UNITED STATES ENVIRONMENTAL PROTECTION AGENCY

 WASHINGTON D.C. 20460

OFFICE OF THE ADMINISTRATOR

SCIENCE ADVISORY BOARD

October 17, 2014

EPA-SAB-15-001

The Honorable Gina McCarthy

Administrator

U.S. Environmental Protection Agency

1200 Pennsylvania Avenue, N.W.

Washington, D.C. 20460

Subject: SAB Review of the Draft EPA Report Connectivity of Streams and Wetlands to 

Downstream Waters: A Review and Synthesis of the Scientific Evidence

Dear Administrator McCarthy:

The EPA’s Office of Research and Development (ORD) requested that the Science Advisory Board 

(SAB) review the draft report titled Connectivity of Streams and Wetlands to Downstream Waters: A 

Review and Synthesis of the Scientific Evidence (September 2013 External Review Draft) (“Report”). 

The Report is a review and synthesis of the peer-reviewed literature on the connectivity or isolation of 

streams and wetlands relative to large water bodies such as rivers, lakes, estuaries, and oceans. The 

Report was developed by ORD to summarize the current scientific understanding of connectivity to 

inform EPA and U.S. Army Corps of Engineers rulemaking related to the jurisdiction of the Clean 

Water Act. 

In response to the EPA’s request, the SAB convened an expert panel to review the Report. The SAB was 

asked to comment on the clarity and technical accuracy of the Report; whether it includes the most 

relevant peer-reviewed literature; whether the literature has been correctly summarized; and whether the 

findings and conclusions are supported by the available science. The enclosed report provides the SAB’s 

consensus advice and recommendations.

The EPA Report is a thorough and technically accurate review of the literature on the connectivity of 

streams and wetlands to downstream waters. The SAB agrees with two of the three major conclusions in 

the Report. The SAB finds that the review of the scientific literature strongly supports the conclusions

that streams and “bidirectional” floodplain wetlands are physically, chemically, and/or biologically 

connected to downstream navigable waters; however, these connections should be considered in terms 

of a connectivity gradient. The SAB recommends revisions to improve the clarity of the Report, better 

reflect the scientific evidence, expand the discussion of approaches to quantifying connectivity, and

make the document more useful to decision-makers. The SAB disagrees with the conclusion that there is 

insufficient information available to generalize about the connectivity of wetlands in “unidirectional,” 

non-floodplain settings. In that case, the SAB finds that the scientific literature supports a more 

definitive statement that reflects how numerous functions of non-floodplain wetlands sustain the 
physical, chemical, and/or biological integrity of downstream waters, although the degree of 

connectivity can vary widely. The SAB’s major comments and recommendations are provided below.

• The Report often refers to connectivity as though it is a binary property (connected versus not 

connected) rather than as a gradient. In order to make the Report more technically accurate, the SAB 

recommends that the interpretation of connectivity be revised to reflect a gradient approach that 

recognizes variation in the frequency, duration, magnitude, predictability, and consequences of those 

connections. The SAB notes that relatively low levels of connectivity can be meaningful in terms of 

impacts on the chemical, physical, and biological integrity of downstream waters.

• The SAB recommends that the EPA consider expanding the brief overview of approaches to 

measuring connectivity. This expansion would be most useful if it provided examples of the 

dimensions of connectivity that could most appropriately be quantified, ways to construct 

connectivity metrics, and the methodological and technical advances that are most needed.

• The Report presents a conceptual framework that describes the hydrologic elements of a watershed 

and the types of connections that link them. The literature review supporting the framework is 

technically accurate and clearly presented. However, to strengthen and improve its usefulness, the 

SAB recommends that the framework be expressed as spatially continuous physical, hydrological

(surface and subsurface), chemical, and biological flowpaths that connect watersheds. Layers of 

complexity should be included in the conceptual framework to represent important aspects of 

connectivity such as spatial and temporal scale. The water body classification system used in the 

Report (i.e., classification of waters according to landscape settings) should be integrated into the 

flowpath framework to show that continuous phenomena interact across landscape settings. In 

addition, the SAB recommends that each section of the Report be clearly linked to the conceptual 

framework.

• The SAB recommends that the Report more explicitly address the scientific literature on cumulative 

and aggregate effects of streams, groundwater systems, and wetlands on downstream waters. In 

particular, the Report should contain a discussion of the spatial and temporal scales at which 

streams, groundwater systems, and wetlands are functionally aggregated. The SAB also recommends

that, throughout the Report, the EPA further discuss several important issues including the role of 

biological connectivity, biogeochemical transformation processes, and the effects of human 

alteration of connectivity.

• In the Report, the EPA has classified waters and wetlands as having the potential for either 

“bidirectional” or “unidirectional” hydrologic flows with rivers and lakes. The SAB finds that these 

terms do not adequately describe the four-dimensional (longitudinal, lateral, vertical, and temporal)

nature of connectivity, and the SAB recommends that the Report use more commonly understood 

terms that are grounded in the peer-reviewed literature. 

• The SAB commends the EPA for the comprehensive literature review in the Report, although 

additional citations have been suggested to strengthen it. To make the review process more 

transparent, the EPA should more clearly describe the approach used to screen, compile, and

synthesize the information. The Report should also clearly indicate that the definitions used for 

rivers, streams, and wetlands are scientific, rather than legal or regulatory definitions, and may differ 

from those used in the Clean Water Act and associated regulations.
• The SAB finds that the review and synthesis of the literature describing connectivity of streams to 

downstream waters reflects the pertinent literature and is well grounded in current science. The 

literature review provides strong scientific support for the conclusion that ephemeral, intermittent,

and perennial streams exert a strong influence on the character and functioning of downstream 

waters and that tributary streams are connected to downstream waters. However, the EPA should 

recognize that there is a gradient of connectivity. The SAB also recommends that the literature 

review more thoroughly address hydrologic exchange flows between main channels and off-channel 

areas, the influence of stream connectivity on downstream water temperature, and the movement of 

organisms throughout stream systems to use critical habitats.

• The SAB finds that the review and synthesis of the literature on the connectivity of waters and 

wetlands in floodplain settings is somewhat limited in scope (i.e., focused largely on headwater 

riparian wetlands) and should be expanded. However, the literature review does substantiate the 

conclusion that floodplains and waters and wetlands in floodplain settings support the physical, 

chemical, and biological integrity of downstream waters. The SAB recommends that the Report be 

reorganized to clarify the functional role of floodplain systems in maintaining the ecological

integrity of streams and rivers and that the Report more fully reflect the literature on lateral exchange 

between floodplains and rivers.

• The SAB finds that, in general, the review and synthesis of the literature on the connectivity of nonfloodplain (“unidirectional”) waters and wetlands is technically accurate. However, additional 

information on biological connections should be included. The SAB has provided numerous 

additional literature citations addressing the roles of multiple biological taxa in this regard, such as

transporting propagules and nutrients and providing critical habitat. 

• The SAB disagrees with the EPA’s conclusion that the literature reviewed did not provide sufficient 

information to evaluate or generalize about the degree of connectivity (absolute or relative) or the 

downstream effects of wetlands in “unidirectional” non-floodplain landscape settings. The SAB 

finds that the scientific literature supports a more definitive statement about the functions of 

“unidirectional” non-floodplain wetlands that sustain the physical, chemical and/or biological 

integrity of downstream waters. In this regard, the SAB recommends that the EPA revise the 

conclusion to better articulate: (1) what is supported by the scientific literature and (2) the issues that 

still need to be resolved.

The SAB appreciates the opportunity to provide the EPA with advice on this important subject. We look 

forward to receiving the agency’s response.

Sincerely,

/s/ /s/

Dr. David T. Allen, Chair Dr. Amanda D. Rodewald, Chair

Science Advisory Board SAB Panel for the Review of the EPA

 Water Body Connectivity Report

Enclosure
NOTICE

This report has been written as part of the activities of the EPA Science Advisory Board (SAB), a public 

advisory group providing extramural scientific information and advice to the Administrator and other 

officials of the Environmental Protection Agency. The SAB is structured to provide balanced, expert 

assessment of scientific matters related to problems facing the Agency. This report has not been 

reviewed for approval by the Agency and, hence, the contents of this report do not necessarily represent 

the views and policies of the Environmental Protection Agency, nor of other agencies in the Executive 

Branch of the Federal government, nor does mention of trade names of commercial products constitute a 

recommendation for use. Reports of the SAB are posted on the EPA Web site at 

http://www.epa.gov/sab. 

i
U.S. Environmental Protection Agency

Science Advisory Board

Panel for the Review of the EPA Water Body Connectivity Report

CHAIR

Dr. Amanda D. Rodewald, Director of Conservation Science, Cornell Lab of Ornithology and 

Associate Professor, Department of Natural Resources, Cornell University, Ithaca, NY

PANEL MEMBERS

Dr. Allison Aldous, Freshwater Scientist, The Nature Conservancy, Portland, OR

Dr. Genevieve Ali, Junior Chair, Manitoba's Watershed Systems Research Program, Department of 

Geological Sciences, University of Manitoba, Winnipeg, MB, Canada

Dr. J. David Allan, Professor, School of Natural Resources & Environment, University of Michigan, 

Ann Arbor, MI

Dr. Lee Benda, Research Geomorphologist, Earth Systems Institute, Mt. Shasta, CA

Dr. Emily S. Bernhardt, Associate Professor of Biogeochemistry, Department of Biology, Duke 

University, Durham, NC

Dr. Robert P. Brooks, Professor of Geography and Ecology, Department of Geography, Pennsylvania 

State University, University Park, PA

Dr. Kurt Fausch, Professor, Department of Fish and Wildlife and Conservation Biology, Colorado 

State University, Fort Collins, CO

Dr. Siobhan Fennessy, Jordan Professor of Environmental Science, Biology Department, Kenyon 

College, Gambier, OH

Dr. Michael Gooseff, Associate Professor, Department of Civil and Environmental Engineering, 

Colorado State University, Fort Collins, CO

Dr. Judson Harvey, Research Hydrologist, National Research Program, U.S. Geological Survey, 

Reston, VA

Dr. Charles Hawkins*

, Professor, Department of Watershed Sciences and Director, Western Center for 

Monitoring and Assessment of Freshwater Ecosystems, Quinney College of Natural Resources, Utah 

State University, Logan, UT

Dr. Lucinda B. Johnson, Center Director, Center for Water and the Environment, Natural Resources 

Research Institute, University of Minnesota Duluth, Duluth, MN

Dr. Michael Josselyn, Principal and Senior Scientist, Wetlands Research Associates, Inc., San Rafael, 

CA

* Resigned from Panel March 2014 ii
Dr. Latif Kalin, Associate Professor, School of Forestry and Wildlife Sciences, Auburn University, 

Auburn, AL

Dr. Kenneth Kolm, President and Senior Hydrogeologist, Hydrologic Systems Analysis, LLC, Golden, 

CO

Dr. Judith L. Meyer, Professor Emeritus, Odum School of Ecology, University of Georgia, Lopez 

Island, WA

Dr. Mark Murphy, Principal Scientist, Hassayampa Associates, Tucson, AZ

Dr. Duncan Patten, Professor Emeritus, School of Life Sciences, Arizona State University, Bozeman, 

MT

Dr. Mark Rains, Associate Professor of Ecohydrology, School of Geosciences, University of South 

Florida, Tampa, FL

Dr. Ramesh Reddy, Graduate Research Professor & Chair, Soil and Water Science Department, 

University of Florida, Gainesville, FL

Dr. Emma Rosi-Marshall, Associate Scientist, Cary Institute of Ecosystem Studies, Millbrook, NY

Dr. Jack Stanford, Jessie M. Bierman Professor of Ecology, Flathead Lake Biological Station, 

University of Montana, Polson, MT

Dr. Mazeika Sullivan, Associate Professor, School of Environment & Natural Resources, The Ohio 

State University, Columbus, OH

Dr. Jennifer Tank, Galla Professor, Department of Biological Sciences, University of Notre Dame, 

Notre Dame, IN

Dr. Maurice Valett, Professor of Systems Ecology, Division of Biological Sciences, University of 

Montana, Missoula, MT

Dr. Ellen Wohl, Professor of Geology, Department of Geosciences, Warner College of Natural 

Resources, Colorado State University, Fort Collins, CO

SCIENCE ADVISORY BOARD STAFF

Dr. Thomas Armitage, Designated Federal Officer, U.S. Environmental Protection Agency, 

Washington, DC

Ms. Iris Goodman, Designated Federal Officer, U.S. Environmental Protection Agency, Washington, 

DC

iii
U.S. Environmental Protection Agency

Science Advisory Board

CHAIR

Dr. David T. Allen, Gertz Regents Professor of Chemical Engineering and the Director of the Center 

for Energy and Environmental Resources, The University of Texas, Austin, TX

MEMBERS

Dr. George Alexeeff, Director, Office of Environmental Health Hazard Assessment, California 

Environmental Protection Agency, Oakland, CA

Dr. Pedro Alvarez, Department Chair and George R. Brown Professor of Engineering, Department of 

Civil & Environmental Engineering, Rice University, Houston, TX

Dr. Joseph Arvai, Svare Chair in Applied Decision Research, Department of Geography, University of 

Calgary, Calgary, Alberta, Canada

Dr. Thomas Burbacher, Professor, Department of Environmental and Occupational Health Sciences, 

School of Public Health, University of Washington, Seattle, WA

Dr. Ingrid Burke, Director and Wyoming Excellence Chair, Haub School and Ruckelshaus Institute of 

Environment and Natural Resources, University of Wyoming, Laramie, WY

Dr. Edward T. Carney, Departmental Senior Science Leader and Director of Predictive Toxicology 

Center, Toxicology & Environmental Research and Consulting, The Dow Chemical Company, Midland, 

MI

Dr. Peter Chapman, Principal and Senior Environmental Scientist, Golder Associates Ltd, Vancouver, 

BC, Canada

Dr. Terry Daniel, Professor of Psychology and Natural Resources, Department of Psychology, School 

of Natural Resources, University of Arizona, Tucson, AZ

Dr. George Daston, Victor Mills Society Research Fellow, Global Product Stewardship, The Procter & 

Gamble Company, Mason, OH

Dr. Costel Denson, Managing Member, Costech Technologies, LLC, Newark, DE

Dr. Otto C. Doering III, Professor, Department of Agricultural Economics, Purdue University, W. 

Lafayette, IN

Dr. Michael Dourson, President, Toxicology Excellence for Risk Assessment, Cincinnati, OH

Dr. Joel Ducoste, Professor, Department of Civil, Construction, and Environmental Engineering, 

College of Engineering, North Carolina State University, Raleigh, NC

Dr. David A. Dzombak, Walter J. Blenko, Sr. University Professor and Head of Civil and

Environmental Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, PA

iv
Dr. T. Taylor Eighmy, Vice Chancellor for Research and Engagement, Office of Research, University 

of Tennessee, Knoxville, TN

Dr. Elaine M. Faustman, Professor and Director, Environmental and Occupational Health Sciences, 

University of Washington, Seattle, WA

Dr. R. William Field, Professor, Department of Occupational and Environmental Health, and 

Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA

Dr. H. Christopher Frey, Distinguished University Professor, Department of Civil, Construction and 

Environmental Engineering, College of Engineering, North Carolina State University, Raleigh, NC

Dr. John P. Giesy, Professor and Canada Research Chair, Veterinary Biomedical Sciences and 

Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

Dr. Steven Hamburg, Chief Scientist, Environmental Defense Fund, Boston, MA

Dr. Cynthia M. Harris, Director and Professor, Institute of Public Health, Florida A&M University, 

Tallahassee, FL

Dr. Robert J. Johnston, Director of the George Perkins Marsh Institute and Professor, Economics, 

Clark University, Worcester, MA

Dr. Kimberly L. Jones, Professor and Chair, Department of Civil Engineering, Howard University, 

Washington, DC

Dr. Catherine Karr, Associate Professor - Pediatrics and Environmental and Occupational Health 

Sciences and Director - NW Pediatric Environmental Health Specialty Unit, University of Washington, 

Seattle, WA

Dr. Madhu Khanna, Professor, Department of Agricultural and Consumer Economics, University of 

Illinois at Urbana-Champaign, Urbana, IL

Dr. Nancy K. Kim, Independent Consultant, Albany, NY

Dr. Francine Laden, Mark and Catherine Winkler Associate Professor of Environmental 

Epidemiology, Harvard School of Public Health, and Channing Division of Network Medicine, Brigham 

and Women's Hospital and Harvard Medical School, Boston, MA

Dr. Lois Lehman-McKeeman, Distinguished Research Fellow, Discovery Toxicology, Bristol-Myers 

Squibb, Princeton, NJ

Dr. Cecil Lue-Hing, President, Cecil Lue-Hing & Assoc. Inc., Burr Ridge, IL

Dr. Elizabeth Matsui, Associate Professor, Pediatrics, School of Medicine, Johns Hopkins University, 

Baltimore, MD

Dr. Kristina D. Mena, Associate Professor, Epidemiology, Human Genetics, and Environmental 

Sciences, School of Public Health, University of Texas Health Science Center at Houston, El Paso, TX

v
Dr. Surabi Menon, Director of Research, ClimateWorks Foundation, San Francisco, CA

Dr. James R. Mihelcic, Professor, Civil and Environmental Engineering, University of South Florida, 

Tampa, FL

Dr. Christine Moe, Eugene J. Gangarosa Professor, Hubert Department of Global Health, Rollins 

School of Public Health, Emory University, Atlanta, GA

Dr. H. Keith Moo-Young, Chancellor, Office of Chancellor, Washington State University, Tri-Cities, 

Richland, WA

Dr. Eileen Murphy, Director of Research Development, Office of Research and Economic 

Development, Rutgers University, Piscataway, NJ

Dr. James Opaluch, Professor and Chair, Department of Environmental and Natural Resource 

Economics, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI

Dr. Duncan Patten, Emeritus Professor, School of Life Sciences Arizona State University, Montana 

State University, Bozeman, MT

Dr. Martin Philbert, Dean and Professor, Environmental Health Sciences, School of Public Health, 

University of Michigan, Ann Arbor, MI

Mr. Richard L. Poirot, Air Quality Planning Chief, Air Quality and Climate Division, Vermont 

Department of Environmental Conservation, Montpelier, VT

Dr. Stephen Polasky, Fesler-Lampert Professor of Ecological/Environmental Economics, Department 

of Applied Economics, University of Minnesota, St. Paul, MN

Dr. Amanda D. Rodewald, Director of Conservation Science, Cornell Lab of Ornithology and 

Associate Professor, Department of Natural Resources, Cornell University, Ithaca, NY

Dr. James Sanders, Executive Director, Skidaway Institute of Oceanography, University of Georgia, 

Savannah, GA

Dr. William Schlesinger, President Emeritus, Cary Institute of Ecosystem Studies, Millbrook, NY

Dr. Gina Solomon, Deputy Secretary for Science and Health, Office of the Secretary, California 

Environmental Protection Agency, Sacramento, CA

Dr. Daniel O. Stram, Professor, Department of Preventive Medicine, Division of Biostatistics, 

University of Southern California, Los Angeles, CA

Dr. Peter S. Thorne, Director, Environmental Health Sciences Research Center and Professor and 

Head, Department of Occupational and Environmental Health, College of Public Health, University of 

Iowa, Iowa City, IA

vi
Dr. Paige Tolbert, Professor and Chair, Department of Environmental Health, Rollins School of Public 

Health, Emory University, Atlanta, GA

Dr. Jeanne VanBriesen, Professor, Department of Civil and Environmental Engineering, Carnegie 

Mellon University, Pittsburgh, PA

Dr. John Vena, Professor and Founding Chair, Department of Public Health Sciences, Medical 

University of South Carolina, Charleston, SC

Dr. Peter J. Wilcoxen, Associate Professor, Economics and Public Administration, The Maxwell 

School, Syracuse University, Syracuse, NY

SCIENCE ADVISORY BOARD STAFF

Dr. Angela Nugent, Designated Federal Officer, U.S. Environmental Protection Agency, Science 

Advisory Board, Washington, DC

vii
Table of Contents

1. EXECUTIVE SUMMARY ................................................................................................................. 1

2. INTRODUCTION................................................................................................................................ 7

3. RESPONSES TO EPA’S CHARGE QUESTIONS.......................................................................... 8

3.1. OVERALL CLARITY AND TECHNICAL ACCURACY OF THE DRAFT REPORT ................................... 8

3.2. CONCEPTUAL FRAMEWORK: AN INTEGRATED, SYSTEMS PERSPECTIVE OF 

WATERSHED STRUCTURE .......................................................................................................... 12

3.3. EPHEMERAL, INTERMITTENT, AND PERENNIAL STREAMS: REVIEW OF 

THE LITERATURE........................................................................................................................ 26

3.4. EPHEMERAL, INTERMITTENT, AND PERENNIAL STREAMS: REVIEW OF 

THE FINDINGS AND CONCLUSIONS ............................................................................................. 35

3.5. WATERS AND WETLANDS IN FLOODPLAIN SETTINGS: REVIEW OF THE 

LITERATURE .............................................................................................................................. 38

3.6. WATERS AND WETLANDS IN FLOODPLAIN SETTINGS: REVIEW OF THE 

FINDINGS AND CONCLUSIONS .................................................................................................... 47

3.7. WATERS AND WETLANDS IN NON-FLOODPLAIN SETTINGS: REVIEW OF 

THE LITERATURE........................................................................................................................ 51

3.8. WATERS AND WETLANDS IN NON-FLOODPLAIN SETTINGS: REVIEW OF 

THE FINDINGS AND CONCLUSIONS ............................................................................................. 58

REFERENCES........................................................................................................................................ 62

APPENDIX A: THE EPA’S CHARGE QUESTIONS..................................................................... A-1

APPENDIX B: ADDITIONAL LITERATURE CITATIONS REGARDING 

BIOLOGICAL CONNECTIVITY...................................................................................................... B-1

viii
1. EXECUTIVE SUMMARY

The National Center for Environmental Assessment in the EPA Office of Research and Development 

(ORD) has developed a draft report titled Connectivity of Streams and Wetlands to Downstream Waters:

A Review and Synthesis of the Scientific Evidence (September 2013 External Review Draft). The draft 

report (hereafter referred to as the “Report”) is a review and synthesis of the peer-reviewed scientific 

literature on the connectivity or isolation of streams and wetlands relative to large water bodies such as 

rivers, lakes, estuaries, and oceans. The purpose of the Report is to summarize the current understanding 

of these connections, the factors that influence them, and the mechanisms by which connected waters 

affect the function or condition of downstream waters. The Report was developed by ORD to inform

EPA and U.S. Army Corps of Engineers rulemaking related to the jurisdiction of the Clean Water Act. 

The Report is a scientific review and, as such, it does not set forth legal standards for Clean Water Act 

jurisdiction.

The literature review and synthesis in the Report focuses on describing: (1) a conceptual framework that 

represents the hydrologic elements of a watershed, the types of physical, chemical and biological 

connections that link them, and the watershed climatic factors that influence connectivity at various 

spatial and temporal scales; (2) the downstream connectivity and effects of ephemeral, intermittent, and

perennial streams; (3) the downstream connectivity and effects of waters and wetlands in floodplain 

settings; and (4) the downstream connectivity and effects of waters and wetlands in non-floodplain 

settings. Six case studies from the literature are included in the Report to illustrate the connectivity of 

water bodies in different landscape settings and geographic regions. 

The EPA asked the SAB to review the Report and comment on: the clarity and technical accuracy of the 

document; whether it includes the most relevant peer-reviewed literature; whether the literature has been 

correctly summarized; and whether the findings and conclusions in the Report are supported by the 

available science. This Executive Summary highlights the findings and recommendations of the SAB in 

response to the charge questions provided in Appendix A.

Overall Clarity and Technical Accuracy of the Report

The SAB was asked to provide its overall impressions of the clarity and accuracy of the Report. The 

Report is an extensive review of the literature on the connectivity of streams and wetlands to 

downstream1 waters; the SAB finds that the literature review is generally thorough and technically 

accurate. However, the Report could be strengthened by careful editing to ensure that it is more clearly 

organized, concise, and written in a consistent style. Some terms and definitions are not used 

consistently throughout the document. The SAB has proposed a revised conceptual framework which 

describes the hydrologic elements of a watershed and the connections that link them, and recommends 

that it be used to integrate the entire Report. Each section of the document should be clearly linked to 

this framework. In addition, the key points in each chapter of the Report should be clearly stated at the 

end of the chapter and the EPA should consider including in the Executive Summary a succinct table 

summarizing all of the key findings and the levels of certainty that could be associated with the findings.

1 In this SAB report, the term ”downstream” is used to refer broadly to connectivity that is both downstream and 

downgradient. All water (e.g., surface water, hyporheic flows, and groundwater) flows downgradient toward lesser hydraulic 

head than at the point of origin or point of interest. For most surface water flows, downgradient is also downstream. 

Sometimes the term “downgradient” is used in this SAB report to emphasize instances where hyporheic and groundwater

flows are especially important.

1

 
The EPA should also consider summarizing and displaying the conclusions in the Report in matrix form 

with brief characterizations of the temporal and spatial scales over which given functions or phenomena 

occur. In addition, the SAB recommends that the conclusions be more empirically and/or specifically 

described by providing a clearer indication of the breadth of support in the literature.

The Report is a science, not policy, document that was written to summarize the current understanding 

of connectivity or isolation of streams and wetlands relative to large water bodies such as rivers, lakes, 

estuaries, and oceans. Given the policy context, however, the Report could be more useful to decisionmakers if it brought more clarity to the interpretation of connectivity, especially with respect to

approaches for quantifying connectivity. The language used in the Report often suggests that

connectivity is a binary property (connected versus not connected) rather than a gradient. The SAB 

recommends that the interpretation of connectivity be revised to reflect a gradient approach that 

recognizes variation in the frequency, duration, magnitude, predictability, and consequences of physical, 

chemical, and biological connections. Moreover, relatively low levels of connectivity can be meaningful 

in terms of impacts on the chemical, physical, and biological integrity of downstream waters. The SAB 

also recommends that the Report more explicitly address: the cumulative effects of streams and wetlands 

on downstream waters and the spatial and temporal scales at which functional aggregation should be 

evaluated; the extent to which biological connections affect the integrity of downstream waters; the 

necessity of adopting watershed, riverscape, riverine landscape, and groundwater basin perspectives to 

understand connectivity; and the influence of human alterations on connectivity.

The literature review in the Report could be strengthened by more clearly describing the approach used 

to screen, compile, and synthesize the information and by including additional references recommended

by the SAB. The SAB finds that the case studies in the Report provide helpful illustrations of the 

connectivity of streams and wetlands in certain geographic areas to downstream waters. However, the 

case studies would be more useful if they were selected to represent geographically relevant examples of 

systems spanning the connectivity gradient. It also would be helpful to present the case studies more 

succinctly in text boxes throughout the document.

Clarity and Technical Accuracy of the Conceptual Framework in the Report

The SAB was asked to comment on the clarity and technical accuracy of the conceptual framework of 

watershed structure and function presented in the Report. The literature review supporting the 

conceptual framework is technically accurate but the SAB recommends some revisions to improve the 

clarity, accuracy, and usefulness of the framework. The SAB recommends clearly delineating the 

Report’s scope in terms of the types of wetlands and water bodies covered and focusing on functional 

roles of floodplains and riparian areas irrespective of their classification as waters and wetlands under 

the Clean Water Act. Connectivity should be defined at the beginning of the Report. The SAB 

recommends that this definition be systems-focused and, as such, include connections within and among 

entire watersheds and underlying aquifers. Different descriptors of connectivity drawn from the 

literature on disturbance ecology (e.g., frequency, magnitude) also might be helpful. The SAB also 

recommends expanding the discussion of approaches to measuring or otherwise quantifying 

connectivity. 

The SAB recommends that the conceptual framework in the Report be expressed as continuous physical, 

hydrological (surface and subsurface), chemical, and biological flowpaths connecting landscapes. The 

framework should illustrate the importance of climate, geology, and topographic relief on flow and 

transport and highlight the four-dimensional (longitudinal, lateral, vertical, and temporal) nature of 

connectivity. In the Report, the EPA discusses connectivity within a classification system based on 

2
discrete landscape settings (i.e., rivers and streams; waters and wetlands in floodplain settings; and 

waters and wetlands in non-floodplain settings). The SAB recommends that this classification system be 

mapped onto the flowpath framework to show that continuous phenomena interact across these discrete 

landscape settings. In the conceptual framework there should be more emphasis on the importance of 

groundwater mediated connectivity and biological connectivity. Additional layers of complexity also

should be included in the conceptual framework to reflect important issues such as spatial and temporal 

scales and human alteration of the hydrological landscape.

In the conceptual framework, the EPA has classified waters and wetlands based on their potential to 

have “bidirectional” or “unidirectional” hydrologic flows with rivers and lakes. Some “unidirectional”

wetlands are also called “geographically isolated wetlands.” However, the terms “bidirectional” and 

“unidirectional” do not adequately describe the four-dimensional nature of connectivity and therefore 

should be replaced with more commonly understood terms that are grounded in the peer-reviewed 

literature (e.g., waters and wetlands in floodplain settings). The term “geographically isolated wetlands”

is also misleading because connectivity occurs along a gradient. Therefore, “geographically isolated 

wetlands” should not be used as an organizational term in the Report. The SAB recommends that the 

EPA carefully define “geographically isolated wetlands” in terms of the literature and explain that the 

term does not imply functional isolation. In addition, the SAB recommends that a summary and 

synthesis of the conceptual framework be added to the end of Chapter 3 of the Report.

Ephemeral, Intermittent, and Perennial Streams: Review of the Literature

The SAB was asked to comment on whether the Report includes the most relevant literature on the 

connectivity and effects of ephemeral, intermittent, and perennial streams and whether the literature has 

been correctly summarized. The Report contains an extensive review of the scientific literature 

describing the connectivity of streams to downstream waters. However, further discussion of the 

literature on several specific topics is warranted. The Report should be expanded to include a more 

complete discussion of temporal dynamics of connectivity of streams as well as the processes involved 

in hydrologic exchange flows between main channels and off-channel areas. The discussion of naturally 

occurring chemical constituents, contaminants, contaminant transformation processes, and the influence 

of stream connectivity on downstream water temperature also should be expanded. In addition, the 

Report should more thoroughly document the evidence that the biological integrity of headwater streams 

and downstream waters is affected by the movement of biota throughout the lotic system. Other 

important topics that should be further discussed include: the consequences of human alteration of 

headwater streams; aggregate and cumulative effects of headwater streams on downstream waters; the 

effects of streamside vegetation on stream ecosystems; the importance of reciprocal food-web linkages 

between streams and their adjacent riparian areas; the role of groundwater and sediments in determining 

connectivity; and the degree or strength of downstream connections.

Ephemeral, Intermittent, and Perennial Streams: Review of the Findings and Conclusions

The SAB was asked to comment on whether the conclusions and findings concerning the connectivity of 

ephemeral, intermittent, and perennial streams are supported by the available science. The Report 

concludes that these streams exert a strong influence on the character and functioning of downstream

waters, and indeed that all tributary streams are physically, chemically, and biologically connected to 

downstream waters. Strong scientific support has been provided for this overall conclusion and related 

findings. The SAB notes that there is a gradient of connectivity that is a function of the frequency, 

duration, magnitude, predictability, and consequences of physical, chemical, and biological connections. 

The SAB recommends that the conclusions and findings concerning ephemeral, intermittent, and

3
perennial streams be quantified when possible, related to the four dimensions of connectivity

(longitudinal, lateral, vertical and temporal), and discussed with additional detail on biogeochemical 

transformations and biological connections. In addition, some hydrologic aspects of connectivity require 

additional detail; these include descriptions of key linkages and exchanges in tributary streams, such as 

groundwater-surface water interactions, and the role of transition areas between uplands and headwaters. 

Likewise, the Report should explain how hydrologic connectivity sustains both streams and aquifers, 

particularly in alluvial systems in the Southwest and in karst systems in the eastern United States. 

Selecting specific case studies to represent the gradient of connectivity and articulating the rationale for 

choosing the case studies would also help ensure that the key points are well illustrated.

Waters and Wetlands in Floodplain Settings: Review of the Literature

The SAB was asked to comment on whether the Report includes the most relevant literature on the 

connectivity and effects of waters and wetlands in floodplain settings and whether the literature has been 

correctly summarized. The SAB finds that the literature review substantiates the Report’s conclusion 

that floodplains and waters and wetlands in floodplain settings support the physical, chemical and

biological integrity of downstream waters. That said, the literature review and synthesis on the 

connectivity and downstream effects of waters and wetlands in floodplain settings is somewhat limited 

in scope (i.e., focused largely on headwater riparian wetlands) and should further consider the 

frequency, magnitude, duration, predictability, and consequences of connectivity pathways. This section

should be expanded to include the following topics: channel migration zones (which demonstrate the 

variable nature of connectivity of floodplains); the importance of lateral connections that support the 

biological integrity of downstream waters by creating a diversity of habitats for a wide array of species; 

and human impacts on connectivity. A more recent and diverse review of the biogeochemical 

implications of exchange flow (including the literature on the role of wetlands and floodplains as 

sources, sinks and transformers of nutrients and other chemical contaminants) should be included in the 

Report.

The SAB also recommends that the examples used in the Report be broadened to make it more 

representative of the United States. In particular, studies on peatlands in floodplain settings in northern 

tier states and Alaska, forested wetlands (including bottomland hardwoods), and coastal lowland 

wetlands in Hawaii could be incorporated. In addition, the functional role of floodplain systems in 

maintaining the ecological integrity of streams and rivers would be clearer if the literature on floodplain 

wetlands were reorganized. The text on low-order riparian areas and the effects of headwater, streamside 

areas on in-stream structure and function could be moved to the chapter of the Report that addresses 

ephemeral, intermittent, and perennial streams.

The SAB suggests that the term “bidirectional wetlands” be replaced with the term “waters and 

wetlands in floodplain settings” to reflect landscape position. The Report should also more explicitly 

discuss how floodplain environments are intimately linked to river systems both spatially and temporally 

by means of flood pulses. In this regard, the importance of the short-duration, high-intensity and longduration, low-intensity events should be compared and contrasted. In addition, the Report should 

emphasize the effects of floodplains not only on river flows, but also on hydrological connections and 

processes affecting biota, chemistry and sediment movement through downstream as well as lateral, 

vertical and temporal dimensions.

4
Waters and Wetlands in Floodplain Settings: Review of the Findings and Conclusions

The SAB was asked to comment on whether the conclusions and findings concerning the connectivity of 

waters and wetlands in floodplain settings are supported by the available science. The Report concludes 

that “bidirectional” wetlands and waters in floodplain settings are physically, chemically and

biologically connected with rivers through multiple pathways. There is strong scientific support for this

overall conclusion. However, additional literature could be included in the Report to bolster the

conclusion and the related findings. Many of the conclusions and findings concerning waters and 

wetlands in floodplain settings are drawn from literature related to non-floodplain riparian wetlands (i.e., 

within headwater riparian zones). 

A discussion of river-floodplain systems as integrated ecological units would be a useful addition to the 

Report, and the science of larger river (i.e., high-order) floodplain systems is a good starting point. The 

discussion of the findings and conclusions concerning waters and wetlands in floodplain settings should 

further address a number of other issues, including: the temporal dimension of connectivity of these 

waters and wetlands; the role of these waters and wetlands in storing and transforming chemical 

constituents; the role of biological connectivity (including food webs); quantification of groundwater

linkages; the effects of human alteration of connectivity; and the importance of considering 

aggregate/cumulative downstream effects of these waters and wetlands. In addition, the SAB 

recommends that consistent terminology be used throughout the Report to describe floodplain wetlands.

Waters and Wetlands in Non-floodplain Settings: Review of the Literature

The SAB was asked to comment on whether the Report includes the most relevant literature on the 

connectivity and effects of waters and wetlands in non-floodplain settings and whether the literature has 

been correctly summarized. In general, the EPA’s review and synthesis of the literature on the

downstream connectivity and effects of wetlands and waters in non-floodplain settings is technically 

accurate. The SAB recommends that the EPA consider reviewing and adding some additional literature. 

In particular, the SAB recommends reviewing publications that analyze bulk exchange of materials by 

biota, movement of nutrients by biota, introduction of disease vectors, and the provisioning of habitat 

essential for biological integrity and completion of life cycles of downstream species. Numerous 

additional literature citations addressing the roles of multiple biological taxa have been provided by the 

SAB for the EPA’s consideration. The review of the literature should also be expanded to include 

quantitative tools such as surface water quantity and quality modeling, sediment transport modeling, 

groundwater quantity and quality modeling, and biological/habitat/landscape modeling. These tools are

used by hydrogeologists, watershed scientists and engineers to assess the structure and function of nonfloodplain wetlands. The term “unidirectional wetlands” as used in the Report is misleading because it 

implies one-way hydrologic flows when, in fact, connectivity can have many spatial and temporal 

dimensions. The SAB recommends that the terms “unidirectional” and “geographically isolated” waters 

and wetlands be replaced in the Report; the term “non-floodplain waters and wetlands” is suggested as 

an alternative. The SAB also recommends that the EPA frame the discussion about the temporal and 

spatial scales and gradients of various connections between and among floodplain wetlands and nonfloodplain wetlands and downstream waters by considering the frequency, magnitude, duration, 

predictability, and consequences of connectivity pathways. The Report also should recognize that all 

aquatic habitats have some degree of connection, although such connections may not be relevant if they 

do not have important effects on the physical, chemical, and/or biological integrity of downstream 

waters. In addition, the Report should discuss the importance of assessing non-floodplain wetland 

connectivity and connectivity pathways in terms of aggregated wetland complexes and the legacy effects 

of human disturbances.

5
Waters and Wetlands in Non-floodplain Settings: Review of the Findings and Conclusions

The SAB was asked to comment on whether the conclusions and findings concerning the connectivity of 

waters and wetlands in non-floodplain settings are supported by the available science. The Report 

concludes that the literature reviewed does not provide sufficient information to evaluate or generalize 

about the degree of connectivity (absolute or relative) or the downstream effects of wetlands in nonfloodplain settings. The SAB disagrees with this overall conclusion. To the contrary, the SAB finds that 

the scientific literature provides ample information to support a more definitive statement (i.e., 

numerous functions of non-floodplain waters and wetlands have been shown to benefit the physical, 

chemical, and biological integrity of downgradient waters). Thus, the SAB recommends that the EPA 

revise the conclusion to focus on what is supported by the scientific literature and articulate the specific 

knowledge gaps that must be resolved (e.g., degree of connectivity, analyses of temporal or spatial 

variability). The SAB also recommends that the Report explicitly discuss the pathways by which nonfloodplain waters and wetlands can be connected to downstream waters and state that the evaluation of 

connectivity should be based on the frequency, magnitude, duration, predictability, and consequences of 

water, material, and biotic fluxes to downstream waters and their impact on the physical, chemical, 

and/or biological integrity of those waters.

The SAB recommends several additional revisions to improve the findings concerning non-floodplain

waters and wetlands. References to specific studies should be synthesized rather than individually 

reported, as they are intended to summarize general themes arising from the diverse literature. The key 

findings should be more explicitly presented and clearly explained in the text of the Report. In addition,

the key findings should address: the biological functions and biological connectivity of non-floodplain

wetlands; differences between natural and manmade wetlands; the importance and temporal dynamics of 

spatial proximity as a determinant of connectivity; and the importance of cumulative or aggregate 

impacts of non-floodplain wetlands.

6
2. INTRODUCTION

The National Center for Environmental Assessment in the EPA Office of Research and Development 

(ORD) has developed a draft report titled Connectivity of Streams and Wetlands to Downstream Waters: 

A Review and Synthesis of the Scientific Evidence (September 2013 External Review Draft). The draft 

report (hereafter referred to as the “Report”) is a review and synthesis of the peer-reviewed scientific 

literature on the connectivity or isolation of streams and wetlands relative to large water bodies such as 

rivers, lakes, estuaries, and oceans. The purpose of the Report is to summarize the current understanding 

of these connections, the factors that influence them and the mechanisms by which connected waters 

affect the function or condition of downstream waters. The Report was developed by ORD to inform

EPA and U.S. Army Corps of Engineers rulemaking related to the jurisdiction of the Clean Water Act. 

The Report is a scientific review and, as such, it does not set forth legal standards for Clean Water Act 

jurisdiction.

The literature review and synthesis in the Report focus on describing: (1) a conceptual framework that 

represents the hydrologic elements of a watershed, the types of physical, chemical, and biological 

connections that link them, and the watershed climatic factors that influence connectivity at various 

spatial and temporal scales; (2) the downstream connectivity and effects of ephemeral, intermittent, and 

perennial streams; (3) the downstream connectivity and effects of waters and wetlands in floodplain 

settings; and (4) the downstream connectivity and effects of waters and wetlands in non-floodplain 

settings. Six case studies from the literature are included in the Report to illustrate the connectivity of 

water bodies in different landscape settings and geographic regions. 

The EPA asked the SAB to review the Report and comment on: the clarity and technical accuracy of the 

document, whether it includes the most relevant peer-reviewed literature, whether the literature has been 

correctly summarized, and whether the findings and conclusions in the Report are supported by the 

available science. In response to the EPA’s request, the SAB convened an expert panel to conduct the 

review. The Panel held a public meeting on December 16-18, 2013 and teleconference meetings on 

April 28, May 2, and June 19, 2014 to deliberate on the charge questions and develop a consensus report

of its findings and recommendations. A large number of public comments were received for the SAB’s 

consideration (Docket EPA-HQ-OA-2013-0582). During Panel deliberations a number of issues 

identified in the public comments were raised for discussion. The Panel’s draft report was reviewed and 

discussed by the chartered SAB at a teleconference on September 26, 2014. This SAB report provides 

the findings and recommendations of the SAB in response to the EPA charge questions (Appendix A). 

The SAB recommendations are highlighted at the end of each section of this report.

7
3. RESPONSES TO EPA’S CHARGE QUESTIONS

3.1. Overall Clarity and Technical Accuracy of the Draft Report

Charge Question 1. Please provide your overall impressions of the clarity and technical accuracy 

of the draft EPA Report, “Connectivity of Streams and Wetlands to Downstream Waters: A Review 

and Synthesis of the Scientific Evidence.” 

The EPA’s Report is an extensive review of the literature that is generally thorough and technically 

accurate. That said, the Report could be improved with additional effort to: (1) ensure consistency and 

continuity in style and organization throughout the document; (2) improve the usefulness of the 

document to decision-makers; (3) strengthen the literature review in several key places; (4) provide 

further detail and clarification of concepts in some parts of the document; and (5) restructure the case 

studies. Each of these points is discussed below.

3.1.1. Style and Organization of the Draft Report

There are stylistic differences among the chapters of the Report, and the writing needs to be reworked 

for consistency and continuity so that it is written in a single voice. There also is a strong need to check 

for consistent use of terms and definitions among the chapters, subchapter sections, and the glossary. To 

prevent confusion, the EPA should avoid using words that may denote particular legal or regulatory 

meanings (e.g., significant, adjacent) unless a definition is provided. The Report is long and repetitive in 

places, with the main points easily lost in the volume of material presented. Superfluous or redundant 

information should be removed, being careful that only concise text supporting the key findings is 

included. A technical editor could provide great support for this process.

Several organizational changes will improve the readability of the Report. First, each section of the

Report should be clearly linked to and consistent with the conceptual framework. Second, each 

paragraph and/or subsection of the Report should have parallel structure where main points are clearly 

articulated at the end – perhaps even in bold or underlined text. Third, key points should be stated 

simply and directly at the end of each chapter. Fourth, the authors should consider including in the 

executive summary a succinct table that summarizes the key findings and levels of certainty of each 

finding within the Report. The report of the Intergovernmental Panel on Climate Change (IPCC 2007) is 

an excellent model for this approach. 

Key Recommendations

• The Report should be edited to ensure that it is written in a consistent style and each section should 

be clearly linked to the conceptual framework. 

• Terms and definitions should be used consistently throughout the Report and, to avoid confusion,

caution should be exercised when using words that may have legal or regulatory meanings.

• Key points should be clearly stated at the end of each chapter and the EPA should consider including 

in the Executive Summary a succinct table summarizing the key findings and level of certainty 

associated with each.

8
3.1.2. Improving the Usefulness of the Report to Decision-Makers

Although the Report is a science, not policy, document, the SAB recognizes that it was written to inform

the EPA’s efforts to clarify the jurisdiction of the Clean Water Act. This objective of the Report should 

be clearly stated and more information should be included to provide greater insight on complex or 

nuanced issues to be addressed in evaluating connectivity. For example, throughout the Report there 

could be greater focus on the literature that addresses various aspects of quantifying the frequency, 

duration, magnitude, predictability, and consequences of connectivity. The authors might consider an 

approach similar to that used in the report of the Intergovernmental Panel on Climate Change (IPCC 

2007), which would provide an estimate of the relative certainty of connectivity or a downstream effect,

and other approaches (e.g., Keeney and Gregory 2005; Gregory et al. 2012) which would be more 

flexible and useful from the standpoint of informing decisions. As written, the Report uses language that 

often suggests that connectivity is a binary property – something either present or absent, rather than a

gradient. Many of the public commenters remarked that the binary perspective in the Report implies that 

any connectivity must significantly affect the biological, physical, or chemical integrity of downstream1

waters. This is not always the case. Although connectivity is known to be ecologically important even at 

the lower end of the gradient, the frequency, duration, predictability, and magnitude of connectivity will 

ultimately determine any consequences to downstream waters. 

The SAB also finds that the Report would be strengthened if it contained: (1) additional review of the 

scientific literature that quantifies the frequency, duration, predictability, and magnitude of physical, 

chemical, and biological connections for each type of “water” and consequences of that connectivity for 

the physical, chemical, and biological integrity of downstream waters, with key uncertainties made 

explicit; (2) a more explicit discussion of the cumulative effects of streams and wetlands on downstream 

waters (i.e., multiple streams and/or wetlands considered in aggregate) including a discussion of the 

spatial and temporal scales at which the functional aggregation should be evaluated; and (3) an 

explanation that the definitions used for rivers, streams, and wetlands are scientific, rather than legal or 

regulatory definitions, and may differ from those used in the Clean Water Act and associated 

regulations.

Key Recommendations

• As further discussed in Section 3.8.1 of this report, the SAB recommends that the interpretation of 

connectivity be revised from a binary, categorical distinction (connected versus not connected) to a 

gradient that is a function of the frequency, duration, magnitude, predictability, and consequences of 

physical, chemical, and biological connections. Approaches to measuring or otherwise quantifying 

connectivity are discussed in Section 3.2.3 of this SAB report.

• The Report should clearly indicate that the definitions used for rivers, streams, and wetlands are 

scientific rather than legal or regulatory definitions, and may differ from those used in the Clean 

Water Act and associated regulations.

1 In this SAB report, the term ”downstream” is used to refer broadly to connectivity that is both downstream and 

downgradient. All water (e.g., surface water, hyporheic flows, and groundwater) flows downgradient toward lesser hydraulic 

head than at the point of origin or point of interest. For most surface water flows, downgradient is also downstream. 

Sometimes the term “downgradient” is used in this report to emphasize instances where hyporheic and groundwater flows are 

especially important.

9

 
3.1.3. Strengthening the Literature Review

The literature review in the Report can be strengthened by clarifying what was considered as peerreviewed literature, the kinds of evidence used to support the findings and conclusions in the Report, and 

the number and types of studies selected for review. The approach used for screening, compiling, and 

synthesizing information should be made explicit. In particular, the “weight of evidence” approach used 

to evaluate multiple references should be described in more detail. In this regard, the SAB finds that the 

EPA Report appears to take a somewhat unconventional approach to the “weight of evidence” review. 

This concern is magnified by the report’s reliance on solely peer-reviewed literature, together with the 

lack of clearly described selection and screening criteria. Peer-reviewed literatures and associated 

literature reviews are often subject to some degree of publication and selection bias (Begg and Berlin 

1988; Møller and Jennions 2001). In such contexts, unsystematic “weight of evidence” reviews can 

provide misleading results. 

The extent to which an exhaustive literature review was performed should be clearly stated in the 

Report. The SAB recommends that the EPA report include a separate section that details methods used 

to identify, screen, compile and synthesize evidence from the literature. This should address both the 

studies used to derive “weight of evidence” conclusions and those used for illustrative case studies. This 

section should include, as applicable, details such as databases searched, keywords used, screening 

criteria applied, and additional approaches used to identify relevant literature. These and related details 

would help engender confidence that the report’s conclusions are based on an objective and systematic 

review of the available evidence. It would also clarify the extent to which potentially confounding issues 

(e.g., selection effects; Rosenberger and Johnston 2009) might influence the results of the report. The 

SAB has provided numerous additional references for the EPA’s consideration, and other references 

have been suggested in written comments from the public.

The SAB also finds that the EPA could better highlight gaps in the understanding of certain wetland and 

stream systems and/or geographic areas by including in the Report a table that shows the distribution of 

the scientific literature for various regions of the United States. 

Key Recommendations

• The literature review in the Report should clearly describe the approach used to screen, compile, and 

synthesize the information and indicate: (1) what was considered to be peer-reviewed literature; and 

(2) the number and types of studies selected for review.

• EPA should include in the Report appropriate additional information from references provided by 

the SAB and members of the public.

3.1.4. Additional Detail and Clarification of Text Needed in the Report

As further discussed in other sections of this SAB report, the following topics in the EPA Report need 

clarification and/or additional detailed information:

a) The importance and relevance of different spatial and temporal scales. The EPA should discuss the 

relevant spatial and temporal scale for assessing connectivity in different water systems and the 

spatial scales and time frames over which wetlands are functionally aggregated. Understanding the 

spatial and temporal scales at which connectivity affects the physical, chemical, and biological 

10
integrity of downstream waters is central to evaluating and predicting connectivity and its 

consequences. The relevant scale of connectivity may be clarified by considering the most important 

consequences or problems over particular temporal and spatial scales.

b) The extent to which biological connections among water systems affect the integrity of downstream

waters. The movement of birds, mammals, and other fauna (e.g., amphibians, fish, and 

invertebrates), among systems can mediate important material transfers to downstream waters. This 

movement can also be a critical source of organisms necessary to support viable populations and 

functions that contribute to ecological integrity of downstream waters. Biological connectivity 

should be evaluated across complete annual and full life cycles, as well as through food web 

interactions. The SAB also notes that free-flowing freshwaters ultimately drain into the sea; between 

marine and fresh waters are transitional waters that have a gradation from slightly salty to almost 

fully marine. Saltwater can move upstream under freshwater in salt wedge estuaries. Biota and 

substances move up and down stream differently in transitional waters than in fresh water (Chapman 

et al. 2013). Literature references concerning biological connectivity are provided in Appendix B 

and in other sections of this SAB report.

c) The necessity of adopting watershed, riverscape, riverine landscape, and groundwater basin 

perspectives to understand connectivity. Viewing systems as part of these larger basins, riverscapes

and watersheds permits a greater understanding of interactions and feedbacks with floodplain and 

riparian vegetation, groundwater and subsurface waters, and other surface water features that can 

ultimately impact downstream waters.

d) The importance of considering water bodies in aggregate (e.g., groups of tributaries, floodplains, 

floodplain wetlands and non-floodplain wetlands) for evaluations of connectivity.

e) The role and temporal dynamics of groundwater, sediments, and chemical and biological 

parameters in establishing connectivity of water bodies.

f) The influence of human alterations on connectivity. Examples of human alterations that could affect 

connectivity in ways that impact the integrity of downstream waters include directly eliminating, 

restoring, or altering connectivity via roads, agricultural tiles, dams, pumping groundwater, 

irrigation, channelization, and other manmade infrastructure (piped streams, stormwater pipes). 

Certain systems, such as those sustained by human wastewater effluents, are more closely tied to 

human alterations than others. Functions associated with these human-altered systems and their 

natural counterparts should be evaluated using the scientific literature.

g) Approaches to assess or measure connectivity. It would be useful to provide examples of the various 

dimensions of connectivity that are most appropriately quantified, ways to construct connectivity 

metrics (e.g., retrospective or prospective analyses, model simulations, spatial analyses), and the 

scientific, methodological, and technical advances most needed to understand and estimate

connectivity.

h) Reporting the literature findings more quantitatively. When detailed information is available it 

would be useful to report the literature findings quantitatively rather than as simple qualitative 

statements. For example, as discussed in Section 3.5.4 of this SAB report, rather than stating that 

nitrogen levels increased or decreased, it would be helpful to indicate the percent concentration 

change.

11
3.1.5. Restructuring the Case Studies 

The SAB finds that the case studies in the Report provide helpful illustrations of connectivity between 

downstream waters and geographically specific types of systems. That said, case studies could be even 

more helpful if they were selected and organized to illustrate different points along the gradient of 

connectivity (i.e., less to more connected) and examples of different types of water bodies, including at 

least one where intermittent connectivity is important. As further discussed in Sections 3.3.9 and 3.5.6 of 

this SAB report, it would be useful to include case studies representing a greater range of geographic 

regions and systems such as Southwest arid, Midwest mesic, Arctic permafrost, human-modified 

systems, forested wetlands, and bottomland forests. As discussed in Section 3.2.5 of this SAB report, 

comparisons among geographic regions could be accomplished by using climate, geology, and relief,

which vary regionally and form the basis of the concept of Hydrologic-Landscape Regions, i.e., HLRs, 

(Wolock et al. 2004) as a framework for the case studies. 

An alternative approach would be to present case study summaries as brief textboxes to clearly and 

simply articulate key points, with reference to the expanded versions in appendices if deemed necessary. 

The rationale for selecting different case studies and the key points illustrated by each should be 

explicitly stated early in the text. If expanded in the appendices, each case study could have a conceptual 

model diagram showing the surface and subsurface flowpaths illustrating the connectivity 

between/among systems. 

Key Recommendations

• The rationale for selecting different case studies and the key points illustrated in each should be 

clearly stated early in the text.

• The EPA should consider distilling case studies into brief summaries presented in text boxes that: (1) 

provide short, clear illustrations of where different systems lie along the gradients of connectivity,

and (2) highlight differences in the ecologically relevant temporal and spatial scales. The reader also 

should be able to see how the case studies align with hydrological, chemical, and biological 

flowpaths connecting watersheds (discussed in Section 3.2 of this SAB report). If expanded case 

studies are desired, these should be presented in the appendices. Case studies could serve to 

highlight areas of certainty in the EPA’s conclusions as well as knowledge gaps.

• The EPA should consider including case studies of a greater range of geographic regions.

3.2. Conceptual Framework: An Integrated, Systems Perspective of Watershed Structure

and Function

Charge Question 2. Chapter 3 of the draft Report presents the conceptual basis for describing 

the hydrologic elements of a watershed; the types of physical, chemical, and biological 

connections that link these elements, and watershed climatic factors that influence connectivity 

at various temporal and spatial scales (e.g., see Figure 3-1 and Table 3-1). Please comment on 

the clarity and technical accuracy of this Chapter and its usefulness in providing context for 

interpreting the evidence about individual watershed components presented in the Report. 

The SAB finds that the literature review in Chapter 3 of the Report is technically accurate and readable, 

although it could be strengthened with technical editing. However, the conceptual framework needs to 

12
be revised and clearly articulated at the beginning of the Chapter. As further discussed below, the SAB 

finds that the following revisions are needed to improve the clarity, accuracy, and usefulness of the 

conceptual framework in the Report: (1) connectivity should be clearly defined at the beginning of 

Chapter 3; (2) the scope of the Report (i.e., the types of waters and wetlands covered) should be clearly 

defined at the beginning of Chapter 3; (3) the conceptual framework should be expressed as 

hydrological, chemical, and biological flowpaths; (4) certain terms (e.g., “unidirectional” and 

“bidirectional”) used in the Report should be replaced with more commonly understood terminology 

from the peer-reviewed literature; (5) additional layers of complexity (e.g., water and wetland function, 

spatial and temporal scales, the influence of human activities, Hydrologic Landscape Regions, aggregate 

and cumulative effects, and map resolution) should be represented in the conceptual model; and (6) a 

summary and synthesis of the conceptual framework should be added at the end of Chapter 3. 

3.2.1. Conceptual Framework

A typical conceptual framework is a concise tool used to make conceptual distinctions and organize 

ideas. The best conceptual frameworks draw simple analogies and are easy to remember. Although

Chapter 3 of the Report certainly includes a great deal of information that supports a conceptual 

framework, the framework should be strengthened and made more explicit (see Section 3.2.3 below). In 

addition, the SAB recommends that the Chapter be retitled “An Integrated Systems Perspective of 

Watershed Structure and Function” to better reflect the content, which includes both the conceptual 

framework and attendant details that support the remainder of the Report. 

3.2.2. Defining Connectivity and Isolation

Because “connectivity” and “isolation” can be defined in many ways, the Report must concisely define 

them at the beginning of Chapter 3. Currently, only connectivity is defined, but long after much of the 

conceptual framework has been presented and discussed (page 3-28). The definition of connectivity also 

should be extended to the entire landscape (i.e., not just to waters and wetlands but to entire watersheds 

and underlying aquifers) through a broader vision of local- to landscape-scale physical, chemical, and 

biological exchanges. The definition and discussion of connectivity at the beginning of Chapter 3 should

be brief, with the many details and nuances addressed later. SAB concerns associated with EPA’s 

definition and use of the term “geographically isolated wetlands” have been previously noted and are 

further discussed below.

The definition of connectivity used in the Report seems to follow that of Pringle (2001, 2003); i.e., the 

transfer of matter, energy, and/or organisms within or between elements of the landscape. The scientific 

literature shows that connectivity is a scalable quantity ranging continuously from fully connected to 

completely isolated, rather than a binary condition of either connected or isolated. The Report should 

articulate that connectivity is spatially and temporally scale dependent, and all elements of the landscape 

are connected when considered at sufficiently long temporal scales. Moreover, elements that appear 

isolated at one time (e.g., a dry season) might otherwise be connected at another time (e.g., during an 

intense rainstorm, during a wet season). This point could be expressed in a simple conceptual figure in 

Chapter 3, and then again as more specific figures in chapters on each water and wetland type covered in 

the Report (see, for example, Figure 3 in Section 3.7.3 of this SAB report.) 

The definitions of connectivity and isolation can be clarified by drawing more upon the literature on 

quantitative metrics of connectivity, Ali and Roy (2010) and Larsen et al. (2012) and references therein, 

or alternatively from the literature on disturbance ecology (see Stanley et al. 2010 and references 

therein). Reiners and Driese (2006) outline physical transport processes in nature. Larsen et al. (2012) 

13
review many definitions of connectivity and associated metrics in hydrology and ecology beginning 

with the conceptual definition of Pringle (2001) and extending to more precise definitions that are more 

amenable to quantification. For example, Larsen et al (2012) define connectivity as transport or dispersal 

potential along a given direction in a patchy or complex landscape, which can be quantified by a 

directional connectivity index that varies between zero and one. A complementary viewpoint is 

apparent from the literature of disturbance ecology, given that disturbances change the physical, 

chemical, and/or biological environment and are commonly quantified in terms of physical measures of 

the disturbance itself (e.g., frequency, magnitude, duration). Predictability and the rate of change are

often part of this definition (e.g., Resh et al. 1988; Poff 1992). By adding these details, connectivity and 

isolation could be viewed conceptually along a continuum ranging from fully connected to completely 

isolated, with a transition somewhere in between that varies case-by-case and is defined by whether or 

not a perturbation is outside the normal range and relevant to the biota.

Key Recommendations

• Connectivity and isolation should be defined and discussed at the beginning of Chapter 3 of the 

Report.

• The definition of connectivity in the Report should be extended to the entire landscape through a 

broad vision of local- to landscape-scale physical, chemical, and biological exchanges.

• The definition of connectivity and isolation could be clarified by connecting to literature on 

quantitative metrics of connectivity and disturbance ecology.

3.2.3. Measuring or Otherwise Quantifying Connectivity

The Report should discuss approaches to measuring or otherwise quantifying connectivity. Such 

approaches should recognize that connectivity is, in part, determined by the extent to which impacts to

one water body will affect chemical, physical, and/or biological integrity of downstream waters. In 

addition, multiple dimensions of connectivity should be described as sources and mechanisms of 

transport and transformation (i.e., fluxes of water, material, biota) and associated ecological functions 

(e.g., lag, refuge, and transformation) manifest along multiple flowpaths (e.g., via surface water, the 

hyporheic zone, and groundwater). Moreover, assessments should occur at spatial and temporal scales 

that permit evaluation of the cumulative effects of connectivity over time and the aggregate effects of 

connectivity over space. Therefore, the EPA should expand the brief overview of approaches to 

measuring connectivity that is provided on pages 6-6 and 6-7 of the Report. This expansion would be 

most useful if it provided examples of the dimensions of connectivity that are most appropriately 

quantified, ways to construct connectivity metrics (e.g., retrospective or prospective analyses, model 

simulations, spatial analyses), and the most needed methodological and technical advances. 

Insights from Hydrologic Systems

Future efforts to quantify connectivity can be informed by the wide variety of conceptual models and 

quantitative tools that have been developed to evaluate the connectivity of both surface and subsurface 

hydrological systems in different settings, including non-floodplain wetlands. The standard approach 

involves first characterizing the surface and subsurface elements of landscapes. Important elements are

climate, geology, topographic relief, and the amount, distribution and types of waters and wetlands. 

These elements can then be integrated to create a flowpath network that describes connectivity (Heath 

1983; ASTM 1996; Kolm et al. 1996; Winter et al. 1998). This approach has been extended to biological 

14
connectivity and hydrogeomorphic (HGM) wetland classifications (e.g., Kolm et al. 1998). Of course, 

the approach to quantifying hydrologic connectivity is not identical across systems, and careful attention 

must be given to identifying the most appropriate techniques (Healy et al. 2007; Bracken et al. 2013) 

and metrics (Lexartza-Artza and Wainwright 2009; Ali and Roy 2010; Wainright et al. 2011; Larsen et 

al. 2012). 

The Report also can draw on examples related to water quantity and quality modeling (Appel and Reilly 

1994; Sun et al. 1997; Harbaugh 2005; Parkhurst et al. 2010; Cunningham and Schalk 2011), integrated 

surface water groundwater modeling (Markstrom et al. 2008; Ely and Kahle 2012; Huntington and 

Niswonger 2012; Woolfenden and Nishikawa 2014), sediment transport modeling (Nelson et al. 2003; 

McDonald et al. 2005), and watershed and biological/habitat/landscape modeling (Kinzel et al. 1999,

2005; Hunt et al. 2013). Approaches have also been developed to quantify linkages due to groundwater

movement and storage (Heath 1983) and the effects of “flood pulses” (Kolm et al. 1998). Likewise, the 

role of chemical movement and storage to groundwater systems in floodplains has been quantified by 

flow and transport modeling (Winter et al. 1998; Markstrom et al. 2008; Woolfenden and Nishikawa 

2014) as well as with steady-state and transient analyses that simulate temporal changes (Appel and 

Reilly 1994; Winter et al. 1998; Nelson et al. 2003; Conaway and Moran 2004; Harbaugh 2005; 

McDonald et al. 2005; Markstrom et al. 2008; Huntington and Niswonger 2012). 

A growing number of studies are using graph-theory-based indices of connectivity to better understand 

aquatic systems. These studies should be considered in developing the discussion of approaches to 

quantify connectivity. For example, Van Looy et al. (2013) used the Integral Index of Connectivity to 

quantify connectivity and habitat availability in a dendritic river network across varying spatial scales. 

Wainwright et al. (2011) demonstrated how responses of river systems to vegetation removal, runoff, 

and erosion were better predicted by measures of structural and functional connectivity. Other metrics 

integrate hydrological and ecological connectivity using the Directional Connectivity Index and 

connectivity-orientation curves, which effectively quantified physical-biological feedbacks in the 

Everglades (Larsen et al. 2012). Malvadkar et al. (2014) recently examined numerous metrics drawn 

from graph-theory, including Betweenness Centrality, Integral Index of Connectivity, Coincidence 

Probability, Eigenvector Centrality, Probability of Connectivity, and Influx Potential. 

Connectivity also can be described using six metrics commonly used in hydrology and disturbance 

ecology – frequency, magnitude, timing, duration, rate of change, and predictability (e.g., Resh et al. 

1988; Poff 1992; Poff et al. 1997). These can be defined in hydrological, chemical, or biological terms. 

For example, in hydrological terms, frequency describes how often a flow of a particular magnitude

occurs, magnitude is the amount of water moving past a fixed location per unit time, duration is a 

measure of how long such a flow persists, and the rate of change is how quickly one flow gives way to 

another. These first five metrics comprise the components of the natural flow regime (Poff et al. 1997). 

The last metric, predictability, takes all of these into account (e.g., predictability of a given flow can be

indicated by the presence or absence of flow-dependent biota).

The temporal and spatial predictability of connectivity is especially important to quantify when 

assessing potential for downgradient effects in systems without permanent or continuous flowpaths (e.g., 

Poff and Ward 1989; Lytle and Poff 2004; Poff et al. 2006). Predictability refers to the regularity at 

which certain flows occur. Some mechanisms of connectivity are predictable (e.g., migration of 

anadromous fish and waterfowl, spring flood pulses and late summer low flows, seasonal peaks of 

aquatic insect emergence), whereas others are less so (e.g., flood events from storms, short-term and/or 

stochastic movement of organisms, nutrient spiraling dynamics). Predictable events can profoundly 

shape systems. For example, sequential and predictable seasonal flooding and drying events over an 

15
annual cycle are formative processes of physical, chemical, and biological attributes of streams in 

Mediterranean biomes, including parts of the western United States (Gasith and Resh 1999). Large 

seasonal waterfowl migrations can move nutrients, plants (seeds), and invertebrates between wetlands 

and downgradient waters (e.g., Figuerola et al. 2003; Green et al. 2008). A predictability axis could be 

folded into the current “gradient of connectivity” framework suggested by the SAB (Figure 3 in Section 

3.7.3 of this report).

Key Recommendations

• The Report should discuss approaches to measuring or otherwise quantifying connectivity. This 

could be done by expanding the brief overview of approaches to measuring connectivity that is 

provided on pages 6-6 and 6-7 of the Report. 

• Approaches to measuring or otherwise quantifying connectivity should be drawn from both the 

hydrological and disturbance ecology literature.

3.2.4. Defining the Scope of the Report

The SAB finds that the scope of the Report, with respect to the types of waters and wetlands covered, 

needs to be clearly defined and discussed at the beginning of Chapter 3. As a synthesis of the scientific 

literature, the Report appropriately includes discussion of the relevant literature on processes that occur 

across landscapes to connect various waters and wetlands, relying on science-based and ecological (i.e., 

Cowardin et al. 1979) rather than regulatory definitions of waters and wetlands. That said, the Report is 

unclear about the degree to which its definitions of waters and wetlands include broader portions of the 

landscape (e.g., whether wetlands or rivers include their floodplains), and this could be clarified with 

discussion of functional roles of landscape elements. Many public commenters have expressed concern 

about the potential expansion of the scope of jurisdiction of the underlying Clean Water Act – from 

“three-parameter” to “one-parameter” waters and wetlands2

. These concerns could be addressed in a 

separate section outlining the scope of the Report immediately after the section defining connectivity. 

The Report should discuss the functional role of floodplains and riparian areas (i.e., the riverine 

landscape) regardless of their regulatory status. However, it should be made clear that this discussion 

does not imply an expansion of the definition of waters and wetlands under the jurisdiction of the Clean 

Water Act. The SAB recognizes that the Report is a scientific and not a policy document, but finds that 

ignoring this distinction only serves to create unnecessary confusion and concern among the readership.

Key Recommendations

• The scope of the Report should be clearly delineated, with special attention paid to defining the 

types of wetlands and water bodies covered.

• The Report should consider the functional role of floodplains and riparian areas (i.e., the riverine 

landscape) irrespective of their classification as waters and wetlands under the Clean Water Act (see 

discussion in Section 3.5.2 of this SAB report). 

2 The “one parameter” wetland classification system (Cowardin et al., 1979) classifies an area as a wetland if it has one or 

more of the following three attributes: (1) the area supports predominantly hydrophytes 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. The “three parameter” classification system 

(33CFR 328.3(b); USACE 1987) requires that an area have all three of these attributes to be classified as a wetland.

16

 
3.2.5. Revising and Defining the Terminology Used in the Report

With regard to the discrete categories of systems discussed in the Report (i.e., rivers and streams, waters

and wetlands in floodplain settings, and waters and wetlands in non-floodplain settings), the SAB finds 

that “bidirectional” and “unidirectional” are misleading terms. The Report uses these terms to describe 

wetlands and open waters with: (1) the potential for non-tidal, “bidirectional” hydrologic flows with 

rivers and lakes; or (2) the potential for “unidirectional” hydrologic flows to rivers and lakes. The fourdimensional nature of connectivity (longitudinal, lateral, vertical, and temporal) is a foundational aspect 

of freshwater ecology (e.g., Ward 1989). “Bidirectional” and “unidirectional” hydrologic flow certainly 

describes a key difference among wetland and open water systems. Indeed, in some landscape settings, 

there are two-way fluxes of water and water-borne materials between the landscape and the rivers and 

streams, while in other landscape settings there are only one-way fluxes of water and water-borne 

materials from the landscape to the rivers and streams. Although this is an important difference, it does 

not adequately characterize the four-dimensional fluxes in both landscapes. The key difference in the 

respective settings is landscape position, with some waters and wetlands having flood-pulse exchanges 

with rivers and streams and other waters, and wetlands not having flood-pulse exchanges with rivers and 

streams. Therefore, the SAB recommends that the terms “unidirectional” and “bidirectional” be changed 

to terms reflecting a commonly understood classification system that is grounded in the literature. This 

is important not only for communication purposes but also because it is consistent with the peerreviewed, literature-based focus of the Report. One possibility is that, after defining the term 

“floodplain” at the beginning of the Report, “bidirectional” wetlands could be called “waters and 

wetlands in floodplain settings” and “unidirectional” wetlands could be called “waters and wetlands in 

non-floodplain settings.”

Use of the term “geographically isolated wetlands” in the Report is problematic. “Geographically 

isolated wetlands” technically means “wetlands isolated in space” but the term is defined in the Report 

to mean “wetlands surrounded by uplands.” These are very different definitions. The SAB 

acknowledges that the term “geographically isolated wetlands” has been established in the literature, and 

is commonly used (e.g., Tiner 2003a,b). However, as discussed in other sections of this SAB report, at 

sufficiently large spatial and temporal scales, all waters and wetlands are connected. More important are

the degree of connection (e.g., frequency, magnitude, timing, duration) and the extent to which those 

connections affect the chemical, physical, and biological integrity of downstream waters. A final point is 

that the term “geographically isolated wetlands” does not fit into the current conceptual framework in 

the Report because the Report explicitly states that geographically isolated wetlands can occur in both 

floodplain settings and non-floodplain settings. Therefore, “geographically isolated wetlands” should not 

be used as an organizational term in the Report. The SAB recommends that the EPA carefully define 

“geographically isolated wetlands” in terms of the literature, explain that the term “geographically 

isolated wetlands” does not imply functional isolation. The SAB further recommends that the EPA then 

remove the term from later sections of the Report or, at the very least, ensure that the term is used 

consistently and not interchangeably with other terms, as it has been on occasion in the section of the 

Report on “unidirectional” wetlands.

Key Recommendations

• The terms “bidirectional” and “unidirectional” should be replaced in the Report with more 

commonly understood terms that are grounded in the peer-reviewed literature. The SAB suggests

that “bidirectional” wetlands be called “waters and wetlands in floodplain settings” and 

“unidirectional” wetlands be called “waters and wetlands in non-floodplain settings.”

17
• The term “geographically isolated wetlands” is misleading because it implies functional isolation 

and does not directly map onto the organizational terminology in the Report. The EPA should not 

use “geographically isolated wetlands” as an organizational term in the Report. The EPA should 

draw upon the literature to carefully define “geographically isolated wetlands” and explain that the 

term does not imply functional isolation.

3.2.6. Use of a Flowpath Framework

Chapter 3 of the Report contains detailed information about river system characteristics, the effects of 

streams and wetlands on downstream waters, and factors influencing connectivity. However, the 

conceptual framework is not explicit, which makes it difficult to categorize and organize this detailed 

information. Thus, the SAB recommends that a conceptual framework be established and discussed at 

the beginning of Chapter 3. This conceptual framework could be expressed as continuous hydrological 

(surface and subsurface), chemical, and biological flowpaths connecting watersheds from “ridge to 

reef,” (i.e., highlands to lowlands) and therefore connecting waters and wetlands to downgradient 

waters. The flowpath framework should highlight the four-dimensional nature of connectivity, because 

four-dimensional connectivity scaled in a habitat-to-watershed context is a foundational aspect of 

freshwater ecology (e.g., Ward 1989). The flux and transformation of water, materials, and organisms –

which fundamentally control the integrity of downgradient freshwater ecosystems – occur at varying 

rates primarily determined by climate, geology, topographic relief, and biology and are expressed in 

terms of surface water and groundwater storage and flow through the landscape (e.g., uplands, wetlands, 

lakes, rivers, and floodplains). Therefore, these flowpaths are inherently four-dimensional (i.e., 

longitudinal, lateral, vertical, and through time). 

The flowpath framework could be briefly presented and discussed in the context of a revised Figure 1-1 

(currently on page 1-2 of the Report), which could be moved to the beginning of Chapter 3 and 

expanded to include at least some representation of hydrological, chemical, and biological flowpaths. In 

the revised figure, each representative type of flowpath could be color-coded (e.g., blue for hydrological, 

red for chemical, and green for biological). The revised Figure 1-1would thus become Figure 3-1. In the 

conceptual framework, hydrological flowpaths should be expressed in terms of both surface water and 

groundwater flowpaths, with the latter including the potential for groundwater connections to cross 

watershed boundaries (McDonnell 2013). Chemical flowpaths should be expressed as largely following 

hydrological flowpaths, with subtle differences such as the typically tight nutrient spiraling transitioning 

to increasingly open spiraling from the headwaters to the outlet (Newbold et al. 1981). Chemical 

flowpaths also could be expressed as sometimes following biological flowpaths, with examples 

including marine-derived nutrients being transported to headwater streams by anadromous fish and 

nutrients being transported between waters and wetlands by birds that eat in one location and defecate in 

another (Helfield and Naiman 2001). Biological flowpaths should be expressed as aquatic, terrestrial, 

and aerial flowpaths connecting watersheds internally “ridge to reef” and “reef to ridge” and including 

the potential for biological connections to cross watershed boundaries (Skagen et al. 2008). Taken to the 

extreme, the revised Figure 1-1 could become almost infinitely complex and equally incomprehensible, 

so it is important to clearly state that this is a conceptual framework with representative rather than 

complete flowpaths.

Groundwater connectivity, in particular, could be better represented in the Report. The U.S. Geological 

Survey (USGS) has published numerous reports and learning tools on groundwater connectivity, 

including examples of flowpath frameworks expressed in block diagrams (Heath 1983, 1984; Winter et 

al. 1998), that contain flows through floodplains. Care should be taken not to imply that bedrock is 

impermeable because groundwater flows through bedrock are important flowpaths that connect 

18
hydrologic landscapes over long distances and often across watershed boundaries (e.g., Roses et al. 

1996). 

An important next step is to state how the revised conceptual framework is used in the Report. 

Connectivity should be discussed as a continuous phenomenon. However, the SAB recognizes that the 

EPA has chosen to discuss landscape settings discretely in the Report, with separate sections for “rivers 

and streams,” “waters and wetlands in floodplain settings,” and “waters and wetlands in non-floodplain 

settings.” This approach is workable as long as the discrete classification is mapped onto the continuous 

conceptual framework. The integration of the discrete classification and continuous framework could be 

achieved by adding two panels to the revised Figure 1-1 described above, using the same base block 

diagram. In the second block diagram, all flowpaths could be removed and the classification system 

showing the three landscape settings (i.e., rivers and streams, waters and wetlands in floodplain settings, 

and waters and wetlands in non-floodplain settings) could be added. Then, in the third block diagram, 

the first and second block diagrams could be merged, clearly showing that the continuous phenomena 

(i.e., the hydrological, chemical, and biological flowpaths) interact across the discrete landscape settings 

(i.e., connect rivers and streams, waters and wetlands in floodplain settings, and waters and wetlands in 

non-floodplain settings to one another at the landscape scale). 

Suggested editorial or technical corrections have been identified in the line-by-line preliminary written 

comments provided by SAB Panel members. Hillslope hydrology is discussed independently here 

because it is so central to the flowpath framework connecting all parts of the watershed, with water 

flowing from the “ridge to the reef” and potentially passing through or otherwise interacting with waters 

and wetlands along the way. The EPA Report should clearly describe the following four pathways 

through which water flows across the landscape: 

1) Infiltration-Excess Overland Flow: This is the overland flow that occurs when the rainfall rate 

exceeds the infiltration rate, resulting in excess rainfall running overland despite a below-surface 

water table. This flow is also known as Hortonian overland flow because it was first described in the 

literature by Horton (1945). 

2) Saturation-Excess Overland Flow: This is the overland flow that occurs when the water table rises to 

the surface, so that all additional rainfall runs overland. This is also known as Dunne’s mechanism 

because it was first described by Dunne and Black (1970).

3) Interflow: This is rapid lateral flow in the unsaturated zone of soil and rock. Interflow commonly 

occurs because above a low-permeability layer there are interconnected macropores that intercept 

and channel rainfall as would a subsurface pipe (e.g., Beven and Germann 1982). 

4) Saturated Groundwater Flow: This is the normal saturated groundwater flow, where infiltrating 

rainfall reaches the water table and then flows laterally along with the general flow in the aquifer.

The Report should further explain how areas contributing runoff expand and contract, changing the way 

that landscapes connect through storms and seasons (Dunne and Black 1970). The expansion of runoffproducing areas in non-floodplain settings can intermittently or ephemerally change the extent of 

headwater streams (e.g., Dunne 1978; Van der Kwaak and Loague 2001; Rains et al. 2006, 2008). This 

type of variability suggests that connectivity should be discussed within a continuum of runoff 

producing mechanisms. As previously noted, the EPA elected to discuss landscape settings discretely, 

focusing on rivers and streams, waters and wetlands in floodplain settings, and waters and wetlands in 

19
non-floodplain settings; however, the lines delineating these landscape categories are conceptual and 

without scientific consensus.

The Report focuses primarily on the site and subregional scales, perhaps due to cost of and access to 

data and model results. This tends to either ignore or at least downplay the potential significance of 

regional-scale hydrologic connectivity, especially as it relates to groundwater. This is a problem because 

regional groundwater flows commonly interact with the surface environment at sinks and springs. For 

example, the Floridan aquifer underlies all of Florida as well as portions of Mississippi, Alabama, 

Georgia, and South Carolina and commonly interacts with the surface environment through sinks, 

springs, and outcrops (see Sun et al. 1997 and references therein). To provide a better understanding of 

groundwater connectivity, and the way that groundwater connectivity might vary spatially, the SAB 

recommends that the EPA also consider using the ASTM D5979-96 Standard Guide for 

Conceptualization and Characterization of Ground Water Systems (ASTM 1996; Kolm et al. 1996). To 

better characterize regional-scale groundwater connectivity, the SAB recommends that the EPA also 

consider using findings from the U.S. Geological Survey Regional Aquifer Systems Analysis (RASA) 

Program. An understanding of regional groundwater flow systems is critical to the understanding of 

four-dimensional hydrologic connectivity on both the local and regional scales. Understanding 

groundwater flow in unique hydrogeologic settings, including the Floridan aquifer system (karst 

systems), the High Plains aquifer system (semi-arid systems), and the Snake River Plain aquifer system 

(volcanic bedrock systems), is especially important. These and other unique hydrogeological settings are 

covered by the RASA Program (Sun et al. 1997). 

The SAB recommends that biological connectivity be better defined, illustrated with examples from a 

broader range of taxa, and described in the context of consequences to downstream waters. As written, 

the Report emphasizes the importance of hydrological connectivity, but organismal movement can 

connect waters and wetlands across uplands and between watersheds in unique and important ways. 

Indeed, many organisms meet life-history requirements by moving among habitats (i.e., their life cycles 

cannot be completed without these habitats) that are often dispersed throughout watersheds (e.g., 

Schlosser and Angermeier 1995; Falke and Fausch 2010). Habitats that are seasonally dry or even dry 

for several years in a row can be critical to the biological integrity of downgradient waters because a 

wide range of species (e.g., fish, amphibians, reptiles, birds, mammals, and invertebrates) use them to 

complete certain annual or life-cycle stages (Falke and Fausch 2010). When these upstream, lateral, and 

disconnected aquatic habitats are degraded or destroyed, populations decline and species can become 

threatened or endangered (or otherwise imperiled), or are extirpated (Fausch and Bestgen 1997). Thus, 

degradation or destruction of upstream, lateral, and disconnected aquatic habitats can result in the listing 

of new threatened and endangered species, not only for highly imperiled vertebrate groups like 

amphibians, but also invertebrates like mussels that are transported by fish (as glochidia, their larval 

stage) throughout watersheds.

Key Recommendations

• The conceptual framework should be fully described at the beginning of Chapter 3. The framework 

should have a flowpath focus showing that watersheds are connected from “ridge to reef,” and that 

waters and wetlands in the landscape are therefore connected to downgradient waters by hydrologic 

(surface and subsurface), chemical, and biological flowpaths.

• The conceptual framework in the Report should generally express the importance of climate, 

geology (surface and subsurface), topographic relief, and biology on flow and transport. The 

resulting three-dimensional structure should show potential surface, near surface, and subsurface 

20
pathways, which then can be analyzed in terms of hydrological, chemical, and biological 

connectivity in four dimensions (i.e., with the temporal dimension included). 

• The discrete-landscape classification system should be mapped onto the revised conceptual 

framework in the Report, with explicit acknowledgment that the classification system serves only as 

a communication tool. 

• Groundwater mediated connectivity, including regional groundwater mediated connectivity across 

watershed divides, should be better defined, and described in the context of connectivity between 

waters and wetlands and downgradient waters.

• Biological connectivity should be better defined, illustrated with examples representing a broader 

range of taxa, described in the context of consequences to downstream waters, and recognized as 

supporting the biological integrity of connected waters.

3.2.7. Layers of Complexity in the Conceptual Framework

Once the EPA has described the flowpath framework and explained how the framework is used in the 

Report, additional layers of complexity (focusing on the issues discussed below) should be represented 

in the conceptual model. The SAB recognizes that some of these issues are already addressed in various 

parts of the Report. In those cases, the SAB recommends expanding upon or moving the discussion to 

the section of the Report that outlines the major concepts underlying the conceptual framework.

Functions

The SAB recommends layering water and wetland function on the flowpath framework. The Report 

should indicate that each water and wetland performs functions broadly categorized as source, sink, lag, 

transformation, and refuge, and that the degree to which each function is performed is dependent upon 

landscape position and related connectivity. The importance of including this in the discussion of the 

conceptual framework is to explain up front that some hydrological, chemical, and biological functions 

are enhanced by connectivity while others are enhanced by relative isolation. This is an important point, 

one that is implicit throughout the Report and explicit in the section on “unidirectional” wetlands. 

Including a functions layer in the conceptual framework will help clarify the later discussion of 

functions that are enhanced by connectivity or relative isolation. 

Spatial and Temporal Scales

Spatial and temporal scales are critical aspects of connectivity and its role in maintaining the chemical, 

physical, and biological integrity of downgradient waters. However, spatial and temporal scales vary by 

flowpath type and flowpath characteristics (Figure 1). An illustration similar to Figure 1, focused on the 

spatial and temporal scale of connectivity, should be included in the Report, with a particular focus on 

the differences in the spatial and temporal scales of surface water and groundwater connectivity as they

relate to the chemical, physical, and biological integrity of downgradient waters. Similar figures could 

also be created for chemical and biological connectivity.

21
Figure 1. Schematic of selected atmospheric, surface, and subsurface hydrologic processes and 

their temporal and spatial scales of occurrence. (Source: U.S. Global Change Research Program 

2001)

The Report should carefully discuss how connectivity is a function of spatial and temporal scale. For 

example, a complex of depressional wetlands might appear connected at the complex scale but might 

nevertheless be collectively isolated at the watershed scale. Alternatively, a depressional wetland might 

appear isolated in the dry season but connected by surface water for long duration during the wet season 

(e.g., Rains et al. 2008).

The Report should clearly state that low-frequency events affecting the chemical, physical, and 

biological integrity of downgradient waters can be particularly important if the effects are essential, 

long-lived, and/or cumulative. Excellent examples can be found in the stream and river literature, though

similar examples for other types of waters and wetlands (e.g., Winter and Rosenberry 1998; Winter 

2000) can be found. Low-frequency, high-magnitude flows connect channels to the furthest reaches of 

the floodplains (Poff et al. 1997), thereby controlling species composition and abundance in forests 

(Darst and Light 2008) and aquatic habitats in the floodplain (Light et al. 1998) and transporting large 

clasts and/or woody debris that otherwise cannot be transported by more-frequent, lower-magnitude 

flows (Wolman and Miller 1960). Long-lived effects are exemplified by debris flows, which are lowfrequency events that nevertheless can be important mechanisms that connect headwaters to rivers, 

serving as important sources of sediment to downgradient waters (Benda et al. 2005). Although such 

debris flows occur infrequently, the consequences can be long lived, and can play important roles in 

controlling the structure and function of downgradient waters over the scale of decades (Leibowitz et al.

2008). Important cumulative effects are exemplified by ephemeral flows in arid landscapes, lowfrequency events that may nevertheless provide most of the subsidies to downgradient waters 

(Schlesinger and Jones 1984; Izbicki 2007). 

The SAB recommends that the Report compare and contrast the temporal scales of connectivity in the 

East and the Southwest. In the East, precipitation is weakly seasonal and the weighted-average flux of 

22
materials, energy, and/or water-borne organisms is therefore likely greatest in response to moderatefrequency rainfall events; in the Southwest, precipitation is strongly seasonal and the weighted-average 

flux of materials, energy, and/or water-borne organisms is therefore likely greatest in response to lowfrequency rainfall events. The latter are no less important to the integrity of the downgradient waters, 

even though their frequency and duration may be negligible in comparison. Therefore, the importance of 

the connectivity is not just a function of the frequency or duration of the connection but, rather, the 

relative magnitude of the connection. Consider, for example, a river with total annual flow of 200,000 

m3, 150,000 m3 of which originates as ephemeral flows in headwater streams. In this case, these 

headwater streams, though infrequently connected to the river, would nevertheless be critical to the 

maintenance of the chemical, physical, and biological integrity of that river.

One way to conceptualize this point in the Report is by developing a matrix of relative likelihood × 

relative consequence (e.g., Figure 2), which would facilitate a discussion of spaces occupied by given 

waters and wetlands. Such a figure would help readers understand the regional context of the spatial and 

temporal scale of connectivity. 

Figure 2. Relative likelihood × relative impact of global-scale phenomena. (Source: Lenton 2011. 

Reprinted by permission from Macmillan Publishers Ltd: Nature Climate Change 1(4):201-209, 

copyright 2011.)

Human-Altered Systems

There are few, if any, ecosystems unaltered by humans. The role that these alterations play in the 

conceptual framework should be addressed explicitly in the Report. Waters and wetlands are 

"connected" in the sense that they are integrated into the broader hydrological landscape and therefore 

23
can play important roles in maintaining the chemical, physical, and biological integrity of downgradient 

waters. They perform a variety of functions (which are broadly classified in the Report as source, sink, 

lag, transformation, and refuge functions) at rates that are a characteristic of where these waters and 

wetlands are located on the gradient of connectivity. Therefore, downgradient waters might suffer 

consequences if the degree of connectivity is altered by human activities. Alterations can be of three 

types: some can directly decrease connectivity, such as dams (Ward and Stanford 1983) and 

groundwater pumping that lowers local water tables and causes surface-water connections to cease 

(Haag and Pfeiffer 2012); some can directly increase connectivity, such as ditches (Min et al. 2010) and 

tile drains (Randall et al. 1997); and some can indirectly change the frequency, magnitude, timing, 

duration, and/or rate of change of connectivity, such as impervious surfaces in the contributing 

watershed (Walsh et al. 2012). Each of these types of human alterations affect connectivity, modify the 

surface water network, and therefore impact the chemical, physical, and biological integrity of the 

downgradient waters. 

Regionalization

The SAB finds that the conceptual framework in the Report is not amenable to considering connectivity 

in a regional context, especially for regions with unique conditions such as the permafrost regions of 

Alaska. This issue was identified by a number of public commenters. The EPA therefore should 

consider expressing forcings of connectivity in terms of Hydrologic-Landscape Regions (HLRs; Wolock 

et al. 2004), or an equivalent system (e.g., Wigington et al. 2013). This would not represent a large 

departure from the approach used in the Report because HLRs are fundamentally a function of climate, 

geology, and topographic relief, which are already recognized as central controls on watershed 

hydrology. Using HLRs to consider flow and transport functions would ground the discussion to 

consistent terminology. Use of terminology in the Report is currently inconsistent, sometimes referring 

to climate, geology, and relief, sometimes to climate and watershed characteristics, and other times 

focusing only on climate. Using the HLRs also would ground the discussion in the Report to peerreviewed literature, which could then serve as a means to discuss regionalization and the reality that

generalizations about chemical, physical, and biological phenomena are limited to particular 

environmental settings (i.e., context dependent). Associated with this issue is the fact that much more is 

known about connectivity in some settings than others. The Report could be improved by explicitly 

recommending that HLRs be used to better understand the relevance of the findings in the document to 

their respective regions.

Aggregate or Cumulative Effects

The aggregate or cumulative effect of many waters and wetlands on the chemical, physical, and 

biological integrity of downstream waters is sufficiently important to merit its own subsection in the 

Report. Mainstem rivers integrate and accumulate the materials, energy, and organisms that flow by 

surface-water and/or groundwater flowpaths from numerous waters and wetlands. This is an important 

concept because the individual effect of any single water or wetland on downstream waters might be 

negligible, but the cumulative effects of many similarly situated waters and wetlands on downstream

waters might nevertheless be important. For example, the degradation of a single small, headwater 

stream in the watershed might have a negligible effect on the physical, chemical, and biological integrity 

of downstream waters, but the aggregate or cumulative effect of the degradation of all small, headwater 

streams would have a large effect on downstream waters (Alexander et al. 2007).

Cumulative effects can be defined as an emergent property of headwater streams in a watershed (i.e., a 

river network statistical attribute). A measurable effect on the integrity of downstream waters may not 

24
be detected if only a small number of headwater streams within a watershed were impacted, whereas 

there could be substantial and possibly cascading effects on downstream waters were a larger number of 

headwater streams impacted. Moreover, the extent of downstream effects reflects a convolution – both 

in space and time – of each headwater stream’s time-varying flux of mass, materials, and organisms. For 

example, in a watershed with a 200-year recurrence interval of debris flows on headwater streams, the 

probability of a debris flow on any given headwater stream in a given year is 0.5% - likely a negligible 

effect on fish habitat in downstream waters in a given year. However, at the watershed scale, there are 

hundreds of headwater streams, which means that the annual probability of a debris flow in the group of 

headwater streams is much higher and more likely to substantially affect downstream fish habitats. 

Studies have been published on these kinds of cumulative effects, such as the aggregate effects of 

individually occurring debris flows in headwater streams controlling the long term sediment flux and 

storage in higher order channels (Benda and Dunne 1997a,b) and the cumulative effects of wetlands on 

watershed hydrology (e.g., Johnston et al. 1990). Therefore, any evaluation of changes to individual 

waters and wetlands must consider past and future (e.g., as a consequence of climate change) alterations 

of other waters and wetlands in the watershed. The SAB recommends that the EPA review the following 

additional studies on the cumulative and aggregate effects of streams and wetlands on downstream 

waters: Ahmed (2014); Bedford and Preston (1988); Benda et al. (2003); Brinson (1988); Dietch et al.

(2013); Dunne et al. (2001); Gabet and Dunne (2003); Johnston (1994); Lancaster and Casebeer (2007); 

Reid (1998); Squires and Dubé (2013); and Schindler (2001). 

Map Scale

The important issue of map resolution, mentioned throughout the Report, needs to be more clearly and 

thoroughly presented in a separate section, or perhaps in a figure comparing the results of using different 

technologies. A related topic that could be addressed in the Report is the increasing availability of light 

detection and ranging (LiDAR) digital elevation models (DEM) and thus the increasing ability to create 

more accurate water and wetland maps; this illustrates how new technologies may influence the 

scientific understanding of connectivity. 

The Report should clearly indicate that many existing databases do not include small streams and thus 

do not represent the full extent and magnitude of the river and stream network. For example, Meyer and 

Wallace (2001), estimating stream extent in a North Carolina watershed using maps with different 

resolution, found 0.8 km of stream channel on a 1:500,000 scale map and 56 km of stream channel on a 

1:7200 scale map. The increasing availability of high resolution DEM, including the USGS National 

Elevation Dataset (NED) 10 m DEM (USGS 2014) and more robust flow routing algorithms means that 

more accurate stream maps are becoming increasingly available. Thus the ability to predict (and discern) 

hydrological, chemical, and biological connections between small and large streams is increasing 

rapidly. Mapping scale also applies to wetlands in non-floodplain settings. Frohn et al. (2009, 2012), 

Lane et al. (2012), and Martin et al. (2012) tried to map geographically isolated wetlands but found that 

currently available spatial data were inadequate for the task, in large part due to the limitations of the 

scale and/or accuracy of the maps used to determine whether or not a wetland was surrounded by 

upland. Hence, the assessment of the degree of connectivity will be determined in some part by the 

database and/or data collection technology used for the analysis.

Key Recommendations

• After describing the structure and use of the flowpath framework, additional layers of complexity 

should be developed with particular focus on the following issues:

25
- Water and wetland function should be represented on the flowpath framework. EPA should 

indicate that each water and wetland performs functions broadly categorized as source, sink, lag, 

transformation, and refuge, with the degree to which each function is performed being dependent 

upon landscape position and related connectivity. 

- Spatial and temporal scales should be addressed in the discussion of connectivity including 

effects on the chemical, physical, and biological integrity of downstream waters. The Report 

should discuss the potential importance of low-frequency events. 

- The role that human alterations play in the conceptual framework should be addressed explicitly.

- The EPA should consider expressing forcings of connectivity in terms of Hydrologic-Landscape 

Regions (HLRs) to help readers understand the regional relevance of findings in the Report.

- The aggregate or cumulative effect of many waters and wetlands on the chemical, physical, and 

biological integrity of downgradient waters is sufficiently important to merit its own subsection 

in the Report. 

- The important issue of map resolution is mentioned in several parts of the Report, but it should 

be more clearly and thoroughly presented in a separate section.

3.2.8. Summary and Synthesis of the Conceptual Framework

Chapter 3 of the Report ends abruptly, without summary or synthesis of the conceptual framework. The 

SAB recommends that the EPA consider moving Figure 6.1 (The role of connectivity in maintaining the 

physical, chemical, and biological integrity of water) to the end of Chapter 3. The figure could then be 

used as a means of summarizing and synthesizing the conceptual model and explaining how the model 

guides the way that the EPA is thinking about and presenting evidence of connectivity between waters 

and wetlands and downgradient waters. This figure succinctly shows the role played by connectivity in 

maintaining the chemical, physical, and biological integrity of downgradient waters and hence would 

serve this purpose well.

Key Recommendation

• A summary and synthesis of the conceptual framework should be added to the end of Chapter 3 of 

the Report using what is currently Figure 6.1 to frame the discussion.

3.3. Ephemeral, Intermittent, and Perennial Streams: Review of the Literature

Charge Question 3(a). Chapter 4 of the draft Report reviews the literature on the directional 

(downstream) connectivity and effects of ephemeral, intermittent, and perennial streams (including flowthrough wetlands). Please comment on whether the Report includes the most relevant published 

literature with respect to these types of streams. Please also comment on whether the literature has been 

correctly summarized. Please identify any published peer-reviewed studies that should be added to the 

Report, any cited literature that is not relevant to the review objectives of the Report, and any 

corrections that may be needed in the characterization of the literature. 

Chapter 4 of the Report is an extensive review of the literature that describes the connectivity of 

headwater streams to downstream waters. The Report documents the current scientific understanding 

that there are numerous ways headwater streams are connected to downstream ecosystems and that these 

connections can be essential in promoting the physical, chemical, and biological integrity of downstream 

ecosystems. The connections between headwaters and downstream ecosystems are well established as a 

foundational concept in stream ecology. 

26
The EPA’s review is based on pertinent literature and is strongly grounded in current science. However, 

the SAB provides a number of recommendations to improve the literature review in Chapter 4 of the 

Report. The SAB has identified additional references to relevant peer-reviewed literature that the EPA 

should consider citing in the Report. 

3.3.1. Hydrologic Exchange Flows between Main Channels and Off-Channel Areas

The SAB recommends that the literature review in Chapter 4 of the Report be expanded to include the 

description of exchanges between main channels and off-channel surface and shallow subsurface waters 

located at channel margins (e.g., pools, recirculating eddies, subsurface hyporheic flow paths) and in 

upstream or off-channel areas that may become connected during wet periods (e.g., variable source areas 

or off-channel sloughs or riparian areas). The Report should include a more complete discussion of the 

soil-water processes involved (e.g., processes that establish temporary sinks for chemical constituents, 

provide water to riparian vegetation, or facilitate contaminant transport) and more attention should be 

given to spatial and temporal variability that could affect connectivity of streams. The revised text also 

should include broader discussion of associated biogeochemical transformations that change the form 

and mobility of dissolved chemicals that affect downstream water quality. The discussion should go 

beyond solely discussing nitrate removal to include phosphorus removal and examples of fate and 

transport of inorganic and organic contaminants. The Report should also discuss the geomorphological 

control of soil moisture and patch diversity that impacts riparian plant communities (Stromberg 2001). 

In addition, the Report should describe how surface-subsurface water interactions affect stream 

temperature and habitat for fish and other organisms, particularly when surface water flows diminish but 

subsurface flow is present. The following references (and others that are appropriate and relevant) 

should be considered for inclusion in a broader discussion of hyporheic processes: Buffington and 

Tonina (2009); Karwan and Saiers (2012); Poole et al. (2006); Sawyer et al. (2011); Stonedahl et al. 

(2010); and Stromberg (2001). As further discussed in Section 3.5 of this SAB report, the material on 

the physical and chemical influence of riparian areas (Sections 5.3.1 and 5.3.2 of the EPA Report) is 

more appropriately located in Chapter 4 of the EPA Report.

Key Recommendations

• The review of hydrologic exchange flows between main channels and off channel areas should be 

expanded in the Report and should include a more complete discussion of: soil-water processes,

biogeochemical transformation processes, and surface-subsurface water interactions that affect 

stream temperature and habitat for fish and other organisms.

• Additional references recommended by the SAB, and others that are appropriate and relevant, should

be considered for inclusion in a broader discussion of hyporheic processes.

3.3.2. Naturally Occurring Chemical Constituents, Contaminants, Contaminant 

Transformations, and Sediment Transport

The EPA should revise the Report to include discussion of contaminants and naturally occurring 

chemical constituents other than nutrients (i.e., nitrogen and phosphorus), and to consider nutrient and 

contaminant transformation processes, the effects of these processes on downstream water quality, if 

known, and sediment transport. The Report needs a more thorough characterization of upslope (surface 

and subsurface) effects of geology, soils, and hydrology (e.g., sediment transport) on overall water 

chemistry (e.g., conductivity, alkalinity, pH, major cations) and the consequences of altering these 

upslope processes on downstream water chemistry and associated ecological responses. The role of 

27
nutrient spiraling as a demonstration of connections between headwaters and downstream ecosystems is 

covered in the Report. However, the Report could be strengthened if more attention were given to the 

important transformations that affect mobility, toxicity, and time lags of storage or degree of removal 

that occurs and how it affects downstream loading of nutrients and contaminants. The Report also

should further discuss both sediments and sediment-bound contaminants and their downstream 

movement and effects on downstream waters. 

The review and synthesis of the literature on connectivity of streams should also be expanded to provide 

information on the physical, chemical, and biological effects and quantification of sediment transport as 

related to surface water connectivity. This review and synthesis should include the geology and 

sedimentology literature on three types of sediment: dissolved, suspended and bedload (based on type of 

movement and size). 

The following references (and others that are appropriate and relevant) should be considered for 

inclusion in the discussion of naturally occurring chemical constituents, contaminants and contaminant 

transformation processes: Baker et al. (2000); Bourg and Bertin (1993); Conant et al. (2004); Doyle et 

al. (2003); Ensign et al. (2008); Findlay (1995); Fuller and Harvey (2000); Harvey and Fuller (1998); 

Harvey et al. (2013); Hedin et al. (1998); Kim et al. (1992, 1995); Kimball et al. (1994); Lautz and 

Fanelli (2008); Malcolm et al. (2005); and O’Connor and Harvey (2008).

Key Recommendations

• The review of the literature on connectivity of streams should be revised to include discussion of

contaminants and naturally occurring chemical constituents other than nutrients (i.e., nitrogen, 

phosphorus) and to consider nutrient and contaminant transformation processes and the effect of 

these processes on downstream water quality, if known. 

• Additional references recommended by the SAB, and others that are appropriate and relevant, should 

be considered for inclusion in the discussion of naturally occurring chemical constituents, 

contaminants and contaminant transformation.

3.3.3. Factors that Influence Stream Temperature

Stream temperature is an important component of ecosystem integrity because it controls many 

ecosystem properties and processes. Upslope factors affect the relative contributions of surface, shallow 

and deeper subsurface waters to channel flow and can affect stream temperature and downstream 

connectivity. The SAB recommends that discussion of this topic be expanded to (1) discuss the 

treatment of the direct and indirect effects of upstream/upslope riparian shading, channel morphology, 

and channel network topology on stream temperature; (2) expand the discussion of how environmental 

alterations in channels and upslope areas influence connectivity, and thus, stream temperature dynamics;

(3) directly address interactions between stream temperature and downstream connectivity; and (4) more 

explicitly describe the effects of hyporheic flow and storage and resulting lag and attenuation effects that 

buffer temperature extremes within streams. The discussion of these latter subsurface hyporheic effects 

should include a comparison to direct groundwater discharge in terms of their effects on stream 

temperature dynamics (Callahan et al. in press). The following references (and others that are 

appropriate and relevant) should be considered for inclusion in the discussion of factors that influence 

stream temperature: Arrigoni et al. (2008); Hester et al. (2009); and Sawyer et al. (2012).

28
Key Recommendations

• The discussion of upslope factors that influence stream temperature should be expanded to include 

hyporheic flow and storage, a comparison to groundwater effects on stream temperature,

upstream/upslope riparian shading, channel morphology, channel network topology, and 

environmental/human alterations in upslope areas and channels. 

• The Report should explicitly discuss interactions between stream temperature and downstream 

connectivity. 

• Additional references recommended by the SAB (and others that are appropriate and relevant) 

should be considered for inclusion in the discussion of factors that influence stream temperature.

3.3.4. Clarifying the Temporal Dynamics of Flow-Related Aspects of Connectivity 

The Report lacks a succinct yet comprehensive paragraph that covers the temporal dynamics of 

connectivity for headwater streams (e.g., headwaters that connect perennial, intermittent, and ephemeral 

channels with their variable source areas) that affect the physical, chemical, and biological integrity of 

downstream waters. Connections that are highly variable in time affect the transport of materials and 

sediments and can also be important to biota (e.g., fish or amphibians breed in habitats that otherwise are 

dry most of the year or for several years). The timescale of these temporally variable connections (i.e.,

connected at certain times) could range from seasons, years, or decades to centuries. In addition, some 

aspects of connectivity occur over relatively short times frames and are highly stochastic but can 

represent important connections to downstream ecosystems. For example, major erosion or woody 

debris fluxes that occur infrequently during high runoff events may represent major sources of sediments 

or large wood to downstream ecosystems. 

Chapter 4 of the Report would benefit from a separate section on the temporal dynamics of connectivity. 

The SAB recommends that the Report characterize the temporal dynamics of streamflow (i.e., 

magnitude, frequency, duration, and timing) that explicitly connect these ecosystems to downstream 

waters. For example, the Report correctly describes how headwater streams can contribute a large 

fraction of the water in downstream ecosystems over an annual cycle, even though they are periodically 

dry. However, the Report should also explore the effect of short duration connections on downstream 

ecosystems. More discussion and additional literature citations should be included to describe how even 

short duration and highly episodic flow connections and longer duration periods of dry conditions can be 

important to downstream ecosystems. The SAB also recommends that the Report be revised to explicitly 

recognize the important role of variable hydraulic residence times in river networks and their effects on 

the storage and transformation of organic matter and nutrients in downstream waters.

In addition, the Report should discuss how natural or human-caused interruptions of flow affect the 

temporal dimensions of connectivity. In many streams that experience flow regulation, groundwater

capture, or any rapid longitudinal change in discharge, riverine habitat can become discontinuous and 

aquatic and riparian communities can lose connectivity. For example, in the arid Southwest, the San 

Pedro and Santa Cruz Rivers include long reaches of ephemeral flow bounded by intermediate-toperennial sections. In the volcanic terrains of the Snake River Plain in Idaho or the Hawaiian Islands and 

karst regions of central Kentucky, stream flow can be captured by bedrock aquifers. These streams, 

defined as “interrupted” (Meinzer 1923; Hall and Steidl 2007), can be strongly or weakly connected 

depending upon a variety of biological and physical factors; the Report should discuss ways commonly 

29
used to spatially and temporally characterize the impacts to riverine habitat of natural and human 

interruption of flow.

Overall, the SAB recommends that the Report include a clear discussion of how intermittent and 

ephemeral streams are connected in space and time to downstream ecosystems and the consequences of 

these connections for physical, chemical, and biological integrity. The following references (and others 

that are appropriate and relevant) should be considered for inclusion in the Report to illustrate the ways 

in which intermittent and ephemeral streams are connected to downstream ecosystems and the effects of 

time-varying flow connections: Brooks et al. (2006); Constantz (2008); Harvey et al. (2012); Levick et 

al. (2008); McDonough et al. (2011); O'Connor et al. (2012); PCRWRD (2002); and Walker et al. 

(2005). 

Key Recommendations

• The Report should include a new section that explicitly examines the temporal dynamics of 

connectivity for headwater streams (e.g., headwaters that connect perennial, intermittent, and 

ephemeral channels with their variable source areas) that affect the physical, chemical, and 

biological integrity of downgradient waters. The new section should note that it is the effect of flows 

that determines their importance to downstream connectivity.

• The Report should be revised to explicitly recognize the important role of variable hydraulic 

residence time in river networks including effects on the storage and transformation of organic 

matter and nutrients in downstream waters.

• The Report should include discussion of how human alterations affect the temporal dimensions of 

connectivity, e.g., via water withdrawal or augmentation and effluent-dependent or effluentdominated stream flow.

• Additional references recommended by the SAB (and others that are appropriate and relevant) 

should be considered for inclusion in the Report to illustrate the ways in which intermittent and 

ephemeral streams are connected in space and time to downstream ecosystems and the effects of 

time-varying flow connections.

3.3.5. Strengthening the Review of Biological Connectivity of Ephemeral, Intermittent, and 

Perennial Streams

As mentioned in Section 3.2.6, the Report should be revised to more thoroughly document evidence that 

biota move throughout aquatic and riparian systems (e.g., in upstream, lateral, and downstream waters) 

to use critical habitats and that these movements have strong and important effects on biological 

integrity. A more thorough treatment of biological connectivity would strengthen Chapter 4 of the 

Report. The following key points should be included in the Chapter: 

a) Organisms require habitats that are dispersed throughout watersheds (i.e., their populations cannot 

persist without these habitats), and many species move among these habitats during their life cycles 

(e.g., Fausch et al. 2002; Kanno et al. 2014).

b) Some species maintain populations in downstream waters, but move upstream or laterally to use 

habitats that are dry seasonally and in some cases are dry several years in a row. Thus, these 

30
intermittent or ephemeral habitats often can be critical to the biological integrity of downstream 

waters (Falke and Fausch 2010).

c) A wide variety of downstream mobile species move among aquatic habitats dispersed throughout 

watersheds, including ephemeral or intermittent streams, to meet critical needs during different 

stages of life and/or annual cycles. 

d) Data from comparative studies and experiments show that some animal populations decline or are 

extirpated when upstream, lateral, and disconnected habitats are degraded or destroyed, or the 

connections are lost (e.g., owing to constructed barriers, Fausch and Bestgen 1997). Thus, 

connectivity to these habitats is key to the biological integrity of downstream waters. Dam and damremoval literature may be helpful to illustrate this point.

e) A failure to recognize the importance of biological and habitat connections can result in the listing 

of new threatened and endangered species, especially for highly imperiled vertebrate groups like 

amphibians, but also highly imperiled groups of invertebrates like mussels whose larvae are 

transported throughout watersheds by their fish hosts (Vaughn 2012; Schwalb et al. 2013).

f) Biological connections, in particular the migration of fish, can be significant pathways for the 

transport of persistent bioaccumulative toxics. 

Key Recommendation

• The Report should more thoroughly document evidence that biota move throughout the lotic system 

in all directions (e.g., in upstream, lateral, and downstream waters) in order to use critical habitats 

and that these movements have strong and important effects on biological integrity of downstream 

waters, as detailed in the points above.

3.3.6. Review of the Human-Modified Headwater Stream Literature

The current version of the Report generally excludes the many studies that have been conducted in 

human-modified stream ecosystems. This literature (e.g., Blann et al. 2009) should be included in the 

Report in order to provide information about the consequences of alterations of headwater systems to the 

physical, chemical, and biological integrity of downgradient waters. Many headwater stream ecosystems 

are altered by land-use change and human activity that often disrupts connectivity. Consideration of 

appropriate temporal scales and disturbance ecology could help the Report provide direction on 

discrimination between short-term, erosional features like rills and gullies, which are initiated by human 

or natural disturbance, and longer-term, integrated headwater channels with more ecologically effective 

connectivity to downstream waters. Poesen et al. (2003) and Schumm et al. (1987) provide information 

on the transition from gullies to headwater streams. The SAB finds that there are many insights to be 

gained about the importance of connectivity to downstream waters when connections are either severed 

or enhanced. Including additional information from this large area of research will provide more 

examples of the importance of connectivity, and the SAB recommends that information about humanmodified systems be included in the Report. 

The SAB recommends that the Report authors consider including examples from at least some of the 

following human alterations affecting the connectivity of streams: agricultural ditches and tile drains, 

urban lined channels and buried streams, removal of riparian trees, cattle grazing, gravel mining, 

channel diversions, low-head dams, grade control structures, roads, stream restoration, accelerated 

31
erosion, sediment transport and storage, stream restoration, and effluent dominated streams. The 

following references (and others that are appropriate and relevant) could be considered for inclusion in 

the Report to illustrate the effects of human alterations to headwater streams: Booth (1990); Bull and 

Scott (1974); Chin and Gregory (2001); Croke et al. (2005); Doyle et al. (2000); Faulkner (2004); Graf 

(2006); Gregory (2006); Horner et al (2001); Lautz and Fanelli (2008); Montgomery (1994); Paul and 

Meyer (2001); Schumm et al. (1984); Thompson et al. (2008); Wemple et al. (1996, 2001); Wigmosta 

and Perkins (2001); Williams and Wolman (1984); and Wohl (2005).

Key Recommendations

• The Report should be revised to include information about the consequences of human alteration of 

headwater systems to connectivity and concomitant effects on the water quantity and quality and 

biota of downstream ecosystems. 

• Additional references, including those recommended by the SAB, should be considered for inclusion 

in the Report to illustrate the effects of human alterations to headwater streams.

3.3.7. Aggregate and Cumulative Effects of Headwater Streams on Downstream Ecosystems

The SAB recommends that a new section on the aggregate and cumulative effects of headwater streams 

on downstream ecosystems be added to Chapter 4 of the Report. This new section should draw upon the 

large body of literature on cumulative watershed effects of land use, based on both modeling and 

empirical approaches. In addition, the existing section on watershed modeling should be improved by 

expanding the discussion to include results from models beyond just the SPARROW (SPAtially 

Referenced Regressions On Watershed attributes) model and encompass the numerous other modeling 

and empirical approaches that have been used. In addition, the Report could draw upon examples from

the literature that investigates the movement of sediments through watersheds to examine aggregate and 

cumulative effects on downstream waters. The following references (and others that are appropriate and 

relevant) should be considered for inclusion in the Report to document the aggregate and cumulative 

effects of headwater streams on downstream ecosystems: Alexander et al. (2009); Böhlke et al. (2009); 

and Helton et al. (2011). 

Key Recommendations

• A new section on aggregate and cumulative effects of headwater streams on downstream ecosystems 

should be added to Chapter 4 of the Report. Additional references recommended by the SAB should 

be considered for inclusion in the new section.

• The findings of the modeling and empirical studies on the cumulative effects of land use on the 

physical, chemical, and biological integrity of downgradient waters should be summarized in the 

Report. 

• The modeling section of the Report should be expanded to include results from a broader set of 

models.

3.3.8 Connections to the Adjacent Riparian Landscape 

The Report focuses primarily on the connections among components of the aquatic system, including 

not only hydrologic connections but also those made by organisms that walk, crawl, or fly between 

32
water bodies. However, the physical, chemical, and biological integrity of downstream waters also 

depends on the presence of intact headwaters, and the integrity of these headwater ecosystems depends 

on critical connections between streams and the adjacent riparian landscape. Given this, the SAB finds 

that more emphasis could be placed on the importance of these connections to the integrity of 

downstream waters. 

For example, the positive ecological effects of streamside vegetation are not limited to riparian wetland 

function, but also include effects of inputs of leaf litter and terrestrial insects on downstream food 

resources, effects of woody debris on channel morphology, sediment and organic matter storage, 

hydrologic retention, and modulation of stream temperature. These benefits occur along the entire 

longitudinal stream profile, but are especially important to headwater streams. The SAB recommends 

that the Report be revised to expand the discussion of the effects of streamside vegetation on stream 

ecosystems. Some information about this topic is already provided in Section 5.3.1.3 of the Report. This 

information should be moved to Chapter 4, which discusses the physical, chemical, and biological 

connections of low-order streams and riparian areas.

The SAB also recommends adding information that addresses the importance of food-web connections 

from riparian zones to streams that support aquatic organisms. Organisms that define the biological 

integrity of downstream waters are embedded in food webs and these food webs transcend aquaticterrestrial boundaries. Following are key points that should be included:

a) Streams receive organic matter in the form of leaves, wood, and other plant litter from riparian 

vegetation, and these supply essential carbon and nutrients to biota ranging from microbes to 

invertebrates, which in turn feed larger invertebrates, fish, amphibians, reptiles, birds, and mammals 

(e.g., Wallace et al. 1997; Cole and Caraco 2001; Baxter et al. 2005; Cole 2013). 

b) Streams also receive terrestrial invertebrates, which are used directly as prey by fish and amphibians, 

either in the same reach, or after flowing downstream from headwaters into reaches that support 

these predators (e.g., Nakano and Murakami 2001; Wipfli and Baxter 2010).

c) These linkages between riparian zones and streams are critical to maintaining the biological integrity 

of the Nation’s waters. Data from comparative studies and experiments support the generalization 

that cutting off these connections can cause emigration or extirpation of organisms that rely on food 

web connections between streams and riparian zones (Fausch 2010). 

Overall, these food webs integrate key connections across aquatic and terrestrial landscapes and 

therefore provide a useful framework through which to view the role of riverine landscapes in 

connectivity among aquatic ecosystems.

Key Recommendations

• The Report should be revised and additional references should be added to expand the discussion of 

the effects of streamside vegetation on stream ecosystems.

• The SAB recommends adding information to the Report to document the importance of reciprocal 

food-web connections between riparian zones and streams to the integrity of the ecosystems that are 

connected to downstream waters

33
3.3.9. Clarifying How Case Studies Were Selected 

As previously discussed, the SAB recommends the addition of text that clarifies how case studies were 

selected. In addition, a case study that focuses on human-dominated systems should be added to the 

Report to illustrate the effect of human-dominated systems on downstream waters. For example, the Rio 

Grande case study on arid rivers provides excellent examples of human-modified systems and its 

description of human effects could be expanded. Other examples include the Baltimore and Central 

Arizona Long Term Ecological Research Projects (Cary Institute of Ecosystem Studies 2014; LTER 

Network 2014). The SAB notes that the San Pedro River example in Section 4.8.4 of the EPA Report is 

never mentioned or interpreted in other parts of the Report. It may be useful to illustrate the effects of 

human-dominated systems on downstream waters by comparing the ecosystem services provided with 

and without human alteration. A relevant publication in this regard is Auerbach et al. (2014).

Key Recommendations

• The Report should discuss the rationale used to select the case studies. 

• The Report should contain a case study that illustrates the downstream effects of human-modified 

systems. The Baltimore and Central Arizona Long Term Ecological Research Projects are good 

examples. 

3.3.10. Clarifying the Report Findings Concerning the Strength or Degree of Downstream 

Connectivity

The SAB recommends that the Report be revised to address the strength or degree of downstream 

connectivity. In particular, the Report needs a more focused discussion of the relative strength/degree of 

connectivity of intermittent and ephemeral streams, including streams with evaporative losses, and their 

variable source areas. This could be achieved through a discussion of the frequency, duration, 

magnitude, predictability, and consequences of surface and subsurface connections. It is important to 

note that subsurface flows often persist after surface flows wane; further, these subsurface flows may 

provide important connectivity functions from ephemeral and intermittent streams to downstream 

waters. As previously mentioned, even ephemeral and intermittent streams and short duration surface 

water connections in source water areas may have substantial effects on the chemical and biological 

integrity of downstream waters. The SAB recommends that the following references (and others that are 

appropriate and relevant) be considered for inclusion in the Report to document the strength or degree of 

downstream connectivity: Goodrich et al. (2004); Graf (1988); Hernandez et al. (2000); Larsen et al. 

(2012); Osterkamp et al. (1994); and Stratton et al. (2009). 

Key Recommendations

• The SAB recommends that the degree/strength of downstream connections be highlighted or 

discussed in each major subsection of Chapter 4 (e.g., for subsections on temperature, chemical, and 

biological connections). In particular, the SAB recommends that the Report contain a more focused 

discussion of the relative strength/degree of connectivity of intermittent and ephemeral streams to 

downstream waters.

• Additional references recommended by the SAB (and others that are appropriate and relevant)

should be considered for inclusion in the Report to document strength or degree of downstream 

connectivity.

34
3.4. Ephemeral, Intermittent, and Perennial Streams: Review of the Findings and Conclusions 

Charge Question 3(b). Conclusion (1) in section 1.4.1 of the draft Report Executive 

Summary discusses major findings and conclusions from the literature referenced in 

Charge Question 3 (a) above. Please comment on whether the conclusions and findings 

in section 1.4.1 are supported by the available science. Please note alternative wordings 

for any conclusions and findings that are not fully supported. 

Conclusion 1 in Section 1.4.1 of the Report states that: “The scientific literature demonstrates that 

streams, individually or cumulatively, exert a strong influence on the character and functioning of 

downstream waters.” The Report further states that: “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.” The SAB finds that the Report provides strong 

scientific support for these conclusions and findings. However, the EPA should recognize that there is a 

gradient of connectivity that is a function of the frequency, duration, magnitude, predictability, and 

consequences of physical, chemical, and biological connections. The SAB strongly supports the current 

emphasis in this Section of the Report on the importance of considering cumulative impacts and 

recommends minor but nevertheless important changes in the conclusions and findings in Section 1.4.1.

The Report should be revised so that the conclusions and findings in Section 1.4.1 are clearly linked to 

the foundational concept that connectivity is expressed in four dimensions (i.e., three-dimensional space, 

plus time) within the context of a watershed. The SAB recommends that the conclusions emphasize not 

only hydrologic linkages but also biogeochemical transformations and diverse biological connections. 

The text in Section 4.6 of the Report, “Synthesis and Implications,” (p. 4-35) could be improved through 

the use of bullets to highlight the main findings as well as underscore the key stream functions (sources, 

sinks, refuges, transformations, and lags; Table 4.1) and their effect on downstream waters. The SAB 

recommends adding connectivity itself to Table 4.1, perhaps using both hydrological and biological 

connections as examples. In addition, the Report’s five key functions and linkages (six if connectivity is 

included) should be reiterated succinctly and consistently across the relevant Report chapters; Sections 

4.6, “Streams: Synthesis and Implications” (p. 4-35); Section 1.4.1, “Key Findings” (p.1-7); and Section 

6.1, “Major Conclusions” (p. 6-1). At present, these summaries vary in content, length, writing and 

presentation style, and number of literature citations; the summary should not include reference to 

literature already cited in the Report. Most importantly, these inconsistencies obscure the Report’s 

conclusions. 

Key Recommendations

• The conclusions in Section 1.4.1 of the Report should be clearly linked to the foundational concept 

that connectivity is expressed in four dimensions (i.e., three dimensional space plus time) within the 

context of a watershed. 

• The conclusions in Section 1.4.1 should emphasize not only hydrologic linkages but also 

biogeochemical transformations and diverse biological connections.

• Bullet points should be used to highlight main findings in the text on “Synthesis and Implications.” 

35
• Different types of connectivity (e.g., hydrologic, biological) should be added to Table 4.1 of the 

EPA report. In addition, the EPA Report should explain that not all connectivity in the watershed is 

hydrologic; biological connectivity should be mentioned as an example.

• The Report’s key functions and linkages should be succinctly and consistently summarized across 

all the relevant Report chapters. 

3.4.1. Recommendations to Strengthen the Findings and Conclusions Concerning Ephemeral, 

Intermittent, and Perennial Streams

The SAB recommends that the Report be revised to strengthen the findings and conclusions concerning 

ephemeral, intermittent, and perennial streams by addressing the specific issues discussed below.

Connectivity, Boundaries, and Linkages

The SAB recommends that the statements in the Report that support conclusions about the connectivity 

of streams should be stated in quantitative terms wherever possible (For example: of X studies, X% 

support a particular conclusion.) 

The SAB also recommends that the text of the Report be revised to provide better definition of 

boundaries (e.g., transitions between uplands and headwaters) and acknowledge where boundaries are 

difficult to define. The Report should also better define and emphasize key linkages and exchanges that 

influence connectivity (e.g., groundwater-surface water interactions, flooding or other episodic events, 

and the influence of riparian zones) and how these linkages influence biota and food webs and vice 

versa. For example, the first sentence in Section 4.6, “Streams: Synthesis and Implications,” should be 

revised to state “A substantial body of evidence unequivocally demonstrates connectivity above and 

below ground.” The conclusions should also reiterate how these linkages and exchanges influence 

physical, chemical, and biological connectivity with downstream systems. 

The SAB finds that neither connectivity linkages that occur during flooding, nor the lack thereof during 

droughts, are well-recognized in the conclusions. Although drought is a natural disturbance, its effects 

can be exacerbated by human activities (e.g., water extraction, wetland drainage) with impacts on 

connectivity. The SAB recommends that text be added to the Report to explain hydrologic connectivity 

where surface water sustains aquifers in some environments and aquifers sustain streams in other 

environments. Alluvial systems in the southwest and karst systems in the eastern United States could be 

used as examples. In addition, the perennial streams in the Colorado Plateau and the Rocky Mountain 

and High Plains systems could be used as specific examples of aquifers sustaining streams. Floodplains 

may connect surface and groundwater locally or regionally in one or both of the directions discussed 

above, particularly during spring runoff/flooding (groundwater recharge and water table rise) or fall 

baseflow (groundwater discharge and water table lowering).

Ephemeral Streams

The Report concludes that existing evidence supports a sufficient link between ephemeral streams and 

downstream systems. This conclusion could be strengthened in three ways: (1) by adding text that 

describes spatial and temporal variation in linkages of ephemeral streams with downstream waters; (2) 

by summarizing existing evidence of the frequency, predictability, and duration of these connections; 

and (3) by identifying where further research is needed. For example, the Report currently emphasizes 

the important role of variable source areas (e.g., swales) in downstream connectivity; this role should be 

36
reiterated in the conclusions. In addition, the conclusions in the Report should emphasize that dynamic 

groundwater-surface water connections not only maintain the ecological integrity of ephemeral streams, 

but also connect them structurally and functionally to downstream waters, whether or not the upstream 

channels are perennial. Finally, the SAB recommends that the conclusions concerning ephemeral 

streams be strengthened by clarifying how and when ephemeral headwaters provide critical habitat and 

corridors for biota commonly connected to habitats associated with downstream rivers. 

Chemical Connectivity and Nutrients

The SAB finds that the summary of chemical functions that has been included in the Report could be 

strengthened by adding details about how headwater streams influence sediment-bound nutrients, 

dissolved organic matter (DOM), and contaminants; the text now focuses primarily on nitrogen, with 

detailed examples provided only for nitrate as it related to denitrification. 

The SAB also finds that Chapter 4 of the Report is currently too focused on headwaters as hotspots for 

uptake and transformation of nitrogen; more breadth across solutes should be added. The text should 

also be revised to include nutrient removal processes in the discussion on the importance of nutrient 

spiraling because both assimilatory and dissimilatory processes are important. Currently, the text focuses 

on the role of denitrification processes in removing nitrate-N from streams.

Treatment of Uncertainty

The SAB recommends that the EPA consider summarizing and displaying the Report’s conclusions in 

matrix form. A well-designed matrix would better communicate: the evidence underlying each 

conclusion, the uncertainty for a given conclusion across different functions (i.e., source, sink, refuge, 

lag, and transformation), and the confidence in conclusions across different system types (e.g., streams 

versus adjacent wetlands). The SAB also recommends including in the Report brief characterizations of 

the temporal or spatial scales over which given functions or phenomena occur as well as their sizes, 

intensities, and effects. Use of graphical methods to convey the level of confidence in the Report’s 

conclusions, e.g., similar to those in the Intergovernmental Program on Climate Change report (IPCC 

2007) would also help to better communicate findings. 

Case Studies and Context

The SAB finds that it is difficult to discern the intended illustrative points of the Report’s case studies 

within the broader discussion of streams in Chapter 4. The case studies should be presented earlier and 

the SAB suggests that text boxes be used to present the findings of case studies within the main body 

text. The longer case studies would have more impact if the key points of each were highlighted. In 

addition, the SAB also finds that some case study conclusions appear to be overreaching; for example, 

real-world management scenarios can contrast greatly with the situations described in the case study for 

arid streams. 

For the summary conclusions in case studies, the SAB recommends that the EPA consider 

distinguishing flow-, geology- and climate-dependent conclusions that integrate with the broader more 

general conclusions provided elsewhere. As previously mentioned, the SAB finds that conclusions for 

the case studies could be improved by being explicit about how human activities alter (both increase and 

decrease) above- and below-ground connectivity of streams with downstream waters. This could ideally 

be accomplished through the use of specific examples and/or case studies. The SAB notes that each case 

37
study has its own unique bulleted list of conclusions, which makes it difficult to draw conclusions across 

the case studies or to relate individual case studies to the Report’s general conclusions. 

Consistent Statement of Conclusions throughout the Text of the Report

The SAB also notes that it is essential that descriptions of functions and linkages be consistently and 

succinctly stated in Section 4.6 “Streams: Synthesis and Implications” (pages 4-35 and 4-36) and 

Section 1.4 of the Report.

Key Recommendations

• Statements in the Report that support conclusions about the connectivity of streams should be 

expressed in quantitative terms wherever possible. Descriptions of functions and linkages should be 

consistently and succinctly stated in Section 4.6 (pages 4-35 and 4-36) and Section 1.4.

• The SAB suggests that the EPA consider summarizing and displaying the Report’s conclusions in 

matrix form. Brief characterizations of the temporal or spatial scales over which given functions or 

phenomena occur, and their sizes, intensities, and effects, should be included.

• The EPA’s Report should analyze the scientific literature and discuss how differences in flows affect 

connectivity. This discussion should emphasize key linkages and exchanges that influence the 

magnitude and frequency of connectivity (e.g., groundwater-surface water interactions, flooding or 

other episodic events, and the influence of riparian zones) and how these linkages influence biota 

and food webs and vice versa. The conclusions in the Report should then reiterate how these 

linkages and exchanges influence physical, chemical, and biological connectivity with downstream 

systems.

• The conclusions concerning ephemeral streams should be strengthened by: (1) adding text that 

describes spatial and temporal variations in linkages of ephemeral streams with downstream waters; 

(2) summarizing existing evidence of the frequency, duration, and predictability of these 

connections; (3) identifying where further research needed; and (4) clarifying how and when 

ephemeral headwaters provide critical habitat and corridors for biota to move among and within their 

habitats associated with downstream waters. 

• Text should be added to the Report to explain how hydrologic connectivity can sustain aquifers as 

well as streams. Alluvial systems in the southwest and karst systems in the eastern United States

should be used as examples that influence the physical, chemical, and biological integrity of 

downgradient waters.

• The summary of chemical functions that has been included in the Report should contain more 

detailed information about the ways that headwater streams influence sediment-bound nutrients, 

dissolved organic matter (DOM), and contaminants.

3.5. Waters and Wetlands in Floodplain Settings: Review of the Literature

Charge Question 4(a). Section 5.3 of the Report reviews the literature on the directional 

(downstream) connectivity and effects of wetlands and certain open waters subject to non-tidal, 

“bidirectional” hydrologic flows with rivers and lakes. Please comment on whether the Report 

includes the most relevant published peer-reviewed literature with respect to these types of 

38
wetlands and open waters. Please also comment on whether the literature has been correctly 

summarized. Please identify any published peer-reviewed studies that should be added to the 

Report, any cited literature that is not relevant to the review objectives of the Report, and any 

corrections that may be needed in the characterization of the literature.

The SAB generally finds that literature on the connectivity of waters and wetlands in floodplain settings 

included in the Report is limited in scope (i.e., focused largely on headwater riparian wetlands) and 

should consider the gradient of connectivity that is a function of the frequency, duration, magnitude, 

predictability, and consequences of physical, chemical, and biological connections. That said, the 

literature substantiates the conclusion that, in an overwhelming number of cases, floodplains and waters 

and wetlands in floodplain settings support the physical, chemical, and biological integrity of 

downstream waters. Additional emphasis, discussion, and reorganization of the information presented 

(and in some cases review of more recent and diverse literature recommended by the SAB in the 

response to this charge question) is needed to address the significance of multi-dimensional

connectivity. The SAB has not identified any literature citations in Section 5.3 that are irrelevant to the 

review objectives.

3.5.1. Structure of Section 5.3 of the Report 

Chapter 5 of the Report addresses the physical, chemical, and biological connections of wetlands to 

rivers. Section 5.3 focuses on wetlands in riparian and floodplain settings and covers a wealth of topics. 

This Section could be strengthened by reorganizing the information presented, incorporating key 

literature that is now missing and, as with other sections, by technical editing of both the text and 

glossary. In the response to this charge question the SAB has provided additional literature citations.

The SAB recommends that Section 5.3 of the Report be reorganized to clarify the functional role of 

floodplain systems in maintaining the ecological integrity of streams and rivers. Much of the text in 

Section 5.3 is focused on headwater riparian zones and the importance of headwater, streamside areas to

in-stream structure and function. As written, Section 5.3 of the Report is 16 pages in length, with only 6 

pages that focus specifically on floodplain dynamics. The SAB recommends that the material on loworder stream riparian areas be moved from Section 5.3 to Chapter 4 of the Report, which discusses the 

physical, chemical, and biological connections of low-order streams and riparian areas (see also 

recommendations in Section 3.3.8 of this SAB report). In particular, the material in Sections 5.3.1 and 

5.3.2, which focus on the physical and chemical influence of riparian areas, is more appropriately 

located in Chapter 4. Chapter 4 already includes discussions of the role of riparian forests in regulating 

water temperature and providing inputs of large woody debris, but leaves the discussion of other 

functions, such as ability of these areas to act as nutrient sinks and transformers, to Chapter 5. 

Consolidating the entirety of the literature review on the dynamics of low-order stream riparian areas 

into Chapter 4 would help organize and clarify the text. This will leave the emphasis of Section 5.3 on 

the structure and function of larger river systems, particularly floodplains and their lateral dimensions. 

This will also require editing throughout the Report for consistency so that the use of headwater riparian 

terminology is separated from discussion of waters and wetlands in floodplain settings as much as 

possible. 

The EPA should consider reorganizing the information on the different taxonomic groups (plants and 

phytoplankton, vertebrates, and invertebrates) that are described in Sections 5.3.3.1-5.3.3.3 of the Report 

to integrate the functional attributes of floodplains as habitats, rather than addressing each group 

separately, textbook style (Amoros and Bornette 2002). The EPA should also consider reviewing the 

following additional selected references on fauna in waters and wetlands in floodplain settings: Brooks 

39
et al. (2013); Baxter et al. (2005); Bestgen et al. (2006, 2007); Bottom et al. (2005); Fausch (2010); 

Flecker et al. (2010); McIntyre et al. (2007); Mion et al. (1998); Modde et al. (2001, 2005); Spinola et 

al. (2008); Strayer et al. (2004); and Zelasko et al. (2010).

Key Recommendations 

• Section 5.3 of the Report should be reorganized by moving the text on low-order riparian areas and 

the role of headwater, streamside areas vis-à-vis in-stream structure to Chapter 4 of the Report. 

Section 5.3 should focus on the functional role of floodplains in maintaining the ecological integrity

of higher-order rivers and the literature review should more fully reflect the physical, chemical and 

biological linkages between floodplains and downstream waters (i.e., lateral exchange between

floodplains and rivers followed by downstream transport) within riverscape (Wiens 2002) and 

riverine landscape (Ward et al. 2002; Thorp 2006) perspectives. 

• EPA should consider reorganizing the information on the different taxonomic groups (plants and 

phytoplankton, vertebrates, invertebrates) that are described in Sections 5.3.3.1-5.3.3.3 of the Report 

to integrate the functional attributes of floodplains as habitats, rather than addressing each group

separately. 

• Additional references on fauna in waters and wetlands in floodplain settings have been 

recommended by the SAB and should be considered for inclusion in the Report.

3.5.2. Terminology in Section 5.3 of the Report 

A broad view of the ecological and functional roles of floodplains, irrespective of their regulatory status,

allows a more representative cross section of the literature to be included. This approach is consistent 

with including a wide range of wetlands (Cowardin et al. 1979) rather than exclusively those meeting 

the federal regulatory definition. The Report should contain a statement that the text refers to riverine 

landscape settings in their entirety, with its characteristic four-dimensions of connectivity (Ward 1989); 

however, the SAB also recommends that the authors clearly indicate these areas are covered in the 

Report because of functional linkages and not policy goals. 

As previously mentioned, the SAB recommends that “bidirectional” wetlands on floodplains be called 

“waters and wetlands in floodplain settings. “Unidirectional” wetlands as defined in the EPA Report are 

discussed in Sections 3.7 and 3.8 of this SAB report. This change in terminology is needed to 

acknowledge the multi-dimensional flux of water and materials between floodplains and riparian areas 

and their associated rivers and streams. Consistent use of these terms is important for clarity, as the 

inconsistent uses of “riparian/floodplain wetlands,” “riparian areas,” or “floodplains” in some sections of 

Chapter 5 is confusing. The definitions of “Riparian Area,” “Riparian Wetland,” “Floodplain,” 

“Floodwater,” and “Floodplain Wetland” in the glossary of the Report should also be revised to be 

consistent. 

Key Recommendations:

• The Report should discuss the functional role of floodplains and riparian areas regardless of their

regulatory status. However, it should be made clear that this discussion does not imply an expansion 

of the definition of waters and wetlands under the jurisdiction of the Clean Water Act. 

40
• The terms “unidirectional” and “bidirectional” wetlands should be revised to reflect the landscape 

position of the water body and/or wetland in question. Thus, it is suggested that “bidirectional”

wetlands be called “waters and wetlands in floodplain settings.”

• The definitions of “Riparian Area,” “Riparian Wetland,” “Floodplain,” “Floodwater” and 

“Floodplain Wetland” in the glossary of the Report should align with the ways the terms are used in 

the text.

3.5.3. Spatial and Temporal Connectivity of Floodplain Environments to River

Systems

Spatial and temporal connectivity between the stream and floodplain are the primary determinants of 

physical and biological processes occurring within both the stream and the floodplain (e.g., Junk et al. 

1989). Thus, Section 5.3 of the Report should include a new subsection that explicitly discusses how 

floodplain environments (including the terrestrial components thereof) are functionally linked to river 

systems, both spatially and temporally, for example, by means of the lateral “flood pulse” for surface 

water connections, and vertical connections to alluvial aquifers. The more current, integrated view of 

“riverscapes” (Wiens 2002) and “riverine landscapes” (Ward et al. 2002, Thorp et al. 2006) as a mosaic 

of patches that are shaped by the four components of connectivity at the habitat, floodplain, and river 

corridor scales, as well as disruptions caused by drought, could also be addressed in the new subsection.

This riverine landscape perspective (Ward et al. 2002; Thorp et al. 2006) can provide the organizational

backbone of the subsection, stressing higher order river structure and function while recognizing that 

there exist gradients of floodplain development along the drainage network. Although the flood pulse 

concept is acknowledged in the Report as a fundamental paradigm in river ecology (page 5–6, line 5; 

page 6–4, lines 1-2), the conceptualization and hydrologic characterization of floodplain wetlands in 

either spatial or temporal dimensions remain undeveloped. The Report also recognizes the extension of 

the flood pulse concept to include “flow pulses” (Tockner et al. 2000) but does little to recognize how 

riverine landscapes (including floodplains and the wetlands within them) function through storm–related 

changes in flow, seasonal variation in water abundance and river discharge, and longer–term changes 

related to climate shifts and precipitation regimes. The references to “flood pulse” in the Report are 

limited, relating to flood attenuation in the main channel (page 5–6, lines 5, 29; Table 5–3, page 5–38), 

or the influence of the flood pulse on biological entities (e.g., page 5–20, lines 16, 22, 29).

Short-duration, high-intensity flood events for surface waters and long-duration, low-intensity lateral 

discharge for groundwater need additional emphasis in the Report. This should include descriptions of

the influence of the flooding on residence time of surface water, seasonal exchanges with groundwater, 

chemical and biological linkages, and ecosystem processes. For example, effects of low-frequency,

high-intensity flood events on downstream waters chiefly affect physical connectivity, including water 

storage, peak flow attenuation, and sediment and wood transport and/or deposition. This occurs on a 

decadal or centennial return interval and the spatial scale of this type of flood event tends to be 

extensive, dictated largely by topography, and covering all available habitats. At the other end of the 

spectrum, the effects of high-frequency, low-intensity forms of connectivity (such as hyporheic 

groundwater flow) may drive biological or biogeochemical functions, including nutrient and 

contaminant transformation and organic matter accumulation. The spatial scale of this type of 

connectivity depends on whether groundwater discharge in the floodplain is discrete (e.g., an alluvial

spring) or diffuse, and whether it travels through the floodplain as channelized flow or in the hyporheic 

zone. As previously mentioned, the SAB recommends that the Report discuss approaches to measuring 

or otherwise quantifying connectivity. In this regard, the SAB notes that the role of groundwater

movement and storage, including the effects of flood pulses on the hydrologic differences between, for 

41
example, “slope” (primarily groundwater fed) and “riverine” (primarily surface water fed) wetlands (per 

the hydrogeomorphic classification scheme; Brinson 1993), and the role of chemical/contaminant 

movement and storage related to groundwater systems in floodplains, have been quantified via flow and 

transport modeling using both steady-state and transient analysis to simulate temporal changes. 

Finally, the potential for drought to disrupt connectivity by reducing water availability and disrupting 

hydrologic connectivity should be acknowledged. Drought has both direct and indirect effects, including 

the loss of available habitat, changes in water quality, and alterations in the strength and structure of 

species interactions (Lake 2003). Climate change is expected to exacerbate the impacts of drought in 

some regions of the U.S. by increasing the frequency and intensity of low flows (van Vilet and 

Zwolsman 2008). In other regions, such as the Northeast, climate change may cause increased 

precipitation (Kunkel et al. 2013) and flooding that could also affect hydrologic connectivity.

Placing floodplain wetland environments into the context of the “riverine landscape” requires a 

perspective that considers how lateral flows caused by flood events influence the expansion of and 

linkages among these environments. The Report should clearly articulate the “bidirectional” nature of 

fluxes of water, materials, and biota to and from the river channel, as well as the temporal pattern of 

flows relative to the flood pulse. The manner in which the riverine landscape view fits within the 

conceptual framework can be illustrated by highlighting in Section 5.3 of the EPA Report the effects of 

floodplains not only on river flows, but also on chemistry, sediments, and biota of downstream waters.

The SAB provides a number of specific recommendations to more clearly articulate the importance of 

lateral flows. Flood-forecasting methods can be used as a means to quantify the strength of connectivity

(spatial and temporal) between floodplains and rivers. Hydrological measures of flood frequency and

floodplain inundation can provide estimates of water residence time (or hydroperiod) on floodplains, 

with implications for fluxes of biota and biogeochemical processing of nitrogen (N), phosphorus (P), 

and other constituents. The results of flood forecasting are measures of vertical and lateral connectivity. 

Flood forecasting analyses require that recurrence intervals be explicitly defined, for example making 

estimates over a reasonable range of overbank flows (2 years out of 3, to 10-yr and 100-yr events), to

establish variability in the time scales of connectivity. Such analyses would focus much needed attention 

on magnitude-frequency relationships.

The EPA should consider incorporating into the Report examples of floodplain classification systems 

(e.g., Nanson and Croke 1992) that address floodplain geomorphological and functional diversity and 

emphasize the continuum of floodplains along stream networks. Describing the ways in which

floodplain/channel geomorphology and the duration of flooding or saturation shape the degree of 

connectivity between floodplains and downstream waters also would be useful. The SAB also 

recommends addressing flood frequency-floodplain inundation science as a means to estimate the degree 

of connectivity. Channel migration zones (Rapp and Abbe 2003; Brummer et al. 2006), which describe 

the movement of channels within floodplains and their valley floors over time, explain the variable 

nature of connectivity (in space and time) of floodplains and the waters/wetlands that they contain. In 

one year a floodplain can exist on one side of the channel and the next year, following a large flood, the 

active channel may have migrated 100 meters to the opposite side, stranding the former floodplain and 

creating new floodplains on that side. Thus floodplains, including wetlands, are temporally variable and 

transient, and connectivity could include what has been referred to as the “channel migration zone.” 

Some state and local governments have developed guidelines (e.g., Rapp and Abbe 2003) or regulations 

to define and protect (regulate development of) channel migration zones that are non-floodplain portions 

of the valley floor

42
The Report should emphasize the importance of floodplain connections and processes - such as sediment 

movement, erosion and deposition - that operate through downstream, lateral, vertical and temporal 

dimensions. Additional literature should be reviewed and cited in Section 5.3 of the Report to 

demonstrate that lateral connections create a diversity of lotic, semi-lotic and lentic habitats within the 

riparian zone, supporting a wide array of taxa (e.g., fish, amphibians, birds, mammals) and high levels of

diversity. As discussed by Bestgen et al. (2007) and Modde et al. (2001, 2005), floodplain wetlands and

off-channel waters play an important role as spawning grounds and fish nurseries during high-water 

seasons for species (including several endangered fishes) that ultimately populate downstream fisheries.

The SAB also recommends that a broader range of examples of waters and wetlands in floodplain 

settings be used in the Report to make it more representative of the United States as a whole. For 

instance, the EPA could incorporate studies on peatlands in floodplain settings that have “bidirectional”

flows, as in northern tier states and Alaska, and coastal lowland wetlands of Hawaii that serve as barriers 

to sediment and nutrient loading to seagrass and coral reef habitat (e.g., Bruland 2008).

The SAB recommends that the EPA consider reviewing the following selected references (and others 

that are appropriate and relevant) to document how the hydrologic phenomenon of the flood pulse links 

rivers to the floodplain (and consequently to wetlands within them): Alford and Walker (2013); 

Anderson and Lockaby (2012); Benke et al. (2000); Bunn et al. (2006); Ellis et al. (2001); Galat et al. 

(1998); Granado and Henry (2014); Heiler et al. (1995); Henson et al. (2007); Hudson et al. (2012, 

2013); Magana (2013); Nanson and Croke (1992); Opperman et al. (2010); Power et al. (1995a,b); 

Powers et al. (2012); Rooney et al. (2013); Schramm and Eggleton (2006); Sullivan and Rodewald 

2012; Sullivan and Watzin (2009); Thorp et al. (2006); Tockner et al. (2000); Toth and van der Valk 

(2012); and Valett et al. (2005).

The SAB also recommends that the EPA consider reviewing the following references that provide 

information concerning quantification of groundwater mediated linkages of waters and wetlands in 

floodplain settings: Appel and Reilly (1994); Conaway and Moran (2004); Harbaugh (2005); Huntington 

and Niswonger (2012); Kolm et al. (1998); Markstrom et al. (2008); McDonald et al. (2005); Nelson et 

al, (2003);Winter et al. (1998); and Woolfenden and Nishikawa (2014).

Key Recommendations:

• Section 5.3 of the Report should contain a new subsection that explicitly discusses how floodplain 

environments (including the terrestrial components thereof) are intimately linked to river systems, 

both spatially and temporally, by means of the “flood pulse” and recent extensions thereof. The 

“riverine landscape” framework should be employed as the conceptual backbone of the new 

subsection, stressing dynamic lateral connections between the floodplain (surface and groundwater) 

and downstream waters, recognizing the full range of temporal and spatial variability (e.g., short 

duration, high-intensity floods for surface waters; long-duration, low-intensity lateral discharge for 

groundwater; drought).

• Section 5.3 of the Report should emphasize the effects of floodplains not only on river flows, but 

also on hydrological connections and processes affecting biota, chemistry, and sediment movement

through downstream as well as lateral, vertical and temporal dimensions. Flood-forecasting methods 

could be used as a means to quantify the strength of connectivity (spatial and temporal) between 

floodplains and rivers. 

43
• The EPA should consider incorporating into the Report examples of floodplain classification 

systems to address the geomorphological and functional diversity of floodplains, and to place 

emphasis on the continuum of floodplains along stream networks. Channel migration zones could be 

used to demonstrate the variable nature of connectivity (in space and time) of floodplains and the 

waters/wetlands that they contain. 

• Additional literature should be reviewed and cited in Section 5.3 of the Report to demonstrate how 

lateral connections create a diversity of lotic, semi-lotic and lentic habitats, supporting a wide array 

of taxa (e.g., fish, amphibians, birds, mammals) and high levels of diversity. More emphasis is 

needed in Section 5.3 of the Report on these biotic exchanges.

• The range of examples of waters and wetlands in floodplain settings in the Report could be 

broadened to make it more representative of the United States as a whole. For instance, the EPA 

could incorporate studies on peatlands in floodplain settings that have “bidirectional” flows, as in 

northern tier states and Alaska and coastal lowland wetlands of Hawaii. 

• The EPA should consider reviewing and including in the Report additional references recommended 

by the SAB to document how the hydrologic phenomenon of the flood pulse links rivers to the 

floodplains.

3.5.4. Chemical Linkages

Wetlands and floodplains serve as sources, sinks and transformers of nutrients and other chemical 

contaminants, and have a significant impact on the physical, chemical, and biological integrity 

(including ecosystem productivity) of downstream waters. The primary driver of chemical linkages is 

ecosystem biogeochemistry, which involves the exchange or flux of materials between living and nonliving components. These fluxes involve interaction of complex physical, chemical, and biological 

processes in various components of the ecosystem. Biota (plants, microbes, and fauna) can be considered 

as exchange pools that are small in size and undergo rapid turnover and cycling. Abiotic components of 

wetlands and floodplains (e.g., soil), which are large in size, undergo slow turnover and provide longterm storage similar to a reservoir. The amount of a given constituent in these pools depends on its 

residence time. It is important to acknowledge these issues in the Report. 

The SAB recommends that the authors of the Report provide a more recent and diverse assessment of 

the biogeochemical implications of exchange flows. This can be accomplished by enhancing the review 

of the literature on the role of wetlands and floodplains as sources, sinks, and transformers of materials 

including: nutrients, metals, organic contaminants, and sediments. The Report sections on microbial 

nitrogen processing (denitrification), phosphorus cycling, and sediments (including legacy sediments 

and associated chemicals) should be strengthened with an expansion of the literature reviewed. The 

review on nitrogen processes in Section 5.3.2.2 of the Report is of particular concern due to its very 

heavy reliance on a single paper by Vidon et al. (2010), cited 20 times in that section, on the fate and 

fluxes of nitrogen in riparian areas. There is an extensive literature on this subject and while the Report 

correctly characterizes nitrogen transformations in a general sense, there are many key references that 

could be included. For example, the Report should be updated to provide a more recent and diverse 

assessment of biogeochemical implications of “hot-spots and hot-moments” in nitrogen fluxes that are 

associated with hydrologic exchanges between surface and subsurface waters, and the residence time of 

water in those locations (e.g., Groffman and Hanson 1997; Groffman et al. 2003, 2009; McClain et al. 

2003; Capps et al. 2014). This information may best be located in Chapter 4 with the review of low order 

riparian zones. The SAB also recommends that, in general, the literature findings in this section (as in 

44
much of the Report) be more quantitative and not reported by simple qualitative statements; for example, 

rather than stating that nitrogen levels increased or decreased, the Report should indicate the percent 

concentration change. The SAB notes that, depending on hydrologic connectivity and water residence 

time, floodplain soils exhibit a range of redox conditions, which then regulate biogeochemical cycling of 

key nutrients, metals, and organic compounds. 

The Report should indicate that changing climatic conditions may stimulate or alter rates, fluxes and 

storage pools of key elements (carbon, nitrogen phosphorus, and sulfur) involved in biogeochemical 

processes and services provided by wetlands. For example, accelerated decomposition of organic matter 

can potentially increase nutrient generation, which may lead to increased nutrient/contaminant loading 

to adjacent water bodies. Important inorganic elements in wetlands are mobile and thus their 

concentrations may increase upon flooding and drainage cycles, water withdrawals, sea level rise, and 

increases in temperature. The bioavailability of many inorganic elements required for key biological 

processes (e.g., plant growth and decomposition) will respond to these changing conditions. Drainage 

also increases enzyme and microbial activities, which facilitates oxidation of organic matter and leads to 

subsidence and loss of organic soils. Oxidation of organic matter in wetlands is dependent on watertable depth, temperature, nutrient loading, vegetation communities and release of nutrients. 

“Bidirectional” exchange of particulate organic matter (POM) and dissolved organic matter (DOM) in

floodplains can be an important source of organic matter to streams and rivers. Further treatment of the 

residence time of water should also be considered. Water residence time is a critical concept that can 

have significant biological impacts, which can be particularly relevant to downstream waters. Powers et 

al. (2012) point out that aquatic ecosystem components that have relatively high nutrient processing 

rates may not contribute substantially to total ecosystem retention unless enabled by hydrological 

connections.

The SAB recommends that the EPA consider including in the Report the following references on 

biogeochemistry: Aitkenhead-Peterson, et al. (2003); Billett et al. (2004); Bridgham et al. (2001, 2006); 

Buresh et al. (2008); Fennessy and Cronk (1997); Freeman et al. (20004a,b); Hefting et al.(2004); 

Osborne (2005); Qualls and Richardson (2003); Reddy et al. (1999, 2005, 2011); Strack et al. (2008); 

and Wetzel (1990, 2002).

Key Recommendations:

• The discussion of the chemical implications of exchange flows should include literature on the

biogeochemistry of wetlands and floodplains, and their role as sources, sinks, and transformers of 

materials including: nutrients, metals, organic contaminants, and sediments (additional references 

are provided in Sections 3.5.4 and 3.5.8 of this SAB report).

• The Report could further discuss how changing climatic conditions may stimulate or alter rates, 

fluxes and storage pools of key elements (carbon, nitrogen, phosphorus, and sulfur) involved in 

biogeochemical processes and services provided by wetlands (additional references are provided in 

Sections 3.5.4 and 3.5.8 of this SAB report). 

• The Report sections on nitrogen processing (denitrification), phosphorus cycling, and sediments 

(including legacy sediments and associated chemicals) should be strengthened by expanding the 

literature reviewed. In particular, Section 5.3.2.2 of the Report should be updated to provide a more 

recent and diverse assessment of biogeochemical implications of “hot-spots and hot-moments” in 

nitrogen fluxes that are associated with residence time and hydrologic exchanges between surface 

and subsurface waters (see references in this section above). The discussion about water residence 

45
time also could be expanded given its significant impacts on downstream water chemistry and 

biology (additional references are provided in Section 3.5.8 of this SAB report). 

• The Report should make quantitative, rather than simple, qualitative statements whenever possible 

(e.g., nitrogen levels increased by 25%).

3.5.5. Export versus Exchange

Floodplains as well as waters and wetlands in floodplain settings are shaped by repeated inundation, 

saturation, erosion and deposition of sediment, and movement of biota. Water and materials flow 

laterally between floodplains and rivers (i.e., downstream waters), moving onto the floodplain in periods 

of high flows and back to the channel as floods recede. As mentioned previously, the Report does not 

clearly articulate the multi-dimensional nature of connectivity between the floodplain and channel. The 

SAB recommends strengthening the focus of the Report on the fluxes of water, materials and biota to 

emphasize how exchange flows respond to the temporal progression of the flood pulse. 

Key Recommendation

• There should be a stronger focus in the Report on the multi-directional fluxes of water, materials and 

biota to emphasize how exchange flows respond to the temporal progression of the flood pulse.

3.5.6. Case Studies

The SAB finds that the Report would benefit from more discussion of forested wetlands, including 

bottomland hardwoods, given their ecological importance, rate of loss, and unique attributes. These

wetlands represent a significant portion of remaining United States wetlands. A case study could 

address this gap and illustrate the role of bottomland forests on river biogeochemistry and flood storage. 

Key Recommendation

• It would be useful to include in the Report a case study illustrating the role of forested wetlands 

(including bottomland hardwoods) in river biogeochemistry and flood storage.

3.5.7. Human Impacts and Aggregate Effects on Waters and Wetlands in Floodplain Settings

The manner in which human activities impact the connectivity of waters and wetlands in floodplain 

settings is an important issue that should be addressed in the Report. An example of such an impact is 

channel incision or levee construction that breaks the link between floodplain waters and wetlands with 

downstream waters. Alterations that reduce the connectivity of floodplains and waters and wetlands in 

floodplain environments provide some of the clearest demonstrations of the functional role of these 

areas with respect to downstream waters (for example, through degraded water quality as urban and 

agricultural runoff increases, leading to downstream sediment and nutrient enrichment). A key approach 

to this analysis is to provide examples of the aggregate effects of watershed land use change and 

floodplain impacts on downstream waters in terms of flooding, biodiversity, and materials flux

(Barksdale et al. 2013). The water quality benefits of riparian areas and floodplains should also be 

highlighted in the Report by explicitly pointing out that their destruction exacerbates nutrient runoff

from agricultural lands by reducing or eliminating nutrient uptake, dentrification, and sedimentation

of adsorbed phosphorus. The EPA should consider including the following references on human 

46
impacts to waters and wetlands in floodplain settings: Dudley and Platania (2007); and Verhoeven et al. 

(2006).

Key Recommendations 

• The Report should address how human activities impact the connectivity of waters and wetlands in 

floodplain settings. Additional references recommended by the SAB should be considered for 

inclusion in the Report.

• The Report should highlight how the destruction of riparian areas and floodplains can impair water 

quality by exacerbating nutrient runoff from agricultural lands, reducing or eliminating nutrient

uptake, dentrification, and sedimentation of adsorbed phosphorus.

3.6. Waters and Wetlands in Floodplain Settings: Review of the Findings and Conclusions

Charge Question 4(b). Conclusion (2) in section 1.4.2 of the Report Executive Summary 

discusses major findings and conclusions from the literature referenced in Charge Question 4(a) 

above. Please comment on whether the conclusions and findings in section 1.4.2 are supported 

by the available science. Please suggest alternative wording for any conclusions and findings 

that are not fully supported.

3.6.1. Scientific Support for the Findings and Conclusions Concerning Waters and Wetlands in

Floodplain Settings

The SAB finds that there is strong scientific support for the conclusion that floodplain water bodies and 

wetlands are connected to downstream waters through multiple pathways (including hydrological, 

chemical, and biological connectivity). However, as further discussed below, the SAB recommends that 

additional literature be included in the Report to bolster these findings, particularly as related to 

chemical and groundwater connectivity. The EPA should also recognize that there is a gradient of 

connectivity between wetlands and waters in floodplain settings and downstream waters that is a 

function of the frequency, duration, magnitude, predictability, and consequences of physical, chemical, 

and biological connections. In addition, the SAB notes that the key findings and conclusions presented 

in Section 1.4.2 of the executive summary of the Report should be directly related and parallel to the 

information presented in Section 5.3 on floodplain wetlands. Any conclusions presented in Section 1.4.2 

of the executive summary should also align with conclusions presented in Sections 5.5, the wetlands 

synthesis and implications discussion, and 6.1, the discussion of major conclusions.

The SAB recommends that the EPA Report discuss river-floodplains as integrated ecological units,

following riverscape (sensu Wiens 2002) and riverine landscape (sensu Ward et al. 2002; Thorp 2006) 

perspectives. Currently, many of the conclusions in the Report are drawn from literature related to nonfloodplain riparian zones (i.e., headwater riparian wetlands), which potentially undermines the ability to

speak to connectivity between waters and wetlands in floodplain settings and downstream systems. 

Thus, the SAB recommends replacing the current riparian focus with a discussion focused on the science 

of larger river (i.e., high-order) floodplain systems, and moving the riparian focus to Chapter 4, where 

the focus can largely remain on the dynamics of low-order streams. 

Key Recommendations 

• There is strong scientific support for the conclusion that waters and wetlands in floodplain settings 

47
are highly connected to downstream waters through multiple pathways including hydrological, 

chemical, and biological connectivity. However, a broad discussion of river-floodplain systems as 

integrated ecological units should replace the current headwater riparian focus and be included in 

Section 5.3 of the Report. The riverine landscape framework (Ward et al. 2002; Thorp et al. 2006)

should be employed as the conceptual backbone of the section. Additional literature should be 

included in the Report to bolster findings as related to chemical and groundwater connectivity.

• Key findings and conclusions presented in Section 1.4.2 of the executive summary of the Report 

should be directly related to the information presented in Section 5.3 on floodplain waters and 

wetlands. Conclusions presented in Section 1.4.2 of the executive summary should also align with 

conclusions presented in Sections 5.5, the wetlands synthesis and implications discussion, and 6.1, 

the discussion of major conclusions.

3.6.2. Additional Recommendations for the Findings and Conclusions for Waters and Wetlands 

in Floodplain Settings

The SAB recommends that the EPA address the following issues in the discussion of the findings and 

conclusions for waters and wetlands in floodplain settings. 

Inconsistent Terminology

As previously mentioned, the Report’s use of terms should remain consistent both within the key 

findings and conclusions sections as well as throughout Section 5.3. The terms “riparian areas,” 

“riparian and floodplain areas,” and “riparian/floodplain waters” are used inconsistently in Tables 5.1 

and 5.3. The SAB encourages consistent use of these (and other) terms and suggests providing 

clarification of the differences among them in the definitions. The SAB notes that the glossary 

definitions in the Report distinguish between “riparian areas” and “riparian wetlands” as well as among 

“floodplain,” “floodwater,” and “floodplain wetland.” “Upland” is also defined in the glossary as: (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) 

three-attribute wetland definition. These are examples of the use of multiple definitions that, while not 

incorrect, are sufficiently different to potentially cause confusion. Most importantly, the SAB suggests

that “bidirectional” wetlands be called “waters and wetlands in floodplain settings” and that headwater 

riparian terminology be disentangled from this section to the degree possible. The terminology used in 

the key findings and conclusions of the Report should align with the glossary definitions and the 

conceptual framework.

Temporal Component

As previously mentioned, the key findings and conclusions in the Report should recognize the temporal 

dimension of waters and wetlands in floodplain settings relative to downstream connectivity, consistent 

with the four-dimensional nature of the conceptual framework set forth in Chapter 2. Water residence 

times and the transient nature of floodplains should be key points. This temporal perspective, combined 

with an emphasis on developing and illustrating the strength of connectivity, could be done using the 

well-developed science of flood forecasting (probability) as a function of vertical and lateral 

connectivity. Incorporating discussion of flood frequency-floodplain inundation science into the Report 

would be effective for highlighting how hydrologists estimate the degree of connectivity. Brief reference 

to the flood-pulse and riverine landscape concepts, discussed within the conceptual framework (Chapter 

2), would reinforce the functional significance of regular or episodic floodplain inundation. 

48
Discussion of “channel migration zones,” which describe the movement of channels within floodplains 

over time as a result of large floods (Rapp and Abbe 2003, Brummer et al. 2006, Washington 

Department of Ecology 2011), would further address the lateral connectivity of rivers to their valley 

floors and the variable nature of connectivity in both space and time. The role of groundwater movement 

and storage should also be highlighted. This discussion should include the effects of flood pulses on the 

hydrologic differences between slope and riverine wetlands and the role of chemical/contaminant 

movement and storage related to groundwater systems in floodplains. These effects have been quantified 

by flow and transport modeling using both steady-state and transient analysis to simulate temporal 

changes. 

Overall, the EPA’s conclusions concerning connectivity of waters and wetlands in floodplain settings

should reflect the main message of a new spatial and temporal subsection in Section 5.3, as 

recommended in Section 3.5 of this SAB report.

Further Quantification of Key Conclusions

The key conclusions for waters and wetlands in floodplain settings should be more empirically and/or 

more specifically described. Whenever possible, the degree of and/or strength of evidence for 

connectivity should be quantified (e.g., of X studies, X% support a particular conclusion).

Chemical Linkages (including biogeochemical cycling)

The role of waters and wetlands in floodplain settings in storing and transforming chemical constituents, 

including the biogeochemical implications of exchange flows, should be expanded under Key Finding 

(d) in Section 1.4.2 of the Report. This may require additional literature review (in Section 5.3) to 

incorporate literature on floodplain wetlands and water bodies rather than relying on headwater riparian 

examples. Changes to nutrients (both N and P) and sediments should be easily documented. Some 

references have been recommended in Section 3.5.4 of this SAB report. There is ample literature on the 

improved water quality function of wetlands and this is the rationale for constructed wetlands. 

Additionally, there is an opportunity to link the discussion of the role of wetlands and other water bodies 

in storing and transforming chemical constituents to the regulation and management of chemical 

contaminants.

Biological Linkages Including Food Webs

The role of biological connectivity between waters and wetlands in floodplain settings and downstream

systems should be further highlighted in the key findings and conclusions. In particular, the SAB 

encourages the EPA to highlight the point that waters and wetlands in floodplain settings and 

downstream systems are intimately linked through biological connections (including integrated wetlandriver food webs) across a range of spatial and temporal scales. In this regard, the Report should 

explicitly discuss linkages to downstream waters. For example: “Floodplain wetlands can provide 

critical nursery habitat for fish, which then disperse into downstream waters, becoming part of river 

food webs and serving as a biological vector of nutrients.” There also may be an opportunity to mention 

the importance of waters and wetlands in floodplain settings to species that are economically important 

or listed as endangered, but this would have to be first developed in the body of the Report. 

49
Export versus Exchange

As previously discussed, an “exchange” versus “export” framework (i.e., reciprocal exchanges between 

waters and wetlands in floodplain settings and downstream waters) should be used in the Report. In this 

way, the EPA can clearly indicate that multi-directional biological, chemical, and hydrological transfers 

characterize the connections between the two systems. 

Case Studies

 

The SAB finds that the case studies in the Report are useful. However, the findings from the case studies 

should be more explicitly linked to the overall conclusions in Section 1.4 of the Report. As previously 

mentioned, the SAB finds that the Report would benefit from more discussion of forested wetlands, 

including bottomland hardwoods, given their ecological importance and their rate of loss. The SAB 

recommends that key information from all of the case studies be presented in side boxes, with more 

detailed information included as appendices.

Human Impacts 

In some cases, human alteration of connectivity provides the clearest demonstration of how waters and 

wetlands in floodplain settings are functionally linked to adjacent waters. Thus, the conclusions in the 

Report could be strengthened by explicitly mentioning how human activities (impairment as well as 

restoration) alter connectivity of waters and wetlands in floodplain settings with downstream waters. 

Mention should be made of alterations that both increase connectivity, such as ditches, and decrease 

connectivity, such as levees and water extraction activities that reduce the water table. Again, using the 

flood frequency-lateral connectivity argument, this might represent a strong opportunity to illustrate how 

diking has clearly diminished connectivity both in individual river segments as well as in the aggregate. 

Many floodplains along stretches of rivers, if not entire rivers, may be affected by diking. Other 

modifications should also be considered, including routine dredging/channelization, which can severely 

impair (or eliminate) floodplain function.

Aggregate/Cumulative Effects

The importance of considering waters and wetlands in floodplain settings in the aggregate should be 

underscored in the key findings and conclusions of the Report. For example, these sections could briefly 

illustrate how floodplain storage in the aggregate (e.g., floodplains in dozens to hundreds of individual 

channel reaches) yields many ecological services, including flood attenuation.

Key Recommendations 

• The key findings and conclusions in the Report should better recognize the temporal dimension of 

waters and wetlands in floodplain settings relative to downstream connectivity, consistent with the 

four-dimensional nature of the conceptual framework set forth in Chapter 2. Water residence times 

and the transient nature of floodplains should be key points. The well-developed science of flood 

forecasting (probability) as a function of vertical and lateral connectivity could be particularly useful 

in developing this temporal perspective.

• The role of waters and wetlands in floodplain settings in storing and transforming chemical 

constituents (i.e., their biogeochemical functions) should be expanded under key findings in Section 

1.4.2 of the Report. The role of biological connectivity between waters and wetlands in floodplain 

50
settings and downstream waters should also be further highlighted in the key findings and 

conclusions.

• The importance of considering waters and wetlands in floodplain settings in the aggregate, as well as 

the ways in which human activities (impairment as well as restoration) alter connectivity of waters 

and wetlands in floodplain settings with downstream waters, should be underscored in the key 

findings and conclusions of the Report.

• Report language referring to floodplain waters and wetlands should remain consistent both within 

the key findings and conclusions sections as well as throughout Section 5.3. The terminology used in 

the key findings and conclusions of the Report should align with the glossary definitions and the 

conceptual framework. The findings from the case studies in the Report should be explicitly linked

to the overall conclusions. 

• The key conclusions for waters and wetlands in floodplain settings should be more empirically 

and/or more specifically described. Wherever possible, the degree of and evidence for connectivity 

should be quantified (e.g., of X studies, X% support a particular conclusion).

3.6.3. Alternative Wording for Findings and Conclusions

The SAB recommends the following specific revisions to clarify the conclusions in Section 1.4.2 of the 

Report:

• Section 1.4.2 should consistently refer to “waters and wetlands in floodplain settings.”

• Section 1.4.2 should indicate that waters and wetlands in floodplain settings form integral 

components of river food webs.

• The text in finding (c) should indicate that waters and wetlands in floodplain settings can reduce 

flood peaks by storing and subsequently releasing floodwaters.

• The example in finding (d) appears to be an agricultural best management practice. A more relevant 

example may be provided from the text on page 5-7.

• In finding (e) the lead sentence emphasizes ecosystem function but the body of the paragraph 

describes biological connectivity. Finding (e) should discuss the importance of waters and wetlands 

in floodplain settings to birds, and how birds can spatially integrate the watershed landscape.

3.7. Waters and Wetlands in Non-floodplain Settings: Review of the Literature

Charge Question 5(a). Section 5.4 of the draft Report reviews the literature on the directional 

(downstream) connectivity and effects of wetlands and certain open waters, including 

“geographically isolated wetlands,” with potential for “unidirectional” hydrologic flows to 

rivers and lakes. Please comment on whether the Report includes the most relevant published 

peer-reviewed literature with respect to these types of wetlands and open waters. Please also 

comment on whether the literature has been correctly summarized. Please identify any published 

peer-reviewed studies that should be added to the Report, any cited literature that is not relevant 

to the review objectives of the Report, and any corrections that may be needed in the 

characterization of the literature.

51
The SAB finds that the review and synthesis of the literature on the downstream connectivity and effects 

of “unidirectional” wetlands and open waters in non-floodplain settings is technically accurate and in 

general the cited literature has been correctly summarized. As previously mentioned, the SAB 

recommends the authors reconsider use of the terms “unidirectional” and “geographically isolated 

wetlands” and suggests replacing them with the term “non-floodplain wetlands.” The SAB finds that the 

focus on surface water hydrologic connections in Section 5.4 of the Report and elsewhere does not 

adequately account for important groundwater and non-hydrologic biological exchanges that can 

strongly influence the integrity of downstream waters. As also previously discussed, the SAB 

recommends that the Report be reorganized to reflect the types of connections between wetlands and 

downstream waters via surface water, shallow subsurface flowpaths, shallow or deep groundwater

flowpaths, or through the movement of biota, with specific attention paid to the magnitude, duration, 

frequency, predictability, and consequences of these connections. Throughout the Report, landscape 

position, spatial scale, and temporal scale should be considered in the evaluation of the degree of 

connectivity, given that regional context (e.g., geology, climate, landforms, and surficial sediments) is a 

major driver of linkages. Consideration of landscape position and scale will likely provide further 

justification for treating wetland complexes as aggregates rather than as individual units based on 

geographic distribution. Likewise, human alterations of watersheds may change the types of connections 

to downstream waters as well as the magnitude, frequency, duration, predictability, and consequences of 

the connections, and the SAB recommends that the Report be revised to acknowledge the role of 

humans in these changes. In addition the Report should discuss the differences between manmade 

wetlands and those found in natural settings. 

3.7.1. Summary of the Literature on Non-floodplain Wetlands

Section 5.4 of the Report captures the most relevant peer-reviewed literature on non-floodplain 

“unidirectional” wetlands” and “geographically isolated wetlands.” The SAB has not identified any 

citations in Section 5.4 that are irrelevant to the review objectives of the Report. However, the SAB 

recommends adding additional citations on biological connections (e.g., Naiman et al. 1994; Polis et al. 

1997), many of which are referenced throughout this SAB report. Additional evidence from the large 

and growing literature on biological exchanges between non-floodplain wetlands should be included in 

the Report. In particular, the SAB recommends including literature addressing: the bulk exchange of 

materials via biota, e.g., energy (Norlin 1967; Mason and MacDonald 1982; Polis et al. 1997; Sabo and 

Power 2002; Baxter et al. 2005; Lowe et al. 2005; Spinola et al. 2008; Pearse et al. 2011); the movement 

of nutrients by biota (McColl and Burger 1976; Johnston and Naiman 1987; Davis 2003; Vrtiska and 

Sullivan 2009); the introduction of disease vectors (Blanchong et al. 2006); and the provisioning of 

habitat essential for biological integrity and completion of life cycles of downstream species (Brooks et 

al. 1998; Miyazano et al. 2010; Julian et al. 2013).

In addition, the SAB recommends that the EPA review and, as appropriate, add to the Report the 

following selected references that are particularly pertinent to the discussion of non-floodplain wetlands: 

Brunet and Westbrook (2012); Conly et al. (2001); Fang and Pomeroy (2008); Gray et al. (1984); 

Hayashi and Van der Kamp (2000); Hayashi et al. (2003); Shaw et al. (2012); Spence (2007); Spence 

and Woo (2003); Stichling and Blackwell (1957); Van der Kamp et al. (2003, 2008); Winter and 

LaBaugh (2003); Woo and Rowsell (1993); and Yang et al. (2010).

52
Key Recommendations

• The literature review in Section 5.4 of the Report is technically accurate; however, the SAB has 

recommended additional literature references that should be considered for inclusion in the Report to 

address: bulk exchange of materials via biota, the movement of nutrients by biota, the introduction 

of disease vectors, and the provisioning of habitat essential for biological integrity and completion of 

life cycles of downstream species. 

• The literature review should address the relative degree of connectivity for various non-floodplain 

wetlands. 

3.7.2. Clarification of Terms in Section 5.4 of the Report

The SAB finds that the term “unidirectional wetlands “ as used in the Report implies the presence of 

only one-way hydrologic flows, when in fact, connectivity can have many physical, chemical, and 

biological dimensions far beyond surface and shallow subsurface hydrologic flowpaths. As previously 

discussed, the SAB recommends that the draft Report’s “uni- and bi-directional” terminology be 

replaced by terms that better describe landscape position. In this case, “bidirectional wetlands” could be 

redefined as those within riparian and floodplain settings, and “unidirectional wetlands” as those not 

within riparian zones and floodplains (i.e., non-floodplain settings). The influence of floodplain and 

non-floodplain wetlands on downstream connectivity can then be explained in the context of their 

landscape settings and with respect to the conceptual framework, as described below.

Key Recommendation

• The SAB recommends that the terms “unidirectional” and “geographically isolated” wetlands be 

replaced in the Report and suggests using the term “wetlands in non-floodplain settings.”

3.7.3. Recommended Conceptual Model for Synthesizing Types and Gradients of Connectivity

As discussed in Section 3.2 of this report, the SAB recommends the EPA Report be revised to use the 

multiple flowpath conceptual framework that describes the multiple dimensions of connectivity. The 

five functions used to describe connectivity in the Report (i.e., source, sink, refuge, lag, transformation) 

are differentially affected by the types and characteristics of connections. The framework recommended 

by the SAB is envisioned as a potential way to map the five functions across different regional settings 

in order to assess the consequences and relative extent of hydrologic, biological, and chemical flowpaths 

provided by non-floodplain wetlands to downstream waters. 

Similarly, the SAB recommends that a second conceptual model be developed and used to frame the 

discussion about the type and gradient of various connections between and among floodplain wetlands 

and non-floodplain wetlands and downstream waters (or “bidirectional” and “unidirectional wetlands,” 

respectively, using the Report’s original nomenclature). Figure 3 illustrates a conceptual model that the 

SAB finds to be useful in this regard.

The multiple dimensions of connectivity to downstream waters include connections provided by surface 

waters, deep and shallow subsurface groundwater, and movement of biota. Each dimension of 

connectivity should be arrayed as a gradient, as illustrated in Figure 3. This approach could be used to 

synthesize findings from the literature in terms of the degree of connectivity pathways (e.g., magnitude, 

53
duration, frequency3

) rather than just the presence of any connection. The SAB finds that such an 

analysis is possible and would be useful for summarizing the effects of such connections in semiquantitative terms. 

Figure 3: Hypothetical illustration of connectivity gradient and potential consequences to 

downstream waters. Panel A illustrates changes to downstream waters with increases in the 

magnitude, duration, and frequency of surface and subsurface connections. Panel B illustrates

transfers mediated by biota to downstream waters. All streams (including perennial, intermittent, 

and ephemeral streams) have a connection to downstream waters. Within non-floodplain wetlands 

the degree of connectivity and implications for integrity of downstream waters vary considerably. 

Key Recommendations

• When describing connectivity for floodplain and non-floodplain wetlands and certain open waters, 

the EPA should refer to the conceptual framework the SAB has recommended for the EPA Report 

(see Section 3.2.3 of this SAB report).

3 Note that, in this context, frequency, magnitude, and duration apply to all five functions used to describe connectivity in the 

Report and not to hydrologic connectivity alone.

54

 
• The EPA should consider using Figure 3 in this SAB report (or a similar figure) to frame the 

discussion of connectivity gradients as a function of the frequency, magnitude, duration, 

predictability, and consequences of physical, chemical, and biological connections among floodplain

wetlands and non-floodplain wetlands and downstream waters.

• The EPA should identify endpoints for each connectivity gradient, quantify each connection to the 

degree possible, and identify research and data gaps. 

3.7.4. Temporal and Spatial Scales of Connections among Non-Floodplain Wetlands and Open 

Waters

Wetlands that are situated alongside rivers and their tributaries are likely to be connected to those waters 

through the exchange of water, biota and chemicals. As the distance between a wetland and a flowing 

water system increases, these connections become less obvious. Wetlands that are not contained within 

river floodplains or stream riparian zones and that lack a permanent surface water connection may still 

be connected to downstream waters through groundwater flowpaths and through the exchange of 

organisms. These water bodies can become connected to downstream waters during floods or as a result 

of rising water tables.

The EPA Report suggests that determining the “connectedness” of each non-floodplain wetland must be 

done on a case-by-case basis. The SAB suggests that the vast majority of non-floodplain wetlands can 

be classified with respect to some degree of hydrologic, chemical or biological connections to 

downstream waters; however, some hydrologically and spatially disconnected wetlands may need to be 

considered on a case-by case basis. The challenge for the EPA is to describe the hierarchy of decisions 

and the tools necessary to assess the degree of connection necessary to warrant case-by-case analysis. 

The SAB notes that despite individual differences among wetlands that warrant case-by-case analysis, 

there are useful (and essential) general principles and “models” that can and should be relied upon for 

making predictions and for guiding policy decisions and actions.

The SAB recommends that EPA establish relevant baselines for temporal intervals that are likely to 

connect a non-floodplain wetland to downstream waters. Current technology exists to map these 

baselines using empirical observations (e.g., use of LandSat imagery to map extent of high water 

regimes receiving precipitation greater than the annual mean plus two standard deviations versus low 

water regimes receiving precipitation less than the annual mean minus two standard deviations, five or 

ten-year flood return interval, or results of hydrologic models). Such maps would be similar to the 

Federal Emergency Management Agency (FEMA) floodplain maps, and would need to be recalibrated 

for changing climate and land cover conditions.

For wetlands outside of these flood boundaries, there may still be important subsurface or biological 

connections. The degree of groundwater connectivity between a wetland and downstream waters varies 

considerably. For example, ombrotophic bogs, which by definition are rain-fed, have minimal 

groundwater connections to downstream waters, while groundwater-fed wetlands are clearly exchanging 

materials with the same groundwater systems that feed downstream waters. EPA scientists should 

consider where along this gradient, the connections are of sufficient magnitude to impact the integrity of 

downstream waters. This may represent an important research need for the agency. Past this threshold, 

groundwater connections will need to be evaluated on a case-by-case basis.

For those non-floodplain wetlands where the only significant connection is via the exchange of biota 

(e.g., the movement of plants and animals between wetlands and rivers), the degree of connection will 

55
require an assessment. There is abundant scientific literature documenting that organisms move between

these habitats and downstream waters (many relevant references are cited in this SAB report), that these 

connections are essential for the survival of many species, and that these connections serve to exchange 

materials across these boundaries; however, there has been insufficient scientific research to date to 

predict the magnitude of these connections and their effects on downstream ecosystems. A case-by-case

evaluation will be required to establish whether these biological connections are of sufficient magnitude 

to affect the integrity of downstream waters.

Key Recommendations

• The Report should recognize that all aquatic habitats have some degree of connection, although they 

may vary widely through space and time in terms of effects on the integrity of downstream waters. 

As a result, the Report should assess connectivity in terms of downstream effects with an emphasis 

on frequency, magnitude, duration, predictability, and consequences of connections. 

• Because the majority of non-floodplain wetlands can be classified with respect to some degree of 

hydrologic, chemical, or biological connections to downstream waters, the SAB recommends that 

the EPA describe the hierarchy of decisions and tools necessary to assess the degree of connection in 

case-by-case analyses.

• The SAB recommends that the EPA initiate research to understand the gradient of connectivity of 

non-floodplain wetlands to downstream waters and to examine the relationships between the degree 

of connectivity and impacts on downstream waters.

3.7.5. Assessing Wetland Connectivity Based on Aggregate Analysis of Wetland Complexes

Many watersheds have a large number of non-floodplain wetlands that are collectively responsible for:

the maintenance of base flows; the attenuation of floods; the production of organic material that fuels 

downstream food webs; and the trapping or removal of sediments, nutrients and contaminants that 

would otherwise contribute to the degradation of the physical, chemical, or biological integrity of 

downgradient waters. Although individually these wetlands may have minimal connections to 

downstream waters, the cumulative impact of these diffuse connections is tremendously important to the 

maintenance of downstream biota and ecosystem integrity. Historically, the destruction of wetlands has 

caused serious declines in the water quality of downstream waters and has had a substantial effect on 

flood regimes. The EPA report should describe the rich literature on historic wetland loss (e.g., Dahl and 

Allord 1996; USFWS 2014) and the resulting consequences for the water quality, biodiversity, and flood 

impacts on downstream waters. This literature should be provided as a preface to a discussion of the 

need to consider the aggregate or cumulative impacts of wetlands that may each individually have 

minimal hydrologic, chemical or biological connections to downstream waters.

Assessment of the degree of wetland connectivity is best conducted on aggregated wetland complexes 

rather than on individual wetlands because over a range of precipitation regimes the boundaries of any 

single wetland may vary through space and time (e.g., Drexler et al. 2013). The regional context (e.g., 

geology, climate, landforms, and surficial sediments) is a major driver of the temporal and spatial scales 

of hydrologic linkages. Thus, regional context and spatial landscape position and scale should also be 

considered when evaluating the degree of connectivity, e.g., distance from and size of wetlands (or 

similar wetland types). As previously discussed, various frameworks for regionalization exist (e.g., 

Hydrologic Landscape Regions) and these include characterizations of landscapes at nested scales, such 

56
as regional, sub-regional, and local. These nested scales can be used to summarize variability in 

connectivity identified in the peer-reviewed literature. 

Key Recommendations

• The Report should articulate the importance of assessing wetland connectivity in terms of 

aggregated wetland complexes, rather than individual wetlands. 

• The Report should discuss the usefulness of regionalization methods to summarize information 

about wetland connectivity at nested scales. 

• The Report should analyze the scientific literature to determine whether there is an appropriate 

scaling that should be used for determining how non-floodplain wetlands may be aggregated when 

considering their effects on downstream waters. A discussion on how the scaling may vary 

geographically, and on the basis of factors affecting connectivity, should be included. 

3.7.6. Discussion of Human Alteration of Landscapes in Section 5.4 of the Report

The Report tends to focus on natural wetland systems or those with minimal disturbance. As previously 

discussed, human modifications alter the type, strength and magnitude of connectivity pathways. The 

EPA Report should discuss the effects of human alterations on the connectivity of non-floodplain waters 

and wetlands. Some types of disturbances promote connections where none previously existed; others 

alter existing types of connections or trigger the transport of novel chemical or biological species. 

Creating connections where none previously existed, or where they were of low frequency through time, 

can affect the biological integrity of downstream waters. For example, such connections can be a key 

problem for amphibians that must breed and rear in wetlands free of fish (i.e., vernal pools). There is a 

large literature on the importance and conservation of ephemeral habitats for amphibians and other 

species and functions (e.g., Semlitsch 1998, 2000, 2002; Semlitsch and Bodie 2003; Calhoun and 

deMaynadier 2008). Most of these references are from the eastern United States. There is also a suite of 

species, mostly toads, that rely on ephemeral aquatic habitats in the Western and Great Plains region, but 

they are less well known. In addition, there are many instances where man-made isolated wetlands occur 

within the landscape. These features are often found behind levees or within isolated parcels within 

urban landscapes and may not provide the same ecosystem functions as natural wetlands. Some features 

considered as wetlands are man-made and specifically designed to reduce connectivity, such as 

detention basins, excavated ponds, or ponds related to industrial processes. The SAB recommends that 

Section 5.4, as well as other sections of the Report, acknowledge these types of alterations or man-made 

habitats and include a discussion of current and past (legacy) human alterations of watersheds and how 

they affect the type, strength, and magnitude of connectivity pathways. In particular, human activities 

such as water diversion or water extraction may influence the water table, thereby reducing the potential 

for connections within and among wetlands and downstream waters. Extractive activities or those that 

alter hydrologic flow paths (diking, channelization, damming) may influence the magnitude of natural 

disturbances such as floods or droughts, and subsequently affect the integrity of downstream waters.

Key Recommendation

• Section 5.4, and other sections of the Report, should be revised to discuss the legacy effects of 

human activities and their effect on the type, strength, and magnitude of connectivity pathways.

57
3.8. Non-floodplain Waters and Wetlands: Review of the Findings and Conclusions

Charge Question 5(b). Conclusion (3) in section 1.4.3 of the Report Executive Summary discusses 

major findings and conclusions from the literature referenced in Charge Question 5(a) above. Please 

comment on whether the conclusions and findings in section 1.4.3 are supported by the available 

science. Please suggest alternative wording for any conclusions and findings that are not fully 

supported.

In commenting on the EPA’s findings and conclusions regarding connectivity among open waters and 

“unidirectional” non-floodplain wetlands and downstream waters (Section 1.4.3 of the Report), the SAB 

focused on knowledge drawn from the peer-reviewed literature, especially that: (1) connectivity extends 

beyond hydrologic connectivity, (2) each connectivity flowpath can be described as a gradient that 

varies over space and time, and (3) multiple low magnitude connections can have large aggregate effects 

on integrity of downstream waters.

3.8.1. Scientific Support for the Conclusions Concerning Non-floodplain Waters and Wetlands 

The SAB disagrees with the overall conclusion in Section 1.4.3 of the Report (Conclusion 3) indicating 

that, “The literature we reviewed does not provide sufficient information to evaluate or generalize about 

the degree of connectivity (absolute or relative) or the downstream effects of wetlands in 

“unidirectional” landscape settings.” This statement is inconsistent with the text immediately preceding 

it, which describes numerous scientifically-established functions of non-floodplain wetlands that can 

benefit the physical, chemical, and biological integrity of downstream waters. Furthermore, the 

conclusion largely overlooks the effects of deep aquifer connections and non-hydrologic biological 

connections on downstream waters. The SAB finds that the scientific literature, including references 

cited in the EPA Report, provides ample information to support a more definitive statement, and 

strongly recommends that the authors revise this conclusion to focus on what is supported by the 

scientific literature and then articulate the specific gaps in our knowledge that must be resolved (e.g., 

degree of connectivity, analyses of temporal or spatial variability). 

The SAB recommends that Conclusion 3 in the Report explicitly recognize that the connectivity of nonfloodplain waters to downstream ecosystems varies widely. Because of this the connectivity of nonfloodplain waters should be evaluated along a gradient rather than as a dichotomous, categorical 

variable. 

The SAB recommends that all of the Report’s conclusions recognize connections beyond hydrologic 

ones, and that the frequency, magnitude, and duration of these connections, as well as their predictability

and consequences, be considered. The SAB recommends that, within the text of Conclusion 3 in the 

Report, the authors explicitly state the four pathways by which non-floodplain wetlands can be 

connected to downstream waters: via surface water and subsurface (shallow or deep groundwater)

flowpaths, or through the movement of biota. It is the magnitude and effect of material, water or biotic 

fluxes rather than the simple presence or absence of a flux that determines the strength of the connection 

between a wetland and downstream waters.

The SAB disagrees with the notion, implied within the Report, that even minimal hydrologic 

connections are more important than biological connections, no matter how large the flux. The SAB 

recommends that this emphasis shift in order to account for strong connections that affect any one of the 

five functions used to describe connectivity in the EPA Report. If the goal of defining and estimating 

connectivity is to protect downstream waters, the interpretation must move from a dichotomous, 

58
categorical distinction (connected vs. not connected) towards a gradient approach that recognizes 

variation in the frequency, duration, magnitude, predictability, and consequences of those connections. 

The SAB recommends that an integrated systematic approach be taken to conceptualize the structure and 

function of non-floodplain wetlands. The systems approach, which evaluates connectivity at the 

landscape scale, is used by hydrogeologists, and by surface water and groundwater hydrologists, who 

have the quantitative tools and conceptual models to determine the connectivity of both surface and 

subsurface hydrological systems to non-floodplain wetlands (ASTM, 1996; Kolm et al. 1996). Such an 

approach could be extended to include biological connections and HGM wetland classifications (Kolm 

et.al. 1998). The flowpath driven conceptual framework recommended by the SAB would provide a 

useful starting point for development of a landscape scale approach to conceptualize the structure and 

function on non-floodplain wetlands.

Key Recommendations

• The overall conclusion for non-floodplain wetlands (Conclusion 3 in Section 1.4.3) should be 

revised to focus on what is supported by the scientific literature and to provide more specifics on 

data and research gaps (e.g., degree of connectivity, analyses of temporal or spatial variability). 

• Conclusion 3 of the Report should explicitly discuss the four pathways by which non-riparian/nonfloodplain wetlands can be connected to downstream waters: i.e., via surface water, shallow 

subsurface flowpaths, shallow or deep groundwater flowpaths, or through the movement of biota. 

• The conclusions in the Report should state that the determination of connectivity should be based on 

the magnitude, duration, frequency, predictability, and consequences of water, material, and biotic 

fluxes to downstream waters, and their impact on the integrity of downstream waters. 

3.8.2. Recommendations Concerning Findings for Waters and Wetlands in Non-floodplain 

Settings

The SAB provides a number of recommendations to improve the presentation of findings in Section 

1.4.3 of the Report. 

The SAB recommends that conclusions be stated as concise, declarative statements. To accomplish this, 

the Report authors should remove references to specific studies within the text of the key findings. The 

Report’s conclusions are intended to summarize general themes arising from a broad synthesis of 

diverse literature. The SAB finds that it is not necessary to attribute these overarching findings to one or 

a few specific studies. 

The SAB also recommends that the key findings be more explicitly presented in the text of the Report. 

Conclusions about non-floodplain wetlands are summarized in Table 5-4, but these same summary 

points are not clearly explained in the text itself. In addition, Table 5-4 discusses functions of wetlands 

but does not present conclusions on how those functions translate to an effect on the physical, chemical, 

or biological integrity of downstream waters based on the magnitude or duration of any of the modes of

connection discussed in the literature. For example, the statement that “unidirectional wetlands can 

remove, retain, and transform many nutrient inputs” refers to such functions, but there is no conclusion 

about how these would affect downstream waters. 

59
The SAB recommends that the EPA revise the following key findings in Section 1.4.3 of the Report. 

These revisions are consistent with the literature synthesis performed and the SAB’s knowledge of the 

subject.

Key Finding (b)

The SAB recommends including the following statement in the Report as an additional key finding on 

the biological functions of “unidirectional” wetlands.

Suggested statement: Wetlands provide unique and important habitats for many organisms, both 

common and rare. Some of these organisms require multiple types of waters to complete their full life 

cycles, including downgradient waters. Other organisms, especially abundant and/or highly mobile 

species, play important roles in transferring energy and materials between wetlands and downstream 

waters.

The SAB also notes that the Report’s conclusion on the similarity between wetlands and other water 

bodies needs further substantiation from the literature as the functions within each are different, 

especially in nutrient and organic matter production. In addition, this conclusion should recognize the 

differences between natural wetland systems and those that are man-made or are found in urban 

environments. 

Key Finding (c)

The SAB recommends including the following statement in the Report as an additional key finding 

about non-floodplain wetlands and downgradient waters to parallel the preceding finding on “hydrologic 

connectivity.”

Suggested statement: Biological connections are likely to occur between all non-floodplain wetlands 

and downstream waters. 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.

Key Finding (f)

The SAB recommends including the following two additional key findings that summarize important 

information from the main body of the document that were not emphasized in the original wording of 

the key finding (f).

 

Suggested additional key finding on spatial proximity of non-floodplain wetlands: 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.

Suggested additional key finding on the cumulative or aggregate impacts of non-floodplain wetlands: 

The cumulative influence of many individual wetlands within watersheds can strongly affect the spatial 

scale, magnitude, frequency, and duration of hydrologic, biologic and chemical fluxes or transfers of 

water and materials to downstream waters. Because of their aggregated influence, any evaluation of 

60
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.

The SAB recommends that the Report authors cite the following references in support of this last 

statement; Lee and Gosselink (1988); Preston and Bedford (1988).

Key Recommendations

• The authors should remove references to specific studies within the text of the key findings in the 

Report. The Report’s conclusions are intended to summarize general themes arising from a broad 

synthesis of diverse literature.

• The key findings should be more explicitly presented in the text of the Report. Conclusions about 

“unidirectional” wetlands are summarized in Table 5-4, but these same summary points are not 

clearly explained in the text itself.

• The SAB recommends revising three of the key findings in Section 1.4.3 of the Report and has 

provided specific text.

61
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APPENDIX A: THE EPA’S CHARGE QUESTIONS

Connectivity of Streams and Wetlands to Downstream Waters:

A Review and Synthesis of the Scientific Evidence 

Technical Charge to External Peer Reviewers

Understanding the physical, chemical, and biological connections by which streams, wetlands, and 

open-waters affect downstream waters such as rivers, lakes, and oceans is central to successful 

watershed management and to meeting water quality goals. It is also central to informing policy 

decisions that guide our efforts to meet these goals. The purpose of this Report, titled Connectivity of 

Streams and Wetlands to Downstream Waters: A Review and Synthesis of the Scientific Evidence is to 

summarize the current scientific understanding of broadly applicable ecological relationships that affect 

the condition or function of downstream aquatic ecosystems. The focus of the Report is on small or 

temporary non-tidal streams, wetlands, and open-waters. Examples of relevant connections include 

transport of physical materials such as water or wood, chemical compounds such as nutrients or 

pesticides, movement of biological organisms such as fish or insects, and processes or interactions that 

alter material transport, such as nutrient spiraling. Materials reviewed in this Report are limited to peerreviewed scientific literature. Findings from this Report will help inform EPA and the U.S. Army Corps 

of Engineers in their continuing policy work and efforts to clarify what waters are covered by the Clean 

Water Act. As a scientific review, the Report does not consider or make judgments regarding legal 

standards for Clean Water Act jurisdiction. 

The Report is presented in six chapters. Key findings and major conclusions are summarized in Chapters 

1 (Executive Summary) and 6 (Conclusions and Discussion). Chapter 2 (Introduction) describes the 

purpose and scope of the document and the literature review approach. Chapter 3 presents a conceptual 

framework that describes the hydrologic elements of a watershed, the types of physical, chemical, and 

biological connections that link them, and watershed climatic factors that influence connectivity at 

various temporal and spatial scales. Chapter 4 surveys the literature on stream networks with respect to 

physical, chemical, and biological connections between upstream and downstream habitats. Chapter 5 

reviews the literature on connectivity and effects of non-tidal wetlands and certain open waters on 

downstream waters. All terms are used in accordance with standard scientific meanings, and definitions 

which are in the Report glossary. 

A-1
TECHNICAL CHARGE QUESTIONS

Overall Clarity and Technical Accuracy of the Draft Report

1. Please provide your overall impressions of the clarity and technical accuracy of the draft EPA 

Report, Connectivity of Streams and Wetlands to Downstream Waters: A Review and Synthesis of 

the Scientific Evidence. 

Conceptual Framework: An Integrated, Systems Perspective of Watershed Structure and 

Function

2. Chapter 3 of the draft Report presents the conceptual basis for describing the hydrologic 

elements of a watershed; the types of physical, chemical, and biological connections that link 

these elements, and watershed climatic factors that influence connectivity at various temporal 

and spatial scales (e.g., see Figure 3-1 and Table 3-1). Please comment on the clarity and 

technical accuracy of this chapter and its usefulness in providing context for interpreting the 

evidence about individual watershed components presented in the Report. 

Lotic Systems: Ephemeral, Intermittent, and Perennial Streams

3(a) Chapter 4 of the Report reviews the literature on the directional (downstream) connectivity and 

effects of ephemeral, intermittent, and perennial streams (including flow-through wetlands). 

Please comment on whether the Report includes the most relevant published peer-reviewed 

literature with respect to these types of streams. Please also comment on whether the literature 

has been correctly summarized. Please identify any published peer-reviewed studies that should 

be added to the Report, any cited literature that is not relevant to the review objectives of the 

Report, and any corrections that may be needed in the characterization of the literature.

3(b) Conclusion (1) in section 1.4.1 of the Report Executive Summary discusses major findings and 

conclusions from the literature referenced in Charge Question 3(a) above. Please comment on 

whether the conclusions and findings in section 1.4.1 are supported by the available science. 

Please suggest alternative wording for any conclusions and findings that are not fully supported.

Lentic Systems: Wetlands and Open Waters with the Potential for Non-tidal, “Bidirectional” 

Hydrologic Flows with Rivers and Lakes

4(a) Section 5.3 of the Report reviews the literature on the directional (downstream) connectivity and 

effects of wetlands and certain open waters subject to non-tidal, “bidirectional” hydrologic flows 

with rivers and lakes. Please comment on whether the Report includes the most relevant 

published peer-reviewed literature with respect to these types of wetlands and open waters. 

Please also comment on whether the literature has been correctly summarized. Please identify 

any published peer-reviewed studies that should be added to the Report, any cited literature that 

is not relevant to the review objectives of the Report, and any corrections that may be needed in 

the characterization of the literature.

4(b) Conclusion (2) in section 1.4.2 of the Report Executive Summary discusses major findings and 

conclusions from the literature referenced in Charge Question 4(a) above. Please comment on 

whether the conclusions and findings in section 1.4.2 are supported by the available science. 

Please suggest alternative wording for any conclusions and findings that are not fully supported.

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Lentic systems: Wetlands and Open Waters with Potential for “Unidirectional” Hydrologic Flows 

to Rivers and Lakes, Including “Geographically Isolated Wetlands”

5(a) Section 5.4 of the draft Report reviews the literature on the directional (downstream) 

connectivity and effects of wetlands and certain open waters, including “geographically isolated 

wetlands,” with potential for “unidirectional” hydrologic flows to rivers and lakes. Please 

comment on whether the Report includes the most relevant published peer-reviewed literature 

with respect to these types of wetlands and open waters. Please also comment on whether the 

literature has been correctly summarized. Please identify any published peer-reviewed studies 

that should be added to the Report, any cited literature that is not relevant to the review 

objectives of the Report, and any corrections that may be needed in the characterization of the 

literature.

5(b) Conclusion (3) in section 1.4.3 of the Report Executive Summary discusses major findings and 

conclusions from the literature referenced in Charge Question 5(a) above. Please comment on 

whether the conclusions and findings in section 1.4.3 are supported by the available science. 

Please suggest alternative wording for any conclusions and findings that are not fully supported.

A-3
APPENDIX B: ADDITIONAL LITERATURE CITATIONS REGARDING 

BIOLOGICAL CONNECTIVITY

The following additional literature citations addressing biological connectivity are provided for the 

EPA’s consideration in developing the Report. These papers represent combinations of floodplainstream, wetland-stream, and wetland-wetland interactions, but in many cases provide evidence of 

connectivity among multiple aquatic habitats. The citations are organized by major taxonomic groups 

and in some cases by topics.

General

Mason, C.F. and S.M. MacDonald. 1982. The input of terrestrial invertebrates from tree canopies to a 

stream. Freshwater Biology 12:305-11.

Winemiller, K.O. 1990. Spatial and temporal variation in tropical fish trophic networks. Ecological 

Monographs 60:331-67.

Birds

Waterbird foraging

Anteau, M.J., M.H. Sherfy, and A.A. Bishop. 2011. Location and agricultural practices influence spring 

use of harvested cornfields by cranes and geese in Nebraska. Journal of Wildlife Management

75:1004-1011, doi: 10.1002/jwmg.135

Austin, J.E., and A.L. Richert. 2005. Patterns of habitat use by whooping cranes during migration: 

summary from 1977-1999 site evaluation data. Proceedings North American Crane Workshop

9:79-104.

Vrtiska, M.P., and S. Sullivan. 2009. Abundance and distribution of lesser snow and Ross’s geese in the 

Rainwater Basin and Central Platte River Valley of Nebraska. Great Plains Research 19:147-155.

Waterfowl freshwater drinking to dilute salt loads

Adair, S.E., J.L. Moore, and W.H. Kiel, Jr. 1996. Wintering diving duck use of coastal ponds: An 

analysis of alternative hypotheses. The Journal of Wildlife Management 60(1):83-93. 

http://www.jstor.org/stable/3802043. [accessed October 8, 2014]

Ballard, B.M.., J.D. James, R.L. Binghan, M.J. Petrie, B.C. Wilson. 2010. Coastal pond use by redheads 

wintering in the Laguna Madre, TX. Wetlands 30:669-674.

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

Hydrobiologia 279/280: 279-287.

Waterbird foraging

Aldrich, T.W., and D.S. Paul. 2002. Avian ecology of Great Salt Lake. In Great Salt Lake: an Overview 

of Change, J.W. Gwynn, (ed.) pp. 343-374. Utah Department of Natural Resources and Utah 

Geological Survey Special Publication, Salt Lake City, Utah, USA.

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Vest, J.L., and M.R. Conover. 2011. Food habits of wintering waterfowl on the Great 

Salt Lake, Utah. Waterbirds 34:40-50.

Sandhill Cranes

Folk, M.J, and T.C. Tacha. 1990. Sandhill crane roost site characteristics in the North Platte River 

Valley, Nebraska. Journal of Wildlife Management 54:480-486.

Subcommittee on Rocky Mountain Greater Sandhill Cranes. 2007. Management Plan of the Pacific and 

Central Flyways for the Rocky Mountain Population of Greater Sandhill

Cranes. [Joint] Subcommittees, Rocky Mountain Population Greater Sandhill Cranes, 

Pacific Flyway Study Committee, Central Flyway Webless Migratory Game Bird Technical

Committee, Migratory Bird Management Office, U.S. Fish and Wildlife Service, Portland, OR.

Tacha, T.C., S.A. Nesbitt, and P.A. Vohs. 1994. Sandhill cranes. In Migratory Shore and Upland Game 

Bird Management in North America, T.C. Tacha and C.E. Braun (eds.) pp. 77-94. International 

Association of Fish and Wildlife Agencies, Washington D.C.

Waterbird movements among multiple waters - Prairie Pothole Shorebirds

Farmer, A.H., and A.H. Parent. 1997. Effects of the landscape on shorebird movements at spring 

migration stopovers. Condor 99:698-707.

Waterbird abundance moving among waters

Jorgensen, J.G., J.P. McCarty, and L.L. Wolfenbarger. 2008. Buff-breasted Sandpiper density and 

numbers during migratory stopover in the Rainwater Basin, Nebraska. Condor 110: 63-69.

Pearse, A.T., G.L. Krapu, D.A. Brandt, and P.J. Kinzel. 2010. Changes in agriculture and abundance of 

snow geese affect carrying capacity of sandhill cranes in Nebraska. Journal of Wildlife 

Management 74(3):479-488.

Waterfowl abundance using multiple wetlands

Fairbairn, S.E. and J.J. Dinsmore. 2001. Local and landscape-level influences on wetland bird 

communities of the prairie pothole region of Iowa, USA. Wetlands 21:41-47. 

Haramis G.M. 1990. Breeding ecology of the wood duck: a review. In Proceedings of the 1988 North 

American Wood Duck Symposium, L.H. Fredrickson, G.V. Burger, S.P. Havera, D.A. Graber. R.E

.Kirby, T.S. Taylor (eds.) pp. 45–60. St. Louis, MO.

Krapu, G.L., K.J. Reinecke, D.G. Jorde, and S.G. Simpson. 1995. Spring staging ecology of midcontinent Greater White-fronted Geese. Journal of Wildlife Management 59:736-746. 

LaGrange, T.G. and J.J. Dinsmore.1989. Habitat use by mallards during spring migration through 

central Iowa. Journal of Wildlife Management 53:1076-1081. 

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Skagen, S. K. and S. K. Knopf. 1993. Toward conservation of midcontinental shorebird migrations. 

Conservation Biology 7:533-541. 

Webb, Elisabeth K., L.M. Smith, M.P. Vrtiska, and T.G. LaGrange. 2010. Effects of local and landscape 

variables on wetland bird habitat use during migration through the Rainwater Basin. Journal of 

Wildlife Management 74(1):109-119.

Fish

Importance of connectivity between river and floodplain for fish

Babar, M.J., D.L. Childers, K.J. Babbit, and D.L. Anderson. 2002. Controls on the distribution and 

abundance of fish in temporary wetlands. Canadian Journal of Fisheries and Aquatic Sciences 

59:1441-1450. 

Boltz, J.M., and R.R. Stauffer, Jr. 1989. Fish assemblages of Pennsylvania wetlands. In Wetland 

Ecology and Conservation: Emphasis in Pennsylvania, S.K. Majumdar, R.P. Brooks, F.J. 

Brenner, and R.W. Tiner, Jr. (eds.) Chapter 14. Pennsylvania Academy of Science, Easton, PA.

Langston, M.A., and D.M. Kent. 1997. Fish recruitment to a constructed wetland. Journal of Freshwater 

Ecology 12:123-129.

Vilizzi, L., B.J. McCarthy, O. Scholz, C.P. Sharpe, and D.B. Wood. 2012. Managed and natural 

inundation: benefits for conservation of native fish in a semi-arid wetland system. Aquatic 

Conservation Marine and Freshwater Ecosystems 23:37–50, doi: 10.1002/aqc.2281

Connectivity of floodplain habitats with rivers

Groom, J.D., and T.C. Grubb Jr. 2002. Bird species associated with riparian woodland in fragmented, 

temperate-deciduous forest. Conservation Biology 16(3):832-836.

Keller, C.M.E., C.S. Robbins, and J.S. Hatfield. 1993. Avian communities in riparian forests of different 

widths in Maryland and Delaware. Wetlands 13:137-144.

Steven, D.D., and R. Lowrance. 2011. Agricultural conservation practices and wetland ecosystem 

services in the wetland-rich Piedmont-Coastal Plain region. Ecological Applications 21(3):S3-

S17.

Mammals

Brooks, R.P., and T.L. Serfass. 2013. Wetland-riparian wildlife of the Mid-Atlantic Region: an 

overview. In Mid-Atlantic Freshwater Wetlands: Advances in Science, Management, Policy, and 

Practice, R.P. Brooks and D.H. Wardrop (eds.) pp. 259-268. Chapter 7 Springer 

Science+Business Media, 491+xiv pp. 

Serfass, T.L., M.J. Lovallo, R.P. Brooks, A.H. Hayden, and D.H. Mitcheltree. 1999. Status and 

distribution of river otters in Pennsylvania following a reintroduction project. Journal of the 

Pennsylvania Academy of Science 73:10-14.

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Stevens, S.S., E.H. Just, R.C. Cordes, R.P. Brooks, and T.L. Serfass. 2011. The influence of habitat 

quality on the detection of River otter (Lontra canadensis) latrines near bridges. American 

Midland Naturalist 166:435-445.

Swimley, T.J., R.P. Brooks, and T.L. Serfass. 1999. Otter and beaver interactions in the Delaware Water

Gap National Recreation Area. Journal of the Pennsylvania Academy of Science 72:97-101

Toweill, D.E., and J.E. Tabor. 1982. The northern river otter Lutra canadensis (Schreber). In Wild 

Mammals of North America, J.A. Chapman and G.A. Feldhamer (eds.) pp. 688–703.

Johns Hopkins University Press, Baltimore, MD, 

Amphibians and Reptiles

Knutson, M.G., J.R. Sauer, D.A. Olsen, M.J. Mossman, L.M. Hemesath, and M.J. Lannoo. 1999. Effect 

of landscape composition and wetland fragmentation on frog and toad abundance and species 

richness in Iowa and Wisconsin, U.S.A. Conservation Biology 13:1437-1446.

Connectivity among wetlands increases aquatic snake abundance

Attum, O., Y.M. Lee, J.H. Roe, and B.A. Kingsbury. 2007. Upland–wetland linkages: relationship of 

upland and wetland characteristics with water snake abundance. Journal of Zoology 271(2):134-

139.

Movement of materials and how interplay of aquatic species among different habitats changes

community composition

Kurzava, L.M., and P.J. Morin. 1998. Tests of functional equivalence: complementary role of 

salamanders and fish in community organization. Ecology 79:477-489.

Movement of stream salamanders upstream, downstream, and into upland areas

Lowe, W.H., G.E. Likens, M.A. McPeek, and D.C. Buso. 2006. Linking direct and indirect data on 

dispersal: isolation by slope in a headwater stream salamander. Ecology 87:334-339.

Macoinvertebrates

Bunn, S.E., and A.H. Arthington. 2002. Basic principles and ecological consequences of altered flow 

regimes for aquatic biodiversity. Environmental Management 30(4):492-507.

Smock, L.A. 1994. Movements of invertebrates between stream channels and forested floodplains. 

Journal of the North American Benthological Society 13:524=531.

Stanford, J.A., and J.V. Ward. 1993. An ecosystem perspective of alluvial rivers: connectivity and the 

hyporheic corridor. Journal of the North American Benthological Society 12:48-60.

Ward J.V., K. Tockner, D.B. Arscott, and C. Claret. 2002. Riverine landscape diversity. Freshwater 

Biology 47:517-539

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Yetter, S. 2013. Freshwater macroinvertebrates in the Mid-Atlantic Region. In Mid-Atlantic Freshwater 

Wetlands: Advances in Science, Management, Policy, and Practice, R.P. Brooks and D.H. 

Wardrop (eds.) Chapter 10, pp. 339-379. Springer Science+Business Media, 491+xiv pp. 

Example from arid environment

Jackson, J.K., and S.G. Fisher. 1986. Secondary production, emergence and export of aquatic insects of 

a Sonoran Desert stream. Ecology 67:629-38.

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