk and Pederson, 2003; Herwig et al., 2010). Dispersal of waterborne organisms also can occur 

through manmade waterways (i.e., ditches) that connect potholes to stream networks (Hanson et al., 

2005; Hentges and Stewart, 2010; Herwig et al., 2010). Most of these studies cite only anecdotal 

evidence for dispersal through ditches. Populations of aquatic plants in agricultural ditches in Europe, 

Stream and Wetland Connectivity:

A Review and Synthesis B-20 January 2015
however, are genetically highly structured along these man-made waterways, suggesting that these 

watercourses determine dispersal pathways (Gornall et al., 1998). 

Finally, overland dispersal of amphibians and mammals can connect potholes. Eight of twelve amphibian 

species were able to quickly recolonize restored potholes near source populations (Lehtinen and 

Galatowitsch, 2001). Although muskrat territories in the PPR are usually restricted (less than 100 m 

from the home stream or wetland), they can disperse longer distances to feed and breed in prairie 

wetland habitat under certain conditions (Clark, 2000 and references therein). In North Dakota, 

muskrats have been observed taking up residence in potholes for a series of years, provided suitable 

water levels and vegetation existed, and then emigrating, presumably to more permanent and larger 

lakes and streams (Winter and LaBaugh, 2003). Not all wetland animals disperse widely, however. 

Populations of the pothole-dwelling salamander Ambystoma tigrinum (studied in small, non-pothole 

wetlands, in this case) can be genetically differentiated from each other down to 1.5 km, indicating low 

dispersal (Routman, 1993). 

Landscape features, including distance, relief, and human alterations, can promote or restrict biological 

connections between wetlands and larger bodies of water. Spatial distance is one important factor to 

consider. For a given species, wetlands located closer together will exchange more organisms than 

wetlands that are farther apart. Therefore, landscapes in which potholes are located in relative 

proximity to each other and to the river network are likely to be connected more frequently and by 

more species. For example, restored potholes in pothole-dense areas tend to be recolonized by plants 

more efficiently (Mulhouse and Galatowitsch, 2003), and high pothole density promotes greater 

movement of waterfowl (Krapu et al., 1997). Unfortunately, quantification of biological effects of 

potholes on larger waters is severely limited. In most cases, studies involving biological isolation or 

connectivity in the PPR have focused on the potholes themselves as sources and recipients of organisms. 

B.3.4 Prairie Potholes: Synthesis and Implications

The key findings for this case study are as follows:

 The degree to which prairie potholes are connected or could connect to river networks depends 

on many factors. These factors include distance to rivers or streams, topography, precipitation, 

climate cycles (seasonal and on longer time scales), biotic community composition, and artificial 

drainage. Within the PPR, distance to rivers and streams is strongly influenced by the three 

major physiographic regions (Red River Valley, Drift Prairie, and Missouri Coteau), which vary 

in the number of potholes and stream density (e.g., Figures 2-20A and 2-20B).

 On a watershed scale, unaltered potholes often function as hydrologic sinks, sequestering water 

and reducing annual streamflow, but can become sources as they spill overland under high 

precipitation or low relief, or both. When artificially drained or ditched, potholes can become 

sources of water, nutrients, sediment, and pesticides. Their roles as sinks and sources affect 

river geomorphology and biological communities. 

Stream and Wetland Connectivity:

A Review and Synthesis B-21 January 2015
 Potholes also might have direct biological effects on river networks via connectivity of resident 

populations, although these effects are less well known and studied.

Because of wide variation in the conditions that determine the incidence or magnitude of connections 

between prairie potholes and river networks, pothole complexes in some watersheds are more likely to 

have important effects on associated rivers and lakes than others are. Given evidence in the current 

literature, however, when proper climatic or topographic conditions occur, or biotic communities are 

present that promote potential or observed connections, measurable influence on the physical, chemical, 

and biological condition and function of downstream waters is highly likely. 

B.4 Case Study: Prairie Streams 

B.4.1 Abstract

Prairie streams drain temperate grasslands in the central United States. Periods of flooding and drying 

characterize their hydrology, with spring-fed, perennial pools and reaches embedded within more 

intermittently flowing reaches; thus, water flow along prairie stream networks exhibits high temporal 

and spatial variability. Existing evidence indicates that small prairie streams are connected to 

downstream reaches, most notably via flood propagation and the extensive transport and movement of 

fish species throughout these networks. Nutrient retention in small prairie streams also significantly 

influences nutrient loading in downstream rivers. 

B.4.2 Introduction

B.4.2.1 Geography and Climate 

Prairies are temperate grasslands located in the Great Plains physiographic region of the central United 

States and Canada (Figure B-2). Grasses and forbs (broad-leaf plants other than grasses) dominate the 

region, particularly in upland areas. Shrubs and trees can be found in lowlands, and are commonly called 

gallery forests. Native prairie ecosystems once covered approximately 1.62 million km2 in North 

America but have been lost almost completely since European settlement, mainly replaced by row-crop 

agriculture (Samson and Knopf, 1994). Because of drastic alterations to much of the historical eastern 

plains (Iowa, Illinois, Missouri, Indiana, Minnesota), our discussion centers principally on river networks 

in the high plains subregion of the Great Plains (Subregion 2 in Figure B-2), where drier climate and 

thin, rocky soil have limited row-crop agriculture.

Prairies generally can be characterized by their relatively low topographic relief, although areas such as 

the Flint Hills in eastern Kansas, the Arikaree Breaks in northwestern Kansas, and the Arbuckle 

Mountains in south-central Oklahoma have relatively steep terrain compared to that of western Kansas 

or the Oklahoma panhandle (Osterkamp and Costa, 1987; Matthews, 1988). The underlying geology 

consists of extensive limestone deposits, but sandstone and shale deposits or unconsolidated sands, 

silts, and clays characterize other areas (Brown and Matthews, 1995). Soils in the Great Plains are 

predominantly loess, but some areas such as Nebraska’s Sand Hills have high percentages of sand 

(Wolock et al., 2004). Although prairie soils tend to be less permeable than more humic forest soils, 

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A Review and Synthesis B-22 January 2015
Figure B-2. Map of the United States showing physiographic subregions and major rivers of the Great 

Plains: (1) glaciated prairie; (2) high plains; (3) eastern plains; and (4) Ozark Plateau. Modified from 

Covich et al. (1997). 

fractures and macropores of the limestone geology in some prairie areas, such as the Flint Hills, allow 

for relatively rapid percolation and recharge of local ground water (Macpherson and Sophocleous, 

2004). 

Most of the large rivers draining the high plains subregion (e.g., the Missouri, Yellowstone, Milk, 

Cheyenne, White, Niobrara, Platte, Kansas-Republican, Arkansas, Cimarron, Canadian, Red, and Washita 

Rivers) are major tributaries to the Mississippi River. The southern portions of the subregion contain 

the headwaters of the Rio Grande River (Pecos River) or rivers that flow directly into the Gulf of Mexico 

(the Guadalupe, San Antonio, Colorado of Texas, Brazos, and Nueces Rivers). Some rivers in the northern 

portions of the glaciated prairie flow north, eventually into the Hudson Bay (notably the Red River of the 

North).

The climate in this region ranges from semiarid in the western portions to moist subhumid in the 

eastern portions. Mean annual precipitation ranges from 200 to 1,000 mm y−1 from west to east across 

the Great Plains (Lauenroth et al., 1999). Potential evaporation typically exceeds precipitation 

(Transeau, 1905, 1935). Mean annual temperatures increase from north (4−8 °C) to south (16–20 °C; 

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A Review and Synthesis B-23 January 2015
Lauenroth et al., 1999). Winters tend to be dry, with less than 20% of the annual precipitation (Borchert, 

1950; Lauenroth et al., 1999; Boughton et al., 2010). Most precipitation falls in late spring and early 

summer (Borchert, 1950; Lauenroth et al., 1999), and much of the summer precipitation results from 

localized convective thunderstorms. Because of the region’s geographic location relative to the Gulf of 

Mexico and the Rocky Mountains, however, substantial interannual variation exists, particularly in 

terms of summer rainfall deficit (Borchert, 1950). 

B.4.2.2 Hydrology and Geomorphology

The hydrology of most prairie river networks is highly variable (Matthews, 1988; Brown and Matthews, 

1995; Dodds et al., 2004). These systems are frequently subjected to the extremes of drying and 

flooding, and intermittent or flashy hydrology is prevalent in river networks throughout most of the 

Great Plains (Matthews, 1988; Zale et al., 1989; Poff, 1996; Dodds et al., 2004). The topology of most 

prairie river networks is dendritic due to the relatively flat landscape and uniform geology (Brown and 

Matthews, 1995). Prairie river networks tend to have high drainage density (Section 2.4.2), and are 

therefore efficient at transferring rainfall from uplands to downstream reaches (Gregory, 1976; 

Osterkamp and Friedman, 2000). Flood magnitudes tend to be higher in the semiarid Great Plains than 

in other regions, despite comparable rainfall intensities, due to low infiltration and vegetation 

interception (Osterkamp and Friedman, 2000). Although floods tend to occur in late fall through late 

spring, they can occur any time during the year (Brown and Matthews, 1995; Poff, 1996). Like most 

river networks, those draining prairie landscapes often contain ephemeral, intermittent, and perennial 

streams. Although many headwater prairie streams are ephemeral or intermittent (Matthews, 1988; 

Brown and Matthews, 1995; Dodds et al., 2004), some have perennial spring-fed reaches located at the 

network origins or distributed between intermittent reaches along headwater streams (Matthews et al., 

1985; Sawin et al., 1999; Dodds et al., 2004; Bergey et al., 2008). 

The flow regimes of streams draining the Rocky Mountains, Black Hills, and northern prairies are largely 

tied to snowmelt. Most systems originating in the mountains quickly transition in flow and morphology 

as they cross the Great Plains, becoming intermittent and then slowly gaining flow from large streams 

before joining the Mississippi River (Brown and Matthews, 1995). Some areas, however, have stable 

streamflow with few intermittent streams because flow is derived from large, permeable ground-water

sources (e.g., Sand Hills in Nebraska; Winter, 2007). 

The High Plains (Ogallala) aquifer system and other aquifers (e.g., Edwards-Trinity) are important 

hydrologic features interconnected with Great Plains river networks. The High Plains aquifer system is 

the largest (450,658 km2) and most intensively pumped U.S. aquifer, underlying much of the Great 

Plains from southern South Dakota and southeastern Wyoming to central Texas (Sophocleous, 2005; 

Ashworth, 2006; Sophocleous, 2010). The High Plains aquifer is composed of blanket sand and gravel 

derived mainly from alluvial deposits and ancient marine sands. It is unconfined regionally, but locally 

can be confined where beds of silt, clay, or marl are present. Regional movement of water through the 

aquifer is from west to east, but locally the water moves toward major tributaries. Northern areas of the 

Great Plain are underlain by glacial deposit aquifers that can be a mixture of till (unsorted material 

Stream and Wetland Connectivity:

A Review and Synthesis B-24 January 2015
ranging from clay to boulders) and outwash (stratified sand and gravel) that was deposited by glacial 

meltwater.

Most headwater streams originating in the prairie have riffle-pool morphology with alluvial gravel; only 

headwater streams originating in the western mountains have high gradient, cobble-boulder channels 

(Brown and Matthews, 1995). Southern prairie headwater streams tend to have finer substrate than 

those in the northern and central Great Plains (Brown and Matthews, 1995). Larger streams tend to 

have broad sand beds that are frequently braided (Section B.4.2.5). In contrast to headwater streams in 

forested regions, the riparian areas of prairie headwater streams typically lack overhanging trees.

Grasses and shrubs are the dominant riparian vegetation, so channels lack woody debris and generally 

receive direct sunlight. Because of intense flooding, prairie streams tend to form wide, deep channels 

relative to their drainage areas, regardless of flow permanence (Hedman and Osterkamp, 1982; Brown 

and Matthews, 1995). Because of similarity in topography, climate, geology, and soils, stream 

geomorphology across the Great Plains is largely comparable (Miller and Onesti, 1988). High plains 

channels, however, tend to be slightly steeper in gradient and more sinuous than wider and deeper 

channels of the eastern plains (Miller and Onesti, 1988). During floods, the relatively incised channels 

and lack of woody debris in prairie headwater streams make them less retentive of organic matter and 

other materials than those of high-gradient forested channels; their pool-riffle morphology, high 

sinuosity, and seasonal drying, however, can enhance retention (Brown and Matthews, 1995). 

B.4.2.3 Physicochemistry

The factors discussed above are strong drivers of prairie stream physicochemistry (Matthews, 1988; 

Brown and Matthews, 1995). Hot summers and cold winters in this region cause substantial direct and 

indirect changes in water temperature, dissolved oxygen, and nutrient concentrations. Isolation of 

surface water into pools during summer drying exacerbates these changes (Zale et al., 1989; Ostrand 

and Marks, 2000; Ostrand and Wilde, 2004). For example, water surfaces can be covered with ice in 

winter, whereas summer water temperatures can reach 35−40 °C with 9−10 °C diel (i.e., daily) 

fluctuations (Matthews, 1988; Matthews and Zimmerman, 1990). Concomitant fluctuations in dissolved 

oxygen occur, which when combined with stream respiration, contribute to dissolved oxygen values 

approaching anoxic conditions.

Prairie rivers and streams naturally have higher concentrations of dissolved solids (e.g., calcium, 

carbonate, bicarbonate, sodium, chloride, magnesium, sulfate) due to dissolution of the underlying 

geologic layers (Huntzinger, 1995). Associated with these high levels of dissolved ions are elevated 

alkalinity and pH. Mean total dissolved solids concentrations for many Great Plains rivers are among the 

highest in the United States, exceeding 500 mg L−1; many Great Plains rivers, however, also receive 

anthropogenic total dissolved solid inputs from wastewater treatment effluents, agricultural runoff, 

irrigation contributions to baseflow, and disposal of produced water associated with fossil fuel 

production (Mathis and Dorris, 1968; Huntzinger, 1995; Farag et al., 2010). Some river networks, such 

as the headwaters of the Red River in Texas and Oklahoma, are saline because they derive from brine 

springs (Taylor et al., 1993). 

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A Review and Synthesis B-25 January 2015
Streams and rivers of the central United States are often cited as having elevated nutrient (i.e., nitrogen 

and phosphorus) loads. These loads are primarily attributable to nonpoint source runoff from fertilizer 

application and livestock waste, especially during higher flows in winter and spring (Huntzinger, 1995; 

Royer et al., 2006; Alexander et al., 2008). Data from streams draining native prairie indicate that 

nitrogen and phosphorus concentrations and fluxes are lower or comparable to other intact ecosystems 

(McArthur et al., 1985a; Dodds et al., 1996a; Kemp and Dodds, 2001). 

B.4.2.4 Ecology

The low diversity of aquatic flora and fauna of prairie river networks, especially compared to 

assemblages in the eastern and southeastern United States (Jewell, 1927; Fausch and Bestgen, 1997), is 

likely due to the environmental instability of these river networks, their evolutionary history, and the 

magnitude and extent of human alterations. Most organisms have adapted to erratic hydrologic regimes 

and harsh physiochemical conditions in prairie streams by having rapid growth, high dispersal ability, 

resistant life stages, fractional or extended reproduction (i.e., spawn multiple times during a 

reproductive season), broad physiological tolerances, and life cycles timed to avoid predictably harsh 

periods (Matthews, 1988; Dodds et al., 1996b; Fausch and Bestgen, 1997). 

Algae are foundational components of prairie streams, acting to retain nutrients and provide an 

important energy source to consumers (Gelwick and Matthews, 1997; Dodds et al., 2000; Evans-White et 

al., 2001; Evans-White et al., 2003). Flooding and drying in prairie streams reset algal assemblages, spur 

successional sequences, and maintain high levels of primary production (Power and Stewart, 1987; 

Dodds et al., 1996b; Murdock et al., 2010). Algal assemblages are composed primarily of diatoms (e.g.,

Cymbella, Cocconeis, Pinnularia, Achnanthes, Navicula, and Gomphonema), filamentous green algae (e.g., 

Cladophora, Spirogyra, Rhizoclonium, Stigeoclonium, Zygnema, and Oedogonium), and cyanobacteria (e.g., 

Oscillatoria, Nostoc). 

Because of high light availability, algal primary production in prairie streams occasionally can be 

substantially higher than in forested headwaters (Hill and Gardner, 1987a; Dodds et al., 1996b; 

Mulholland et al., 2001; Bernot et al., 2010). Gallery forests farther downstream provide shade and 

contribute organic matter. Shade from the gallery forests lowers light transmission to algae, resulting in 

lower algal primary production in these reaches than in unshaded prairie headwater reaches. Thus, in 

contrast to conventional longitudinal paradigms like the River Continuum Concept, the organic matter 

driving prairie headwater streams derives mainly from within the channel (autochthonous production), 

whereas leaf litter and other detritus from nearby gallery forests (allochthonous production) dominate 

in intermediate-sized streams (Gurtz et al., 1982; Gurtz et al., 1988; Wiley et al., 1990). Despite having 

greater primary production than forested headwaters, prairie streams—like forested ones—tend to be 

net heterotrophic systems (Mulholland et al., 2001), but those that agricultural activities (e.g., elevated 

nutrients, channelization) influence can at times be net autotrophic (Prophet and Ransom, 1974; Gelroth 

and Marzolf, 1978; Wiley et al., 1990). 

Invertebrates in prairie streams are represented by various aquatic insect groups (e.g., Diptera, 

Coleoptera, Plecoptera, Ephemeroptera, Trichoptera), crustaceans (crayfish, isopods, amphipods), 

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A Review and Synthesis B-26 January 2015
mollusks, and oligochaetes. Consumers of fine benthic organic matter, epilithic algae, and other 

invertebrates tend to dominate invertebrate communities (Gray and Johnson, 1988; Harris et al., 1999; 

Stagliano and Whiles, 2002). Diversity and abundance of invertebrates tend to increase with flow 

permanence, but species composition generally highly overlaps, with intermittent stream assemblages 

representing a nested subset of those from perennial streams (McCoy and Hales, 1974; Miller and 

Golladay, 1996; Fritz and Dodds, 2002). 

As with algae, flooding and drying are important drivers of invertebrate assemblages in prairie streams.

Distinct successional transitions are apparent following these disturbances (Chou et al., 1999; Fritz and 

Dodds, 2002), and recovery to predisturbance levels can be rapid (Miller and Golladay, 1996; Miller and 

Nudds, 1996; Fritz and Dodds, 2004). Woody debris is often rare in prairie streams, but where it is 

present, invertebrates tend to be more abundant and more resistant to flooding, relative to those 

associated with less stable sand and gravel substrates (Golladay and Hax, 1995; Hax and Golladay, 1998; 

Johnson and Kennedy, 2003). 

Fish are a well-studied component of river networks in the Great Plains, and are among the most 

threatened (Rabeni, 1996; Fausch and Bestgen, 1997; Hubert and Gordon, 2007; Hoagstrom et al., 

2010). Approximately 200 fish species are found across prairie river networks, about 50 of which are 

endemic to these streams. The most common taxa are minnows (Cyprinidae), suckers (Catastomidae), 

darters (Percidae), sunfishes (Centrarchidae), and catfishes (Ictaluridae). 

Longitudinal organization of fish assemblages has been recognized widely in Great Plains river networks 

(Harrell et al., 1967; Smith and Powell, 1971; Schlosser, 1987), and like macroinvertebrates these 

assemblages often are nested such that intermittent headwater communities are subsets of those in 

downstream perennial segments. Unlike algae and macroinvertebrates, fish inhabiting intermittent 

headwater streams have no terrestrial or drying-resistant life stages. Fish, however, are highly mobile 

and avoid desiccation by moving into downstream perennial reaches or perennial spring-fed pools in 

upstream segments (Deacon, 1961; Fausch and Bramblett, 1991). Periodic floods are important for 

creating perennial refuges and providing connectivity between habitats for the dispersal of fish and 

their eggs in prairie stream networks (Section B.4.3.3; Labbe and Fausch, 2000; Franssen et al., 2006). 

B.4.2.5 Human Alterations

Human alterations to prairie river networks have affected physical, chemical, and biological connectivity 

in these systems both directly and indirectly. Crop and livestock agriculture are predominant land uses 

in the Great Plains (Galat et al., 2005; Matthews et al., 2005) and represent major nonpoint sources of 

nutrients, sediment, and pesticides (Battaglin et al., 2003; U.S. EPA, 2006; Alexander et al., 2008). 

Livestock concentrate in and near streams for shade, food, and water, leading to bank erosion, increased 

soil bulk density, sedimentation, and elevated fecal bacteria concentrations (Armour et al., 1991; Strand 

and Merritt, 1999). 

To support these agricultural enterprises, water has been diverted from channels, withdrawn from 

regional aquifers, and stored in reservoirs. Ground-water withdrawals in the Great Plains are the highest 

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A Review and Synthesis B-27 January 2015
in the United States (Sophocleous, 2010), causing many once perennial river segments to regularly dry 

up completely during summer months, particularly in the drier western portions of the Great Plains 

(Cross and Moss, 1987; Ferrington, 1993; Falke et al., 2011). Nearly all river networks in prairie regions 

have been altered by impoundments for irrigation storage and flood control, from small farm ponds in 

headwaters to large reservoirs on river mainstems (Smith et al., 2002; Galat et al., 2005; Matthews et al., 

2005). Decline in flood magnitude, altered flow timing, and reduced flow variability and turbidity are 

evident in many prairie rivers compared to historically documented conditions (Cross and Moss, 1987; 

Hadley et al., 1987; Galat and Lipkin, 2000). Reductions in peak discharge derived from prairie streams 

have contributed to the narrowing of the region’s once broad and shallow river channels (Friedman et 

al., 1998; Wohl et al., 2009). Dynamic mosaics of sand bars common in most prairie rivers have become 

stabilized and coalesced islands. The establishment of trees along prairie river riparian zones was 

limited by floods prior to settlement, but now dense zones of native and invasive trees and shrubs 

further reduce flows through high evapotranspiration (Johnson, 1994; Dahm et al., 2002). 

B.4.3 Evidence

B.4.3.1 Physical Connections

B.4.3.1.1 Water

As in other river systems, water is the primary medium by which materials are transported from 

streams to rivers in prairie networks. Floods are common in Great Plains streams (Fausch and 

Bramblett, 1991; Hill et al., 1992; Fritz and Dodds, 2005), and propagation of these floods from streams 

to downstream rivers demonstrates hydrologic connectivity. Fritz and Dodds (2004, 2005) 

characterized the hydrology of intermittent streams draining native tallgrass prairie in a study that 

coincided with the highest flow on record (on May 13, 1995, with a return interval of at least 50 years).

Kings Creek and one of its headwater streams (N01B) are both headwater streams draining into the 

Kansas River, downstream of the USGS gaging station at Fort Riley and upstream from the confluence of 

the Big Blue and Kansas Rivers and the USGS gaging station at Wamego (Figure B-3). The peak-flow 

rising and descending limbs were very rapid at Kings Creek and N01B compared to those recorded for 

the Kansas River at Wamego, where the peak arrived approximately 12 hours later (Figure B-4).

Hydrographs for the upstream Fort Riley gage on the Kansas River and the Big Blue River indicate that 

the May 13, 1995 peak at the downstream Wamego gage was associated with floods propagating from 

Kings Creek and other small streams (Figure B-4). The subsequent peak at the Wamego gage that 

occurred 5 days later was associated with a storm mainly affecting portions of the Kansas River basin 

upstream of the Fort Riley gage, which elicited only a slight increase in discharge at Kings Creek and 

N01B (Figure B-4).

A flood occurring June 14−20, 1965 on the Platte River (Colorado and Nebraska) is among the largest 

U.S. floods in recorded history, with a recurrence interval of 900 to 1,600 years (Matthai, 1969). This 

flood originated from runoff of intense rainfall (360 mm in 4 hours) over headwater portions of the 

drainage south of Denver, CO. Normal annual precipitation for this area is approximately 400 mm. Flows

in Plum Creek, one of the intermittent headwater streams to the Platte River that received the heaviest

Stream and Wetland Connectivity:

A Review and Synthesis B-28 January 2015
Figure B-3. Map showing the location of Kings Creek and N01B, intermittent tributaries to the Kansas 

River.

rains, rose from <5 m3 s−1 to 4,360 m3 s−1 in only 40 minutes. Under the Federal Flood Control Act of 

1944, detention impoundments were extensively constructed on headwater streams in the Great Plains 

to retard flooding in downstream rivers (Schoof et al., 1978; Van Haveren, 1986). Headwater 

impoundments reduced runoff to the Washita River in Oklahoma by 36%, but channel dredging of 

streams offset these reductions by increasing flow from ground water and reducing transmission loss 

(Schoof et al., 1978). 

Machavaram et al. (2006) examined hydrologic connectivity between intermittent prairie streams, a 

headwater pond, and a perennial stream reach approximately 10 km downstream using chemical and 

isotopic tracers in a southeastern Kansas system. They found that, following precipitation, 20% of 

downstream water originated from the upstream pond, fed by ephemeral and intermittent streams; 

elevated oxygen stable isotope tracer associated with the pond water took 26−31 hours to reach the 

downstream site (Machavaram et al., 2006). Streams connected to lakes and wetlands contributed

proportionally more flow to a southeastern Minnesota river in summer, when other water sources were 

minimal, than in spring (Lenhart et al., 2010). Flow from these streams has a delayed or lagged release 

because of storage in lakes and wetlands, and stream flow backed up because of high mainstem flows 

(Lenhart et al., 2010). 

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A Review and Synthesis B-29 January 2015
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. Also shown are hydrographs from upstream gages on the Kansas River at Fort Riley and 

the Big Blue River (see Figure B-3 for all site locations). Instantaneous data were not available at Kings 

Creek immediately following the flood because of damage to the USGS gage and were not available 

from Big Blue River. The peak instantaneous discharge for Kings Creek was estimated by USGS.

B.4.3.1.2 Temperature (heat energy) 

Water temperatures represent a substantial stress to biotic communities in Great Plains rivers (Section 

B.4.3.3). Rivers to the north experience cold winters, and those to the south and west experience hot 

summers. Streams, particularly those strongly connected to more stable ground water, can provide 

thermal refuges for avoiding temporary hypothermic and hyperthermic stress (Section B.4.3.3.2). Wide, 

shallow channels with little overhead canopy can result in high water temperatures under summer low 

flows. Over a 1-km reach of the South Canadian River in Oklahoma, summer (August 18−19, 1976) 

maximum mainstem water temperatures were 36−37 °C, with cooler water (32−35 °C) in backwater 

pools and a tributary stream (Matthews and Zimmerman, 1990). Mean water temperatures of seven 

streams immediately upstream from confluences with the Missouri River (at the Kansas-Missouri 

border) did not differ from water temperatures in the mainstem river, 200−300 m downstream of the 

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confluences, except during March when streams were warmer than the river (Braaten and Guy, 1999). 

Mean water temperature was determined to be homogeneous with no relationship between drainage 

area and water temperature across two agriculturally dominated drainages in Illinois, where most flow 

was derived from surface and shallow subsurface runoff (agricultural tiles) rather than deeper ground 

water (Wiley et al., 1990). 

B.4.3.1.3 Sediment 

Great Plains rivers are naturally turbid (Jewell, 1927; Cross and Moss, 1987; Huntzinger, 1995), with 

suspended sediment derived from the fine soils through which these river networks flow. Turbidity and 

suspended sediment concentration increase in prairie networks with increasing discharge and drainage 

area (Hill and Gardner, 1987b; Wiley et al., 1990; Lenhart et al., 2010), and can vary seasonally (Lenhart 

et al., 2010). Seasonal turbidity levels at tributary outlets and nearby mainstem reaches, however, were 

not related across seven Missouri River confluences in Kansas and Missouri (Braaten and Guy, 1999), 

suggesting that these streams did not influence river turbidity at baseflow conditions. In contrast to 

other studies in the prairie region, no relationship was found between suspended particle concentration 

and stream size among 22 sites ranging in land use and network position (second- to eighth-order) in 

the Kansas River basin (Whiles and Dodds, 2002). A significant positive relationship did exist when the 

authors excluded suburban sites and sites influenced by impoundments. Concentrations of suspended 

fine inorganic and organic matter were highest in the smallest stream draining suburban land use, 

whereas a comparably small stream draining native tallgrass prairie had among the lowest 

concentrations (Whiles and Dodds, 2002). 

The downstream transport of metal-contaminated sediment was documented from mine tailings near a 

South Dakota headwater stream down through the river network to a reservoir approximately 200 km 

downstream, at the confluence of the Cheyenne and Missouri Rivers (Horowitz et al., 1988; Marron, 

1989). The total amount of mine tailings transported from the headwater stream to downstream waters 

and floodplains over a 100-year span was estimated to be approximately 100 million metric tons 

(Marron, 1989). Contributions from streams to large rivers can therefore depend on the quantities 

available for transport from headwater streams from surrounding land uses.

B.4.3.2 Chemical Connections

B.4.3.2.1 Nutrients and other chemicals 

Studies show that chemical constituents are exported from small prairie streams (Dodds et al., 1996a) 

and these chemical connections, or the downstream, flow-associated transport of nutrients, ions, 

dissolved and particulate organic matter, and other substances along prairie stream drainage networks, 

can significantly influence downstream water quality (Kemp and Dodds, 2002; Dodds et al., 2004; Dodds 

and Oakes, 2006). 

Small prairie streams also can be important in preventing downstream nutrient transport. Studies 

conducted in Kings Creek, a stream draining a 1,060-ha tallgrass prairie catchment in Kansas, indicate 

that small prairie streams are highly nitrogen retentive (Tate, 1990; Dodds et al., 1996a; Dodds et al., 

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2000). For example, Dodds et al. (1996a) found that nitrogen transport through four second- and thirdorder streams in the Kings Creek watershed ranged from 0.01 to 6.0% of the total nitrogen supplied by 

precipitation, the balance being retained by the stream system. Similar patterns of nutrient retention 

have been demonstrated at larger spatial scales, as well. Alexander et al. (2000; 2008) modeled the 

contribution of different-sized streams and rivers (including prairie streams) to nutrient loading in the 

Gulf of Mexico. They found that large rivers deliver more of their nitrogen and phosphorus loads to the 

Gulf of Mexico than small streams, largely due to increased instream nutrient uptake and removal by 

small streams (Alexander et al., 2000). Despite their relative retentiveness, however, small streams do 

make substantial contributions to downstream nutrient loading due to their large numbers, with small 

to mid-sized streams in the western regions of the Mississippi River basin (which includes the Great 

Plains) delivering approximately 25−50% of their nitrogen loads to the Gulf (Alexander et al., 2008). 

Correlations between water quality and upstream land use also indicate that prairie stream headwaters 

affect downstream reaches. Dodds and Oakes (2006, 2008) examined relationships between water 

quality and watershed land use at different spatial scales, along one fifth-order prairie stream network 

(Dodds and Oakes, 2006) and across 68 small prairie streams (Dodds and Oakes, 2008) in eastern 

Kansas. In the single drainage study, they found that concentrations of total nitrogen and nitrate were 

significantly related to riparian cover in the 2 km upstream of sampling sites, even when controlled for 

catchment land cover at each site (Dodds and Oakes, 2006). In the cross-drainage study, riparian cover 

along first-order streams was more closely correlated with total nitrogen, nitrate, ammonium, total 

phosphorus, atrazine, dissolved oxygen, and fecal coliform concentrations than riparian cover 2 or 4 km 

immediately upstream of sites across the 68 drainages (Dodds and Oakes, 2008). Nutrients are elevated 

in most prairie streams and rivers and nutrient concentrations in these systems are related to nonpoint 

land uses (Dodds and Oakes, 2004). These, along with widespread nature of headwater streams in river 

networks, are highly indicative that streams have strong chemical connection, functioning as important 

links between the surrounding lands to downstream waters.

Because prairie streams frequently experience intermittent flow, their influence on downstream waters 

is often discharge-dependent and temporally variable. For example, nitrate concentrations tend to be 

higher in intermittent prairie streams immediately after flows resume, versus when flow recedes (Tate, 

1990). In addition, nitrogen uptake lengths (Dodds et al., 2000) and total phosphorus loads (Banner et 

al., 2009) increase with discharge. The effect of precipitation-driven flows on downstream water quality 

can depend on the relative contributions of surface water delivered from upstream channels and ground 

water. Prairie streams typically are tied closely to ground-water sources (Section B.4.2.2), so the 

influence of headwaters can be especially pronounced during periods of high precipitation. Kemp and 

Dodds (2001) found that nitrate concentrations in fourth- and fifth-order lowland prairie reaches were 

lowest during periods of high precipitation, when more low-nitrate water was delivered downstream 

from second- and third-order reaches and high-nitrate ground-water influences were minimized. 

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B.4.3.2.2 Dissolved and particulate organic matter 

Differences in DOC inputs along the prairie stream longitudinal gradient provide further indirect 

evidence of chemical connections between prairie stream headwaters and downstream reaches.

McArthur et al. (1985b) isolated bacteria from stream sediments of grassland reaches and gallery forest 

reaches of a prairie stream and exposed them to leachates derived from grasses and bur oak (a common 

gallery forest species). Grassland bacteria only grew when provided with grass leachates as a carbon 

source, whereas gallery forest bacteria grew when provided with either grass or bur oak leachates. This 

finding suggests that either (1) grass-derived DOC-consuming bacteria are transported downstream and 

then coexist with bacteria consuming forest-derived DOC, or (2) grass-derived DOC is transported 

downstream, and local bacterial communities have adapted to use more refractory DOC exported from 

upstream reaches (McArthur et al., 1985b). 

Studies measuring POM exported from low-order prairie stream reaches show significant temporal and 

spatial variability. For example, Golladay (1997) documented little POM export from a third-order 

prairie stream in Kansas, whereas two prairie streams in Texas had much higher rates of POM transport 

(Hill and Gardner, 1987b). In part, these differences might reflect variability between stormflow and 

baseflow sampling, as organic matter concentrations can be positively correlated with stream discharge 

(Hill and Gardner, 1987b; Golladay, 1997). Whiles and Dodds (2002) examined seston (suspended fine 

particles) dynamics along the Kansas River drainage network (second- to eighth-order), and found that 

seston concentrations showed a significant positive relationship with stream size, increasing 

approximately 17-fold along the longitudinal gradient. This increase in seston was correlated with an 

increase in the taxa richness of filter-feeding invertebrates (Whiles and Dodds, 2002), illustrating that 

detrital transport along the stream gradient can influence invertebrate assemblages, which is a basic 

tenet of the River Continuum Concept (Vannote et al., 1980). 

Stagliano and Whiles (2002) found that the standing stock of fine particulate organic matter FPOM in a 

perennial reach of a tallgrass prairie stream was insufficient to support the annual secondary 

production (i.e., the rate of heterotrophic biomass formation) of collector-gatherers (Cummins and Klug, 

1979), the dominant group of macroinvertebrates feeding on deposited FPOM. The replenishment of 

FPOM standing stocks, at least in part from upstream sources via algal senescence, the transport and 

settlement of suspended POM, and the breakdown and transport of coarse POM, likely accounted for this 

apparent imbalance: Turnover of FPOM standing stocks was estimated to occur every 20 days (Stagliano 

and Whiles, 2002). Whiting et al. (2011) examined organic matter dynamics and trophic structure along 

a tallgrass prairie stream network (first- to fifth-order). They found that collector-filterers 

(macroinvertebrates that feed on suspended POM; Cummins and Klug, 1979) in upstream reaches 

consumed <1% of suspended POM flux; gatherers that feed on fine and very fine POM dominated 

secondary production in downstream reaches; and predators in downstream forested reaches 

consumed 107% of locally derived macroinvertebrate production. Predators in the upstream and 

middle reaches consumed 65% and 74% of available macroinvertebrate production, respectively. These 

findings support the idea that downstream secondary production depends in part on the export of 

Stream and Wetland Connectivity:

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energy sources (i.e., POM and invertebrates) from upstream reaches (in order for downstream 

predators to consume >100% of locally derived macroinvertebrate production).

As discussed earlier (Section B.4.2.4), prairie stream headwaters typically are open-canopied systems 

that receive little organic matter from terrestrial inputs, relative to forested headwaters (Jewell, 1927). 

Given the importance of autochthonous production in these systems, that algal-based contributions to 

prairie stream seston can be significant (Swanson and Bachmann, 1976; Hill and Gardner, 1987b; 

Lenhart et al., 2010) is not surprising. In four Iowa streams, export of chlorophyll a (a measure of algal 

biomass) was positively correlated with upstream channel bottom area, suggesting that downstream 

suspended algae originated as benthic algae in upstream portions of the network (Swanson and 

Bachmann, 1976). This downstream transport of algae also can provide colonists for downstream 

reaches after flooding or drying of stream channels. For example, Dodds et al. (1996b) examined the 

recovery of periphyton biomass upon channel rewetting in an intermittent prairie stream. Within 2 

weeks, chlorophyll had returned to maximum levels on rocks placed in the stream, even when the rocks 

had been treated and scrubbed to remove desiccation-resistant propagules; this finding suggests that 

algal colonists in this stream were transported downstream from permanent upstream pools (Dodds et 

al., 1996b). 

Coarse POM can connect prairie stream headwaters to downstream reaches. Johnson and Covich (1997)

examined detrital inputs along a second- to fifth-order prairie stream network in Oklahoma. They found 

that leaves in the stream originated from farther upstream than expected, with the percentage of whole 

leaves at a site best explained by riparian forest cover in reaches 500 and 1,000 m upstream. The 

percentage of leaf fragments >1 mm was best explained by downstream distance along the stream 

network (Johnson and Covich, 1997), suggesting increased processing and fragmentation of leaves as 

they move down the longitudinal gradient.

B.4.3.3 Biological Connections

B.4.3.3.1 Invertebrates 

Existing evidence for invertebrate-mediated biological connectivity along prairie stream networks 

mainly comes from studies of invertebrate assemblage recovery following flooding and drying in small 

prairie streams. Recovery from these disturbances tends to be relatively rapid, with substantial gains in 

invertebrate taxa richness and density observed within days to weeks (Miller and Golladay, 1996; Hax 

and Golladay, 1998; Fritz and Dodds, 2004), suggesting that these reaches are quickly repopulated by 

invertebrate drift from upstream sources, aerially dispersing adults, or disturbance-resistant survivors.

Fritz and Dodds (2002, 2004, 2005) examined postflooding and postdrying recovery of invertebrates in 

small intermittent and perennial prairie streams along an approximately 5-km stretch of Kings Creek in 

Kansas. They found that initial recovery of invertebrate taxa richness in intermittent reaches, and taxa 

richness of invertebrate drift and aerially colonizing insects, were negatively related to distance from 

upstream perennial water (Fritz and Dodds, 2002, 2004). Distance from upstream refuges, however, 

was not a significant predictor of invertebrate diversity measures across annual time scales (Fritz and 

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Dodds, 2005); they speculated that movement of water along the entire stream network (i.e., 

maintenance of hydrologic connectivity) makes proximity to colonists less important over longer time 

scales. These findings suggest that recovery from disturbance in these systems depends on biological 

connectivity via both downstream drift of colonizers and downstream (and potentially upstream) 

movement of aerially dispersing, egg-depositing adults (Miller and Golladay, 1996; Dodds et al., 2004). 

B.4.3.3.2 Fishes 

Research on fish assemblages in prairie streams provides perhaps the strongest and most well-studied 

evidence of biological connections throughout these networks. Much of this evidence focuses on two 

related aspects of the ecology of prairie stream fish: the dispersal and recruitment of pelagic-spawning 

prairie stream fish and the recovery of fish assemblages after disturbance, especially flooding and 

drying. 

Many prairie stream fish broadcast spawn nonadhesive, semibuoyant eggs, which develop (typically 

hatching within 1 to 2 days) as they are transported downstream with water flow (Cross and Moss, 

1987; Fausch and Bestgen, 1997; Platania and Altenbach, 1998; Durham and Wilde, 2006). The distance 

these eggs travel downstream depends on discharge and several other factors (e.g., development time); 

Platania and Altenbach (1998) estimated, however, that unimpeded eggs could travel as far as 144 km 

before 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. Without adequate water flow along 

sufficient lengths of the stream network, eggs can drop out of suspension before hatching (Platania and 

Altenbach, 1998; Durham and Wilde, 2006). Based on historical and contemporary fish surveys, eight 

species of pelagic-spawning cyprinids require a minimum length of greater than approximately 100 km 

(ranging from 103 to 297 km, depending on the species) of undisrupted stream channel (e.g., channels 

with no impoundments and no drying associated with human withdrawal) to support persistent 

populations (Perkin and Gido, 2011). 

This pelagic-spawning reproductive strategy also necessitates upstream movement by adult fish, if 

populations are to be maintained in small prairie streams (Fausch and Bestgen, 1997; Durham and 

Wilde, 2008). Prairie stream fishes generally are highly vagile, with adults capable of long-distance 

migrations. For example, individuals of one species of prairie fish (Hybognathus placitus) in the South 

Canadian River, NM were observed to move approximately 250 m upstream over a 15-minute period, 

illustrating that prairie fishes can move substantial distances over relatively short periods (Fausch and 

Bestgen, 1997). 

The effect that impoundment of prairie streams and rivers has had on the region’s native fish 

assemblages highlights the importance of hydrologic connectivity in these systems. Many studies have 

documented statistically significant associations between impoundment of prairie streams and loss of 

native fishes (Winston et al., 1991; Luttrell et al., 1999; Schrank et al., 2001; Falke and Gido, 2006; 

Matthews and Marsh-Matthews, 2007). For example, Schrank et al. (2001) found that, across 26 streams 

in the Flint Hills region of Kansas, sites from which Topeka shiners (Notropis topeka) had been 

extirpated had significantly more small impoundments on them and higher largemouth bass 

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A Review and Synthesis B-35 January 2015
(Micropterus salmoides) catch-per-unit-effort than sites at which the shiners were extant. Fewer studies 

have specifically examined the mechanisms by which impoundments affect these changes, although 

impoundments likely disrupt both the downstream transport of developing eggs and larvae (Platania 

and Altenbach, 1998) and the upstream and downstream movement of adult fish. 

Because many small prairie streams have intermittent flow, maintenance of fish populations often 

depends on dispersal out of intermittent reaches before drying occurs and recolonization of these 

habitats once water flow resumes—both of which require hydrologic connectivity along the stream 

network. Many fishes also require different habitats during different life stages, further necessitating 

hydrologic connectivity across these areas (Labbe and Fausch, 2000; Falke et al., 2010). 

For dispersal and recolonization to occur, fishes must be able to access refuge habitats under adverse 

conditions, and then expand into newly habitable areas once adverse conditions abate. Small, spring-fed 

prairie streams serve as key refuges for endemic prairie fishes (Hoagstrom et al., 2010), because they 

are ground water fed and maintain permanent pools that can provide habitat during periods of channel 

drying (Wohl et al., 2009). This ground-water influence also allows these spring-fed streams to provide 

refuge from adverse temperatures. For example, a spring-fed stream in Missouri had more stable 

temperatures than the mainstem river, with cooler summer and warmer winter temperatures; in winter, 

fish from the mainstem river moved into this habitat, where their food availability, growth, and average 

egg size were greater than those of fish that stayed in the mainstem (Peterson and Rabeni, 1996). 

During and after floods, juvenile and adult fishes can move upstream or downstream (or get displaced 

downstream) into newly available habitat (Fritz et al., 2002; Franssen et al., 2006). Once channels are 

rewetted, prairie stream fishes can move quickly into these previously unoccupied habitats (Harrell et 

al., 1967; Fritz et al., 2002; Franssen et al., 2006). For example, Harrell et al. (1967) examined fish 

response to channel drying in third- to sixth-order reaches of Otter Creek, an intermittent prairie stream 

in north-central Oklahoma, and found that most fish species collected after 8 months of flow prior to 

channel drying were already present 3 days after channel rewetting (Harrell et al., 1967). After a flood in 

an intermittent prairie stream in Kansas, fish dispersed into the headwaters from a perennial reach 

approximately 5 km downstream (Franssen et al., 2006). 

B.4.4 Prairie Streams: Synthesis and Implications

Prairie streams typically represent a collection of spring-fed, perennial pools and reaches, embedded 

within larger, intermittently flowing segments (Labbe and Fausch, 2000). Due to the region’s geographic 

location, substantial interannual variation in rainfall exists. Expansion (flooding) and contraction 

(drying) of these systems, particularly in terms of summer rainfall deficit (Borchert, 1950), determine 

the timing of hydrologic connectivity at any given time. Because of this temporal variability, connectivity 

in prairie river networks must be considered over relatively long time scales (multiple years). 

 Studies have demonstrated significant physical, chemical, and biological connections from 

prairie headwater streams to larger rivers, despite extensive alteration of historical prairie 

regions by agriculture, water impoundment, water withdrawals, and other human activities 

Stream and Wetland Connectivity:

A Review and Synthesis B-36 January 2015
(Matthews and Robinson, 1998; Dodds et al., 2004), and the challenges these alterations create 

for assessing connectivity.

 The most compelling evidence for connectivity along prairie river networks comes from 

examples of streams as sources of water via flood propagation (Matthai, 1969; Fritz and Dodds, 

2004, 2005), sources of contaminated sediment transport (Horowitz et al., 1988; Marron, 1989), 

sites of nutrient lags and transformation (Dodds et al., 1996a; Alexander et al., 2008), the 

downstream transport of prairie fish eggs and larvae (Platania and Altenbach, 1998; Perkin and 

Gido, 2011), and refuges for prairie fishes (Fausch and Bestgen, 1997; Franssen et al., 2006). 

 Impoundments for irrigation storage and flood control have altered flood magnitude, altered 

flow timing, and reduced flow variability and turbidity across the prairie regions (Cross and 

Moss, 1987; Hadley et al., 1987; Galat and Lipkin, 2000). The effect that impoundment of prairie 

streams and rivers has had on the regions’ native fish assemblages highlights the importance of 

hydrologic connectivity in these systems. Maintenance of fish populations often depends on 

dispersal out of intermittent reaches before drying occurs and recolonization of these habitats 

once water flow resumes―both of which require hydrologic connectivity along the stream 

network―and many fishes also require different habitats during different life stages (Labbe and 

Fausch, 2000; Falke et al., 2010). 

B.5 Case Study: Southwestern Intermittent and Ephemeral 

Streams 

B.5.1 Abstract

Ephemeral and intermittent streams are abundant in the arid and semiarid landscapes of the West and 

particularly the Southwest (Figure B-5.). These areas are characterized by low and highly variable 

precipitation where potential evapotranspiration exceeds precipitation. Based on the National 

Hydrography Dataset; 94%, 89%, 88%, and 79% of the streams in Arizona, Nevada, New Mexico, and 

Utah are intermittent or ephemeral (NHD, 2008). The heavily studied Upper San Pedro Basin in 

southeastern Arizona is discussed in detail because it is a well-understood example of the hydrologic 

behavior and connectivity of rivers common to the southwestern United States where ephemeral and 

intermittent tributaries comprise the majority of the basin’s stream reaches. Flows and floods from 

ephemeral and intermittent streams are also major drivers of the dynamic hydrology of the relatively 

few perennial reaches in the Southwest. These streams also supply water to mainstem alluvial aquifers 

and regional ground-water aquifers. Both alluvial and regional aquifers, in turn, supply baseflow to 

perennial mainstem stream reaches over extended periods (sometimes months) when little or no 

precipitation occurs. It is this baseflow and shallow ground water that supports the limited naturally 

occurring, vibrant riparian communities in the region. In addition, ephemeral streams export sediment, 

which contributes to shaping the fluvial geomorphology and alluvial aquifers of streams in the regions 

(Shaw and Cooper, 2008), and nutrients, which contribute to river productivity. Several studies found

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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 

(http://nhd.usgs.gov/). Lower: maps of mean precipitation and the precipitation coefficient of variation 

(equal to the standard deviation divided by the mean) of annual precipitation from 1895 to 2012. Note 

that the NHD might not accurately reflect the total extent of ephemeral or intermittent streams, as it 

does not include stream segments less than 1.6 km (1 mile) long, combines intermittent and 

ephemeral streams, and is based on 1:100,000-scale topographic maps.

that native fishes and invertebrates are well adapted to the variable flow regimes common in rivers of 

the Southwest and are heavily influenced by ephemeral tributary streams (Turner and List, 2007). 

B.5.2 Introduction

This case study addresses the hydrologic and ecological influence of ephemeral and intermittent 

streams on perennial or intermittent rivers in the arid and semiarid southwestern United States with 

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A Review and Synthesis B-38 January 2015
particular emphasis on Arizona and New Mexico. The structure of this case study differs slightly from 

the other case studies because of the uniquely thorough understanding of one particular southwestern 

river system, the San Pedro River, which has been the subject of a long-term research program 

(Goodrich et al., 2000; Stromberg and Tellman, 2009). Hence, evidence for the function and connectivity 

of ephemeral and intermittent tributaries to the San Pedro River is described in detail, and its 

application to other river systems in the Southwest is subsequently explored.

B.5.3 Southwestern Rivers 

Understanding the unique characteristics of southwestern American rivers is necessary to evaluate the 

connectivity and influence of ephemeral and intermittent streams on these rivers (Levick et al., 2008). 

Southwestern rivers differ in many ways from rivers in the humid eastern United States or in the 

Midwest and West. Southwestern rivers typically can be divided into two main types, particularly in the 

Basin and Range geologic province. The first type comprises rivers in the mountainous upper basins that 

receive more precipitation, often as snow, and the second type comprises those rivers located in the arid 

or semiarid plateau regions and valley plains dominated by ephemeral streams (Blinn and Poff, 2005). 

For example, more than 80% of the Gila River corridor in New Mexico and Arizona meanders through 

desert scrublands. Precipitation is seasonal. In summer, precipitation is strongly influenced by 

atmospheric moisture flowing from the Gulf of Mexico and the Gulf of California (Mexican monsoon), 

where local heating triggers high-intensity air-mass thunderstorms. In fall, tropical depressions, often

remnants of hurricanes, can bring infrequent but long-duration rainfall events; such storms are 

responsible for many of the larger floods in the region (Webb and Betancourt, 1992). Cyclonic storms 

from the Pacific Ocean, resulting in large frontal systems, dominate winter precipitation in the form of 

snow in higher elevations and typically as low-intensity rainfall in lower elevations (Blinn and Poff, 

2005). Figure B-6 illustrates the 2003 calendar year hydrograph from the White River near the Fort 

Apache USGS gaging station (upper) in east-central Arizona, and the San Pedro River near Tombstone, in 

southeastern Arizona (lower). Although the two gaging stations differ in elevation by less than 200 m, 

the watershed contributing to the White River is substantially larger and is higher in elevation than the 

San Pedro watershed, resulting in long-duration spring runoff from snowmelt. Monsoon-generated,

short-duration runoff dominates the San Pedro watershed but monsoonal influence also is apparent in 

the White River hydrograph. Runoff generated from late monsoon precipitation in September caused a 

major increase in discharge in the White River and a minor increase in the San Pedro. Most perennial 

and intermittent rivers in the Southwest are ground water dependent, flowing primarily in a baseflow 

regime and supported by discharge from a connected regional or alluvial aquifer or both. As discussed in 

more detail below, part of the baseflow is often sustained or augmented by slow drainage of a shallow 

alluvial aquifer from past flooding. In arid and semiarid regions, the riparian areas that perennial and 

intermittent streams support occupy a small percentage of the overall landscape but they host a 

disproportionately greater percentage of the biodiversity than the areas surrounding them (Goodrich et 

al., 2000; Stromberg et al., 2005). Reservoir construction, irrigation withdrawals, and the cumulative 

impacts of ground-water pumping have converted many historical, perennially flowing reaches into 

intermittently flowing reaches (Blinn and Poff, 2005). 

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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.

Abrupt changes in streamflow regimes (i.e., a change from perennial to intermittent or ephemeral and 

back again) can also result from underlying geology. Streams with abrupt changes are often referred to 

as interrupted streams (Meinzer, 1923; Hall and Steidl, 2007). A constriction and rise in bedrock geology 

can force regional ground water to the surface resulting in perennial flow while streamflow 

encountering highly fractured bedrock or a highly porous karst system can virtually disappear over very 

short distances. Another relatively abrupt transition in arid and semiarid stream hydrology and 

morphology occurs where steep mountain slopes transition into lower valley slopes. At this transition, 

watersheds with high sediment transport out of the mountainous portion often form alluvial fans. The 

stream channel system above the transition is typically dendritic and below the transition, the channel 

Jun

Jun

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A Review and Synthesis B-40 January 2015
system often becomes a diffusive set of shallow braided channels. Runoff over alluvial fans typically 

becomes less concentrated or confined to a single large channel but more diffuse and shallower turning 

into broad sections of sheet flow (Parker et al., 1998). The diffuse runoff is more likely to infiltrate into 

the alluvial fan. Very large flows may be required for runoff to cross the alluvial fan and connect to 

downstream waters.

Dominant hydrologic flowpaths vary with location within southwestern river basins. After climate and 

weather, recharge and infiltration mechanisms are the next most important factors determining the 

occurrence of ephemeral, intermittent, and perennial streams. Recharge over longer time scales 

(months to centuries) is essential to replenishing regional ground water and near-stream alluvial 

aquifers, which in turn are essential to maintaining baseflow in perennial streams. Primary recharge 

mechanisms include mountain block recharge, mountain front recharge, diffuse hillslope or interchannel 

recharge, and ephemeral channel recharge. Key advances brought forth in a recent synthesis of research 

on ground-water recharge in the southwestern and western United States include (1) desert vegetation 

effectively eliminates diffuse recharge in most areas of the basin floor; (2) ephemeral channel recharge 

can be very important in wet years and greatly dominates recharge in basin-floor environments; and 

(3) environmental tracers are now available to “fingerprint the sources and amounts of ground-water 

recharge at the basin scale” (Phillips et al., 2004). 

Mountains with deeper soils or those consisting of fractured rock will have higher infiltration capacities, 

less frequent occurrences of overland flow, and serve as recharge areas for regional ground water

(Wilson and Guan, 2004; Blasch and Bryson, 2007; Wahi et al., 2008). Mountains with shallow soils and 

more consolidated rock will shed stormflow and shallow ground water off the mountain block onto the 

valley, which often consists of deep alluvium, particularly in the basin and range geologic province. This 

area is where mountain-front recharge occurs. High-elevation perennial streams often become 

intermittent or ephemeral at this transition, with their downstream disappearance of surface flow 

dependent on the flow rates coming off the mountain block and the permeability of the valley alluvium 

into which they enter. During periods of high flow, they can reconnect with other perennial stream 

reaches maintained by ground-water flow (Blinn and Poff, 2005; Blasch and Bryson, 2007; Yuan and 

Miyamoto, 2008). 

Runoff generation in arid and semiarid valley floors and lowlands where basin alluvium is relatively 

porous and deep is dominated by the infiltration-excess mechanism in which precipitation rates exceed 

infiltration rates. In the arid and semiarid Southwest, high-intensity convective thunderstorms typically 

trigger this situation. Generally, such storms are relatively short in duration, resulting in ephemeral 

flows with short runoff duration (Goodrich et al., 1997). As water flows down dry ephemeral channels, it 

infiltrates the channel bottom and sides (i.e., channel transmission losses occur) where channel 

substrate is porous. If restricting soil or geologic layers underlying the channel do not substantially 

inhibit downward motion, channel transmission losses will recharge either the regional or alluvial 

ground water (Tang et al., 2001; Constantz et al., 2002; Harrington et al., 2002; Goodrich et al., 2004; 

Coes and Pool, 2005; Vivoni et al., 2006; Blasch and Bryson, 2007). In this influent stream environment 

typical of many southwestern streams, the volume of transmission water losses in ephemeral channels 

Stream and Wetland Connectivity:

A Review and Synthesis B-41 January 2015
increases as watershed size increases, resulting in a losing stream environment as opposed to a gaining 

stream environment encountered in wetter hydroclimatic regimes (Goodrich et al., 1997). As noted 

above and discussed in Phillips et al. (2004), these ephemeral tributary channels are the dominant 

source of recharge in valley floors, and at the basin scale they can provide substantial recharge during 

wet years. Typically, as stream drainage area increases, the alluviums under and next to streams begin 

to serve as important shallow aquifers that receive and store streamflow infiltration during hydrologic 

events and sustain baseflow and riparian communities between storms (Stromberg et al., 2005; Baillie 

et al., 2007; Dickinson et al., 2010). 

The magnitude of aquifer recharge is highly temporally variable in the Southwest. Winter precipitation, 

which has a predominant effect on mountain-block and mountain-front recharge in the Arizona-New 

Mexico portion of the Southwest, is correlated with the El Niño/Southern Oscillation (Woolhiser et al., 

1993) at interannual time scales. Over decadal climate cycles, winter precipitation also is related to the 

Pacific Decadal Oscillation (Pool, 2005). The magnitude of ephemeral channel recharge varies widely 

from year to year, depending on the strength of the monsoon season (Goodrich et al., 2004) and the 

occurrence of relatively infrequent and prolonged precipitation events resulting from tropical 

depressions. Floods and large runoff events caused by any of these mechanisms can have a long-lasting 

influence (6 to 10 months) on baseflow of southwestern rivers by recharging near-stream alluvial 

aquifers and thereby sustaining streamflow as they drain (Brooks and Lemon, 2007). 

B.5.4 San Pedro River 

B.5.4.1 Basin Characteristics

Because of a rich research and long-term monitoring history, the San Pedro Basin and River in 

southeastern Arizona represents an excellent case study of the hydrologic behavior and connectivity of 

southwestern rivers (Goodrich et al., 2000; Stromberg and Tellman, 2009; Brookshire et al., 2010). The 

San Pedro River originates in Mexico, flowing undammed north to its confluence with the Gila River. The 

San Pedro is the only significant un-impounded river in Arizona and the last remaining stream in 

southern Arizona with long perennial reaches (Figure B-7; Kennedy and Gungle, 2010). Most tributaries 

to the river are ephemeral at their confluence with the mainstem. The river basin, located in the Basin 

and Range Province, has a valley that is generally 30−50 km wide, comprising sedimentary fill deposits, 

and slopes upward from the river to mountains with elevation ranging from 2,000 to 2,900 m. The San 

Pedro Basin consists of 93% nonperennial reaches (including ephemeral and intermittent), 6.3% 

artificial path (canals, diversions, pipeline, connectors), and 0.7% perennial reaches in the U.S. portion of 

the basin as derived from the USGS NHD1 (Figure B-8). The percentage of streams types is not static but 

varies from year-to-year. The Nature Conservancy and its partners annually map the wet and dry 

reaches along the San Pedro mainstem and several large tributary streams since 2007 

1

Based on USGS National Hydrography Dataset (NHD) stream map (http://nhd.usgs.gov/). Note that the NHD 

might not reflect the total extent of ephemeral or intermittent streams accurately, as it does not include stream 

segments less than 1.6 km (1 mile) long, combines intermittent and ephemeral streams, and is based on 

1:100,000-scale topographic maps.

Stream and Wetland Connectivity:

A Review and Synthesis B-42 January 2015

 
Figure B-7. San Pedro River basin map showing major physiographic features and current and 

historical perennial reaches. From Levick et al. (2008), courtesy of The Nature Conservancy, Arizona.

Available online at 

http://azconservation.org/map_gallery/current_and_formerly_perennial_san_pedro_river_surface_water. 

(Turner and Richter, 2011). The wet-dry mapping is conducted roughly in the middle June, historically 

the time of lowest streamflow, prior to the onset of the monsoon. For 2014, about 25% (54.1 km) of the 

214 km surveyed were found to be wet (214 km is ~1.1% of the stream length plotted in Figure B-8). 

Stream and Wetland Connectivity:

A Review and Synthesis B-43 January 2015
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/).

The wet-dry survey data is accessible at:

(http://azconservation.org/downloads/category/san_pedro_river). 

Annual precipitation within the basin ranges from 300 to 750 mm with highest amounts occurring in the 

mountains. Vegetation includes desert scrub, grasslands, oak woodland savannah, mesquite woodland, 

riparian forest, coniferous forest, and agriculture (Kepner et al., 2000; Kepner et al., 2004). Brush and 

grasses typical of southwestern semiarid landscapes (Goodrich et al., 1997) dominate the valley floor 

vegetation. 

Nonperennial

Perennial

Stream and Wetland Connectivity:

A Review and Synthesis B-44 January 2015
At the Walnut Gulch Experimental Watershed (WGEW―a subwatershed of the San Pedro watershed 

near Tombstone, Arizona), operated by U.S. Department of Agriculture, Agricultural Research Service 

(USDA-ARS), approximately two-thirds of the annual precipitation on the watershed occurs as highintensity, convective thunderstorms of limited aerial extent (Goodrich et al., 1997). Winter rains (and 

occasional snows) are generally low-intensity events associated with slow-moving cold fronts and are 

typically of greater aerial extent than summer rains. Runoff on the lower elevations of the WGEW is 

generated almost exclusively from convective storms during the summer monsoon season via 

infiltration excess that produces overland flow. The hydrogeology of the San Pedro River basin is typical 

of many alluvial basins in the Southwest (Dickinson et al., 2010). Ground water flows through the basinfill aquifer (regional aquifer) from recharge areas near the mountains and beneath ephemeral 

tributaries to perennial reaches of the San Pedro River (Wahi et al., 2008; Dickinson et al., 2010). A 

narrow band of highly permeable stream alluvium is incised into the basin-fill along the major stream 

channels (Figure B-9). The stream and floodplain alluvium is an important alluvial aquifer that receives 

discharge from the basin-fill aquifer and streamflow via streambank infiltration occurring during high 

stream stages. 

This bank and alluvial aquifer storage supports riparian vegetation during periods lacking runoff 

(Dickinson et al., 2010). The San Pedro River network with associated shallow alluvial aquifers 

(mainstem and portions of some tributaries) supports extensive riparian vegetation communities 

(Stromberg et al., 2005) that provide habitat for more than 350 species of birds, 80 species of mammals, 

and 40 species of reptiles and amphibians (Kennedy and Gungle, 2010). Alluvial aquifers also are zones 

of extensive hyporheic exchange (Stanford and Ward, 1988; Fernald et al., 2001). 

Figure B-9. Generalized east-west section and stratigraphic units in the middle San Pedro watershed.

From Dickinson et al. (2010). 

B.5.4.2 Ephemeral Stream Connections and Their Influence on the San Pedro River 

Overland runoff generation and associated ephemeral streamflow is common in San Pedro tributary 

streams. Goodrich et al. (1997) examined hundreds of hydrologic events in different-sized catchments at 

the USDA-ARS WGEW and found that the relationship between watershed area and runoff volume was 

Stream and Wetland Connectivity:

A Review and Synthesis B-45 January 2015
increasingly nonlinear as drainage area increased. The authors found a critical threshold watershed area 

of approximately 36−60 ha, at which runoff responses became much less linear and channel 

transmission losses increased more rapidly with increasing watershed area. This relationship is very 

different from commonly observed relationships in humid streams of the East, where runoff generally is 

proportional to watershed area (Section 3.3.1). Two reasons for this variability in runoff produced per 

unit watershed area are: (1) the spatial variability and limited spatial extent of runoff producing 

precipitation, and (2) the loss of runoff by infiltration into the bed of ephemeral channels (transmission 

losses). Figure B-10 illustrates this process. During a major rainstorm on 17 August 2006, most of the 

precipitation from multiple air-mass thunderstorm cells occurred over relatively localized areas in the 

upper and lower portions of the USDA WGEW. As overland flow occurred and became concentrated in 

the ephemeral tributary network, streamflow dramatically diminished as the runoff hydrograph 

traveled downstream through the channel network. However, a substantial amount of runoff from this 

storm traversed the ephemeral Walnut Gulch tributary and reached the mainstem of the San Pedro 

River, augmenting the flow as measured at the USGS Tombstone stream gage. Runoff in Walnut Gulch 

(149 km2 drainage area) and many arid and semiarid streams is characterized by short duration, highly 

episodic flows. The longitudinal extent of the effects of these flows on downstream waters is a function 

of the flow magnitude, its duration, the depth, conductivity and antecedent moisture conditions of the 

ephemeral channel substrate that the runoff flows across, and the depth to ground water. For example, 

in 2006 there were 23 runoff flows measured at Walnut Gulch flume 1 (the outlet of the WGEW). The 

average volume, peak runoff rate, and duration of these runoff events was 31,460 m3, 7.23 m3/s, and 

239 minutes, respectively. Four (4) of the 23 runoff events recorded at Flume 1 were estimated to have 

measureable impacts on flows measured at the downstream USGS Tombstone stream gage (4510 km2) 

on the San Pedro River (including the event shown in Figure B-10).

Evidence is strong that transmission losses in ephemeral tributary streams recharge alluvial and 

regional aquifers (Goodrich et al., 1997; Callegary et al., 2007). Using three fundamental approaches to 

estimate ephemeral channel recharge (1—closing the water balance for the channel reach, 2—

measuring changes in ground-water volume directly [well levels] or indirectly [microgravity], and 3—

using geochemical tracers), Goodrich et al. (2004) estimated that during the relatively wet 1999 and 

2000 monsoon seasons, regional aquifer ground-water recharge from ephemeral streams ranged from 

approximately 15 to 40% of total average annual recharge as estimated from a calibrated regional 

ground-water model (Pool and Dickinson, 2007). During the dry monsoon seasons of 2001 and 2002, 

limited ephemeral runoff and stream channel infiltration occurred, but no discernible deep aquifer 

recharge was detected.

The influence of stormflows from ephemeral tributary streams extends to the San Pedro River 

mainstem. As stormflow is exported from the tributaries to the mainstem and water moves 

downstream, transmission losses and bank recharge occur within the mainstem river itself and supply 

water to the alluvial aquifer of the mainstem (Kennedy and Gungle, 2010). Using geochemical tracers 

(chloride, sulfate, and stable isotopes of hydrogen and oxygen in water), Baillie et al. (2007) found two 

main sources of water in the alluvial aquifer for the upper San Pedro River: (1) regional ground water 

Stream and Wetland Connectivity:

A Review and Synthesis B-46 January 2015
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. Inset 

photos show a typical air-mass thunderstorm and the front of surface flow progressing down an 

ephemeral channel. Photo of ephemeral stream from Levick et al. (2008). 

recharged along the Huachuca Mountains (mountain block, mountain front) to the west, and (2) local 

recharge from monsoon floodwaters. Alluvial ground-water composition varied between gaining and 

losing reaches. Locally recharged floodwater comprised 60 to 85% of the alluvial ground water in losing 

reaches but only 10 to 40% in gaining reaches. Baseflow also contained a significant component of 

monsoon floodwater throughout the year, from 80% in upstream reaches to 55% after passing through 

several gaining reaches. 

Ephemeral tributary stormflows are also sources of sediment and alluvium for the main San Pedro 

River. Only the largest, less frequent events can flush sediment completely through ephemeral 

tributaries (Lane et al., 1997). For example, a reach-scale study in the WGEW estimated sand transport 

distances of only 401 and 734 m in nine floods over two consecutive years (Powell et al., 2007). In 

another study, Lekach et al. (1992) found that more than 90% of the bedload yield originated from the 

mid-watershed channels during larger runoff events from an arid watershed in Israel. Ephemeral 

tributary stormflows and their associated sediment loads influence the character of river floodplains 

and alluvial aquifers (Nanson and Croke, 1992; Shaw and Cooper, 2008). 

Extensive riparian plant communities along the mainstem San Pedro River depend on the availability of 

water in the alluvial aquifer along the river, including water derived from ephemeral stream stormflows 

(Stromberg et al., 2005; Baillie et al., 2007). These riparian areas, in turn, strongly influence river 

Aug. 17, 2006 

Stream and Wetland Connectivity:

A Review and Synthesis B-47 January 2015
attributes through stream shading, channel stabilization, nutrient cycling, inputs of invertebrates and 

other organisms, and inputs of detritus, wood, and other materials (Gregory et al., 1991; National 

Research Council, 2002; Naiman et al., 2005). 

Ephemeral tributary stormflow inputs heavily influence the nutrient and biogeochemical status of the 

San Pedro River. Brooks and Lemon (2007) performed synoptic sampling on a 95-km reach of the San 

Pedro River to identify the effects of regional hydrology and land use on dissolved carbon and nitrogen 

concentrations. They found that, during the summer monsoon season, baseflow increased 5- to 10-fold, 

and dissolved organic matter and inorganic nitrogen increased 2- to 10-fold. The fluorescence index of 

water samples indicated a large input of terrestrial solutes with the onset of monsoon runoff inflows, 

and values of both chloride and oxygen isotope tracers indicated that stream water and alluvial ground 

water were well mixed along the entire 95-km reach. Meixner et al. (2007) used chloride tracer samples 

and mixing analyses to examine sources of San Pedro River water during six summer floods in 2001 

(wet year) and 2002 (dry year). Results of mixing models indicated that both a ground water-soil water 

end-member and a precipitation end-member (indicative of overland flow) contributed to the floods.

The highest percentage of ground water-soil water in the flood flow (46%) occurred during an early 

2001 flood and the lowest during large monsoonal floods of 2002. They noted that ground water

probably made lower contributions than soil water to streamflow, because high river stage during flood 

events created hydraulic gradients from the river to alluvial ground water in the riparian area (water 

moved from the river to alluvial ground water via bank storage, Figure 2-13B). During the first floods of 

each year, nitrate and dissolved organic carbon increased dramatically in the river, whereas dissolved 

organic nitrogen did not exhibit increases in 2001 but did in 2002. During floods, nitrate-nitrogen (NO3-

N) concentrations in river water were 0.2−0.5 mg NO3-N L−1 higher in 2002 than during 2001. This 

result was consistent with higher observed nitrate-nitrogen concentrations in soil water of the riparian 

zone (alluvial aquifer) in 2002 than in 2001. 

In summary, ephemeral tributary streams have strong physical and chemical connections to the San 

Pedro River. The river ecosystem, including its abiotic and biotic components, depends on the influences 

exerted by the ephemeral tributary streams on the river environment. 

B.5.5 Other Southwestern Rivers 

B.5.5.1 Physical Connections

Hydrologic behavior and river-system connectivity similar to the San Pedro River have been observed in 

other southwestern rivers, increasing confidence that the observations made within the San Pedro are 

applicable to other southwestern river systems.

Plummer et al. (2004) found that the Rio Grande in New Mexico has two primary sources of regional 

ground water: (1) recharge from mountains and (2) seepage from the Rio Grande and Rio Puerco, and 

from Abo and Tijera Arroyos (arroyos are ephemeral streams). Vivoni et al. (2006) observed groundwater recharge processes in the Rio Puerco, a tributary river to the Rio Grande, and in the Rio Grande 

itself. They note that a summer monsoonal rainstorm produced a flood event on the Rio Puerco that, in 

Stream and Wetland Connectivity:

A Review and Synthesis B-48 January 2015
turn, generated a pulse of floodwaters along a losing reach of the Rio Grande (Figure 3-2). Forty-nine

percent (49%) of flood volume was lost to the shallow alluvial aquifer of the Rio Grande. Loss of river 

water to the alluvial aquifer was observed to decrease with distance down the river reach. 

Another important drainage basin type in the western and southwestern United States is endorheic or 

closed drainage basins draining to lakes and playas having no outlet to the ocean. The largest of these 

western basins is the Great Basin, which is approximately 490,000 km2 (~5% of the area of the United 

States) and covers most of Nevada and parts of Oregon, Utah, and California (Atwood, 1994). Closed 

basins can contain ephemeral, intermittent, and perennial stream reaches. Although endorheic streams 

do not drain into oceans, many support downstream waters and habitat and numerous large perennial 

lakes such as Lake Tahoe in California and Nevada and the Great Salt Lake in Utah.

The Pecos River basin in eastern New Mexico and western Texas comprises part of southern Rocky 

Mountains in the north and grasslands, irrigated farmlands, deserts, and deep canyons in the southern 

lower reaches of the river (Yuan and Miyamoto, 2008). Precipitation occurs as snow in the mountains 

and summer monsoonal rainfall in the lower river valley. Based on hydrogen and oxygen isotope 

composition of river water, Yuan and Miyamoto (2008) separated the river basin into three subbasins: 

(1) the upper basin, (2) the middle basin, and (3) the lower basin. Snowmelt dominates the mountainous 

upper basin. The river in the topographically gentle middle basin had mixed sources of water. Thirtythree percent (33%) of river water was lost through evaporation occurring in the streams channels and 

irrigated fields of the middle basin. Similar to the San Pedro River, up to 85% of streamflow in the lower 

basin was estimated to derive from local freshwater sources, mainly monsoonal rainfall. This finding is 

consistent with significant contributions of flow from ephemeral tributary streams. 

Shaw and Cooper (2008) studied the 14 ephemeral stream reaches in the Little Colorado River Basin in 

northeastern Arizona. As derived from the USGS National Hydrography Dataset, this basin contains a 

lower percentage of ephemeral and intermittent stream reaches (70%) as compared to the ~93% of 

such reaches in the Upper San Pedro. Shaw and Cooper (2008) related watershed characteristics of the 

Little Colorado to downstream reaches and the riparian plant communities of those reaches. They found 

that, as the watershed area draining to the studied reaches increased, the overall basin channel slope 

deceased, which resulted in less erosive capacity due to channel transmission losses and a decrease in 

the variability of alluvial ground water in these channels. This resulted in “decreased disturbance 

potential and increased moisture availability in the downstream direction,” and these reaches had a 

greater abundance of obligate riparian vegetation. Shaw and Cooper (2008) went on to develop a stream 

classification system that related the functional linkages between contributing upstream watersheds, 

stream reaches, and riparian plant ecology. Type I stream reaches have relatively small drainage areas 

(less than 10 km2), which have the greatest disturbance potential with in-channel and near-channel 

plants resembling those of surrounding upland species. Between 10 and 100 km2, Type II streams 

exhibit “more moderate shear stresses and more persistent alluvial groundwater” with riparian 

vegetation that is a mixture of upland and riparian species. Having larger areas (greater than 100 km2), 

Type III reaches are “controlled mainly by upstream hydro-climatic conditions” with wetland tree and 

shrub communities. Shaw and Cooper (2008) concluded that the connection of streamflow and groundStream and Wetland Connectivity:

A Review and Synthesis B-49 January 2015
water regimes to riparian vegetation in the larger Type III watersheds, draining greater than 100 km2, to 

upstream reaches far removed from larger regional floodplain rivers “... were driven by climatic 

patterns from distant portions of the upper watershed and were relatively insensitive to local rainfall.” 

This finding reinforces the fact that stream-reach characteristics are influenced and connected, often 

episodically, to distant portions of the contributing watershed. 

B.5.5.2 Human Alterations

Anthropogenic uses and activities on arid and semiarid landscapes can have significant effects—both 

good and bad—on downstream waters and overall health of watersheds. Human alteration to arid and 

semiarid watersheds occurs in many forms and includes livestock grazing, land clearing, mining, timber 

harvesting, ground-water withdrawal, streamflow diversion for water supply and irrigation, 

channelization, urbanization, agriculture, roads and road construction, off-road vehicle use, camping, 

hiking, and vegetation conversion (Levick et al., 2008). Climate change likely will have increasing 

influence on streams and their connectivity in the Southwest. Most climate models predict important 

changes for the southwestern United States, including increased warming and drying, intensification of 

droughts, and increased variability of precipitation (Seager et al., 2007). These changes will result in less 

runoff, reduced snowpack, and changes in streamflow patterns. Reduced snowpack will result in shorter 

periods of longitudinal stream connectivity in intermittent streams, as snowmelt will occur more rapidly 

in a warmer climate.

Streamflow augmentation can occur in human-dominated watersheds in the form of treated municipal 

and industrial wastewater effluent discharges. Streams that would dry without these discharges are

effluent-dependent streams, whereas those that receive most, but not all, of their flow from effluent are 

effluent-dominated streams (Brooks et al., 2006). Streams draining human-dominated areas also can 

acquire baseflow from ground water recharged by over-irrigation and leaky infrastructure (Lerner, 

1986; Roach et al., 2008; Townsend-Small et al., 2013). 

Riparian areas near mainly perennial streams, but also in many cases intermittent streams, historically 

have been attractive for human development, leading to their alteration on a scale similar to that of 

wetlands degradation nationally (National Research Council, 2002). This situation is especially true in 

arid and semiarid regions because riparian areas typically are indicative of water availability either as 

surface water or as shallow ground water. Riparian areas in arid and semiarid regions are also greener 

and cooler than most upland areas. Riparian areas are more sensitive to development impacts than 

wetter areas, however, because of their limited geographical extent, drier hydrologic characteristics, and 

fragile nature (e.g., erodible soils). Historically, riparian habitats represented about 1% of the landscape 

in the West, and within the past 100 years, an estimated 95% of this habitat has been lost due to a wide 

variety of land-use practices such as river channelization, unmanaged livestock grazing, agricultural 

clearing, water impoundments, and urbanization. The following subsections present some of the types 

of human-caused impacts on ephemeral and intermittent streams and their associated riparian areas.

Stream and Wetland Connectivity:

A Review and Synthesis B-50 January 2015
B.5.5.2.1 Land development

Land development includes urban, suburban, and exurban development but is referred to here 

collectively as urban development. Before the 2008 recession, the Southwest was one of the fastest 

growing regions of the United States, having an increase in population of approximately 1,500% over 

the previous 90 years. In contrast, the population of the country as a whole grew by just 225% over that 

time. Arizona and Nevada have grown the most, with population increases of 2,880% and 2,840%, 

respectively. Typical urban development significantly changes the hydrologic characteristics of a 

watershed by covering uplands with impervious surfaces, and removal, channelization, or armoring of 

headwater streams (Box 3-1; Kennedy et al., 2013). Alteration of the natural stream network disrupts 

natural flow patterns and sediment transport and storage, resulting in downstream flooding and 

changes to the clarity and quality of the downstream flows and receiving waters. These effects can 

damage downstream water supplies and habitat. The aerial photograph presented in Figure B-11 shows 

a network of ephemeral streams that flows through a small community southeast of Tucson, AZ, to 

Cienega Creek, a protected perennial stream.

Figure B-11. Aerial photograph showing ephemeral tributaries to Cienega Creek, a perennial stream, 

flowing through the small community of Vail, southeast of Tucson, AZ. Photograph: Lainie 

Levick/Aerial flight courtesy of Lighthawk, www.lighthawk.org.

The impact of urbanization increases as the percentage of impermeable surface increases. Various 

studies have shown that semiarid stream systems become irreparably impaired once the impervious 

surfaces within the watershed exceed about 10% and experience dramatic morphological changes once 

those surfaces exceed about 20% (Schueler, 1994; Miltner et al., 2004). 

As the amount of impervious surface increases, runoff increases and infiltration decreases (Kennedy et 

al., 2013), starting a chain of events that includes flooding, erosion, stream-channel alteration, increases 

in human-caused pollutants, and ecological damage. Floods become more severe and more frequent, and 

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A Review and Synthesis B-51 January 2015
peak flows and runoff volumes will be many times greater than in natural basins. The greater volume 

and intensity of flooding causes increased erosion and sediment transport downstream. To 

accommodate the increased flow and sediment load, streams in urbanized areas tend to become deeper 

and straighter over time. The resulting bank erosion can destroy established streamside habitat and tree 

cover, leading to higher temperatures, sedimentation, and disruption of wildlife corridors.

Storm sewers and lined drainages increase the rate of water delivery to the downstream channel 

network. Erosion and sedimentation increases during construction and road building for new urban 

areas. Improperly constructed and maintained roads, especially unpaved roads, can alter hillslope 

drainage, and change baseflow and precipitation-runoff relationships, causing erosion and 

sedimentation in streams (USDA, 2002). The primary geomorphic consequence of these hydrologic 

changes is the erosional entrenchment of nearby channels and associated transportation of the 

excavated sediment downstream, causing a significant increase in sediment load. Sediment is of 

particular concern in arid and semiarid regions because many other pollutants tend to adhere to eroded 

soil particles. Additional pollutants from urban runoff can include pathogens, nutrients, toxic 

contaminants, sediment, and debris. Consequently, urban areas require stormwater management plans 

both during and after construction to control runoff and offsite pollution.

Streams are channelized in urbanizing areas to protect private property and control streambank 

erosion. Channelization typically straightens and steepens the stream, however, resulting in increased 

flow velocity and sediment movement. These changes transfer flooding and bank erosion downstream 

of the protected area. In the channelized reaches, the greatly reduced out-of-bank flow disrupts water, 

sediment, organic matter, and nutrient enrichment of the flood plain (National Research Council, 2002). 

In addition, removal of vegetation as part of the channelization process degrades wildlife habitat.

Habitat fragmentation is a common consequence of urbanization (Hilty et al., 2006). New developments 

can alter large areas of land, removing natural drainage systems and wildlife habitat, and replacing them 

with houses and roads. Altering, bisecting, or channelizing streams effectively can eliminate the main 

biological functions of the stream channel by disrupting vegetation communities and hydrologic 

function. Habitat fragmentation reduces wildlife diversity and abundance and might cause sensitive 

species to disappear (England and Laudenslayer, 1995). 

B.5.5.2.2 Land use

In addition to urbanization, agriculture (livestock and crops) and mining, including sand and gravel 

operations, are major land uses in the desert Southwest. Livestock grazing is one of the more common 

uses of rural land in the Southwest. Late 1800s estimates of cattle numbers in Arizona and New Mexico 

exceeded 1.5 million and 2 million, respectively. During this period, the region experienced both 

significant droughts and floods. During drought, the resulting desiccation of the uplands drove cattle to 

the riparian areas, which were heavily damaged as a result. When the rains returned to the denuded 

landscape, erosive processes were greatly enhanced. The overgrazing that occurred during this time is 

one of the factors attributed to a relatively widespread period of channel downcutting, forming deep 

arroyos and lowering ground-water levels (Schumm and Hadley, 1957; Hastings, 1959; Graf, 1988). 

Stream and Wetland Connectivity:

A Review and Synthesis B-52 January 2015
In modern grazing-land management, livestock are provided with watering sources away from streams 

when possible, but frequently they must depend on the streams for water. Livestock management 

efforts attempt to avoid overuse of an area, but because water is scarce in arid environments, cattle and 

wildlife tend to linger near water sources. Where not properly managed, cattle can remain too long in a 

riparian area and trample streambanks, eat the riparian vegetation to the ground, contaminate the 

water with wastes, and compact the soil (Levick et al., 2008). Several literature sources have stressed 

that the cumulative impacts of unmanaged livestock in southwestern riparian ecosystems for the past 

several hundred years probably have been the single most important factor in riparian ecosystem 

degradation (Wagner, 1978; Ohmart, 1995). 

Mining is another activity that historically has played a large role in the economy and land use in the 

Southwest. Some of the largest copper and gold mines in the world are found in this region, and some 

cover many thousands of hectares. Mining can cause major impacts on riparian areas along tributaries 

and downstream waters by altering the local hydrology. Mining not only dewaters the area, it removes 

vegetation and soil and changes the topography, severely affecting the watershed. Instream and 

floodplain gravel mining can alter channel dimensions, increase sediment yield, and increase fine 

sediment loading and deposition that can reduce infiltration into ephemeral channels (Bull and Scott, 

1974). 

Cultivated agriculture has had a long history in the southwestern deserts, and areas such as the Central 

Valley in California provide much of the country’s food supply. Most crops, however, must be irrigated 

due to the low annual rainfall. Impacts to local hydrology from agricultural activities include (Levick et 

al., 2008): 

 Increased salinity caused by clearing of native vegetation that raises the ground-water 

reservoir;

 Reduced flows from ground-water pumping or stream diversions for irrigation;

 Increased nutrients and turbidity from the use of fertilizers that run off into the streams across 

the land surface or through the soil, causing excessive algal growth; and

 Fish, aquatic invertebrate, and bird kills from pesticides that run off into the streams or leach 

into the ground water.

Due to the abundant solar resources in the arid and semiarid Southwest, numerous, large-scale solar 

energy projects are envisioned or already under development. O'Connor et al. (2014) note that 

development of solar energy zones will significantly affect ephemeral channel systems; the authors have 

developed a scoring system to conduct ephemeral stream assessments using publicly available 

geospatial data and high-resolution aerial imagery.

B.5.5.2.3 Water resources impacts

The Southwest has experienced rapid growth over the past several decades. This growth can be 

sustained only with reliable water supplies. Lack of surface-water flows has placed increased reliance on 

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A Review and Synthesis B-53 January 2015
ground water for human and agricultural uses. The percentage of population dependent on ground 

water for domestic water needs in New Mexico, Arizona, and California is 90%, 60%, and 45% 

respectively (Anderson and Woosley, 2005). When ground-water pumping is sufficiently large or 

prolonged, it can result in lower water-table levels in regional and alluvial aquifers. If these aquifers are 

a primary source of water for sustaining surface-water flow in perennial or intermittent streams and if 

the drop in aquifer water levels is large enough, the pumping can effectively dewater these stream 

reaches, severing longitudinal and vertical connectivity (Winter et al., 1998; Scanlon et al., 2012). The 

perennial and intermittent streams effectively become ephemeral streams, and the habitat supported by 

reliable surface flow or shallow ground water is lost (Stromberg et al., 1996). 

The impact of aquifer water-level declines is illustrated in Figure B-12 with repeat photography of the 

Santa Cruz River south of Tucson from 1942 and 1989 showing changes in riparian vegetation. Tucson’s 

population in 1940 was roughly 36,000 and increased to approximately 405,000 by 1990. Until the 

Central Arizona Project brought Colorado River water to Tucson in the early 1990s, Tucson’s domestic 

water supply was solely provided by ground water. As ground-water pumping increased to supply the 

growing population, the aquifer water level dropped by more than 25 meters and the riparian habitat 

was completely altered, as all phreatophytic vegetation died out. The growing population of Tucson also 

resulted in proportional increases in discharge of treated effluent. Portions of the Santa Cruz River 

downstream of the reach photographed in Figure B-12 near treatment plant outfalls are now effluentdependent perennial stream reaches. Depending on the level of treatment, effluent can have various 

effects on the stream ecosystem (Brooks et al., 2006). Without careful water management and reuse 

(Bischel et al., 2013), the benefits of baseflow augmentation can be overshadowed by potential risks, 

such as increased contaminant and pathogen exposures (Jackson and Pringle, 2010). 

Dams and retention or detention basins frequently are used to store water or as flood-control devices in 

the Southwest. They disrupt natural surface flow and sediment transport, interfere with natural 

geomorphic processes, alter water temperatures, and fragment the natural stream systems both 

upstream and downstream of the structure (Williams and Wolman, 1984). Upstream locations can 

experience flooding, whereas downstream locations can be dewatered and become starved of sediment 

(Sections 2.4.4 and 3.3.2).

Stream and Wetland Connectivity:

A Review and Synthesis B-54 January 2015
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. Photographs of the Santa Cruz River looking south from 

Tucson, AZ, provided by Robert H. Webb, U.S. Geological Survey Anderson and Woosley (2005).

B.5.5.3 Biological Connections

Much of the material in this section, as in Section B.5.5.2, is derived from the material presented in 

Levick et al. (2008). As noted in Chapter 3, ephemeral and intermittent streams perform many of the 

same functions in a watershed as perennial streams. In particular, in arid and semiarid regions, riparian 

areas, including those near ephemeral and intermittent streams, support the vast majority of wildlife 

species, are the predominant sites of woody vegetation including trees, and surround what are often the 

only available surface-water sources, even if they are available only for limited periods. Desert washes 

are easily recognizable by their dense corridors of vegetation that strongly contrast with the more 

sparsely vegetated uplands (Figure B-13). In contrast to the nearby uplands, these stream corridors and 

their associated vegetation communities provide structural elements of food, cover, nesting, and 

breeding habitat, and movement/migration corridors for organisms. These corridor vegetation 

communities moderate soil and air temperatures, stabilize channel banks, provide seed banking and 

trap silt and fine sediment that favor the establishment of diverse floral and faunal species, and dissipate 

stream energy (Levick et al., 2008). The resulting microclimates in and around ephemeral and 

intermittent stream vegetation corridors are used extensively by fauna. In arid climates, such conditions 

often benefit less mobile species that cannot avoid the harsh desert environment by moving to 

microclimates that are more favorable. These stream corridors provide primary habitat, predator 

protection, breeding and nesting sites, shade, travel corridors, migration stopover sites, and food 

sources.

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A Review and Synthesis B-55 January 2015
Figure B-13. Aerial photograph showing dense corridor of vegetation lining ephemeral washes in 

southeastern Arizona. Image accessed from Google Earth from May 2005 imagery date.

Both passive and active biological connections exist in the intermittent and ephemeral streams network. 

Passive connections involve the transport of organisms and organic matter driven by water flow; these 

connections thus depend on hydrologic connectivity. Active connections do not depend on flowing 

water; instead, dispersal of organisms and organic matter occurs throughout the stream network 

through walking, flying, or hitchhiking on mobile organisms. All these organism-mediated connections 

form the basis of biological connectivity between headwater streams and downstream waters. 

Movement can be both longitudinal along the stream network and lateral, and can occur over the life 

cycles of numerous organisms (Schlosser, 1991; Fausch et al., 2002). 

Meyer et al. (2007) noted the importance of headwater streams, including ephemeral and intermittent 

streams, as vital parts of the biological integrity of U.S. waterways. Ephemeral and intermittent stream 

channels are bordered by a zone of continuous or near-continuous vegetation, and thus they provide 

important wildlife movement corridors as they afford both cover and food. Summer monsoons in the 

Southwest coincide with periods when herptofauna such as snakes and amphibians are most active; the 

episodic flows provide a generally continuous aquatic corridor for their dispersal. The translocation and 

dispersal of species enables genetic interchange between subpopulations that are often isolated for most 

of the year. In addition, recolonization of sites can occur when subpopulations are lost due to drought or 

disturbance. Degradation of these habitats and loss of their connections to larger streams can have 

negative consequences for the diversity of downstream and riparian ecosystems and for the biological 

integrity of the entire river network. Nearly 81% of all streams are ephemeral or intermittent in the six 

Southwestern states (USGS, 2006). From a strictly numerical viewpoint, therefore, degradation of these 

ephemeral streams diminishes ecosystem functions in most southwestern watersheds.

Stream and Wetland Connectivity:

A Review and Synthesis B-56 January 2015
B.5.5.3.1 Physical features important to biological connectivity and integrity

Ephemeral and intermittent riverbanks in the arid Southwest provide shelter for numerous species of 

wildlife, including reptiles, amphibians, birds, mammals, and invertebrates. These shelters typically are 

independent of whether the streams contain water year-round. Shelters are created through the action 

of water, wind, and gravity. Ephemeral dry-wash embankments notoriously are full of small caves and 

crevices critical in the life of desert animals such as the desert tortoise (Gopherus agassizii) (Van 

Devender, 2002). The alluvium in ephemeral and intermittent streams is often looser than the soils or 

colluvium of surrounding uplands. These conditions provide enhanced habitat by specialized sandburrowing species of wildlife. High-value shelters also are created when woody debris is swept in from 

the watershed and collects in the floodplain and stream channel. In cases of deep ephemeral stream 

incision, cooler canyon-type environments might be created in which moisture loss is retarded.

B.5.5.3.2 Vegetation habitat features important to biological connectivity and integrity

Large ephemeral washes with shallow ground-water zones often are colonized with a variety of 

phreatophytic trees, such as Fremont cottonwood (Populus fremontii), Arizona sycamore (Platanus 

wrightii), and Arizona ash (Fraxinus velutina). These washes also include distinctive shrubs, such as 

willow (Salix spp.), seepwillow (Baccharis spp.), burrobrush (Ambrosia monogyra), and saltcedar 

(Tamarix ramosissima), and dense grass stands of sacaton (Sporobolus spp.). Those washes that lack a 

shallow ground-water system or water augmentation by effluent discharge nonetheless give rise to a 

distinctive vegetative habitat from the surrounding uplands. These environments often are referred to 

as xeroriparian habitat.

The floral species in these habitats is moderated by the frequency and magnitude of runoff events. 

Common tree species in xeroriparian habitat include subtropical legumes such as mesquite (Prosopis

spp.), catclaw acacia (Acacia greggii), ironwood (Olneya tesota), and blue palo verde (Cercidium 

floridum). Mesquite has been identified as the key provider of food for numerous migrating birds (Van 

Riper and Cole, 2004). Netleaf hackberry (Celtis reticulatata) and Arizona sycamore (Platanus wrightii) 

have been identified as providing exceptional cover for nesting birds on intermittent streams (Powell 

and Steidl, 2002). 

B.5.5.3.3 Hydrologic habitat features important to biological connectivity and integrity

Stanley et al. (1997) provide an excellent overview of the expansion and contraction of flowing waters 

within southwestern streams in response to variable precipitation events. This phenomenon commonly 

results in reaches of streams or rivers that have flow or residual pools with water surrounded by 

reaches without water. This phenomenon is common in dryland rivers across the globe (Arthington et 

al., 2005; Bunn et al., 2006). The isolated pools often serve as refuges for fish to survive in intermittent 

streams during dry periods (Labbe and Fausch, 2000). 

Episodic stream flow might be the most visually prominent hydrologic aspect of a stream but is seldom 

the only hydrologic habitat feature of biological significance. An arid stream wash with a shallow 

ground-water system also might have moist banks fed by capillary flow that provide sites for turtle or 

Stream and Wetland Connectivity:

A Review and Synthesis B-57 January 2015
insect reproduction. Distinct invertebrate fauna can inhabit the hyporheic (subsurface) zone of flow 

beneath a dry streambed. Episodic flooding, human excavations, and channel scour can produce inchannel or off-channel pools where amphibians breed. Within-channel or floodplain springs can provide 

distinct chemical compositions or thermal refuges from the main ephemeral or intermittent stream.

The natural episodic and intermittent flow regime in the arid Southwest is a competitive factor of native 

species over exotics adapted to lake and pond conditions (Minckley and Meffre, 1987; Poff et al., 1997). 

Louw and Seely (1982) and Williams (2005) concluded most desert species have developed adaptations 

to the water-limited conditions of these regions that enable them to survive under harsh environmental 

conditions. Fauna using ephemeral or intermittent waters include fish, mammals, amphibians, reptiles, 

birds, and invertebrates. The variability of climate and flow regime, which influences species abundance 

and diversity, however, makes evaluation difficult unless surveys are conducted over years in different 

community types (Boulton and Lake, 1992). 

B.5.5.3.4 Fish and aquatic insects

As discussed in the previous section, the interplay between stormflow from ephemeral tributary 

streams, water from alluvial aquifers, and water from regional ground water control the distribution 

and timing of flowing water in southwestern rivers. Native fish species of southwestern streams and 

rivers are adapted to these dynamic environments (John, 1964; Meffe, 1984). Rinne and Miller (2006)

compared fish assemblage data in river networks for two southwestern rivers, the Gila River (New 

Mexico and Arizona) and the Verde River (Arizona) over 7 to 12 years. They included river hydrology 

and geomorphology data in their analysis and found that variable streamflows and higher flow volumes 

favor native fish species over nonnatives. They also noted that the presence of unconstrained alluvial 

valley river reaches with shallow pools favored native fish. Furthermore, when humans alter the 

hydrologic dynamics of ephemeral and intermittent tributaries such that flows connecting them to the 

river network are more frequent or more consistent, nonnative fish can invade (Turner and List, 2007). 

Recent nonnative invasion and a corresponding decline in native fish species diversity were observed in 

the lower reaches of Aravaipa Creek, a tributary of the San Pedro River, which historically was only 

rarely connected to the mainstem (Eby et al., 2003). 

Lytle et al. (2008) found a similar adaptation strategy in populations of an aquatic insect (Abedus 

herberti) occupying sites along a natural gradient of disturbance predictability. In their study, 

predictability was defined as the ability of a signal or cue (rainfall) to cause a disturbance. In this case, 

the disturbance was a flash flood. Using signal detection theory, they found that for 13 of 15 insect 

populations, the observed insect response times “were an optimal compromise between the competing 

risks of abandoning versus remaining in the stream, mediated by the rainfall-flood correlation of the 

local environment.” They concluded that these aquatic insect populations could evolve in their 

responses to changes in the flow disturbance regime, providing evidence that these aquatic populations 

can adapt to “among-stream differences in flow regime.”

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B.5.6 Southwestern Intermittent and Ephemeral Streams: Synthesis and 

Implications

Rivers of the arid and semiarid Southwest are products of a highly variable and dynamic environment.

Ephemeral and intermittent streams and their tributaries in the American Southwest provide a wide 

range of functions that are critical to the health and stability of arid and semiarid watersheds and 

ecosystems. Most importantly, they provide hydrologic connectivity within a basin, linking ephemeral, 

intermittent, and perennial stream segments. This linkage and the corridor of connectivity facilitates the 

movement of water, sediment, nutrients, debris, fish, wildlife, and plant propagules throughout the 

watershed. The relatively more vegetated streams corridors connected to downstream perennial 

reaches provide wildlife habitat and more humid environment than do the surrounding uplands. During 

ephemeral and intermittent streamflow, energy dissipates as part of natural fluvial adjustment, and 

sediment, organic matter, and debris are transported. The variability of the hydrologic regime in these 

streams is the key determinant of spatial and temporal distribution of plant community structure and 

the types of plants and wildlife present. Some of the major ways in which ephemeral streams are 

connected with and influence rivers are as follows:

 Flows from ephemeral streams are a major driver of the dynamic hydrology of southwestern 

rivers. Ephemeral tributary streamflows are especially important drivers of downstream floods 

during monsoon seasons. 

 Fishes and invertebrates native to mainstem rivers are adapted to the variable flow regimes that 

ephemeral tributary streams strongly influence. Ephemeral flows prevent or mitigate invasion 

by introduced species.

 Ephemeral tributary streams supply water to mainstem river alluvial aquifers; these alluvial 

aquifers help sustain river baseflows. 

 Ephemeral streams export sediment to rivers during major hydrologic events; the sediment 

contributes to materials that comprise alluvial aquifers and shape the fluvial geomorphology of 

rivers. 

 Ephemeral tributaries export nutrients to mainstream rivers during hydrologic flow events; 

nutrients occur in many forms and contribute to river productivity. 

 Ephemeral and intermittent streams and their associated vegetation communities provide 

structural elements of food, cover, nesting and breeding habitat, and movement/migration 

corridors for organisms. 

 Water, sediment, and nutrients exported to the river from ephemeral tributaries support 

riparian communities of mainstem rivers; the riparian communities profoundly influence river 

attributes through shading and allochthonous inputs of organic matter, detritus, wood, and 

invertebrates to the river. 

Stream and Wetland Connectivity:

A Review and Synthesis B-59 January 2015
 Regional ground-water aquifers are in part recharged through infiltration of water to the 

streambed of ephemeral stream channels during wet years; the regional aquifer supplies a 

varying but critical portion of baseflow for perennial river reaches.

B.6 Case Study: Vernal Pools 

B.6.1 Abstract

Vernal pools are shallow, seasonal wetlands that accumulate water during colder, wetter months and 

gradually dry down during warmer, dryer months. Despite differences in geology, climate, and biological 

communities, some common findings about the hydrologic connectivity of vernal pools in different 

regions include evidence for temporary or permanent outlets, frequent filling and spilling of higher 

pools into lower elevation swales and stream channels, and conditions supporting subsurface flows 

through pools without perched aquifers to nearby streams. Insects and amphibians that can live in 

streams or permanent pools opportunistically use glaciated vernal pools as alternative breeding habitat, 

refuge from predators or environmental stressors, hunting or foraging habitat, or stepping-stone 

corridors for dispersal and migration. Nonglaciated vernal pools in western states are reservoirs of 

biodiversity and can be connected genetically to other locations and aquatic habitats through wind- and 

animal-mediated dispersal. 

B.6.2 Introduction

The term “vernal pool” is broadly used to describe shallow, fishless pools situated on bedrock or lowpermeability soils that lack continuous surface-water connection to permanent water bodies but have a 

seasonal period of inundation on which aquatic species depend for completion of their life cycles 

(Zedler, 2003). This case study reviews evidence for physical and biological relationships between 

vernal pools and downstream waters in the western United States (western vernal pools) and glaciated 

areas of northeastern and midwestern states (northern vernal pools), where vernal pools are 

particularly abundant (Zedler, 2003). 

B.6.2.1 Geography and Geology

B.6.2.1.1 Western vernal pools 

Zedler (1987) used the term vernal pool to describe basin/swale systems in California’s Mediterranean 

climate that flood in winter, host diverse communities of aquatic plants and animals in early spring, 

transition to terrestrial ecosystems in late spring, and desiccate during hot, dry summer months.

Western vernal pools are seasonal wetlands associated with topographic depressions; soils with poor 

drainage; mild, wet winters; and hot, dry summers in western North America from southeastern Oregon 

to northern Baja California, Mexico (Bauder and McMillan, 1998). Locally, wetlands that fit this 

definition might be known by other names, such as the upland playas in Oregon (Clausnitzer and 

Huddleston, 2002). 

Stream and Wetland Connectivity:

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Historically, vernal pools covered 518 km2, or 5−6% of the total land surface in southern California and 

northern Baja, but losses in that area have been substantial (Bauder and McMillan, 1998). Pools occur on 

impermeable or slowly permeable soils or bedrock (Smith and Verrill, 1998) that limit percolation and 

thus produce surficial aquifers that perch above regional ground-water aquifers. Pool-forming soil 

layers in this region include clay-rich soils, silica-cemented hardpans (duripans), volcanic mudflows, or 

bedrock (Weitkamp et al., 1996; Hobson and Dahlgren, 1998; Smith and Verrill, 1998; Rains et al., 2006). 

Because their hydrology and ecology are so tightly coupled with the local and regional geologic

processes that formed them, western vernal pools typically occur within “vernal pool landscapes” 

(Smith and Verrill, 1998), or complexes of pools in which swales connect pools to each other and to 

seasonal streams (Weitkamp et al., 1996; Rains et al., 2008). 

B.6.2.1.2 Northern vernal pools

The geologic formations underlying northern vernal pool landscapes were formed by the movement of 

glaciers across the northeastern and north-central states approximately 12,000 years ago. Retreating 

glaciers scoured basins in rock ledges and mountaintops, or left behind large pieces of ice that later 

collapsed to form topographic depressions containing deposits of gravel, sand, or mud (Colburn, 2004). 

Although not all vernal pools in these areas were formed by glaciers, the soils, geology, and evolutionary 

history of plants and animals in northern vernal pools have been profoundly affected by glacial events.

Like western vernal pools, northern vernal pools are significantly grouped or clustered (Brooks, 2005). 

Grant (2005) found that pools in Massachusetts are more likely to occur in more porous substrates 

(alluvial, fine grained, or sand/gravel soils) than glacial till or impermeable bedrock, increasing their 

hydrologic connection to shallow ground water.

Unlike western vernal pools, which typically occur in open grasslands, most northern vernal pools are 

detrital wetlands fully contained within forest ecosystems that depend on the pulse of organic matter 

from leaf fall that coincides with initial filling of temporary pools in these regions. 

B.6.2.2 Temporal Dynamics

Zedler (1987) identified four distinct ecosystem phases in the annual hydrologic cycle of western vernal 

pools, which we have generalized here (with additional citations) to describe the temporal dynamics of 

northern vernal pools as well:

 Wetting or newly flooded phase: Rainwater, snow, runoff, or snowmelt infiltrate upper layers of 

permeable soil and, when topsoils are saturated, collect in pool basins formed by impervious 

rock, clay, or till layers (aquitards or aquicludes; Rains et al., 2008). In early spring, perennial 

plants sprout and stored seeds germinate in wet soils. Aquatic invertebrate communities 

develop from resting eggs and seed banks (Colburn, 2004). 

 Aquatic phase: Soils are saturated and pools hold standing water, in many locations filled to 

capacity. In some western vernal pools, surface and subsurface flows from upland pools through 

swales feed downgradient pools, connecting pools at a site and extending the aquatic phase of 

Stream and Wetland Connectivity:

A Review and Synthesis B-61 January 2015
the pool complex (Weitkamp et al., 1996; Hanes and Stromberg, 1998). Pools are colonized by 

dispersing insects and breeding amphibians.

 Terrestrial phase: Evapotranspiration rates increase and pool water recedes, although soils 

remain saturated. In western pools, aquatic plants flower and seed. Aquatic animals disperse or 

become dormant. Terrestrial plant communities persist.

 Dry phase: Pools and soils dry to moisture levels similar to uplands, and many plants senesce or 

die. Summer rains produce no new ponding or plant growth.

In the western United States, vernal complexes saturate and begin to pool during winter rains, reach 

maximum depth by early spring, and lose all standing water by late spring (Zedler, 1987). The timing of 

filling and drying of northern vernal pools varies, depending on pool type. Colburn (2004) proposed five 

hydrologic classes for northern vernal pools, based on time of filling and average duration of flooding: 

(1) short-cycle, spring-filling pools that stay wet for 3−4 months; (2) long-cycle, spring-filling pools that 

stay wet for 5−8 months; (3) short-cycle, fall-filling pools that stay wet for 7−9 months; (4) long-cycle, 

fall-filling pools that stay wet for 9−11 months; and (5) semipermanent pools that stay wet for 36−120 

months. Many northern vernal pools do not dry down completely, but retain areas of saturated sediment 

or standing water in part of the basin. Such pools are considered “incompletely dry,” to differentiate 

them from pools that are “continuously flooded” or “dry.”

B.6.2.3 Ecology

Vernal pool ecosystems support large breeding populations of amphibians, aquatic invertebrates, and 

aquatic or semiaquatic plants, including many rare or endemic taxa (King et al., 1996; Zedler, 2003; 

Colburn, 2004; Calhoun and DeMaynadier, 2007). The annual cycle of basin flooding and drying plays an 

important role in structuring biological communities in vernal pools. The wet phase prevents 

establishment of upland plant species in pool basins, while the dry phase limits colonization by aquatic 

and semiaquatic plant and animal species that occur in permanent wetlands, ponds, or streams (Keeley 

and Zedler, 1998; Bauder, 2000). Despite their cyclical nature, vernal pool habitats are species rich and 

highly productive, in part because they provide relatively predator-free breeding habitat for 

invertebrates and amphibians (Keeley and Zedler, 1998; Calhoun et al., 2003). Many resident species are 

locally adapted to the timing and duration of inundation, soil properties, and spatial distribution of 

vernal pools in a specific geographic subregion. Other species that are widespread across regions and 

aquatic habitat types (including streams or lakes) use inundated pools periodically for refuge, 

reproduction, or feeding (King et al., 1996; Williams, 1996; Colburn, 2004). 

B.6.3 Evidence

B.6.3.1 Physical Connections

Vernal pools are primarily precipitation fed and typically lack permanent inflows from or outflows to 

streams or other water bodies. They can be connected temporarily, however, to permanent waters by 

surface or shallow subsurface flow (flow through) or ground-water exchange (recharge; Weitkamp et al., 

1996; Brooks, 2005; Rains et al., 2008). Hydrologic connectivity is typically limited to flow through in 

Stream and Wetland Connectivity:

A Review and Synthesis B-62 January 2015
vernal pools formed by perching layers; ground-water exchange can occur in vernal pool systems 

without perching layers (Brooks, 2005). 

B.6.3.1.1 Western vernal pools

Rains et al. (2006; 2008) examined the hydrology and biogeochemistry of two vernal pool complexes in 

the northern end of California’s Central Valley (Smith and Verrill, 1998). The 2006 study evaluates water 

balance and the relative importance of direct precipitation, evaporation, surface flow, and shallow 

subsurface flow in a hardpan vernal pool complex (Rains et al., 2006). The 2008 study contrasts the role 

of geology and soil type—specifically, clay-rich versus hardpan soils—in controlling vernal pool 

hydroperiod, hydrodynamics, and water chemistry (Rains et al., 2008). Clay-rich and hardpan

complexes are common vernal pool types in California’s Central Valley (Smith and Verrill, 1998). In both 

studies, study sites were pool complexes located in the upper portion of the watersheds. Within each 

complex, upland (feeder) pools were connected to lower (collector) pools by ephemeral swales, and the 

lowest pool was connected by swale to a seasonal stream. 

Results showed that high and low pools were connected via surface flows 10−60% of the time; surface 

water flowed through swales connecting low-elevation pools to streams during 60% of the inundation 

period (Table B-1). Underlying geology and soil type influenced ponding rates and inundation periods: 

In water year 2003, pools in clay-rich soils accumulated water at the onset of rainfall and held water 

longer than pools in hardpan soils, which have higher soil infiltration rates (Table B-1; Rains et al., 

2008). Horizontal subsurface flows reduced the number and volume of higher elevation surface flows 

into hardpan pools, relative to the clay-rich pools. Most water discharging from the swale to the seasonal 

stream at the hardpan site was perched ground water that had flowed around, rather than through, the 

pool basins. In both soil types, however, vernal pool basins, swales, and seasonal streams were shown to 

be part of a single surface-water and shallow ground-water system connected to the river network when 

precipitation exceeds storage capacity of the system (Rains et al., 2006; Rains et al., 2008). Pyke (2004)

reported that a complex of 38 vernal pools north of Sacramento was filled to capacity in 10 of 11 years 

from November 1999 to June 2001. A direct precipitation-evaporation model for another hardpan 

complex near this Sacramento site showed that direct precipitation could fill pools beyond capacity in 

most years (Hanes and Stromberg, 1998). Pools located at the lower end of a complex (and thus more 

likely to be directly connected to streams) can receive surface water through stepping-stone spillage in 

addition to direct input from precipitation; thus, they can remain wetted longer than upper pools. For 

example, Bauder (2005) found that “collector” pools with no outlet held water longer than headwater 

pools with no inlet. Collectively, these findings suggest that filling and overflow of vernal pools are not 

rare phenomena. Filling and spilling also can occur in other vernal pool types because all vernal pools 

are underlain by aquitards (Rains et al., 2008). 

B.6.3.1.2 Northern vernal pools

Northern vernal pools include both perched and ground water-connected aquifers (Brooks, 2004; Boone 

et al., 2006). As in western vernal pools, rainfall or snowmelt in excess of pool capacity is lost to surface 

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runoff or subsurface flows into shallow, nearby ground water (Brooks, 2005). Studies of surface and

subsurface inflows and outflows were not found in the literature. Brooks (2004) reports that

precipitation and potential evapotranspiration alone could not account for large observed water losses 

in four vernal pools he studied for 10 years. These losses could have been due to inaccurate estimates of 

precipitation or evapotranspiration (both of which were significantly related to water depth) or to 

surface overflow and soil infiltration, which were not measured. In a separate study, Boone et al. (2006)

used a classic water-budget model to predict vernal pool hydroperiods in Minnesota and found that, 

although precipitation and evapotranspiration were good predictors of pool inundation in most cases, 

errors in model estimates for a few pools suggested that surface outflows or infiltration might have been 

occurring at some sites.

Individually small, temporary storage of heavy rainfall and snowmelt in vernal pool systems (pools plus 

soils) can attenuate flooding, provide a reservoir for nearby vegetation during the spring growth period, 

and increase nutrient availability (Hobson and Dahlgren, 1998). 

B.6.3.2 Biological Connections

Dispersal of vernal pool organisms can be active or passive and occurs at multiple scales: local scale 

(among nearby pools), neighborhood scale (among pools in a geographic cluster or complex), or 

regional (outside of the complex, to other ecosystem types; Compton et al., 2007). Examples of active 

regional dispersal include insect flight or juvenile dispersal by amphibians. Passive transport is of 

particular interest for regional-scale dispersal, as it enables plants and low-vagility animals such as 

microcrustaceans to move long distances. Examples of passive transport to and from unidirectional 

wetlands and pools include water-mediated dispersal of larvae (Hulsmans et al., 2007); transport of 

diapausing (dormant) eggs by waterbirds (Figuerola et al., 2005; Frisch et al., 2007) or flying insects 

(Van De Meutter et al., 2007); and wind-mediated dispersal of dormant eggs, larvae, and adult 

zooplankton from dry rock pools (Vanschoenwinkel et al., 2009). 

Table B-1. California vernal pool inundation and hydrologic connectivity. Summarized from Rains et al. 

(2008)

Soil; hydrology Inundation period 

(days/water yeara) 

Flow-through paths 

(pool-pool and poolstream)

Surface flows 

between high- and 

low-elevation poolsb

Surface flows 

between lowest 

elevation pool and 

stream networkb 

Fine-grained, clayrich soils; perched 

surface water 

200−205 surface only 120 (60%) 120−123 (60%)

Coarse-grained, 

hardpan soils;

perched surface

water and ground

water 

150−154

surface and 

horizontal 

subsurface

15 (10%) 90−92 (60%)

aOctober 1 2002−September 30, 2003.

b Units = days/water yeara, % of inundation period. 

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Western vernal pools are highly productive ecosystems that have evolved in what Zedler (2003)

describes as a “balance between isolation and connectedness.” Pacific vernal pool landscapes are tightly 

coupled with variable climate, soils, and geologic formations in the western United States, producing 

diverse habitats for organisms with different life-history strategies (Bauder and McMillan, 1998). 

Seasonal wetlands in this region might have served as evolutionary refuges since Mesozoic times (King 

et al., 1996). As a result, present-day vernal pool communities have a large proportion of passively 

dispersing, endemic (i.e., restricted to small geographic area) species in genera that are widely 

distributed across continents and aquatic systems (King et al., 1996; Keeley and Zedler, 1998; Zedler, 

2003). This apparent paradox is explained by the fact that individuals transported passively over long 

distances have colonized, and through time have become locally adapted to, different vernal pool 

landscapes, creating new endemic species from the rootstock of ancient lineages. As a result, Pacific 

vernal pools are now rich reservoirs of genetic and species diversity connected to other locations and 

aquatic habitats through continuing dispersal. The existence and connectivity of such reserves are 

especially important at a time when changing climatic conditions are likely to increase intermittency of 

stream flows and decrease duration of wetland inundations in other areas. 

Western vernal pools also support generalist invertebrate communities, including crustaceans and 

insects that are widely distributed in permanent wetlands, ponds, lakes, and streams (Zedler, 1987; 

2003). Invertebrates and zooplankton can be flushed from vernal pools into streams or other water 

bodies during periods of overflow, carried by animal vectors (including humans), or dispersed by wind.

Wind-mediated dispersal can be of particular importance in seasonal wetlands: during the dry phase, 

dry soils containing large numbers of transportable seeds, resting eggs, cysts, diapausing larvae, and 

adults are picked up and blown away (Vanschoenwinkel et al., 2009). The maximum distance such 

propagules can travel is not known, but, from currently available literature, pool-pool or pool-stream 

transport is clearly possible, and the potential for long-distance transport also exists.

Food webs in northern vernal pools include highly fecund amphibians and insects that convert detrital 

organic matter inputs into biomass that subsidizes terrestrial and aquatic ecosystems in other parts of 

the watershed (Semlitsch and Bodie, 1998; Brooks, 2000; Gibbons et al., 2006). 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. For example, Gahl et al. (2009)

reports that bullfrog (Rana catesbeiana) densities per unit wetland perimeter were greater in two small 

seasonal pools than in a larger, permanent breeding wetland. Regular use of seasonal pools by bullfrogs 

throughout this study offers compelling evidence for the role of seasonal pools as a component of their 

nonbreeding habitat. Spotted turtles (Clemmys guttata) used seasonal pools for foraging, basking, and 

mating at two sites in Massachusetts (Milam and Melvin, 2001). Many insects and amphibians found in 

streams, lakes, or riparian/floodplain wetlands are facultative users of vernal pool habitats (Table 4-2).

Stream and Wetland Connectivity:

A Review and Synthesis B-65 January 2015
B.6.4 Vernal Pools: Synthesis and Implications

The key findings from this case study are as follows: 

 In the aquatic phase, some western vernal pools are filled to capacity in most years, creating 

conditions under which water flows from pools into swales and stream channels.

 Documented evidence of surface flows connecting western vernal pool complexes to the river 

network via swales and seasonal streams is available in the literature.

 Indirect evidence indicates that surface and subsurface flows connect northern pools without 

perched aquifers to shallow ground water and thus to nearby streams. 

 Many insects and amphibians that can live in streams or pools that are more permanent 

opportunistically use northern vernal pools as alternative breeding habitat, refuge from 

predators or environmental stressors, hunting or foraging habitat, or stepping-stone corridors 

for dispersal and migration.

 Nonglaciated vernal pools in western states have achieved a long-term “balance between 

isolation and connectedness” and have functioned as refuges for plant and animal diversity since 

the Mesozoic era. They are current reservoirs of biodiversity connected genetically to other 

locations and aquatic habitats through continuing dispersal. 

Direct evidence supports the existence of seasonal hydrologic connections and indirect evidence 

supports the movement of organisms between western vernal pool complexes and streams. Indirect 

evidence supports the existence of hydrologic and biological connections between northern vernal pools 

and river networks, with potential for storing water during the wet season, and providing alternative 

breeding habitat or food resources for stream organisms. 

Stream and Wetland Connectivity:

A Review and Synthesis B-66 January 2015
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