UNITED STATES ENVIRONMENTAL PROTECTION AGENCY WASHINGTON D.C. 20460

OFFICE OF THE ADMINISTRATOR SCIENCE ADVISORY BOARD

October 17, 2014

EPA

- SAB

- 15

- 001

The Ho norable Gina McCarthy Administrato r 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 Synthe s is 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 resp onse 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 b een 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.

T he EPA Report is a thorough and technically accurate review of the lit erature 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 support s the conclusion s 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. T he SAB recommend s revisions to improve the c larity o f the Report , better reflect the scientific evidence, expand the discussion of approaches to quantifying connectivity

, and make the document more useful to decision

- makers. T he SAB disagrees with the conclusion that there is in sufficient information available to generalize about the connectivity of wetlands in “unidirectional

, ”

non

- floodplain settings. In that case, the SAB finds that the s cientific literatur e support s a more definitive statement that reflects how numerous function s of non

- floodplain wetlands sustain thephysical, chemical

, and /or biological integrity of downstream waters , although the degree of connectivity can vary widely

. The SAB’s major comments and r ecommendations are provided below.

• The Report often refe rs 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 ap proach that recognizes variation in the frequency, duration, m agnitude

, p redictability

, 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 bio logical 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

c onnectivity 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 o f 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. L ayers of complexity should be included in the conceptual framework to re present important aspects of connectivity such as spatial and temporal sc ale. The water body classification system used in the R eport (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 e ach 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

, a nd 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 recommend s 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 (longitu dinal, 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

, al though additional citations have been suggested to strengthen it

. T o 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 als o 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 t he 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 connectiv ity

. Th e SAB also r ecommend s that t he 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 move ment of organisms throughout s tream 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 s ubstantiate the conclusion that floodplains and waters and wetlands in floodplain settings support the physical, chemical

, and biological integrity of downstream waters. The SAB recommend s 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 non

floodplain (“unidirectional”) waters and wetlands is technically accurate

. However, a dditional information on biological connections shou ld be included . T he SAB h as provided numerous additional literature citations addressing the role s of multiple biological taxa in this regard , such as transporting propagules and nutrients and providing critical habitat.

• T he SAB disagrees with the EPA’s conclusion that the literature reviewed did not provide sufficient information to evaluate or generalize about the degree of connectiv ity (absolute or relative) or the downstream effects of wetlands in “ unidirectional ” non

- floodplain landscape settings. Th e SAB finds that the scientific literature support s 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, t he SAB re commends that the EPA revise the conclusion to better articulate : ( 1) what is supported by the scientific literature and ( 2) th e 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 Pa nel for the Review of the EPA Water Body Connectivity Report

EnclosureNOTICE

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 Environm ental 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 n ecessarily 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 Michiga n, 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 Geogr aphy 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 P rofessor 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 Hydrol ogist, 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 iiDr. Latif Kalin , Associate Professor, School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL

Dr. Kenneth Kolm , President and Senior Hydrogeologist, Hydrologic Systems Analysi s, 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 Sci ences, 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, Pol son, 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. Mau rice 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 Uni versity, 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, Schoo l 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 L td, 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 St ewardship, 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 Dourso n , 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. Dzomb ak , Walter J. Blenko, Sr. University Professor and Head of Civil and Environmental Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, PA

ivDr. 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 Hea lth, 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 Ca rolina 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, Cla rk 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 Direct or

- 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 , Independ ent 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 Schoo l, 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, Pedia trics, 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

vDr. 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 Developme nt, 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 Islan d, 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 Econo mics, 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

viDr. 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 Ch air, 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

viiTable of Contents

1. EXECUTIVE SUMMAR Y

................................ ................................ ................................ ................. 1

2. INTRODUCTION

................................ ................................ ................................ ................................ 7

3. RESPONSES TO EPA’S C HARGE QUESTIONS

................................ ................................ .......... 8

3.1. O VERALL C LARITY AND T ECHNICAL A CCURACY OF THE D RAFT R EPORT

................................ ... 8 3.2. C ONCEPTUAL F RAMEWORK : A N I NTEGRATED , S YSTEMS P ERSPECTIVE OF W ATERSHED S TRUCTURE

................................ ................................ ................................ .......... 12 3.3. E PHEMERAL , I NTERMITTENT , AND P ERENNIAL S TREAMS : R EVIEW OF
THE L ITERATURE

................................ ................................ ................................ ........................ 26 3.4. E PHEMERAL , I NTERMITTENT , AND P ERENNIAL S TREAMS : R EVIEW OF
THE F IND INGS AND C ONCLUSIONS

................................ ................................ ............................. 35 3.5. W ATERS AND W ETLANDS IN F LOODPLAIN S ETTINGS : R EVIEW OF THE L ITERATURE

................................ ................................ ................................ .............................. 38 3.6. W ATERS AND W ETLANDS IN F LOODPLAIN S ETTINGS : R EVIEW OF THE F INDINGS AND C ONCLUSIONS

................................ ................................ ................................ .... 47 3.7. W ATERS AND W ETLANDS IN N ON

- FLOODPLAIN S ETTINGS : R EVIEW OF
THE L ITERATURE

................................ ................................ ................................ ........................ 51 3.8. W ATERS AND W ETLANDS IN N ON

- FLOODPLAIN S ETTINGS : R EVIEW OF
THE F INDINGS AND C ONCLUSIONS

................................ ................................ ............................. 58

REFERENCES

................................ ................................ ................................ ................................ ........ 62

APPENDIX A: THE EPA ’S CHARGE QUESTIONS

................................ ................................ ..... A

- 1

APPENDIX B : ADDITIO NAL LITERATURE CITAT IONS REGARDING BIOLOGICAL CONNECTIV ITY

................................ ................................ ................................ ...... 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 (Septem ber 2013 External Review Draft). T he 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 str eams and wetlands relative to large water bodies such as rivers, lakes, estuaries

, and oceans. The purpose of the R eport 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 R eport is a scientific review and, as such, it d oes 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 hydro lo gic ele ments 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 o f e phemeral, i ntermittent

, and perennial streams ; (3) the downst ream c onnectivity and effects of w aters and w etlands in f loodplain

s ettings ; 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 R eport to illustrate t he 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 techn ic al 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 th e charge questions provided in Appendix A.

Overall Clarity and Technical Accuracy of the Report

The SAB was asked to provide its overall impression s of the clarity and accuracy of the Report

. T he Report is an extensive review of the literature on the con nectivity of streams and wetlands to downstream 1 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

, conc ise

, and written in a consistent style. Some t erms and definitions are not used consistently throughout the document. The SAB has proposed a revised conceptual framework which describ es 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 t he 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. S ometimes the term “ downgradient ” is used in this SAB report to emphasize instances where hyporheic and groundwater flows are especially important.

1T he 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 t he conclu sions 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 c ould be more useful to decision

ma kers 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 (conn ected versus not connected) rather th an 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. T he SAB also recommends that the Report more explicitly address : the cumulative eff ects 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, rive r scape, riverine landscape, and groundwater basin perspectives to understand connectivity; and the influence of human alterations on connectivity

. The literature review in the Report co uld be strengthened by more clearly describing the approach used to screen, compile

, and synthesize the inform ation 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 st reams 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 p resent 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 t echnically accurate but the SAB recommends some revision s to improve the clarity, accuracy

, and usefulness of the framework. T he SAB recommends clearly delineating the Report’s scope in terms of the types of wetlands and water bodies covered and focus ing on functional roles of floodplains and riparian areas irrespective of their classification as waters and wetlands under the Clean Wate r Act

. Connectivity should be defined at the beginning of the Report . T he SAB recommends that this definition be systems

- focused and, as such, include connections within and among entire watersheds and underlying aquifers. Different descriptors of connecti vity drawn from the literature on disturbance ecology (e.g., frequency, magnitude) also might be helpful . The SAB also recommends expand ing the discussion o f 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 discuss es connectivity within a classification system based on

2discrete 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 sys tem be mapped onto the flowpath framework to show that continuous phenomena interact across the se discrete landscape settings. In the conceptual framework t here should be more emphasis on the importance of groundwater mediated connectivity and biological connectivity

. A dditional 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 w aters and wetlands based on their potential to ha ve “ bidirectional ” or “ unidirectional ” hydrologic flows with rivers and lakes. S ome “ unidirectional ” wetlands are also called “geographically isolated wetlands.” However, the terms “bidirectional” and “unidirectional” do not adequately describe the four

- di mensional 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 t he 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 cor rectly summarized. T he Report contains an e xtensive review of the scientific literature describ ing the connectivity of streams to downstream waters

. H owever, 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 chemi cal constituents, contaminants, cont aminant 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 l o tic system . Other important topics that should be further discussed include: the consequences of human alteration of headwater streams; aggregate an d 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 sedimen ts 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

. S trong scientific support has been provided for th i s overall conclusion and related findings

. T he 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

3perennial streams be quantified whe n 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 ; t hese 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, t he R eport 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 a rticulating the rationale for choosing the case studies would also help ensure that the key points are well illustrated

.

Waters and Wetlands in F loodplain 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. T he SAB finds that the literatu re review substantiate s the Report’s conclusion that flo odplains and waters and wetlands in floodplain settings support the physical, chemical and biological integrity of downstream waters

. That said, t he 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 c onnectivity of floodplains); the importance of lateral connections that support the biological integrity of downstream waters by creat ing a diversity of habitats for a wide array of species; and human impacts on connectivity. A more recent and diverse revi ew 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 recom mends 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 i ntegrity of streams and rivers would be clearer if the literature on floodplain wetlands were reorganized

. T he text on low

- order riparian areas and the effects of headwater, streamside areas on in

- stream structure and function could be moved to the c hapter of the Report that addresses ephemeral, intermittent

, and perennial streams

.

The SAB suggests that the te rm “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 spatial ly and temporally by means of flood pulse s . In this regard, t he importance of the short

- duration

, high

- intensity and long

duration

, low

- intensity events should be compared and contrasted. In addition, t he 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

.

4Waters and Wetlands in F loodplain 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 Repor t concludes that “bidirectional” wetlands and waters in floodplain settings are physically, chemically and biol ogically connected with rivers through multiple pathways

. T here is strong scientific support for th is overall conclusion

. However, additional literature could be included in the Report to b olster the conclusion and the related findings

. M any 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 i ssues , including: the temporal dimension of connectivity of these waters and wetlands ; the role of these waters a nd 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/c umulative downstream effects of these waters and wetlands

. In addition, the SAB recommends that consistent terminology be used throughout the R eport 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, t he EPA’s revi ew 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. N umerous additional literature citations addressing the role s 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 th e structure and function of non

floodplain wetlands

. The term “unidirectional wetlands” as used in the R eport is misleading because it implies one

- way hydrologic flows when

, in fact

, connectivity can have many spatial and temporal dimensions. The SAB recom mends that the terms “unidirectional” and “geographically isolated” waters and wetlands be replaced in the R eport ; the term “ n on

- 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 non

floodplain 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 R eport 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.

5Waters 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. T he Report conclud e s 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 non

floodplain settings. The SAB disagrees w ith this overall c onclusion

. To the contrary, the SAB finds that the scientific literature provide s 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 down gradient water s ) . 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 resolve d (e.g., degree of connectivity, analyses of temporal or spatial variability). The SAB also recommends that the Report explicitly discuss the pathways by which non

floodplain waters and wetlands can be connected to downstream waters and state that the eval uation 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 water s.

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

- floodplain waters and wetlands

. Reference s to specific studies should be synthesized rather than individually reported, as they are intended to summarize general the mes 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

- floodpl ain 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 Synthesi s of the Scientific Evidence (Septem ber 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 rela tive 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 funct ion 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 connecti ons that link them, and the watershed climatic factors that influence connectivity at various spatial and temporal scales; (2) the downstream connectivity and effects of e phemeral, i ntermittent, and perennial streams; (3) the downstream connectivity and ef fects of w aters and w etlands in f loodplain

s ettings ; 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 R eport 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 d ocument, whether it includes the most relev ant 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, t he 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 th e 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 r ecommendations are highlighted at the end of each section of this report.

7

### 3. RESPONSE S 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 severa l 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 dif ferences 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, sub chapter 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, w ith 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 th is 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 shoul d 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 th e 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 Recommen dations

• The Report should be edited to ensure that it is written in a consistent style and e ach 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 st ated 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.

83.1.2. 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. T h is o bjective of the R eport 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 address es 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 20 05; Gregory et al. 2012) which would be more flexible and useful from the standpoint of informing decisions . As written, the R eport 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 down stream 1

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 th e 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 consequ ences 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., multipl e streams and/or wetlands considered in aggregate) including a discuss ion 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 fur ther dis cussed in Section 3.8.1 of this re port , 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, magni tude, 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 t hat 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 S AB 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 origi n 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.

93.1.3. Strengthening the Literature Review

The literature r eview in the Report can be strengthened by clarifying what was considered as peer

reviewed 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 u sed 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. Pee r

- reviewed literature s 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 ev idence 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, sc reening 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 w ould 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 ot her references have been suggested in written comments from the public.

T he 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 includ e in the Repo rt 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 i n 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 frame s over which wetlands are functionally aggregated

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

10integrity 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 wh ich biological connections among water systems affect the integrity of downstream
waters

. The movement of b irds, mammals, and other fauna (e.g., amphibians , fish, and invertebrates )

, among systems can mediate important material transfers to downstream wate rs . Th is
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 wat ers that ha ve 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 p rovided 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 cons idering 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 h uman alterations on connectivity. E xample s 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 susta ined by human wastewater effluent s , are more closely tied to human alterations than others. F unctions associated with these hu man

- altered systems and their natural counterparts should be evaluated using the scientific literature.

g) Approaches to assess or m easure 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 an alyses), 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.

113.1.5. Restructuring the Case Studies

The SAB finds that the case studies in the Report provide helpful illustrations of connectivity between downstream waters and geographica lly 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, A rctic 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 stud y summaries as brief textboxe s 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 tex t

. If expanded in the appendices, e ach 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. T he reader also should be able to see how the case studies align with hydrological, chemical, and biological flowpaths connect ing watersheds (discussed in Section 3.2 of this SAB report)

. If expanded case studies are desired, these should be presented in the appendices. C ase studies could serve to highlight areas of certainty in the EPA’s conclusions as well as knowledge gaps.

• T he EPA should consider including c ase 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

12b e revised and clearly articulated at the beginning of the C hapter. 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) connectivit y 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 hydrologica l, 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 synthes is 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 frame works draw simple analogies and a re 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 s trengthened and made more explicit ( see Section 3.2.3 belo w )

. In addition, the SAB recommends that the Chapter be retitled “An Integrated Systems Perspective of W atershed Structure and Function ” to better reflect the content , which includes both the conceptual framework and attendant details that support the rema inder 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 aquifer s) 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 an d nuances addressed later. SAB conce rns 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., t he transfer of matter, energy, and/or organisms within or between elements of the landscape. T he scientific literature shows that connectivity is a scalable quantity ranging continuously from fully connected to completely isolated, rather than a binary con dition 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 tha t 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 speci fic figures in chapter s on each water and wetland type covered in the Report ( s ee, for example, Figure 3 in Section 3.7.3 of this SAB report

. )

The definition s 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 physic al transport processes in nature. Larsen et al. (2012)

13review 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 mor e 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 chang e the physical, chemical, and/or biological environment and are commonly quantified in terms of physical measures of the disturba nce 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 continu um 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

• Connectivit y 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 biol ogical integrity of downstream waters. In addition, multiple dimensions of co nnectivity 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, r efuge, 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 prov ided 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 techni cal advances.

Insights from H ydrologic S ystems

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 h ydrological 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 biologic al

14connectivity 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 appropr iate 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 (A ppel 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)

. A pproaches have also been developed to quantify linkages due to groundwater

mo vement 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 ; Markstro m 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; Ma rkstrom 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 a l. (2011) demonstrated how r esponses 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 Directi onal 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 Be tweenness Centrality, Integral Index of Connectivity, Coincidence Probability, Eigenvector Centrality, Probability of Connectivity, and Influx Potential

.

C onnectivity also can be described using six metrics commonly used in hydrology and disturbance ecol ogy

– frequency, magnitude, timing, duration, rate of change , and predictability (e.g., Res h et al. 1988; Poff 1992; Poff et al

. 1997)

. These can be defined in hydrological, chemical, or biological terms. For example, i n hydrological terms, f requency descr ibes how often a flow of a particular magnitude
occurs, m agnitude is the amount of water moving past a fixed location per unit time, d uration 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. 199 7 ). 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

- dep endent biota).

The temporal and spatial predictability of connectivity is e specially 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 certa in 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 fr om 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

15annual cycle are formative pro cesses 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 betwe en 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 Recommen dation s

• 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 t o 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 con nect 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 wetla nds 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

. M any public commenters have expressed concern about the poten tial expansion of the scope of jurisdiction of the underlying Clean Water Act

– from “three

- parameter” to “one

- parameter” waters and wetlands 2 . 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 exp ansion 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 confusio n 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” we tland 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 h as substrate that is predomina ntly 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) require s that an area have all three of these attributes to be classified as a wetland. 163.2. 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 “unidi rectional” 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 r ivers and lakes. T he four

dimensional 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 describe s a key di fference 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” a nd “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 peer

reviewed, literature

- bas ed focus of the Report. One possibility is that , after defining the term “floodplain” at the beginning of the R eport, “bidirectional” wetlands could be called “ waters and wetlands in floodplain settings ” and “unidirectional” wetlands could be called “ waters and wetlands in

non

- floodplain settings

. ”

U se of the term “geographically isolated wetlands” in the Report is problematic

. “ G eographically isolated wetlands” technically mean s “wetlands isolated in space” but the term is defined in the Report
to m ean “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 2003 a,b ). However, a s discussed in o ther 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 biol ogical 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 geog raphically 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 “geog raphically 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 th e 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 f loodpla in settings” and “unidirectional” wetlands be called “waters and wetlands in n on

- floodplain settings.”

17• The term “geographically isolated wetlands” is misleading because it implies functional isolation and does not directly map onto the organizational term inology in the Report. The EPA should not use “geographically isolated wetlands” as an organizational term in the Report. T he EPA should draw upon the literature to carefully define “geographically isolated wetlands” and explain that the term does not impl y 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 framew ork 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. Th e 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 wa ter 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, chemic al, 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). C hemical flowpaths also cou ld 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 loc ation and defecate in another (Helfield and Naiman 2001). Biological flowpaths should be expressed as aquatic, terrestrial, and aerial flowpaths c onnecting 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 e xamples 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

18hydrologic 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. C onnectivity should be discu ssed as a con tinuous phenomenon. However, the SAB r ecognize s 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 wetl ands 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 p anels 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 wetland s 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, chem ical, 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 e ditorial 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 connect ing 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 whic h 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 flo w 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 rainfal l 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 l ayer 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 t hrough storms and seasons (Dunne and Black 1970). The expansion of runoff

producing areas in non

- floodplain settings can intermittently or ephemerally change the extent of headwater streams (e.g., Dunne 1978; Van der K waak and Loague 2001 ; Rains et al. 200 6
, 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 w etlands in floodplain settings, and waters and wetlands in

19non

- floodplain settings; however, the lines delineating these landscape categories are conceptual and without scientific consensus.

The Report focus es 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 surf ace 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 EP A also consider using the ASTM D5979

- 96 Standard Guide for Conceptualization and Characterization of Ground W ater Systems (ASTM 1996; Kolm et al. 1996). To better characterize regional

- scale groundwater connectivity, the SAB recommends that the EPA also

co nsider 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 b iological 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,
t he Report emphasizes the importance of hydrological connectivity , but organismal movement can connect waters and wetlands across uplands and between watersheds in unique and impor tant ways. Indeed, m any 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 Fa usch 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 impe riled), 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 subsurfac e), 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 str ucture should show potential surface, near surface, and subsurface

20pathways, 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

- landscap e 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 groundwat er 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 Framew ork

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 so me 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 funct ions 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 conceptua l 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 criti cal aspects of connectivity and its role in maintaining the chemica l, physical, and biological integrity of downgradient waters. However, spatial and temporal scales vary by flowpath type and flowpath characteristics (Figure 1 ) . A n 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. Simil ar figures could also be created for chemical and biological connectivity.

21Figure 1

. Schematic of selected atmospheric, surface, and subsurface hydrologic processes and their temporal and spatial scales of occurrence. ( Source: U.S. Glob al 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 iso lated at the watershed scale. Alternatively, a depressional wetland might appear isolated i n 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

- frequenc y events affect ing 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 f ound in the stream and river literature, though similar examples for other types of waters and wetlands (e.g., Winter and Rosenberry 199 8 ; 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 (W olman and Miller 19 60 ). Long

- lived effects are exemplified by debris flows, which are low

frequency events that nevertheless can be important mechanisms that connect headwaters to rivers, serving as important sources of sediment to downgradient waters (Ben da et al. 2005). Al t hough 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 c umulative effects are exemplified by ephemeral flows in arid landscapes, low

frequency events that may nevertheless provide most of the subsidies to downgradient waters ( Schlesinger and Jones 1984; Izbicki 2007).

The SAB recommends that the Report compar e and contrast the temporal scale s of connectivity in the East and the Southwest. In the East, precipitation is weakly seasonal and the weighted

- average flux of

22materials, energy, and/or water

- borne organisms is therefore likely greatest in response to mod erate

frequency 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 low

frequency 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 bu t, rather, the relative magnitude of the connection. Consider, for example, a river with total annual flow of 200,000

m 3 , 150,000 m 3 of which originates as ephemeral flows in headwater streams. In this case, these headwater streams, though infrequently con nected 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 conseq uence (e.g., Figure 2) , which would facilitate a discussion of spaces occupied by given waters and wetlands. Such a figure would help readers u nderstand 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 Publishe rs Ltd: Nature Climate Change 1(4):201

- 209 , copyright 2011. )

H

uman

- 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

23can 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, tra nsformation, 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); so me 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.

Regionaliza tion

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 sho uld 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. 201 3 ) . This would not represent a large depart ure 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 wou ld 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 climat e. Using the HLRs also would ground the discussion in the Report to peer

reviewed literature , which could then serve as a means to discuss regionalization and the reality that generalizations about chemical, physical, and biological phenomena are limited t o 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 down str eam 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 down stream waters might be negligible, but the cumulative effects of many similarly situated waters and wetlands on down stream 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 water s , but the aggregate or cumulative effect of the degradation of all small, headwater streams would have a large effect on down stream water s (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 t he integrity of down stream waters may not

24be detected if only a small number of headwater streams within a watershed were impacted, whereas there could be substantial and possibly cascading effects on down stream waters were a larger number of headwater str eams impacted. Moreover, the extent of down stream 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 d ebris 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 down stream 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 down stream fish habitats. Studies have been published on these kinds of cumulative effec ts, 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 hydrolo gy (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 t hat 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

. (20 1 3); Dunne et al

. (2001); Gabet and Dunne (2003); Johnston (1994); Lancaster and Casebeer (2007); Reid (1998); Squires and Dub é (2013) ; and Schindler (2001)

. Map Scale

The important issue of map resolution

, mentioned throughout the Report, needs to be more clearly and
t horoughly 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 ele vation 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.

T he Report should clearly indicate that many exis ting da tabases 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 r outing 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 al so applies to wetlands in non

- floodplain settings. Frohn et al. (2009

, 2 012), 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- W ater 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 pe rformed 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 down stream waters. The Rep ort 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

- Landsc ape Regio ns ( 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 import ant to merit its own subsection in the Report.

- The important issue of map resolution is mentioned in several parts of the R eport, 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, with out 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 suc cinctly 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 flow

through wetlands). Please comme nt 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 head water streams are connect ed 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 foundatio nal concept in stream ecology.

26The 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 i dentified additional references to relevant peer

- reviewed literature that the EPA should consider citing in the Report.

3.3.1. Hydrologic Exchange Flow s 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

s oil

- 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 c ould 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 g o 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 subsurfac e 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); Sawye r et al. (2011); Stonedahl et al. (2010) ; and Stromberg ( 200 1 )

. As further discussed in Section 3.5 of this SAB report , the m aterial 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 con taminants and naturally occurring chemical constituents other than nutrients (i.e., nitrogen and phosphorus), and to consider nutrient and contaminant transformation processes, the e ffect s of t hese 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

27nutrient 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 contam inants. The Report also should further discuss both sediments and sediment

- bound contaminants and their downstream movement and effects on downstream waters.

T he 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 se diment: 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, cont aminants 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); Hedi n 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.

• A dditional 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 contaminan t 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 surfa ce , shallow and deeper subsurface waters to channel flow and can affect stream temperature and downstream connectivity. The SAB recommends that discussion of this topic b e 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) d irectly address interactions between stream temperature and downstr eam 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 d iscussion 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).

28Key Recommendations

• The discussion of upslope factors th at 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 al terations 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 con sidered 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 w ith their variable source areas) that affect the physical, chemi cal, and biological integrity of downstream waters. Connections that are highly variable in time affect the transport of materials and sediment s and can also be important to biota (e.g., fish or amphibians breed in habitats that otherwise are dry most of t he 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 f rames 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 R eport characterize the temporal dynamics of streamflow (i.e., magnitude, frequency, duration, and timing) that explicitly connect these ecosystems to downstream
waters

. For example, the R eport correctly describes how headwater streams can contribute a large fraction of the water in downstream ecosystems over an annual cycle, even though they are period ically dry. However, t he R eport 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 conne ctions 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 interruption s of flow affect the temporal dimensions of connectivity. In many streams that e xperience 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

- to

perennial 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 bedr ock 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

29used to spatially and tempo rally characterize the impacts to riverine habitat of natural and human interruption of flow.

Overall, the SAB recommends that the R eport include a clear discussion of how intermittent and ephemeral streams are connected in space and time to downstream e cosystems 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 i ntermittent 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); PC RWRD (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 down gradient water s . 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 r iver 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 withdrawa l or augmentation and effluent

- dependent or effluent

dominated stream flow.

• A dditional 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 interm ittent 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 mentio ned in Section 3 .2.6 , the R eport 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 R eport. 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 wate rs, 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

30intermittent or ephemeral habitats often can be critical to the biological integrity of downstream waters (Falke and Fa usch 2010).

c) A wide variety of downstream m obile 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 comp arative 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 19 97). Thus, connectivity to these habitats is key to the biological integrity of downstream waters. Dam and dam

removal literature may be helpful to illustrate this point.

e) A failure to recognize the importance of biological and habitat connections can resu lt 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 h osts (Vaughn 2012; Schwalb et al. 2013).

f) B iological connections, in particular the migration of f ish

, can be significant pathway s 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 effec ts on biological integrity of downstream waters, as detailed in the points above.

3.3.6. Review of the Human

- Modified Headwater Stream Literature

T he current version of the R eport 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 head water systems to the physical, chemical, and biological integrity of down gradient 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 ecolo gically effective

con nectivity 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 import ance of connectivity, and the SAB recommends that information about human

modified systems b e included in the R eport.

The SAB recommends that the R eport authors consider including examples from at least some of the following human alterations affecting t he 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, acc elerated

31erosion, 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

. (19 8 4); 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.

• A dditional references , inclu ding 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. A ggregate and C umulative E ffects of H eadwater S treams on D ownstream E cosystems

The SAB recomm ends 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, b ased 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 att ributes) model and encompass the numerous other modeling and empirical approaches that have been used

. In addition, the R eport could draw upon examples from the literature that investigates the movement of sediments through watershed s to examin e 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 downst ream 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. Add itional 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 w ater s 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 R eport 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

32water 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

. Gi ven 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, b ut 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 ben efits 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 informati on 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 ad ding 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 transc end aquatic

terrestrial 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 ran ging 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 ripar ian 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 ri verine 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 recomm ends 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

333.3.9

. 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 includ e 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.

3.3.1 0

. 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 intermitt ent 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. A s 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 Str atton 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 R eport to document strength or degree of downstream connectivity

. 343.4. E phemeral, 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 se ction 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

stre ams, 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 the se 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 st rongly 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 h ighlight 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: S ynthesis 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 ; t he summary should not include reference to literature already cited in the Report

. M ost 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 foundat ional 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 transforma tions 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 acros s 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 s treams 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 R eport should also better define and emphasize key linkages and exchanges that influence connectivity (e.g., groundwater

- surface water interactions, flooding or o ther 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 th at 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

. T he 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 U nited S tates 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 sus taining 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. T his 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 duratio n 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
36reiterated in the concl usions. 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 co nnected 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 infl uence 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 Repo rt 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 nutri ent 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, la g, 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 fun ctions 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

T he 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 studie s 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

. T he longer case studies would have more impact if the key points of each were highlighted. In addition, the SAB al so 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, t he SAB finds that conclusions for the case studies coul d 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

37study 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.

Cons istent Statement of Conclusions t hroughout 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 a nd 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 display ing the Report’s conclusions in matrix form

. B rief 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 R eport should analyze the scientific literature and discuss how differences in flows affect connectivity . This discussion should emphas iz e 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 strengthen ed 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 sh ould 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 U nited States should be used as examples that influence the physical, chemical, a nd biological integrity of downgradient waters

.

• The summary of chemical functions that has been included in the Report should contain more detail ed information about the ways that headwater streams influence sediment

- bound nutrients, dissolved organic mat ter (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 publis hed peer

- reviewed literature with respect to these types of

38wetlands 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 floodplai n settings included in the R eport 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 phys ical, chemical, and biological connections . That said, the literature substantiate s the conclusion that , in an overwhelming number of cases, floodplains and waters and wetlands in floodplain settings support the physical, chemical, and bio logical i ntegrity of downstream waters. A dditional 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 r iparian and f loodplain settings and covers a wealth of topics

. This Section could be strengthened by reorganizin g 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 ques tion the SAB has provided additional literature citations.

The SAB recommend s 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 t he 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 low

order 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 appropriate ly located in Chapter 4 . Chapter 4 already includes discussions of the role of riparian forests in regulating
wat er 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 dyna mics 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 dimension s. This will also require editing throughout the R eport 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 inf ormation 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 eac h 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

39et al. (2013); Baxter et al. (2005); Bestgen e t 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 headwate r, streamside areas vis

- à

- vis in

- stream structure to Chapter 4 of the Report. Section 5.3 should focus on the functional role of floo dpla ins 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, vert ebrates, 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

r ecommended 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 role s 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 w etlands ( Cowardin et al. 1979) rather than exclusively those meeting the f ederal regulatory definiti on

. The Report should contain a s tatement 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 a reas are covered in the R eport because of functional linkages and not policy goals.

As previously mentioned, t he 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 re port . This change in terminology is needed to acknowledge the multi

- dimensional flux of water and materials betwe en floodplains and riparian area s and their associat ed rivers and streams. Consistent use of th ese term s is important for clarity, as the inconsistent uses of “ ripa rian/floodplain wetlands,” “riparian areas

, ” or “floodplains” in some sections of Chapter 5 is confusing. The definitions of “Riparian Area,” “R iparian Wetland,” “Floodplain,” “Floodwater,” and “Floodplain Wetland” in the glossary of the Report should also be revised to be consistent.

Key Recommendations :

• The R eport should discuss the functional role of floodplains and riparian area s 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• T he 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 R iver Systems

S patial 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 Repor t should include a new sub section 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 puls e” for surface water connections, and vertical connections to alluvial aquifers. T he 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 f our 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 sub section, 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 acknowledg ed 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 character ization of floodplain wetlands in either spa tial or temporal dimensions remain undeveloped

. The Report also r ecognize s the extension of the flood pulse concept to include “ flow pulses ” (Tock ner 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, seas onal variation in water abundance and river discharge, and longer

– term changes related to climate shifts and precipitation regimes. T h e references to “flood pulse” in the Report are limited, relat ing 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).

S hort

- duration

, high

- intensity flood events for surface waters and long

- duration

, low

- intensity lateral discharge for grou ndwater need a dditional emphasis in the Report. This should includ e descriptions of the influence of the flooding on residence time of surface water, seasonal exchanges with groundwater

, chemical and biological linkages, and ecosystem process es . Fo r exampl e, effects of low

- frequency

, high

- intensity flood event s 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 connectivi ty (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 disch arge in the floodplain is discrete (e.g., a n 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 measurin g or otherwise quantifying connectivity. In this regard, t he SAB notes that t he role of groundwater movement and storage, including t he effects of flood pulses on the hydrologic differences between, for

41example, “ slope ” (primarily groundwater fed) and “riv erine” (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

, ha ve been quantified via flow and transpor t 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. D rought has b oth 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). C limate change is expected to exacerbate the impacts of drought in

some r egions 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 hydr ologic connectivity

. Placing floodplain wetland environments into the context of the “ river ine 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 articulat e 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 w ithin 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 r ecommendations 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 frequ ency 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 c onsider 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 recommend s addressing flood frequency

- floodplain inundation science as a means to estimat e the degree of connectivity

. C hannel 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) o f 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 fl oodplain 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

42The 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 l ateral 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 Modd e et al. (2001

, 2005 ), floodplain wetlands and off

- channel waters play an important role as spawning grounds and fish nurseries d uring high

- water

seasons for species (including several endangered fishes) that ultimately populat e 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 habita t (e.g., Bruland 2008).

The SAB recommends that the EPA consider reviewing the following selected reference s (and others that are appropriate and relevant ) to document how the hydrologic phenomenon of the flood pulse links rivers to the floodplain (and c onsequently 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 “r iverine landscape” framework should be employed as the conceptual backbone of the new sub section, stressing dynamic lateral connections between the floodplain (surface and groundwater ) and downstream waters, recognizing the full range of temporal and spati al variability ( e.g., short duration

, high

- intensity flood s for surface waters ; long

- duration

, low

- intensity lateral discharge for groundwater ; drought)

.

• S ection 5.3 of the Report should emphasize the effects of floodplains not only on river flows, but

a lso on hydrological connections and processes affect ing bio ta , che mistry

, 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 c onsider 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 . C hannel 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 s hould be reviewed and cited in Section 5.3 of the Report to demonstrate how l ateral 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 diversi ty

. 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 in stance, 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 floodplain s.

3.5.4. Chemical L inkages

Wetlands and floodplains serve as sources, sinks and transformers of nutrients and other c hemical 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 exchan ge or flux of materials between living and non

living 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 exch ange 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 long

term storage similar to a reservoir. The amount of a give n constituent in these pool s depends on its residence time

. It is important to acknowledge t hese issues in the Report.

The SAB recommends that the authors of the Report p rovide 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, a nd 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 extensi ve literature on this subject and while the R eport 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

ass essment 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 ) . T his 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

44m uch 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 , d epend ing 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 c hanging 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 flo oding and drainage cycles, water withdrawals, sea level rise, and increases in temperature. The bioavailability of m any inorganic elements required for key biological processes (e.g., plant growth and decomposition) will respond to these changing conditions . Drainage also i ncreases enzyme and microbial activities, which facilitates oxidation of organic matter and leads to subsidence and loss of organic soils. O xidation of organic matter in wetlands is dependent on water

table 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 o f 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 : Aitkenhe ad

- 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 c hemical 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 S ection s 3.5.4 and 3.5.8 of this SAB report).

• The Report could further discuss how c hanging climati c conditions may stimulate or alter rates, fluxes and storage pools of key elements (carbon, nitrogen

, phosphorus, and sulfur) involved in biogeochemical processes an d services provided by wetlands (additional references are provided in S ection s 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 expan ding the literature reviewed. In particular, S ection 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 w ater residence

45time also could be expanded given its significant impact s on downstream water chemistry and biology (additional referen ces are provided in S ection 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 wat ers 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 f loodplain 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 n ature of connectivity between the floodplain and channel. The SAB recommends strengthening t he f ocus 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 t he R eport would benefit from more discussion of forested wetlands, including bottomland hardwoods, given their ecological importance, rate of loss, and unique attributes. T hes e

w e tl and s r ep r esen t a si gn i f i can t po rti o n o f remaining United States w e tl ands

. 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 (includ ing 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 wate rs. 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 degrade d 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 down stream waters in terms of flooding, biodiversity, and material s flux ( Barksdale et al. 2013)

. The water quality benefits of riparian areas and floodplains should also be highlighted in the Report by exp li c itl y po i n ting ou t t ha t t h e ir des tr uc ti o n exace r ba t es nu tri en t runoff fr o m ag ri cu lt u r a l l and s b y r educ i n g o r e li m ina ti n g nu tri en t up t ak e , den trifi ca ti on , an d sed i m en t a ti o n

o f adso r be d phospho r u s

. The EPA should consider including the following references on human

46impacts 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 des tr uc ti o n of riparian areas and floodplains can impair water quality by exacerbating nu tri en t runoff fr o m ag ri cu lt u r a l l and s , r educ i n g o r e li m ina ti n g nu tri en t up t ak e , den trifi ca ti on , an d sed i m en t a ti o n o f adso r be d phospho r u s

.

3.6. Waters and Wetlands in Floodplain Settings : Review of the Fin dings 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 a nd Conclusions Concerning Waters and W etlands i n Floodplain S ettings

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 ( inc luding hydrological, chemical, and biological connec tivity ) . 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 f loodplain w etlands. Any conclusions p resented 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 d iscu ss 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 non

floodplain 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 ripa rian 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

• T here is strong scientific support for the conclusion that waters and w etlands in floodplain s ettings

47are highly connected to downstream w aters 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. Th e riverine landscape framework (Ward e t al. 2002 ; Thorp et al. 2006) should be employed as the conceptual backbone of the s ection . Additional literature should be included in the Report to bolster findings as related to chemical and groundwater connectivity.

• Key findings and conclusions prese nted 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 f loodplain w aters and

w etlands. Conclusions presented in Section 1.4.2 of the executive summary should also align with

co nclusions 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 W aters and Wetlands i n Floodplain S ettings

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 T erminology

As previously mentioned, the Report ’s use of terms should remain cons istent 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 me e t 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 , com bined 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 freq uency

- floodplain inundation science into the Report would be effective for highlight ing how hydrologists estimate the degree of connectivity . Brief reference to the flood

- pulse and riverine landscape concepts, discussed within the conceptual framework (Cha pter 2), would reinforce the functional significance of regular or episodic floodplain inundation.

48Discussion 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 includ e t he 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 ha ve been quantified by flow and transport modeling using both steady

- state and transient analysis to simulate temporal changes.

Overall, the EPA’s conclusion s c oncerning connectivity of w aters and w etlands in f loodplain s ettings should r eflect the main message of a new spatial and temporal sub section in Section 5.3, as recommended in Section 3.5 of this SAB report

.

Further Q uantification of K ey C onclusions

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 biogeo chemical 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 Repor t. This may require additional literature review (in Section 5.3) to incorporate literature on floodplain wetlands and water bodies rather than rely ing on headwater riparian examples. Changes to nutrients (both N and P) and sediments should be easily docum ented. Some references have been recommended in Section 3.5.4 of this SAB report. There is ample lite rature 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 betw een waters and wetland s 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 do wnstream systems are intimately linked through biological connections (including integrated wetland

river food webs) across a range of spatial and tempor al scales. In this regard, the R eport should explicitly discuss linkages to downstream waters. For exam ple: “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.

49Export versus E xchange

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

- direct ional biological, chemical, and hydrological transfers characterize the connections between the two systems.

Case S tudies

The SAB finds that the case studies in the Report are useful. However, the findings from the case studies should be more explicit ly link ed 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 r ate 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 I mpacts

In some cases, human alteration of connectivity provides the clear est demonstrat ion 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 c onnectivity 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 floo dplains 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/Cumulati ve 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 th e aggregate (e.g., floodplains in dozens to hundreds of individual channel reaches) yields many ecological service s, including flood attenuation.

Key Recommendations

• The key findings and conclusions in the Report should better recognize the temporal dim ension 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 b e 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 k ey f indings in Section 1.4.2 of the Report. The role of biological connectivity between waters and wetlands in floodplain

50settings 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 h uman activities (impairmen t 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 consi stent 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 link ed 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 conc lusion).

3.6.3. A lternative W ording for F indings and Concl usions

The SAB recommends the following specific revisions to clarify the conclusions in Section 1.4.2 of the R eport:

• Section 1.4.2 s hould 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 connec tivity. 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 wa ters, 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 objective s of the Report, and any corrections that may be needed in the characterization of the literature.
51The 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 r eplac ing 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 biolog ical exchanges that can strongly influence the integrity of downstream waters. As also previously discussed, t he SAB recommends that the Report be reorganized to reflect the types of connections between wetlands and downstream waters via surface water, sha llow 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 lands cape 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 type s of connections
t o 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 disc uss 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 t he 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, t he 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 e vidence from the large and growing literature on biological exchanges between non

- floodplain wetlands should be included in the Report

. In particu lar, t he SAB recommend s 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 ; Pears e 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 biologi cal integrity and completion of life cycles of downstr eam 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 (200 0); 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); Winte r and LaBaugh (2003); Woo and Rowsell (1993); and Yang et al. (2010).

52Key Recommendations

• The l iterature review in Section 5.4 of the Report is technically accurate; however, the SAB has recommend ed a dditional 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, t he SAB recommends that the draf t Report’s “ uni

- and bi

- directional ” terminology be replaced by terms that better describe landscape position. In this case, “bidirectional wetlands” c ould be redefined as those within riparian and floodplain settings, and “unidirectional wetlands” as thos e 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 setting s and with respect to the concept ual 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 type s and characteristics of connections. The framework recommende d 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 down stream waters.

Similarly

, t he 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 downstrea m 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 f indings from the literature in terms of the degree of connectivity pathways (e.g., magnitude,

53duration, frequency 3 ) rather than just the presence of any connection. The SAB finds that such an analysis is possible and would be useful for summarizing the eff ects of such connections in semi

quantitative terms.

Figure 3 : Hypothetical illustration of connectivity gradient and p otential 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. A ll streams ( including perennial , intermittent, and ephemeral streams) have a connection to downstream waters. Within no n - f loodplain wetlands the degree of connectivity and implications for integrity of d ownstream waters var y 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 t he Report and not to hydrologic connectivity alo ne. 54• The EPA should consider us ing 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 Co nnections 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 becom e 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
organ isms. 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 S AB 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 receiv ing precipitation greater than the annual mean plus two st andard deviation s versus low water regimes r eceiv ing precipitation less than the annual mean minus two standard deviations , five or
ten

- year flood return interval, or result s of hydrologic models ) . Such maps would be similar to the Federal Emergency M anagement Agency ( FEMA ) floodplain maps, and would need to be recalibrated for changing cli mate 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 conne ctions 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 magnitud e 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

55require 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, t here 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 Recommendation s

• The Report should recognize that all aquatic habitats have some degree of connection

, al though 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 a nalyses.

• 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 impact s 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 f or : the maintenance of base flows ; the attenuation of flood s ; the produc tion 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 down gradient waters . Alt hough 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 ; USFW S 2014) and th e 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 indi vidually 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 cha racterizations of landscapes at nested scales, such

56as 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 wat ers. 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 w etland 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

- floodp lain 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). T here 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 West ern 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 ec osystem 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 connect ivity 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

a lter 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

.

573.8. 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 tha t 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 th e 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 litera ture 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 o f non

floodplain waters to downstream ecosystems varies widely. Because of this the connectivity of non

floodplain 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 th e 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 R eport, 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 u sed 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,

58categorical distinction (connected vs. not connected) towards a gradient a pproach 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 a l

. 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 n on

- floodplain wet lands (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).

• Conclu sion 3 of the Report should explicitly discuss the four pathways by which non

- riparian/non

floodplain 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 find ings in Section 1.4.3 of the Report.

The SAB recommends that conclusions be stated as concise, declarative statements. To accomplish this, the R eport authors should remove references to specific studies within the text of the key findings. The Report’s c onclusions 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 addi tion, 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 down stream 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

.

59The 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 a nd rare. Some of these organisms require multiple types of waters to complete their full life cycle s , including downgradient waters. Other organisms, especially abundant and/or highly mobile species, play important roles in transferring energy and material s 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 follow ing 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 t he 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 o f 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 down stream 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 dur ation of hydrologic, biologic and chemical fluxes or transfers of water and materials to downstream waters. Because of their aggregated influence, any evaluation of

60changes to individual wetlands should be considered in the context of past and predicted ch anges (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 fi ndings 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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84

### 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 curre nt 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 re levant 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, suc h as nutrient spiraling. Materials reviewed in this Report are limited to peer

reviewed 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 w aters 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 s ummarized 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 hydrol ogic 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

- 1TECHNICAL CHARGE QUE STIONS

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, S ystems 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 connectiv ity 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 component s 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 scie nce

. 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 sh ould 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 wordin g for any conclusions and findings that are not fully supported.

A

- 2Lentic 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 river s 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 ide ntify 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

. T hese papers represent combinations of floodplain

stream, wetland

- stream, and wetland

- wetland interactions, but in many cases provide evidence of connectivity among multiple aquatic habitats. The citations are org anized 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, a nd 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., a nd A.L

. Richert

. 2005

. Patterns of h abitat use by whooping cranes during migration: summary from 1977

- 1999 site evaluation data

. Proceedings North American Crane Workshop 9:79

- 104.

Vrtiska, M.P., a nd S. Sullivan

. 2009. Abu ndance 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, a nd 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 foragi ng
Aldrich, T.W., and D.S. Paul. 2002. Avian ecology of Great Salt Lake

. I n Great Salt Lake: an O verview of C hange

, J.W. Gwynn, (ed

. ) pp. 343

- 374. Utah Department of Natural Resources and Utah Geological Survey Special Publication, Salt Lake City, Utah, U SA.

B

- 1Vest, 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 P lan of the Pacific and Central Flyways for the Rocky Mountain P opulation of G reater S andhill C ranes

. [Joint] Subcommittees, Rocky Mountain Population Greater Sandhill Cranes, Pacific Flyway Study Committee, Central Flyway Webless Migratory Game Bird Tech nical 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. I n 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.

Wate rbird 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

- 7 07.

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 a gricultur e and a bundance of

s now g eese a ffect c arrying c apacity of s andhill c ranes 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 W ood D uck S ymposium
, 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 mid

continent 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.

B

- 2Skagen, 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. 20 02. Controls on the distribution and abundance of fish in temporary wetlands. Canadian Journal of Fisheries and Aquatic Sciences 5 9:1441

- 1450

.

Boltz

, J

. M

. , and R.R. Stauffer

, Jr

. 1989

. Fish assemblages of Pennsylvania wetlands. In Wetland E cology and C onservation: E mphasis in Pennsyl vania

, 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 o f 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 s pecies a ssociated with r iparian w oodland in f ragmented,
t emperate

- d eciduous f orest

. 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 we tland

- rich Piedmont

- Coastal Plain region. Ecological Applications 21(3):S3

- S17.

M ammals

Brooks, R

. P

. , and T

. L

. Serfass. 2013. Wetland

- riparian wildlife of the Mid

- Atlantic Region: an overview. I n Mid

- Atlantic Freshwater Wetlands: Advances in S cience, M an agement, P olicy, and P ractice
, 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.

B

- 3Stevens

, 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 Rive r 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 A cademy of Science 72:97

- 101

Toweill

, D

. E

. , and J.E. Tabor

. 1982

. The northern river otter L utra canadensis (Schreber). In Wild M ammals 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 . Co nservation 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 change s 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: isol ation by slope in a headwater stream salamander . Ecology 87:334

- 339.

Macoinvertebrates

B unn , 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 chann els 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 river s: connectivit y 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

B

- 4Yetter, S. 2013. Freshwater macroinvertebrates in the Mid

- Atlantic Region. I n Mid

- Atlantic Freshwater Wetlands: Advances in S cience, M anagement, P olicy, and P ractice

, R.P. Brooks and D.H. Wardrop (eds.) Chapter 10, pp. 339

- 379

. Springer Science+Business Me dia, 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.

B

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