Protecting
       Healthy Watersheds
       Concepts, Assessments, and Management Approaches
       February 2012
Watersheds

-------
 Disclaimer

 This document provides information for states, territories, and federally recognized tribes for identifying and
 protecting healthy watersheds. At times, this document refers to statutory and regulatory provisions, which
 contain legally binding requirements. This document does not substitute for those provisions or regulations,
 nor is it a regulation itself. Thus it does not impose legally-binding requirements  on EPA, states, territories,
 authorized tribes, or the public and may not apply to  a particular situation based upon the circumstances.
 EPA, state,  territory, and  authorized tribe  decision makers retain the discretion to adopt approaches  to
 identify and protect healthy watersheds that differ from this document. EPA may change  this document in
 the future.

 Reference herein to  any specific commercial products, process,  or service by trade name, trademark,
 manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation,  or
 favoring by the United States Government. The  views and opinions of authors expressed herein do not
 necessarily state or  reflect those of the United States Government,  and shall not  be used  for advertising  or
 product endorsement purposes.

 Some of the photos, figures, tables, and other graphics  that are used in this document are copyrighted
 material for which  permission was obtained from the copyright owner for use in  this  document.  Specific
 materials reproduced by permission are marked, and are  still under copyright by the original authors and
 publishers. If you wish to use any of the copyrighted photos, figures, tables, or other graphics in any other
 publication, you must contact the owner and request permission.
Main front cover photo courtesy of Kristin Godfrey. Inset front cover photos courtesy of US DA NRCS (top), USFWS
(middle), and Kristin Godfrey (bottom). Some of the photographs used on the chapter title pages are courtesy of Ben
Fertig (Chapter 2)  and Jane Hawkey (Chapter 4 and Chapter 5), Integration and Application Network Image Library
(ian.umces.edu/imagelibrary/). The six symbols  used in Chapter 3 are  courtesy of the Integration and Application
Network (ian.umces.edu/symbols/).

-------
Identifying and Protecting
     Healthy Watersheds

     Concepts, Assessments, and
      Management Approaches
                Contact Information
       For more information, questions, or comments about this document, contact
       Laura Gabanski, at U.S. Environmental Protection Agency, Office of Water,
       Office of Wetlands, Oceans, and Watersheds, 1200 Pennsylvania Avenue, Mail
       Code 4503T, Washington, DC 20460, or by email at gabanski.laura@epa.gov.
                 February 2012

                 EPA841-B-l1-002

-------

-------
Acknowledgements
This document was prepared by the U.S. Environmental Protection Agency (EPA), Office of Water, Office
of Wetlands, Oceans, and Watersheds.  The EPA Project Manager for this document was Laura Gabanski,
who provided overall direction and coordination. EPA was supported in the development of this document
by The Cadmus Group, Inc. Laura Blake and Corey Godfrey of The Cadmus Group, Inc. were responsible
for creating most of the content  of this  document. Mike Wireman (EPA Region 8), Leslie Bach and Allison
Aldous (The Nature Conservancy), and Christopher Carlson (U.S. Forest Service) were responsible for writing
sections on hydrology, ground water, and ground water dependent ecosystems. Jonathan Higgins (The Nature
Conservancy) wrote the sections on freshwater conservation priorities. Joe Flotemersch (EPA Office of Research
and Development) designed the healthy watersheds logo. A draft of this document underwent an external peer
review, as well as was released for public review. Comments and recommendations from the peer review and
public review were taken into consideration during the finalization of this document.

Peer Reviewers
Paul Blanchard, Missouri Department of Conservation
Gail Cowie, Georgia Department of Natural Resources
David Bradsby, Texas Parks and Wildlife Department
Mark VanScoyoc, Kansas Department of Wildlife
Karen Larsen, California State Water Resource Control Board
Peter Ode, California Department of Fish and Game
Tim Beechie, National Oceanic and Atmospheric Administration
James O'Connor, U.S. Geological Survey
Julian Olden, University of Washington
Chris Yoder, Midwest Biodiversity Institute
Gerrit Jobsis, American Rivers, Inc.
Special appreciation is extended  to the  following individuals, who provided technical information, reviews,
and recommendations during the preparation of this document:
U.S. Environmental Protection Agency
Jim Carleton, Office of Water
Tommy Dewald, Office of Water
Laura Dlugolecki, Office of Water
Chris Faulkner, Office of Water
Robert Goo, Office of Water
Heather Goss, Office of Water
Susan Jackson, Office of Water
Tracy Kerchkof, Office of Water
Stuart Lehman, Office of Water
Sarah Lehmann, Office of Water
Fred Leutner, Office of Water (retired)
John McShane, Office of Water
Mike Muse, Office of Water
Doug Norton, Office of Water
Rich Sumner, Office of Water
Ellen Tarquinio, Office of Water
Don Waye, Office of Water
Dov Weitman, Office of Water
Naomi Detenbeck, Office of Research and
Development
Joe Flotemersch, Office of Research and
Development
Susan Julius, Office of Research and Development
Betsy Smith, Office of Research and Development
Wayne Davis, Office of Environmental Information
Ralph Abele, Region 1
Trish Garrigan, Region 1
Eric Perkins, Region 1

-------
Identifying and Protecting Healthy Watersheds
       U.S. Environmental Protection Agency (cont.)
       Tom DeMoss, Region 3
       Bill Jenkins, Region 3
       Sue McDowell, Region 3
       Matt Nicholson, Region 3
       Susan Spielberger, Region 3
       Stephanie Fulton, Region 4
       Christine McKay, Region 4
       John Richardson, Region 4
       Cynthia Curtis, Region 5
       Betsy Nightingale, Region 5
       Paul Thomas, Region 5
       Brian Fontenot, Region 6
       Leah Medley, Region 7
       Jill Minter, Region 8
       Mike Wireman, Region 8
       Carolyn Yale, Region 9
       Christina Yin, Region 9
       Tracy Nadeau, Region 10
       U.S. Forest Service
       Christopher Carlson
       John Potyondy
       Nancy Stremple
       Natural Resources Conservation Service
       Jan Surface
       Richard Weber
       U.S. Fish and Wildlife Service
       Megan  Estep
       Will Duncan
       Vincent Mudrak
       Ron Nassar
       Cindy Williams
       U.S. Geological Survey
       Stacey Archfield
       Alex Covert
       Jonathan Kennen
       Donna Meyers
       Columbia River Inter-Tribal Fish Commission
       Dianne Barton
       Connecticut Department of Environmental
       Protection
       Christopher Belluci
       Kansas Department of Health and Environment
       Bob Angelo
Louisiana Department of Environmental Quality
Jan Boydstun
Maine CDC Drinking Water Program
Andrews Tolman
Maine Department of Environmental Protection
Susan Davies (retired)
Maryland Department of Natural Resources
Catherine McCall
Christine Conn
Paul Kazyak
Scott Stranko
Massachusetts Department of Fish and Game
Russ Cohen
Michigan Department of Natural Resources
Paul Seelbach
Gary Whelan
Troy Zorn
Minnesota Department of Natural Resources
Sharon Pfeifer
Beth Knudsen
Minnesota Pollution Control Agency
Stephen Heiskary
New Hampshire Department of Environmental
Services
Ted Walsh
Oregon Watershed Enhancement Board
Bonnie Ashford
Ken Bierly
Tennessee Department of Environment and
Conservation
Robert Baker
Texas Parks and Wildlife
Dan Opdyke
Vermont Agency of Natural Resources
Tim Clear
Neil Kamman
Mike Kline
Leslie Matthews
Eric Sorenson

-------
Virginia Department of Conservation and
Recreation
Jason Bulluck
Jennifer Ciminelli
Rick Hill
Washington Department of Ecology
Stephen Stanley
Anne Arundel County, MD
Dawn Thomas
Cleveland Metroparks, OH
Jessica Ferrato
Delaware River Basin Commission
Robert Tudor
Hampton Roads Planning District Commission,
VA
Sara Kidd
Eric Walberg
New York City Department of Environmental
Protection
Paul Rush
Orange County Water District, CA
Michael Markus
Triangle J Council of Governments
Sarah Bruce
Warren County Conservation District, PA
Jean Gomory
Association of State Drinking Water
Administrators
Jim Taft
Board of Alliance for the Great Lakes
Jack Bails
The Conservation Fund
Will Allen
Campaign to Safeguard America's Waters
Gershon Cohen
Delaware Riverkeeper Network
Faith Zerbe
Environmental Law and Policy Center
Brad Klein
Gulf Restoration Network
Matt Rota
Kentucky Waterways Alliance
Judith Petersen
Licking River Watershed Watch
Barry Tonning
The Nature Conservancy
Allison Aldous
Colin Apse
Leslie Bach
Jonathan Higgins
Eloise Kendy
Mark Smith
Scott Sowa
Openlands
Stacy Meyers-Glen
River Network
Merritt Frey
Superior Watershed Partnership and Land Trust
Carl Lindquist
The Trust for Public Lands
Kelley Hart
Water Environment Federation
Tim Williams
Wild Utah Project
Jim Catlin
Allison Jones
Wells National Estuarine Research Reserve
Christine Feurt
Colorado State University
LeRoy Poff
Michigan State University
Peter Esselman
Oregon State University
Jimmy Kagan
University of California at Davis
Fraser Shilling
                                                                                                    in

-------
Identifying and Protecting Healthy Watersheds
       University of Kansas
       James Thorp
       University of Maryland Center for Environmental Science
       Ken Barton
       University of New England, Australia
       Martin Thorns
       University of New Mexico
       Peter Stacey
       University of North Carolina at Pembroke
       Patricia Sellers
       University of Tennessee at Knoxville
       Tracy Walker Moir-McClean
       University of Washington
       James Karr
       Virginia Commonwealth University
       Greg Garman
       The Cadmus Group, Inc.
       Elisabeth Cianciola
       Kristina Downing
       Tracy Mehan
IV

-------
Table of Contents
Acknowledgements	i
Table of Contents	v
Figures	vii
Tables	xi
Foreword	xiii
1.      Introduction	1-1
 1.1      Background	1-2
 1.2      Healthy Watersheds Initiative	 1-3
 1.3      Characteristics of a Healthy Watershed	 1-4
 1.4      Benefits of Protecting Healthy Watersheds	 1-4
 1.5      Purpose and Target Audience	 1-6
 1.6      How Does the Healthy Watersheds Initiative and this Document Relate to What Others
          are Doing?	1-6
 1.7      How to Use this Document	1-6
2.      Key Concepts and Assessment Approaches	2-1
 2.1      A Systems Approach to Watershed Protection	2-2
 2.2      Landscape Condition	2-4
   2.2.1       Green Infrastructure	2-5
   2.2.2       Rivers as Landscape Elements	2-7
   2.2.3       Natural Disturbance	2-8
   2.2.4       Connectivity and Redundancy	2-9
 2.3      Habitat	2-9
   2.3-1       Fluvial Habitat	2-9
   2.3-2       Lake Habitat	2-14
   2.3-3       Wetland Habitat	2-15
 2.4      Hydrology 	2-16
   2.4.1       Hydroecology	2-16
   2.4.2       Ground Water Hydrology	2-19
 2.5      Geomorphology	2-24
 2.6      Water Quality	2-26
 2.7      Biological Condition	2-27
 2.8      Watershed Resilience...                                                       .. 2-30

-------
Identifying and Protecting Healthy Watersheds
        3.      Examples of Assessment Approaches	3-1
         3.1       Landscape Condition	3-3
         3.2       Habitat	3-19
         3-3       Hydrology	3-33
         3.4       Geomorphology	3-51
         3.5       Water Quality	3-56
         3.6       Biological Condition	3-58
         3.7       National Aquatic Resource Assessments	3-74
        4.      Healthy Watersheds Integrated Assessments	4-1
         4.1       Integrated Assessment	4-2
         4.2       Moving Towards Integrated Assessments	4-31
        5.      Management Approaches 	5-1
         5.1       Implementing Healthy Watersheds Programs in States	5-3
         5.2       Protection Programs	5-5
           5.2.1        National	5-5
           5.2.2        State and Interstate	5-12
           5.2.3        Local	5-28
           5.2.4        Other Protection	5-39
         5.3       Restoration Programs	5-41
           5.3-1        National	5-41
           5.3-2        State and Interstate	5-42
           5-3-3        Local	5-43
         5.4       Education, Outreach, and Collaboration	5-44
        References	R-l
        Acronyms & Abbreviations	AA-1
        Appendix A. Examples of Assessment Tools	A-l
        Appendix B. Sources of National Data	B-l
        Appendix C. Cited Assessment and Management Examples	C-l
VI

-------
Figures
Figure 1-1      Numbers of imperiled North American freshwater and diadromous fish taxa	1-2

Figure 1-2      Gap between impaired and delisted waters in EPA Region 3	1-2

Figure 2-1      Spatial and temporal scales of watershed processes	2-2

Figure 2-2      The five major factors that determine integrity of the aquatic resource	2-3

Figure 2-3      Essential ecological attributes	2-3

Figure 2-4      Healthy watersheds assessment components	2-4

Figure 2-5      Landscape condition	2-5

Figure 2-6      Green infrastructure network design	2-5

Figure 2-7      Map of the Chicagoland area showing land cover and currently protected areas	2-6

Figure 2-8      Components and dominant processes of the Active River Area	2-8

Figure 2-9      Cool water rivers	2-9

Figure 2-10     The River Continuum Concept	2-10

Figure 2-11     Hierarchy defining spatiotemporal scales of hydrogeomorphic patches	2-11

Figure 2-12     A conceptual riverine landscape	2-12

Figure 2-13     Distribution of the various Functional Process Zones in the Kanawha River, West
               Virginia	2-13

Figure 2-14     Schematic of a lakeshore and the three habitat zones of a typical lake	2-15

Figure 2-15     Relation  between water table and stream type	2-17

Figure 2-16     Different components of the natural flow regime	2-17

Figure 2-17     Ecological model of the Savannah River, Georgia	2-18

Figure 2-18     Geomorphic and ecological functions provided by different levels of flow	2-19

Figure 2-19     Different scales of ground water flow systems	2-20

Figure 2-20     Streambeds and banks are unique environments	2-21

Figure 2-21     Common locations for ground water dependent ecosystems	2-23

Figure 2-22     Lane's Balance	2-24

Figure 2-23     Channel evolution model	2-24
                                                                                                     vn

-------
Identifying and Protecting Healthy Watersheds
Figure 2-24
Figure 2-25
Figure 2-26
Figure 2-27
Figure 3-1
Figure 3-2

Figure 3-3
Figure 3-4
Figure 3-5
Figure 3-6
Figure 3-7
Figure 3-8
Figure 3-9

Figure 3-10
Figure 3-11
Figure 3-12
Figure 3-13
Figure 3-14
Figure 3-15
Figure 3-16
Figure 3-17
Figure 3-18
Figure 3-19
Figure 3-20
Figure 3-21
Figure 3-22
Figure 3-23
Rosgen stream types 	
Conceptual model of the Biological Condition Gradient 	
Maine Index of Biotic Integrity (IBI) scores 	
Sprawling development 	
Green infrastructure in Maryland 	
Comparison of proposed greenways and green infrastructure in Anne Arundel
County, MD 	
Map of results from the Virginia Natural Landscape Assessment Model 	
Green infrastructure in the Hampton Roads region 	
Three-zone buffer showing the protection, conservation, and stewardship zones 	
Components and dominant processes of the Active River Area 	
The Active River Area in the Connecticut River Basin 	
National output of the Fire Regime Condition Class Mapping Method 	
Map of stream habitat condition in Maryland, as determined with the Physical
Habitat Index 	
Map of focal wetland complexes shown by wetland density 	
Wyoming's wetlands 	
Framework for the Ecological Limits of Hydrologic Alteration Process 	
Thermal and fish assemblage based classification of streams in Michigan 	
Example flow alteration-ecological response curves from Michigan 	
Diagram of the Texas Instream Flows Program process 	
Environmental flow regime recommendations for the San Antonio River 	
Classification tree showing the seven naturalized hydrologic classes 	
Ground water dependent ecosystem clusters in Oregon 	
Decision tree for identifying ground water dependent river ecosystems 	
Ground water dependent biodiversity in the Whychus Creek Watershed 	
Phase 3 data gathering for Vermont Stream Geomorphic Assessments 	
Intact and incised streambeds 	
Map of Oregon Water Quality Index results for water years 1998-2007 	
2-25
2-29
2-29
2-30
	 3-6

	 3-7
	 3-9
	 3-10
	 3-12
	 3-14
	 3-15
	 3-18

	 3-21
	 3-31
	 3-32
	 3-34
	 3-38
	 3-38
3-40
3-42
3-44
3-46
3-48
	 3-50
	 3-53
	 3-54
	 3-57
Vlll

-------
Figure 3-24     Human activities alter five water resource features, resulting in alteration offish
               communities	3-60

Figure 3-25     Conceptual model of the Biological Condition Gradient	3-63

Figure 3-26     Maine Tiered Aquatic Life Uses in relation to Biological Condition Gradient Levels	3-64

Figure 3-27     Maps of Missouri showing levels four through seven of the aquatic ecological
               classification hierarchy	3-66

Figure 3-28     Predicted aquatic species richness  for HUC12 watersheds in Ohio	3-68

Figure 3-29     Map of watershed integrity in Virginia based on modified Index of Bio tic Integrity
               scores	3-73

Figure 3-30     Status  of healthy waters and watersheds in Maryland and Virginia	3-73

Figure 3-31     Biological quality results from EPA's Wadeable Streams Assessment	3-75

Figure 3-32     National Rivers and Streams Assessment sample sites	3-76

Figure 3-33     Biological condition of lakes nationally and based on lake origin	3-79

Figure 3-34     Sites for Regional and National Monitoring and Assessments of Streams and Rivers	3-82

Figure 4-1      Healthy watersheds integrated assessment and management framework	4-2

Figure 4-2      National Fish Habitat Assessment scores for Vermont	4-4

Figure 4-3      Blocks of contiguous natural land cover in Vermont	4-8

Figure 4-4      Percent natural land cover in the Active River Area of Vermont	4-9

Figure 4-5      Location of dams in Vermont	4-11

Figure 4-6      Class I and Class II significant wetlands in Vermont	4-12

Figure 4-7      Phase 1 stream geomorphic assessment  results for Vermont	4-14

Figure 4-8      Reference and non-reference water quality sites in Vermont	4-16

Figure 4-9      Results of bioassessment scores at  stream monitoring sites in Vermont	4-17

Figure 4-10     Relative watershed health scores for Vermont	4-19

Figure 4-11     Normalized watershed  health scores for Vermont, with normalized attribute scores	4-20

Figure 4-12     Relative watershed vulnerability scores for Vermont	4-23

Figure 4-13     Example of a management priorities matrix for setting protection and restoration
               priorities	4-24

Figure 4-14     Example of potential management guidance for Vermont	4-25

Figure 4-15     Regional results of the VCLNA Vulnerability Model overlain with results  from
               Virginia's  Healthy Waters Program	4-27
                                                                                                           IX

-------
Identifying and Protecting Healthy Watersheds
        Figure 4-16     Business as usual development pattern and compact center scenario used for the
                       alternative growth scenario evaluations	4-29

        Figure 4-17     Virginia Watershed Integrity Model final output	4-34

        Figure 4-18     Indicators used by the Watershed Assessment Tool for calculating watershed health
                       scores	4-36

        Figure 4-19     Results of Minnesota's statewide watershed health assessment	4-37

        Figure 4-20     Minnesota's watershed health assessment results for the Rapid River and Redwood
                       River watersheds	4-38

        Figure 4-21     Oregon's Watershed Assessment Manual methodology framework	4-39

        Figure 4-22     Example conceptual model for riparian forest indicator selection	4-42

        Figure 4-23     Map of Pennsylvania's least disturbed streams	4-44

        Figure 4-24     Watershed conservation priorities in Pennsylvania	4-45

        Figure 4-25     Conceptual model of the effect of impervious cover on stream quality.	4-47

        Figure 4-26     Map of Connecticut showing stream classes and management classes by watershed	4-47

        Figure 4-27     Location of Kansas' least disturbed watersheds within individual ecoregions	4-49

        Figure 4-28     Reach cumulative landscape disturbance scores summarized by local catchments for
                       the United States	4-51

        Figure 4-29     Three-dimensional bubble plot comparing recovery potential among subwatersheds	4-53

        Figure 4-30     Bubble plot of recovery potential screening of 94 non-tidal watersheds in Maryland	4-54

        Figure 5-1      Areas of Freshwater Biodiversity Significance in the Upper Mississippi River Basin	5-8

        Figure 5-2      The Delaware River as a Special Protection Water.	5-17

        Figure 5-3      Example fish response curves	5-19

        Figure 5-4      Illustration of the water withdrawal assessment process and resulting actions	5-20

        Figure 5-5      Map and  orthophoto  depicting the meander belt width-based river corridor being
                       considered for protection in the Town of Cabot	5-22

        Figure 5-6      Maryland's GreenPrint map of targeted ecological areas	5-25

        Figure 5-7      Identification of targeted ecological areas	5-26

        Figure 5-8      Green infrastructure identified for water quality protection	5-34

        Figure 5-9      Map of Lower Meramec Conservation Priority Index Areas	5-36

        Figure 5-10     Map of Cecil County Green Infrastructure Plan	5-38

        Figure 5-11     Chesapeake Bay report card results for 2007	5-45

-------
Tables
Table 1-1       Estimated cost of pollutant cleanup in the Chesapeake Bay Watershed	 1-2

Table 1-2       Estimated range of values for ecological services provided by healthy watersheds	 1-5

Table 3-1       List of assessment approach summaries and case studies included in Chapter 3	3-2

Table 3-2       Parameters and weights used to rank overall ecological significance of each hub
               within its physiographic region	3-5

Table 3-3       Fire regime groups and descriptions	3-16

Table 3-4       Example reference condition table	3-17

Table 3-5       Management implications for the stand-level fire regime condition class based on
               the S-Class relative amount	3-17

Table 3-6       Metrics for the Physical Habitat Index in each of the three stream classes in
               Maryland	3-21

Table 3-7       Proper Functioning Condition checklist worksheet	3-23

Table 3-8       The four primary environmental flow components considered in the Texas
               Instream Flows Program and their hydrologic, geomorphic, biological, and water
               quality characteristics	3-39

Table 3-9       Criteria used to identify HUC12s in Oregon where ground water is important for
               freshwater ecosystems	3-45

Table 3-10     Essential ecological attributes associated with ground water	3-47

Table 3-11     Parameters and variables in the Vermont Reach Habitat Assessment Protocol	3-52

Table 3-12     Eleven metrics included in the human-threat index	3-67

Table 3-13     Assessment criteria used for prioritizing and selecting aquatic ecological system
               polygons and valley-segment type complexes for inclusion in the portfolio of
               conservation opportunity areas	3-67

Table 4-1       Datasets used to identify healthy watersheds in Vermont	4-5

Table 4-2       Metrics calculated for each healthy watersheds assessment component	4-6

Table 4-3       Descriptions of the stream geomorphic condition categories	4-13

Table 4-4       Ecoregional water quality criteria used to screen for reference sites in Vermont	4-15

Table 4-5       Healthy watersheds assessment components addressed  in each of the eight
               assessments summarized in this section	4-32
                                                                                                         XI

-------
Identifying and Protecting Healthy Watersheds
        Table 4-6       Data layers in Minnesota's Watershed Assessment Tool	4-35




        Table 4-7       Parameters and criteria used to identify least disturbed watersheds in Connecticut	4-46




        Table 4-8       Landscape alteration variables used in KDHE's reference stream assessment	4-49




        Table 4-9       Example Recovery Potential Indicators	4-53




        Table 4-10      Recovery potential indicators used to screen Maryland watersheds	4-54




        Table 5-1       Management approaches and case studies summarized in Chapter 5	5-2
xn

-------
Foreword
Forty years ago, the U.S. Environmental Protection Agency (EPA) was created and tasked with implementing
programs designed to repair the damage already done to the environment and to help Americans make their
environment cleaner and  safer. The  objective of the  1972 Clean Water Act amendments was "to restore
and maintain the chemical, physical, and biological  integrity of the nation's waters." Through restoration of
impaired water bodies, vast environmental improvements have been seen in the last 40 years. However, the
rate at which new waters are being listed for water quality impairments exceeds the  pace at which waters are
removed from the list. It has  become clear  that a broader view of aquatic ecosystems is critical if we are to
truly protect the chemical, physical, and biological integrity of our waters. As we look forward to the future,
EPA remains strongly committed to protecting and preserving our country's environment. On March 29,
2011, EPA released the Coming Together for Clean Water Strategy as the  framework for  guiding the Agency's
implementation efforts and actions  to  meet the 2011-2015 Strategic Plan  objectives for protecting and
restoring our waters. One of the key areas of the Agency's strategy is to increase protection of healthy waters,
including healthy watersheds. The Healthy Watersheds Initiative was launched to place a renewed emphasis on
the protection of our nation's healthy waters and to leverage these natural resources to  accelerate our restoration
successes. Through the Healthy Watersheds Initiative, EPA is working with state, tribal, and other partners to
take proactive measures to identify and protect healthy watersheds based on integrated assessments  of habitat,
biotic communities, water chemistry, and watershed  processes such as hydrology, fluvial  geomorphology, and
natural disturbance regimes.

The integrity of aquatic  ecosystems  is  directly affected by their landscape context and the processes that
occur in their watershed.  Natural land  cover maintains hydrologic and  sediment regimes within a natural
range of variation that shape the aquatic habitat upon which biological communities have evolved and can't
live without. Conversion from natural to anthropogenic land  cover typically results in altered flow  regimes,
changes in sediment supply and transport, increased loading of nutrients and other pollutants, and ultimately
leads to degradation of the biological community. Recognizing these connections and the role of watershed
processes and functions on water quality, the Healthy Watersheds Initiative augments EPA's traditional focus
on regulating specific pollutants and pollutant sources, emphasizing protection of critical watershed processes
that support chemical, physical, and biological integrity. Healthy, functioning watersheds  provide the  building
blocks that  anchor water  quality restoration  efforts. Without  this ecological  support system,  we will have
more  limited success in restoring impaired waters  and  will lose the many socio-economic benefits  of healthy
ecological systems.

This document is  a technical  resource  that provides information  for  assessing, identifying, and  protecting
healthy  watersheds. It is not program implementation guidance. EPA, state, territory, and authorized tribal
decision makers retain the discretion to adopt approaches to identify and protect healthy watersheds that differ
from those described in this document. This document can assist in those efforts by providing a wealth of
information and examples that we hope will inspire and motivate aquatic resource scientists and managers
to conduct  integrated healthy watersheds  assessments and  initiate protection programs that are cognizant
of the systems context. Chapter 1 introduces the  Healthy Watersheds  Initiative, discusses the characteristics
of a healthy watershed, and reviews  the benefits of protecting healthy watersheds.  Chapter 2 describes the
healthy  watersheds conceptual framework and discusses, in  detail, each of the six assessment components  —
landscape condition, habitat,  hydrology, geomorphology, water quality,  and biological  condition. A sound
understanding of these concepts is necessary for the appropriate application of the methods described in later
chapters. Chapter 3 summarizes a range  of assessment approaches currently being used to assess the health of
watersheds, and are provided as examples of different assessment methods that can be used as part of a healthy
watersheds integrated assessment. Chapter 4  presents  an example screening level method for conducting a
healthy  watersheds integrated assessment  and  identifying  healthy  watersheds, and includes  examples  of
                                                                                                         xin

-------
Identifying and Protecting Healthy Watersheds
        state assessments that approximate integrated assessments. Chapter 5 summarizes  a variety of management
        approaches for protecting healthy watersheds. Lastly, the appendices contain a summary of assessment tools,
        sources of data, and a compilation of assessment and management examples cited in the document. Readers
        can navigate between the chapters depending on their needs and priorities.

        The term integrated assessment is used in this document to describe a holistic evaluation of system components
        and processes that results  in  a more complete  understanding of the aquatic ecosystem, and allows  for the
        targeting of management actions to protect healthy watersheds. The healthy watersheds integrated assessment
        and management framework, shown below,  requires collaboration with multiple partners throughout the
        entire process. Critical first steps include framing the scale and context of the assessment and ensuring that
        all relevant data and expertise have been identified and obtained. The data are then used to evaluate  each of
        the six healthy watersheds  assessment components - landscape condition, habitat, hydrology, geomorphology
        water quality, and biological condition. The results of the individual assessments are synthesized to provide an
        overall assessment of watershed health. From here, strategic watershed protection priorities can be identified
        by evaluating vulnerability alongside the  identified healthy watersheds.  As watershed protection  measures
        are implemented, it will be important to  collect new data  and information that help  to  demonstrate the
        effectiveness of watershed protection  activities and that can be used to refine future assessments. The  healthy
        watersheds integrated  assessment and management framework is not  a linear effort with a defined endpoint.
        Assessment and management of healthy watersheds is an adaptive and iterative process, with new data and
        improved methodologies providing refined assessment results and more effective  protection  strategies over
        time.
                                                  Involve partners to
                                                 identify available data
                                                 & scale of assessment
                                                                                       Evaluate each of the
                                                                                      six healthy watersheds
                                                                                          components
Measure progress &
 collect new data
                            Implement strategic
                           watershed protection
                                 priorities
                                                           Integrate results to
                                                             identify healthy
                                                          watersheds & evaluate
                                                              vulnerability
xiv

-------
1.   Introduction
                           Introduction
                           This chapter introduces the Healthy Watersheds Initiative, discusses the
                           characteristics of a healthy watershed, and reviews the benefits of protecting
                           healthy watersheds. This chapter also describes the purpose, target audience, and
                           intended use of this document.
                           Overview of Key Concepts
                           This chapter describes the healthy watersheds conceptual framework. It then
                           discusses, in detail, each of the six assessment components - landscape condition,
                           habitat, hydrology, geomorphology, water quality, and biological condition.
                           A sound understanding of these concepts is necessary for the appropriate
                           application of the methods described in later chapters. This chapter concludes
                           with a discussion of watershed resilience.
                           Examples of Assessment Approaches
                           This chapter summarizes a range of assessment approaches currently being used
                           to assess the health of watersheds. This is not meant to be an exhaustive list of all
                           possible approaches, nor is this a critical review of the approaches included. These
                           are provided solely as examples of different assessment methods that can be used
                           as part of a healthy watersheds integrated assessment. Discussions of how the
                           assessments were applied are provided for some approaches. Table 3-1 lists all of
                           the assessment approaches included in this chapter.
                                                                                             —

                           Healthy Watersheds Integrated Assessments
                   •L
This chapter presents two examples for conducting screening level healthy
watersheds integrated assessments. The first example relies on the results of a
national assessment. The second example demonstrates a methodology using
state-specific data for Vermont. This chapter also includes examples of state
efforts to move towards integrated assessments.
                           Management Approaches
                           This chapter includes examples of state healthy watersheds programs and
                           summarizes a variety of management approaches for protecting healthy
                           watersheds at different geographic scales. The chapter also includes a brief
                           discussion of restoration strategies, with focus on targeting restoration towards
                           degraded systems that have high ecological capacity for recovery. The results of
                           healthy watersheds integrated assessments can be used to guide decisions on
                           protection strategies and inform priorities for restoration.
                                                                                                   1-1

-------
Identifying and Protecting Healthy Watersheds
        1.1   Background

        The  stated  objective  of  the  Clean Water
        Act  (CWA) is  "to  restore and maintain the
        chemical, physical,  and  biological  integrity
        of the Nation's waters"  (33 U.S.C. Section
        1251 (a); CWA Section 101 (a)). Since the 1972
        amendments to the CWA (known then as the
        Federal Water Pollution Control Act), federal
        water quality regulations have led to significant
        reductions   in   pollutant   levels  in many
        impaired lakes,  rivers, and streams.  Further,
        significant  efforts  have been undertaken  to
        restore  aquatic  ecosystems  in  our  nation's
        impaired watersheds. Despite these efforts, our
        aquatic ecosystems are declining  nationwide
        (Figure 1-1). This trend has been  documented
        by many, including the Heinz Center (2008)
        and the American Fisheries Society (Jelks et al.,
        2008). Further,  the rate at which new waters
        are being listed for water quality impairments
        exceeds  the pace  at  which restored waters
        are removed from the list  (Figure 1-2), and
        restoring impaired waters is costly (Table  1-1).
        In addition to  pollution,  threats  such as loss
        of habitat   and its  connectivity, hydrologic
        alteration, invasive species, and climate change
        continue to increase.  A  better  strategy  is
        needed if we are to achieve the objective of the
        Clean Water Act.
       Vulnerable
                   Threatened
                              Endangered
                                          Extinct    Delisted
    300
              1979
                              1989
                                              2008
Figure 1-1 Numbers of imperiled North American freshwater
and diadromous fish taxa (modified from Jelks et al., 2008).
  7000-r
  5000 - -
S 3000--   „-
  1000--
                                Impaired Waters
G
A
P
I
            1998
                     2000
                              2002
                                        2004
                                                 2006
                                                      Figure 1-2 Gap between impaired and delisted waters in EPA
                                                      Region 3.
        Table 1-1 Estimated cost of pollutant cleanup in the Chesapeake Bay Watershed (EPA Region 3).
Water Body
Corsica River, MD
Little Laurel Run, PA
Conewago Creek, PA
Bear Creek, PA
Catawissa Creek, PA
Thumb Run, VA
Willis River, VA
Muddy Creek, VA
Impairment
Nutrients
Metals
Nutrients
Metals
Metals
Bacteria
Bacteria
Bacteria
Miles
7.6
3
17
5
57.9
17
30
9
Cost
$17,500,000
$1,048,013
$4,300,000
$964,000
$3,500,000
$2,450,000
$2,794,160
$2,612,000
Average Cost/Mile
$2,302,632
$349,338
$252,941
$192,800
$60,449
$144,118
$93,139
$290,222
1-2

-------
                                                                                                1  Introduction
1.2    Healthy Watersheds Initiative

                                                      EPA's Healthy Watersheds Website
                                                            www.epa.gov/healthvwatersheds
The Section 101 (a) objective of the CWA is "...to restore and maintain the chemical, physical, and biological
integrity of the Nation's waters." The Committee Report written in support of the 1972  Federal Water
Pollution Control Act amendments clarified that the term integrity "...refers to a condition in which the
natural structure and function of ecosystems is [sic] maintained," rather than simply improving water quality in
a narrow sense (U.S. Government Printing Office,
1972; Doppelt, Scurlock, Frissell, &  Karr, 1993).
The U.S. Environmental Protection Agency (EPA),
in partnership  with others,  launched  the Healthy
Watersheds  Initiative  to protect  and  maintain
remaining healthy watersheds having natural, intact
aquatic  ecosystems; prevent  them from becoming
impaired; and accelerate  restoration successes. This
initiative is being implemented  by promoting a
strategic, systems approach to identify and protect
healthy  watersheds based on  integrated assessments
of habitat,  biotic  communities,  water  chemistry,
and watershed  processes  such as hydrology, fluvial
geomorphology, and natural disturbance  regimes.
Once healthy watersheds or healthy  components
of watersheds are identified, priorities can be set for
protection and  restoration, with the best chances of
recovery likely to be in waters near existing healthy
aquatic  ecosystems (Roni et al., 2002; Norton et al.,
2009; Sundermann, Stoll, &  Haase, 2011).

The key components of the Healthy Watersheds Initiative are as follows:

    1.   Partnerships are established to  identify and protect healthy watersheds.
    2.   Healthy watersheds  are identified state-wide using  scientifically-sound integrated
        assessment techniques.
    3.   Healthy watersheds  are listed, tracked, maintained, and increased  in  number over
        time.
    4.   Healthy watersheds  are  protected and enhanced using both regulatory and non-
        regulatory tools.
    5.   Progress on protecting healthy  watersheds is measured and  tied to achieving the
        overall goals of EPA's Water Program and Strategic Plan.

While the Healthy Watersheds Initiative is intended to be implemented to support strategic statewide and tribal
decisions, the assessment data and other information generated as part of a healthy watersheds  assessment can
also be  used to inform management decisions at the basin or local watershed levels, including implementing
water quality and other programs. The anticipated outcomes of the Healthy Watersheds Initiative are integrated
aquatic  ecosystem protection programs that maintain and increase the number of healthy watersheds in our
nation.
                                                                                                        1-3

-------
Identifying and Protecting Healthy Watersheds
        1.3   Characteristics of a  Healthy Watershed
        A healthy watershed is one in which natural land cover supports dynamic hydrologic and geomorphic processes
        within their natural range of variation; habitat of sufficient size and connectivity supports native aquatic and
        riparian species; and  water quality supports healthy biological communities. An interconnected  network of
        natural land  cover throughout a watershed, and especially in the riparian zone, provides critical habitat and
        supports maintenance of the natural flow regime and fluctuations in water levels. It also helps to maintain
        natural geomorphic processes,  such as sediment storage and deposition, which  form the basis  of aquatic
        habitats. Connectivity of aquatic and riparian habitats,  in  the longitudinal, lateral, vertical, and temporal
        dimensions helps to ensure that biotic refugia are available during floods, droughts, and other extreme events.
        In addition to connectivity, redundancy of ecosystem types helps to ensure that the characteristics of a healthy
        watershed  will persist into the future.  Processes that are  maintained within their  natural range of variation,
        connectivity, and redundancy are thus critical characteristics of healthy watersheds.

        1.4   Benefits of Protecting Healthy Watersheds
        Motivation to protect ecosystems comes  from a variety of sources,  including intrinsic value, the services
        ecosystems provide to humans, and legal  mandates. There is growing  recognition that functionally  intact
        and  biologically  complex  freshwater
                                                New York City Watershed: Economic Benefits and
                                                Cost Savings of Protecting the Clean Water  Supply
ecosystems      provide     valuable
commodities and services to  society
(Baron  et  al.,  2002).  In 2000,  the
United Nations Secretary General Kofi
Annan called for a global assessment of
ecosystems and implications for human
health and well-being. The  resulting
Millennium  Ecosystem  Assessment
documents   worldwide  trends   in
ecosystem  integrity  and  the  services
they provide (Millennium Ecosystem
Assessment,    2005).    Ecosystems
provide raw products,  including food,
fuel,  fiber,  fresh  water,  and  genetic
resources.  They  regulate   processes
affecting  air  quality,  climate,   soil
erosion, disease, and water purification.
Non-material cultural  benefits derived
from   ecosystems  include  spiritual
enrichment,  cognitive development,
reflection,  recreation,   and  aesthetic
experiences   (Millennium  Ecosystem
Assessment, 2005). Research indicates
that the  short-term economic benefits
from  exploiting  natural resources pale
in comparison to the long-term loss of
ecosystem services (Daily et al., 1997).
                                              their drinking water source  through a  unique agreement  that links
                                              ecosystem service providers and beneficiaries. The New York City case
                                              study demonstrates that watershed protection can  be a  highly cost-
                                              effective alternative to technological treatment in meeting water quality
                                              standards that can work for both upstream and downstream parties.
                                              New York City was faced with building an estimated $6 billion filtration
                                              plant with an annual operating cost of $300 million to ensure compliance
                                              with the Safe Drinking Water Act. However, the City  had the option of
                                              requesting a waiver if they could demonstrate that they can meet water
                                              quality standards through protection of their source watersheds.  The
                                              City went through a long agreement-building  process with the private
                                              landowners and communities within the Catskill-Delaware watersheds,
                                              which supply the City with 90% of its drinking water.
                                              Terms of the agreement included that the  City would not  condemn
                                              any land through the  state's  health eminent domain  process. The  City
                                              would also purchase properties for their actual face value from willing
                                              sellers and pay taxes on the properties  so that it would not  erode the
                                              local tax revenues. The total amount of land purchased was  estimated
                                              at $94 million, which  doubled  the area of  the protected buffer.  The
                                              overall investment  was estimated to  be $1 billion.  The  City  also
                                              initiated other programs and a trust fund within the area to promote
                                              best management practices. These practices, along with the  protected
                                              lands, increased property values, provided additional income, created
                                              healthier  streams and habitats, and  provided additional  recreational
                                              opportunities. Future  protection of this area will  be dependent on
                                              population and development growth and any future regulations.
1-4

-------
                                                                                                   1 Introduction
Watersheds  are   coupled  social-ecological   systems,
meaning  that  the  health and  well-being of human
societies are dependent on the health and well-being of
the watersheds they live within,  and vice versa (Bunch,
Morrison, Parkes, &Venema, 2011). Key to maintaining
this  relationship  is  a  diverse  ecological  and   social
structure, as well as the ability to adapt to the change and
uncertainty characteristic  of natural processes (Berkes,
2007)-  A  systems  approach for  understanding  social-
ecological systems forms  the backbone  of sustainability
science  and modern-day  adaptive  management (Berkes
& Folke, 2000). The healthy watersheds approach draws
from and builds on this work to protect the  ecological
infrastructure that society depends on.
                                      The Economic Impact of Recreational
                                        Trout Angling in the Driftless Area
                                     -pi

                                     Iowa, Wisconsin, and Illinois. According to a study
                                     by  Trout  Unlimited  and  Northstar Economics
                                     (2008), direct spending of $647 million per year on
                                     recreational angling, plus a "ripple effect" of nearly
                                     $3,000 per angler, in  the Driftless Area generates
                                     a $1.1 billion annual economic benefit to the local
                                     economy. The ripple effect is a result of the money
                                     spent by anglers flowing through the local economy,
                                     stimulating additional spending by local businesses.
                                     Trout Unlimited attributes these economic benefits
                                     to the natural potential of the Driftless Area streams,
                                     good land  stewardship, public access, and wise
                                     investment  in restoration. Trout fishing  has very
                                     limited impact on natural  resources. Anglers tend
                                     to treat the Driftless Area  with respect, and many
                                     release the  fish they catch back to the stream. It
                                     is clear that the thriving economy of the  Driftless
                                     Area is at least partially  supported by clean water,
                                     resilient streams, and healthy fish populations.
There are many economic benefits to protecting healthy
watersheds,  including  the  avoidance   of  expensive
restoration activities. Healthy watersheds sustain water-
related recreation opportunities, such as fishing, boating,
and  swimming, and provide hiking,  birding,  hunting,
and  ecotourism opportunities.  Vulnerability to  floods,
fires, and other natural disasters  is minimized, thereby
reducing costs to communities.  Healthy watersheds can also help to assure availability of sufficient amounts
of water for human  consumption  and industrial uses.  By protecting aquifer recharge zones and surface water
sources, costs of drinking water  treatment may be reduced. A survey of 27 drinking water utilities found that
for every 10% increase in forest cover of the source area, chemical and treatment costs decrease by 20% (Ernst,
2004). The functions that healthy watersheds provide,  and the benefits they create, are often taken for granted
when they exist in natural systems, but are  difficult and expensive to achieve when they must be reproduced
(Table 1-2).
Table 1-2 Estimated
provided by healthy
& Bergkamp, 2006).
range of values for ecological services
watersheds (Smith, de Groot, Perrot-Matte,
     Service Provided        Estimated Value ($/acre/year)
 Drinking Water
 Fisheries
 Water quality control
 Flood mitigation
 Carbon sequestration
 Recreation and tourism
                  $18 - $3,035
                     $81
                  $24 - $2,711
                  $6 - $2,227
                  $53 - $109
                  $93 - $1,214
The recognition of climate change as a serious
threat  to  ecosystem structure and  function
provides  additional motivation to  protect
healthy watersheds. Natural vegetative  cover
(including forests, wetlands, and grasslands)
sequesters large amounts  of carbon,  and the
soil resources that this vegetation maintains
can hold even larger  amounts of  carbon.
Protection of  these resources  can   help  to
mitigate increased carbon dioxide  emissions
(U.S.   Environmental  Protection   Agency,
201 la).
Water is the primary medium through which climate change will be seen and felt. Both droughts and large
storm events are expected to increase in frequency and severity in some parts of the country. Wetlands and
forested areas have a profound effect on watershed hydrology, regulating flows during droughts and large storm
events. This regulating function has far-reaching effects on provision of drinking water, flood reduction, and
other natural hazard reductions. Protection of watershed processes can help to maintain and increase resilience
to climate change (e.g., keeping ecosystems healthy can reduce management costs to sustain these benefits).
                                                                                                            1-5

-------
Identifying and Protecting Healthy Watersheds
        1.5   Purpose and Target Audience

        The purpose of this document is to provide state water quality and aquatic resource scientists and managers
        with an overview of the  key concepts behind the Healthy Watersheds Initiative, examples of approaches for
        assessing components of healthy watersheds, integrated assessment options for identifying healthy watersheds,
        examples of management approaches, and some assessment tools and sources of data. With this information,
        scientists and managers will be  able to conduct healthy watersheds assessments and initiate protection programs.
        The results of healthy watersheds assessments can be used by local land use managers to  inform protection
        priorities. This document is not a guide, nor does it provide step-by-step instructions, but  it does  identify
        example  approaches and sources for scientists and managers to obtain detailed information on assessment
        methods and management tools. Finally, this document is not EPA program implementation guidance, but
        rather a resource  that states and other entities may choose to use for assessing, identifying, and protecting
        healthy watersheds.

        1.6   How Does the Healthy Watersheds Initiative  and this

               Document Relate to What Others are Doing?

        The book Entering the Watershed (Doppelt et al., 1993) outlines many of the  concepts necessary for a truly
        holistic approach to riverine ecosystem protection. Since its publication, various aquatic ecosystem assessment
        approaches and protection strategies have been developed. Some of the many examples include the Ecological
        Limits of Hydrologic Alteration, The Nature Conservancy's  Active River Area and Freshwater Ecoregional
        Assessments, Virginia's Conservation Lands Needs Assessment,  Ohio's Primary Headwaters Habitat Assessment,
        and State Wildlife Action Plans (see Chapters 3 and 5). The Healthy Watersheds Initiative builds on this body
        of work.  The integrated  assessment approaches presented in Chapter 4 expand the value of other approaches
        by linking the assessments of  biota, habitat,  and functional processes together to  evaluate  aquatic ecosystem
        integrity within a watershed context. The Healthy Watersheds  Initiative also includes  strategic implementation
        of protection and restoration measures to maintain and increase the number of healthy watersheds. Many state
        agencies and other organizations are already implementing initiatives that are similar to  the healthy watersheds
        approach, and this document  highlights their projects as examples. Further, complementary approaches have
        also been adopted by other federal agencies.  For example, along with the Association of Fish and Wildlife
        Agencies,  the  U.S. Fish and  Wildlife  Service  and National Marine Fisheries Service developed  and  are
        implementing the National Fish Habitat Action Plan, which  takes a holistic systems approach to protecting
        and restoring fish habitat (Association of Fish and Wildlife Agencies, 2006). Also, the U.S. Forest Service
        developed the Watershed  Condition Framework,  which employs an integrated,  systems-based approach
        for classifying watershed condition based on an evaluation  of the underlying ecological, hydrologic, and
        geomorphic functions and processes (U.S. Forest Service, 2011). The U.S. Forest Service is using the results of
        a national reconnaissance-level assessment of watershed condition, based on the Framework, to identify high
        priority watersheds on national forests and grasslands for restoration starting with the "best" watersheds first.

        1.7   How to Use this  Document

        Every organization has a unique combination of strengths in aquatic ecosystem assessment  and protection.
        Many have solid grounding in the  field of water quality, while others have strengths in landscape ecology or
        biodiversity conservation. This document should be used as a reference for expanding capabilities beyond a
        specific area of expertise  to include a holistic approach for identifying and protecting healthy watersheds. It is
        recommended that all users read Chapter 2 to familiarize or refresh themselves  with the concepts underlying
        the Healthy Watersheds  Initiative.  Chapter 3 provides examples of assessment approaches in use across  the
        country, and Chapter 4 provides examples of ways in which integrated assessments can be conducted and used
        to identify healthy watersheds  and set protection priorities. Chapter 5 presents some of the many management
        approaches that can be used at the national, state,  or local level to protect healthy  watersheds. Appendix A
        contains  assessment tools, Appendix  B identifies sources of data, and Appendix C includes a compilation of
        resources and sources of information mentioned in  this document for use in assessing and protecting healthy
        watersheds. Readers can navigate between these chapters depending on their needs and priorities.
1-6

-------
2.   Key Concepts and  Assessment
       Approaches
                         Introduction
                         This chapter introduces the Healthy Watersheds Initiative, discusses the
                         characteristics of a healthy watershed, and reviews the benefits of protecting
                         healthy watersheds. This chapter also describes the purpose, target audience, and
                         intended use of this document.
                         Overview of Key Concepts
                         This chapter describes the healthy watersheds conceptual framework. It then
                         discusses, in detail, each of the six assessment components - landscape condition,
                         habitat, hydrology, geomorphology, water quality, and biological condition.
                         A sound understanding of these concepts is necessary for the appropriate
                         application of the methods described in later chapters. This chapter concludes
                         with a discussion of watershed resilience.
                         Examples of Assessment Approaches
                         This chapter summarizes a range of assessment approaches currently being used
                         to assess the health of watersheds. This is not meant to be an exhaustive list of all
                         possible approaches, nor is this a critical review of the approaches included. These
                         are provided solely as examples of different assessment methods that can be used
                         as part of a healthy watersheds integrated assessment. Discussions of how the
                         assessments were applied are provided for some approaches. Table 3-1 lists all of
                         the assessment approaches included in this chapter.
                         Healthy Watersheds Integrated Assessments
                         This chapter presents two examples for conducting screening level healthy
                         watersheds integrated assessments. The first example relies on the results of a
                         national assessment. The second example demonstrates a methodology using
                         state-specific data for Vermont. This chapter also includes examples of state
                         efforts to move towards integrated assessments.
                         Management Approaches
                         This chapter includes examples of state healthy watersheds programs and
                         summarizes a variety of management approaches for protecting healthy
                         watersheds at different geographic scales. The chapter also includes a brief
                         discussion of restoration strategies, with focus on targeting restoration towards
                         degraded systems that have high ecological capacity for recovery. The results of
                         healthy watersheds integrated assessments can be used to guide decisions on
                         protection strategies and inform priorities for restoration.
                                                                                           2-1

-------
Identifying and Protecting Healthy Watersheds
        2.1   A Systems Approach to  Watershed Protection

        The healthy watersheds conceptual framework is based on a holistic systems approach to watershed assessment

        and protection that recognizes the  dynamics  and interconnectedness  of aquatic ecosystems. Maintenance

        of aquatic ecological integrity requires that we understand not only the biological, chemical, and physical

        condition of water bodies, but also landscape condition and critical watershed attributes and functions, such as

        hydrology, geomorphology,  and natural disturbance patterns.


        Watersheds provide a useful context for managing aquatic ecosystems. Rivers, lakes, wetlands, and ground water

        are sinks  into which water  and materials from the surrounding landscape drain (U.S. EPA Science Advisory

        Board, 2002). Landform, hydrology, and geomorphic processes generate and maintain freshwater ecosystem

        characteristics, including stream channel habitat structure,  organic matter inputs,  riparian soils, productivity,

        and invertebrate community composition (Montgomery & Buffington,  1998; Vannote, Minshall, Cummins,

        Sedell, & Gushing,  1980).  Consequently,  the  ecosystem protection approaches described in  this document

        focus  on  assessing and managing landscape conditions, including connectivity, and key functional processes

        in the watershed  of which the aquatic ecosystem  is a part and cannot function without. These processes are

        hierarchically nested and occur at  multiple spatiotemporal scales (Beechie et al., 2010) (Figure 2-1). Therefore,

        assessment and management must also occur at multiple spatial and temporal scales.
             Large
                        Reach scale:
                        riparian and channel-
                        floodplain processes
                                                                                   Shade
                                   Channel
                                  migration.
                                  Floodplain
                                   building
                     Pool formation
                      Bar depostion
                                                         Watershed scale:
                                                         erosion and runoff
                                                         processes
                                                                         Sot) creep Ove
                                                                            Jjf flow
                                                                    Laiirislklinrj
EslaDlishmem
 Succession
                        Shading
                    Wood recnjitmenl
                        Litterfall
                                                         Litho-topograpntc
                                                         template
            Migration
           Colonization
                                  Population
                                  dynamics
                                                                  Valley
                                                                  confinement
                      abilat selection,
                    Trophic dynamics
             Small
                   Short *
                                                              Dnving variables controlled by
                                                              reach-scale processes
                                                                 - root reinforcement
                                                                 - wood supply

                                                              Reach-scale processes:
                                                                 - nparian processes
                                                                 - channel-floodplain
                                                                  Interactions

                                                              Spatial scale of processes:
                                                                 10-1 -10'km2

                                                              Temporal scale of processes
                                                                 10' -10'yr
Dnving variables controlled by
watershed-scale processes:
   - sediment supply
   - discharge

Watershed-scale processes:
   - runoff processes
   - erosion

Spatial scale of processes1
   10-1 -10" km2

Temporal scale of processes:
   10-' -10'yr
                                                              Driving variables controlled by
                                                              the [lino-topographic template
                                                                 - channel slope
                                                                 - valley confinement

                                                              Landscape-scale processes:
                                                                 - tectonics
                                                                 -erosion

                                                              Spatial scale of processes
                                                                 »Id1km'

                                                              Temporal scale of processes:
                                                                 >103yr
                                Temporal scale
         Figure 2-1 Spatial and temporal scales of watershed processes. Watershed and ecosystem processes
         operate at a variety of spatial and temporal scales, with processes operating at larger spatial scales generally
         influencing processes operating at smaller scales. In some instances, processes operating at smaller scales
         may also influence processes operating at larger spatial scales. This is perhaps best illustrated in fishes,
         where processes such as habitat selection and competition influence survival of individuals, which influences
         population dynamics at the next larger space and time scale (Beechie et al., 2010). Reprinted with permission
         of University of California Press.
2-2

-------
                                                                        2 Key Concepts and Assessment Approaches
                                                                        ECOLOGICAL
Although  EPA's  watershed  approach has traditionally focused
primarily  on the management of the chemical,  physical,  and
some biological  aspects of water  quality, the importance of
pattern, connectivity, and process for integrated management of
watershed health is emerging (e.g., California's Healthy Streams
Partnership and Virginia's Healthy Waters Program). Assessments
of landscape condition,  hydrology,  geomorphic condition,  and
natural disturbance regimes provide complementary information
to the chemical,  physical, and biological parameters commonly
measured by water quality monitoring programs. Integrating the
results of all of these assessment approaches can help to provide a
more comprehensive understanding of aquatic ecosystem health.

The healthy watersheds conceptual framework is consistent with
recommendations by EPA's Science Advisory Board (SAB) (U.S.
EPA Science Advisory Board, 2002). Building on previous work
to describe aquatic resource integrity (Figure 2-2), the EPA SAB
identified six essential ecological attributes (EEAs)  to describe factors that support healthy ecosystems (Figure
2-3). These include  landscape condition, biotic condition, chemical and physical characteristics, ecological
                                                            Figure 2-3 Essential ecological attributes
                                                            (U.S. EPA Science Advisory Board, 2002).
    Solubilities
         W
    Adsorption
                          Alkalinity
                                      Temperature
                                          D.O.
      Nutrients
    Sunlight
    Organic Matter
        Inputs
                                                                                 Precipitation &
                                                                                      Runoff
                                                         INTEGRITY OF THE
                                                        WATER RESOURCE
                                                      "Principal Goal of the Clean Water Act
                                                      Riparian
                                                    Vegetation
                            1°and2°
                           Production
                                            Siltatiori
                                              Sinuosity
                                                     ^
                                                   Current
                                                                  Canopy
Width/Depth
 	
 Bank Stability
       Channel
     Morphology

   Gradient
 In stream
  Cover
Figure 2-2 The five major factors that determine integrity of the aquatic resource (modified from Karr, Fausch,
Angermeier, Yant, & Schlosser, 1986).
                                                                                                     2-3

-------
Identifying and Protecting Healthy Watersheds
        elements  (e.g., energy and material flow), hydrologic and geomorphic condition, and natural disturbance
        regimes. The healthy watersheds concept views watersheds as integral systems that can be understood through
        the dynamics of these essential ecological attributes.

        The systems approach to healthy watersheds assessment and protection is based on an integrated evaluation of:
        1) Landscape Condition, 2) Habitat, 3) Hydrology, 4) Geomorphology, 5) Water Quality, and 6) Biological
        Condition (Figure 2-4). Ecological processes and natural disturbance regimes are addressed in the context of
        these six components. Background information on each of these components is provided in the pages that
        follow.
                               Landscape Condition
                   Patterns of natural land cover, natural disturbance regimes,
                      lateral and longitudinal connectivity of the aquatic
                     environment, and continuity of landscape processes.
                                    Habitat
                    Aquatic, wetland, riparian, floodplain, lake, and shoreline
                            habitat. Hydrologic connectivity.
                                   Hydrology
                    Hydrologic regime: Quantity and timing of flow or water
                    level fluctuation. Highly dependent on the natural flow
                   (disturbance) regime and hydrologic connectivity, including
                           surface-ground water interactions.
           Geomorphology
Stream channels with natural geomorphic dynamics.
            Water Quality
  Chemical and physical characteristics of water.
          Biological Condition
   Biological community diversity, composition,
 relative abundance, trophic structure, condition,
          and sensitive species.
         Figure 2-4 Healthy watersheds assessment components.


        2.2   Landscape Condition

        Natural vegetative  cover stabilizes soil, regulates watershed hydrology, and provides habitat to terrestrial and
        riparian species. The type, quantity, and structure of the natural vegetation within a watershed have important
        influences on aquatic habitats. Land cover is  a driving factor in determining the  hydrologic and chemical
        characteristics of a water  body. Vegetated landscapes cycle nutrients, retain sediments, and regulate surface
        and ground water hydrology. Riparian forests regulate temperature, shading, and input of organic matter to
        headwater streams  (Committee on Hydrologic Impacts of Forest Management, National Research Council,
        2008). Conversely, agricultural and urban landscapes serve as net exporters of sediment and nutrients, while
        increasing surface runoff and decreasing infiltration to ground water stores.

        Recognition of these landscape influences has shaped previous aquatic ecosystem management efforts. Adequate
        protection of a range of aquatic ecosystem types is a widely accepted conservation approach (Noss, LaRoe III,
        & Scott, 1995). The Center for Watershed Protection (2008c) recommends conservation of multiple landscape
        areas: 1)  critical habitats; 2) aquatic corridors; 3) undeveloped  areas, such as forests, which help maintain
        the pre-development hydrologic response of a watershed; 4) buffers to separate water pollution hazards from
        aquatic resources; and 5) cultural  areas that sustain both aquatic and terrestrial ecosystems.

        It  is important  that forest patches, wetlands, and  riparian zones are of sufficient size, quantity,  and quality
        to sustain ecological communities and processes. Interconnections among habitat patches  are also important.
        For many species, an isolated forest patch is not a high quality habitat. However, a number of forest patches
        interconnected by forested corridors can provide outstanding habitat for a number of species. This is  because
        species need to  migrate, feed, reproduce, and  ensure genetic diversification. Native habitat in the  landscape
        provides a variety of benefits for aquatic ecological integrity, including maintenance of the natural watershed
        hydrology, soil and nutrient retention, preservation of habitat for both aquatic and terrestrial species, and
        the prevention of other adverse impacts associated with development. The photos in Figure 2-5 illustrate the
        difference between  intact habitat in the landscape and fragmented habitat.
2-4

-------
                                                                           2 Key Concepts and Assessment Approaches
            Figure 2-5 These photos provide an example of intact landscape condition (on the
            left) and fragmented landscape condition (on the right).

2.2.1  Green Infrastructure
The concept of linked landscape elements and ecological networks has evolved into the green infrastructure
movement in land conservation. Green infrastructure is "an interconnected network of natural areas and other
open spaces that conserves natural ecosystem values and functions, sustains clean air and water, and provides
a wide array of benefits to people and wildlife" (Benedict & McMahon, 2006). The natural areas are typically
referred to as "hubs," and the connections, or links, between the hubs are termed "corridors" (Figure 2-6). The
green infrastructure movement is rooted in: 1) Frederick Law Olmsted's idea of linking parks for the benefit
of people  (e.g., Boston's famous Emerald Necklace) and 2)  the recognition by wildlife biologists and ecologists
that interconnected habitat patches are essential for maintaining viable ecological communities (Benedict &
McMahon, 2002). The evolution of the green infrastructure movement has coincided with the development
of geographic information system  (GIS) technology and conceptual developments in landscape ecology and
conservation biology.

The green infrastructure approach considers open and green space as a system to be managed to meet the needs
of both ecosystems  and humans.  It can provide information  to  assist community planning, and to identify
and prioritize conservation opportunities. It can be mapped as a network of key ecological areas, or hubs, and
corridors  connecting them.  For example,  the  Green Infrastructure Vision of Chicago Wilderness  identifies
1.8 million acres of potential areas for protection and restoration throughout the  region (Figure 2-7; Chicago
Wilderness,  2009).

The   greenways   movement,   an  evolution
of  Olmsted's   idea,  has   influenced  green
infrastructure considerably, linking people with
their landscape  through  recreational activities.
Greenways  are   recreational  and  alternative
transportation    corridors    surrounded    by
vegetation. An example of a popular greenway
approach  is  the Rails-to-Trails Conservancy's
acquisition of abandoned railways to create bike
paths for local  transportation and  recreation.
Green infrastructure is different from greenways
in that green infrastructure emphasizes ecology
over  recreation.  Further, green  infrastructure
focuses    on  large,   ecologically  important
hubs  and planning  for  growth  around the
green  infrastructure,  as  opposed  to  "fitting"
Figure 2-6 Green infrastructure network design (modified
from Maryland Department of Natural Resources, 2011).
                                                                                                         2-5

-------
Identifying and Protecting Healthy Watersheds

                       Land Cover
                       • Forested Land
                       • Urban Open Space
                          Rural Grassland orShrublan'
                          Water
                       • Wetland
                          Agricultural Land
                       • Urban Developed Land
                       • Bare Rock/Sand/Clay

                       Protected Land
                       CD Protected Land Overlay
                        Figure 2-7 Map of the Chicagoland area showing land cover and currently protected
                        areas (Chicago Wilderness, 2009).
2-6

-------
                                                                            2 Key Concepts and Assessment Approaches
conservation areas into developed landscapes (Benedict & McMahon,  2002).  Identification of hubs  in  a
green infrastructure program typically involves a land cover and human infrastructure assessment to identify
interior habitat patches, which are areas of forest or wetland that have not been fragmented by roads or other
development. These hubs often serve as  core habitat for a number of species. The links, or corridors, between
these hubs provide opportunities for movement of fauna and flora between the habitat patches, thus allowing
for dispersal and genetic diversity, which are essential for ecological integrity.

The  1990s saw the development of a number of green infrastructure programs, the most notable of which
were in Florida and Maryland (Benedict & McMahon, 2006). Ecologists Larry Harris and Reed Noss at the
University of Florida conceptualized an integrated habitat conservation system to address the fragmentation of
natural areas that they saw as the primary cause of biodiversity decline across the state (Benedict & McMahon,
2006). This  vision led to the development of Florida's Ecological Network Project and, later, the  Southeastern
Ecological Framework Project, the  first regionally-based green infrastructure study (John Richardson,  EPA
Region 4, Personal Communication). Maryland's  green infrastructure assessment built off of the success of
these pioneering programs  (John Richardson,  EPA  Region 4,  Personal Communication).  These programs
also  drew upon work by The Nature Conservancy on an ecoregional approach to selecting wildlife reserves
(Benedict & McMahon,  2006). The original  green  infrastructure  approaches  contain  five basic steps, as
outlined by  Benedict and McMahon (2006):

    1.   Develop network design goals and identify desired features.
    2.   Gather and process data on landscape types.
    3.   Identify and connect network elements.
    4.   Set  priorities for conservation action.
    5.   Seek review and input.

Green  infrastructure assessments utilize a weighted overlay technique in GIS that identifies the most ecologically
valuable lands based on co-occurrence  of multiple ecological attributes. For  example, creating a map  that
overlays the  state's road network with land cover data allows one to identify those areas with remaining natural
land cover that contain the  fewest road crossings. Additional data layers can be added to this analysis,  with
each layer weighted according to the importance of its features for ecological integrity. The final result is a  map
that shows the areas with the highest priority for conservation. This approach has been replicated and modified
for use in a number of states, local communities, and regions throughout the United States.

2.2.2  Rivers as Landscape Elements
Although the term landscape implies a focus on terrestrial features, aquatic systems are just as much landscape
elements as  forested patches and corridors (Wiens, 2002). Rivers interact with other landscape elements  over
time through their natural floodplains, migrating meander belts, and riparian wetlands (Smith, Schiff, Olivero,
& MacBroom, 2008). Natural hydrology provides connectivity among aquatic habitats and between terrestrial
and  aquatic elements. Many aquatic organisms  depend on being  able to move through  connected systems
to habitats in response to variable environmental  conditions.  Forested riparian zones are often some of the
best  remaining  green infrastructure links, or corridors, for connecting hubs on the landscape. Furthermore,
maintenance of natural land cover protects aquatic ecosystems from nonpoint sources of pollution, including
urban  and agricultural runoff.

Recognizing the importance of connectivity, The Nature Conservancy advocates a systems approach to  river
protection, exemplified by the Active River Area (Figure 2-8), which includes not only the river channel but
also  floodplains, riparian wetlands, and other parts  of the river corridor where key habitats and processes
occur  (Smith et al., 2008).  The Active  River Area concept can  be applied at  different scales, from basin to
catchment or reach.  For example, identification of intact riparian areas and headwaters  in the Connecticut
River Basin  was accomplished using standard GIS techniques, available models, and national datasets (Smith
et al.,  2008). A more detailed analysis,  using techniques such as Vermont's Stream Geomorphic Assessment
protocols (see Chapter 3), can then be used to identify specific conservation priorities on a subwatershed scale.
                                                                                                          2-7

-------
Identifying and Protecting Healthy Watersheds
                              MATERIAL
                              • CONTRIBUTION
• V-SHAPED CONFINED VALLEY
    - HEADWATER CATCHMENT AREAS

          - WETLANDS
                                                                          ALLUVIAL FAN

                                                                            NCISED TRIBUTARY
                LATERAL
              MIGRATION
             BACKSWAMP
             FLOOOPLAIN
                               FLOODPLA1N FOREST
                               RIPARIAN WETLAND
                                                                                         OX BOW ABANDONED
                                                                                         CHANNEL
                                                                                                     BRAIDED RIVER
                                                                                                     FLOODPLAIN DELTA
          HEADWATERS
          • CPOM I.-vi -v !."'*'.! MWn
          • 3040 METERS FROU CHAM-4EL
          . <1 YEAR RECURRENCE WTERVAL
           MID • WATERSHED
           . UEMOBl H--I i
           SEDIMENT EROSION. STORACE DEPOSITION.
           AND TRANSPORT IN THE CHANEL AND FlOODfVAIW
           . MEAnoeft KIT (« CHMI.VB. IWDTHSI «
           ADJACEWTUJW ACTIVE fLOQORAIN
           . * 1 TO 1  ID YEAR RECLP.RENCE
                             LONG-TERM SEDIMENT STORAGE
                             • ENTIRE VALLEV BOTTOM
                             • 1.10 YEARS RECURRENCE
                              INTERVAL
                                                                         NATURAL SEDIMENTARY
                                                                         LEVEE
                                                                                    I	1  LOCATION OF THE
                                                                                        J  ACTIVE RIVER AREA

          Figure 2-8 Components and dominant processes of the Active River Area (Smith et al., 2008).

        Active River Areas, in their natural state, maintain the ecological integrity of rivers, streams, and  riparian areas
        and the connection of those areas to the local ground water system. They also provide a variety of ecosystem
        services,  such as flood prevention and hazard avoidance, recreation and open space, and other habitat values.
        The Active  River  Area is essential to healthy and productive fish  populations. Preserving riparian wetlands
        and a river  channel's connection with its floodplain provides surface and subsurface floodwater storage and
        reduces stream power during flood events. This is  especially important in temperate regions, where increases
        in average annual  precipitation and frequency of extreme storm events have been observed  and are expected to
        continue as  a result of climate change (IPCC, 2007). Also, warming temperatures will increase the importance
        of these  undeveloped areas as zones  of ground water discharge provide refugia for coldwater aquatic species.
        Maintaining natural vegetation  in the entire Active River Area and in the wider watershed provides  water
        quality improvements through reduced surface runoff and increased opportunity for ground water infiltration
        and storage.

        2.2.3  Natural  Disturbance
        The natural disturbance regime  is an important consideration in assessment and management of landscape
        condition. Ecosystems are naturally dynamic and depend  on recurrent disturbances to maintain their health.
        Natural disturbance  events that affect watershed ecosystems include fires, floods, droughts, landslides, and
        debris flows. The frequency,  intensity, extent,  and duration  of the events are  collectively referred to as the
        disturbance regime  (U.S. EPA Science Advisory Board, 2002). The natural fire regime, particularly in some
        regions of the United States (e.g., longleaf pine/flatwoods ecosystems of the southeast), helps to maintain
        healthy landscape condition through a process of ecological renewal that creates opportunities for some species
        while scaling back the prevalence of others. Fire dependant ecosystems require this periodic disturbance to
        maintain their natural state and composition.  Suppression of the natural  fire regime may cause an excessive
        build-up of nutrients on the forest floor due to decomposition of organic matter (Miller et al.,  2006).  These
2-8

-------
                                                                            2 Key Concepts and Assessment Approaches
nutrients  can then be transported to aquatic ecosystems during rainfall/runoff events,  causing  eutrophic
conditions. Fire disturbances of natural frequency and intensity remove the excess organic matter causing the
nutrient build-up and may actually improve long-term water quality, although water quality will be temporarily
worsened  immediately following a fire (Miller et al., 2006). The Fire Regime Condition Class methodology is
an example of a landscape condition assessment that focuses on the natural disturbance regime (see Chapter 3).
This approach assesses a landscape's degree of departure from the natural fire regime and suggests management
approaches for emulating that regime.

2.2.4  Connectivity and Redundancy
Connectivity of landscape  elements, including aquatic ecosystems,  provides  organisms with access  to  the
habitats and resources necessary for the different stages of their life cycle  (e.g., breeding, feeding, nesting). It
also helps  to ensure that ecosystems and species have the ability to recover and recolonize following disturbance
(Poiani, Richter, Anderson,  & Richter, 2000). Lateral (floodplain access), vertical (hyporheic exchange), and
longitudinal (stream flow) connectivity are equally important for supporting these processes. Physical barriers,
such as dams and levees, isolate aquatic populations and prevent dispersal of organisms (Frissel, Poff,  & Jensen,
2001). Further,  these barriers prevent the flow of water, sediment,  nutrients, and heat loads that support
ecosystem processes (Frissel, Poff,  & Jensen, 2001).  As a result, non-native species are often  better able to
compete with native species (Frissel, Poff, & Jensen,  2001).  Connectivity is therefore critical to ensuring the
persistence of native species by  providing habitat refugia and recolonization access. Redundancy refers to the
presence of multiple examples of functionally similar habitat and ecosystem types that help to "spread the risk"
of species loss following major ecological disturbances. This can allow populations of the same species to persist
in the presence of disturbance or environmental change.

2.3   Habitat

Habitat extent is directly related to  hydrologic and  geomorphic processes. The  number and  distribution of
different habitat  types, or patches, and their  connectivity influence species population health (Committee
on Hydrologic Impacts of Forest  Management, National Research Council, 2008). Habitat quality is also
affected by the physical  and chemical characteristics of water (e.g.,  water temperature). Water quality and
geomorphic and hydrologic processes are all affected
by landscape condition, which  also shapes riparian
and  terrestrial  habitat.  Thus,  habitat  condition
serves as an integrating indicator of other watershed
variables, upon which biological condition is highly
dependent.

Protection efforts must consider a variety of habitat
types that serve  different needs  of an  ecosystem,
such as  cool water rivers for trout foraging  (Figure
2-9), riffles in cold headwater streams for breeding,
and  springs for thermal refuge during low water
conditions (Montgomery & Buffington,  1998). In
addition,  natural variability within a habitat patch
provides  opportunities  for  species  with different
requirements and tolerances (Aber et al., 2000).

2.3.1  Fluvial Habitat
Figure 2-9 Cool water rivers provide important trout
foraging habitat.
Hydrologic and geomorphic processes create the physical habitat template that supports aquatic communities
in fluvial systems. As described by the River Continuum Concept (RCC), physical habitat variables can change
predictably along the longitudinal gradient of the riverine system (Figure 2-10) (Vannote et al., 1980). Changes
in biological communities generally correspond  with this physical  gradient. For example, a characteristic
community of macroinvertebrates (dominated  by shredders and collectors) is typically found in headwater
                                                                                                          2-9

-------
Identifying and Protecting Healthy Watersheds
                                                                      shredders
                                                                                       grazers
                      •S 4
                       01
                      f
                       o
                         10
                         11
                         12
                                                        course
                                                     A   paniculate
                                                        matter
                                         I I I I I I I  I I I I I I I  I I I
                                          Relative Channel Width
                        Figure 2-10 The River Continuum Concept (Vannote et al., 1980).
                        Canada.
2008 NRC
        streams. These species are dependent on sufficient shade and inputs of terrestrial vegetation (e.g., large woody
        debris) from riparian areas. As a stream  channel widens,  allowing more sunlight to penetrate into the open
        water, algae and rooted vascular plants become the primary sources of energy input, and the macroinvertebrate
        community  reflects this transition (dominated by collectors and grazers). As a river becomes larger and wider,
        fine particulate matter from upstream becomes more important as an energy source for the macroinvertebrate
        community  (dominated by collectors).

        This predictable change in community structure has been shown to be generally true at broad scales. However,
        the influence of tributary  confluences and watershed disturbances  on aquatic habitat must be understood
        to explain the many deviations  from the habitat type and expected biological community predicted by the
        River Continuum Concept. Inputs of sediment and large woody debris at river confluences create  habitat
2-10

-------
                                                                            2 Key Concepts and Assessment Approaches
heterogeneity, allowing for the existence of communities that would not otherwise be expected to occur in a
given stream order. Additionally, flood pulses and other aspects of the natural flow regime create a lateral and
temporal gradient of habitat from the stream channel and out on to the floodplain. Ground water input in the
hyporheic zone also creates unique habitats that cannot be explained from a purely longitudinal perspective
of riverine habitat. This inherent complexity of riverine ecosystems is responsible for the diversity of aquatic
habitats and resultant  biological communities found within them.

Understanding riverine ecosystems in a landscape context can help to elucidate the complex relationships that
define aquatic habitat. The RCC conceptual model has been improved upon in recent years to include  not
only the longitudinal  dimension of river systems, but also the lateral (floodplain and  riparian zone), vertical
(hyporheic zone), and temporal (flow regime) dimensions (Thorp, Thorns, & DeLong, 2006). The Riverine
Ecosystem Synthesis (RES) (Thorp, Thorns, & Delong, 2008) builds on the RCC and other leading concepts in
river ecology to explain the spatial and temporal distribution  of species, communities, and ecosystem processes
as a function of hydrogeomorphic differences in
the  riverine  landscape.  Heterogeneous  patches
of habitat  result  from  unique  combinations of
hydrologic and geomorphic processes, including
the dynamics of watershed disturbance  and the
structure of the river network within a watershed.
                                                                Organizational Levels
The   geomorphic,  hydrologic,   and  ecological
processes  that  form these patches operate at a
variety of scales. Thus, hydrogeomorphic patches
exist  at  multiple spatial  and  temporal  scales,
such as drainage basins or watersheds, functional
process zones  (FPZ),  reaches, functional  units,
and   individual  habitats  (Thorp,  Thorns,  &
DeLong,  2006)  (Figure  2-11). Hierarchically-
organized units,  such  as  watersheds, are  most
affected by the scale immediately below that of
interest and the scale immediately above it (Thorp,
Thorns, & Delong, 2008). As FPZs are the level
immediately  below watersheds  or  basins, they
are an appropriate scale for integrated watershed
assessments  and receive special  attention in the
RES.  These  FPZs are  not necessarily distributed
in a manner  predictable by longitudinal  theories
of river ecology, such as the RCC (Figure 2-12).
Rather, all four dimensions of the riverine system
influence their distribution.
                                                 Figure 2-11 Hierarchy defining spatiotemporal scales
                                                 of hydrogeomorphic patches (Thorp, Thorns, & Delong,
                                                 2008). Reprinted with permission of Elsevier.
Through a collaborative effort, EPA and the University  of Kansas developed  a computer program that
statistically delineates FPZs using precipitation, geology, elevation, and remote sensing data. The program
extracts 14 hydrogeomorphic variables from these datasets and uses multivariate cluster analysis to identify the
distinct FPZ types. This approach minimizes human bias in the classification. See Figure 2-13 for an example
of the various FPZs delineated in the Kanawha River Basin of West Virginia.

Stratifying a field sampling program based on FPZs can be a useful method for ensuring that scale is adequately
considered in the data collection process. Data can be collected at reaches within each FPZ and averaged to
get a condition score for the FPZ. FPZs can then be compared  across the watershed to understand watershed
condition.  Important habitat variables at the reach scale  (and smaller) include substrate  composition and
riparian vegetation, both of which are dependent on processes operating at larger scales.
                                                                                                         2-11

-------
Identifying and Protecting Healthy Watersheds
                        Anabranch
                                    Braidec

                                       Anabranch
                                                            Meandering
                                                                                Distributary
                         Distributary
                       Flow
                       Pulse
 Flow
History
                              Flow
                             Regime

                          HYDROLOGY

                                              INFORMATION KEY
                    Lateral
                                                         Longitudinal
                    Vertical
             CONNECTIVITY
 FCL  Food chain length


    | Nutrient spiralling


QijSjpJ Species Diversity

ECOSYSTEM FUNCTION
        Figure 2-12 A conceptual riverine landscape is shown depicting various functional process zones (FPZ) and
        their possible arrangement in the longitudinal dimension. Note that FPZs are repeatable and only partially
        predictable in location (corrected copy from Thorp, Thorns, & Delong, 2008). Reprinted with permission of
        Elsevier.
2-12

-------
                                                                           2 Key Concepts and Assessment Approaches
 Functional Process Zones
       Constricted High Energy Upland Zone
       Lowland Alluvial River
       Lowland Constricted Zone
       Open Valley Upland Zone
       Resen/oirZone
       Upland Constricted Zone
                                                                              A
                                                                               N
                                                          0   12.5  25
50
75
 100
• km
Figure 2-13 Distribution of the various Functional Process Zones in the Kanawha River, West Virginia (from
in-review manuscript by J.H. Thorp, J.E. Flotemersch, B.S. Williams, and L.A. Gabanski entitled "Critical role for
hierarchical geospatial analyses in the design of fluvial research, assessment, and management").
                                                                                                        2-13

-------
Identifying and Protecting Healthy Watersheds
        Headwater streams represent more than half of the nation's stream miles  and are fundamental to a healthy
        watershed. Properly functioning headwater streams are one of the primary determinants of downstream flow,
        water quality, and biological communities (Cohen, 1997)- Headwater streams provide sediment, nutrient, and
        flood control and help to maintain base flow in larger rivers downstream. They support macroinvertebrate,
        amphibian, and plant populations that contribute to regional and local  biodiversity.

        Riparian zones are strongly influenced by the flow regime of a river, as  well as the geomorphology of the river
        network, including the river banks and floodplain elevations. Riparian zones provide organic material as input
        to the riverine system,  providing both energy and habitat to stream dwelling organisms. Riparian vegetation
        stabilizes the banks of the river channel and provides important nutrient and mineral cycling functions (Mitsch
        &  Gosselink,  2007). Riparian habitats support diverse plant  and animal species that  provide  important
        ecological  functions and also regulate inputs to  the aquatic system. These unique habitats require  hydrologic
        connectivity with the river channel to be maintained.

        Substrate composition is a physical habitat variable that is highly dependent on flow, geomorphic stability, and
        sediment inputs from the watershed. Many macroinvertebrates  and aquatic plants require specific substrates
        for attachment and anchoring, while  fish use cobble and boulders  for shelter from currents and predators.
        Some fish  species lay their eggs, which require unrestricted flow of well-oxygenated water, in gravel substrates.
        When these gravel substrates become  embedded in  finer sediment,  the eggs do not have access to sufficient
        oxygen and die.

        2.3.2   Lake  Habitat
        Lakeshores also have riparian zones that serve as a source of organic material to the lake's aquatic habitat and
        stabilize the lake's perimeter. Lakeshore vegetation creates stable habitat  conditions in the peripheral waters of a
        lake by buffering it from exposure to environmental elements such as wind and sunlight. EPA's National Lakes
        Assessment (NLA) indentified poor lakeshore habitat as the most prominent stressor to the biological health of
        lakes (U.S. Environmental Protection Agency, 2009a).

        Lakes are typically thought of as having three habitat zones: the littoral zone, the limnetic zone, and the benthic
        zone (Figure 2-14). The littoral zone is  the  nearshore area where sufficient sunlight reaches  the substrate,
        allowing aquatic plants to grow. This zone provides habitat for fish, invertebrates, and other aquatic  organisms.
        The limnetic zone is the open water area where light does not penetrate  to the substrate.  Although rooted
        aquatic plants cannot live in this zone, plankton and nekton are found here and serve as  sources of food for
        many fish  species. Habitat in the benthic zone (the lake bottom) consists of mostly mud and sand, which can
        support diverse invertebrate and algal communities, which in turn serve as primary food sources for many fish
        and other vertebrates.

        The three  lake habitat  zones are tightly coupled, with organic matter from the limnetic zone serving as an
        important food source  for animals in the benthic zone and many organisms spending different parts of their
        life cycles in different zones. Many fish species, for example, spend their time in the limnetic zone as juveniles,
        taking advantage of the abundant plankton found there. As they grow, they shift to feeding in the benthic zone
        and may spend their nights in the littoral zone,  while other species may spend the day in the near  shore zone
        and the  night in the limnetic zone.

        Lakes with greater, and more varied, shallow water habitat are able to more effectively support aquatic life (U.S.
        Environmental  Protection Agency, 2009). Lakeshore habitat is strongly influenced by natural fluctuations in
        lake  levels, with characteristic plant communities existing in the transition zone where the water rises  and
        recedes.  The natural fluctuation helps to prevent establishment of invasive species that are not adapted to such
        fluctuations and provides seasonal cues for reproduction  of native species. Lake level fluctuation is  influenced
        by ground water inputs, precipitation, evaporation, and  runoff from storm events or snowmelt. Like riverine
        habitats, the physical and chemical characteristics of the water also contribute to the quality of a lake's aquatic
        habitat.
2-14

-------
                                                                            2 Key Concepts and Assessment Approaches
                                                                                           trophic zone
     Figure 2-14 Schematic of a lakeshore and the three habitat zones of a typical lake (U.S. Environmental
     Protection Agency, 2009a).

2.3.3  Wetland Habitat
Wetland habitat characteristics are largely affected by their hydrologic connectivity to surrounding landscape
features. The hydrogeomorphic wetland classification and assessment approach defines seven types of wetlands
based on their geomorphic setting and dominant water sources: riverine wetlands primarily receive overbank
flow from the stream channel, depressional wetlands receive return  inflow from ground water and interflow,
slope wetlands receive return inflow from ground water, mineral soil flats and organic soil flats primarily receive
inputs from precipitation, estuarine fringe wetlands receive their water from overbank flows from the estuary,
and lacustrine fringe wetlands receive their water primarily from overbank flows  from lakes (Smith, Ammann,
Bartoldus, and Brinson, 1995).

The biological communities that occur in wetlands are uniquely adapted to their environmental conditions
because wetland habitats offer essential resources in limited forms and quantities. Soil saturation reduces the
availability of oxygen to plants, and nutrient  availability is low in some wetland types because decomposition
rates are slowed in these low-oxygen conditions.  Bogs,  in particular, are characterized by their low nutrient
concentrations. In other wetlands, the combination of shallow water, high levels of nutrients, and primary
productivity  is  ideal for the development of organisms that form the base of the food web  and feed many
species offish, amphibians, shellfish,  and insects. Many species of birds and mammals also rely on wetlands for
food, water, and shelter, especially during migration and breeding. Variations in the biological communities of
different wetland types provide unique  habitat structures. For example, swamp communities are dominated
by woody vegetation, whereas marshes are dominated by herbaceous vegetation. More than one third of the
United States' threatened and endangered species live only in wetlands, and nearly half use wetlands at some
point in their lives (U.S. Environmental Protection Agency, 1995).
                                                                                                         2-15

-------
Identifying and Protecting Healthy Watersheds
        2.4    Hydrology

        Watershed hydrology is driven by climatic processes; surface and subsurface characteristics, such as topography,
        vegetation, and geology; and human processes, such as water and land use. A watershed can be thought of as a
        surface catchment (drainage basin) plus a subsurface catchment. A drainage basin can be defined as the surface
        area that, on the basis of topography, contributes all the runoff that passes through a given cross section of a
        stream (Dingham, 2002). Drainage that occurs via subsurface flow, controlled by hydrogeology, is called the
        subsurface catchment (Kraemer et al., 2000). Precipitation that falls within the watershed can be stored on the
        land surface (e.g., lakes or wetlands), infiltrate to the subsurface, move as overland flow to stream channels, or
        be lost to evapotranspiration. Ground water can also enter and exit a watershed via inflow and outflow through
        aquifers that extend beyond the surface  catchment. Rain and  snowmelt produce runoff that moves through a
        variety of surface and subsurface pathways as it flows through the drainage network, eventually exiting the
        watershed via stream or ground water flow.

        An important conceptual framework for understanding and evaluating watershed structure and function is the
        water  budget (see Appendix A). A water budget can be developed for any hydrologic feature and accounts for
        all water inputs and  outputs. A watershed scale water budget includes the following components:
                                           P  + Gin - (Q + ET + Gout) = AS,
        where  P is  precipitation,  G  is ground  water  inflow  to  the  watershed,  Q is  stream  outflow, ET is
        evapotranspiration, Gou(is ground water outflow from the watershed and AS  is change in storage over time.

        Spatial and temporal variation in evapotranspiration, infiltration, and overland flow is determined by the size
        of the watershed, the surface  topography and vegetation, the underlying geology, climatic  conditions, and
        water  and land uses. Small watersheds are more dynamic than large watersheds, responding  more rapidly to
        inputs from  precipitation. Hydrographs for streams dominated  by snowmelt and base flow follow a  more
        predictable pattern than those for streams dominated by surface runoff (Healy, Winter, LaBaugh, & Franke,
        2007). Surface and  ground  water interact in a variety of ways. Overland flow to surface waters results  from
        both saturation-excess and  infiltration-excess runoff processes. Water that infiltrates  to the subsurface can
        discharge to  a nearby stream  as  interflow or move vertically to  the water  table providing aquifer recharge.
        Water that recharges aquifers flows through the subsurface to discharge areas, such as springs,  seeps, wetlands,
        fens, streams, and lakes.

        Stream flow can be affected by surface runoff, interflow discharge, and base flow discharge. The contribution of
        ground water to stream flow varies significantly, but is estimated to be 40% to 50% in small- to medium-sized
        streams (Alley, Reilly, & Franke, 1999).  A given reach of stream can be perennial,  intermittent, or ephemeral
        (Figure 2-15) and the ground water contribution can vary over an annual hydrograph.

        2.4.1  Hydroecology
        Hydroecology is a  new  discipline  that examines the relationship of hydrology and  ecology. Although
        hydroecology as a distinct discipline is new,  this interdisciplinary field has, at its roots, the applied science of
        instream  flows. With increasingly large  withdrawals from surface and ground  water,  protection of sufficient
        instream  flow became a major concern  during the middle of the last century. The difficulty in determining
        ecologically relevant instream flow requirements initially led to the development of "rule of thumb" hydrologic
        statistics  serving as  the basis  of minimum flows requirements  (Annear, et  al.,  2004).  The 7Q10 rule is
        an example of this  kind of thinking. 7Q10 refers to the lowest 7-day  average flow that  occurs on average
        once every 10 years. It is calculated based on historic flows and does not  necessarily "protect"  because it is
        unrelated to any explicit biological needs or thresholds. Increased knowledge of aquatic ecosystems and access
        to computers led to more sophisticated techniques for assessing  instream flow requirements in the 1970s
        and 1980s (Annear, et al., 2004). The National Biological Service published its Instream Flow Incremental
        Methodology (IFIM) in 1995- The IFIM uses a suite of models to evaluate physical habitat availability in
        riverine systems  based on recent historical stream flows (Stalnaker, Lamb,  Henriksen,  Bovee, & Bartholow,
        1995). It was developed in response to the National Environmental Policy Act's mandate that  all federal water
2-16

-------
                                                                             2 Key Concepts and Assessment Approaches
Losing Stream
   (ft-A'J
Gaining Stream in Spring
  Losing Stream in Fall
      (B-B')
                                                                   Gaining Stream
                                                                      (C-C)
                   in Fall (F)
 Figure 2-15 Relation between water table and stream type (U.S. Environmental Protection Agency, 1987).

resource management agencies consider alternative water development and management schemes (Stalnaker
et al., 1995). IFIM was designed to predict the flow/habitat relationships for different species and lifestages,
evaluate flow management alternatives, and reach agreement on preferred flow regime(s). This method  is data
intensive, requiring substantial fieldwork and multidisciplinary expertise.

Ecosystems are naturally dynamic and depend on recurrent natural disturbances to maintain their health. The
publication of The Natural Flow Regime (Poff, et al., 1997) contributed  greatly to the understanding that a
dynamic river is a healthy river. Natural flow regimes are composed of seasonally varying environmental flow
components  (Matthews &  Richter, 2007),  including high flows, base flows, pulses, and  floods.  Each flow
component serves critical ecological functions such as creating habitat and providing cues  for spawning and
migration during discrete times of the year  (Figure 2-16 and Figure 2-17). Environmental flow components can
be characterized in terms of their magnitude, frequency, duration, timing, and rate of change. The Indicators
of  Hydrologic  Alteration   (IHA)
(Richter et al.,  1996) quantifies these
characteristics   of    environmental
flow components,  as well  as other
ecologically  relevant   stream  flow
statistics, based on daily stream flow
data.  IHA can  also  calculate   the
degree  to  which  flow  components
have been altered  from  a  reference
condition.   The    Hydroecological
Integrity     Assessment     Process
(Henriksen,  Heasley,  Kennen,  &
Nieswand,  2006)  also   calculates
stream flow statistics, and uses them
to  classify  streams  into   regional
hydrologic  types.   The  Ecological
Limits   of  Hydrologic  Alteration
(Poff, et al., 2010)  is  a  framework
that relates hydrologic alteration to
ecological  response  to support  the
                                            Principle 3
                                       lateral connectivity
                                       longitudinal connectivity
                                                              spates
                                                        Principle 1
                                             channel form
                                             habitat complexity—
                                             patch disturbance
                                                                                            biotic diversity
                                                                                     Principle 2
                                                                                 Life history patterns
                                                                                 • spawning
                                                                                 • recruitment
                                                                                J"
                                                                             stable baseflcws
                                                                                             drought
                                                               Time
                                                               Principle 4
                                                      natural regime discourages invasions
                                    Figure 2-16 Different components of the natural flow regime support
                                    different ecological processes and functions (Bunn & Arthington, 2002).
                                    Reprinted with permission of Springer Science and Business Media B.V.
                                                                                                           2-17

-------
Identifying and Protecting Healthy Watersheds
                        110,000
                                   Prothonotary warbler in          return
                                   Central and South America        migration
                                     wintering grounds          j»
                        100,000
                        90,000
breeding/nesting
                                                                              f \
fledging     fall
       migration
                                   Bald cypress peak seed fall       seed dispersal
                                                       and germination
                                                                          growing season
                                                                                                 seed fall
                                                                         1944 (pre-dam average year)

                                                                                    1972 (post-dam average year]
                                 :ober  November December January  February  March   April    May   June   July    August  September
                      Figure 2-17 Ecological model of the Savannah River, Georgia illustrating the ecological
                      importance of the natural flow regime. Note the loss of high and low flows during
                      critical bioperiods for the post-dam hydrograph (The Nature Conservancy). Illustrations
                      from the National Audubon Society: Sibley Guide to Birds, by David Allen Sibley,
                      published by Alfred A. Knopf, Inc. Copyright © 2000 by Andrew Stewart Publishing,
                      Inc. All rights reserved. Reproduced with permission of the copyright holder.

        determination of environmental  flow standards  or targets. Recognition of the role  that flow variability and
        disturbance play on the health of aquatic and riparian species initially led to flow prescriptions focused on one
        or a few species (Richter, Baumgartner, Powell,  & Braun, 1996). More recent, holistic assessment methods
        (Tharme, 2003) focus on maintaining the natural flow regime, or the flow variation that existed prior to human
        modification, by relating flow statistics to a variety of biological community metrics (Richter et al., 1996).

        The natural disturbance regime  is  a vital component of instream flow assessments. Holistic assessments
        determine  the flow variability  and magnitude necessary to maintain aquatic and riparian communities over
        time (Figure 2-18). In the higher order reaches  of large river/floodplain systems, aquatic biota have adapted
        their life history strategies to cope with, and even take advantage of, the predictable flood regime. For example,
        a gradient  of plant species exists along  the aquatic/terrestrial transition zone as a result  of seasonal  degrees
        of inundation, nutrients, and light (Bayley, 1995). The littoral zone in rivers is a moving zone of alternating
        flooding and  drying as the water level rises and  falls.  This  zone provides excellent nursing grounds for many
        fish species, which have adapted their life  histories to spawn just before or during the rising, flooding phase.
        During the drawdown phase,  nutrient runoff from  the littoral zone increases primary production of algae,
        which in turn increases production of aquatic invertebrates that feed on these algae. Not only does periodic
        flooding affect biological communities directly, but it also  affects the distribution of habitat patches  through
        sediment deposition and scouring. In order for this natural  regime of flood disturbance to effectively influence
        riparian biodiversity, it is essential that the  river channel maintain lateral connectivity with its floodplain (Junk
        &Wantzen, 2004).
2-18

-------
                                                                           2 Key Concepts and Assessment Approaches
                                                                                          Frequency
                                                                                           Annual
  Figure 2-18 Geomorphic and ecological functions provided by different levels of flow. Water tables that
  sustain riparian vegetation and that delineate in-channel baseflow habitat are maintained by ground water
  inflow and flood recharge (A). Floods of varying size and timing are needed to maintain a diversity of riparian
  plant species and aquatic habitat. Small floods occur frequently and transport fine sediments, maintaining
  high benthic productivity and creating  spawning habitat for fishes (B). Intermediate-sized floods inundate
  low-lying floodplains and deposit entrained sediment, allowing for the establishment of pioneer species
  (C). These floods also import accumulated organic material into the channel and help to maintain the
  characteristic form of the active stream channel. Larger floods that recur on the order of decades inundate
  the aggregated floodplain terraces, where later successional species establish (D). Rare, large floods can
  uproot mature riparian trees and deposit them in the channel,  creating high-quality habitat for many aquatic
  species (E) (Poff et al.,  1997). Reprinted  with permission of University of California Press.

2.4.2  Ground Water  Hydrology
It is estimated that ground water represents about 97% of all the  liquid freshwater on earth (Dunne & Leopold,
1978). Water stored in rivers, lakes, and as soil moisture accounts for less than  1% of the planet's freshwater.
Ground water is an important source of water for meeting human needs, including drinking water, irrigation,
and industrial  use. In the United States,  approximately 50% of  the drinking water supply comes from ground
water; in rural areas, 99% of the population relies on ground water to meet their drinking water needs (Kenny
et al., 2009). Ground water  is equally important to conservation of aquatic and terrestrial  ecosystems and
species. Many aquatic,  riparian, and wetland  ecosystems  rely  on ground  water  to  meet  their water needs.
Ground water is also important for maintaining the water temperature and chemical conditions required by
these ecosystems and the  plants and animals they support. Describing the link between ground water and
ecosystems, understanding and documenting the key processes and functions  that ground water provides, and
identifying the critical threats are key components of a healthy watersheds assessment.

Spatial and temporal distribution of ground water recharge is influenced significantly by geomorphic landforms,
soil conditions, vegetation patterns,  and  land use. Direct recharge occurs when  precipitation infiltrates to the
water table at  or near the point of impact and does  not run off. Direct recharge, more common in humid
areas, is controlled by soil moisture, plant communities, and landform type. Indirect  recharge occurs when
precipitation flows as surface  runoff and infiltrates to the water table at some distance from its original point
of impact. More common in semi-arid  regions, indirect recharge can occur in two ways: 1) infiltration of
overland flow  into  fractures,  joints, faults, and macropores;  and 2)  seepage  through the beds and  banks of
recognizable streams, lakes, or wetlands  (Younger, 2006). This  happens in beds of ephemeral streams during
flood flow and through multiple channel  beds  in alluvial fans  along mountain fronts. Recharge  to regional
aquifers underlying a watershed may also occur by ground water inflow from aquifers outside the boundaries of
the surface catchment. Adequate recharge is fundamental to ensuring that sufficient ground water is available
to support ecosystems.
                                                                                                        2-19

-------
Identifying and Protecting Healthy Watersheds
        Ground water flows from areas of recharge to locations of discharge. Depending on the size and geology of
        a watershed, multiple aquifers may be found within the  boundaries of a surface  catchment.  Conversely, a
        single aquifer may underlie multiple watersheds. Watersheds of moderate to large size and significant relief
        typically contain multiple ground water flow systems of different scales (Figure 2-19). Flow system boundaries
        are controlled by topography, type, and distribution of geomorphic land forms within the watershed, and  the
        underlying geology. Ground water discharge is dynamic and occurs at a variety of locations within a watershed,
        including springs and seeps, streams, wetlands, and lakes. Discharge from local and intermediate ground water
        flow systems is likely to fluctuate over an annual hydrograph while discharge from deeper, regional aquifers is
        likely to be more stable. Travel times from ground water recharge areas to ground water  discharge areas can
        vary greatly, from days to millennia.
                                                                       LOCAL AND
                                                                      INTERMEDIATE
                                                                       RECHARGE
                                                                 LOCALAND
                                                                  REGIONAL
                                                                 DISCHARGE
                         LOCAL
                       RECHARGE
                                              LOCAL
                                            RECHARGE
           LOCALAND
           REGIONAL
           DISCHARGE
 LOCAL AND
INTERMEDIATE
 RECHARGE
          Figure 2-19 Different scales of ground water flow systems (modified from U.S. Geological Survey, 1999).

        Discharge to Springs

        Springs are focused points of ground water discharge. The locations of springs within a watershed are controlled
        primarily by topography and geology. Springs are the principal type of natural discharge for confined aquifers
        and are also important discharge features in unconfined aquifers. Springs can be divided into  four types: 1)
        depression springs occur where the water table intersects the land surface;  2) contact springs occur along the
        geologic contact between an  aquifer and a confining layer, usually  at the lowest point where  the confining
        layer intersects the land surface; 3) fault springs occur where faulting has brought an aquifer in contact with
        a confining layer; and 4) sinkhole springs occur in karst terrains where natural vertical shafts connect the land
        surface to underlying, confined karst aquifers. In watersheds underlain by consolidated  bedrock, springs often
        occur where preferential flow paths composed of fractures and joints intersect  the land surface. In semi-arid
        regions underlain  by extensive bedrock  formations, regional springs  are critical  for sustaining important
        ecological resources.

        Discharge to Streams

        Ground water discharges to streams via seepage faces above  the channel  and by direct inflow through the
        streambed.  Streams can also lose water to underlying aquifers. Temporal and spatial distribution of ground
        water discharge can vary over the annual hydrograph. Perennial flow in  most streams  is due to base flow
        provided by ground water discharge. In arid areas or areas where aquifer water levels have been significantly
        lowered due to pumping, streams can be disconnected from the underlying aquifer.
2-20

-------
                                                                           2 Key Concepts and Assessment Approaches
An important hydrologic process affecting the chemical and biological conditions within a stream system is
hyporheic flow (Figure 2-20). In streams with coarse bed sediments, there is strong mixing between ground
water and stream water within the bed sediment in response to local head conditions. Within the hyporheic
zone: 1) water in the channel can flow into the coarse bed sediment and back into the channel a short distance
later; 2) ground water discharge can flow upwards through the bed sediment and into the channel; and 3)
water from the open channel can flow downward though the bed sediment and infiltrate into the underlying
aquifer.
                            Interface of local and regional
                              round-water flow systems,
                             hyporheic zone, and stream
                                                                                         Direction of
                                                                                         round-water
                                                                                            flow
 Figure 2-20 Streambeds and banks are unique environments because they are found where ground water
 that drains much of the subsurface of landscapes interacts with surface water that drains much of the surface
 of landscapes (Winter, Harvey, Franke, & Alley, 1998).

Discharge to Wetlands

Wetlands  generally occur where hydrologic and geologic/topographic settings facilitate the  retention of soil
water and/or surface water. Wetlands commonly  occur in topographic depressions and flat lying lowlands.
However, wetlands can also occur on slopes and topographic high points. Sources of water to wetlands include
rainfall, surface water inflow, and ground water discharge. Many wetlands occur where there is  a perennial
ground water discharge. Ground water supports wetlands by either focused discharge at the ground's surface or
discharge from an underlying aquifer.

Discharge to Lakes and Ponds

Ground water discharge to lakes and ponds occurs primarily by preferential or diffuse inflow through the
lakebed sediments in the littoral zone, and less commonly from seepage faces or springs above or below the
water line. In humid, temperate areas there are typically four types of lake-ground water relationships (Younger,
2006): 1)  lakes that receive most inflow from ground water and all outflow is to surface water, 2) lakes that
receive most inflow from surface water and most outflow is to ground water, 3) lakes that receive most inflow
from ground water and all outflow goes back to ground water (through-flow lakes), and 4) lakes that receive
inflow from ground water and surface water and outflow is to ground water.

Ground Water Dependent Ecosystems

Ecosystems and  species that depend on ground water to sustain their ecological structure and function are
termed Ground Water Dependent Ecosystems,  or GDEs  (Murray, Hose, Eamus, & Licari, 2006). GDEs often
harbor high species richness for their overall size, contributing significantly to  the ecological diversity of a
region. GDEs often contain endangered, threatened, or rare plants and animals. In addition, GDEs can act
as  natural  reservoirs, storing water during wet periods and releasing it during dry periods, and can  function as
refugia during periods of environmental stress.  In some circumstances, the flora and fauna of GDEs can help
clean up contaminants and sediments.
                                                                                                        2-21

-------
Identifying and Protecting Healthy Watersheds
        Eamus and Froend (2006) identified six ecosystems that depend on ground water: springs, wetlands,  rivers,
        lakes, phreatophytes, and subterranean systems. These ecosystems can be classified as either obligately ground
        water dependent or facultatively ground water dependent. Obligately ground water dependent ecosystems are
        found only in association with ground water. Facultatively ground water dependent  ecosystems may receive
        some or all of their water supply from ground water, depending on the hydrogeologic setting.

        Springs, including seeps, are ecosystems where ground water discharges at the surface. Thus, they are obligately
        ground water dependent by definition. The water supply of springs comes solely from ground water, and often
        this water has chemical or temperature characteristics that support uncommon communities or species (Sada
        et al.,  2001; Williams & Williams, 1998). With some exceptions (e.g., arid regions), wetlands are generally
        facultative GDEs that, depending on their setting, may rely on ground water to create specific hydroperiods
        or chemical conditions, which govern wetland structure and function (Wheeler, Gowing, Shaw, Mountford,
        & Money, 2004; Mitsch & Gosselink, 2007). Some types of wetlands are obligately ground water dependent,
        such as  fens,  which receive their water supply almost exclusively from ground water (Bedford & Godwin,
        2003). In some ecosystems, such as calcareous fens, the influx of ground water creates unusual water chemistry
        (Almendinger & Leete, 1998).

        In general, rivers, lakes, and areas of phreatophytic plants are facultatively ground water dependent. However,
        perennial rivers and streams are often obligately dependent on ground water to maintain late-season base flow,
        maintain moderate temperature regimes, create certain water chemistry conditions, or produce thermal refugia
        for fish  and  other species during temperature extremes (Power, Brown, & Imhof, 1999). Lakes can receive
        significant inputs of ground water during certain times of the year under specific hydrologic, geologic, and
        topographic conditions (Grimm et al., 2003;  Riera, Magnuson, Kratz, & Webster, 2000; Winter, 1978; Winter,
        1995). Phreatophytic plants have deep roots that can  access water in the capillary fringe, immediately above
        the water table;  if these plants use this deep water  at some  point during the year or the plant life cycle, they
        are considered to be ground water dependent (Zencich & Froend, 2001).  These species have been identified
        in arid climates, and recent work in more humid climates suggests this phenomenon may be more widespread
        than is generally acknowledged (Brooks, Meinzer, Coulombe, & Gregg, 2002).

        Subterranean GDEs consist of aquatic ecosystems that are found in  the free water of caves and karst systems,
        and within aquifers themselves (Gilbert, Danielopol, & Stanford, 1998). Aquifer ecosystems represent the most
        extended array of freshwater ecosystems across the entire planet (Gilbert, 1996). Their fauna largely consists
        of invertebrates and microbes  (Humphreys, 2006). The ecological importance of subterranean  ecosystems has
        only recently emerged in the  scientific literature (Tomlinson & Boulton, 2008;  Goldscheider et al.,  2007;
        Hancock, Boulton, & Humphreys, 2005).

        The type and location of GDEs  depends on the hydrogeologic setting of the ecosystem in the watershed and
        its climate context. The hydrogeologic setting is defined by factors that control the flow of surface water and
        ground  water to ecosystems.  These factors  include: elevation and  slope of the land surface; composition,
        stratigraphy,  and structure of subsurface geological materials in the watershed and  underlying the  GDE;
        and position of the GDE in the landscape (Winter, Labaugh, & Rosenberry, 1988; Komor, 1994; Bedford,
        1999).  Some common locations for GDEs  to occur are landscape depressions,  breaks in slope,  and areas of
        stratigraphic change (Figure 2-21).

        In general, there are three ecological attributes related to ground water that can be important to GDEs:

            1.   Water quantity: This includes timing, location, and duration of ground water discharge. In rivers and
                streams,  ground water provides  the base flow component  of the  hydrograph. In wetlands, ground
                water may partly or fully control the hydroperiod,  or water table fluctuation. Shallow ground water
                can support terrestrial and riparian  vegetation, either permanently or seasonally. Healthy watershed
                assessments  and actions need to consider the  relationship  of ground water quantity to aquatic
                ecosystems.
2-22

-------
                                                                         2 Key Concepts and Assessment Approaches
              Slope break
                              General direction of
                              ground-water (low
                          --- Average water table

                              Forest vegetation

                              Scrub-Shrub vegetation
EXPLANATION
         Jl|/l,\| Emergent vegetation
         II Peat
            I Glacial till
            I (low permeability)

            | Sand and gravel
             (high permeability)
Figure 2-21 Common locations for ground water dependent ecosystems to occur include landscape
depressions, breaks in slope, and  areas of stratigraphic change (modified from U.S. Geological Survey, 1999).

 2.  Water chemistry: When ground water discharges at the surface,  its  chemical composition represents
    a mixture affected by the quality of the recharge water  and the interaction of ground water with the
    geologic materials through  which it  flows. Many ground water fed wetlands  (e.g., calcareous fens)
    have chemical compositions that support a unique suite of flora and fauna. In some settings, ground
    water can be the principal source of dissolved chemicals to a lake, even in cases where ground water is
    a small component of the lake's water budget (Striegl & Michmerhuizen, 1998).
 3-  Water  temperature:  Ground water  emerging at  the  surface  often  maintains a  fairly constant
    temperature year round. This low variability can be important as  ground water dependent species can
    be adapted to these stable conditions. Localized areas of ground water discharge often provide areas of
    thermal refugia for fish in both winter and summer (Hayashi & Rosenberry, 2002). This is particularly
    important for species  such as  salmonids, including bull trout, which  have  specific  temperature
    requirements  for spawning  and egg incubation (U.S. Fish & Wildlife Service, 2002; King County
    Department of Natural Resources, 2000). In some settings, ground water emerges at the surface as hot
    springs, which support a unique set of flora and fauna (Springer, Stevens, Anderson, Parnell, Kreamer,
    & Flora, 2008).
                                                                                                      2-23

-------
Identifying and Protecting Healthy Watersheds
        2.5   Geomorphology
        Fluvial   geomorphology   seeks   to
        explain   river  forms   and   processes
        through an understanding  of landscape
        characteristics,  water  movement,  and
        sediment transport (Leopold, Wolman, &
        Miller, 1964). Watershed inputs (water,
        sediment, and organic matter) and valley
        characteristics  (valley slope and width,
        bedrock and surficial geology, soils, and
        vegetation)  determine  a  river  channel's
        form  (pattern,  profile,  and dimension)
        (Vermont Department of Environmental
        Conservation, 2007)- Although watershed
        inputs and  channel  form vary over time,
        they are often considered to be balanced
        in natural systems. This natural balance is termed "dynamic equilibrium" and is illustrated by Lane's Balance
        (Figure 2-22), where sediment size and volume are in balance with stream slope and discharge. Any time one
        of these variables changes, the other variables will respond to bring the stream back to a dynamic equilibrium.
        Disturbances such as floods or forest fires are natural, episodic events that cause a stream to become unbalanced.
        After such disturbances, the stream will "seek" equilibrium conditions through adjustment of the components
        of Lane's Balance  until  the stream is once again in a form that allows it to efficiently perform its functions
   Sediment Supply
      (Volume)
  Discharge
(Volume/Time)
Figure 2-22 Lane's Balance (1955). Modified from Rpsgen (1996).
Reprinted with permission of American Society of Civil Engineers.
        1
                     Equilibrium Channel
                               Incised due to berming
                               or headcutting
                                    Widening due to
                                    bank failures
                                       Continued
                                       widening &
                                       aggrading
                      . Terrace 2
                                     Stage 1
                                       Terrace 1
            New flood plain
                                   Stage 3
        Figure 2-23 This channel evolution model
        shows the stages of channel adjustment due to
        a disturbance (modified from Schumm, 1977).
    of water and sediment discharge. This form may or may not
    be the same as the pre-disturbance form. There are instances
    where a threshold is crossed, pushing the stream into a new,
    metastable  state  (Hugget, 2011).  Periodic  disturbances,
    of natural  intensity and  frequency, can  increase  aquatic
    biodiversity by creating opportunities for some  species and
    scaling back the prevalence of others.

    As a result of its watershed inputs and valley characteristics,
    a stream will typically have a predictable and characteristic
    form. When watershed inputs or valley characteristics change,
    or when disturbances are of extreme intensity or frequency, as
    many human disturbances are, a stream channel will undergo
    adjustment to a new form. Assessing a stream's watershed
    inputs and valley characteristics  allows the resource manager
    to determine the predicted form of the stream channel. If
    the existing channel does not match  the predicted form, it is
    likely undergoing adjustment  to a new form, which will be
    evidenced by head cuts or channel incision (bed degradation),
    sedimentation or deposition (bed aggradation), or  channel
    widening (Figure 2-23). The channel may also have already
    undergone adjustment and be in a stable new form. Factors
    that may initiate channel adjustment include changes in land
    use/cover (e.g., urbanization  or agriculture), channel  and
    floodplain encroachment (e.g., bank armoring and riverside
    development), and  flow alteration (e.g., dam construction
    or large municipal  withdrawals) (Vermont Department of
    Environmental Conservation,  2007).
2-24

-------
                                                                            2 Key Concepts and Assessment Approaches
Before the publication of Fluvial Processes in  Geomorphology (Leopold, Wolman, & Miller, 1964), the field
was primarily descriptive. The  new quantitative focus drew the interest of engineers, which resulted  in the
development of engineered approaches to  river restoration over the next few decades. David Rosgen's 1996
publication Applied River Morphology is one of the most influential in modern river restoration practice. His
ideas  built off of Luna Leopold's classification and Stanley Schumm's concept of channel evolution. Rosgen
developed  a  classification system for  describing channel form and sequences of adjustment in disturbed
channels. The underlying principles in Rosgen's Applied River Morphology have been used by a number of states
in their own river protection programs. The following are the objectives of the Rosgen  stream classification
system:

    •   Predict a river's behavior from its appearance.
    •   Develop specific hydraulic and sediment relationships  for a given stream type and its
        state.
    •   Provide a mechanism to extrapolate site-specific data to stream reaches having similar
        characteristics.
    •   Provide a consistent frame of reference for communicating stream morphology and
        condition among a variety of disciplines.

This four-level, descriptive classification system is analogous to  the Linnaean classification system in biology, in
which each species receives one Latin name for its genus and one for its species. Level I of the Rosgen system
classifies a channel as one of seven letters (A through G)  based on channel slope, entrenchment, width/depth
ratio, and sinuosity. The width/depth ratio and entrenchment refer to the amount of erosion that has shaped the
stream channel and relate to the stream's power. There are then  six numerical categories based on the dominant
bed material (Rosgen, D.,  1994) (Figure  2-24). An  A3  stream, for  example,  is one in which the dominant
substrate is cobble, the slope  is steep, does not have  much sinuosity (the channel is relatively straight), has a
low width/depth ratio, and is well entrenched. These streams  are typically found in mountainous headwater
areas. Level II classifies stream types to a finer level of detail based on slope ranges. Levels III and IV then assess
   Figure 2-24 Rosgen stream types (Rosgen, D., 1996).
                                                                                                          2-25

-------
Identifying and Protecting Healthy Watersheds
        the  stream's condition and validate the predictions based on field  measurements. The Rosgen classification
        system is a valuable tool for communicating stream characteristics to others. However, it has been criticized for
        focusing too heavily on form without sufficient regard to variation in the processes affecting streams, such as
        flow hydraulics, sediment transport, and bank stability (Simon et al., 2007).

        The mechanisms  by which streams adjust to altered inputs of energy  (stream slope and discharge) and
        materials (sediment size and volume) are just as important as the form of the channel. Quantitative linkages
        between sediment transport (the combination of energy and materials) and the driving  and resisting forces
        (flow hydraulics and bank stability) acting on the stream channel can enhance the understanding of processes
        controlling channel form  (Simon et al., 2007). For example, three streams with the same original morphology
        and similar altered sediment transport scenarios may adjust to different morphologies  because of differences in
        bank materials (e.g., clay vs. silt vs. sand) (Simon et al., 2007).

        2.6   Water Quality

        Aquatic ecosystems  are substantially affected by the quality of their water, but also by the chemical and
        physical characteristics of the air, surrounding watershed soils, and sediment transported through the aquatic
        system. EPA and states have established water quality criteria for freshwater ecosystems that address important
        ecological  constituents.  Chemical  and  physical constituents include:  (1)  concentrations  of organic and
        inorganic constituents, such as nutrients, trace metals, and dissolved organic matter; (2) additional chemical
        parameters indicative of habitat suitability, such as pH and dissolved oxygen; and  (3) physical parameters,
        including water temperature and turbidity. Many of these  constituents are dynamic and related to natural
        watershed hydrology. For example, dissolved oxygen fluctuations in streams are related to watershed nutrient
        loading, biotic activity, stream flow, and temperature. Monitoring methods for  many of these parameters are
        well established and  should be part of an ecosystem assessment and management  approach (MacDonald,
        Smart, & Wissmar, 1991).

        Physical and  chemical  water  quality is strongly influenced  by hydrology, geomorphology, and  landscape
        condition. Forested landscapes cycle nutrients and retain sediments, while riparian forests regulate temperature,
        shading, and  input  of organic matter to headwater  streams (Committee on Hydrologic Impacts of Forest
        Management,  National Research Council,  2008).  Natural quantities of suspended and  bedded  sediments
        (SABS) transport nutrients, detritus, and other organic matter, which are critical to the health of a water body.
        Natural quantities of SABS also replenish sediment bed loads and create valuable microhabitats, such as pools
        and sand bars.

        Material flows, such as the cycling of organic matter and nutrients, are very important ecosystem functions. As
        described in  The River Continuum Concept (Vannote et al., 1980), the flow of energy and materials is closely
        linked by downstream  transport of biomass created by primary productivity  in headwater streams. These
        areas contain  unique assemblages of organisms that begin  the processing of coarse particulate organic matter,
        providing the nutrients required by other assemblages  of organisms downstream.

        Chemical and physical water quality parameters are common in water quality monitoring programs. The
        ecological  information  derived from  chemical/physical monitoring will become  more valuable as  more
        sophisticated  monitoring designs,  sampling  instruments,  modeling tools,  and analytical  procedures  are
        developed. Chemical and physical  assessment  information has  been well integrated  into assessments  of
        biological condition, hydrology, geomorphology, and the importance of vegetative cover.
2-26

-------
                                                                            2 Key Concepts and Assessment Approaches
2.7   Biological Condition

Ecosystem protection efforts are often driven by concerns over biodiversity. Though originally defined simply
as the number of species in a given region, the term biodiversity is now commonly used to refer to the diversity
of life  at all levels (from genes to ecosystems). Biological condition is defined here as the ability to support
and  maintain a balanced, integrated, and adaptive community with a biological diversity, composition, and
functional organization comparable to  those of natural  aquatic ecosystems in the region (Frey, 1977; Karr
& Dudley, 1981;  Karr, Fausch, Angermeier, Yant, & Schlosser, 1986). Thus, biodiversity is one  aspect of
biological condition.

Large river basins that contain a distinct assemblage of aquatic communities and species are referred to as
freshwater ecoregions. Freshwater  ecoregions are a useful  organizational unit for  conducting biodiversity
assessments, as a given ecoregion contains similar species, ecosystem processes, and environmental conditions.
Freshwater ecoregional assessments identify the suite of places that collectively best represent the biodiversity
and  environmental processes of a large river basin.  Efforts to protect "enough of everything"  (The  Nature
Conservancy, 201 la) should consider ecoregional patterns and processes when assessing and prioritizing areas
for ecosystem protection actions.

Biological condition can refer to individual organisms, species, or entire communities. The health of individuals
may provide an indication of future trends affecting an entire  population or supporting ecological  process
(e.g., the spread of a virus in fish populations). Species are a common focus because they may be endangered or
game species, or because they exert an important influence on an ecosystem (e.g., indicator species or keystone
species).  Measures of species health include population size and genetic diversity. The condition of an entire
ecological community depends upon species composition, trophic structure, and habitat extent  and pattern.
A balanced ecological  community, as naturally occurs, reflects good water quality and  a naturally expected
hydrologic regime.  Habitat variables such as substrate  and vegetative cover also impact the biological health
of aquatic ecosystems. Moreover, landscape conditions in  the watershed will affect aquatic habitat through the
dynamic linkage of terrestrial and aquatic elements that defines a watershed. Biology and habitat are intricately
entwined, with habitat structural  elements often composed of biotic components themselves. For example,
certain invertebrate communities live out their lives on the leaves of wetland vegetation. If it were not for the
existence of the wetland vegetation, which has its own habitat requirements, these invertebrate communities
would  likely not exist.

Biological  assessments typically  rely on bioindicators  (U.S.  Environmental Protection Agency, 201 Ib).
Bioindicators are groups of organisms used to assess environmental condition.  Fish, invertebrates, periphyton,
and  macrophytes  can all  be  used as  bioindicators.  Species  within these
groups  are  used to  calculate  metrics,  such as percent  Ephemeroptera,
Plecoptera, Trichoptera (EPT) or an Index of Biotic Integrity (IBI), which
convey important information on the  state of a  water body. Bioindicators
are useful measurements of environmental condition because they integrate
multiple effects  over time. An  assessment of biotic organisms can often
detect  ecosystem degradation  from unmeasured stressors  and unknown
sources of stressors. Many biological assessments rely on  the concept  of
reference conditions to determine the  relative biological health of a given
water body. Reference conditions  are  the expected conditions of aquatic
biological communities in the absence of human disturbance and pollution.
Reference conditions may be modeled or determined through an assessment
of minimally-impacted sites that represent characteristic stream types in a
given ecoregion.  Identifying  reference conditions provides some  of  the
information for the biological condition assessment component of a healthy
watersheds assessment.
                                                                                                          2-27

-------
Identifying and Protecting Healthy Watersheds
        The Biological Condition Gradient (BCG) is a conceptual, scientific model for interpreting biological response
        to increasing levels of stressors. It has been shown to assist with more accurate assessments of aquatic resource
        condition, a primary objective of the CWA  (Davies & Jackson, 2006). The BCG (Figure 2-25) describes six
        different levels of biological condition along  a generalized stressor  gradient ranging from biological conditions
        found at no or low stress  (level 1) to those found at high levels of stress  (level 6). This generalized stressor
        gradient consists of the sum of all aquatic resource stressors, including chemical, hydrologic, and geomorphic
        alterations. Biological  condition can be evaluated through the use of new or  existing biological  assessment
        methods that have  been calibrated  to  the  BCG, such as an IBI, the River Invertebrate Prediction and
        Classification System (RIVPACS), or Threshold Indicator Taxa Analysis (TITAN).

        The BCG  is  characterized by  a description  of how 10 attributes of aquatic ecosystems change in response
        to increasing levels of anthropogenic stress. The attributes  include several aspects of community structure,
        organism condition, ecosystem function, spatial and  temporal attributes of stream  size, and connectivity
        (Davies & Jackson, 2006). A BCG can be used in conjunction with biological assessments to more precisely
        define designated aquatic life uses, establish  biological criteria, and measure the effectiveness of controls and
        management actions aimed at  protecting the aquatic biota (U.S.  Environmental Protection Agency, 201 Ib).
        This approach, often called tiered aquatic life uses, when applied  to water  quality standards (WQS), consists
        of bioassessment-based statements of expected biological condition in specific water bodies and is based on the
        following concepts:

            •   Surface waters and the biological communities they support  are predictably and
                consistently different in different parts of the country (classification along a natural
                gradient, ecological region concept);
            •   Within the same ecological regions,  different types of water bodies  (e.g., headwaters,
                streams, rivers, wetlands) support predictably different  biological communities (water
                body classification);
            •   Within a given class of water bodies, observed biological condition in a specific water
                body is a function  of  the level of stress  (natural and anthropogenic) that the water
                body has experienced (the biological condition gradient);
            •   Similar stressors at similar intensities produce  predictable and consistent biological
                responses in waters  within a class, and those responses can be detected and  quantified
                in terms of deviation from an expected condition (reference condition); and
            •   Water bodies exposed to higher levels of stress will have lower biological performance
                compared to the reference condition than those waters experiencing lower levels of
                stress (the biological condition and stressor gradients).

        The results of biological  assessments based  on the BCG  approach can be used in state healthy  watersheds
        assessments to identify high quality biological condition (e.g., BCG levels I and II)  (Figure 2-26).
2-28

-------
                                                                                  2 Key Concepts and Assessment Approaches
 Levels of Biological Condition

Level 1. Natural structural, functional,
andtaxonomic integrity is preserved.
Level 2. Structure & function similar to
natural community with some additional
taxa & biomass; ecosystem level
functions are fully maintained.

Levels. Evident changes in structure
due to loss of some rare native taxa;
shifts in relative abundance; ecosystem
level functions fully maintained.
Level4. Moderate changes in structure
due to replacement of some sensitive
ubiquitous taxa by more tolerant taxa;
ecosystem functions largely
maintained.
Level 5. Sensitive taxa markedly
diminished; conspicuously unbalanced
distribution of major taxonomic groups,
ecosystem function shows reduced
complexity &redundancy.
Level 6. Extreme changes in structure
and ecosystem function; wholesale
changes in taxonomic composition;
extreme alterations from normal
densities


                                Watershed, habitat,flow regime
                                   and water chemistry as
                                      naturally occurs
Ch emistry, h abitat, an d/or flow
 regime severely altered from
     natural conditions
   Figure 2-25 Conceptual model of the Biological Condition Gradient (U.S. Environmental  Protection
   Agency, 2011c).
                         Allagash
                       Aroostook
                  Reference Sites
                          St John
                  W Br Penobscot
              E & N Br Penobscot
             Upper Androscoggin
                      Upper Saco
                      Lower Saco
                  Penobscot Tribs
                  Upper Kennebec
             Moose R/E-W Outlets
                       Penobscot
                          St Croix
                            Sandy
             Lower Androscoggin
                    Presumpscot
                     Sebasticook
                  Lower Kennebec
                                 100          80          60          40          20          0

                                            Maine Rivers Index of Biotic Integrity (IBI)

             Figure 2-26 Box-and-whisker plots of Maine Index of Biotic Integrity (IBI) scores
             arranged, and color coded, according to the six Biological Condition Gradient
             (BCG) tiers (Chris Yoder, Midwest Biodiversity Institute, Personal Communication).
             The dark blue watersheds can be considered the healthy watersheds.
                                                                                                                   2-29

-------
Identifying and Protecting Healthy Watersheds
        2.8   Watershed Resilience
        A key component of watershed health is the
        ability  to withstand, recover from, or adapt
        to  disturbances,  such as fires,  floods,  and
        droughts.  Healthy  ecosystems  are naturally
        dynamic and  often  depend on  recurrent
        natural disturbances to maintain their health.
        However,  natural  disturbance regimes have
        been severely altered in many watersheds due
        to dam construction, fire suppression, surface
        and ground water withdrawals, and land use
        change  (Figure  2-27).  This  can  increase a
        watershed's vulnerability to future disturbance
        events,  whether  natural  or  anthropogenic.
        Anthropogenic disturbances  may  take years
        to be recognized and can persist for decades
        or   centuries  (Committee  on  Hydrologic
        Impacts  of Forest  Management,  National
        Research Council, 2008).
Figure 2-27 Sprawling development results in significant land
use change, which can alter natural disturbance regimes.
        Broadly speaking, stressors from human activity can be classified into two categories: 1) changes in the natural
        variability of ecological attributes; and 2)  introduction of pollutants or species that interfere with ecological
        processes (Center for Watershed Protection, 2008c). The former  can include urbanization impacts on the
        magnitude and frequency of stormwater runoff events, habitat conversion and fragmentation, climate change,
        and over-harvesting. If perturbations  are large enough to reach a  threshold, ecosystems can change rapidly
        to a new state (e.g., fishery collapse),  and  these changes are typically difficult to reverse  (Noss, LaRoe III, &
        Scott, 1995). Pollutants that disrupt  ecosystem  function can be physical (e.g., sediment from construction
        sites) or chemical (e.g., pesticides). Salt Cedar, an example of a  biological stressor, is an invasive tree that has
        spread throughout the western United States and uses long taproots to take advantage of deep water tables. Its
        invasion not only disrupts the native vegetative community, but also disrupts the natural hydrology of the area,
        affecting aquatic habitat as well.

        The impact  of climate change and other stressors on different  ecosystems  and regions of the United  States
        depends on  the vulnerability of those systems and their ability to  adapt to the changes imposed on  them.
        As temperature  and precipitation  regimes change, so too will the ecological processes that are driven  by
        these regimes.  These processes are assumed to have a natural range of variability that may be exceeded when
        disturbances, changes, and shocks occur to  a system. In such cases, the system may still recover because its
        adaptive capacity has not been exceeded, or it  could pass a threshold and change  into another ecosystem
        state. Although some ecosystems can rely on their size for resistance to climate change, other ecosystems will
        need to rely on resilient processes. Resistance is distinguished  from resilience in that  resistant systems  persist
        and remain  relatively stable when  faced with  stresses, whereas  resilient systems are affected by  stresses, but
        are able to recover from the impacts of stress and adapt  to new conditions. Increasing a system's  resilience to
        pressures includes ensuring that watersheds have adaptive attributes such as meander  belts, riparian wetlands,
        floodplains,  terraces, and material contribution areas. For example,  a disturbance may lead to changes  in the
        timing,  volume, or  duration of flow  that are  outside the natural range of variability. In a  healthy, resilient
        watershed, these perturbations would not cause a permanent change because riparian areas and floodplains
        would help  to absorb some of the disturbance.  Managing to optimize resilience includes both minimizing
        threats and protecting the most essential or sensitive areas.
2-30

-------
                                                                             2 Key Concepts and Assessment Approaches
An example of managing for resilience is the Massachusetts Division of Fisheries and Wildlife's process for
identifying and prioritizing land protection and stewardship actions needed for long-term conservation of the
state's biodiversity, and for climate adaptation (Massachusetts Department of Fish & Game and The Nature
Conservancy, 2010):

    1.  Prioritize habitats, natural communities, and ecosystems of sufficient size. Larger
        ecosystems are more likely to provide the tracts of intact habitat and functioning
        ecosystem processes  needed to support larger numbers of organisms and a broader
        diversity of native  species. Climate refugia,  which organisms can use  to endure
        extreme conditions, are likely to be more prevalent in larger ecosystems than they are
        in smaller ecosystems as well.
    2.  Select habitats, natural  communities,  and ecosystems that support ecological
        processes. Healthy functioning of ecological processes  allows an ecosystem to persist
        through conditions of environmental stress or adapt to the  stresses imposed  on it.
        Natural flow regime is an ecological process that is particularly  important to healthy
        watersheds. Ecosystems that have the least potential to be disturbed by anthropogenic
        influences often have the greatest potential to maintain functioning processes in the
        long term and are thus  most likely to have the resilience needed to recover  from
        climate change impacts.
    3.  Build connectivity  into habitats and ecosystems. Connectivity is a conservation
        priority for  the same reason that large  ecosystems are a conservation priority:  it
        maximizes  the accessibility of resources populations  can  use to survive periods
        of environmental  stress.  Many species  representing  diverse classes  of organisms,
        including amphibians, aquatic insects, and anadramous and catadramous fish require
        multiple habitat types to carry out their life  cycles. In addition to connectivity to
        other habitat sources, wildlife populations need connectivity  to other populations of
        their own species in  order to maintain levels of genetic diversity sufficient to sustain
        viable populations.
    4.  Represent a diversity of species, natural communities, ecosystems, and ecological
        settings. Conserving a representative set of species  and habitats creates a diversified
        "savings bank" of physical and genetic resources that  provides the greatest chances
        for successful ecosystem adaptation and recovery. In addition, protecting a variety of
        habitat conditions provides a coarse filter for  protecting the  diversity of biota  these
        conditions support.
                                                                                                          2-31

-------
Identifying and Protecting Healthy Watersheds
2-32

-------
3.   Examples of Assessment
       Approaches
                         Introduction
                         This chapter introduces the Healthy Watersheds Initiative, discusses the
                         characteristics of a healthy watershed, and reviews the benefits of protecting
                         healthy watersheds. This chapter also describes the purpose, target audience, and
                         intended use of this document.
                         Overview of Key Concepts
                 m.
                         This chapter describes the healthy watersheds conceptual framework. It then
                         discusses, in detail, each of the six assessment components - landscape condition,
                         habitat, hydrology, geomorphology, water quality, and biological condition.
                         A sound understanding of these concepts is necessary for the appropriate
                         application of the methods described in later chapters. This chapter concludes
                         with a discussion of watershed resilience.
                         Examples of Assessment Approaches
                         This chapter summarizes a range of assessment approaches currently being used
                         to assess the health of watersheds. This is not meant to be an exhaustive list of all
                         possible approaches, nor is this a critical review of the approaches included. These
                         are provided solely as examples of different assessment methods that can be used
                         as part of a healthy watersheds integrated assessment. Discussions of how the
                         assessments were applied  are provided for some approaches. Table 3-1 lists all of
                         the assessment approaches included in this chapter.
                         Healthy Watersheds Integrated Assessments
This chapter presents two examples for conducting screening level healthy
watersheds integrated assessments. The first example relies on the results of a
national assessment. The second example demonstrates a methodology using
state-specific data for Vermont. This chapter also includes examples of state
efforts to move towards integrated assessments.
                         Management Approaches
                         This chapter includes examples of state healthy watersheds programs and
                         summarizes a variety of management approaches for protecting healthy
                         watersheds at different geographic scales. The chapter also includes a brief
                         discussion of restoration strategies, with focus on targeting restoration towards
                         degraded systems that have high ecological capacity for recovery. The results of
                         healthy watersheds integrated assessments can be used to guide decisions on
                         protection strategies and inform priorities for restoration.
                                                                                            3-1

-------
Identifying and Protecting Healthy Watersheds
         Table 3-1 List of assessment approach summaries and case studies included in Chapter 3.
          Landscape Condition
            Maryland Green Infrastructure Assessment
              Cose Study: Anne Arundel County Greenways Master Plan
            Virginia Natural Landscape Assessment
              Cose Study: Green Infrastructure in Hampton Roads
            Beaver Creek Green Infrastructure Plan
            The Active River Area
            Interagency Fire Regime Condition Class
 3-4
 3-7
 3-8
3-10
3-11
3-13
3-16
            Ohio's Primary Headwaters Habitat Assessment                                                                   3-20
            A Physical Habitat Index for Freshwater Wadeable Streams in Maryland                                              3-21
            Proper Functioning Condition                                                                                  3-22
            Rapid Stream-Riparian Assessment                                                                             3-24
            Ohio Rapid Assessment Method                                                                                3-26
            California Rapid Assessment Method                                                                            3-28
            Wyoming Wetland Complex Inventory and Assessment                                                            3-30
          Hydrology
            Ecological Limits of Hydrologic Alteration                                                                        3-34
              Cose Study: A Regional Scale Habitat Suitability Model to Assess the Effects of Flow Reduction on Fish Assemblages in      3-37
              Michigan Streams
            Texas Instream Flow Assessments                                                                               3-39
              Cose Study: San Antonio River Basin                                                                           3-41
            Hydrogeomorphic Classification of Washington State Rivers                                                        3-43
            Ground Water Dependent Ecosystems Assessment                                                                3-45
              Cose Study: Identifying GDEs and Characterizing their Ground Water Resources in the Whychus Creek Watershed         3-49
          Geomorphology
            Vermont's Stream Geomorphic and Reach Habitat Assessment Protocols                                             3-52
              Cose Study: Geomorphic Assessment and River Corridor Planning of the Batten Kill Main-Stem and Major Tributaries      3-55
          Water Quality
            Oregon Water Quality Index                                                                                    3-57
          Biological Condition
            Index of Biotic Integrity                                                                                        3-59
              Cose Study: Ohio Statewide Biological and Water Quality Monitoring and Assessment                                 3-61
            The Biological Condition Gradient and Tiered Aquatic Life Uses                                                     3-62
              Cose Study: Maine Tiered Aquatic Life Use Implementation                                                        3-64
            Aquatic Gap Analysis Program                                                                                  3-65
              Cose Study: Ohio Aquatic GAP Analysis: An Assessment of the Biodiversity and Conservation Status of Native Aquatic      3-68
              Animal Species
            Natural Heritage Program Biodiversity Assessments                                                               3-69
              Cose Study: Oregon Natural Heritage Information Center                                                         3-71
            Virginia Interactive Stream Assessment Resource and Healthy Waters Program                                        3-72
          National Aquatic Resource Assessments
            National Rivers and Streams Assessment                                                                         3-75
              Cose Study: Oklahoma National Rivers and Streams Assessment                                                   3-77
            National Lakes Assessment                                                                                    3-78
              Cose Study: Minnesota National Lakes Assessment                                                               3-80
            Regional and National Monitoring and Assessments of Streams and Rivers                                           3-81
3-2

-------
                                                                                            3 Examples of Assessment Approaches
3.1  Landscape Condition

This section provides summaries for some examples of approaches currently being  used to  assess landscape
conditions. See Chapter 2 for background information on landscape condition.
                         Landscape Condition
            Patterns of natural land cover, natural disturbance regimes,
               lateral and longitudinal connectivity of the aquatic
              environment, and continuity of landscape processes.
                               Habitat
             Aquatic, wetland, riparian, floodplain, lake, and shoreline
                      habitat. Hydrologic connectivity.
                             Hydrology
             Hydrologic regime: Quantity and timing of flow or water
             level fluctuation. Highly dependent on the natural flow
            (disturbance) regime and hydrologic connectivity, including
                     surface-ground water interactions.
            Geomorphology
Stream channels with natural geomorphic dynamics.
             Water Quality
  Chemical and physical characteristics of water.
           Biological Condition
   Biological community diversity, composition,
 relative abundance, trophic structure, condition,
           and sensitive species.
                             Large patches of natural
                                vegetative land
                                   cover stabilize
                                    soil, regulate
                                     watershed
                                       hydrology, and
                                       provide habitat
                                       for terrestrial
                                       and aquatic
                                       species.
                                   Photo: BLM.
               Ecosystems in some
                  parts of the country
               ^  require a natural
                      fire regime to
                       help maintain
                        habitat,
                         biodiversity,
                         and nutrient
                         cycling
                         properties.
                                                                                               Photo: BLM.
                              Wetlands provide
                                 important fish and
                                   wildlife habitat,
                                     improve water
                                      quality, and
                                       help regulate
                                       water levels
                                       within
                                       watersheds.
                                   Photo: Jane Hawkey, IAN.
                Natural land cover
                  within the Active
                     River Area
                       maintains
                       connectivity
                        between
                        terrestrial
                        and aquatic
                        elements of
                        the landscape.
                                                                                               Photo: USFWS.
                                                                                                                          3-3

-------
Identifying and Protecting Healthy Watersheds
          Maryland Green Infrastructure Assessment
          Author or Lead Agency: Maryland Department of Natural Resources (DNR)
          More Information: http://www.greenprint.maryland.gov/

        The Maryland Green Infrastructure Assessment is a proactive approach  to  addressing the state's  growing
        forest fragmentation, habitat degradation, and water quality problems. By determining those  areas that are
        most critical to protecting the ecological integrity of Maryland's natural resources, the conservation programs
        operating through the Maryland  Department of Natural Resources (Program Open Space and the Rural
        Legacy Program) can strategically and defensibly pursue the acquisition and easement of lands that are among
        the  most ecologically valuable in the state.  In addition, this assessment, joined with other natural  resource
        assessments, now forms the foundation for the Governor's GreenPrint initiative in Maryland. As part of the
        GreenPrint initiative, an interactive mapping tool was developed to identify high priority conservation lands,
        provide performance measures to track the success of state land conservation programs, and facilitate united
        and integrated land conservation strategies among all conservation partners in Maryland. As part of its Coastal
        Atlas program, Maryland DNR is also mapping the state's "blue infrastructure." The state's blue infrastructure
        is defined as the critical near-shore habitat that serves as a link between the aquatic and terrestrial environments
        of Maryland's coast. By combining the green infrastructure assessment with  the blue infrastructure assessment,
        a "complete ecological network" is being identified to prioritize lands for acquisition that protect both terrestrial
        and aquatic resources.

        Conservation of habitats and multiple species is a more cost-effective and  less reactive  approach than single
        species  management and  engineering-based  solutions  to  ecosystem  degradation (Jennings,  2000).  This
        proactive approach has shown significant success  in Maryland in recent years. In addition, surveys have shown
        that the majority of Maryland's citizens support public land conservation programs. Preservation of open space
        is considered a worthwhile expenditure of public funds by most residents. Several land conservation programs
        exist in Maryland; however, only 26% of the state's green infrastructure was protected in 2000. Many of the
        larger tracts of land are becoming more fragmented over time. By protecting the remaining tracts of contiguous
        land, or hubs, and connecting them with natural corridors, many of the same benefits of larger conservation
        areas can be realized, including maintenance of natural watershed hydrology and thermal regimes.

        Based  on the principles of landscape ecology and conservation biology, Maryland's  Green  Infrastructure
        Assessment tool uses GIS to identify the ecologically important hubs and  connecting corridors in the state.
        Hubs are defined by Maryland DNR as:

            •    Large blocks  of contiguous  interior forest containing at least 250 acres, plus  a
                transition zone of 300 feet.
            •    Large wetland complexes, with at least 250 acres of unmodified wetlands.
            •    Important animal and plant habitats of at least 100 acres, including rare, threatened,
                and endangered species locations; unique ecological communities; and  migratory
                bird habitats.
            •    Relatively pristine stream and river segments (which, when  considered with adjacent
                forests and wetlands, are at least 100  acres in size) that support trout, mussels, and
                other sensitive aquatic organisms.
            •    Existing protected natural resource lands that contain one or more of the  above; for
                example,  state parks and forests, National Wildlife Refuges, locally owned reservoir
                properties, major stream valley parks, and Nature Conservancy preserves.

        The corridors  connecting these  hubs are typically streams with wide riparian forest buffers,  ridge  lines, or
        forested valleys. They are  at least  1,100 feet wide, which allows for the dispersal of organisms that require
        interior cover. These areas were identified in Maryland  using a GIS technique called "least cost path." With
        this technique, each landscape element is assigned  different values ("costs") based on its ability  to provide for
        movement of wildlife. For example, a road is assigned a value reflective of a "high cost" for wildlife movement,
3-4

-------
                                                                                         3 Examples of Assessment Approaches
while a forested area is assigned a "low cost" value. The algorithm then determines the least cost path from one
hub to another.
Hubs and corridors in Maryland were given ecological scores based on their relative importance in the overall
green infrastructure network (Table  3-2). Each hub or corridor's ecological score was  evaluated alongside an
assessment of development risk to rank and prioritize lands for protection actions.  The lands outside of the
network (developed,  agricultural, mined, or cleared lands) were also evaluated for their restoration potential
by considering watershed condition,  landscape  position,  local  features,  ownership,  and programmatic
considerations.
Table 3-2 Parameters and weights used  to rank overall ecological significance of each  hub within its
physiographic region (Weber, 2003).
                                   Parameter
 Heritage and Maryland's Biological Stream Survey element occurrence (occurrences of rare,
 threatened and endangered plants and animals; rated according to their global or range-
 wide rarity status; state-specific rarity status; and population size, quality, or viability)
 Area of Delmarva fox squirrel habitat
 Fraction in mature and natural vegetation communities
 Area of Natural Heritage Areas
 Mean fish IBI score
 Mean benthic invertebrate IBI score
 Presence of brook trout
 Anadromous fish index
 Proportion of interior natural area in hub
 Area of upland interior forest
 Area of wetland interior forest
 Area of other unmodified wetlands
 Length of streams within interior forest
 Number of stream sources and junctions
 Number of GAP vegetation types
 Topographic relief (standard deviation of elevation)
 Number of wetland types
 Number of soil types
 Number of physiographic regions in hub
 Area of highly erodible soils
 Remoteness from major roads
 Area of proximity zone outside hub
 Nearest neighboring hub distance
 Patch shape
 Surrounding buffer suitability
 Interior forest within 10 km of hub periphery
 Marsh within 10 km  of hub periphery
Weight
   12

   3
   6
   6
   1
   1
   2
   1
   6
   3
   3
   2
   4
   1
   3
   1
   2
   1
   1
   2
   2
   2
   2
   1
   1
   1
   1
                                                                                                                     3-5

-------
Identifying and Protecting Healthy Watersheds
        Maryland's Program Open Space,  operating  since  1969, funds land conservation through the real estate
        transfer tax. Since the completion of the green infrastructure assessment, Program Open Space and other land
        conservation  efforts have continued to refine  targeting and acquisition/easement approaches for conserving
        and protecting the most ecologically significant lands in the  state. In addition to mapping out the highest
        priorities, a GIS-based parcel evaluation scores the potential project based on the property's importance in the
        green infrastructure network and on other natural resource values. These assessments are validated through field
        visits before additional decisions are made. As the project is prepared for approval, a conservation scorecard,
        documenting conservation  values, is presented to the Board of Public Works (consisting of the Governor,  the
        Treasurer, and the Comptroller) to justify the expenditure of state funds on protection efforts.  In addition to
        Program Open Space and the Rural Legacy Program, the Maryland Environmental Trust and the Maryland
        Agricultural Land Preservation Foundation form  an  "implementation  quilt"  of state land conservation
        programs that  bring  together  different resources to implement the protection  strategies identified by  the
        green infrastructure assessment. The GreenPrint  initiative provides transparency  and accountability through
        performance measures, and clearly identifies and maps land conservation goals that bolster the integration and
        effectiveness of Maryland's  conservation programs. The results of the green infrastructure assessment (Figure
        3-1) are being used by other counties and municipalities in their  local land use planning efforts as well. Private
        land  trusts  are using  the results to help  prioritize their land  acquisition strategies.  Private citizens  can  also
        use the online  mapping tool to see the ecological value of the  land they  own and make  wise decisions for
        future use of their land. Since 1999, 88,000 acres have been protected in Maryland through the use of green
        infrastructure assessment information.
                                            I Kilometers
                 0   20   40   60  80  100
         Figure 3-1 Green infrastructure in Maryland (Maryland Department of Natural Resources, 2011).
3-6

-------
Case   Study
 Anne Arundel  County Greenways Master
 Plan
 More Information: Anne Arundel County, 2002 (http://www.aacounty.org/PlanZone/MasterPlans/
 Greenways/Index.cfm)
 Anne Arundel County was the first county in the State
 of Maryland to base its Greenways Plan on the results
 of the Maryland green infrastructure assessment. The
 Plan won an award from the Maryland chapter of the
 American Planning Association in 2003- Greenways
 are  typically focused  on recreational  and scenic
 opportunities as priorities.  Anne Arundel  County,
 in its Greenways Plan, takes an ecological approach
 to identifying  its  potential greenways,  using the
 following criteria:
    1.   Habitat value.
    2.   Size.
    3-   Connections   to   other  land  with
        ecological value.
    4.   Future potential.
    5.   National and countywide trails.

 The county used  habitat requirements of indicator
 species (downy woodpecker, bobcat, and red-spotted
 newt) to identify the "best" lands for inclusion in the
 greenways system. These species were chosen because
 their  habitat requirements  are general enough to
 provide protection to most other species as well. Using
 the five criteria for identifying potential greenways,
 a network of hubs and corridors was designed. This
 network  closely  reflects the  green  infrastructure
 assessment  network  (Figure  3-2).  One  of the
 advantages of the Anne Arundel County Greenways
 Plan is  that it makes explicit the  added benefit of
 low impact  recreational and scenic use to the general
 public, which can greatly increase public support of
 the plan. In addition, it protects and improves water
 quality and wildlife habitat.
I   | Green Infrastructure
t=l Proposed Greenways
Figure 3-2 Comparison of proposed greenways and
green infrastructure in Anne Arundel County, MD
(modified from Anne Arundel County, 2002).
                                                                                           3-7

-------
Identifying and Protecting Healthy Watersheds
          Virginia Natural Landscape Assessment
          Author or Lead Agency: Virginia Department of Conservation and Recreation (DCR) - Division of Natural Heritage
          More Information: http://www.dcr.virginia.gov/natural heritage/vclnavnla.shtml

        The Virginia Conservation Lands  Needs Assessment (VCLNA)  is a  flexible  GIS tool for integrated  and
        coordinated modeling and mapping of land conservation priorities and actions in Virginia. The VCLNA is
        currently composed of seven separate, but interrelated models: 1)  Natural Landscape Assessment Model, 2)
        Cultural Model, 3) Vulnerability Assessment Model, 4)  Forest Economics Model, 5) Agricultural Model, 6)
        Recreation Model, and 7) Watershed Integrity Model. Together, these models are used to identify and assess the
        condition of Virginia's green infrastructure.  The Natural Landscape Assessment Model  is described here.  The
        Watershed Integrity Model is described in Chapter 4. All VCLNA models, along with Virginia's Conservation
        Lands and a variety of reference layers, can be viewed on an interactive  mapping site called the Virginia Land
        Conservation Data Explorer at www.vaconservedlands.org.

        The VCLNA Natural Landscape Assessment Model is  a geospatial inventory of the  remaining patches of
        natural land and the links between those patches throughout Virginia. Large patches  are those with interior
        cover of at least 100 acres, while small patches are identified as areas containing between 10 and 99 acres of
        interior cover. Interior cover, also known as the core area, is defined as  the natural land cover beginning  100
        meters inside of a habitat patch. As large patches of core area tend to  have  a greater variety of habitats  and
        increased protection from adjacent disturbances, biodiversity in these areas typically doubles for every 10-fold
        increase in habitat size. In addition, certain species require large areas deep within interior habitat patches to
        carry out their life histories. Large patches of natural land cover also prevent erosion, filter nutrients and other
        pollutants in runoff, provide pollinators for crops, and  sequester carbon in  their biomass. Fewer and fewer
        large patches of natural vegetation remain in Virginia, as fragmentation resulting from roads and suburban
        development continues to spread at an advancing rate. As more habitat is fragmented, the interior area to edge
        perimeter ratio decreases  to such an extent that, while there continue to be patches of vegetation  scattered
        across the landscape, there will be virtually no interior cover remaining for species that require this  core area to
        survive and reproduce.

        Although conservation of larger natural  areas  is typically an effective strategy for preserving biodiversity and
        ecological integrity, patchwork patterns of human development make it  necessary to conserve many modestly-
        sized natural areas. By connecting  these smaller areas  with  corridors of natural vegetation, the  levels of
        biodiversity maintained in large conservation  areas can be approached. However, these corridors  should  also
        contain nodes,  or smaller habitat patches interspersed along these  links that facilitate dispersal of organisms
        between ecological cores. Through the evaluation  of ecologically significant attributes (such as species diversity,
        presence of rare habitats, and water quality benefits), a prioritization scheme was developed by Natural Heritage
        biologists for use in selecting those lands most critical for maintaining ecological integrity across the landscape
        of the Commonwealth of Virginia.  One of five scores was given to each ecological core area, and corridors
        between patches receiving the two highest rankings were designated using a  GIS  technique called "least  cost
        path." This technique employs a variety of user defined attributes for determining the easiest routes for wildlife
        to migrate between the ecological core areas. Wherever possible, lower-ranked ecological core areas were used
        as nodes in the corridors connecting the larger ecological  cores.

        The landscape assessment  results are provided in GIS data, hard copy, and digital maps (Figure 3-3), which can
        be explored with an online interactive  tool called Land Conservation Data Explorer (Virginia Department of
        Conservation and Recreation, 2009).
3-8

-------
                                                                                  3 Examples of Assessment Approaches
The results  of the Natural Landscape Assessment  provide  guidance on lands to prioritize for conservation
actions in Virginia. A number of municipalities, counties, land trusts, and other organizations are using the
methods and  results from the Virginia Natural Landscape Assessment. Ranked cores and corridors are used
by  the Virginia Land Conservation  Foundation and various conservation organizations (e.g., land trusts)
throughout  the commonwealth to help assure that conservation efforts are concentrated on the areas with high
ecological integrity. Furthermore, the cores are  an essential component of the State Wildlife Action Plan. The
Virginia Natural Landscape Assessment identifies and ranks ecological integrity statewide, while also providing
a tool that can be used to better inform local conservation planning efforts.

Cores and Habitat FngmtMs by
Ecological Integrity
04 C1: Outstanding
O4 C2: Very High
03 High
04 C4' Moderate
04 C5: General
LEGEND
Other VaNLA Features
^^^^ Landscape Corridor
: • Corridor Node
*^^P Natural Landscape Block



Reference Features
f ' „ Locality Boundary
^\^s Interstate Highway
Primary Road
C~^) Open Water
(^^) Land Without VaNLA Features
 Figure 3-3 Map of results from the Virginia Natural Landscape Assessment Model (Virginia Department of
 Conservation and Recreation, 2008).
                                                                                                            3-9

-------
                                                Case   Study
                    Green Infrastructure in  Hampton  Roads
                    More Information: Kidd, McFarlane, & Walberg, 2010 (http://www.hrpdc.org/PEP/PEP
                    Green InfraPlan2010.asp)
       The Hampton Roads Green Infrastructure Plan was
       undertaken to expand upon the Southern Watershed
       Area Management  Program Conservation Corridor
       System previously  developed  as  a  collaborative
       state, federal, and local effort. The corridor  system
       identified  in  that study was contained to southern
       Chesapeake   and Virginia Beach,  Virginia.  The
       Hampton Roads Green Infrastructure Plan identifies
       green infrastructure throughout the entire Hampton
       Roads region (Figure 3-4). With  conservation and
       restoration of water quality as a primary goal, the
       technical development and stakeholder involvement
       process focused  on riparian areas  as they provide
       multiple benefits including water quality protection,
       wildlife habitat, and flood storage.

       The Hampton Roads green infrastructure model uses
       the output layer from the VCLNA project to identify
       ecological  cores. It also uses  wetlands,  land cover,
       and a riparian  corridor layer  developed specifically
for the project. Each of these four layers was ranked
and prioritized by stakeholders for use in a weighted
overlay analysis in GIS. Given the riparian focus, the
links between ecological cores  were  mostly found
along streams and rivers.

The   green   infrastructure  network   is   being
implemented through several parallel efforts including
provision of GIS data  to Hampton Roads localities
for  use  in comprehensive  plan updates  and other
planning efforts, working with  the Department of
Defense  to include the regional network in efforts to
buffer military facilities from encroachment, and use
of the network as a basis for obtaining grant funding
to purchase lands based on habitat value.  Efforts are
also underway to improve the integration of the green
infrastructure network with the implementation of
wetlands mitigation and stormwater and water quality
regulatory programs.
                         Hampton Roads
                     Green Infrastructure Network

                      ££ High Value-Water Quality

                      Q^l Higli Value-Habitat Protection

                      AA Higli Value-Both

                                                               ••"
                                                                          \

            Figure 3-4 Green infrastructure in the Hampton Roads region (Kidd, McFarlane, & Walberg, 2010).
3-10

-------
                                                                                3 Examples of Assessment Approaches
   Beaver Creek Green Infrastructure Plan
   Author or Lead Agency: Tracy Moir-McClean and Mark DeKay of University of Tennessee's College of Architecture
    and Design
   More Information: http://ww2.tdot.state.tn.us/sr475/library/bcgitdot.pdf

The Beaver Creek Green Infrastructure Plan was created in 2006 to protect and restore naturally functioning
ecosystems in  the Beaver Creek watershed along the northern  border of Knox County, TN for the purposes
of improving water quality, mitigating floods, protecting wildlife habitat, and connecting communities and
neighborhoods. The underlying perspective of the plan is "the idea that the form of settlement grows out of
an understanding of landscape context, both ecological and social." The three primary elements of the plan are
the water network, open space network,  and settlement network. Analyzing these networks and basing land
use decisions around them can help to create a sustainable and livable community.

A Land Stewardship Network was identified based on a composite of four assessments identifying: 1) stream
protection corridors,  2)  ground water protection  corridors, 3)  ridge protection corridors, and 4) heritage
protection corridors. This network represents the most ecologically and culturally valuable conservation land
in the watershed, forming a framework around which to base  development and protection strategies. Three-
zone buffers were created around each of the four corridor types.  The innermost zone is a protection zone,
followed by a conservation zone, and a stewardship zone at the interface with surrounding developed land uses
(Figure 3-5).

As a result of development patterns in the Beaver Creek watershed, water quality has degraded and flooding
has become severe. The full length of Beaver Creek is included on Tennessee's list  of impaired waters and the
floodplain has expanded as a result of the increased runoff from growing impervious areas in the  watershed.
The stream and ground water protection corridors  in the Green Infrastructure Plan address  these issues by
protecting and restoring vegetated riparian areas, which slow runoff and filter pollutants,  and by protecting
wetlands and sinkholes that help to maintain the watershed's natural hydrology. Stream and ground water
protection corridors were created by buffering first and second order streams, wetlands, and sinkholes with
100 foot protection zones. Third order streams were buffered with a 125 foot protection zone and springs were
given a 500 foot radius protection zone. In order to create a continuous network of protected waters, features
adjacent to streams and  chains of related features were all linked to the zone 1  protected stream network.
The boundaries of the zone 2 conservation network were extended 75 feet for streams with defined Federal
Emergency Management Agency  (FEMA) floodways and 50 feet for smaller streams. This  distance is in
addition to the first zone buffer distances and is extended to the edges of the FEMA floodplain when present.
A 50 foot conservation buffer was added to sinkholes and wetlands and 450 feet was added to the uphill sides
of springs. The final zone 3 buffer adds an additional 25 feet to the network.

Ridge protection corridors were created  by identifying all  land with slopes greater than 25% plus adjacent
forested areas with slopes greater than 15%. Heritage protection corridors were identified as areas with prime
or good farmland, remaining forests,  prime grassland habitat,  and riparian habitat areas. Ground water and
stream protection corridors were  identified  and linked with the ridge  and  heritage  protection corridors.
The composite of the ground water, stream,  ridge, and  heritage protection corridors provides the final land
stewardship network.

Parcels that intersect  the land stewardship  network were  identified for  consideration in conservation and
development decisions such as conservation easements and proposed town, village, and neighborhood centers.
A proposed future settlement pattern was created to guide land  use planning decisions in the coming years.
This involves a density gradient of neighborhood types that allows for the most ecologically important areas to
be protected while allowing other areas to be developed at reasonable and desirable densities.
                                                                                                         3-11

-------
Identifying and Protecting Healthy Watersheds
        Green infrastructure plans, such as  the one developed for Beaver Creek, can help communities to plan for
        smart growth and sustainable development that preserves the socially and ecologically valuable lands that will
        provide recreational, aesthetic, and ecosystem services to future generations. This kind of planning is necessary
        for maintaining healthy watersheds while  allowing  for the economic  growth that is  necessary to support
        growing populations.
                                FLOODWAY
                                                     ZONE1
                                                                     ZONE 2
                                                                              ZONE 3
                               STEWARDSHIP
                                  ATTITUDES
                                   CLIMAX of
                                     NATIVE
                                 VEGETATION
PROTECT, STABILIZE
       and
  SHADE STREAM
CONSERVE
   and
 RESTORE
ENCOURAGE
LANDOWNER
CONSERVATION
                                                                              ADJACENT LAND-USE

                         Figure 3-5 Three-zone buffer showing the protection, conservation, and
                         stewardship zones (Moir-McClean & DeKay, 2006).
3-12

-------
                                                                                 3 Examples of Assessment Approaches
  The Active River Area
  Author or Lead Agency: The Nature Conservancy
  More Information: http://conserveonline.org/workspaces/freshwaterbooks/documents/
    active-river-area-a-conservation-framework-for/view.html

The Nature Conservancy's Active River Area  approach is  a framework for protecting rivers and  streams.
The health of a stream or river depends on a variety of physical and ecological processes that operate within
the dynamic environment of the water/land interface. This environment has been termed the "Active River
Area" and is  formed and  maintained by disturbance events and regular variations in flow. The Active River
Area includes the river channel itself, as well as the riparian lands necessary for the physical and ecological
functioning of the river system. The approach complements other programs that seek to protect natural
hydrologic regimes, maintain connectivity, improve water quality, eradicate invasive species,  and maintain
riparian lands in natural cover.

The proper functioning  of rivers and riparian areas depends on  the  dynamic  ecological  interactions  and
disturbance events that characterize natural flowing water systems. The Active River Area focuses on five key
processes: hydrology and fluvial action, sediment transport, energy flows, debris flows, and biotic  actions and
interactions. The approach identifies the places  where these processes occur based on valley setting, watershed
position, and geomorphic stream type. The five  primary components of the Active River Area are:

    1.   Material contribution areas.
    2.   Meander belts.
    3.   Floodplains.
    4.   Terraces.
    5.   Riparian wetlands.

Material contribution areas are small headwater catchments  in the uppermost reaches  of the watershed, as
well as upland areas immediately adjacent to streams and rivers that are not floodplain, terrace, or riparian
wetlands. Material contribution areas provide food and  energy (e.g., falling leaves) to aquatic organisms  that
is then transported downstream through  ecological processes. Meander belts are  the most active  part of the
Active River Area and are defined as the area within which the river channel will migrate, or meander,  over
time. The meander belt width is the cross-channel distance that spans the outside-most edges of existing or
potential meanders and can be easily measured and mapped for both healthy and altered rivers,  providing a
basis for  management decisions (e.g., implementation of no-build zones). Floodplains are expansive, low-slope
areas with deep sediment deposits. Low floodplains are immediately adjacent to  the stream channel and are
typically flooded annually, while high floodplains are at somewhat higher elevations and flooded every one to
10 years  on average. Terraces are former floodplains that may be flooded and provide storage capacity during
very large events (e.g., the 100-year flood). Riparian wetlands are areas with hydric soils  that support wetland
plant species.  Riparian wetland soils  are flooded by the adjacent river water and/or high ground water levels.
These areas support a high biodiversity with a variety of aquatic and terrestrial habitat types.

The physical and ecological  processes  occurring in each  of these five  areas  differ depending on watershed
position  (Figure 3-6). The Active River Area framework uses Schumm's (1977) system of classifying watershed
position  to organize the five Active River Area components into upper-watershed, mid-watershed, and low-
watershed zones. This system of organization helps to understand the Active River Area in the context of the
landscape of which it is a part. The mosaic of habitat patches formed by the dynamic interactions in the Active
River Area could be considered landscape  elements, with the river corridor itself serving  as a link between the
elements.

The methods  used to delineate the Active River Area involve GIS  techniques and analyses  of elevation, land
cover, and wetlands data. The meander belt/floodplain/riparian wetland/terrace area can be identified using a
Digital Elevation Model (DEM) and a technique that calculates the area within which the river is  expected to
interact dynamically with  the land surface. It is  based on both the lateral and vertical distance (elevation) from
                                                                                                          3-13

-------
Identifying and Protecting Healthy Watersheds
                                                    - V-SHAPED CONFINED VALLEY
                                                       -HEADWATER CATCHMENT AREAS
                                                             - WETLANDS
                                                                          ALLUVIAL FAN

                                                                            INCISED TRIBUTARY
                                                                                  FLOODPLAIN FOREST
                                                                                  RIPARIAN WETLAND
                                                                                                    BRAIDED RIVER
                                                                                                    FLOODPLAIN DELTA
             HEADWATERS
             • CPOM LWD, SEDIMENT
             . 30-60 METERS FROM Cl
             • <1 YEAR RECURRENCE
             MID - WATERSHED
             .MEANDER BELT ADJUSTMENTS DUE TO
              SEDIMENT EROSION. STORAGE. DEPOSITION,
              AND TRANSPORT IN THE CHANNEL AND FLOODPLAIN
             • MEANDER BELT (4-6 CHANNEL WIDTHS) S
              ADJACENTLOW ACTIVE FLOODPLAIN
             • < 1 TO 1 - 10 YEAR RECURRENCE INTERVAL
                              LOW - WATERSHED
                              • FLOODPLAIN INUNDATION fi
                               LONG-TERM SEDIMENT STORAGE
                              • ENTIRE VALLEY BOTTOM
                              • 1-10 YEARS RECURRENCE
                               INTERVAL
                                                                         NATURAL SEDIMENTARY
                                                                         LEVEE
                                                                                   |	1 LOCATION OF THE
                                                                                       J ACTIVE RIVER AREA

           Figure 3-6 Components and dominant processes of the Active River Area (Smith et al., 2008).

        the stream and user-supplied cutoff distances that are determined based on stream size (Strager, Yuill, & Wood,
        2000). By considering stream size, the dominant physical processes occurring in each zone of the watershed
        are accounted for. Since the extent of riparian wetlands is dependent not only on overbank flows, but also on
        ground water and runoff from adjacent uplands, a second technique is used to determine those areas expected
        to be wet based  on slope and a flow moisture index. Combining  these identified areas  with the known
        occurrence of wetlands from the National Land Cover Database (NLCD) and National Wetlands  Inventory
        (NWI) data and a distance cutoff based on stream size, riparian-associated wetlands can be identified.

        Material contribution areas can also be identified using GIS techniques. The DEM data layer for a watershed
        is  divided  into 10 equal elevation groups. Headwater catchments can be defined based on size relative to the
        watershed  and inclusion in the appropriate elevation group. The appropriate elevation group and headwater
        catchment size depends on area-specific conditions and is determined by the user.  For example, a headwater
        catchment area of <10 m2 falling mostly  within the top 40% of elevation bands  could be  used as the criteria
        for identifying headwater material contribution areas. For the streamside areas not yet  included in either of
        the above  methods, an area with a width of 30-50 meters can be  used  as  a cutoff for identifying  streamside
        material contribution areas.

        These GIS techniques identify the material contribution areas, riparian wetlands,  and the combined area
        consisting  of the  meander belt/floodplains/terraces.  Distinguishing  between  the meander belt, floodplains,
        and terraces  requires more detailed field assessments such as the  Vermont Stream Geomorphic Assessment
        Protocols (Kline, Alexander, Pytlik, Jaquith, &  Pomeroy, 2009). However, these simple GIS techniques alone
        are enough to delineate the Active River Area and begin to prioritize lands for conservation.

        The Nature Conservancy has demonstrated the technique in the Connecticut River Basin to highlight the utility
        of the methodology for identifying and prioritizing lands within the Active River Area for conservation actions
        (Figure 3-7). The Active River Area was  delineated using the GIS techniques described above. A  condition
3-14

-------
                                                                                    3 Examples of Assessment Approaches
analysis using land cover data was then performed to identify the largest intact areas with minimal developed
or agricultural lands. For example, riparian areas with less than 25% agricultural land use could be considered
most intact and prioritized for conservation. Similarly, headwater areas with less than 1 % impervious surfaces
and  less than 5% agricultural land use could be considered very good, while those headwater areas with less
than 3%  impervious surfaces and less than 25% agricultural land use could be considered  good. This is a
simple method for identifying priority conservation lands within the Active River Area. Other  prioritization
methodologies are available to address more specific objectives. Prioritization methodologies should be based
on local knowledge and data whenever possible.

Combining the Active River Area approach with other approaches such as a green  infrastructure assessment
or GAP analysis can provide a  comprehensive framework for identifying  those  areas critical for maintaining
watershed and river  ecological  integrity. Water quality, habitat,  and biomonitoring data can further refine
the analysis of healthy components  of the watershed. Identifying those areas within  the Active River Area
that  are not currently protected, but that are comprised of land uses compatible for conservation, as well as
the corridors  connecting the Active River Area with other hubs, or habitat patches, on the landscape creates
the outline of a strategy to protect aquatic ecosystems. The Active River Area components  can be used to
design freshwater protected areas that support natural disturbance regimes, natural hydrologic and geomorphic
variability, and a connected network of healthy areas.
     Active River Area
          Riparian Areas and
          Headwater Areas

Headwater Areas by Intactness
  | Very Good
    Good
Largest Riparian Areas by Intactness
  • <25% Agriculture
    >25% Agriculture
                                                                   VT
    Figure 3-7 The Active River Area in the Connecticut River Basin (Smith et al., 2008).
                                                                                                             3-15

-------
Identifying and Protecting Healthy Watersheds
          Interagency Fire Regime Condition Class
          Author or Lead Agency:  Hann et al., 2008. U.S. Forest Service,  U.S. Department of the Interior, The Nature
            Conservancy, and Systems for Environmental Management
          More Information: http://frames.nbii.gov/documents/frcc/documents/FRCC+Guidebook 2008.10.30.pdf

        The Fire Regime Condition Class (FRCC) methodology relies upon concepts that define the natural fire regime
        as "the role fire would play across a landscape in the absence of modern human mechanical intervention but
        including the possible  influence of aboriginal fire use."  The FRCC field and  mapping assessment  methods
        describe the departure of fire disturbance regime  from reference  periods or the natural range  of variability
        (as determined through  modeling).  These results  allow land managers to  focus  management  strategies on
        maintaining or restoring the natural  disturbance regime of the forest or rangeland ecosystem.  These  methods
        were developed by an interagency working group and The Nature Conservancy, and managed by the  National
        Interagency Fuels Coordination Group.

        The FRCC methodology allows for the assessment  of the  fire  disturbance regime  and resultant vegetation
        at the  stand  and landscape scales. Two procedures  exist for determining the FRCC.  The FRCC  Standard
        Landscape Worksheet Method provides the background understanding necessary to use the other tools in the
        FRCC Guidebook, as well as allows for assessment at both the landscape and stand scales. The FRCC  Standard
        Landscape Mapping Method determines  FRCC based on vegetation departure alone, while  the Worksheet
        Method assesses both vegetation departure and fire  regimes directly. However, methods are under development
        for assessing the fire regime through the Mapping Method. Outputs from the Mapping Method are consistent,
        objective, and spatially explicit at multiple scales. The  Mapping Method  can also  be employed for larger
        geographic scales with much less staff time. Maintenance or restoration of the natural fire regime is important
        for preventing severe fires that  can destroy entire forest ecosystems, contribute vast quantities  of sediment  to
        streams from surface erosion, and damage public  and private infrastructure. Areas that have departed from
        their natural fire regime have also been shown to cause excessive build-up of nutrients on the forest floor due
        to decomposition of organic matter  (Miller et al.,  2006). These nutrients can then be transported to aquatic
        ecosystems during rainfall/runoff events, causing eutrophic conditions. The continual build-up  of nutrients on
        the forest floor provides a constant source of pollution to streams and lakes in the watershed. Fire  disturbances,
        of natural frequency and intensity, remove the excess organic matter causing the nutrient build-up  and may
        actually improve long-term water quality, although it will  be temporarily  worsened immediately following
        a fire  (Miller et al., 2006). These are important considerations  for watershed managers seeking to  maintain
        overall watershed health.

        Five  natural  fire  regimes are classified based on  frequency and  severity, which  reflect the replacement  of
        overstory  vegetation (Table 3-3). The natural fire regime for a landscape  unit is determined  based on  its
        biophysical setting. A biophysical setting, in the FRCC  methodology, is described based on the vegetation
        composition and structure associated with particular fire regimes.
        Table 3-3 Fire regime groups and descriptions (Hann et al., 2008).
         Group     Frequency
                    0-35 Years
                    Severity
            II

            III

            IV
 0-35 Years

35-200 Years

35-200 Years
Low/Mixed


Replacement

Mixed/Low

Replacement
                                    Severity Description
Generally low-severity fires replacing less than 25% of the
dominant overstory vegetation; can include mixed-severity
fires that replace up to 75% of the overstory.

High-severity fires replacing greater than 75% of the
dom inant overstory vegetation.
Generally mixed-severity; can also include low-severity fires.
High-severity fires replacing greater than 75% of the
dom inant overstory vegetation.
                    200+Years    Replacement/Any Severity
3-16

-------
                                                                                 3 Examples of Assessment Approaches
The LANDFIRE Program  (U.S. Department of Agriculture; U.S. Department of the Interior, 2009) models
reference conditions for biophysical settings for the entire United States based on five characteristic succession
classes of forest and rangeland ecosystems:

    1.  S-Class A: Early serai, post-replacement.
    2.  S-Class B: Mid serai, closed canopy.
    3.  S-Class C: Mid serai, open canopy.
    4.  S-Class D:  Late serai, open canopy.
    5.  S-Class E: Late serai, closed canopy.

Evaluating the vegetation across the project landscape allows for the delineation of biophysical settings, which
can be compared to the relative amounts of each succession class for reference conditions in that biophysical
setting. For example, Table 3-4 shows the percent coverage of each succession stage (columns A-E) within the
biophysical setting. The last column displays the "fire regime group" for each biophysical setting's  reference
conditions, which has a frequency range of 35-200 years and an average severity of mixed to low.
Table 3-4 Example reference condition table (Hann et al., 2008).
                  Biophysical Setting
 Rocky Mountain Aspen Forest & Woodland
 Rocky Mountain Lodgepole Pine Forest
 Rocky Mountain Alpine Dwarf Shrubland
34%
29%
14%
                             Fire Regime Group
20%   8%   26%  12%           3
47%   26%   0%   0%           4
86%   0%   0%   0%           5
Weighted averages  for percent coverage of succession classes in all biophysical  settings within  the project
landscape and weighted averages of the fire frequency and severity for all biophysical settings in the project
landscape are used to determine the degree of departure from  reference conditions. The FRCC is  then
determined based on this degree of departure:

    1.  FRCC 1: < 33% (within reference condition range of variability).
    2.  FRCC 2: > 33% to < 66% (moderate departure).
    3.  FRCC 3: > 66% (high departure).

Management implications are then defined based on the FRCC and relative amount of succession  class (Table
3-5). For example, an FRCC of 3 and an abundant amount of the succession class would suggest that thinning
of the forest stand would improve the condition. Conversely, an FRCC of 1 with only trace amounts of the
succession class does not require any action.

Table 3-5 Management implications for the stand-level fire regime condition
class based on the S-Class relative amount (Hann et al., 2008).
S-Class Relative Amount
Trace
Under-represented
Similar
Over-represented
Abundant
Stand FRCC
1
1
1
2
3
Improving Condition if Stand is:
Maintained
Maintained
Maintained
Reduced
Reduced
The relative amount of each S-Class (A, B, C, D, and E) is determined for the stand and evaluated against the
reference conditions for its biophysical setting (e.g., Table 3-4). Five natural fire regimes are classified based
on frequency and severity, which reflect the replacement of overstory vegetation  (Table 3-3). The  natural
fire regime for a landscape unit is determined based on its biophysical setting. A biophysical setting, in the
FRCC methodology, is described based on the vegetation composition and structure associated with particular
                                                                                                          3-17

-------
Identifying and Protecting Healthy Watersheds
        fire regimes (Table 3-4). The FRCC for the stand is then determined based on the departure from reference
        conditions (e.g., under-represented or over-represented).

        The entire process involves a significant amount of data gathering and input that can be greatly facilitated
        through the use of the GIS-based FRCC Mapping Tool. Outputs of the FRCC Mapping Tool include:

           1.  Succession class relative amount.
           2.  Succession class relative departure.
           3-  Stand FRCC.
           4.  Biophysical setting departure.
           5.  Biophysical setting FRCC.
           6.  Landscape departure.
           7-  Landscape FRCC.

        The FRCC Mapping Method provides condition class outputs at three scales (stand,  biophysical setting, and
        landscape). Figure 3-8 displays an example of the landscape scale output.

        The results of the FRCC assessment are used to prioritize fire suppression activities across the United States.
        They can also be used to help manage invasive species through the use of controlled burns without destroying
        natural ecosystem components. The methodology also  provides a foundation on which other disturbance
        regime assessments can be built.
                                   Fire Regime  Condition  Class
                                             Coarse  Scale - 2000
            Legend
            ^| Condition Class 1
            I    | Condition Class 2
            ^H Condition Class 3
            I    I Agriculture, Barren, Alpine, & Urban
            ^H Water

         Figure 3-8 National landscape-scale output of the Fire Regime Condition Class Mapping Method. (Hann et al.,
         2008).
3-18

-------
                                                                                              3 Examples of Assessment Approaches
3.2 Habitat

This  section provides summaries for some examples of approaches currently being used to  assess habitat. See
Chapter 2 for background information on habitat.
                          Landscape Condition
             Patterns of natural land cover, natural disturbance regimes,
                lateral and longitudinal connectivity of the aquatic
               environment, and continuity of landscape processes.
                               Habitat
             Aquatic, wetland, riparian, floodplain, lake, and shoreline
                      habitat. Hydrologic connectivity.
                              Hydrology
              Hydrologic regime: Quantity and timing of flow or water
              level fluctuation. Highly dependent on the natural flow
            (disturbance) regime and hydrologic connectivity, including
                     surface-ground water interactions.
            Geomorphology
Stream channels with natural geomorphic dynamics.
             Water Quality
  Chemical and physical characteristics of water.
           Biological Condition
   Biological community diversity, composition,
  relative abundance, trophic structure, condition,
           and sensitive species.
                             Headwater streams
                                maintain water quality,
                                   attenuate flooding,
                                     maintain water
                                      supplies, trap
                                       and retain
                                        sediments,
                                        process
                                        organic
                                        matter, and
                                        maintain
                                       aquatic
                                      biodiversity.
                                    Photo: Adrian Jones, IAN.
               Large woody debris
                 increases stream
                    habitat diversity,
                      helps control
                       the grade of a
                        stream channel,
                         and protects
                         streambanks
                         from erosion.
                     Photo: USFS.
                             Isolated wetlands
                               provide habitat for
                                  many threatened
                                    and endangered
                                      species,
                                       including plants,
                                        amphibians,
                                        and birds.
                                    Photo: USFWS.
               Vegetated riparian
                areas provide habitat
                   for turtles, birds,
                     and a variety of
                       fish species;
                        they also can
                         trap sediment
                         and reduce
                         nutrients
                         and other
                         pollutants
                        from runoff.

                     Photo: USFWS.
                                                                                                                           3-19

-------
Identifying and Protecting Healthy Watersheds
          Ohio's Primary Headwaters Habitat Assessment
          Author or Lead Agency: Ohio Environmental Protection Agency
          More Information: http://www.epa.state.oh.us/dsw/wqs/headwaters/index.aspx

        Ohio  EPA's  Primary Headwater Habitat (PHWH) Assessment procedure  uses a rapid Headwater Habitat
        Evaluation Index (HHEI) along with two optional levels of biological assessment (order-family level or genus-
        species level) to assign a headwater stream to one of three classes. Primary headwater streams comprise over 80%
        of all stream miles  in Ohio and provide a variety of ecosystem services and  benefits (Meyer, Wallace, Eggert,
        Helfman, & Leonard, 2007)- Most primary headwater  streams in Ohio have not been assigned a designated
        beneficial use. Additionally,  due to habitat differences, biological criteria and methods of sampling used in
        larger streams are not applicable to many primary headwater streams. In response to these limitations, Ohio
        EPA conducted a statewide evaluation of PHWH and developed the HHEI. The HHEI uses  a combination
        of three  habitat variables to predict  the  presence or absence of an assemblage of cold-cool  water adapted
        vertebrates and benthic macroinvertebrates. Using the results of the HHEI, a. potential existing aquatic life use
        can  be assigned to  the stream reach. When biological assessment data are available, these data will be used to
        determine the actual existing aquatic life use designation.

        Primary headwater streams are defined by  Ohio EPA as streams having a watershed area of less than one square
        mile, with a defined stream bed and bank, and a natural pool depth of less than 40 cm.  Streams with a larger
        watershed area or natural pool depths greater than 40 cm should be evaluated using the Qualitative Habitat
        Evaluation Index, as opposed to the HHEI.  For  the purposes of the HHEI, stream reaches of up to 200 ft.
        should be delineated for assessment.  Tributaries of the PHWH stream should be evaluated separately from
        the  main stem. The evaluation should be conducted at a time when base flow conditions are present. Once
        the watershed drainage area has  been calculated and the stream reaches delineated, physical habitat conditions
        including bank full width, maximum pool depth, and substrate  composition  are recorded on the PHWH
        form.  Additional habitat parameters may be  measured and recorded if desired.  These include gradient, flood
        prone width, and pebble counts. Water chemistry, salamander, fish, and macroinvertebrate survey data can also
        be collected  if desired or deemed appropriate. The data from the HHEI and/or the biological survey data (if
        available) should be used to  determine  the appropriate  Class I, II, or III existing aquatic life use designation
        (Class III being of  the highest quality).  The HHEI is calculated based on a scoring system using the bank full
        width, maximum pool depth, and substrate composition.

        Biological survey data can be  collected  for a more detailed evaluation of primary headwater  streams. A
        Headwater Macroinvertebrate Field Evaluation Index can be calculated to refine a PHWH stream classification.
        Based on the taxa present, a scoring system places the stream reach into one of the three classes of PHWH. The
        presence  of cold water fish indicator species automatically places the stream in the Class  III PHWH category.
        In the absence of fish, aquatic and semi-aquatic  salamanders are the primary vertebrate predator functional
        group in  Ohio's headwater streams. Therefore, a salamander survey  is  used  to evaluate  the  biological health
        of headwater habitats. Three different assemblages  of salamander species have been identified by Ohio EPA
        as corresponding to the  three PHWH Classes. The goal of the salamander survey is simply to document the
        presence or absence of the species representing the three assemblages.

        The output of the Primary Headwaters Habitat Assessment is a classification of:

            •   Class I PHWH - ephemeral stream, normally dry channel.
            •   Class II PHWH - warm water adapted native fauna.
            •   Class III PHWH - cool-cold water adapted native fauna.

        These classifications  help  to protect Ohio's primary headwater streams through  the  state's water quality
        standards, which are chemically  and biologically based.
3-20

-------
                                                                                 3 Examples of Assessment Approaches
  A Physical Habitat Index for Freshwater Wadeable Streams in Maryland
  Author or Lead Agency: Maryland Department of Natural Resources
  More Information: http://www.dnr.md.gov/streams/pubs/ea03-4phi.pdf

The Maryland Biological Stream  Survey developed a multimetric index to describe stream physical habitat.
The effort resulted in a Physical  Habitat Index  (PHI) that relates metrics of geomorphology, visual habitat
quality, and riparian condition to classify streams compared to reference conditions in the state. The PHI is
significantly correlated with the benthic IBI and fish IBI. This correlation can help  to elucidate the effects of
physical habitat attributes and chemical stressors on biological condition.

Based on the understanding that physical habitat degradation is one of the leading causes of stream impairment,
the Maryland Biological Stream Survey began collecting a variety of physical habitat variables as  part of its
routine biomonitoring program in 1994. Based on  a statistical evaluation of these data, the Coastal  Plain,
Piedmont, and Highland regions  were chosen to represent three biologically distinct stream classes. Reference
and degradation criteria were determined based on the amount of forested, agricultural, and urban land use.
Different reference criteria were developed  for each of the  three stream classes. The metrics selected for each
stream class are shown in Table 3-6. The final PHI for a stream is calculated by averaging the individual metric
scores.

Table 3-6 Metrics for the Physical  Habitat Index in each of the three stream classes in  Maryland (Maryland
Department of Natural Resources, 2003).
| Coastal Plain
Bank stability
Instream wood
Instream habitat quality
Epibenthic substrate
Shading
Remoteness

Piedmont
Riffle quality
Bank stability
Instream wood
Instream habitat quality
Epibenthic substrate
Shading
Remoteness
Highland |
Bank stability
Epibenthic substrate
Shading
Riparian width
Remoteness


Embeddedness
The relationship between the PHI, fish IBI, and benthic IBI were examined by ecoregion and river basin.
These  relationships  were found to
be significantly correlated. However,
the degree to which the PHI predicts
fish or benthic IBI  depends on the
presence and levels of other stressors,
such  as  low dissolved   oxygen or
high  temperatures.  Given that the
PHI was found  to  be significantly
correlated with biological condition,
the analysis was completed statewide
(Figure 3-9).  The  PHI   is  used in
Maryland's statewide monitoring and
assessment program  and,  along with
biological and chemical assessments,
is   used  to  communicate   the
condition of Maryland's  streams to
the public and decision makers.
         Severely Degraded
         Degraded
         Partially Degraded
         Minimally Degraded
Figure 3-9 Map of stream habitat condition in Maryland, as determined
with the Physical Habitat Index (Maryland Biological Stream Survey,
2005).
                                                                                                         3-21

-------
Identifying and Protecting Healthy Watersheds
          Proper Functioning Condition
          Author or Lead Agency: U.S. Bureau of Land Management, U.S. Fish and Wildlife Service, and Natural Resources
            Conservation Service
          More Information: ftp://ftp.blm.gov/pub/nstc/techrefs/Final%20TR%201737-9.pdf

        The  Proper Functioning Condition  (PFC) assessment method  is a checklist-based  evaluation of riparian
        wetland functional status that was  developed by the Bureau of Land Management,  U.S.  Fish  and Wildlife
        Service, and the Natural Resources Conservation Service (NRCS). It is a qualitative, field-based methodology
        developed by an interdisciplinary team around the  principles  of the quantitative  Ecological Site Inventory
        (Habich, 2001) method. The method was developed with  the purpose of restoring  and managing riparian
        wetlands in 11 western states.

        The  PFC process requires an interdisciplinary team of soil, vegetation,  hydrology,  and  biology specialists
        and  follows three overall steps: 1) review existing documents,  2) analyze the PFC definition, and 3) assess
        functionality using the checklist. The PFC method  defines  a  riparian wetland  area as being in  proper
        functioning condition when adequate vegetation, landform, or large woody debris is present to:

            •   Dissipate stream energy associated with high water flow, thereby reducing erosion
                and improving water quality.
            •   Filter sediment, capture bedload, and aid floodplain  development.
            •   Improve flood-water retention and ground water recharge.
            •   Develop root masses that stabilize stream banks against  cutting action.
            •   Develop diverse ponding and channel characteristics to provide the habitat and the
                water  depth, duration,  and  temperature  necessary for fish production, waterfowl
                breeding, and other uses.
            •   Support greater biodiversity.

        The  PFC  method evaluates  a specific riparian wetland area  against its capability and potential.  Capability is
        defined as "the highest ecological status an area can attain given political, social, or economical constraints,
        which are often referred to as limiting factors." Potential is defined as "the  highest ecological status a riparian-
        wetland area can attain given no political, social,  or economical constraints, and is often referred to as the
        potential natural community." Restoration goals resulting from the assessment emphasize achievement of the
        highest level of functioning given the political, social, or economic constraints that are present. Therefore, PFC
        does not necessarily equate to "natural" conditions. Assessing a  specific area's capability and potential involves
        examination of soils for evidence of previous saturation, frequency and duration of flooding, historic record of
        plant and animal species present, relic areas, and historic photos. Table 3-7 contains  the 17 components of the
        PFC checklist.

        Using the checklist and  the definition of PFC, an  assessment of a riparian wetland results in one  of four
        ratings:

            •   Proper functioning condition.       •   Nonfunctional.
            •   Functional - at risk.                 •   Unknown.

        A rating of proper functioning condition means that the riparian area is stable and resilient at high flow events,
        while ratings of functional — at risk or nonfunctional mean that  the area is susceptible to damage at medium to
        high flow events. Rehabilitation strategies  should be  developed  for areas rated as nonfunctional (e.g., riparian
        revegetation). Areas placed  in the functional - at risk category should be evaluated for their trend  toward
        or away from  proper functioning condition and the appropriate protection or  monitoring strategies put in
        place. The results of a  PFC  analysis can be combined with other types of watershed assessments for a better
        understanding of how  the riparian and upland areas  interact. A PFC analysis is also often used as a screening
        level assessment to determine whether or not more intensive, quantitative analyses are necessary.
3-22

-------
                                                                                          3 Examples of Assessment Approaches
Table 3-7 Proper Functioning Condition checklist worksheet (Bureau of Land Management, 1998).
                                                               HYDROLOGY
                           1) Floodplain above bankfull is inundated in "relatively frequent" events
                           2) Where beaver dams are present they are active and stable
                           3) Sinuosity, width/depth ratio, and gradient are in balance with the landscape setting (i.e.,
                           landform, geology, and bioclimatic region)
                           4) Riparian-wetland area is widening or has achieved potential extent
                           5) Upland watershed is not contributing to riparian-wetland degradation
Yes No N/A





















VEGETATION
6) There is diverse age-class distribution of riparian-wetland vegetation (recruitment for
maintenance/recovery)
7) There is diverse composition of riparian-wetland vegetation (for maintenance/recovery)
8) Species present indicate maintenance of riparian-wetland soil moisture characteristics
9) Stream bank vegetation is comprised of those plants or plant communities that have root masses
capable of withstanding high stream flow events
10) Riparian-wetland plants exhibit high vigor
11) Adequate riparian-wetland vegetative cover is present to protect banks and dissipate energy
during high flows
12) Plant communities are an adequate source of coarse and/or large woody material (for
maintenance/recovery)
Yes No N/A















EROSION/DEPOSITION
13) Floodplain and channel characteristics (i.e., rocks, overflow channels, coarse and/or large woody
material) are adequate to dissipate energy
14) Point bars are revegetating with riparian-wetland vegetation
15) Lateral stream movement is associated with natural sinuosity
16) System is vertically stable
17) Stream is in balance with the water and sediment being supplied by the watershed (i.e., no
excessive erosion or deposition)
                                                                                                                      3-23

-------
Identifying and Protecting Healthy Watersheds
          Rapid Stream-Riparian Assessment
          Author or Lead Agency: Wild Utah Project
          More Information: http://wildutahproject.org/files/images/rsra-ug2010v2 wcover.pdf

        The Rapid Stream-Riparian Assessment  (RSRA)  protocol (Stevens  et al., 2005 and  Stacey et al., 2007)  was
        developed to provide a mechanism to objectively determine the functional condition of both the aquatic
        and riparian components of small  and medium  sized streams and  rivers in the American Southwest and in
        other arid and semi-arid regions. It provides a standardized  method to evaluate the existing conditions along
        a particular reach of river to  determine which components of the stream-riparian ecosystem differ from what
        would be expected within the reach under geomorphically similar but unimpacted reference conditions. It
        also creates a yardstick by which to  objectively monitor any future changes within  the system that result either
        from active restoration programs or from allowing the system to follow its current trajectory under existing
        management programs. Because the protocol can be completed in a relatively short time and does not require
        specialized and expensive equipment, it  is possible to  efficiently survey a number of different reaches within
        a particular watershed. This can then provide an understanding of both the variation in conditions within a
        particular watershed, as well as any potential trends that might indicate cumulative impacts of various activities
        upon the stream-riparian ecosystem.

        The RSRA utilizes a primarily qualitative assessment based on quantitative measurements made in the field. It
        focuses upon five functional  components of the stream-riparian ecosystem that provide important benefits to
        humans and wildlife and which, on public lands, are often the subject of government regulation and standards.
        These components are:

            1.  Non-chemical water quality and pollution;
            2.  Stream channel and floodplain  morphology  and the ability of the system to limit
               erosion and withstand flooding without damage;
            3.  The presence of habitat for native fish and other aquatic species;
            4.  Riparian vegetation structure and productivity; including the occurrence and relative
               dominance of exotic or nonnative species; and
            5.  Suitability of habitat for  terrestrial wildlife, including  threatened  or endangered
               species.

        Within each of these areas, the RSRA evaluates between two and seven variables that reflect the  overall function
        and health of the stream-riparian ecosystem. Variables  are measured either along the entire study reach (usually
        around  1  kilometer in  length, depending on
        local conditions)  or along 200  meter sample
        transects. Each variable is assigned a score from
        1 to 5, using pre-defined scoring levels that can
        be scaled  to  the individual  geomorphic and
        ecological conditions of that particular reach. A
        score of 1 indicates that  the ecosystem is highly
        impacted and non-functional for that variable,
        while  a score of 5 indicates that the system is
        healthy and is functioning in  a way that would
        be found in a local and  geomorphically similar
        reference stream that has not been impacted by
        human activities. A complete description of the
        variables and  the  methods  used to  collect and
        score them can be found in Stacey et al. (2007).
       Examples of RSRA Variables
Overbank co\
Plant community cover and structural diversity
Dominant shrub and tree demography
Non-native herbaceous and woody plant cover
Mammalian herbivory impacts on ground cover
Mammalian herbivory impacts on shrubs and small trees
Riparian shrub and tree canopy cover and connectivity
Fluvial habitat diversity
3-24

-------
                                                                                 3 Examples of Assessment Approaches
The RSRA provides information that will be of value to land managers in making policy decisions  and to
help provide guidance for potential restoration programs. The protocol considers features or variables that
not only indicate the ability of the system to provide specific  functions, but ones that also reflect important
ecological processes within the stream-riparian system. For example, the fish habitat section includes a measure
of the relative amount of undercut banks along the reach. Undercut banks not only provide important  habitat
and hiding cover for fish and other aquatic species, but their presence  along a reach  indicates that the banks
themselves are well vegetated and that there is sufficient root mass from vegetation to allow the development
of the hour-glass shape channel  cross-section that is typical of most healthy stream systems. The presence of
this channel shape, in turn, indicates that the fluvial processes of erosion and deposition along that reach are in
relative equilibrium. Thus, when interpreting RSRA surveys, the results of all indicators should be considered
in concert. This will facilitate deciding which parts of the ecosystem within the study reach may be  most out
of balance with natural processes and, therefore, which of those parts may be the most important or the most
suitable for future restoration efforts.

In order to increase the number of survey sites that can be sampled, the protocol uses variables that  can be
measured rapidly in the field and that  do not require specialized equipment. More detailed and  extensive
methods have been developed for several of the individual indicators included in this  protocol. Many of these
analyses may take one or more  days to  complete, just for that single  variable. However, should any of the
individual indicators be found to be particularly problematic or non-functional in a specific reach using the
RSRA protocol, more specialized methods can be used during subsequent  visits to the site in order to collect
additional quantitative information on that particular indicator.

The RSRA protocol measures only the current condition of the ecosystem.  It does not base its scores upon
some hypothesized future state or successional trend within the reach, as is done with several other riparian
assessment methods (e.g., the BLM's Proper Functioning Condition assessment). The RSRA method  addresses
the ability of the ecosystem to provide some important function at the  present time, not whether it would be
likely to do so at some point in the future, if current trends or management practices on the reach continue.
This approach  is used because stream-riparian systems are highly  dynamic, and they are often subject to
disturbances  (e.g., large floods) that can alter successional trends  and make predictions of future conditions
on an individual reach  highly problematic. Also,  by evaluating  only  current conditions, this  protocol  can
serve  as a powerful tool for monitoring and
measuring  future  changes  in   the  functional
status of the  system. For example, if a particular
set of indicators suggest that a reach is  in poor
condition, re-evaluating the system with the same
protocol in subsequent years gives one the ability
to measure the effectiveness of any management
change  or active restoration program  and  to
undertake  corrective action if  the  restoration
efforts are not found to  be producing the desired
changes. This   type  of  adaptive  management
approach  can  be extremely challenging if the
evaluation  and  monitoring measures are based
primarily upon  the expectations of some future,
rather than current, condition.
                                                                                                         3-25

-------
Identifying and Protecting Healthy Watersheds
          Ohio Rapid Assessment Method
          Author or Lead Agency: Ohio EPA Division of Surface Water
          More Information: http://www.epa.ohio.gov/dsw/wetlandsAVetlandEcologySection.aspxtfORAM

        Having worked through five previous versions of a wetlands assessment methodology based on the Washington
        State Wetlands Rating System, Ohio EPA decided to impart a new format and structure on the assessment
        process when the Ohio Rapid Assessment Method (ORAM) for Wetlands Version 5-0 was developed. ORAM
        is designed to measure the  intactness of the hydrologic regime and habitat of a wetland relative to the type
        of wetland in question. The basis for ORAM  is a  ten-page wetland categorization form. The form includes
        worksheets that  direct the  assessor through the process  of identifying background information,  a  scoring
        boundary, and a narrative  rating for the wetland.  The  first  part of the assessment is to use the  wetland's
        hydrologic regime to define the boundary of the area to be assessed. Following the six-step process outlined on
        the form, the assessor:

            1.  Identifies the area of interest;
            2.  Locates physical evidence of rapid changes in hydrology;
            3.  Delineates a  boundary  around all areas within  and contiguous  with the area of
               interest that have the same hydrologic regime as the area of interest;
            4.  Verifies that none  of the  boundaries  of the delineation have  been  defined using
               artificial boundaries;
            5.  Adjusts the  delineation  as  needed to  encompass multiple wetlands  for scoring if
               appropriate;  and
            6.  Consults the current version of the ORAM manual to ensure that  any  complex
               situations (i.e., patchworks, wetlands bounded by water bodies, wetlands transected
               by artificial boundaries, or wetlands that may fit into multiple categories) have been
               handled properly.

        Once the  boundary  to be  used  in  the assessment  has been  defined, the  assessor proceeds to awarding the
        wetland a  narrative rating. Additional information is gathered through site visits, literature searches, and data
        requests from relevant agencies. Site visits should be  carefully scheduled paying close attention to the possibility
        that seasonal  changes may affect the assessor's ability to make unbiased observations.  The narrative rating uses
        the presence or absence of threatened or endangered species to determine whether or not the wetland  should be
        considered for superior function/integrity status (Category 3). Wetlands that are not candidates for Category
        3 are divided between wetlands having  moderate function/integrity (Category 2)  and wetlands with minimal
        function/integrity (Category 1) in the quantitative rating process. As in a dichotomous key, the "Yes" or "No"
        questions used in the narrative rating process form a decision tree that solicits responses from the assessor that
        set him or her up to be able to answer questions appropriately in the quantitative rating process.

        Metrics assessed in the quantitative rating process include:

            •   Wetland size (6 points);
            •   Buffer size and intensity of pressure from surrounding land use (14 points);
            •   Hydrology (30 points);
            •   Habitat alteration and development (20 points);
            •   Special wetlands (i.e.  bogs, fens, old growth forest) (10 points); and
            •   Plant communities, interspersion, and  microtopography (20 points).
3-26

-------
                                                                                  3 Examples of Assessment Approaches
In the hydrology and habitat alteration and development sections of the assessment, there are also tables that
prompt the assessor to identify any disturbances observed during the site visit. After rating the wetland for all
six metrics, the assessor compares the total number of points awarded to the wetland to the set of breakpoints
between categories to place the wetland  into one of the same set  of three categories used in  the  narrative
rating process. The categories  break according to the following point values for emergent wetland vegetation
communities: 0-11 points (Category 1), 12-16  points  (Category 1 or 2), 17-29 points (Category 2),  30-
34 points  (Category  2  or 3),  and 35 or more points (Category 3). In the case of forested and shrub-scrub
wetlands, the categorical breakpoints are as follows: 0-16.9 points (Category 1), 17-0-19-9 points (Category 1
or 2), 20.0-25-9 points (Category 2), 26.0-28.9 points (Category 2 or 3), and 29-0 or more points (Category
3).  In either categorization scheme,  a wetland can earn up to a maximum  of 100 points. The  assessment
questions and point values are based on significant differences in vegetation index of biotic integrity scores,
as developed by Mack et al., (2000). For wetlands that score in point ranges assigned to multiple categories
(i.e., "gray  zones"), the wetland is assigned to the higher (lower quality) of the two categories, unless detailed
assessments and narrative criteria justify assigning the wetland to the lower  (higher quality) category. Even
with this protocol in place, it remains a possibility that a wetland could be under-  or over-categorized because
it in some way defies one of ORAM's underlying assumptions, such as the assumption that human disturbance
degrades biotic integrity and function.

Although the numeric output and  wetland categorization drawn from ORAM  are neither absolute values
nor comprehensive ratings of ecological and human value, but  rather are  most  useful when interpreted in
the context of all available, relevant information, the results of ORAM  assessments nonetheless  are useful for
comparing different types of wetlands because scores are derived using standardized procedures. In  the State
of Ohio, the ORAM categories are used to divide wetlands into regulatory groups. Different antidegradation
procedures are applicable for  Category 1  wetlands, which are held to lower  avoidance, minimization, and
mitigation  standards because they have been so severely degraded. Many of the wetlands that fall into  Category
2 have also been degraded, but have a reasonable  potential for successful restoration. Ohio's stormwater runoff
control also only applies to wetlands in Categories 2 and 3, and demonstration of public need for disturbing
a wetland  only applies  to wetlands in Category  3- In cases where impact cannot be avoided, compensatory
mitigation  is required; however, ORAM is not recommended for use beyond the wetland classification process
(i.e., analyzing the success of a mitigation project).
                                                                                                          3-27

-------
Identifying and Protecting Healthy Watersheds
          California Rapid Assessment Method
          Author or Lead Agency: California Wetland Monitoring Group
          More Information: http://www.cramwetlands.org/

        Like other rapid assessment methods, the California Rapid Assessment Method (CRAM) uses field indicators to
        evaluate the ecological condition of wetlands and associated aquatic resources. CRAM was initially designed for
        use  in assessing the ambient condition of wetlands of seven main types: depressional, estuarine (separated into
        saline and non-saline), lacustrine, playa, riverine and riparian, vernal pool, or wet meadow. More recent work
        has  focused on the use of CRAM assessment to inform regulatory decisions involving dredge and fill projects
        and associated mitigation. The results generated by CRAM  for these uses  have  been found to correspond
        well with other biological and landscape disturbance assessments (Stein et al., 2009).  The assessment can  be
        conducted  at one of four scales: an individual project, watershed, geographic region, or state. Eight key steps
        are involved in implementing CRAM (Collins et al., 2008):

            1.   Assemble background information about the management history of the wetland.
            2.   Classify the type of wetland with the assistance of the CRAM user's manual.
            3.   Determine the appropriate season and other timing aspects of the assessment.
            4.   Estimate the boundary of the area of assessment.
            5.   Conduct an  office assessment  of  stressors and  on-site conditions of the area of
                assessment.
            6.   Conduct a field assessment of stressors  and  on-site conditions  of the  area of
                assessment.
            7-   Complete CRAM scores and perform quality assurance and control procedures.
            8.   Upload CRAM  results to state and regional information systems.

        The user's manual (Collins et  al., 2008) provides guidance, derived from the  Ohio Rapid Assessment Method
        (Mack, 2001) on determining what portions of the wetland should be included in the area of assessment(s).
        The CRAM software package makes assessments  standardized and  cost-effective, requiring a team of two
        trained professionals to  invest half of a day conducting preparations and analyses in the office and half of a
        day collecting data  in the field. Real-time  data collection can be conducted using the PC-based data-entry
        and imagery-delivery system eCRAM, which interfaces with the CRAM website and  eliminates the need  to
        produce hard-copy data  in the field.

        CRAM  evaluates wetland condition through an analysis of the size  and structural  complexity of a wetland
        determined through assessments of buffer  and landscape  context, hydrology, physical structure,  and biotic
        structure. Several metrics are used to assess each of these four wetland attributes. For each metric, the assessor
        matches field observations to one of the condition descriptions (A, B, C, or D)  for that metric.  Landscape
        and buffer context is used to estimate the capacity of area surrounding a wetland to shield it from the impacts
        of pollution and pollutants.  Hydrology metrics strive  to characterize the magnitude, intensity, and duration
        of water movement because these  hydrologic characteristics affect  the wetland's structure  as well as the
        movement  of both nutrients and pollutants through the wetland.  The physical structure and biotic structure
        of wetlands are assessed  for their ability to  support ecosystem functioning as indicated by the  complexity of
        wetland site morphology and plant  community composition respectively. The letter  grades associated with
        each of the descriptions  given to the wetland are then converted into ordinal scores  that can be added across
        metrics to obtain a score for each attribute; the attribute scores are then summed to obtain the wetland's overall
        CRAM score. Since the  scoring characteristics are consistent regardless of the scale at which the assessment is
        conducted, wetland scores are comparable across scales.
3-28

-------
                                                                                  3 Examples of Assessment Approaches
The spectrum of output scores from CRAM encompasses ecologically-intact aquatic systems, severely degraded
aquatic systems, and various conditions between these extremes. In the State of California, CRAM scores are
being used to describe  trends in wetland
condition over  time.  When comparing
the CRAM scores of different wetlands, it
is important to  consider that the context
of a wetland can degrade  its condition.
The stressor checklist developed  as part of
CRAM provides assessors with a means
of identifying possible factors  that may
be causing  a wetland to  score  poorly.
Similarly, in  a  regulatory  context  the
stressor checklist can  be used to evaluate
the ecological suitability of sites  proposed
for compensatory mitigation.
                                                                                                           3-29

-------
Identifying and Protecting Healthy Watersheds
          Wyoming Wetland Complex Inventory and Assessment
          Author or Lead Agency: The Nature Conservancy
          More Information: Copeland et al., 2010

        Wetlands are a key component  to assess when evaluating watershed health,  as they lay at the intersection
        of terrestrial and aquatic ecosystems.  Because wetlands support a hybrid of terrestrial and aquatic features, a
        disproportionately large number of wildlife species depend on wetlands at some point in their life histories. This
        point has been particularly noted in Wyoming, where 90% of the state's wildlife species use wetlands, but most
        of the state is arid and lacks the surface hydrology needed to support wetland  complexes and riparian habitat
        (Hubert,  2004; Nicholoff, 2003). Furthermore, these wetlands face a number of potential threats, including
        impacts from surrounding lands that are irrigated, fertilized, or treated with pesticides; urban runoff; dams and
        water withdrawals;  climate change; permitted mines and  underground injection wells; and fragmentation due
        to development of oil and gas reserves or residential subdivisions. The need to protect the health of Wyoming's
        wetlands  is clear; however, with limited resources  available to support conservation and management, it  is
        critical that resources are strategically allocated to the wetlands where protection and restoration will have the
        greatest impact.

        The Nature Conservancy developed a GIS-based assessment tool to aggregate  all the layers of  geospatial data
        for Wyoming, including current and future conditions that decision makers need to consider when developing
        wetland conservation priorities.  Evaluating all data in the same manner at a consistent level for each wetland
        allows decision makers to compare and rank wetlands for conservation. The assessment is done at the wetland
        complex level, which requires that wetlands be mapped and then grouped into  complexes. To map Wyoming's
        wetlands, National Wetlands Inventory data were merged with National  Hydrography Data via a crosswalk
        table. The protection status of the assessed wetlands was determined using merged and intersected datasets
        from the  1994 Wyoming GAP Analysis, the Bureau of Land Management's Areas of Critical Environmental
        Concern, and conservation easement data from Wyoming Land Trusts and  the Wyoming Game and Fish
        Department.  Wetlands were grouped by hydroperiod, and palustrine systems  were selected for study in this
        assessment. Areas in which the wetland density exceeded one per km2 were designated as wetland complexes.

        Several refinements were made to the resulting  set of wetland complexes  to reach the final set of complexes
        shown in Figure 3-10. Wetland complexes less than 200 hectares in size were excluded from  the assessment
        because the datasets used were poorly  suited for such a small scale.  On the other hand, the three largest
        complexes were partitioned into smaller complexes  by ecoregion because  they encompassed too  much
        environmental variability to be assessed as single units. Furthermore, watersheds larger than 40,500 hectares
        were split into their sixth level hydrologic  unit codes (HUC),  although Yellowstone National Park  was
        maintained as a single unit because it is uniformly managed by the National Park Service.

        Each complex was  divided into  hexagons  259 hectares in size. Distribution data for the 49 species identified
        in Wyoming's 2005 Comprehensive Wildlife Conservation Strategy were generated using geospatial data such
        as ecological systems, watersheds, water features, and elevation to predict the presence of each  species in each
        hexagon.  Shannon's Diversity Index  and  rare species richness were calculated for each hexagon. The mean
        values for these indicators were calculated for each  complex, and mean indicator scores were normalized to a
        0-100 scale (Figure 3-11).

        The most current publicly available geospatial data depicting locations and values of factors known to affect the
        functional integrity of wetlands were compiled. This included irrigated lands, urban areas, golf courses, roads,
        dams, permitted mines and underground injection permits, potential sources of contamination (e.g., oil and
        gas wells, wastewater discharge, hazardous waste sites), pipelines, surface water use, toxic contaminants,  and
        county-wide pesticide use. Overall landscape condition was assessed for each wetland complex by summing the
        scores for individual landscape condition factors and scaling those sums from  1 to 100. Individual condition
        factor scores  were  based on  the  mean distance between the wetland complex and the landscape condition
        factor, and normalizing the distances on a zero to one scale. Area-weighted means were used for county-based
        factors.
3-30

-------
                                                                                  3 Examples of Assessment Approaches
  C~) Wetland Complexes
  Wetland Density
     High : 28.0121

     Low: 0

 Figure 3-10 Map of focal wetland complexes shown by wetland density. Density is defined as the unit area of
 wetlands divided by the area of the wetland focal complex. The labels are unique wetland IDs (Copeland et al.,
 2010). Reprinted with permission of Elsevier.

The assessment also examined the vulnerability of each wetland complex to three key potential environmental
changes: oil and gas development, rural residential subdivision, and climate change. A spatial model of oil and
gas development potential based on geophysical and topographic predictor variables was used  to determine
vulnerability to oil and gas development. Each wetland complex was given an area-weighted score based on the
percent of its area that has high (exceeding 75%) potential for oil and gas development. A model forecasting
exurban subdivision development potential in the  United States for 2030 was used to identify cells of land
vulnerable to subdivision development. The percent cover of exurban development cells was calculated for
each wetland complex. Lastly, climate  change vulnerability was assessed using water balance deficit  trends.
Water  balance  deficit  was calculated  by subtracting  total   monthly  precipitation  (mm)  from potential
evapotranspiration for wetland complexes already experiencing drying trends.

Water  balance deficit values for all months were summed for  each year. The ClimateWizard climate  change
analysis tool was used  to calculate linear trends in water balance  deficit; complexes with a positive trend
(increasing water balance deficit) were  treated as vulnerable to climate change. The vulnerability of wetland
complexes to all three land use changes was documented in maps.
                                                                                                           3-31

-------
Identifying and Protecting Healthy Watersheds
               Number of Wetlands
                                                             Condition
                                                      (a)
(b)
                                                                                                    (d)
           Figure 3-11 Wyoming's wetlands ranked by number (a), condition (b), Shannon diversity (c), and rarity (d).
           All rankings are presented using the Jenks  natural breaks method (Copeland et al., 2010). Reprinted with
           permission of Elsevier.

        Two other key land uses that impact wetland condition are agriculture and hunting. To quantify agricultural
        influence, the area and percent of irrigated lands was calculated for each wetland complex. Hunting potential
        was quantified using duck breeding data and duck harvesting data. Where  "average indicated breeding pair
        density" data were available for  duck species, survey areas were given a 10 kilometer buffer and  data were
        extrapolated to wetland complexes by calculating the maximum buffered survey value per wetland complex. In
        addition, the mean annual duck harvest from 2002 to 2005 was calculated within each waterfowl management
        area using data provided by the Wyoming  Game and Fish  Department. The influence  of agriculture and
        hunting potential were also documented in maps.

        The final step of the assessment  is to integrate the appropriate individual assessments of biological diversity,
        protection status, proximity to  sources of impairment,  and susceptibility to  land  use changes to  make
        conservation decisions. The  results highlight wetlands that are supporting high biodiversity, as well as those
        that are most vulnerable to degradation. Some wetlands, especially at lower elevations, fall into both of these
        categories and would thus make good candidates  for protection. It is intended that this assessment will be used
        in Wyoming not only by the Department of Environmental Quality (DEQ) in the development of its wetland
        assessment protocol, but also to inform the State Wildlife Action Plan and nonpoint source pollution control
        program. At the national level, assessments such as this one may help establish a trend emphasizing landscape-
        scale wetlands mitigation.
3-32

-------
                                                                                              3 Examples of Assessment Approaches
3.3  Hydrology

This section provides summaries for some examples of approaches currently being used to assess hydrology. See
Chapter 2 for background information on hydrology.
                         Landscape Condition
            Patterns of natural land cover, natural disturbance regimes,
                lateral and longitudinal connectivity of the aquatic
               environment, and continuity of landscape processes.
                               Habitat
             Aquatic, wetland, riparian, floodplain, lake, and shoreline
                      habitat. Hydrologic connectivity.
                              Hydrology
              Hydrologic regime: Quantity and timing of flow or water
              level fluctuation. Highly dependent on the natural flow
            (disturbance) regime and hydrologic connectivity, including
                     surface-ground water interactions.
            Geomorphology
Stream channels with natural geomorphic dynamics.
             Water Quality
  Chemical and physical characteristics of water.
           Biological Condition
   Biological community diversity, composition,
 relative abundance, trophic structure, condition,
           and sensitive species.
                             Springs are a type
                                of ground water
                                  dependent
                                    ecosystem that are
                                      characterized by
                                       relatively stable
                                       ground water
                                        discharge,
                                        temperature,
                                        and chemistry.
                                    Photo: USFWS.
               Dams can dramatically
                 alter the natural flow
                    regime of a river
                      and disconnect
                       many aquatic
                        species from
                        upstream
                         habitats.
                                                                                                Photo: Jane Hawkey, IAN.
                             The natural flow regime
                                helps to shape
                                   physical habitat,
                                     provides cues
                                      for spawning
                                       and migration,
                                        and maintains
                                        ecosystem
                                        processes.
                                    Photo: BLM.
               Lake levels fluctuate
                 naturally, resulting in
                   variations in lake
                      shore vegetation,
                       including
                        some plant
                        species whose
                        succession is
                        dependent
                        upon lake
                        level cycles.


                    Photo: Melissa Andreycheck, IAN.
                                                                                                                          3-33

-------
Identifying and Protecting Healthy Watersheds
           Ecological Limits of Hydrologic Alteration
           Author or Lead Agency: International Workgroup comprised of Colorado State University, The Nature Conservancy,
            U.S. Forest Service, U.S. Geological Survey, and seven other U.S. and international organizations
           More Information: http://www.conserveonline.org/workspaces/eloha

        The Ecological Limits of Hydrologic Alteration (ELOHA) is a framework for assessing instream  flow needs
        at the regional level where in-depth, site-specific studies are not  feasible. The approach involves  a scientific
        and social process for classifying river segments,  determining flow-ecology relationships,  and  identifying
        environmental flow targets based on socially  acceptable ecological conditions (Figure 3-12). The process is
        flexible, allowing the user to choose between a  number of tools and strategies for each step of the process.

        The concepts put  forth in The Natural Flow Regime (Poff et al., 1997) have rapidly gained acceptance in the
        scientific and resource management community (see Chapter 2). However, due to the difficulty in determining
        the specific flow requirements of a river and its biota, simple "rules of thumb" are still being used  in place of
        scientifically sound environmental flow requirements for the management  of riverine resources (Arthington,
        Bunn, Poff, & Naiman,  2006). This poses a great threat to the nation's freshwater biodiversity. Many aquatic
        and riparian organisms depend on the natural variability in the flow magnitude, duration, timing, frequency,
        and rate of change that characterize the  natural flow regime. ELOHA addresses  the threats to  freshwater
        biodiversity through an  assessment of flow alteration-ecological response relationships  for different types of
        rivers. Classifying rivers  based on their unaltered hydrology allows for limited ecological information to be
        applied to unstudied rivers in the same hydroecological class. This involves the assumption that  ecosystems
        with similar stream flow  and geomorphic characteristics respond similarly  to flow alterations.
               SCIENTIFIC PROCESS
                        Step 1. Hydrologic Foundation
                                                   Step 2. River Classificat/pn (for each analysis node)
Hydrologic
Classification


Geomorphic
Sub-
classification
                                                                                       *7 River Type  /
                                                   Sfep 3. Flow Alteration (for each analysis node)
                        Step 4. Flow-Ecology Relationships
              Monitoring
                             Flow - Ecology
                             Hypotheses for
                             each river type
:cological Data
  for each
inalysis node
Flow Alteration-Ecological
 Response Relationships
   for each river type
Acceptable
Ecological
Conditions


Societal
Values and
Management Needs
        Figure 3-12 Framework for the Ecological Limits of Hydrologic Alteration Process (Poff et al., 2010). Reprinted
        with permission of John Wiley and Sons.
3-34

-------
                                                                                3 Examples of Assessment Approaches
The scientific and social components of the ELOHA framework may be conducted concurrently. The scientific
component involves four steps:

    1.  Building a hydrologic foundation involves the development of a regional database that
        includes daily or  monthly stream flow hydrographs  from both baseline (i.e., natural)
        conditions and developed conditions. The time period of stream flow data should be long
        enough to represent climatic variability (typically about  20 years). Sites where biological
        data have also been collected  should be  included in order to facilitate development of
        flow alteration-ecological response relationships in step  4. Hydrologic modeling can be
        used to extend stream flow records beyond their  dates of data collection or to estimate
        stream flow records at ungaged sites.
    2.  Classifying river  segments involves grouping  rivers  according to similar flow regimes
        and geomorphic characteristics. A nationwide classification of stream flow regimes (Poff
        N. L., 1996) identifies rivers as: 1) harsh intermittent,  2) intermittent flashy  or runoff, 3)
        snowmelt, 4) snow and rain, 5) superstable or stable ground water, or 6) perennial flashy
        or runoff. Other, region-specific, classifications have used temperature (as a surrogate for
        flow) and catchment geomorphic characteristics to classify stream types  (Zorn, Seelbach,
        Rutherford, Willis, Cheng, & Wiley, 2008).
    3.  Compute hydrologic alteration as the  percentage deviation of developed flows from
        baseline flows for  each river segment. Use  a small set of flow statistics  that are strongly
        correlated with ecological conditions (e.g., frequency of low flow conditions, etc.).
    4.  Develop flow alteration-ecological response relationships by associating the degree of
        hydrologic alteration with changes in ecological condition for each river type. Ecological
        data can come from  aquatic invertebrate  or  fish biomonitoring, riparian vegetation
        assessments,  or other sources, but should be  sensitive to flow alteration  and able to
        be validated with monitoring data. Expert knowledge and  a literature review  should
        supplement ecological data.

The social component of ELOHA involves three steps:

    1.  Determining  acceptable ecological  conditions involves  a stakeholder  process  for
        identifying the goals for each  river segment or  river type. ELOHA does not attempt to
        protect or restore  pristine conditions in all rivers. It recognizes society's needs for water
        as well. Therefore, some  amount of degradation may be acceptable to stakeholders in
        some rivers, while other rivers will receive the highest degree of protection.
    2.  Development of the environmental flow targets is  based on the ecological condition
        goals  determined  in the stakeholder process.  The flow  alteration-ecological response
        curves translate acceptable ecological condition  into allowable degree of flow alteration.
    3.  Implementation of environmental flow management incorporates the environmental
        flow targets into existing or proposed water policies and  planning.

There are many instances where stream flow data are not available for computing the flow statistics required
to implement the methodology. A number of tools have been  developed to address  this, including rainfall-
runoff models such as the Soil and Water Assessment Tool and Hydrologic Simulation Program Fortran; water
budget models such as the Colorado River Decision Support System (CROSS); and regression models such as
the Massachusetts Sustainable Yield Estimator (SYE) (The Nature Conservancy, 201 Ib). The Massachusetts
Sustainable Yield Estimator was developed as a USGS/Massachusetts Department of Environmental Protection
collaboration to estimate the unimpacted daily hydrograph for  any stream in southern New England, gaged
or ungaged. Basin characteristics were related to the flow duration curves in gaged streams in order to estimate
the flow duration curve in ungaged streams. The tool  can be used to evaluate the impacts of proposed and
existing withdrawals to determine the baseline stream flow conditions needed for aquatic  habitat integrity and
to estimate inflows to drinking water supply reservoirs for safe yield analyses at ungaged locations  (Archfield,
2009).
                                                                                                         3-35

-------
Identifying and Protecting Healthy Watersheds
        A variety of tools are available for assessing the degree of flow alteration including USGS' Hydroecological
        Integrity Assessment  Process (HIP) and The Nature Conservancy's Indicators of Hydrologic Alteration (IHA).
        The IHA examines 67 biologically relevant flow statistics, quantified in terms of their magnitude,  duration,
        timing, frequency, and/or rate of change. All 67 flow statistics may be evaluated for pre- and post-development
        timeframes and  are  compared to calculate the degree of hydrologic alteration. IHA is available  as  a free
        download from TNC.

        USGS' HIP uses a Hydrologic Index Tool (HIT) to calculate 171 biologically relevant stream flow statistics,
        stream classification,  and a Hydrologic Assessment Tool  (HAT) to determine the degree of departure from
        baseline conditions. The two tools are available for  download from USGS  (U.S. Geological Survey, 2009b)
        and allow the user to calculate all 171 hydroecological indices using daily and peak stream flow data  imported
        directly from  the  National Water  Information System  (U.S. Geological  Survey,  2009b). 10 statistically
        significant,  non-redundant, hydroecologically relevant indices are then chosen out of these 171.  These 10
        indices may include:
            1.   Magnitude of:                      3-  Duration of:
                •   Average  flow conditions.             •    Low flow conditions.
                •   Low flow conditions.                •    High flow conditions.
                •   High flow conditions.            4.  Timing of:
            2.   Frequency of:                           •    Low flow conditions.
                •   Low flow conditions.                •    High flow conditions.
                •   High flow conditions.            5-  Rate of change in flow events.

        Stream classification in the HIP is conducted according to  Poff (1996)  and requires user expertise in hydrology.
        USGS will work with state agencies and other organizations to develop  their own stream  classification tool to
        facilitate the classification process. Such  a tool was created in New Jersey. Similarly, a state-specific HAT was
        created in New Jersey and can also be created for any other  state wishing to do so (Henriksen et al., 2006).
        However, in the absence of a state-specific HAT, the National HAT can be used. This tool helps to determine
        the degree of departure in stream flow from baseline conditions if they have been determined, for example, via
        rainfall-runoff modeling

        The HAT can be used to  evaluate alternative flow management scenarios.  This evaluation can  be  as simple
        as  modifying the flow data in a  spreadsheet and re-importing the data into the tool or can involve the use
        of a sophisticated watershed  model for  simulating future stream flow  under different land use, climate, or
        withdrawal conditions.

        ELOHA advances  the state of the science by relating ecologically relevant  flow statistics from IHA or HIP
        to  biological responses in the riverine or riparian system. The outcome of the ELOHA process is a set of
        ecological-flow standards for  different river types  and ecological condition  goals determined from the flow
        alteration-ecological response relationships and the acceptable ecological conditions determined through the
        social  process. Environmental flow standards are then implemented through protection or restoration strategies
        as part of an overall water policy.

        The case study from Michigan (see next page) provides an example of the practical application of an ELOHA-
        like framework. The Michigan case study is the closest example to date of carrying the science process through
        to  policy implementation,  but  it differs significantly from  ELOHA in: 1) only fish, not entire biological
        communities were  assessed; 2) only minimum flows were examined,  and; 3) current  condition is considered
        "baseline" so flow restoration is not a goal.
3-36

-------
Case   Study
 A  Regional Scale Habitat  Suitability  Model to
 Assess  the Effects of Flow Reduction on Fish
 Assemblages in  Michigan Streams
 More Information: Zorn et al., 2008 (http://www.michigan.gov/documents/dnr/
 RR2089 268570 7.pdfi
 In response to the 2001 Annex to the Great Lakes
 Charter of 1985, the State of Michigan enacted Public
 Act 33 of 2006. This Act required the creation of an
 assessment model to determine the potential effects of
 water withdrawals on the aquatic natural resources of
 the state. Fish were chosen as the indicator of stream
 health because they are widely recognized as indicators
 of stream health by scientists  and are known and
 appreciated by the general public. The state's Ground
 Water Conservation Advisory Council was charged
 with the development of this assessment model.

 Many of the same steps outlined by the ELOHA
 process   were  followed to  build  a  hydrologic
 foundation, classify river segments based on similar
 ecological characteristics, and develop flow alteration-
 ecological response curves for each river type. River
 segments  were delineated  and  classified  based
 on relationships between  fish  species  and water
 temperature in Michigan according to the following
 four categories:
    •  Cold = July mean  water temperature
       <63-5°F (17-5°C). The fish community is
       nearly all coldwater fishes; small changes
       in temperature  do  not  affect  species
       composition.
    •  Cold-transitional =  July  mean  water
       temperature  >63-5°F   (17-5°C)  and
       <67°F  (19-5°C). The fish community is
       mostly coldwater fishes, but some warm
       water fishes are present; small changes in
       temperature cause significant  changes in
       species composition.
   •   Cool (or warm-transitional) = July mean
       water temperature >67°F (19-5°C) and
       <70°F  (21.0°C). The  fish  community
       is mostly warm water  fishes, but some
       coldwater  fishes  are   present;  small
       changes in temperature cause significant
       changes in species composition.
   •   Warm  =  July mean water temperature
       >70°F  (21.0°C). The fish community is
       nearly  all warm water fishes and is not
       affected by small changes in temperature.

Each of the approximately 9,000 river segments was
also given a size classification as follows:
   •   Stream = Segment catchment area <80
       mi2 (207 km2).
   •   Small river = Segment  catchment area
       >80 mi2 (207 km2) and <300 mi2 (777
       km2).
   •   Large river = Segment  catchment area
       >300 mi2 (777 km2).

The  resulting  11 temperature-size  categories are
the  classification  upon which  the flow alteration-
ecological response modeling was then performed
(Figure 3-13).

Using catchment  size,  baseflow yield, July mean
temperature, and fish survey data, impacts to fish
species  and  assemblages were predicted  for  10%
incremental reductions in base  flow for each river
type. The flow alteration-ecological response  curves
(Figure 3-14) developed from this modeling analysis
were  used as a basis  for determining, for each river
type, the level  of flow reduction that would cause
                           Continued on page 3-38
                                                                                           3-37

-------
        an Adverse Resource Impact on the fish community.
        The river-type specific, flow  reduction limits  were
        linked to a database with flow predictions  for rivers
        statewide and a model that predicts effects of ground
        water  pumping   on  stream  flow  (the  hydrologic
        foundation) to develop a water withdrawal assessment
        tool.  This  water  withdrawal  assessment  tool  is
        available as an online decision support system for use
        by  proposed water  users  to  determine whether the
        impacts  of proposed withdrawals combined with all
        existing  withdrawals will  cause degradation of fish
        communities beyond the allowable amount.

        Using the water withdrawal assessment tool, Michigan
        policy makers are  able   to  use  sound  science to
        determine maximum  allowable withdrawal amounts
        that will maintain  fish communities well into the
        future.
    0.00
               025
                          0.50
                                    075
                                               100
Figure 3-14 Example flow alteration-ecological
response curves from Michigan (Zorn et al., 2008).
For this river type, an Adverse Resource Impact (10%
decline in the fish community metric) occurs when
the index flow declines by about 23%.
                                    Cold stream
                                    Cold small river
                                    Cold transitional stream

                                    Cold transitional small river
                                    Cold transitional large river
                                    Warm transitional stream

                                    Warm transitional small river
                                    Warm transitional large river
                                    Warm stream

                                    Warm small river
                                    Warm large river
                         Figure 3-13 Thermal and fish assemblage based classification of
                         streams, small rivers, and large rivers in Michigan (Zorn et al., 2008).
3-38

-------
                                                                                  3 Examples of Assessment Approaches
  Texas Instream Flow Program

  Author or Lead Agency: Texas Water Development Board

  More Information: http://www.tceq.state.tx.us/permitting/water supply/water rights/eflows/resources.html

Recognizing the substantial risk imposed on the State of Texas by rapid population growth and resultant water
shortages, the Texas Legislature enacted Senate Bill 2 to establish the Texas Instream Flow Program (TIFP) in
2001. The Texas Commission on Environmental Quality  (TCEQ), Texas Parks and Wildlife Department, and
Texas Water Development Board are primarily responsible for the development and implementation of the
Instream Flow Program, which relies on "multidisciplinary studies,  considering a range of spatial and temporal
scales,  focusing on essential ecosystem processes, and recommending a flow regime to meet study goals and
objectives."  These  studies are conducted on individual sub-basins,  recognizing that assessment methods must
be consistent across the state, but adaptable to accommodate the diversity of aquatic ecosystems in Texas.

Due to the  relatively long  time frame required to conduct the sub-basin studies under the TIFP, Senate Bill
3 was enacted in 2007 to  provide for an aggressive, adaptive  management process for generating regulatory
environmental flow standards based  on  the best science  currently available. In  accordance with this statute,
each of the  state's basins has a Basin and Bay Area Stakeholder Committee (BBASC), which appoints a Basin
and Bay Expert Science Team (BBEST) to conduct environmental flow analyses and recommend flow regimes
based solely on the best available science. The BBESTs are not permitted to consider other water needs, such as
drinking water, irrigation,  recreation, etc. Once the BBEST makes their recommendations, the BBASC then
considers these other water needs along with the science-based environmental flow recommendations to make
balanced flow management recommendations  to the TCEQ. TCEQ then adopts environmental flow standards
for each river  basin and bay through  a public  rule-making process. Since the statute requires that the BBEST
complete its work within one year and the BBASC complete its work six months later, environmental flow
standards can  be set before a TIFP sub-basin study has been completed.

The sub-basin studies conducted under the TIFP, which are carried out separately from, but strongly influence,
the BBEST studies, focus on hydrology, geomorphology, biology, water quality, and  four environmental
flow components  (Table 3-8). Connectivity and scale (spatial and temporal) are also considered. There are

 Table 3-8 The four primary environmental flow components considered in the Texas Instream Flows Program
 and their hydrologic, geomorphic, biological, and water quality characteristics (Texas Commission on
 Environmental Quality; Texas Parks and Wildlife Department; Texas Water Development Board, 2008).
Component
Subsistence flows
Hydrology
Infrequent, low flows
Geomorphology
Increase deposition
of fine and organic
particles
Biology
Provide restricted
aquatic habitat; Limit
connectivity
Water Quality
Elevate temperature and
constituent concentrations;
Maintain adequate levels
of dissolved oxygen
 Base flows
 High flow pulses
 Overbank flows
Average flow
conditions, including
variability
In-channel, short
duration, high flows
Infrequent, high
flows that exceed the
channel
Maintain soil moisture
and ground water
table; Maintain a
diversity of habitats
Maintain channel
and substrate
characteristics; Prevent
encroachment of
riparian vegetation
Provide lateral
channel movement
and floodplain
maintenance; Recharge
floodplain water table;
Form new habitats;
Flush organic material
into channel; Deposit
nutrients in floodplain
Provide suitable
aquatic habitat; Provide
connectivity along
channel corridor
Serve as recruitment
events for organisms;
Provide connectivity
to near-channel water
bodies

Provide new life phase
cues for organisms;
Maintain  diversity of
riparian vegetation;
Provide conditions for
seedling development;
Provide connectivity to
floodplain
Provide suitable in-channel
water quality
Restore in-channel water
quality after prolonged low
flow periods
Restore water quality in
floodplain water bodies
                                                                                                           3-39

-------
Identifying and Protecting Healthy Watersheds
                                               Stage 1: Identify and Engage Stakeholders
                                            Stage 2: Conduct Sub-basin Orientation Meetings
                                                                                 Reconnaissance and Information
                                                                                        Evaluation
                                               StageS: Establish Sub-basin Workgroups
                                               and Conduct Study Design Workshops
                                                                                Goal Development Consistent with
                                                                                  SoundEcological Environment
                                                                                       Study Design
                                            Stage 4: Conduct Data Collection Workshops/Field
                                                   Demonstrations (by request)
essentially four steps in the process of conducting a sub-basin study (blue boxes in Figure 3-15) and hydrology,
geomorphology, biology, and water quality are all considered at each step. In addition, stakeholder involvement
and peer review are incorporated throughout the process (yellow and pink boxes in  Figure 3-15)-  The end
result is  a flow regime prescription that includes targets for each of the four environmental flow components:
subsistence flows, base flows, high flow pulses, and overbank flows.

The primary objective of the subsistence flow component is to maintain water quality. Hydrologic and water
quality models are used  to relate biologically-relevant water quality constituents to low flow conditions so that
flow management guidelines that maintain these constituents  within their  natural range can  be identified.
The  primary   objective  of the
base flow component is to ensure
adequate   habitat   conditions,
including their natural  variability.
GIS-based physical habitat models
are  used along  with  biological
and  geomorphic  data  collected
in  the  field  to  determine the
habitat  versus  flow relationships
specific  to each  river basin.  Flow
management     guidelines    are
developed (often  for wet, average,
and  dry conditions)   to  ensure
that base flows adequately protect
the  target species or guilds.  The
primary objective of the high flow
pulse component is to maintain
physical habitat  and longitudinal
connectivity. Hydrologic statistics
that characterize the magnitude,
frequency, timing,  and shape of
high flow pulses can then be used
along with  geomorphic data and
sediment budgets to  ensure  that
habitat structure  and connectivity
adequately  support the   aquatic
biota. The primary objective of the
overbank flows  component  is to
maintain riparian areas  and lateral
connectivity with the  floodplain.
Geomorphic      studies      that
characterize the  active  floodplain
and channel   processes  are  used
with  flood  frequency statistics  to
model  the  extent  of  inundation
during flood events.
Multidisciplinary Data Collection
     and Evaluation
                                             StageS: Conduct Data Integration Workshops
  Data Integration to Generate
   Flow Recommendations
                                                                                     Draft Study Report
Stage 6: Review Study Report

+

Final Study Report
E
                                                                                       Next Steps:
                                                                                 Implementation, Monitoring, and
                                                                                    Adaptive Management
                                             Figure 3-15. Diagram of the Texas Instream Flows Program process.
                                             Blue boxes represent the four primary steps, green boxes represent
                                             deliverables, yellow boxes represent public outreach components,
                                             and pink boxes represent peer review steps (Texas Commission on
                                             Environmental Quality; Texas Parks and Wildlife Department; Texas
                                             Water Development Board, 2008).
3-40

-------
Case   Study
 San  Antonio  River Basin
 More information: http://www.twdb.state.tx.us/instreamflows/sanantonioriverbasin.html
 The San Antonio  River Basin occupies 14 counties
 in south central Texas and  has  experienced rapid
 population  growth and development  over the past
 several decades. The increased use of ground water
 to support  this rapid development, combined with
 increased areas of impervious  surface,  has  led  to
 increased base flows as a  result of the dramatically
 increased wastewater return  flows. Depending  on
 future water management policies in the basin, this
 trend  could  continue  (as population grows even
 further) or  reverse (if water reuse policies are put in
 place). Based  on  these  concerns, development  of
 a TIFP sub-basin  study design for the San Antonio
 River  Basin began  in 2006. A BBASC was named in
 the fall of 2009, a BBEST was named in the spring
 of 2010, the BBEST  recommendations report was
 submitted  on March 1,  2011,  and  the  BBASC
 recommendations report was submitted on September
 1,2011.

 To  maintain consistency  with the  separate  TIFP
 sub-basin  study,  the  BBEST selected  indicators
 representing hydrology, biology,  water quality, and
 geomorphology for the larger Guadalupe River Basin,
 San  Antonio  River  Basin,  San  Antonio—Nueces
 Coastal  Basin, San Antonio  Bay,  and the Mission,
 Copano,  and Aransas  Bays  (the GSA Basins). The
 first step in  the assessment  was to select flow gages for
 which environmental flow recommendations would
 be developed. Sixteen USGS gages in the GSA Basins
 were selected,  ensuring that  a range of hydrologic,
 water  quality, geomorphic, and biological conditions
 were  represented.  Using   the   Hydrology-based
 Environmental Flow Regimes (HEFR) methodology,
 initial recommendations were developed based  on
 the long-term hydrologic data collected from  the
 USGS gages.  The  HEFR  methodology  involves
 hydrograph  separation to  parse  the hydrograph
 into   components  that  provide  the  ecological
 functions described  in Table 3-8. This facilitates
 characterization of the four flow regime components:
 subsistence  flows,  base flows, high flow pulses, and
 overbank flows.  Additional  steps  in the  HEFR
 methodology include  selection  of an appropriate
 period of record  and selection of the appropriate
 length and number of  seasons  for development
of  environmental  flow  recommendations.  Once
the initial  flow  recommendations were  developed
through the HEFR process, a number of ecological
"overlays" were developed and used to refine the flow
recommendations as necessary.

A Biology Overlay was developed based on habitat
suitability   curves.  Habitat suitability  curves  are
created by  identifying habitat guilds, or groups  of
species using similar  habitats, and relating habitat
characteristics  to different  hydrologic  conditions.
For  example,  the Texas  Logperch  and  Burrhead
Chub both rely on shallow riffle  habitat for critical
stages of their life.  Fish abundance and associated
depth, velocity,  and  substrate data are  compiled
from  multiple studies to determine the relationship
between fish use  and  habitat characteristics. A focal
species is then selected for each  habitat guild and
the species-specific habitat suitability curves are used
as the basis for defining overall habitat guild habitat
suitability curves. Habitat-discharge relationships are
then determined  through physical habitat  modeling
and, finally, results of the HEFR analysis are used to
estimate habitat availability for various discharges at
the sixteen flow recommendation sites.

A Water Quality Overlay was  also developed by the
BBEST. This involved  regression  analyses  between
water quality variables of concern and flow. Dissolved
oxygen, pH,  conductivity,  temperature,  ammonia-
nitrogen,  total  phosphorus,  and  total  kjeldahl
nitrogen were all evaluated. Results of these analyses
showed no  significant relationships and thus do not
impact the environmental flow recommendations.

For the BBEST  Geomorphology  Overlay, sediment
transport was evaluated with sediment rating curves.
Sediment rating curves allow for  an examination of
relationships between flow and  transport of sediments
of various  sizes.  Combined with a flow duration
curve, sediment rating curves can be used to estimate
effective discharge — "the (relatively narrow) range of
flows  from  the entire  range  of flows associated with
some  hydrologic  condition that transports the most
sediment over time." This can be  thought of as  the
channel forming  flow that must be attained in order
                             Continued on page 3-42
                                                                                                    3-41

-------
         to maintain stream channel shape over time. Current
         and proposed flow regimes can then be evaluated to
         determine  their impact on the shape  of the  stream
         channel. It was found that maintaining the effective
         discharge within  +/-  10%  of current  conditions
         requires a flow regime that does not fall below 80%
         of the current average annual water yield. While this
         information was included in the BBEST report, there
         was no  formal recommendation to maintain 80% of
         the current average annual water yield.

         The  results  of the  biological,  water  quality,  and
         geomorphology overlays  were  compared with the
         initial  HEFR  recommendations  and  modifications
         were made  to  ensure protection of these attributes.
         In   order   to  account   for  variable   hydrologic
         conditions,  high,  medium,  and  low  flow  criteria
         were determined.  These  flow  levels  are calculated
         on the first day of each season and are based  on the
              previous 12-months of flow data. High flow pulse and
              overbank  flow recommendations  are not subject to
              these hydrologic conditions. The final environmental
              flow recommendations were then developed for the
              16 USGS gage sites in  the Guadalupe-San Antonio
              system (Figure 3-16).

              These matrices form the quantitative recommendations
              of the BBEST. Details on the implementation of these
              values are included in the recommendations report.
              Most importantly, these flow values are solely intended
              as  pass-through  conditions on  new  and  amended
              water rights.  They are not  intended or  expected to
              be achieved all of the time and  these pass-through
              conditions will  not  be  imposed on  existing  water
              rights.  These  matrices were subsequently  modified
              by the BBASC and both reports are under  review at
              TCEQ for future rule-making.
                              Qp: 1,520 cfs with Avera
                               Frequency 1 per season
                             Regressed Volume is 12,800
                                Duration Bound is 19
Qp: 3,540 cfs with Average
 Frequency 1 per season
Regressed Volume is 30,000
  Duration Bound is 24
Qp: 1,640 cfs with Average
 Frequency 1 per season
Regressed Volume is 11,200
  Duration Bound  is 16
Qp: 2,320 cfs with Average
 Frequency 1 per season
Regressed Volume is 17,600
  Duration Bound  is 19
                              Qp: 550 cfs with Average
                               Frequency 2 per season
                              Regressed Volume is 3,940
                                Duration Bound is 11
Qp: 1,570 cfs with Average
 Frequency 2 per season
Regressed Volume is 11,300
  Duration Bound is 16
 Qp: 750 cfs with Average
 Frequency 2 per season
Regressed Volume is 4,450
  Duration Bound is 10
 Qp: 780 cfs with Average
 Frequency 2 per season
Regressed Volume is 5,070
  Duration Bound is 11
                                           High (75th %ile

                                           Medium (50th %ile)
                                           Low (25th %ile)
                                           Subsistence
               Notes:
                 1. Period of Record used: 1/1/1940 to 12/31/1969.
                 2. Volumes are in acre-feet and durations are in days.
                 Figure 3-16. Environmental flow regime recommendations for the San Antonio River at Goliad
                 (GSA BBEST, 2011).
3-42

-------
                                                                                 3 Examples of Assessment Approaches
   Hydrogeomorphic Classification of Washington State Rivers
   Author or Lead Agency: University of Washington, National Oceanic and Atmospheric Administration, Australian
    Rivers Institute, Skidmore Restoration Consulting, United States Geologic Survey, and The Nature Conservancy
   More Information: Reidy Liermann et al., 2011

Hydrologic classification is a necessary prerequisite to the development of regional environmental flow rules. By
determining the stream flow characteristics common amongst rivers across a state or region, limited ecological
response data  can  be  extrapolated to other streams and rivers with similar flow regimes. In addition to the
stream flow characteristics common amongst rivers, aquatic habitat is also strongly influenced by geomorphic
characteristics. Thus, classification systems based on both hydrologic and geomorphic characteristics result in
improved resolution of flow alteration — ecological response relationships used in the development  of regional
environmental flow standards.

Scientists from the University of Washington, National Oceanic and Atmospheric Administration, Australian
Rivers Institute, Skidmore  Restoration  Consulting,  United  States Geologic Survey,  and The Nature
Conservancy developed a statewide hydrogeomorphic classification for streams and rivers in Washington State.
In addition to predicting the unregulated hydrologic and geomorphic characteristics of ungaged streams, the
classification incorporates climate change projections and potential reassignment of streams to different flow
classes in the future. The classification fills data gaps across the state at the resolution of practical management
units  that will support the development of regional environmental flow protection  programs that  are flexible
and responsive to the expected ecological responses that will result from climate change.

Sixty-four reference gages were first selected  out of a total of 372 stream gages with long-term  (>15  years)
flow records. The upstream catchment areas were  delineated for all gages and those with no more than one
dam regulating <5%  mean annual discharge, <10% urban or agricultural land use, and <20% water rights
or permits allocation  were identified as reference  gages. With  a goal of maximizing the spatial coverage of
reference stream gages, these  criteria were then relaxed somewhat to  ensure that a sufficient number of gages
encompassed all ecological drainage units in the state.

Hydrologic classification was performed using Bayesian mixture modeling and a classification tree based on
recursive partitioning (Figure 3-17), while the geomorphic classification was based on whether a channel is
able to migrate and create a  floodplain or not. This was determined based on estimates of the confinement
ratio using a digital elevation model, precipitation, and field measured geomorphic data. The hydrologic and
geomorphic classifications were then combined into a 14-tier  hydrogeomorphic classification. Other than
elevation, drainage basin characteristics did not prove to be as strong predictors of hydrogeomorphic class as
the climatic variables.  This is in contrast  to hydrogeomorphic  classifications conducted in other  states.  The
interactive effects of elevation and precipitation variables in the classification are a result of snowpack typically
melting later in the season at higher elevations. The timing and magnitude of this snowmelt runoff are the most
influential hydrologic metrics in the classification.  This suggests  that climate  change may result in significant
changes to the hydrologic regimes of Washington streams and rivers if high elevation snowmelt occurs earlier
in the season.
                                                                                                          3-43

-------
Identifying and Protecting Healthy Watersheds
                              I     •
      March Precipitation £ 261.7 mm
     •       I          I       ~
                                                                 March Precipitation < 185.6 mm
                        Rainfall
                          r>=7
Rain-Snow
   n=17
                                                       January Temperature
                                                             > -5.0 °C *
                Naturalized
                Hydrologic Classes
                i     i Ultra-Snowmelt
                ^^H Snowmelt
                i     i Snow-with-Rain
                i     i Snow-and-Rain
                I     I Rain-with-Snow
                I     I Rainfall
                ^^H Groundwater
          Annual Snow
      Depth < 1,741 mm**
                                   Snow&Rain
                Minimum Winter       n=14
             Temperature < -7.7 °C
  Groundwater
       r>=3
Snow-Rain
    n=7
                                                  u
                                                                       Ultra-   Snowmelt
                                                                    Snowmelt    n=w
                                                                        n=6
                Figure 3-17 Classification tree showing the seven naturalized hydrologic classes. Combined
                with the geomorphic classification distinguishing between migrating and non-migrating
                channels, the number of stream classes doubles (Reidy Liermann et al., 2011).

        Shifts in hydrologic class as a result of climate change were predicted using both high and low emissions
        scenarios produced  from the  Intergovernmental Panel  on Climate Change's ensemble  of global circulation
        models. The projected changes in precipitation, temperature, and snowfall were input into the random forest
        classifier (i.e., collection of classification trees) to produce the projected future hydrologic classification. Results
        from both climate change scenarios indicated large-scale shifts from streams dominated by snowmelt runoff to
        streams dominated by rainfall runoff. The number of streams that are currently classified as 'ultra-snowmelt',
        for example, decreased by 86% while streams currently classified as 'rainfall' increased by over 125%. Ground
        water-dominated streams were relatively insensitive to climate changes.

        The results of the climate change analysis are generally consistent with other findings for the region and allow
        for management  planning at the reach scale. The affected stream reaches represent one third of the state's total
        river miles and alteration of their flow regimes will have large effects on the timing of water availability. This
        will have far-reaching  effects on both humans and aquatic ecosystems, as earlier snowmelt will result in less
        runoff to water supply reservoirs during the summer months and loss of biological refugia during summer low
        flows. For example, five Pacific Northwest salmon and  steelhead species are currently listed  as threatened  or
        endangered under the Endangered Species Act. With  flow alteration cited as the primary cause of their decline,
        the ability to target specific management actions to specific stream classes that these species depend on will be
        critical.
3-44

-------
                                                                                 3 Examples of Assessment Approaches
   Ground Water Dependent Ecosystems Assessment
   Author or Lead Agency: The Nature Conservancy
   More Information: http://tinyurl.com/GDE-Workspace

Ground water is a vital source of water that sustains ecosystems, aquatic species, and human communities
worldwide. Wetlands, rivers,  and lakes often receive inflow from ground water; it provides late-summer flow
for many rivers, and creates cool water upwelling critical for aquatic species during the summer heat. These
species and ecosystems that rely on ground water discharge for water quantity or quality are collectively called
ground water dependent ecosystems, or GDEs.

The Nature Conservancy has developed tools to map and understand GDEs at two scales. At the landscape
scale (i.e., multiple adjacent  watersheds), a GIS-based  assessment  tool is available to identify  and map all
types of GDEs and the land  uses and human activities that threaten their ecological integrity. At the scale of
individual watersheds,  tools are available to assist in understanding ground water processes and characterizing
the ground water requirements  of individual GDEs. These  tools were developed and tested in the Pacific
Northwest;  detailed analyses  are available  for Oregon and similar assessments were developed in Washington
and California. The assessment tools should be transferable to  most watersheds, providing technical expertise is
available to ensure that the local hydrogeologic context is adequately incorporated.

Landscape  scale assessment. The Oregon Groundwater Dependent Biodiversity Spatial Assessment (Brown ].,
Wyers, Bach, & Aldous, 2009a) is a GIS-based screening methodology  that uses existing datasets to identify
and locate  ground water-dependent ecosystems and describe threats  to their integrity and sustainability. It
describes the assessment processes, and includes a detailed description of the GIS-based analysis methods. A
companion  document, Atlas  of Oregon Groundwater Dependent Biodiversity and Associated Threats (Brown ].,
Wyers, Bach, & Aldous, 2009b; Brown, J., Bach, Aldous, Wyers, DeGagne, 2011) contains all of the maps
that were produced using this assessment protocol for Oregon. The assessment is focused on the landscape scale
and relies on readily available  data sets. These data include physical parameters (e.g., soils, geology, topography,
surface hydrology, and hydrogeology), and biological data (e.g., species distributions maps of wetlands and
springs, and vegetated land cover).

The analysis is carried out in  two steps. First, data are analyzed to determine the distribution of GDEs across
the landscape. Obligate GDEs, such as springs, are ground water-dependent regardless of where they occur.
Facultative GDEs such as certain wetlands, rivers, and lakes, may be fed  by ground water, depending on their
hydrogeologic setting. Thus, further analysis is required to evaluate whether these ecosystems are GDEs. The
assessment  includes analysis tools for determining whether a specific ecosystem is ground water-dependent.
Once each  freshwater ecosystem  is coded as being a GDE or not, the data are aggregated at the  HUC12 scale.
This is done to better understand the relative importance of ground water in different areas of the landscape.
A rule set was developed to classify HUC12 units that contain relatively high densities of GDEs (Table 3-9).
The specific rule sets may need to be modified for other landscapes, depending on  the relative distribution of
GDEs. Once each HUC12 was coded as containing  GDEs,  the data were further aggregated  by number of
GDE types  within the HUC (Figure 3-18). For example, a green HUC12 has three types of GDEs, and can
include springs, a wetland, and a river that are all ground water-dependent.

Table 3-9 Criteria used to identify HUC12s in Oregon where ground water is important for
freshwater ecosystems  (Brown et al., 2009a).
 Springs                 Contains >1 spring/2236 ha (5525 acres)
 Wetlands                Contains a fen OR Area of ground water dependent wetlands >1% of HUC12 area
 Rivers                   Contains ground water dependent river
 Lakes                   Contains a lake
 Species and communities    Contains an  obligately ground water dependent species or community
                                                                                                         3-45

-------
Identifying and Protecting Healthy Watersheds
          Figure 3-18 Ground water dependent ecosystem clusters (blue through red). Number of ground water
          dependent ecosystems present in each HUC12, per criteria in Table 3-9 (Brown et al., 2009a).

        The second step in this landscape-scale assessment is to identify and map threats to ground water and GDEs.
        The  ecological integrity of GDEs  may  be impacted by  activities that threaten their  essential  ecological
        attributes, specifically from alterations to water quantity, water quality (chemistry and temperature),  and direct
        habitat destruction. Specific methods  are  included for evaluating  current and potential future threats such as
        ground water extraction for irrigation and domestic use,  as well as contamination from nutrients,  pesticides,
        and toxic chemicals. This analysis uses available data of the  human fingerprint on the landscape  (e.g., land
        use; municipal, agricultural, and industrial water uses; population projections; and waste disposal  types and
        locations).

        In some cases, further analyses were required to evaluate the threat of certain activities to GDEs. One example
        is the effect of pesticides  on GDEs. Very  few data are available  quantifying the presence of agricultural
        pesticides in ground water outside of drinking water systems. For any one of these pesticides to pose  a threat to
        a GDE, it must be mobile in ground water, toxic to aquatic life, and have the potential to move from its source
        to the GDE. Therefore, the 43 pesticides registered for agricultural uses in Oregon were evaluated. Of those,
        10 were mobile in ground  water and toxic to aquatic life. HUC12 reporting units that  have soils with low
        potential to retain those 10 pesticides (meaning they would be easily transported in ground water)  were then
        identified.  Finally, HUC12 reporting  units meeting all three  of the following criteria were identified: at least
        one of the  10 mobile pesticides is applied in the HUC, the soils do not retain the pesticides, and GDE clusters
        are present. GDEs in these HUCs are at highest risk of pesticide contamination.
3-46

-------
                                                                                 3 Examples of Assessment Approaches
Watershed scale assessment. The Groundwater Dependent Ecosystem Methods Guide (Brown ]., Wyers, Aldous,
& Bach,  2007) was developed to  help  resource  managers and conservation groups identify site-specific
GDEs, understand their ecological requirements, and incorporate this information into water resources and
biodiversity conservation plans. The assessment is focused on the watershed or project  scale,  and utilizes
more site-specific information than  the landscape scale assessment. This protocol includes three sections:  1)
determining if ecosystems within the planning area are GDEs, 2) characterizing the ground water requirements
of each type of GDE, and 3) understanding and mapping the ground water flow systems that provide ground
water discharge to those GDEs.

The  assessment provides a set of decision trees for evaluating whether an ecosystem is dependent on ground
water. This involves a series of yes/no questions in sequence, similar to a dichotomous key used in plant  or
animal taxonomy. Individual decision trees are provided for wetlands, rivers, lakes and species. An example
decision tree is provided for rivers (Figure 3-19). As described above, springs and subterranean ecosystems are,
by definition,  ground water-dependent.

Once an ecosystem or species has been determined to be a GDE, characterizing its ground water requirements
is  an important step  in  protecting  and/or restoring its  ecological integrity, and in conducting adaptive
management  of that resource.  This is  done  by identifying  the  essential  ecological attributes,  or  EEAs,
identifying measurable indicators that can be used to track the status of the EEAs over time, and describing a
desired future condition for each of those EEAs.

While different  types of GDEs will  have different EEAs, two categories of EEAs are common to all GDEs:
water quantity and water quality. Water quantity is a  function of the hydrogeology of the contributing area
and  ground water discharge to the ecosystem,  and water quality is generally expressed in terms of the water
chemistry or water temperature. Indicators specific to a particular GDE can be developed based on  these two
EEAs. Table 3-10 provides an example for ground water-dependent rivers.

Finally, the ground water flow system can be characterized to understand the context of the GDE in relation to
its ground water sources. This includes identifying ground water recharge and discharge areas and developing
conceptual ground water flow paths. These final steps, as well as  the previous two, are illustrated  in the
following case study from Whychus Creek, in the Deschutes Basin, Oregon.

Table 3-10 Essential ecological attributes associated with ground water and potential indicators of the integrity
of rivers: (Brown et al., 2007).
    Essential Ecological Attribute
 Temperature regime


 Hydrologic regime
                             Indicator
Maximum 7-day average of daily maximum temperature
Location and number of thermal refugia
Number of zero-flow days
Trend in annual mean low flow
Location and continued presence of springs/seeps adjacent to the stream.
                                                                                                          3-47

-------
Identifying and Protecting Healthy Watersheds
             Ql: Does the stream
              flow year-round?
        No
                    Low
                 likelihood of
                groundwater
                dependence
                    Yes
               Q2: Are springs
                present in the
              drainage nearthe
                  streams?
Yes
  Q2A: Is summer
  precipitation a
significant source of
      water?
                                   No
    High
 likelihood of
groundwater
dependent—
             Q3: Are snowfields or
                glaciers in the
                headwaters?
                     No
   Yes
                                                           Yes
       likelihood of
       groundwater
       dependence
                Q4: Is summer
                precipitation a
             significant source of
                   water?
               Yes
                                No
                       High
                    likelihood of
                   groundwater
                   dependence
          Figure 3-19 Decision tree for identifying ground water dependent river ecosystems (Brown et al., 2009a).
3-48

-------
Case   Study
 Identifying GDEs and  Characterizing their
 Ground Water  Resources  in the Whychus
 Creek Watershed
 More Information: http://tinvurl.com/GDE-Workspace
 The Whychus Creek Watershed, located in Oregon's
 Upper Deschutes Basin, offers a good illustration of
 how a combination of GIS datasets and decision trees
 can be  used to identify GDEs. Using the decision
 tree for river ecosystems, TNC determined that the
 rivers in the Whychus Creek Watershed  are highly
 likely to be ground water dependent, because they
 are  perennial (determined through examination of
 the National Hydrography Dataset (NHD)), they are
 associated with springs,  and  summer precipitation
 is not a significant  source of water. USGS gage data
 further confirm the high likelihood of ground water
 dependence, because they show that low flow is 59%
 of annual mean monthly flow, and base flow is active
 through  most  of the year. Lastly, seepage-run data
 provided by the Oregon Water Resources Department
 and USGS gage data indicate that stream reaches in
 the  Whychus Creek Watershed are gaining streams
 (i.e., ground water discharges into them).

 To identify ground water dependent wetlands, TNC
 compiled datasets for known and potential wetlands
 from the NWI, the Northwest  Habitat Institute's
 Interactive  Biodiversity System, STATSGO, and the
 Deschutes Wetland Atlas developed by the Deschutes
 River Conservancy. Applying the wetlands ecosystem
 decision  tree, TNC determined that  both subalpine
 parkland and wet meadow wetlands in the Whychus
 Creek Watershed are highly likely to be ground water
 dependent, because they are present year  round and
 they either occur in slope breaks or are associated with
 springs or seepage areas.

 Using the  decision tree for lake  ecosystems,  TNC
 determined  that lakes in the  watershed are  likely
 to depend  on  local ground water for part of their
 water supply, because they are located on permeable
 geologic deposits, no seeps or springs are known to
 discharge into the lakes, and the lakes are located in
 the upper portion of the watershed.
Spring ecosystems, which are ground water dependent
by definition, were mapped  using  data from the
USGS  Geographic Names  Information  System,
the Pacific Northwest  Hydrography  data layer, the
Oregon  Gazetteer, and Forward Looking  Infrared
data.  Phreatophytic  ecosystems  (above  ground
ecosystems that depend on subsurface expressions of
ground water) were not included in  this assessment
because extensive laboratory study would be needed
to confirm  their  dependence  upon  ground water.
Subterranean ecosystems were also not considered in
this assessment, because there are no mapped caves in
the Whychus Creek Watershed.

The assessment also identified ground water dependent
species in the watershed. Species that were potentially
dependent upon ground water were  identified from
TNC's  ecoregional assessment and the U.S. Forest
Service's watershed  analysis.  This list was refined
with input from local experts to consist exclusively of
ground water dependent species by comparing species
distributions with the distributions of ground water
dependent ecosystems in the watershed.

The assessment then used geologic and topographic
maps to delineate the ground water contributing area,
which in this case  matched  the surface watershed
for Whychus  Creek. A layer  of precipitation  data
was used  with the geologic data layer to locate  wet,
permeable areas that are likely sites for ground water
recharge.  Recharge areas were  refined using USGS'
Deep Percolation Model. Horizontal flow paths were
mapped,  connecting ground  water  recharge  and
discharge sites. Hydrogeologic cross-sections  were
developed from geologic and topographic maps using
ground water recharge  and discharge data. Vertical
ground water flow paths were mapped on the cross-
sections. These recharge, discharge, flow path,  and
GDE distribution data  are now available to inform
conservation priorities  for   the Whychus Creek
Watershed (Figure 3-20).
                            Continued on page 3-50
                                                                                              3-49

-------
         Figure 3-20 Ground water dependent biodiversity in the Whychus Creek Watershed (Brown et al., 2007).
3-50

-------
                                                                                            3 Examples of Assessment Approaches
3.4  Geomorphology

This section provides summaries for some examples of approaches currently being used to assess geomorphology.
See Chapter 2 for background information on geomorphology.
                         Landscape Condition
            Patterns of natural land cover, natural disturbance regimes,
               lateral and longitudinal connectivity of the aquatic
               environment, and continuity of landscape processes.
                              Habitat
             Aquatic, wetland, riparian, floodplain, lake, and shoreline
                      habitat. Hydrologic connectivity.
                             Hydrology
             Hydrologic regime: Quantity and timing of flow or water
              level fluctuation. Highly dependent on the natural flow
            (disturbance) regime and hydrologic connectivity, including
                     surface-ground water interactions.
            Geomorphology
Stream channels with natural geomorphic dynamics.
             Water Quality
  Chemical and physical characteristics of water.
           Biological Condition
   Biological community diversity, composition,
  relative abundance, trophic structure, condition,
           and sensitive species.
                              High gradient
                               mountain streams are
                                  characterized by
                                    relatively straight
                                     stream channels
                                      and larger
                                      substrate, such
                                       as cobble and
                                       boulders.
                                   Photo: BLM.
                Meandering is a
                common characteristic
                   of low gradient
                     streams and
                      is critical to
                       the physical
                        stability of the
                        channel and
                        the health of
                        the stream.
                                                                                              Photo: USFWS.
                              Maintenance of a river
                                channel's lateral
                                  connectivity with its
                                    floodplain allows
                                     for the natural
                                      regime of flood
                                       disturbance
                                       to effectively
                                       influence
                                       riparian
                                      biodiversity.


                                   Photo: NRCS.
                Stream geomorphic
                 state and processes
                   are intricately tied
                     to aquatic habitat
                      condition
                       and macro-
                        invertebrate
                        community
                        composition.
                                                                                              Photo: USFWS.
                                                                                                                        3-51

-------
Identifying and Protecting Healthy Watersheds
          Vermont's Stream Geomorphic and Reach Habitat Assessment Protocols
          Author or Lead Agency: Vermont Agency of Natural Resources
          More Information: http://www.vtwaterquality.org/rivers/htm/rv geoassess.htm

        The Vermont Agency of Natural Resources (VTANR) is using fluvial geomorphic-based watershed assessments
        to plan and manage streams toward their natural dynamic equilibrium. The state has developed a series of
        assessment  protocols that are broken down into three phases, facilitating assessment at multiple scales. A
        growing statewide database of fluvial geomorphic and physical habitat data collected through the use of these
        protocols is allowing resource managers across Vermont to understand river systems as integral components of
        the landscape and to classify river segments according  to reference conditions specific to Vermont. Vermont's
        Stream Geomorphic Assessment  Protocols (Kline, Alexander, Pytlik, Jaquith, & Pomeroy, 2009) provide
        resource managers  with a method to characterize riparian and instream habitat, stream-related erosion  and
        depositional process, and fluvial erosion hazards for informing watershed planning and management activities
        that  are ecologically sustainable and that  avoid  conflicts between human investments  and river systems.
        Vermont has fully integrated Reach Habitat Assessment Protocols (Schiff, Kline, & Clark, 2008) with stream
        geomorphic protocols to evaluate habitat connectivity and the departures in natural hydrologic, sediment, and
        woody debris regimes that explain physical processes and alterations to the hydro-geomorphic units associated
        with shelter, feeding, and reproductive habitats (Table 3-11).

        Table 3-11 Parameters and variables in the Vermont Reach Habitat Assessment Protocol
         (Schiff, Kline, & Clark, 2008).
                 Key Ecological Processes
    Aquatic Life Cycle Requirements
Cover/Shelter Habitat based on:
        The Vermont Stream Geomorphic and Reach Habitat Assessment Protocols provide resource managers with
        a scientifically sound, consistent  set of tools to classify, assess the condition of, and design management
        approaches for  the state's flowing water  resources.  The protocols are separated  into  three phases.  Phase 1
        includes watershed-scale assessments that  are based on valley land forms, geology, land use, and channel and
        floodplain modifications,  and are typically conducted with remotely-sensed data. Stream type,  condition,
        fluvial processes, and sensitivity are provisionally assigned and can be refined in phases 2  and 3- Although
        phase 1 assessments  are  primarily desktop analyses, a few months  is typically necessary to assess a large
        watershed. Phase 2 assessments are rapid field assessments. Channel  and floodplain cross-section, as well as
        stream substrate are measured. Qualitative field  evaluations of erosion and depositional processes, changes in
        channel and floodplain geometry, and riparian land use/cover are used to identify geomorphic and physical
        habitat condition, adjustment processes, reach sensitivity, and stage of channel evolution. A phase 2 assessment
        on a one mile reach requires one to two days in the field to complete. Phase 3 assessments are survey-level field
3-52

-------
                                                                                  3 Examples of Assessment Approaches
assessments. Quantitative measurements of channel dimension, pattern, profile, and sediments confirm, and
provide further detail on, the stream types, hydraulic conditions, and adjustment processes identified in phases
1 and 2 (Figure 3-21). Phase 3 assessments are used to characterize reference reaches and to gather intensive
data for river  corridor protection or  restoration projects. Phase 3  assessments require three to four days to
survey a sub-reach of two meander wavelengths, as well as professional level stream survey and geomorphic
assessment skills and equipment.

Interactive web-based data storage, retrieval, and mapping systems, as well as spreadsheets and GIS tools, have
been developed by VT ANR to  facilitate data reporting and analysis for all three  phases of the assessment
process. Whether the user decides to  perform the phase 1 screening level assessment or the detailed  phase 3
assessment, they will have a better understanding of the physical conditions of their streams and the  linkages
of stream channel condition with watershed inputs and floodplain and valley characteristics. Assessing the
streams access to its floodplain; sediment size, quantity, and transport processes; erodibility of the stream bed
and banks; and runoff characteristics  of the watershed allows for a  classification of stream type. The resource
manager then  categorizes the stream type as a reference stream type — the natural stream type in  relation to the
natural watershed inputs and valley characteristics, existing stream type — the stream  type and processes under
current conditions, or modified reference stream type — the stream type that may evolve as a result of the human
imposed channel, floodplain, or watershed changes. The existing stream  type is often the same as the reference
stream type, with the exception that its geomorphic and physical habitat condition  is different. Stream reach
condition can  be assessed as  in regime — exhibiting dynamic equilibrium, in adjustment— changing in form and
process  outside of natural variability,  or active adjustment and stream type departure — exhibiting  adjustment
to a new stream type or fluvial process as a result of a change in floodplain function and/or watershed inputs
(Figure  3-22). In addition,  a stream sensitivity rating  is assigned to each assessed reach. A stream's inherent
sensitivity is related to its setting  and location within the watershed. Sensitivity ratings are assigned based  on
the reference stream type and the degree of departure from that reference. Certain reference stream types, as a
result of their natural characteristics, are more susceptible or sensitive to certain perturbations that may initiate
adjustment and channel evolution.
  Figure 3-21 Phase 3 data gathering (Vermont Department of Environmental Conservation, 2007).
                                                                                                          3-53

-------
Identifying and Protecting Healthy Watersheds
        With the resulting  stream type,  geomorphic and physical habitat  condition,  and  sensitivity rating, an
        assessment indicates what type of stream should exist and why, what type of stream does exist and the watershed
        characteristics that caused it, the type of stream that will evolve if left alone, and the  potential actions that
        can be taken to restore or  accommodate the adjustment of a stream to its reference type or protect it from
        departing from its reference type. A stream that has departed from its reference type, due to excess watershed
        runoff from impervious surfaces or other causes, no longer provides its proper functions (e.g., maintenance of
        habitat, sediment storage and transport, etc.). This type of information is invaluable to the natural resource
        planner evaluating alternative management scenarios for land  use, flow regulation, or channel modification.

        Vermont's River Corridor Planning Guide (Kline & Cahoon,  2010)  provides detailed data reduction methods
        and  mapping tools,  and helps watershed planners make management recommendations to address fluvial
        process-based departures and reach-specific stressors. River corridor plans include watershed-scale strategies for
        prioritizing river corridor protections and restorative actions  aimed at helping the state and its local partners
        manage streams toward their  dynamic equilibrium condition. Plans also include river corridor maps based
        on the meander beltways that provide a critical spatial context for achieving and maintaining equilibrium by
        limiting land use encroachments and channelization (Kline & Cahoon, 2010). The results of Vermont's stream
        geomorphic and reach habitat assessments can be  used to identify:  a) conservation reaches, b)  strategic sites,
        c) reaches with high  recovery potential, and d) moderately to highly degraded sites.  Conservation reaches are
        the least disturbed reaches of a watershed and should be maintained in  their natural state in a protected river
        corridor. Starting from this base of healthy ecosystem components, protection and restoration measures can be
        focused on less healthy reaches.  Strategic sites are  those vulnerable, sensitive sites  where protection strategies
        should be prioritized to avoid impacts to adjacent conservation reaches or to accommodate fluvial processes that
        will lead to a more even distribution of energy and sediments within the watershed (Leopold, 1994). Reaches
        with high recovery potential are those where  active restoration strategies should be prioritized. Moderate or
        highly degraded sites are those where expensive and uncertain restoration actions would be necessary. These
        projects should only be undertaken  after impacts  to  watershed hydrologic and sediment regimes have been
        remediated and upstream sources of instability have been resolved. Working out from conservation reaches to
        strategic sites, reaches with  high recovery potential, and finally to moderate and highly degraded sites provides
        the most efficient method  of protecting and  restoring the dynamic equilibrium  of the watersheds running
        water resources.
                    Figure 3-22. Intact (left) and incised (right) streambeds. (Images courtesy of Ben Fertig
                    (left) and Jane Thomas (right), IAN Image Library (ian.umces.edu/imagelibrary/)).
3-54

-------
 Case   Study
Geomorphic Assessment and  River Corridor
Planning of the  Batten  Kill Main-Stem and
Major Tributaries
More Information: http://www.anr.state.vt.us/dec/watera/rivers/htm/rv  aeoassess.htm
The  Batten  Kill  is  considered Vermont's  best
trout fishing stream and has been rated by Trout
Unlimited as one of the 10 best trout streams in the
United  States (Cox, 2006). However, since the early
1900s the quality of the fishery has been declining
(Jaquith, Kline, Field, & Henderson, 2004). Altered
land  use patterns, channel straightening, floodplain
encroachment,  and  dam  construction  have  been
prevalent in the Batten Kill watershed, as they have
been in much of New England for over a century.
A  phase  1,  watershed-scale,  fluvial  geomorphic
assessment   was  conducted  in  the  Batten  Kill
watershed to understand the extent to which these
disturbances are affecting the geomorphic condition
of the stream and the degradation of physical habitat
due to channel adjustment processes.

The phase  1 assessment identified over half of the
Batten Kill and its tributaries as being in some form
of channel  adjustment. Phase  2 assessments were
conducted on 36 reaches and  phase 3 assessments
were  conducted on eight segments in the watershed
to verify the results of the phase 1 assessment. Likely
causes  of  channel  adjustment  were  determined
through an  examination of historic  channel  and
floodplain modifications including deforestation, dam
construction,  agricultural  practices,  transportation
development,  and  the  more recent straightening,
dredging, and berming of the river for flood control.
As the low  gradient,  meandering  streams of the
Batten  Kill were straightened due to rail and road
construction and berming of the river, the channelized
streams were no longer able  to dissipate the energy
of their flows through lateral migration. Instead, the
energy was dissipated through erosion of the channel
bed, causing channel incision and loss of access to the
streams floodplain. Additionally, watershed  runoff
and sediment supply were historically altered  due
to changing  land use patterns, deforestation,  and
agricultural  practices.  Aggradation  or  deposition
of  sediment  occurred  in  downstream,   low-
gradient reaches, resulting in embedded substrates.
Embeddedness  refers to  the  deposition  of finer
sediments in the spaces between cobbles and boulders.
These spaces are prime habitat for juvenile fish. Deep
pools and other structural elements, such as large
woody debris, have been scoured from the river bed,
reducing habitat for adult fishes. In addition, gravel
substrate critical for spawning in some tributaries of
the Batten Kill has been scoured and lost.

The recommendations resulting from this geomorphic
assessment include strategic river corridor protection
to protect segments that are in regime (exhibiting the
dynamic equilibrium characteristic  of natural stream
channels), and to allow for channel adjustments and
the evolution of the channel and floodplains to a
dynamic equilibrium  condition. The river corridor
plan  also  focuses activities (e.g.,  erosion  control
practices)  on the whole system instead of individual
sites,  in order to restore geomorphically  unbalanced
streams to  equilibrium  conditions.  An education
program to increase public awareness,  perception,
and participation in appropriate watershed  activities
was also identified as critical  to the long-term health
of the Batten Kill.
                                                                                              3-55

-------
Identifying and Protecting Healthy Watersheds
         3.5 Water Quality

         This  section provides summaries for some examples of approaches currently being used to assess water quality.
         See Chapter 2 for background information on water quality.
                                  Landscape Condition
                     Patterns of natural land cover, natural disturbance regimes,
                         lateral and longitudinal connectivity of the aquatic
                        environment, and continuity of landscape processes.
                                        Habitat
                      Aquatic, wetland, riparian, floodplain, lake, and shoreline
                               habitat. Hydrologic connectivity.
                                       Hydrology
                      Hydrologic regime: Quantity and timing of flow or water
                       level fluctuation. Highly dependent on the natural flow
                     (disturbance) regime and hydrologic connectivity, including
                              surface-ground water interactions.
            Geomorphology
Stream channels with natural geomorphic dynamics.
             Water Quality
  Chemical and physical characteristics of water.
           Biological Condition
   Biological community diversity, composition,
 relative abundance, trophic structure, condition,
           and sensitive species.
                                       Riparian buffers filter
                                         pollutants, regulate
                                           water temperature,
                                             and help to
                                               maintain
                                                hydrologic
                                                regimes that
                                                support water
                                                quality.
                As runoff and surface
                 water pass through,
                   wetlands remove
                     or transform
                       pollutants  (e.g.,
                        sediments,
                        nutrients,
                         etc.) through
                         physical,
                        chemical, and
                        biological
                        processes.

                    Photo: NRCS.
                                       A Secchi disk is used to
                                         measure how deep
                                            a person can see
                                             into the water,
                                               and provides an
                                               approximate
                                                evaluation
                                                of the
                                                transparency
                                                of water.
                                            Photo: Adrian Jones, IAN.
                State, tribal, federal,
                 and local agencies,
                    as well as many
                     watershed
                       organizations,
                        conduct
                        water quality
                         monitoring
                         programs.
                                                                                                         Photo: Jane Thomas, IAN.
3-56

-------
                                                                                3 Examples of Assessment Approaches
  Oregon Water Quality Index
  Author or Lead Agency: Oregon Department of Environmental Quality
  More Information: http://www.deq.state.or.us/lab/wqm/wqimain.htm

The  Oregon  Water Quality  Index (WQI) is  a single number that describes water quality by integrating
measurements of eight water quality variables: temperature, dissolved oxygen, biochemical oxygen demand,
pH,  ammonia and nitrate nitrogen, total phosphorus, total solids, and fecal coliform. The purpose of the WQI
is to provide  a simple and concise method for  expressing the ambient water quality of Oregon's streams. The
WQI is useful for answering general questions (e.g., how well does water quality in my stream rate on a scale of
0 to  100?) and for comparative purposes (e.g., comparing several streams within the same watershed; detecting
trends over time, etc.). The WQI  is not, however, suited for site-specific questions that should be based on
the analysis of the original water quality data. The WQI can serve as a useful screening tool for general water
quality conditions,  as well as to help to communicate water quality status and illustrate the need for, and
effectiveness of, protective practices.

The Oregon WQI is calculated in two steps. First, the raw analytical results for each parameter are transformed
into  unitless,  subindex values. These values range from 10 (poor water quality) to 100 (excellent water quality)
depending  on that parameter's contribution to water quality impairment. These subindices  are combined
to give a single water quality index value ranging  from 10 to 100. The unweighted harmonic square mean
formula used to combine subindices allows the most impacted parameter to impart the greatest influence on
the water quality index.  This method  acknowledges that the influence of each water quality parameter on
overall water quality varies with time and location. The formula is sensitive to changing conditions and to
significant impacts on water quality.

Water quality indices, such as the Oregon WQI, when used appropriately, can be powerful tools for comparing
aquatic health conditions in different water bodies and in communicating information to the general  public
(Figure 3-23). A water quality index has the potential to be combined  with other indices  (such as an  IBI or
Index of Terrestrial Integrity)  in order to evaluate the overall health of a watershed.
                              Ambient Water Quality Monitoring Network
                                    Oregon Water Quality Index Results ( WY 1998 - 2007)
                      Oregon Department of Environmental Quality Laboratory May 2008
               Figure 3-23 Map of Oregon Water Quality Index (WQI) results for water years
               (WY) 1998-2007 (Oregon Department of Environmental Quality, 2008).
                                                                                                         3-57

-------
Identifying and Protecting Healthy Watersheds
         3.6  Biological  Condition

         This section provides summaries for some examples  of approaches  currently being used to assess biological
         condition. See Chapter 2 for background information on biological condition.
                                  Landscape Condition
                     Patterns of natural land cover, natural disturbance regimes,
                        lateral and longitudinal connectivity of the aquatic
                       environment, and continuity of landscape processes.
                                       Habitat
                     Aquatic, wetland, riparian, floodplain, lake, and shoreline
                               habitat. Hydrologic connectivity.
                                      Hydrology
                      Hydrologic regime: Quantity and timing of flow or water
                      level fluctuation. Highly dependent on the natural flow
                     (disturbance) regime and hydrologic connectivity, including
                             surface-ground water interactions.
            Geomorphology
Stream channels with natural geomorphic dynamics.
             Water Quality
  Chemical and physical characteristics of water.
           Biological Condition
   Biological community diversity, composition,
 relative abundance, trophic structure, condition,
           and sensitive species.
                                       Macroinvertebrates are
                                        a critical element in
                                           the aquatic food
                                       B^   chain and are
                                              frequently used
                                               as indicators
                                                of aquatic
                                                ecosystem
                                                condition.
                                             Photo: Jane Hawkey, IAN.
                 Native aquatic plants
                 can be an important
                    indicator of
                      biological
                       condition, and
                        also create
                         habitat for
                         other aquatic
                         organisms.
                                                                                                        Photo: Ben Fertig, IAN.
                                       Amphibian species
                                         are an indicator
                                            of biological
                                             condition,
                                               especially in
                                                headwater
                                                streams that
                                                lack fish
                                                populations.
                                             Photo: USFWS.
                 Presence of certain
                  fish species, such as
                    trout and salmon
                      in coldwater
                        streams, can
                        be indicators
                         of good
                         biological
                         condition.
                                                                                                        Photo: USFWS.
3-58

-------
                                                                                  3 Examples of Assessment Approaches
  Index of Biotic Integrity
  Author or Lead Agency: James Karr
  More Information: http://www.epa.gov/bioiwebl/html/ibi history.html

The Index of Biotic Integrity (IBI) is a multi-metric index of aquatic health based on ecological characteristics
of biological communities. It was originally developed by James Karr in 1981 for use in warm water streams
in Illinois and Indiana and has since  been modified for use in other states and  aquatic ecosystem types in
the United  States, as well as  in other countries.  It was  developed to  provide  an alternative  perspective to
physicochemical water quality monitoring programs  that were initially the typical monitoring approach for
addressing the requirements of the Federal Water Pollution Control Act Amendments of 1972 (the Clean
Water Act). The advantage  of integrating biological assessments into physicochemical assessments is a more
complete understanding of the effects of point and nonpoint source pollution in the context of aquatic life.

Biological communities are sensitive to a variety of environmental factors including chemical contamination
from  point and nonpoint sources, physical habitat alteration, flow modification, and disruption of ecological
processes and biotic interactions.  Since chemical  monitoring programs are  not  designed to detect some of
these, such as habitat alteration and flow modification impacts, biological assessments provide a mechanism for
evaluating the effects of all of these factors on ecosystem health. Additionally, biological communities integrate
the cumulative, and sometimes  synergistic, effects of pollutants and other disturbances over time. Chemical
monitoring programs, for example, might miss episodic discharges of untreated wastewater while the resident
biota  can often be affected by those events for an extended period of time.

The original IBI developed by James Karr assessed 12 characteristics offish communities. These 12 metrics
captured  information  about  species  richness  and  composition, indicator species,  trophic  organization,
reproductive behavior, and individual condition. These metrics are  directly affected by human disturbance and
alteration of the aquatic system and its watershed.  Choosing specific metrics within these classes allows for the
development of an IBI  in any region  based on local  ecological and biological conditions. The IBI approach
requires that the fish sample used is representative  of the fish community at the sample site, the sample site is
representative of the stream or watershed, and that the lead biologist is very familiar with the local fish fauna
and stream ecology.

A score is assigned to each of the chosen metrics,  and then summed to arrive at the IBI for the site. The IBI
score  for the site is interpreted relative  to undisturbed, reference conditions for the region. However, reference
sites in many states represent least disturbed conditions so threshold selection needs to take into consideration
the quality of the  reference sites (Stoddard et al., 2006;  U.S.  Environmental Protection  Agency, 201 Ic)
Reference conditions must  be defined for each stream type in  an ecoregion. The final IBI  score represents
the health of the  biological  community relative to reference conditions  for that stream type.  Through careful
selection of metrics, human alteration of the five water resource features can be determined (Figure 3-24).

Ohio  is an example of a state that uses biological data and biocriteria as  the principal mechanism for assessing
aquatic life use attainment for its Water Resource Inventory (CWA Section 305(b) report) (see following case
study). Biocriteria are also used in setting water quality standards, supporting the National Pollutant Discharge
Elimination System  (NPDES) permitting process, performing nonpoint source assessments, and as part of
risk assessments in various states. Other states have used modified  IBIs in integrative assessments of watershed
condition. For example, the Virginia DCR uses a modified IBI in its Watershed Integrity Model (summarized
in Chapter 4). In the Watershed Integrity Model, a spatial representation of the IBI is combined with other
aquatic and terrestrial ecological indicators and a weighted overlay is created in a GIS.  The weighted overlay
provides guidance on watershed  lands that are most valuable for maintaining aquatic ecosystem integrity.

The IBI  approach to assessing the biological health of surface water resources is a valuable and widely  used
method  that can be modified and integrated into region-specific conditions and objectives. Evaluating the
biological condition of a  watershed's streams, lakes, and  rivers allows for the identification of the healthiest
sites that should be prioritized for protection.
                                                                                                          3-59

-------
Identifying and Protecting Healthy Watersheds
            Direct ecological effects
            Channel modifications
            Riparian clearing
            Water withdrawal
            Addition of alien taxa
            Indirect ecological effects
            Changing land use
            Appropriation of water
            Stormwater runoff
            Pollutant generation
              Human activities
                  (stressors)
                                                  Habitat
                                                 Structure
        Flow
      Regime


       Water
       Quality
       Energy
      Sources
       Biotic
    Interactions

  Altered water
resource features
                                 Declining diversity within
                                 feeding and reproductive
                                 guilds
 Loss of migratory species
 Disrupt flow regime
                                                                             Loss of sensitive taxa
                                                                             Increased frequency of
                                                                             tumors, lesions, etc.
 Declining diversity of
 food specialists
 Increase in omnivores
 Loss of top predators
 Decline of harvestable
 species

Biological changes
        (fish)
            Figure 3-24 Human activities alter five water resource features, resulting in alteration of fish
            communities (Modified from Karr & Yoder, 2004).
3-60

-------
Case   Study
 Ohio Statewide Biological  and Water Quality
 Monitoring  and Assessment
 More Information: State of Ohio Environmental Protection Agency, 2009 (http://www.epa.state.oh.us/
 dsw/bioassess/ohstrat.aspx)
 Ohio EPA has  relied on biological  monitoring and
 assessment as a critical component of its water quality
 program  for almost three decades. Ohio  created
 three different  modified versions of Karr's IBI for
 application to headwater streams  (drainage area <20
 mi2), wadeable  sites, and larger non-wadeable sites.
 These three  different versions were necessary due to
 fundamental differences  of the  fauna  at different
 site  types and  consideration of sampling methods.
 However, Karr's original ecological structure  was
 maintained throughout the development of the three
 versions. In addition, Ohio created modified versions
 of an Invertebrate Community Index and a Modified
 Index of Wellbeing. These are conceptually similar to
 the IBI. The IBI and Modified Index of Wellbeing
 are based on assessments of stream  fish assemblages
 while the Invertebrate Community Index is based on
 macroinvertebrate assemblages.

 Ohio  uses   the   IBI,   Invertebrate  Community
 Index,  and Modified Index of Wellbeing biological
 assessments  along with physicochemical assessments
 to assess  compliance with water quality  standards.
Numeric biocriteria have been specified for each of the
three indices, and in each of Ohio's five ecoregions,
using  a system of tiered aquatic life  uses (limited
resource water, modified warm water habitat, warm
water  habitat, and exceptional warm water habitat).
Biocriteria  for the exceptional warm water  habitat
are  derived from biological  assessments  conducted
in undisturbed, reference  reaches for each ecoregion.
Management responses are prioritized along this tiered
aquatic life use gradient. For example, exceptional
warm  water habitats are  of the highest quality and
would merit protection as a management measure.
Warm water habitats are somewhat degraded and
would thus be ideal locations for restoration projects.
Highly degraded sites  would receive  enhancement
management measures and the most severely degraded
sites are  considered  irretrievable.  Ohio  adopted
numeric  biocriteria into its  water quality standards
in  1990,  which has  allowed the  state  to assess
cumulative impacts,  define  appropriate aquatic  life
use  designations,  assess  impacts from altered habitat,
and to identify high quality waters.
                                                                                             3-61

-------
Identifying and Protecting Healthy Watersheds
          The Biological Condition Gradient and Tiered Aquatic Life Uses
          Author or Lead Agency: Susan K. Jackson (U.S. EPA)
          More Information: http://water.epa.gov/scitech/swguidance/standards/criteria/aqlife/biocriteria/uses index.cfm

        The Biological Condition  Gradient (BCG)  is a conceptual,  scientific model for interpreting  the biological
        response of aquatic ecosystems to increasing levels of stressors.  The BCG model was developed by a workgroup
        of aquatic  ecologists and biologists  from different regions  of the United States to represent their empirical
        observations of biological response to ecosystem stress, regardless of the monitoring methodology employed.
        The model evaluates the response of 10 aquatic ecosystem attributes to  locate a stream's condition on  the
        stressor-response  curve  (Figure 3-25). There are six levels, or tiers, of biological condition on the stressor
        response curve. The BCG  model is intended to assist states  and tribes to more precisely define the aquatic
        biota expected along a gradient from undisturbed to severely disturbed conditions and assign goals for a water
        body that better represent its highest achievable condition. The  model accounts for geographical differences
        in ecosystem attributes, so is applicable  across the nation; however, modifications to the levels can  be made
        by individual  states and  tribes to most appropriately characterize their regional conditions (e.g., use of three
        levels, as opposed to six). For example, New Jersey calibrated  a five level BCG for their upland  streams and is
        evaluating  options for application.  Maine has incorporated a three tier BCG to define their aquatic life  use
        classification framework (U.S. Environmental Protection Agency, 201 Ic).

        The ten attributes assessed in the BCG evaluate several aspects of community structure,  organism condition,
        ecosystem function,  and spatial and temporal attributes of stream size and connectivity. The stressor axis of
        the BCG model represents a composite of all of the chemical, physical, and biological factors  that can disrupt
        ecological integrity. Placement of a monitoring site in one of the six BCG levels, as described in Figure 3-25, is
        determined through an examination of the ten attributes:

            1.   Historically documented, sensitive, long-lived or regionally endemic taxa.
            2.   Sensitive-rare taxa.
            3.   Sensitive-ubiquitous taxa.
            4.   Taxa of intermediate tolerance.
            5.   Tolerant taxa.
            6.   Non-native or intentionally introduced taxa.
            7-   Organism condition.
            8.   Ecosystem functions.
            9-   Spatial and temporal extent  of detrimental  effects.
            10. Ecosystem connectance.

        A number of states have, or are in the process of developing, their own  regional or statewide BCG models. The
        initial step in  developing a state-specific  or ecoregional BCG  model is to identify and define, where  possible,
        undisturbed conditions on which the model's level 1 category will be based. Calibration of the model  has
        sometimes resulted in combining BCG level 1 and level II categories to define the upper gradient of a local
        BCG  because  of lack of undisturbed sites.  A workgroup  of professional biologists with considerable field
        experience and knowledge of the local fauna should be assembled  to calibrate the BCG model.  They will define
        the ecological  attributes by, for example, assigning taxa to attributes 1-6. This will involve the examination of
        a variety of bioassessment and stressor data and the classification of different sites into the different levels of
        biological condition along a gradient of increasing stress. It  is often  possible to calibrate existing indices of
        biotic integrity, such as the IBI,  to the levels of biological condition, which  will facilitate the  application of
        the BCG model  to future monitoring endeavors  (e.g., Pennsylvania Case Example in  U.S. Environmental
        Protection Agency, 201 Ic). If a biotic index system  does not exist, an index that corresponds to the newly
        established levels  may be developed. The stressor axis of the  BCG  model represents the composite stressors
        on the aquatic ecosystem. These stressors can originate from: 1) chemical factors, 2)  the flow regime,  3) biotic
3-62

-------
                                                                                        3 Examples of Assessment Approaches
factors, 4) energy sources, and 5) habitat structure (Karr, Fausch, Angermier, Yant, & Schlosser, 1986). Like the
biological condition axis, the stressor axis is based upon deviation from natural (e.g., undisturbed, minimally
disturbed) conditions and thus should be calibrated to the local conditions and stressors.

Once  the BCG model has  been calibrated to local conditions, it can be used by  states  and tribes to more
precisely evaluate  the  current and  potential biological conditions of their streams and more precisely define
aquatic life uses. The BCG is based on 30 years of conceptual development  in  aquatic ecology and represents
the understanding that biological communities differ in a predictable manner across ecoregions, water body
types,  and levels of stressors (Davies & Jackson, 2006). The use of the BCG allows states to  assess the ecological
condition of water bodies from a more holistic standpoint than using chemical and physical water quality data
alone.  The method is scientifically and statistically robust, and can be used to complement existing or develop
new quantitative measures of ecosystem health.
    Levels of Biological Condition

   Level 1. Natural structural, functional,
   and taxonornic integrity is preserved.
   Level 2. Structure & function similar to
   natural community with some additional
   taxa & biornass; ecosystem level
   functions are fully maintained.

   Levels. Evident changes in structure
   due to loss of some rare native taxa;
   shifts in relative abundance; ecosystem
   level functions fully maintained.
   Level 4. Moderate changes in structure-
   due to replacement of some sensitive
   ubiquitous taxa by more tolerant taxa;
   ecosystem functions largely
   maintained.
   Level 5. Sensitive taxa markedly
   diminished; conspicuously unbalanced
   distribution of major taxonomic groups;
   ecosystem function shows reduced
   complexity & redundancy.
   Levels. Extreme changes in structure
   and ecosystem function; wholesale
   changes in taxonomic composition;
   extreme alterations from normal
   densities.
                                   Watershed, habitat,flow regime
                                       and water chemistry as
                                          naturally occurs
Ch ernistry, h abitat, an d/or flow
 regime severely altered from
     natural conditions
Figure 3-25 Conceptual model of the Biological Condition Gradient (U.S. Environmental Protection Agency,
2011c).
                                                                                                                   3-63

-------
                                                   Case   Study
                      Maine Tiered  Aquatic Life Use
                      Implementation
                     More Information: http://www.maine.gov/dep/water/monitoring/biomonitoring/index.
                     html
       The Maine Department of Environmental Protection
       (DEP) has used a tiered approach to water quality
       management since the early  1970s, before adoption
       of the Clean Water Act. Classifications of AA, A,
       B, or C are given to the state's water bodies, with
       Class AA  waters  receiving  the  highest levels of
       protection. Numeric biocriteria have been developed
       based  on  benthic  macroinvertebrate  assessments.
       Over the years, Maine  DEP biologists have  made
       empirical observations of the differences in aquatic
       macroinvertebrate  communities across gradients of
       stressors. At the same time, work in aquatic  stress
       ecology,  particularly  by  Eugene Odum,  helped
       to  reinforce these  observations with  a theoretical
       underpinning.   Narrative  biological  criteria  were
       designed to be  consistent with  these observations
       and ecological  understanding. Maine DEP biologists
       aligned the narrative criteria with a slight modification
       of  the   already-established   four  tier  classification
       system.  Class AA and A were  combined to yield a
       three-tier system of Class A, B, or C (Figure 3-26).
                                 Maine DEP quantified each of their aquatic life use
                                 classes in the  late 1980s using a probability-based
                                 statistical model of 31 biological variables. This model
                                 was developed based on the best professional judgment
                                 of Maine DEP biologists through an  evaluation of
                                 144 samples with 70,000 organisms. The model was
                                 recalibrated with an additional 229 samples in 1999-
                                 Using this model and current biomonitoring data, an
                                 aquatic life attainment classification of A, B, or C is
                                 given to each stream. If the stream is not attaining its
                                 aquatic life use designation, it is listed as impaired on
                                 the state's 303 (d) list of impaired water bodies.

                                 With 51% of the state's water bodies  designated as
                                 Class AA or Class A, Maine maintains a strong focus
                                 on protection  of aquatic life use. Any discharge to
                                 waters with  these classifications must be of equal or
                                 better quality than the receiving water  and any flow
                                 obstructions must not have effects greater than what
                                 would be expected from a natural flow obstruction,
                                 such as a beaver dam.
             Natural
                o
                o
                "TO
                o
                '5)
                £
                o
                ffl
            Severely
             Altered
                       •j  Native or natural condition
                                         Minimal loss of species: some
                                         density changes may occur
Some replacement of   «
sensitive-rare species:  J
functions fully maintained
                              Some sensitive species
                           4  maintained: altered
                              distributions: functions
                              largely maintained
             Tolerant species show
             increasing dominance:
             sensitive species are
             rare: functions altered
                           Severalteration of    -,
                           structure and function  «
                   Low
                                     Stressor Gradient
                                                                       High
                                                                               Class AA/A
                                                                               As naturally occurs.
                                                                               Habitat: "natural"
                                                                               Class B
                                                                               No detrimental change:
                                                                               support all indigenous species
                                                                               Habitat: "unimpaired"
Maintain structure and function:
support all indigenousfish
(salmonids).
Habitat for fish and aquatic life
                                                                               Non-attainment of
                                                                               minimum standards
           Figure 3-26 Maine Tiered Aquatic Life Uses in relation to Biological Condition Gradient Levels (Davies
           and Courtemanch, 2012).
3-64

-------
                                                                                  3 Examples of Assessment Approaches
  Aquatic Gap Analysis Program
  Author or Lead Agency: U.S. Geological Survey (USGS)
  More Information: http://www.gap.uidaho.edu/projects/aquatic/default.htm: http://morap.missouri.edu/Projects.
    aspx

The USGS Gap Analysis  Program (GAP) is designed to keep  common species  common by  proactively
identifying the distribution of habitats and species  not currently represented in conservation networks and
disseminating this information to relevant stakeholders before the organisms become threatened or endangered.
A fundamental concept to the GAP program is that species distributions  can be predicted based on habitat
indicators. Many approaches to biodiversity conservation have focused on single-species management, typically
threatened or endangered species. While these  approaches have their place, a proactive approach to biodiversity
conservation will include methods for identifying habitats that support a diversity of species and ensuring
protection of these areas before the species become  threatened. The availability of remotely sensed data and
the vast improvements in computing power over the past couple of decades have facilitated the possibility of
identifying these areas at multiple scales and with minimal resources. By identifying these areas and comparing
them with the current network of conservation lands, the "gaps" in the network can be identified and these
areas prioritized for conservation.

The terrestrial component of the USGS GAP program began in 1988  and is now operating in every state. The
aquatic component of GAP has only recently begun, with nine state projects and four regional projects. Similar
to the terrestrial component, Aquatic GAP seeks to  identify areas  of high biodiversity within watersheds and
use remotely sensed data to map habitats and predict aquatic biodiversity to provide a biological basis on
which to create aquatic conservation plans. While the terrestrial component relies primarily on vegetation as a
habitat indicator, the Aquatic GAP uses multiple indicators to identify Aquatic GAP habitat types and develop
species-habitat relationships. While each individual project may use a different subset of habitat indicators, the
following are typically used:

    •   Stream size.
    •   Stream gradient.
    •   Watershed  land use.
    •   Riparian forest cover.
    •   Bedrock and surficial geology.
    •   Water quality.
    •   Stream sinuosity.

Remote sensing data are used to determine  the first four indicators.  Digital Elevation Models, which are
available from the USGS,  can be used to  determine stream size and  stream gradient. Watershed land use and
riparian forest cover data are readily available from sources such as the Multi-Resolution  Land Characteristics
Consortium, which is a group of federal agencies working together to produce  and  maintain comprehensive
and current data on land cover. Bedrock surficial geology maps  are available from the USGS. Ambient water
quality data are  typically available from state and national monitoring programs,  as well  as through some
local monitoring programs. Stream sinuosity can be  measured using available stream data layers such as  the
National Hydrography Dataset. These habitat indicators must be combined to establish discrete habitat types
for each delineated  catchment or watershed. Relationships between species  presence and habitat type are then
determined with statistical  models using biomonitoring  data for fish and macroinvertebrate taxa.

An aquatic GAP assessment  for  Missouri (Sowa, Annis,  Morey, & Diamond,  2007), for example, used
indicators such as those mentioned above, along with biological data, to generate a  hierarchical classification
of riverine ecosystems, with the smallest unit representing distinct habitat types. This eight-level classification
was developed in collaboration with TNC's Freshwater Initiative staff (see  Appendix A)  and includes aquatic
subregions, ecological drainage units  (EDUs), aquatic  ecological systems  (AESs),  and valley-segment types
(VSTs) (Figure 3-27). Using this classification system and species-habitat relation models, maps of predicted
                                                                                                          3-65

-------
Identifying and Protecting Healthy Watersheds
        species distribution were then generated. The conservation status (based on ownership/stewardship) of each
        AES was also mapped. A human threat index was created to evaluate the vulnerability of these systems using
        eleven  different metrics (Table 3-12) and AESs and VSTs were prioritized for conservation (Table 3-13).
        Regional experts weighted each of the metrics in the human threat index, which was also calculated for every
        stream reach in the region (Annis et al., 2010). The individual metric data, as well as the index results, can be
        summed cumulatively at any location.

        The results of an Aquatic GAP assessment, such as the  one conducted for Missouri, are intended to be used
        by state and local decision makers for land use planning, conservation management, and public education.
        Partnerships between various agencies and other stakeholders are vital to coordinating collection and analysis
        of the  data required  as well as to the successful use of the assessment in actual management plans. Use of
        this information as part of a comprehensive watershed  assessment strategy can complement other biological
        condition and landscape condition assessment approaches and provide a greater level of protection to healthy
        ecosystems and their components.
                     Aquatic subregions
Ecological drainage units
                     Aquatic ecological system types
   Valley-segment types
         Figure 3-27 Maps of Missouri showing levels four through seven of the aquatic ecological classification
         hierarchy (Sowa et al., 2007). Reprinted with permission of Ecological Society of America.
3-66

-------
                                                                                               3 Examples of Assessment Approaches
Table 3-12 Eleven metrics included in the human-threat index and the criteria used to define the four relative
ranks for each individual metric (Sowa et al., 2007).
•
Number of introduced species
Percentage urban
Percentage agriculture
Density of road-stream crossings (no./km2)
Population change 1990-2000 (no./km2)
Degree of hydrologic modification and/or fragmentation by
Number of Federally licensed dams
Density of coal mines (no./km2)
Density of lead mines (no./km2)
Density of permitted discharges (no./km2)
Density of confined animal feeding operations (no./km2)
Relative Ranks ^^^^1
1 2 3 4-5
0-5 5-10 11-20 0.20
0-25 26-50 51 - 75 0.75
0 - 0.09 0.10 - 0.19 0.2 - 0.4 0.4
-16 - 0 0.04 - 5 6-17 0.17
major impoundment 1 2 or 3 4 or 5 6
0 1-9 10-20 0.20
0 0.1-2 2.1 - 8 0.8
0 0.1-2 2.1 - 8 0.8
0 0.1-2 2.1-8 0.8
0 0.1-2 2.1 - 4 0.4
Table 3-13 Assessment criteria used for prioritizing and selecting aquatic ecological system (AES) polygons and
valley-segment type (VST) complexes for inclusion in the portfolio of conservation opportunity areas (Sowa et
al., 2007).
• AES-level Criteria
Select the AES polygon that:
VST-level Criteria ^^^H
Select an interconnected complex of VSTs that: ^^^^1
Has the highest predicted richness of target species.
Contains known viable populations of species of special
concern.
Has the lowest degree of human disturbance based on human-    Has the lowest degree of human disturbance based on a
threat index value and qualitative evaluation of threats using the   qualitative evaluation of relative local and watershed conditions
full breadth of available human-threats data.                     using the full breadth of available human-threats data.
Has the highest percentage of public ownership.
Is already contained within the existing matrix of public lands.
Overlaps with existing conservation initiatives or high public
support for conservation.
Overlaps with existing conservation initiatives or high public
support for conservation.
                                                                                                                            3-67

-------
                                                 Case   Study
                    Ohio  Aquatic  GAP Analysis: An  Assessment
                    of the Biodiversity and  Conservation Status
                    of Native  Aquatic Animal Species
                    More Information: U.S. Geological Survey, 2006 (http://pubs.er.usgs.gov/usgspubs/ofr/
                    ofr20061385)
       The  Ohio Aquatic GAP  pilot project assessed all
       continuously  flowing streams  in  Ohio to identify
       gaps in the current conservation network that could
       potentially pose a risk to  freshwater biodiversity. A
       classification system was  developed to characterize
       and map the aquatic habitats of 217 freshwater  fish,
       crayfish, and bivalve species. The classification system
       used geomorphic and stream network variables, such
       as stream size and connectivity, sinuosity, and gradient
       to identify physical habitat types.

       Biological data were compiled from multiple sources
       representative of the variety of stream types  and
                           sizes in Ohio. Species distributions were predicted
                           using statistical models that relate the eight habitat
                           indicators to the  occurrence of individual  species.
                           The results of this  analysis were overlain on a map of
                           all  conservation lands in  the state. Predicted species
                           distributions from the GAP Analysis showed that the
                           predicted  distribution of 24 species fell completely
                           outside of these conservation lands. Nine of the 24
                           species  are threatened or  endangered. The  results
                           of  this  analysis were used to  identify  conservation
                           priority lands  based  on  predicted species richness
                           (Figure 3-28).
         Lake Erie drainage basin

         Small stream (1st order)

         I  I fish (95

         l"1 fish (95

         Small AND n edium streams (1st, 2nd, 3rd

               .)
               (95%)

         Medium streams (2nd and 3rd order)

         I  I fish (95%)

         I  I crayfish (95%)

         I  I fish (90%) bivalves (95%)

         Large streams (4th order and larger)

         I  I fish (95%)

         I  I crayfish bivalves (75%) fish (95%)

         I  I crayfish <95%>

         I  I fish (90%) crayfish (95%)

         HI fish (95%) crayfish (95%)

         I  I fish.'crayfish/bivalves (75%)
         I  I fish bivalves (90%)

         ^H bivalves (90%) fish (95%)

         ^H fish (90%) bivalves (95%)

         • fish (95%) bivalves (95%)

         IH crayfish (75%) fish (95%) bivalves (95'
   Ohio River drainage basin

   Sin all streams (1st order)

   E~»1 fish (95%)

   L . I crayfish (95%)

rder) F"5"! bivalves (95%)

   [Medium streams (2nd and 3rd order)

   C3 bivalves (75%) crayfish (90%) fish (95%)

   1  I tish crayfish bivalves (75%)

   I  I fish (95%)

   E-H bivalves (75%) fish (90%) crayfish (95%)

   I  I bivalves (75%) iish.'crayfish (90%)

   I  I crayfish (95%)

   I  I fish (95%) and bivalves (95%)

   Large streams (-Ith order and linger)

   I  I lish.orayfish. bivalves (75%)

   I  I fish (95%)

   I  I crayfish, bivalves (75%) fish (95%)

   dJ bivalves (75°») fish.crayfish (90°»)

   I  I crayfish (95%)

   I  I fish, bivalves (90%)

   ^H bivalves (90%) fish (95%)

   • crayfish (75%) fish/bivalves (90%)

i)  ^M crayfish (75%) bivalves (90%) fish (95%)

   •I aa>lish<75%) fish <95%) and bivalves (95%)

   Cold wafer streams

    I cold water
         Figure 3-28 HUC12 watersheds in Ohio. The different color watersheds represent high predicted aquatic
         species richness for various taxa (U.S. Geological Survey, 2006).
3-68

-------
                                                                                 3 Examples of Assessment Approaches
   Natural Heritage Program Biodiversity Assessments
   Author or Lead Agency: NatureServe and state partners
   More Information: http://www.natureserve.org/aboutUs/network.jsp

When it was formed in 1951, The Nature Conservancy's primary mission was the conservation of biological
diversity through the establishment of nature reserves (Groves, Klein, & Breden, 1995)- Realizing the need for
a scientifically sound data collection and management program on which to base conservation decisions, the
first state Natural Heritage Program was formed in South Carolina in 1974  (Groves, Klein, & Breden, 1995).
Today, the Natural Heritage Network is comprised of 82 independent programs that are located in all 50 U.S.
states, 11 provinces and territories of Canada, and in many countries and territories of Latin  America and
the Caribbean. These programs collect, analyze,  and disseminate information about the biodiversity of their
respective regions. With three decades  of data collection and over 1,000 professional biologists, this network
maintains the most comprehensive conservation database available  in the western hemisphere.  NatureServe,
originally established in 1994 as the Association for Biodiversity Information, is the umbrella organization that
now represents all of the state Natural Heritage Programs in the United States and Conservation Data Centers
internationally.

The Natural  Heritage  Methodology gathers, analyzes, organizes, and manages  information  on biodiversity
through  a network of professional biologists in partner agencies who keep  pace with the growth in scientific
understanding while maintaining an  underlying continuity in the methodology. NatureServe (2008) identifies
the following characteristics  of the Natural Heritage Methodology:

    •   It is designed to support a decentralized  database network that respects the principle
        of local custodianship of data.
    •   It supports the collection and  management of data at multiple geographic  scales,
        allowing decisions to be  made  based on detailed local information, yet within a
        global context.
    •   It encompasses both spatial and  attribute data, but emphasizes the  type of fine-scale
        mapping required to inform on-the-ground decisions.
    •   It includes  multiple quality  control and quality assurance steps to ensure that data
        products have the reliability needed to inform planning and regulatory actions.
    •   It incorporates explicit estimates of uncertainty and targets additional inventory work
        to reduce levels of uncertainty.
    •   It integrates multiple data  types, including: species  and  ecological communities;
        collections and other forms of observational  data; and biological  and non-biological
        data.

                                                                                                         3-69

-------
Identifying and Protecting Healthy Watersheds
        The methodology is based upon the occurrence of "elements of biodiversity," which include both  species
        and communities. These element occurrences are stored in spatial  databases that are maintained by the local
        programs  in  each state. NatureServe maintains  a  central database where  all local programs upload  their
        information at least once per year. The following are the basic steps in the Natural Heritage Methodology as
        defined by NatureServe  (2008):

            1.   Develop  a list of the elements  of biodiversity in a given jurisdiction, focusing  on
                better-known species groups (e.g., vertebrate animals,  vascular plants, butterflies,
                bivalve mollusks), and on the ecological communities present.
            2.   Assess the relative risk of extirpation or extinction of the elements to determine
                conservation status and set initial priorities for detailed inventory and protection.
            3-   Gather information  from all available  sources for priority elements, focusing  on
                known locations, possible locations, and ecological and management requirements.
            4.   Conduct field inventories for these elements and collect data about their location,
                condition, and conservation needs.
            5.   Process and manage all the data collected, using standard procedures that will allow
                compilation and comparison of data across jurisdictional boundaries.
            6.   Analyze the data with a view toward refining previous conclusions about element
                rarity and risk, location, management needs, and other issues.
            7-   Provide access to  data and information products to interested parties so that it can
                be used to guide conservation, management planning, and other natural  resource
                decision-making.

        The information collected, compiled, and distributed  by state Natural Heritage Programs and NatureServe is
        used by land  use and community planners, land owners, and natural area managers. Conservation groups use
        the data to set conservation priorities within their region. Developers and businesses use the data to comply
        with environmental regulations and government agencies use the data to help manage public lands and guide
        policy.  The approach  can be  used to assess the biotic condition of a watershed at the local scale or aquatic
        ecoregions at the state  scale.  The general framework of the approach can  also serve as a useful model for
        other assessment  approaches  that seek to  identify healthy components of watersheds and prioritize sites for
        conservation or protection actions.
3-70

-------
Case   Study
  Oregon Biodiversity Information Center
  More Information: Oregon Biodiversity Program, 2009 (http://orbic.pdx.edu/)
  The  Oregon  Biodiversity   Information   Center
  (ORBIC) works  across  agencies to  identify  the
  biological and ecological resources  of  the state.
  Formed  in 1974, it was  the first Natural Heritage
  Program in the west and is charged with the voluntary
  establishment of natural areas, manages the Rare and
  Endangered  Invertebrate Program, and develops and
  distributes information on species and ecosystems
  throughout  Oregon  and the  Pacific  Northwest.
  ORBIC  is also heavily  involved in the  state Gap
  Analysis  Program  and other conservation assessment
  and planning efforts in the state.

  ORBIC typically identifies elements of biodiversity at
  the community or ecosystem level that represent the
  full range of diversity in the state. While this approach
  captures most species, there are times when individual
  species  must  be  singled  out  as elements.  These
  elements are  mapped where  they occur throughout
  Oregon,  but  examples are selected as  Natural Areas
  at the ecoregional level in order  to ensure that the
  full range of Oregon's  natural  areas is represented.
  Ecoregions are delineated areas  with similar climate,
  vegetation,  geology,  geomorphology,  soils,  and
  ecosystem processes that define  characteristic  natural
  communities of plant and animal life.

  When a community or  ecosystem element makes
  a significant contribution to biodiversity within its
  ecoregion, it  is defined as a natural area ecosystem
  element. Both ecosystems and species are then ranked
  by conservation priority according to: 1)  rarity, 2)
  threats, 3) ecological fragility, and 4) the adequacy and
  viability of protected occurrences. ORBIC then works
  with  landowners  and managers to conserve  a good
example of these in a protected area. Classifications
of terrestrial,  aquatic,  and wetland ecosystems are
organized  according  to  ecoregions.  The  current
classification system used for riverine communities is
based on the system used by the USGS Aquatic GAP
and  identifies  unique  "valley  segment"  types that
contain  distinct fish or aquatic species assemblages.
Valley segment types are defined based on elevation,
stream order, stream gradient,  stream sinuosity, and
the geology of the basin.

A  unique  aspect of  the Oregon Natural Areas
Program's  approach is that,  in  addition  to the
identification   and  ranking   of  ecosystem  cells,
natural  disturbance  processes are  also  identified
and prioritized for conservation.  Ecosystem process
elements are identified  as areas containing landscape
scale disturbance processes that occur with a frequency
that  is shorter than the  life cycle  of the  affected
communities. Wildfires are the most common type of
natural disturbance in  Oregon and typically require
protected areas of several thousand acres to maintain.
Special species lists are also  created to ensure that rare,
threatened, and endangered species receive the level
of protection that they require.

ORBIC  pursues a variety of conservation strategies on
both public and private lands. Lands can be dedicated
as State Natural Areas, Research Natural Areas, Marine
Reserves, Biosphere  Reserves,  Nature Conservancy
Preserves, as well as many other designations. ORBIC
also  seeks  out donations  of land from  individuals
and works with state and federal  land managers to
promote the acquisition of those private lands which
are critical for conservation.
                                                                                                  3-71

-------
Identifying and Protecting Healthy Watersheds
          Virginia Interactive Stream Assessment Resource and Healthy Waters Program
          Author or Lead Agency: Virginia Department of Conservation and Recreation, Virginia Commonwealth University
            Center for Environmental Studies
          More Information: www.dcr.virginia.gov/healthywaters and http://instar.vcu.edu

        The Virginia Department of Conservation and Recreation and Virginia Commonwealth University Center for
        Environmental Studies are collaborating in the development and implementation of a statewide Healthy Waters
        program to identify and protect healthy streams. The Interactive Stream Assessment Resource (INSTAR) is
        an online, interactive database application that evaluates the ecological integrity of Virginia's streams  using
        biological and habitat data. This  web-mapping application is available to the public as a free resource to help
        planners, advocacy groups, and individuals to make wise land use decisions.

        The INSTAR and Healthy Waters program would not be  possible without the substantial investment Virginia
        has  made in the collection of biological and habitat field data. Watershed biotic integrity is  evaluated with a
        modified Index of Biotic Integrity (mlBI) that uses the following six metrics:

            •   Native species richness.
            •   Number of rare, threatened, or endangered species.
            •   Number of non-indigenous species.
            •   Number of significant species (ecologically or economically important).
            •   Number of tolerant species.
            •   Number of intolerant species.

        The mlBI score  can range from  6-30 and scores greater  than 16 are considered to represent high watershed
        integrity. This analysis has been completed for all HUC12 watersheds across the entire State of Virginia (Figure
        3-29). The ecological health of individual stream reaches is also evaluated based on  their comparability to
        virtual  reference streams. These virtual  reference streams are modeled for each ecoregion and stream  order
        and eliminate  many of the limitations of other  bioassessment approaches (e.g., finding appropriate reference
        sites) by relying on  an objective  reference condition  based  on  fish and  macroinvertebrate assemblage
        structure, instream habitat, and geomorphology. A virtual stream assessment is then conducted by evaluating
        the  comparability of the empirical data to the  appropriate virtual reference stream. Streams that are >70%
        comparable are considered healthy and  those that are >80% comparable are considered "Excellent." Due to
        lack of data in the western part of the state, most of the  healthy waters have so far been identified in eastern
        Virginia, but the goal is to expand sampling across the state (Figure 3-30).

        The Virginia Healthy Waters  program  promotes the  protection of headwater areas,  riparian buffers, and
        maintenance of natural stream flow as management strategies for its high quality streams and watersheds. The
        INSTAR assessment identified Dragon Run as one of the highest quality streams in Virginia. The watershed
        is primarily forested, with some agricultural land uses as well, and there are only a few bridge crossings in the
        whole watershed. Maintenance of the wide riparian buffers, core forests, and wildlife corridors will be critical
        in maintaining Dragon Run as a high quality stream. Virginia is working with The Nature Conservancy and
        the residents of the watershed to ensure that this stream remains healthy.
3-72

-------
                                                                                                   3 Examples of Assessment Approaches
  Legend

  Biotic Integrity
  Ranking
        Moderate
        High
        Very High
        Outstanding
        No Score
 This map *as produced by the
 CENTER FOR ENVIRONMENTAL STUDIES at
 \^rginia Commonwealth University.
 Foi additional information, contact the Center at:
 VAVW.VCLI . eclu/cesweb
 Map publication date: FEBRUARY 1, 2011
 Data shown in map can be lound at INSTAR -
Virginia Coostol zone  **
 OCR
                                                      North  Carolina
Distribution of modified Index of Biotic Integrity (rnlBI)
scores for Virginia's 5th order watersheds (HUCs).
The mlBI scores are generated from an  extensive
database offish species occurrences, scoring criteria,
and metrics such as native species richness and the
number of toleranttaxa. Data used to generate this
map were current as of December. 2010.
Figure 3-29 Map of watershed  integrity in Virginia based on modified Index of Biotic Integrity
scores (Greg Garman, Virginia Commonwealth University, Personal  Communication).
 Legend

  •  Healthy Waters

  __S Healthy Watersheds

 £3 MaJ°r Drainages

 ^^ Chesapeake Bay Basin

 Data Description:


 302 Healthy Waters'
 152 Healthy Watersheds-

 Virginia:
 175 Hf-.iltliy Waters'
 205 Healthy Watersheds"




 through Maryland's anii-degradation regulation. Maryland stronghold watersheds



                       University's !NSTAR prog
                       region ally-specific, model refer'
                     the INSTAR program, visit
Figure 3-30 Status of healthy waters and watersheds in Maryland and Virginia (Greg Garman, Virginia
Commonwealth University, Personal Communication).
                                                                                                                                   3-73

-------
Identifying and Protecting Healthy Watersheds
        3.7  National Aquatic Resource Assessments

        This section provides summaries for some  examples  of national programs that monitor and assess aquatic
        resources, including water quality, biology, and habitat. Working with state, tribal, and other federal agency
        partners, EPA is conducting statistical surveys of the nation's streams and rivers, lakes and reservoirs, coastal
        waters,  and wetlands.  Because different organizations  use differing monitoring designs, indicators, and
        methods, EPA cannot  combine their information to  effectively answer questions about the quality of the
        nation's  waters or track changes over time. EPA and its state, tribal,  and federal partners are implementing a
        series of aquatic  resource surveys to address this national information gap. These National Aquatic Resource
        Surveys  (NARS)  use randomized sampling designs, core indicators, and consistent monitoring methods and lab
        protocols to provide statistically-defensible assessments of water quality at the national scale. Additionally, the
        national surveys are helping build stronger monitoring programs across the country by fostering collaboration
        on new  methods, new indicators, and new water quality research. EPA implements the surveys on a five year
        rotation. As the surveys repeat, EPA will be able to track changes over time and advance our understanding
        of important regional  and national patterns  in  water quality. USGS'  National Water  Quality Assessment
        (NAWQA)  Program also conducts national and regional assessments  of status and trends of aquatic ecological
        condition. These national programs can serve as sources of biological,  geological, chemical,  geospatial, and
        physical data, which can be used to assess water quality conditions within a watershed.
                                 Plankton nets are
                                   used to collect
                                     and evaluate for
                                       abundance and
                                        diversity of
                                         phytoplankton
                                         and
                                          zooplankton,
                                          which form
                                          the base
                                         of a lake's
                                         food chain.

                                      Photo: NEIWPCC.
Water quality
 multiprobes are often
   used to collect data
     in the field on
      temperature,
       dissolved
        oxygen,
        conductivity,
        pH, and other
        parameters.
                                                                                          Photo: USFWS.
                                 Working with partner
                                   organizations
                                     increases access to
                                       the specialized
                                        equipment
                                         that can be
                                         needed for
                                         water quality
                                         monitoring.
                                      Photo: USGS.
 in
Examination of diatoms
   cross sections of
     sediment core
     can provide
      insight on a
       lake's historical
       chemical
       and physical
       characteristics,
     =  such as total
       phosphorus
       and clarity.

    Photo: NEIWPCC
3-74

-------
                                                                                 3 Examples of Assessment Approaches
   National Rivers and Streams Assessment
   Author or Lead Agency: U.S. EPA
   More Information: http://water.epa.gov/type/rsl/monitoring/riverssurvey/riverssurvey index.cfm

In 2006, EPA released a report on the Wadeable Streams Assessment (WSA), which was the first statistically
valid  national  survey  of the biological condition  of small  streams throughout  the  United  States (U.S.
Environmental Protection Agency,  2006c).  The WSA  uses  macroinvertebrate communities  to  report  on
biological condition and measures  other key parameters such as riparian and instream habitat, sediments,
nutrients, salinity, and acidity. With  1,392 randomly selected sites, a representative sampling of the condition
of streams  in all ecoregions  established  a national baseline of biological condition. The WSA found that,
compared to best available reference sites in their ecological regions, 42% of U.S. stream miles are in poor
condition,  25% are in fair condition, and 28% are in good condition (Figure 3-31).  The National  Rivers
and Streams Assessment (NRSA) expands on the WSA by including larger streams and rivers.  The NRSA is
designed specifically to:

    •   Assess the condition of the nation's rivers and streams.
    •   Help build state and  tribal capacity for monitoring and assessment.
    •   Promote collaboration across jurisdictional boundaries.
    •   Establish a  baseline to evaluate progress.
    •   Evaluate changes in condition since the first Wadeable Streams Assessment.
        West
   152,425 stream miles
Plains and Lowlands
242,264 stream miles
                                                Eastern Highlands
                                               276,362 stream mile!.
rl.
            TT.
                                                                                  5.0%
                                                                          National Biological Quality
                                                                             Cood
                                                                             Fair
                                                  Not Assessed
 Figure 3-31 Biological quality results from EPA's Wadeable Streams Assessment (U.S. Environmental Protection
 Agency, 2008c).
                                                                                                          3-75

-------
Identifying and Protecting Healthy Watersheds
        The sampling design  for the NRSA survey is  a probability-based  network that provides  statistically valid
        estimates of condition for a population of rivers and streams with a known confidence. A total of 1,800 sample
        sites were selected to represent the condition of rivers and streams across the country (Figure 3-32), 900 in each
        of two categories  of waters: wadeable and  non-wadeable. The survey is measuring a wide variety of variables
        intended to characterize the  chemical, physical,
        and biological condition of the  nation's flowing
        waters. These include  water chemistry, nutrients,
        chlorophyll  a, sediment enzymes,  enterococci,
        fish   tissue,   physical  habitat   characteristics,
        and biological assessments  including  sampling
        of    phytoplankton,     periphyton,    benthic
        macroinvertebrates,   and   fish   communities.
        Sample collection was completed in 2009 and a
        final report is scheduled for 2012. Data collected
        through  the  NRSA  will  be  made  available
        through EPA's Water  Quality Exchange (WQX)
        (see Appendix B). These data can be used by state  ^W               W^ ^  Vf't't ^J  MR^~.
        and local watershed  managers for targeting of
        more intensive monitoring plans and for regional
        comparisons of water quality.
           Figure 3-32 National Rivers and Streams Assessment sample sites (U.S. Environmental Protection Agency,
           2011d).
3-76

-------
Case    Study
 Oklahoma  National  Rivers  and Streams
 Assessment
 More information: http://www.owrb.ok.gov/studies/reports/reports pdf/REMAP-
 OKStreamRiver ProbMonitorNetwork.pdf
 Several  agencies,  including  the  Oklahoma Water
 Resources  Board and  the  Oklahoma Conservation
 Commission,   conduct  water  quality  monitoring
 in the State of Oklahoma. Since the  early 1990s,
 monitoring programs have developed  complementary
 monitoring objectives that  support the  management
 of Oklahoma's  surface waters, including a long-term,
 fixed-station water  quality monitoring  network on
 rivers and  lakes, and a small-watershed rotating basin
 monitoring program that targets smaller streams. As
 part of Oklahoma's long-term water quality monitoring
 strategy, a probabilistic approach to resources has been
 in development since 2001, with the primary objective
 to compliment  other programs.

 Due  to  funding  and  resource  constraints,  full
 implementation of probabilistic monitoring has taken
 a number of years to reach full maturation. As late as
 2003, Oklahoma agencies remained unable to initiate
 further planning and make a long-term commitment,
 even though the need  for the approach  had already
 been  accepted. However, in  2004, Oklahoma  took
 part  in the National WSA, and from 2004-2008, the
 Oklahoma  Water  Resources  Board  received several
 grants to study the feasibility of, and to implement, a
 probabilistic monitoring approach in  rivers,  streams,
 and  lakes.  These  projects  included  CWA  104(b)3
 grants,  a  Regional  Environmental Monitoring and
 Assessment grant, and CWA 106 monies to  perform
 the NARS monitoring  in  lakes (2007)  and rivers/
 streams  (2008-2009).  Over  this  five year  span,  a
 probabilistic approach  was  fully integrated into the
 Oklahoma  Water  Resources  Board's   monitoring
 strategy and has been  adopted by  the  Oklahoma
 Conservation Commission as  part of  their long-term
 monitoring approach. With the assistance of continued
 NARS funding and supplemental 106  monitoring
 funds coupled with  the leveraging of state dollars, the
 various programs have  grown to include monitoring
 of various  resource  types and  sizes.  The statewide
 rivers and  streams probabilistic program will  enter its
fourth study cycle in 2013 and considers both small
and large water bodies separately. The program has
also integrated several  studies to investigate regional
needs.  Additionally,  a  statewide  lakes program
entered its second  study cycle in  2010. The design
considers both large lakes (>500 surface acres)  and
small lakes  (>50 surface acres). Lastly, using CWA
319 funds, the Oklahoma Conservation Commission
has implemented a probabilistic component as part
of its rotating basin monitoring program.

In terms of water  quality management, the most
obvious  outcome of probabilistic design has been
the inclusion of statistically valid surveys for creation
of  the  state's  305(b)  report.   However,  several
technological  enhancements  developed  through
NARS are being used  to benefit  the state in several
ways.  First, biological indicator  development  has
taken a dramatic leap  forward with the inclusion of
probabilistic data. Although Oklahoma has used both
invertebrate and fish indicators in wadeable streams
assessments   for   years,  probabilistic  collections
will facilitate  refinement of reference conditions,
improvement of metrics, and development of other
indicators, such as  phytoplankton and zooplankton.
Also, indicator collection methods  and eventually
assessment indices developed through NARS for both
large rivers and lakes are being implemented widely
throughout  Oklahoma.  Second,  the enhancement
of indicator-stressor relationships through  NARS
is  being used in Oklahoma studies.  Concepts of
relative risk have been included  in several studies
and can be  used to develop  long-term strategies for
toxic monitoring, nutrient criteria development,  and
refinement  of sediment and in-situ water  quality
criteria. Additionally, the NARS quantitative habitat
methodologies  have  been  combined  with rapid
bioassessment  protocols  to  develop more sensitive
habitat  metrics.  Lastly,  use  of multiple  design
strategies (fixed and probabilistic) will improve the
ability  to identify  regional hotspots  for resource
allocations.
                                                                                                 3-77

-------
Identifying and Protecting Healthy Watersheds
          National Lakes Assessment
          Author or Lead Agency: U.S. EPA
          More Information: http://water.epa.gov/type/lakes/lakessurvey index.cfm

        Lakes are an  important water resource to monitor, because  they provide,  among other things,  drinking
        water, habitat for fish and wildlife, recreational opportunities,  and flood control. However, their integrity is
        potentially threatened by the continual expansion of lakeshore development. The National Lakes Assessment
        was conducted in 2007 to survey the biological condition of the nation's lakes, ponds, and reservoirs as part
        of the NARS Program. The NLA incorporates assessments of biological, chemical, and physical integrity; this
        integrated approach is expected to focus attention on the relationships between stressor levels and lake integrity
        and developing management strategies that foster healthy lake  conditions in all three of these aspects of lake
        integrity.

        For the NLA, indicators were selected to measure the biological, chemical, and physical integrity  of lakes and
        their capacity to support recreational opportunities. The NLA is designed to provide information on the entire
        population of lakes, nationally and  at other broad scales; it does not assess the quality of individual lakes.
        The NLA emphasizes the analysis of biological indicators and biological condition, because biological systems
        integrate the affects of multiple stressors over time. Biological indicators included observed versus  expected
        (O/E) phytoplankton  and zooplankton,  the Lake Diatom Condition Index,  benthic macroinvertebrates,
        algal density (chlorophyll a), and invasive species. Chemical  indicators included phosphorus and  nitrogen
        concentrations, characteristics of the water column  profile (dissolved oxygen,  temperature, pH, turbidity,
        acid  neutralizing  capacity, salinity),  and sediment mercury concentrations. Indicators  of physical  integrity
        included lakeshore  habitat cover  and structure, shallow water habitat cover and structure, and lakeshore
        human disturbance. Poor  lakeshore habitat was the most significant stressor among lakes studied, being both
        the  most prevalent  problem  (occurring in one third of studied lakes) and  the stressor  that has  the greatest
        negative  impact on a lake's  biological  health.  This finding implies a need for management strategies  that
        protect and restore  the natural state of lakeshore  habitat to provide essential vegetative cover and buffering
        from human disturbances. Lastly, recreational suitability indicators included pathogens (enterococci), algal toxin
        concentrations (microcystins), and cyanobacteria counts.

        Well-documented sample collection and analysis procedures were used to conduct the NLA. Depth profiles for
        temperature, pH, dissolved oxygen, water clarity, and the depth at which light penetrates the lake's water were
        measured over the deepest point in each lake. Single grab water samples were collected to measure nutrients,
        chlorophyll a, phytoplankton, and the algal toxin microcystin. Zooplankton samples were collected using fine
        and coarse plankton nets. A sediment core was taken to provide data on sediment diatoms and mercury levels.
        Along the perimeter of the lake, crews collected data on the physical characteristics that affect habitat suitability.
        Substrate composition data were  recorded  along the ten peripheral stations. Benthic macroinvertebrates and
        water samples for pathogen analysis were collected at the first and last stations, respectively.

        All of these measurements were made for lakes  selected through the random selection process and for a set of
        least disturbed lakes that exhibit the highest quality condition. The results obtained from analysis of these high
        quality lakes were used to define  a set of reference lakes for biological condition and a set of reference lakes
        for nutrient condition, to which  lower quality lakes were compared. Lakes  which had results above the 25th
        percentile of the reference range values were  considered "good" (56%); those which had results between the
        fifth and 25th percentiles were considered "fair" (21%); and lakes which had results below the fifth percentile of
        the reference range values were considered "poor" (22%) (Figure 3-33).
3-78

-------
                                                                               3 Examples of Assessment Approaches
                          National All Lakes
                                 49,546
Natural Lake
    29,308
Man-Made Lakes
       20,238
       Taxa Loss
       Good = <20%
       Fair = 20% - 40%
       Poor= >40%
 Figure 3-33 Biological condition of lakes nationally and based on lake origin (U.S. Environmental Protection
 Agency, 2009a).

The data produced by the 2007 NLA and future applications of its standardized field and laboratory protocols
contribute  to the kind of statistically valid assessment of lakes that EPA and states need to inform  their
lake management policy decisions. This survey established the  first nationally consistent assessment of both
condition  and extent of stressors to lake biological condition, which may be used to measure the impact of
future management activities. EPA sees the analyses that were developed for the NLA, such as the IBI for lake
diatoms and plankton O/E models, as tools that can be adapted for use within individual states. Data generated
through the NLA can be used to identify regional hotspots for particular stressors  and promote collaboration
between jurisdictional authorities  in those hotspots to reduce the stressors' impacts on  lake integrity. States
can also use NLA data to tailor restoration strategies to address the stressors identified for each of the  lakes
in their jurisdictions, making it easier for them to leverage programs such as the Environmental Quality
Incentives Program and Conservation Reserve and Enhancement Programs managed by the U.S. Department
of Agriculture's (USDA) Natural  Resources Conservation Service and the CWA Section  319 Program and
National Pollutant Discharge Elimination System.
                                                                                                       3-79

-------
                                                 Case    Study
                    Minnesota  National Lakes Assessment
                    More information: http://www.pca.state.mn.us/index.php/water/water-types-and-
                    programs/surface-water/lakes/lake-water-quality/national-lakes-assessment-project-nlap.
                    html?menuid=&redirect=l
       Minnesota's  2007  NLA  effort  was  led  by the
       Minnesota Pollution Control Agency and Minnesota
       Department of Natural Resources (DNR). Other
       collaborators  included  the  U.S.  Forest  Service,
       Minnesota Department of Agriculture, and USGS.
       Minnesota received 41 lakes as a part of the original
       draw of lakes for the national survey—the most of
       any of the  lower 48 states. Minnesota added nine
       lakes to the survey to yield the 50 lakes needed for
       statistically-based statewide estimates of condition. In
       addition to the 50 lakes, 14 reference lakes were later
       selected and sampled by EPA as a part of the overall
       NLA effort. Data from the reference lakes provide
       an additional basis  for assessing  lake condition as a
       part of NLA. Because of its statistically-based nature,
       this dataset provides a good basis for describing the
       typical  range of constituents and interrelationships in
       Minnesota's lakes on a statewide basis.

       Previous  studies  have described regional patterns
       in lake trophic status and the  NLA data reinforce
       these patterns  and provide a basis for statistically
       describing trophic status  on a statewide basis and
       providing estimates at an ecoregion basis. In terms
       of phosphorus-based trophic status, the distribution
       of Minnesota's lakes is similar to that of the Nation
       and about 64% of Minnesota's lakes are considered
       oligotrophic or mesotrophic  (on  a weighted basis).
       The Minnesota NLA phosphorus, chlorophyll a, and
       Secchi  data exhibit relatively strong correlations and
       can be used to describe interrelationships and identify
       thresholds. With  respect to nitrogen, the Minnesota
       data reveal very poor correspondence among nitrogen
and chlorophyll a, and nitrogen:phosphorus ratios
indicate that <10% of the lakes might be considered
"nitrogen-limited"  — both  of which  support  the
need to emphasize phosphorus over nitrogen when
developing nutrient criteria in freshwater lakes.

In addition to the measurements made as a part of the
overall  NLA, Minnesota made several enhancements
to their survey, including:  collaboration with U.S.
Forest  Service  in  sampling the  Boundary  Waters
Canoe  Area Wilderness, which allowed  for inclusion
of hard-to-access  lakes  in this  wilderness  area;
sampling in support of lake  Index of Biotic Integrity
(IBI) development; and a region-wide assessment of
the Prairie Pothole Region conducted in conjunction
with North  Dakota, South Dakota, Montana  and
Iowa  an ongoing effort  with primary  emphasis
on identifying  reference condition  for this  unique
population of lakes.

The NLA data provide a valuable complement to data
collected from  other more  targeted  programs. This
statistically-based dataset allows for  extrapolation to
the entire state or ecoregions. This can provide context
for  data collected from  other programs,  estimate
numbers or  percentages of lakes  that  meet water
quality standards or numbers or percentages of lakes
that may have a chemical make-up or other attributes
that may be of interest to state or local lake managers.
Minnesota's NLA reports also provide information on
other lake attributes that is useful to lake managers
and scientists.
3-80

-------
                                                                               3 Examples of Assessment Approaches
  Regional and  National Monitoring and Assessments of Streams and Rivers
  Author or Lead Agency: U.S. Geological Survey
  More Information: http://water.usgs.gov/nawqa/studies/mrb/

USGS implemented the National Water Quality Assessment (NAWQA) Program in 1991 to develop long-
term, consistent and comparable information on streams, rivers, ground water, and aquatic systems in support
of national, regional, state, and local information needs and decisions related to water quality management and
policy. The current focus of USGS' National Water Quality Assessment Program is on regional and national
scale assessments of status  and trends  in  streams, rivers, and ground  water across  the nation. Under the
NAWQA program, USGS collects and  interprets a variety of biological, geological, chemical, geospatial, and
physical data, which can be used to assess  water quality conditions and trends within a  watershed. Available
ground water quality data are similar to surface water quality data but in addition include volatile organic
compounds, major anions and cations, trace  elements, and selected radionuclides. Chemical, physical, and
aquatic biological parameters collected in surface waters include:
  •   Temperature
  •   Specific conductance
  •   Dissolved oxygen
  •   pH
  •   Alkalinity
  •   Chloride
•   Carbonate
•   Bicarbonate
•   Sulfate
•   Suspended sediment
•   Nitrogen
•   Phosphorus
Fish
Aquatic macrolnvertebrates
Periphyton
Chlorophyll
Stream habitat
Daily stream flow
NAWQA has identified eight large geographic regions  (referred to as "major river basins") as the basis for its
status and trends assessments (Figure 3-34). The most  recent NAWQA assessments (2002-2010) build upon
previous  findings  generated  from 1992-2001  for streams and rivers in smaller basins (referred to  as "study
units"). Primary goals remain the same: characterize the status of surface water quality (stream chemistry and
ecology)  and ground water quality; determine trends at those sites that have been consistently monitored for
more than  a decade; and build an understanding of how natural features and human activities affect water
quality. The number of sites included in NAWQA's status and trends  network totals 113 across the eight major
river basins (Figure 3-34). The NAWQA monitoring network uses a fixed-site, five interval rotational sampling
scheme; therefore,  sampling intensity varies from every year to  one in four years at the different sites.  The
results of regional  and national scale water quality assessments are  published in various USGS and  journal
publications. In addition, data collected through the NAWQA monitoring network are made available through
USGS' National Water Information System (NWIS) and the NAWQA Data Warehouse (see Appendix B).
                                                                                                       3-81

-------
Identifying and Protecting Healthy Watersheds
        An important design element of the NAWQA Program is the integration of monitoring data with modeling
        and other scientific tools to estimate water quality at unmonitored sites based on data collected at comparable
        sites. Many of these tools are designed to evaluate various resource management scenarios and predict how
        management actions are likely to affect water quality. Some specific applications of NAWQA tools include:

            •   The use of a hybrid statistical, GIS,  and process-based model, SPARROW (SPAtially
                Referenced Regressions On Watershed  attributes), to estimate nutrient fluxes  in
                unmonitored streams throughout the conterminous United States (U.S. Geological
                Survey, 2009d).
            •   The use of statistical  and GIS tools for classifying watersheds  into  Hydrologic
                Landscape Regions.

        These modeling tools, based on  the NAWQA data, can provide watershed managers with valuable information
        when site-specific data are not available. National water quality monitoring and  assessment programs such as
        NAWQA and the National Rivers and Streams Assessment are important in the development of these tools, as
        well as for providing information on aquatic ecosystem health.
                                                                                                      MRB1
                  1
          if Urban core sites (14)
          if Agricultural core sites (8)
          A Urban indicator sites sampled every 2 years (12)
          A Agricultural indicator sites sampled every 2 years (3)
          ft. Urban indicator sites sampled every 4 years (12)
          ft Agricultural indicator sites sampled every 4 years (25)
          ftj Integrator sites sampled every 4 years (30)
          ft Reference indicator sites sampled every 4 years (19)

           Figure 3-34 Sites for Regional and National Monitoring and Assessments of Streams and Rivers within
           Major River Basins (MRB) (U.S. Geological Survey, 2009c).
3-82

-------
4.   Healthy  Watersheds  Integrated
       Assessments
                         Introduction
                         This chapter introduces the Healthy Watersheds Initiative, discusses the
                         characteristics of a healthy watershed, and reviews the benefits of protecting
                         healthy watersheds. This chapter also describes the purpose, target audience, and
                         intended use of this document.
                         Overview of Key Concepts
                         This chapter describes the healthy watersheds conceptual framework. It then
                         discusses, in detail, each of the six assessment components - landscape condition,
                         habitat, hydrology, geomorphology, water quality, and biological condition.
                         A sound understanding of these concepts is necessary for the appropriate
                         application of the methods described in later chapters. This chapter concludes
                         with a discussion of watershed resilience.
                         Examples of Assessment Approaches
                         This chapter summarizes a range of assessment approaches currently being used
                         to assess the health of watersheds. This is not meant to be an exhaustive list of all
                         possible approaches, nor is this a critical review of the approaches included. These
                         are provided solely as examples of different assessment methods that can be used
                         as part of a healthy watersheds integrated assessment. Discussions of how the
                         assessments were applied are provided for some approaches. Table 3-1 lists all of
                         the assessment approaches included in this chapter.
                         	s

                         Healthy Watersheds Integrated Assessments


                         This chapter presents two examples for conducting screening level healthy
                         watersheds integrated assessments. The first example relies on the results of a
                         national assessment. The second example demonstrates a methodology using
                         state-specific data for Vermont. This chapter also includes examples of state
                         efforts to move towards integrated assessments.
                         Management Approaches
                         This chapter includes examples of state healthy watersheds programs and
                         summarizes a variety of management approaches for protecting healthy
                         watersheds at different geographic scales. The chapter also includes a brief
                         discussion of restoration strategies, with focus on targeting restoration towards
                         degraded systems that have high ecological capacity for recovery. The results of
                         healthy watersheds integrated assessments can be used to guide decisions on
                         protection strategies and inform priorities for restoration.
                                                                                           4-1

-------
Identifying and Protecting Healthy Watersheds
        4.1    Integrated Assessment

        The term "integrated assessment," as used in this document, refers to a holistic evaluation of system components
        and processes that results in a more  complete understanding of the aquatic ecosystem, and  allows for the
        targeting of management actions  to  protect healthy watersheds. Figure  4-1 shows the healthy  watersheds
        integrated assessment and management framework. Collaboration with multiple partners is critical for framing
        the  scale and context of the assessment and ensuring that all relevant data and expertise are  identified and
        made available. These data are then used to evaluate each of the six healthy watersheds assessment components
        - landscape  condition, habitat, hydrology, geomorphology, water quality, and biological condition.  The results
        of the individual assessments are synthesized to  provide an overall assessment of watershed health. Strategic
        watershed protection priorities  can then  be identified  by evaluating vulnerability alongside  the identified
        healthy watersheds. Examples of watershed  protection strategies  and the role of outreach and education are
        discussed in Chapter 5- It is also important to collect new data for demonstrating the effectiveness of watershed
        protection activities and to refine future assessments. Assessment and management of healthy watersheds is an
        adaptive and iterative process, with new data and improved methodologies providing better assessment results
        and more effective protection strategies over time.
                                                 Involve partners to
                                                identify available data
                                                & scale of assessment
            Measure progress &
             collect new data
                 Evaluate each of the
                six healthy watersheds
                     components
                            Implement strategic
                           watershed protection
                                 priorities
  Integrate results to
   identify healthy
watersheds & evaluate
    vulnerability
         Figure 4-1 Healthy watersheds integrated assessment and management framework.
4-2

-------
                                                                             : Healthy Watersheds Integrated Assessments
Numerous approaches are available for evaluating each healthy watersheds attribute, ranging from screening
level analyses and desktop assessments to field assessments. The National Fish Habitat Assessment (NFHA) is
an example of a screening level analysis that was conducted for the entire United States (National Fish Habitat
Board, 2010). The assessment estimates relative fish habitat condition for all rivers at the reach, catchment, and
HUC12 scale. The following fifteen human disturbance variables were calculated for all reaches represented in
the NHDPlus dataset:
    1.  Population density
    2.  Developed open space
    3.  Road crossing density
    4.  Low intensity development
    5.  Road density
    6.  Medium intensity development
    7-  Dam density
    8.  High intensity development
    9.  Mine density
    10. Impervious surfaces
    11. Toxics Release Inventory site density
    12. Pasture/hay
    13- National Pollutant Discharge Elimination System site density
    14. Cultivated crops
    15- Superfund national priority site density
Canonical correspondence analysis and multiple linear regression were used to  relate  the best subset of the
human disturbance variables  to a fish community metric, percent intolerant species. The fish community data
were available from 2,440 sites sampled since 1995-  The NFHA results can be downloaded by state and used
as a first pass for identifying healthy watersheds (http://ecosystems.usgs.gov/fishhabitat/). NFHA results for
Vermont are shown in Figure 4-2.
                                                                                                            4-3

-------
Identifying and Protecting Healthy Watersheds
              N
             A
                                                                                 Not Scored
                                                                             ^H 5 Best Condition
                                                                                 3.6001 - 4.9999
                                                                                  .3334 - 3.6000
                                                                                 1.0001 -2.3333
                                                                                 1 Poorest Condition
                                                                                               Miles
                                                                                     10
20
             Figure 4-2 National Fish Habitat Assessment (NFHA) scores at the 12 digit hydrologic unit code
             (HUC) scale for Vermont (courtesy of the National Fish Habitat Board).
4-4

-------
                                                                               : Healthy Watersheds Integrated Assessments
NFHA results provide one option for easily identifying  potential healthy watersheds without the need to
collect additional data or conduct an assessment. Many states have detailed datasets available that include more
specific indicators of watershed health and consider additional attributes and habitats (e.g., lakes, wetlands,
etc.). These states are in a good position to perform their own assessment and identify healthy watersheds. This
chapter outlines one example of a GIS-based, screening level methodology for identifying healthy watersheds
statewide. This assessment methodology  uses an index approach for identifying healthy watersheds across the
State of Vermont with existing data collected by state and national  organizations. Indices are a convenient
way to aggregate data and  communicate complex information in  a simplified manner. They are  most useful
for comparative purposes (e.g., healthy or degraded) and to communicate with the  public or decision makers.
By design, indices contain  far less information than the raw data that they summarize;  they do not convey
information about underlying processes.  Statistical methods can be used to better understand the relationships
between individual metrics that  make  up an index. The results of such analyses  can be helpful in estimating
conditions in data-poor watersheds and  can also help to set management goals.  For example, multiple linear
regression can be used to  investigate relationships  between different land  cover classes  in a watershed and
indicators of biological condition such as macroinvertebrate species richness.  Biological conditions can  then
potentially be estimated in similar watersheds that lack biomonitoring  data by applying the regression equation
to available land cover data.  In addition, this type  of analysis provides information on potential land  cover
thresholds  that result in lowered  biological  condition. These thresholds can then be used to  inform land use
planning decisions.

Some of the  datasets  used in this example are unique to the State  of Vermont,  while  others  are  available
nationwide. Most states and tribes will  find that they are able to gather sufficient existing data, from  both
internal sources and from national databases,  to perform screening level assessments for identifying healthy
watersheds. Screening level assessments allow early action to protect healthy watersheds and prioritization of
future  field data collection  efforts that will  be used  to verify and refine the  assessments of individual healthy
watersheds components. It is important to work across programs and agencies in order to identify all potentially
useful datasets. The  datasets used in the  assessment summarized in this chapter come from the organizations
listed in Table 4-1. These data were used  to  calculate metrics for each  of the  six healthy watersheds assessment
components  (Table  4-2). The rest of this section describes how these metrics were calculated and integrated
into an overall index of watershed health.
Table 4-1 Datasets used to identify healthy watersheds in Vermont.
                       Dataset
 Dam inventory

 Water quality monitoring data

 Stream geomorphic assessment data

 Significant Wetlands Inventory

 Biological monitoring data
 Draft results from Vermont's Habitat Blocks and Wildlife
 Corridors Analysis
 National Hydrography Dataset Plus (NHDPIus)

 National Land Cover Dataset (NLCD) 2001 and 2006

 Active River Area delineation for the northeastern U.S

 Climate change projections

 Impervious cover change projections

 Water use change projections
                   Organization
Vermont Department of Environmental Conservation

Vermont Department of Environmental Conservation

Vermont Department of Environmental Conservation

Vermont Department of Environmental Conservation

Vermont Department of Environmental Conservation

Vermont Fish and Wildlife Department

U.S. Environmental Protection Agency

U.S. Geological Survey

The Nature Conservancy

Climate Wizard

U.S. Environmental Protection Agency

U.S. Geological Survey
                                                                                                               4-5

-------
Identifying and Protecting Healthy Watersheds
        Table 4-2 Metrics calculated for each healthy watersheds assessment component.
         Healthy Watersheds Assessment Component
                   Landscape Condition
                          Metric
Percent of watershed occupied by unfragmented natural land cover
Percent natural land cover within the Active River Area

Dam density (#/mi)
Percent of watershed occupied by significant (i.e., high quality) wetlands


Dam storage ratio (days)
                                                      Percent of assessed stream miles in reference condition
                                                      Percent of assessed sites in reference condition
                                                      Percent of assessed sites in BCG Tiers I or II
        Determine the Appropriate Scale

        One of the first steps in any watershed assessment is to decide on the appropriate geographic scale. Depending
        on the specific objectives and the resources available, the assessment can be conducted at a number of scales.
        Watersheds have a hierarchical nature; every watershed is  nested within a larger watershed  and has smaller
        watersheds nested within it. The appropriate scale  for conducting  a healthy watersheds assessment depends
        on the  user and their  specific objectives, as well as the hydrologic characteristics of the region (e.g., larger
        watersheds in  arid regions, smaller  watersheds in regions  with high precipitation). It is also important to
        consider the resolution of available  datasets when choosing the  appropriate scale  for the  assessment.  For
        example, the NLCD layer has a resolution  of 30 meters and should only be used in landscape scale analyses
        (not site-based). Ideally, field data will have been collected under a probabilistic monitoring design that allows
        for statistical estimates of aquatic ecosystem condition at the watershed scale. In the absence of probabilistic
        data, data gaps and uncertainties should be clearly stated. In this example, data were aggregated at the HUC12
        scale to identify healthy watersheds throughout Vermont. Though the field data used here were  not collected
        under  a probabilistic design, the large amount of data collected in all  areas of the  state helps  to  minimize
        uncertainty. A refinement of this analysis would include statistically-based estimates of biological condition at
        the watershed scale using data collected under a probabilistic monitoring design.
4-6

-------
                                                                            : Healthy Watersheds Integrated Assessments
Evaluate Landscape Condition

        The percent natural land cover within a watershed can be an important indicator of watershed health.
        Land cover data are sometimes available from the state or county. When local data are not available,
        the NLCD can be downloaded for free from the Multi-Resolution Land Characteristics Consortium
(http ://www.mrlc.gov). This dataset contains  land cover data for the years  1992, 2001, and  2006, as well
as percent  impervious data for the entire  United States. Impervious surfaces are associated with roads and
residential and urban areas, and can increase watershed runoff, leading to instream flow alteration, geomorphic
instability, and increased pollutant loading. Less than  10% impervious cover throughout a watershed has been
correlated with excellent or very  good IBIs and is suggested as a threshold  beyond which  aquatic ecosystem
health begins to decline (Schueler, 1994). Recent  research has suggested that much lower levels  of impervious
cover may have significant impacts on the aquatic biota (King,  Baker, Kazyak & Weller, 2011). A general
trend of declining IBI scores has also been observed with increasing agricultural land use (Wang & Yin, 1997).
However, generally applicable thresholds have yet to be determined and are likely to vary by region.

The extent and connectivity of natural land  cover within a watershed are very important for ecological integrity.
Natural land cover within the watershed, and especially within headwater areas and riparian corridors, helps to
maintain the hydrologic regime, regulates inputs of nutrients and  organic matter, and provides habitat for fish
and wildlife. Assessing the connectivity of large core areas of natural vegetation involves a green infrastructure
assessment such  as those that have been  conducted  by Virginia,  Florida, and Maryland (see Chapter 3).
Green infrastructure assessments identify large core areas of unfragmented natural vegetation and corridors of
sufficient width to allow for the migration of wildlife between the core areas. A number of CIS tools have been
developed to assist with green infrastructure assessments, such as the University of Connecticut's Landscape
Fragmentation Tool  (University of Connecticut Center for Land Use Education  and Research, 2009).  This
tool delineates areas of contiguous natural land cover, allowing for the identification of core areas or hubs.
Typically,  green infrastructure assessments  then use GIS techniques  to identify corridors  that represent the
easiest migration routes for wildlife to move from one core area to another. For the Vermont example, draft
results from the Fish and  Wildlife Department's Habitat Blocks and Wildlife Corridors analysis were used to
identify contiguous blocks of natural land cover and calculate the percent of each watershed's area occupied by
these blocks (Figure 4-3).  The green infrastructure metric was calculated as follows:

                                             (Acres of contiguous natural land cover in watershed)
                Green infrastructure metric =  	
                                                          (Total acres in watershed)

The amount of natural land cover within the  Active  River Area is  another important indicator of landscape
condition.  The Active River Area framework  was developed by  The Nature Conservancy and includes the
river channel,  lakes and ponds, and the  riparian lands necessary for  the physical and ecological functioning of
the aquatic ecosystem (see Chapter 3). This area is formed and maintained by disturbance  events and regular
variations in flow and water level within the dynamic environment of the water/land interface. The Active River
Area focuses on five key processes: hydrology and fluvial action, sediment transport, energy flows, debris flows,
and biotic actions and interactions (Smith et al., 2008). The analysis identifies the places where these processes
occur based on valley setting, watershed position, and geomorphic stream type.  The Active River Area has
already been delineated by The Nature Conservancy for the entire northeastern United States (Arlene Olivero,
The Nature Conservancy,  Personal Communication).  A set of GIS tools for delineating the Active River Area
in other parts of the country can be obtained by contacting TNC's freshwater program. For the Vermont
example, the percent natural land cover within the Active River Area was calculated for each watershed (Figure
4-4). The Active River Area metric was calculated as follows:

                                              (Acres of natural land cover in Active River Area)
                    Active River Area metric = 	
                                                      (Total acres in Active River Area)
                                                                                                           4-7

-------
Identifying and Protecting Healthy Watersheds
                                                                         Habitat Blocks
                                                                         Water
                                                                         HUC 12 Watersheds
                                                                                      Miles
                                                                            10      20
           Figure 4-3 Blocks of contiguous natural land cover in Vermont (courtesy of Vermont Fish and Wildlife
           Department).
4-8

-------
                                                                        : Healthy Watersheds Integrated Assessments
                                                          % Natural Land Cover
                                                          ^H 9-31
                                                                32-54
                                                                55-77
                                                          ^H 78-100
                                                          H Water
                                                          I     I HUC 12 Watersheds
                                                                             Miles
                                                                   10      20
Figure 4-4 Percent natural land cover in the Active River Area of Vermont (Active River Area delineation
courtesy of The Nature Conservancy)..
                                                                                                      4-9

-------
Identifying and Protecting Healthy Watersheds
        Evaluate Habitat Condition

                The quality of aquatic  habitat is  dependent on the surrounding landscape, and  hydrologic and
                geomorphic processes. Therefore,  habitat  condition is  partly accounted for through  indicators
                representing those assessment  components. The potential for organisms to migrate upstream and
        downstream within a riverine system can also  serve as an indicator  of aquatic habitat condition. For the
        Vermont example, dam density (dams  per  stream mile) was  calculated and used as an indicator  of aquatic
        habitat connectivity (Figure 4-5). The habitat connectivity metric was calculated as follows:

                                                     (Number of dams in watershed)
                       Habitat connectivity metric = 	
                                                   (Total stream miles in watershed)

        Intact wetlands help to maintain natural hydrologic regimes, provide important habitat for fish and wildlife,
        and regulate water quality. The Vermont Department of Environmental Conservation has inventoried and
        classified wetlands in Vermont into one of three classes  according to their overall condition and  ability to
        provide important habitat or maintain important ecosystem functions. Class  I and  Class  II wetlands are
        designated as significant wetlands based on the function and value they provide. For the Vermont example, the
        percent of the  watershed occupied by Class I and Class II wetlands was calculated and used as an  additional
        indicator of habitat condition for each watershed (Figure 4-6).  The wetland metric was calculated as follows:
                                         (Acres of Class I and Class  II significant wetlands)
                       Wetland metric = 	
                                                     (Total acres in watershed)

        Evaluate Hydrologic Condition

        /T\  Where long-term  stream flow data are available, either from a USGS stream gage  or a locally
           ^ 1 operated  stream gage, and predevelopment flow data  are available or have been modeled, the degree
           W/ of hydrologic alteration  can be rigorously evaluated. Where long-term flow data are not  available,
        it can be estimated with a number of modeling techniques. For example, StreamStats  is a web-based USGS
        application that will estimate monthly stream flow statistics at  ungaged sites  across the United States (U.S.
        Geological  Survey, 2009e).  The  Massachusetts  Sustainable Yield Estimator estimates daily stream flow at
        ungaged sites anywhere in Massachusetts (Archfield et al., 2010).  The USGS is  currently working  to expand
        the approach developed in Massachusetts to estimate continuous, daily unimpacted stream flow at any ungaged
        location in the Connecticut River Basin (portions of MA, CT, NH, and VT). This will result in a seamless,
        multi-state GIS-based point-and-click application that will allow users to identify a stream reach of interest in
        the Connecticut River Basin and obtain estimated continuous daily, unimpacted or "natural" stream flow at
        the selected location.

        The ratio of the volume of water impounded by dams and the average annual  predevelopment stream flow
        can also serve  as  an indicator of potential hydrologic alteration.The National Inventory of Dams (NID),
        as  well as many state dam inventories, contains the annual storage volume impounded  behind each dam.
        Summing these values for an entire watershed gives the numerator of the dam storage ratio. Estimated average
        annual predevelopment stream flow can be obtained for any watershed in the country from the National
        Hydrography Dataset Plus (NHDPlus). Dividing the dam storage volume by the predevelopment stream flow
        yields the storage ratio. It is important to keep in mind that these values are only coarse  estimates and that this
        indicator does  not represent the important hydrologic processes that drive aquatic ecosystem condition. More
        sophisticated analyses of hydrologic condition should be conducted when feasible. For  the Vermont example,
        the dam storage ratio was calculated for each watershed  and  used as  a metric of hydrologic alteration. The
        hydrologic alteration metric was calculated as follows:
                                                          (Dam storage volume)
                       Hydrologic alteration metric =
                                                    (Predevelopment annual stream flow)
4-10

-------
                                                                       : Healthy Watersheds Integrated Assessments
                                                           Dams
                                                           Streams
                                                           Lakes
                                                           HUC 12 Watersheds
                                                                        Miles
                                                              10      20
                                                                                   N
                                                                                  A
Figure 4-5 Location of dams in Vermont (courtesy of Vermont Department of Environmental
Conservation).
                                                                                                   4-11

-------
Identifying and Protecting Healthy Watersheds
                                                                       HUC 12 Watersheds
                                                                       Vermont Significant Wetlands
                                                                       Water
                                                                                     Miles
                                                                           10      20
            Figure 4-6 Class I and Class II significant wetlands in Vermont (courtesy of Vermont Department of
            Environmental Conservation).
4-12

-------
                                                                              : Healthy Watersheds Integrated Assessments
Evaluate Geomorphic Condition

         Built infrastructure can fragment  both terrestrial and aquatic habitat throughout a watershed and
         can  modify natural stream geomorphology.  In  the  absence of data on stream geomorphology,  the
         percent natural land cover in the Active River Area can be used as a potential indicator of geomorphic
condition. Detailed assessments of stream geomorphic condition can be performed using procedures such as
the Massachusetts River and Stream Continuity Project protocols (Massachusetts Department of Fish & Game,
2011), Vermont's Stream Geomorphic Assessment protocols (Kline, Alexander, Pytlik, Jaquith, & Pomeroy,
2009), or other similar, region-specific protocols. Most of these protocols typically begin with a desktop based
analysis (Phase 1) of geomorphic condition and are often followed up with detailed field assessments.

Phase 1  stream geomorphic assessments  have  been conducted  for a large number of watersheds in Vermont
using techniques described  in Chapter  3  (Figure 4-7).  Phase 1 assessments are GIS-based analyses using
elevation, land cover,  and stream network data layers to classify stream types and evaluate the  condition of
individual reaches based on a comparison to reference conditions for that stream type. Additional data used
to evaluate stream reach condition include locations of flow regulations  and water withdrawals  (including
dams, bridges, culverts, etc.), USGS topographic maps, and historical information concerning dredging, gravel
mining,  and bank armoring. The  Phase  1  geomorphic condition is determined primarily through  a stream
impact rating based on channel, floodplain, and land use modifications. Low stream impact ratings indicate
reaches that are in good to  excellent condition and may  be candidate reference reaches. The specific  methods
used to determine stream geomorphic condition are described in detail in the Vermont SGA protocols. Table
4-3 describes the stream geomorphic condition categories  that  are determined through the stream impact
rating. For the Vermont example, the percent of assessed stream miles in reference condition was calculated for
each watershed and used as an indicator of geomorphic condition. The geomorphology metric was calculated
as follows:
                Geomorphology metric =
                               (Stream miles in reference condition)

                             (Total stream miles assessed in watershed)
Table 4-3 Descriptions of the stream geomorphic condition categories (Kline et al., 2009).
 Condition
 Reference
 Good
 Fair
 Poor
                                        Description
In Equilibrium - no apparent or significant channel, floodplain, or land cover modifications; channel geometry is
likely to be in balance with the flow and sediment produced in its watershed.

In Equilibrium but may be in transition into or out of the range of natural variability - minor erosion or lateral
adjustment but adequate floodplain function; any adjustment from historic modifications nearly complete.

In Adjustment- moderate loss of floodplain function; or moderate to major plan-form adjustments that could lead
to channel avulsions.
In Adjustment and Stream Type Departure - may have changed to a new stream type or central tendency of fluvial
processes or significant channel and floodplain modifications may have altered the channel geometry such that the
stream is not in balance with the flow and sediment produced in its watershed.
                                                                                                            4-13

-------
Identifying and Protecting Healthy Watersheds
                                                                Stream Geomorphic Condition
                                                                     Poor
                                                                     Fair
                                                                     Good
                                                                     Reference
                                                                     Unassessed
                                                                     Water
                                                                     HUC 12 Watersheds
                                                                                  Miles
                                                                        10      20
          Figure 4-7 Phase 1 stream geomorphic assessment results for Vermont (courtesy of Vermont Department
          of Environmental Conservation).
4-14

-------
                                                                             : Healthy Watersheds Integrated Assessments
Evaluate Water Quality

        Water quality can be evaluated in a number of ways, ranging from statewide probabilistic monitoring
        to the use of complex watershed loading models and empirical analyses of the relationship between
        landscape characteristics and water quality As part of the National Wadeable Streams Assessment and
National Lakes Assessment, EPA has specified ecoregional water quality criteria for identifying least-disturbed
sites throughout the United States (Herlihy,  et al. 2008; in-review manuscript by Herlihy, A., Banks Sobota,
J., McDonell, ^.,  Sullivan, ^., Lehmann, S., and Tarquinio, E.  "An a priori process for selecting candidate
reference lakes for a national survey")- For the Vermont example, these criteria were used to identify streams
and lakes that are likely to be in reference condition based on total phosphorus, total nitrogen, turbidity, and
chloride concentrations (Table 4-4; Figure 4-8). The water quality metric was calculated as follows:
          Water quality metric =
(Number of sites with all parameters less than reference criteria)

        (Total number of sites assessed in watershed)
Table 4-4 Ecoregional water quality criteria used to screen for reference sites in Vermont (Herlihy, et al. 2008;
in-review manuscript by Herlihy, A., Banks Sobota, J., McDonell, T., Sullivan, T., Lehmann, S., and Tarquinio, E. "An
a priori process for selecting candidate reference lakes for a national survey").
  Ecoregion/Ecoarea    Total Phosphorus (ug/L)   Total Nitrogen (ug/L)   Turbidity (NTU)   Chloride (ue/L)
 Northern Appalachian
 Ecoregion (Streams)
 New England Highlands
 Ecoarea (Lakes)
 New York Lowlands
 Ecoarea (Lakes)
 20

 10

 20
                        750
250

20

100
Evaluate Biological Condition

        In areas where IBIs have been developed, these data can be overlain in GIS to identify healthy instream
        conditions in the context of the other healthy watersheds attributes.  Healthy watersheds should have
        IBI scores close to reference conditions. Where such indices have not been developed, biological data
can be used to create them. Examples of approaches for developing IBIs are summarized in Chapter 3-

The Vermont Department of Environmental Conservation uses the Biological Condition Gradient  (BCG) to
characterize biological condition statewide (See Chapter 3). Each assessed stream is placed into one of six tiers
(biological condition categories) based upon the IBI scores from fish and/or macroinvertebrate assessments.
Tiers I and II can be considered  to  be least or minimally disturbed. Where the fish and  macroinvertebrate
scores differ for the same stream, the lower score is used to represent biological condition. This is a conservative
approach  for estimating overall biological condition. For the Vermont example, the percent of Tier I and Tier
II sites in each  watershed was  used  as a  metric to represent  overall  biological condition (Figure  4-9). The
biological condition metric was calculated  as follows:
                Biological condition metric =
                 (Number of Tier I and Tier II sites)

             (Total number of sites assessed in watershed)
                                                                                                           4-15

-------
Identifying and Protecting Healthy Watersheds
                                                                  Water Quality Sampling Locations
                                                                    •  Non-reference
                                                                    •  Reference
                                                                       Streams
                                                                       Lakes
                                                                       HUC 12 Watersheds
                                                                                     Miles
                                                                           10      20
            Figure 4-8 Reference and non-reference water quality sites in Vermont (courtesy of Vermont
            Department of Environmental Conservation).
4-16

-------
                                                                          : Healthy Watersheds Integrated Assessments
                                                        Biological Condition Gradient
                                                         •   Tier 6
                                                         o   Tier 5
                                                         o   Tier 4
                                                             Tier 3
                                                         o   Tier 2
                                                         •   Tier 1
                                                             Streams
                                                             Lakes
                                                             HUC 12 Watersheds
                                                                          Miles
                                                                        20
Figure 4-9 Combined results of fish and macroinvertebrate bioassessment scores at stream monitoring
sites in Vermont (courtesy of Vermont Department of Environmental Conservation).
                                                                                                       4-17

-------
Identifying and Protecting Healthy Watersheds
        Evaluate Overall Watershed Health

        Watershed health was evaluated by normalizing the metric scores to  integrate the data on multiple healthy
        watershed attributes into a composite score. Normalization converts indicator scores into a common scale in
        order to avoid potential bias introduced by the units in which each variable is measured. Normalization can be
        as simple as defining a threshold for the indicator score that is considered healthy. Scores above this threshold
        may receive a one and scores below it, a score of zero. Defining  "healthy" thresholds for each indicator can
        be a difficult  process that may require input from multiple programs  or agencies. Alternatively, the indicator
        scores may be scaled to a value between zero and one by dividing  the observed value for a given watershed by
        the reference  value or maximum value for all watersheds in a state, essentially representing the condition as a
        percentage. The indicator scores must also be directionally aligned,  meaning that higher scores should equate to
        "better" ecological conditions for each metric.  For metrics that are not directionally aligned (e.g., dam storage
        ratio) in their original units, the inverse (1/X) of each value can be taken.

        For the Vermont example, a composite index of watershed health was constructed by averaging the normalized
        indicator scores for each attribute (Figure 4-10). For attributes with more than one indicator, a sub-index was
        first calculated. The sub-indices  were then averaged to obtain the overall health index score. Depending on
        the specific management objectives, it may be appropriate to place more weight on some ecological attributes
        than on others. At that point, the process becomes subjective and a logical decision framework can be  used for
        soliciting and documenting expert opinion (see Smith, Tran, & O'Neill, 2003). Weighting was not used in the
        Vermont assessment. The normalized metrics and sub-index were calculated as follows:

                                                     (Observed  metric for watershed x)
                    Normalized metric value =
                                              (Maximum metric value for all watersheds in state)

                                (Normalized metric 1 + Normalized metric 2 + ... + Normalized metric x)
                    Sub-index =
                    Watershed health index =
        (Total number of metrics)

(Sub-index 1 + Sub-index 2 + ... + Sub-index x)

        (Total number of Sub-indices)
        The final sub-index and watershed health scores for the Vermont HUC12s span varying ranges. For example,
        the habitat condition scores range from  a minimum value of 0.001 to a maximum value of 0.516.  For
        communication purposes, it can be useful to normalize the final sub-index and watershed health index scores
        to range from 0 to 1. This allows for comparison of attribute  scores between different HUC12s, as well as
        allows for direct comparison of one attribute score to another. Figure 4-11 displays the normalized scores for
        each of the six attribute sub-indices and the normalized score for watershed health in three example HUC12s.
4-18

-------
                                                                              : Healthy Watersheds Integrated Assessments
 N
A
                                                                                       Miles
                                                                    0       10       20
  Figure 4-10 Relative watershed health scores for Vermont.
                                                                                                             4-19

-------
Identifying and Protecting Healthy Watersheds
          N
          A
HUC12
Landscape Condition
Habitat
Hydrology
Geomorphology
Water Quality
Biological Condition
010801050102
0.938
0.958
0.381
0.988
0.595
0.862
                                                                          Watershed Health
                                                                                                     1.000
                                                                               Watershed Health
                                                                                            Miles
                                                                                  10      20
         Figure 4-11 Normalized watershed health scores for Vermont, with normalized attribute scores displayed for
         select HUC12s. To facilitate communication of the results, all scores were normalized to range from 0 to 1.
         The final watershed health index scores, for example, were transformed from a minimum value of 0.071 and a
         maximum value of 0.598 to a minimum value of 0 and a maximum value of 1.
4-20

-------
                                                                            : Healthy Watersheds Integrated Assessments
Assess Vulnerability

Though not essential to identifying healthy watersheds and their intact components, a vulnerability assessment
facilitates the prioritization of protection and restoration strategies. Future projections of impervious surface
cover for the  year  2050  from EPA's Integrated Climate and Land Use Scenarios (ICLUS) project  (U.S.
Environmental Protection Agency, 2010) were  compared with current impervious surface cover in the same
dataset to calculate  a percent change metric for each watershed. The threats may include expected population
growth and urban  and suburban development, impacts from climate change, increased water withdrawals,
industrialization, agriculture, etc. Vulnerability assessments can be conducted based on urban growth models,
climate change predictive models, water use forecasts, invasive species threats, pollutant threats and models,
best professional judgment, and other methods.

Areas of vulnerability  can be identified on a map, and the healthy areas that fall  within  those "vulnerable
boundaries" can be prioritized for  protection.  For example, a build-out  analysis is a mapping method for
assessing vulnerability  to  future growth. Build-out analyses identify areas of potential  development  based
on  current zoning regulations and can be instructive to the public and local  governments. Many people are
unaware  of the potential risks that  their local zoning regulations (or lack  thereof) create. Build-out analyses
and the predicted ecological  and social  effects of complete development can prompt action to revise zoning
regulations and  implement other environmental protection ordinances. Some  of these potential actions are
discussed in Chapter 5. To complete a build-out analysis, a GIS layer(s) of current zoning for the watershed(s)
is required. Zoning designates legally allowable land uses for districts within a community. A copy of the land
cover layer used in the landscape condition evaluation can  be modified using  GIS to reflect these potential
future land uses.

For the Vermont example, vulnerability was calculated using data for future projections of impervious cover,
climate change projections, future water use, and recent changes in anthropogenic cover (Figure 4-12). Future
projections of impervious surface cover  for the year 2050 were obtained from EPA's Integrated Climate and
Land Use Scenarios (ICLUS) project (U.S. Environmental Protection Agency, 2010). The projected values of
impervious surface cover were compared with current impervious surface cover in the same dataset to calculate
a percent change metric for each watershed. The impervious change metric was calculated as follows:

                                        (Impervious area in 2050 - Impervious area in 2010)
              Impervious change metric = 	
                                                (Impervious surface acres in 2010)

Similarly, the percent change between current temperature and precipitation  and projected temperature and
precipitation for the year 2050 were also calculated for each watershed in Vermont. These climate projections
are  available for  download from climatewizard.org (Maurer, Brekke, Pruitt, & Duffy, 2007). The temperature
and precipitation change metrics were calculated as follows:

      Temp, change metric = Avg. annual temp.in 2050 - Avg. annual temp, for period of 1961 to 1990

      Precip. change metric = Avg. annual precip.in 2050 - Avg. annual precip. for period of 1961 to 1990

Projected water use estimates are  available for Vermont from  the  USGS for the year  2020  (Medalie  &
Horn, 2010).  In cases where detailed water use projections are not  available, population growth estimates
can be obtained from the U.S. Census Bureau.  Future water use can be estimated based on these population
projections and a per capita water use rate. Projected water use estimates from USGS were used to calculate the
water use change metric as follows:

                                        (Water use in 2020 - Water use  in 2005)
                Water use change metric = 	
                                                 (Water use in 2005)
                                                                                                         4-21

-------
Identifying and Protecting Healthy Watersheds
        The percent change in anthropogenic (e.g., urban and agricultural) land cover between 2001 and 2006 was
        also calculated for each watershed. This metric represents recent landscape alteration, an important indicator
        of aquatic ecosystem degradation (Schueler, 1994; King, Baker, Kazyak & Weller, 2011). While impervious
        surface cover is projected to decrease in many watersheds  throughout Vermont by 2050, recent land cover
        data indicate that anthropogenic land uses have continued to increase throughout Vermont in recent years.
        Therefore, this metric was included to provide a more balanced representation of landscape threats to aquatic
        ecosystem health. The recent land cover change metric was calculated as follows:

                                         (Anthropogenic land cover in 2006 - Anthropogenic land cover in 2001)
         Recent land cover change metric = 	
                                                          (Anthropogenic land cover in 2001)

        Similar to the method used to calculate the watershed health index, the vulnerability index was calculated by
        normalizing and combining the individual metric scores as follows:

                                              (Observed metric value for watershed x)
              Normalized metric value =
               Vulnerability index =
     (Maximum metric value for all watersheds in the state)

(Normalized metric 1 + Normalized metric 2 + ... + Normalized metric x)

                    (Total number of metrics)
        Three additional examples of vulnerability assessment approaches include Virginia's Vulnerability Assessment
        Model,  EPA's Regional Vulnerability Assessment (ReVA),  and Wyoming's  Ground Water Vulnerability
        Assessment. Case studies of these examples are provided on pages 4-26 through 4-30.
4-22

-------
                                                                               : Healthy Watersheds Integrated Assessments
 N
A
                                                                                        Miles
                                                                              10      20
  Figure 4-12 Relative watershed vulnerability scores for Vermont.
                                                                                                              4-23

-------
Identifying and Protecting Healthy Watersheds
        Set Strategic Management Priorities

        The results of watershed  health and  vulnerability assessments can be  used to set strategic management
        priorities at the watershed scale. Figure 4-13 illustrates one way to assign relative priorities  statewide. The
        median watershed health score for the state splits the X-axis in half and  the median watershed vulnerability
        score for the state splits the Y-axis in  half. These two median  lines create four  quadrants that  can be used
        to  classify watersheds according to their relative restoration and protection needs. Other quantiles or break
        points (e.g., 90%) can also be used for classifying the watersheds as healthy or vulnerable. These  break points
        should be carefully defined, and may require input from multiple programs or agencies. Healthy watersheds
        with high vulnerability  can  be  considered a priority for protection actions  before they become degraded.
        Healthy watersheds  with low vulnerability should still be protected, but  the need may not be  as urgent.
        Degraded watersheds with low vulnerability can be  considered a priority  for restoration due to  their high
        potential for recovery while degraded watersheds with high vulnerability  can  be  considered less  of a priority
        when the emphasis is on achieving results and demonstrating management effectiveness. In all of these cases,
        but especially when health  and vulnerability scores are within intermediate ranges, site-specific  determinations
        should be used to verify that the management action is appropriate for the watershed. Figure 4-14 displays the
        results of this management prioritization process for the State of Vermont. The  individual scores for each of the
        metrics and sub-indices can also help guide the selection of specific management actions for a given watershed.
        For example, a watershed identified as a protection priority might have a high geomorphology score, but a
        relatively low water quality score. This indicates  the need for both protection (e.g., river corridor easements)
        and restoration (e.g., TMDL implementation) actions.
              High
                                   Restore
                      Protection
                        Priority
                £
                cu
                c
  Site-specific
Determination
                                 Restoration
                                    Priority
                        Protect
               Low
                        Low
                                                 Watershed Health
                                          High
              Figure 4-13 Example of a management priorities matrix for setting protection and restoration
              priorities using watershed health and vulnerability scores.
4-24

-------
                                                                         : Healthy Watersheds Integrated Assessments
 N
A
                                                                HUC 12 Watersheds
                                                                Management Guidance
                                                                  | Protection Priority
                                                                   | Protect
                                                                   | Restoration Priority
                                                                   ~| Restore
                                                                                  Miles
                                                                        10      20
 Figure 4-14 Example of potential management guidance based on combined watershed health and
 vulnerability scores for Vermont.
                                                                                                      4-25

-------
                                               Case   Study
                    Virginia Conservation  Lands Needs
                    Assessment  Vulnerability  Model
                    More Information: http://www.dcr.virginia.gov/natural heritage/vclnavulnerable.shtml
       The Virginia Conservation Lands Needs Assessment
       (VCLNA)  is  a  flexible, widely  applicable CIS
       tool for integrated and coordinated modeling and
       mapping of land conservation priorities and actions
       in Virginia. The VCLNA is  currently composed of
       seven separate,  but interrelated  models: 1) Natural
       Landscape  Assessment Model, 2) Cultural  Model,
       3) Vulnerability Model, 4) Forest Economics Model,
       5) Agricultural Model, 6) Recreation Model, and 7)
       Watershed  Integrity Model. Together, these models
       are  used to identify and assess the condition of
       Virginia's  green infrastructure.  Additional  models
       can be built to analyze other green infrastructure and
       natural resource-related issues. The Natural Landscape
       Assessment Model is described in Chapter 3 and the
       Watershed Integrity Model is described in Chapter 4.

       The Vulnerability Model informs land conservation
       priorities in the Virginia Conservation Lands Needs
       Assessment by  identifying those  areas most at risk
       from development pressures  and other factors. The
       Vulnerability Model uses three submodels to evaluate
       growth pressures in urban, urban fringe, and suburban
       or rural areas. A composite model integrates all three
       of the submodels to  provide a complete  picture of
       potential growth areas.

       Based on the Chesapeake Bay Program's model, the
       Vulnerability Model  used Rural Area Community
       Codes (U.S. Department of Agriculture  Economic
       Research Service, 2005) to distinguish between urban,
       urban fringe, and suburban  areas. The model used
       land cover, slope, census (housing and population),
       roads, travel time, and parcel data to predict future
       growth across the state.
The outputs of the Vulnerability Model provide an
opportunity for local communities  to proactively
plan for growth. The results of the assessment can be
used to guide a community's master planning process
and can be combined with any of the other models
in the  VCLNA program,  such  as  the Landscape
Assessment Model or Watershed Integrity Model for
use in determining priority conservation areas.  GIS
data, hardcopy,  and digital maps are available for the
Vulnerability Model's results in the Commonwealth
of Virginia and  can be combined with other data or
analyses. The Vulnerability Model can be  used for
targeting  and prioritization of conservation  sites,
guiding local planning and growth assessment,  land
management, and  public  education.  Figure  4-15
shows  how the vulnerability assessment results can
be combined with a healthy waters assessment to
identify high quality streams for protection  priorities
at a regional scale.
4-26

-------
   Virginia   Healthy   Waters   Vulnerable
                      to   Potential   Growth
                                                        Healthy Waters

                                                         •  Exceptional Stream, Highest Growth Threat

                                                         •  Exceptional Stream, High Growth Threat

                                                             Healthy Stream, Highest Growth Threat

                                                             Healthy Stream, High Growth Threat

                                                        	Virginia County Boundaries

                                                        Predicted Growth Threat

                                                        ^^| Highest Growth Threat

                                                             High Growth Threat
                                                            ^"flr"
                                                            fX.
                                                           0  10  20     40
     Virginia Coastal Zone
                    This map was produced by the CENTER FOR ENVIRONMENTAL
                    STUDIES at Virginia Commonwealth University.         *
                    For more information about Virginia's Healthy Waters Initiative.  •
                    visit http://instarvcu.edu.
                    For more information on the VCLNA Growth Prediction Model.visit
                    the OCR Division of Natural Heritage website at
                    http://www.dcr. virginia.gov/natural_herrtage/vclnavulnerable.shtrnl.
Figure 4-15 Regional results of the VCLNA Vulnerability Model overlain with results from Virginia's
Healthy Waters program (Greg Garman, Virginia Commonwealth University, Personal Communication).
                                                                                                 4-27

-------
                                                 Case   Study
                    EPA Regional Vulnerability Assessment
                    Program
                    More Information: http://www.epa.gov/reva/
       The goal of EPA's Regional Vulnerability Assessment
       (ReVA)  Program is to develop and demonstrate an
       approach to comprehensive, regional-scale assessments
       that  effectively  inform decision  makers as to the
       magnitude, extent,  distribution, and uncertainty of
       current and anticipated environmental vulnerabilities.
       By identifying ecosystems within  a  region that are
       most vulnerable to being lost or harmed in the next
       five to 25 years, and determining which stressors are
       likely to pose the greatest risks, ReVA  serves as an
       early warning system for identifying environmental
       changes that can be  expected over  the  next  few
       decades. The objectives of the ReVA program are to:
           1.   Provide   regional    scale,     spatially
               explicit information on the  extent and
               distribution  of stressors  and  sensitive
               resources.
           2.   Develop and  evaluate  techniques to
               integrate information on  exposure and
               effects  so  that  decision makers  can
               better  assess relative risk  and prioritize
               management actions.
           3-   Predict   potential   consequences  of
               environmental changes under alternative
               future scenarios.
           4.   Effectively communicate  economic and
               quality  of life  trade-offs associated  with
               alternative environmental policies.
           5.   Develop techniques to prioritize  areas for
               ecological restoration.
           6.   Identify   information   gaps   and
               recommend    actions    to     improve
               monitoring and focus research.
       Current science indicates that future environmental
       protection efforts must address  problems  that are
       just emerging or are on the horizon. Many of these
       problems are subtle and cumulative, with widespread,
       regional effects and poorly understood implications.
The research approach advocated by ReVA differs
from typical ecological research in that it seeks  to
integrate many different types  of information from
many different sources into a cohesive product.

Much of the last 100 years of ecological research has
focused on examining the effects of single components
of ecosystems one by one. Many of the issues facing
the  environment are chronic conditions such as the
impairment of our nation's waters being affected  by
point sources (e.g., waste water treatment facilities),
nonpoint sources (pollution  generated by activities
such as agriculture), water usage, and climate.

ReVA uses four  interacting functions  to  develop
regional assessments that address  current and future
(projected) chronic environmental problems:
    1.  Landscape: Data on stressors and effects
       from many  sources must  be placed into
       spatial  context  and synthesized using
       GIS techniques.
    2.  Research Gaps: Research must fill critical
       gaps in our ability to apply the data at
       landscape and regional scales, and  to
       understand  how socioeconomic factors
       affect environmental conditions.
    3-  Real World: An assessment component
       must keep the project  grounded in the
       "real world" by applying the data and
       risk  assessment  techniques  to specific
       regions.
    4.  Data and Analytical Tools: This final step
       is  critical to ensuring that the results of
       the research can be applied to continuing
       regional  assessments.  The  data  and
       analytical tools must be transferred into
       the hands of regional  managers;  ReVA
       accomplishes this final step by developing
       web based demonstration projects.
4-28

-------
ReVA   developed   a   web-based   environmental
decision  toolkit  for  the Mid-Atlantic region  that
allows  decision makers to evaluate potential changes
to ecosystems in response  to  various management
decisions under various future development scenarios
(e.g., population increase, land-use  change,  climate
change,  intensity of resource  extraction)  out to
the year 2020.  The  toolkit is now being  used by
states  and  EPA Region 3 to develop  integrated
management  decisions.   For example,  ReVA has
tailored the  environmental  decision  toolkit to fit
the local conditions found within the 15 counties of
the Charlotte/Gastonia/Rock Hill region in  North
and South Carolina.  This region is projected to see
an  85% growth in its  population  by 2030, with
concomitant increases in  sprawl, air quality problems,
and associated concerns  of decreased quality of life
if the  growth is not carefully  managed.  ReVA has
helped to integrate the  pieces  and provide insights
into cumulative impacts  associated with  alternative
patterns of growth and land development by explicitly
considering factors  such as air  quality, amenities,
water quality, infrastructure costs, and human health
factors. Economic  impacts of  alternative  growth
scenarios were  evaluated, along with the effects on
health and natural resources. Many  of the  region's
environmental  concerns, such as air quality, will be
driven by options chosen for  future transportation
needs. Thus, partners envisioned an alternative future
scenario that would encourage both mass transit and
distributed economic development  built around city
centers (Figure 4-16).  ReVA  worked  closely with
its partners to  develop a spatially detailed model of
land use change that reflected realistic challenges and
options. At the same time, local leaders have formed
an alliance to  allow  strategic planning to take place
across regional  boundaries.  Individual jurisdictions
are now able to consider land use and other issues on
a more regional basis, not just by each locality. Now,
questions of land use and other issues that impact the
environment are being looked at on a broader scale.
                                                              6. -V
                                                                         ! tt   .'  ''
 Figure 4-16 Business as usual development pattern (left) and compact center scenario (right) used for the
 alternative growth scenario evaluations (U.S. Environmental Protection Agency, 2011e).
                                                                                                         4-29

-------
                                              Case   Study
                   Wyoming Aquifer Sensitivity and Ground
                   Water Vulnerability Assessment
                   More Information: http://waterplan.state.wv.us/plan/areen/techmemos/swaualitv.html
      The threat of ground water contamination is a major
      concern for Wyoming citizens, as well as local, state,
      tribal,  and  federal water management agencies.
      Use  of  industrial  and  agricultural  chemicals,
      resource  development activities (mining and  oil
      and  gas  development),  and urban  development
      can potentially cause  contamination of  underlying
      ground water resources.  In  1998, the  University
      of Wyoming  Water  Resources  Research Center,
      in partnership with  the Wyoming  Department
      of Environmental  Quality and EPA,  completed
      a statewide  assessment of aquifer sensitivity and
      ground water vulnerability for the shallow aquifers
      in Wyoming.  Aquifer sensitivity is defined as the
      relative ease with which contaminants  can move
      from the  land surface to  the water table based on
      hydrogeologic characteristics of the land surface,
      the vadose zone,  and the aquifer. Ground water
      vulnerability  is defined as  the relative  ease with
      which contaminants can move from the land surface
      to the water table based  on  aquifer  sensitivity
      and  the physical  and chemical properties  of the
      contaminant.
The Wyoming statewide aquifer sensitivity/ground
water vulnerability assessment was developed using
the EPA DRASTIC model. The DRASTIC model
uses seven environmental  parameters  (Depth  to
water,  net  Recharge, Aquifer media, Soil media,
Topography, Impact of vadose zone, and hydraulic
Conductivity)  to  characterize the  hydrogeologic
setting and evaluate aquifer vulnerability. For the
Wyoming Assessments, detailed statewide datasets
were developed for  the hydrogeologic (bedrock
geology,  surficial  geology,  well locations  and
logging information, elevation, and  precipitation)
and land use parameters used for the assessment
(agricultural, urban, oil and gas exploration areas,
etc.). GIS software was used to generate a statewide
aquifer sensitivity map and individual county level
aquifer sensitivity  and ground water vulnerability
maps. These maps  are used for a variety of ground
water management activities, including prioritizing
ground water monitoring and land  use planning
and management of agricultural chemicals. Aquifer
sensitivity and ground water vulnerability maps can
be used to assess the vulnerability of ground water
dependent ecosystems.
4-30

-------
                                                                           : Healthy Watersheds Integrated Assessments
4.2   Moving Towards Integrated Assessments

The following assessment approaches represent state and EPA efforts to move towards integrated evaluations
of watershed health. A summary of each approach  is provided  in the subsequent pages. Table 4-5 lists the
healthy watersheds assessment components addressed by each approach, and pages 4-55 through 4-64 contain
tables listing the indicators used in each assessment approach.  These tables  can be useful  for identifying
similarities and differences between approaches.  States, tribes, and other organizations  may  also find these
useful in developing their own lists of indicators for assessing watershed health. For example, the tables can
form the basis of a "scorecard" for evaluating: a) which components to include in an integrated assessment, b)
an appropriate classification system, c) indicators for which there are available data, and d) indicators that may
require additional monitoring.

Virginia Watershed Integrity Model

The Virginia Watershed Integrity Model uses a green infrastructure approach to evaluate landscape condition
across the watershed and in the riparian corridor specifically. It  incorporates a terrestrial habitat evaluation
and a modified IBI for identifying ecologically important catchments across the landscape. Although it does
not address hydrology, geomorphology, or water quality directly,  the  IBI serves as an integrating indicator of
the condition of these attributes, and the landscape condition is a characteristic that has a large effect on the
condition of these attributes.

Minnesota's Watershed Assessment Tool

Minnesota's Watershed Assessment Tool is an online map viewer that lets users evaluate landscape, habitat,
biology, water quality,  hydrology, and geomorphology in an integrated context. Currently, it only supports
online overlay analyses. However, efforts are underway to create a watershed health index that will use these
data to evaluate the condition of Minnesota's watersheds.

Oregon Watershed Assessment Manual

The Oregon Watershed Assessment Manual addresses landscape, habitat, biology, water quality,  hydrology, and
geomorphology through  field  assessments and follow-up analyses based on a  classification  and condition
assessment of channel habitat types. The classification system is based  on the expected biota of a stream and its
surrounding land uses. Management opportunities are prioritized  to protect, restore, or collect  additional data
based on the condition evaluation.

California Watershed Assessment Manual

The California Watershed Assessment Manual presents an organizational framework for integrated  assessments
of California watersheds. The framework is based on recommendations from EPA's Science Advisory Board
to evaluate the six essential ecological  attributes of landscape condition, hydrology/geomorphology, biotic
condition, chemical/physical condition,  natural disturbance  regimes, and ecological condition. A variety of
assessment approaches and management options are presented.

Pennsylvania Aquatic Community Classification

The Pennsylvania Aquatic  Community Classification approach  is based on biological  and  environmental
variables that categorize watersheds across Pennsylvania to identify the  least disturbed streams and set watershed
conservation, restoration, and enhancement priorities.
                                                                                                        4-31

-------
Identifying and Protecting Healthy Watersheds
        Connecticut Least Disturbed Watersheds

        Connecticut's Least Disturbed Watersheds approach identified the least disturbed watersheds in Connecticut
        based  on  an impervious surface and natural land  cover analysis, an  IBI approach, water  quality, flow
        modifications, and water withdrawals. The assessment identified  watersheds of exceptional  quality that can
        be used as reference sites in the development of a biological condition gradient for the state and that can be
        prioritized for protection.

        Kansas Least Disturbed Watersheds

        Kansas' Least Disturbed Watersheds approach identified the  least  disturbed watersheds in  Kansas using a
        landscape alteration index and taxonomic richness data. The assessment identified candidate reference streams
        in each of Kansas' five ecoregions and condition ratings for all other streams.

        EPA Recovery Potential Screening Tool

        EPA's Recovery Potential Screening Tool uses a wide variety of landscape datasets, impaired waters attributes
        reported by states to EPA, and monitoring data to evaluate ecological, stressor, and social indicators to prioritize
        watersheds  for protection or  restoration. This approach allows for  targeting of limited resources  to protect
        those watersheds that are of the highest ecological integrity and restore watersheds  with highest ecological
        capacity for recovery.

        Table 4-5 Healthy watersheds assessment components addressed in each of the eight assessments
        summarized in this section.
Healthy Watersheds Assessment Component
Landscape Condition
Habitat
Hydrology
Geomorphology
Water Quality
Biological Condition
VA
WIM
y




y
MN
WAT
y
y
y
y
y
y
OR
WAM
y
y
^
Y
y
y
CA
WAM
y
y
y
y
y
y
PA
ACC
y
y
y
y
y
y
CT
LOW
y

y

y
y
KS
LOW
y
y
y

y
y
EPA
RPST
y
y
y
y

y
        VA WIM: Virginia Watershed Integrity Model
        MN WAT: Minnesota's Watershed Assessment Tool
        OR WAM: Oregon Watershed Assessment Manual
        CA WAM: California Watershed Assessment Manual
        PA ACC: Pennsylvania Aquatic Community Classification
        CT LOW: Connecticut Least Disturbed Watersheds
        KS LOW: Kansas Least Disturbed Watersheds
        EPA RPST: EPA Recovery Potential Screening Tool
4-32

-------
                                                                             : Healthy Watersheds Integrated Assessments
  Virginia Watershed Integrity Model
  Author or Lead Agency: Virginia Department of Conservation and Recreation - Division of Natural Heritage
  More Information: http://www.dcr.virginia.gov/natural  heritage/vclnawater.shtml

The Virginia Conservation  Lands Needs Assessment  (VCLNA) is a flexible, widely applicable GIS tool for
integrated and coordinated modeling and mapping of land conservation priorities and actions in Virginia. The
VCLNA is currently composed of seven separate, but interrelated models: 1) Natural Landscape Assessment
Model, 2) Cultural  Model, 3) Vulnerability Model, 4) Forest Economics Model, 5) Agricultural Model,  6)
Recreation Model,  and 7)  Watershed Integrity Model. Together, these models are  used  to identify and
assess the condition of Virginia's green infrastructure.  Additional models can be built to analyze  other  green
infrastructure and natural resource-related issues. The Natural Landscape Assessment is described in Chapter 3
and the Vulnerability Model is described in Section 4.3-

The VCLNA Watershed Integrity  Model  identifies  the  terrestrial resources that should  be conserved  to
maintain  watershed  integrity and water quality. The relationship between land use and aquatic health is well
documented. For  example,  it is well-known that as the area of impervious surface in  a watershed increases,
water quality declines.  This is due to the decreased infiltration capacity of the land and the rapid accumulation
of pollutants, such as heavy metals and salts, on these  impervious surfaces. When it rains, these pollutants are
rapidly washed off of the roads  and parking lots directly into the nearest stream or storm drain, which  often
empties into a stream some  distance away. Other examples of land use characteristics that affect water quality
include erosion and sediment loading from decreased forest cover in a watershed, nutrient loading as a result of
intensive agriculture, and decreased water quality as a result of loss of riparian vegetation.

The Watershed Integrity Model  combines GIS layers representing a modified Index of Biotic Integrity (mlBI),
an Index of Terrestrial  Integrity  (ITI), slope, source water protection zones, ecological cores, and riparian areas
to derive a final weighted overlay grid that identifies the relative value of land in the watershed as it relates to
water quality. The relative weights for the overlay analysis are as follows:

    •   mlBI — 25%                          •   Source water protection zones — 10%
    •   ITI-30%                            •   Ecological cores-15%
    •   Slope-10%                          •   Riparian areas-10%

The mlBI was developed by Virginia Commonwealth University Center for Environmental Studies (Virginia
Commonwealth University,  2009) to evaluate aquatic health and is computed  from six metrics:

    1.  Number of intolerant species.
    2.  Species richness.
    3.  Number of rare, threatened, or endangered species.
    4.  Number of non-indigenous species.
    5.  Number of critical/significant species.
    6.  Number of tolerant species.

The ITI is calculated based on the percent natural cover of the watershed, percent riparian corridor vegetation
remaining, proportion of habitat fragmentation due  to roads,  and percent impervious surface cover in the
watershed. Areas with  steep  slopes are included in the model as an indicator of where small headwater streams
are  likely to occur. Riparian areas and source water protection zones  are also identified and included in the
Watershed Integrity Model. Ecological cores are large patches  of natural land cover that provide significant
interior habitat and are an output  of the VCLNA Natural Landscape Assessment Model. Inclusion of these
large forested areas provides the Watershed Integrity Model with a method for prioritizing forested lands that
provide water quality benefits  in addition to critical wildlife habitat.
                                                                                                           4-33

-------
Identifying and Protecting Healthy Watersheds
        The final output of the Watershed Integrity Model is a weighted  overlay grid identifying areas most critical
        for maintaining watershed health (Figure 4-17)- Lands with a watershed integrity value of 5  are the most
        important areas for maintaining water quality, while lands with a value of 1 do not have  a significant impact
        on  maintaining water quality. The Watershed Integrity Model can be used alone or with other  models, such
        as the VCLNA Vulnerability Model to identify those lands most important for water quality and most at  risk
        from development pressures. The Virginia DCR identifies the following as potential  uses of the Watershed
        Integrity Model:

            •   Targeting — to identify areas important for maintaining or improving water quality.
            •   Prioritizing — to provide justification for key conservation land purchases and other
                protection activities.
            •   Local planning  — guidance  for comprehensive planning and  local ordinance and
                zoning development.
            •   Assessment — to  review proposed projects for potential impacts.
            •   Land management — to guide property owners and public and private  land managers
                in making land management decisions.
            •   Public education — to inform citizens about  the importance of land use and the effect
                on water quality and watershed integrity.

        A number of municipalities, counties, land trusts, and other organizations are beginning to  use the methods
        and results  from  the Watershed Integrity Model to identify and prioritize  conservation and preservation
        opportunities. For example, the Richmond Regional Planning District Commission and the Crater Planning
        District Commission  are using the results of the Watershed Integrity Model and other VCLNA models in their
        planning process.  Combined with an intensive public involvement process, these maps are being used by the
        Commissions to guide land use planning and conservation actions.
                                     DEPARTMENT OF CONSERVATION AND RECREATION
                                 Virginia Conservation Lands Needs Assessment
                                          Virginia Watershed Integrity Model
               Watershed Integrity Value
                Hh
                  J Giunty Huuiuhr y
               'llw.- \ViUtT\hvil tntt^n^ Model rqiri^enlN I In
               rvbrn-e importance/ i-^u*; of lanj .is it c< mcribuio
               tn \ratcr fjualih- or v.itersht'ij integrity. Valuci
               •ire UiM.-d on rookl mpu[ par-ami: ten r.uii^. from
           ECpMtnm a Ontr^an I KettJlian
           £rw.M,ra«M44t.(KB«riM.i!
-------
                                                                              : Healthy Watersheds Integrated Assessments
  Minnesota Watershed Assessment Tool
  Author or Lead Agency: Minnesota Department of Natural Resources
  More Information: http://www.dnr.state.mn.us/watershed tool/index.html

Minnesota's Watershed Assessment Tool (WAT) is an online mapping program with pre-loaded data layers
displaying information relevant to the health of the state's watersheds. Important concepts are explained in
detail throughout the web site, and connections among the components of watershed health are emphasized.
The program  is based  around five components that Minnesota considers essential to an understanding of
watershed health:

    1.   Hydrology
    2.   Connectivity
    3.   Geomorphology
    4.   Biology
    5.   Water quality

Resource  managers and other users can explore the myriad issues affecting natural resources at the watershed
scale by viewing these components and the connections between them. Table 4-6 lists the data layers available
for viewing with this tool. In addition to viewing the various data layers, the user has the option of downloading
most layers for use in a  GIS to perform original analyses at a variety of scales and for a variety of purposes.
Table 4-6 Data layers in Minnesota's Watershed Assessment Tool.
 Well index
               Hydrology Component
Lakes
                                       "ater Quality Component
Water quality stations
LakeTMDL
 USGS gages
                            Wetlands
                                                     Stream assessments
                                                    Potential contaminant sites
 Water use permits
Major river centerline
                                                     Lake assessments
                           Superfund sites
 Precipitation
                            Border watersheds
                                                     Stream TMDL
                                                    Waste water plants
 Minor watersheds
                            Streams
                 Biology Component
                                       Connectivity Component
 Mussel survey
Designated trout streams
Municipal boundaries
Public lands
 Biodiversity significance
Ecological Classification
System subsections
National Inventory of Dams
Bridges/culverts
 Native plant communities
                         FEMA floodway
                           Road/stream intersections
             Geomorphology Componen
                                             Base Layers
 Soils
Ground water recharge
                                                     Counties in Minnesota
                           Land use land cover 1990s
 % change in population
Karst features
Roads
2001 national land cover
 Depth to bedrock
                         2003 air photos
                           USGS topo map 250K
                                                     Shaded relief
                                                                                                            4-35

-------
Identifying and Protecting Healthy Watersheds
        The WAT has also been used to calculate watershed health assessment scores for Minnesota's major watersheds
        based on index values that compare the  relative health of the five components. The steps taken to create the
        watershed health index include:

            1.   Review scientific literature to inform the selection of significant and well-supported
                ecological relationships.
            2.   Review availability of statewide GIS data that support the selected relationship.
            3-   Discuss index development approaches with subject matter experts.
            4.   Compute results by applying an  appropriate GIS method.
            5.   Rank and score results.

        The indicators used to develop the statewide index are listed in Figure 4-18. Scores for each indicator must
        first be normalized to a 0-100 scale by  dividing threshold values  and/or the  maximum value in the range.
        The average of indicator scores for each  of the five components is then calculated to arrive at a component
        score. The five component scores are then averaged to arrive at a watershed  health score. Figure 4-19 displays
        the results for each of Minnesota's major watersheds and Figure 4-20  displays  the detailed component scores
        for two  example watersheds. By viewing and comparing the health scores for each of the components, an
        understanding of the relative condition of the assessment components can be used to direct resources to
        protection and restoration. Minnesota plans  to recalculate all index scores every  five years, incorporating
        enhanced methods and data as available.  This will allow for refinements in the watershed health assessment as
        well as tracking of trends in watershed health over time.

                                          HEALTH INDEX BY COMPONENT
                                                                        Terrestrial Habitat
                                                                          Connectivity
                               QW Contamination
                                 Susceptibility
                                 Stream Type /
                                  Valley Type
                                   (future)
                                  Index scores are combined into a component score:
            HYDROLOGY      GEOMORPHOLOGY
                                                                                         i;
CONNECTIVITY      WATER QUALITY
-J
                            Component scores are combined into a watershed health score:
                                           WATERSHED HEALTH SCORE
         Figure 4-18 Indicators used by the Watershed Assessment Tool for calculating watershed health scores
         (Minnesota Department of Natural Resources, 2011).
4-36

-------
                                                                                    : Healthy Watersheds Integrated Assessments
              fcl      .1  I
                                                                                                    II
                                                                                                     A
                                                                                                     N
                                                                                              Legond
                                                                                              Watershed Mean Score
                                                                                                  80-100
                                                                                                  60-80
                                                                                                  40-60
                                                                                                  20-40
                                                                                               M 0-20
                                                                                              Component Health Scores
                                                                                              _« 50
                                                                                              IB Hydrology
                                                                                              ^H Geomorphology
                                                                                              ••Biology
                                                                                              |H Connectivity
                                                                                              ,^B Water Quality
                                                                                                  Max. Possible (100)
                                                                                                ;.'.',!,;   Si
                                                                                                I\\l> A   ur«»i«»a*ti
                                                                                                    December 2011

Figure 4-19 Results of the statewide watershed health assessment conducted with the Watershed Assessment
Tool (Beth Knudsen, Minnesota Department of Natural Resources, Personal Communication).
                                                                                                                    4-37

-------
Identifying and Protecting Healthy Watersheds
                                                                  Rapid River
                                                        WATERSHED HEALTH ASSESSMENT SCORES
                                                           Mean {average) Health Score    Sd
                                                           Minimum Hearth Index Score    36
                                                          Minimum Health Index: &Gtogy - Al-Risk Species

                                                                 Watershed Assessment Tool
                             waeish^d Health Scores eorwpaf* and rank va/isus $spftd& ct e
                             acicis Mirme&obi index values ate based oo a v^t.ery ot data sources calculations
                             and scientific approaches Each index is scored on a state fromGlo 100. wrtftQbemg
                             the least des--3bl£ f*5Utt o*r rontfto" to 100 being the besi existing eondftan or mosl
                             desirable it-Suit  MiijOf w9ie**h*d SCal* rgnVingt may mas* the *3nge Of condition*
                             iftal occur at me*e focal tales A high *«xe may indicate the least imparted condition
                             m Minnesota rut neces&arity a healthy condition
COMPONENT SCORES
f b- A i* jj
HYDROLOGY
Mean (Ave.) 81
Minimum Index 50
INDEX SCORES
Pefenmal Cover 99
Impervious Cover 1 00*
Withdrawal 100*
Storage 50
Flow Variability 58

Metric Sub-Scores
Storage
StreanVDrtch Ratio 0
Surface storage 100













GEOMORPHOLOGY
Mean (Ave } 94
Minimum Index 88
INDEX SCORES
Sort Erosion 95
Susceptibility
&oundwater QQ
Susceptibility
Climate 10Q


















BIOLOGY
Mean (Ave.J 66
Minimum Index 36
INDEX SCORES
Terrestrial Habrtat
Quality
Stream Species 78
Specjes Rermess 67
At-Ri&k Species •«





CONNECTIVITY
Mean (Ave.) 98
Minimum Index 96
INDEX SCORES
Terrestrial Katxtat gs
Connectivity
Aquatic Connectivity 100



Metric Sub-Scores
Aquatic Connectivity
Bridges/Curverts 100
Darre 100
WATER QUALITY
Mean (Ave.) 82
Minimum Index 54
INDEX SCORES
Non-Point Source 93


Assessments 54


Metric Sub-Scores
Non-Potrrt Source
Nutrient Application 99
Riparian Impervious 36

                                                               Redwood River
                                                        WATERSHED HEALTH ASSESSMENT SCORES
                                                           Mean {average) Health Score    43
                                                           Minimum Hearth Index Score     .'.
                                                          Minimum Hearth Index: &C>!DQV - Kabtal
                                                                 Watershed Assessment Tool
                                       •
                             Wntei&hed Health Scores compar* and tank, vatous, asspscss, ot ecoio^tca.) health
                             aacss Minnesota irtdex values are based oc a variety ot data sources calculations
                             and science apPfoachcs Each index is scored on a scate fnsm 0 to 100. wrtti 0 be»ng
                             the least desoble result o« condbcn to 100 tomg the bcs! f^simg conctitcxn or most
                             desirable- Scores
Aquatic Carmectrvrty
Bridg&yCurverts 5
Dams B

WATER QUALITY
Mean (Ave ) 46
Minimum Index 23
INDEX SCORES
Non-Point Sourc* 25


Assessments 23

Meinc Sub-Scores
Non-Potrrt Source
NcSrient Application 3D
Riparian Impervious 20

                                                                                                                                        Nouemcer 2011
                          Figure 4-20  Minnesota's watershed  health assessment results for the  Rapid River (top) and
                          Redwood  River (bottom) watersheds.
4-38

-------
                                                                            : Healthy Watersheds Integrated Assessments
  Oregon Watershed Assessment Manual
  Author or Lead Agency: Oregon Watershed Enhancement Board
  More Information: http://www.oregon.gov/OWEB/docs/pubs/OR wsassess manuals. shtml#OR Watershed
    Assessment Manual
The Oregon Watershed Assessment Manual was created in 1999 to help the state's watershed councils and other
local groups  to conduct  holistic, screening-level  watershed assessments.  The assessment manual addresses
hydrology, geomorphology, biological condition, chemical and physical water quality, land use, and natural
disturbances. The assessment results in a watershed condition evaluation that prioritizes sites for protection or
restoration actions and provides direction for additional monitoring and assessment activities.

The assessment process contains  a number of steps, many of which can be completed concurrently (Figure
4-21). The initial project startup involves the identification of stakeholders, creation of an assessment team, and
gathering of data. Following the initial project startup, an evaluation of historical conditions in the watershed
is completed. This evaluation provides clues as to the condition of the watershed before European settlement,
the history of development and resource  use, and natural and human disturbances. A channel habitat type
(CHT)  classification is also completed at  this stage of the assessment. Drawing on several established stream
classification  systems, these CRTs were developed by Oregon to describe stream channels in  the context of
their expected biota and the surrounding land uses. This step of the assessment results in a channel habitat
map with different CRTs  identified based on their landscape position, channel slope, confinement, and size.

Following the historical condition evaluation and  CHT classification, watershed hydrology and water use are
evaluated. This component examines the precipitation type that causes peak flows in the watershed (rain, rain
on snow, or spring snowmelt), the types and quantities of different land uses, and water uses in  the watershed.
These analyses result in an assessment  of  flow alteration. The analysis provides guidance  on prioritization of
potential flow restoration  activities. Riparian conditions are also evaluated based  on the CHT  and ecoregion
maps to determine the expected vegetation of a riparian area, resulting in a map  of riparian condition units
and areas of large woody debris recruitment potential. A wetland characterization and  optional functional
assessment is also conducted to identify the locations of wetlands in the watershed and potential opportunities
for restoration based on field and aerial photo observations.
                                    Watershed
                                    Description
           ^  Start-Up and
           f Identification of
              Watershed issues
                                                         Watershed
                                                       Characterization
                                                    f	—v.
                                                  •*«   Hydrology and  1^.
                                                   V—    Wntor- I lea   ^"
       Watershed
       Assessment
                                                           Channel
                                                         Modification
                                                       Sg£&S£g
                                                        Water Quality _
                                                          Fish and
                                                 ^: teg.    Fish Habitat  gftr'
                                                     --ti-tir3!r%-%-^^>-5--

           Figure 4-21 The Watershed Assessment Manual methodology framework (Watershed
           Professionals Network, 1999).
    Watershed Condition |
 y      Evaluation

 ^^^S^l
.(
                                                                                                          4-39

-------
Identifying and Protecting Healthy Watersheds
        A sediment source assessment is conducted, in which eight potential sources of sediment are evaluated using
        maps of roads, peak flow, debris flow, landslides, forest road hazards, soils, stormwater, and fire locations. The
        purpose of this step is to identify areas of human-caused erosion with a priority for restoration or protection
        measures. A channel modification assessment is also completed, which identifies dams, artificial impoundments,
        stream bank protection (riprap), roads next to streams, sand or gravel mining near channels, etc. The affected
        CRTs are then identified and an evaluation of low, moderate, or high impact is assigned to the modified areas.
        A water quality assessment, using chemical and biological data available from relevant agencies,  is conducted
        to determine areas of impairment or at risk of impairment. Maps offish distribution and habitat condition are
        created using available data from relevant fish and wildlife agencies. These maps are also used to identify areas
        of impairment or at risk of impairment. A survey of stream crossings and migration barriers also contributes to
        the habitat condition maps.

        The final product of all of the individual assessment components is the watershed condition evaluation.  This is
        the stage where all of the information is compiled to create a channel habitat — fish use map that also identifies
        threats to water quality and aquatic life. A summary of historical  and current watershed conditions will also
        help in  the creation of a list and map of watershed protection and restoration opportunities.  One of three
        action opportunities is assigned to each item on the list and map:

            1.  Protect stream reaches that are in relatively good condition.
            2.  Restore  stream reaches with habitat or fish populations that  are  currently  in
                degraded condition but have the  potential to  support  high-quality habitat and fish
                populations.
            3.  Survey stream reaches where there are insufficient data to assess stream habitat quality
                or fish population status.

        A number of watershed councils and soil  and water conservation  districts throughout Oregon have used the
        Watershed Assessment Manual to conduct their own analyses. Sometimes these analyses enlist the assistance of
        technical specialists, but typically they are conducted by the local organization and its volunteers.
4-40

-------
                                                                           : Healthy Watersheds Integrated Assessments
  California Watershed Assessment Manual
  Author or Lead Agency: University of California, Davis
  More Information: http://cwam.ucdavis.edu/

The  California Watershed Assessment Manual (CWAM) was written for local watershed  groups, local  and
state agencies, and others to use in performing assessments of rural California watersheds between  10,000
— 1,000,000 acres in size. Building on ideas and techniques outlined in other manuals, including the Oregon
Watershed Assessment Manual, the CWAM was designed to meet the specific needs of California's extraordinary
hydrological, geological, and  biological diversity. The CWAM was  developed by an interdisciplinary team of
scientists from the University of California Davis and the Office of Environmental  Health Hazard Assessment
(within the California Environmental Protection Agency) with assistance from the California Department of
Forestry and Fire Protection.

The  CWAM contains two volumes,  with the first focusing on the overall process of watershed assessment,
reporting, and planning. The second volume focuses on specific assessment techniques and methodologies  that
can be used in an integrative watershed assessment. Key steps covered in the first volume include:

    •   Planning of the assessment (team building, defining purpose, etc.).
    •   Basic watershed concepts.
    •   Collection and organization of existing data.
    •   Data analysis and presentation.
    •   Information integration.
    •   Development of the assessment report.
    •   Decision making.

Beginning with the identification of environmental indicators and conceptual  modeling, the second volume
of the CWAM provides a framework and covers the technical aspects of conducting an integrative watershed
assessment. Without prescribing specific techniques, approaches for assessing water  quality, hydrology  and
geomorphology,  biotic condition, fire ecology (natural  disturbance), and cumulative effects are discussed. In
its discussion of environmental indicators, the manual discusses the importance of basing indicators  around
a framework such as the EPA SAB's Essential  Ecological Attributes. The indicators  chosen should  inform
environmental decision making.

Indicators for the different system components  can be aggregated into  an index  that represents the overall
condition of the watershed. This is accomplished by rescaling each indicator to  a unitless scoring system (e.g.,
1-100) and combining the scores to create an index of overall watershed condition. This process  requires some
knowledge of statistics and should include a validation phase to determine if the index is accurately conveying
the intended information.

The CWAM promotes the use of conceptual modeling in the watershed assessment and adaptive management
process. Conceptual models  can help in the process  of selecting  indicators, as shown in Figure 4-22. An
appendix on the construction and use of conceptual models is provided in the CWAM.

The CWAM is an example of a statewide effort to provide a framework and explanation of tools and methods
for conducting holistic watershed assessments to local watershed groups, local and state agencies, and others.
Rather than focus solely on chemical/physical water quality or aquatic biology, the manual outlines approaches
for all of the components of an integrated watershed assessment. The second volume of the CWAM remains
to be completed, although most of the  chapters are available for download from the  web site. As resources
become available, the remaining chapters will be completed.
                                                                                                        4-41

-------
Identifying and Protecting Healthy Watersheds
         Ecosystem Indicators
                   ,-	
                   Native bird diversity
Restoration Actions
                                                             Riparian Forest
                                                                Growth,
                                                           Regeneration, and
                                                              Habitat Value
                                                            Ecosystem
                                                              Function
         Figure 4-22 Example conceptual model for riparian forest indicator selection (Shilling, 2007).
4-42

-------
                                                                            : Healthy Watersheds Integrated Assessments
  Pennsylvania   Aquatic   Community   Classification   and   Watershed   Conservation
  Prioritization
  Author or Lead Agency: Pennsylvania Natural Heritage Program
  More Information: http://www.naturalheritage.state.pa.us/aquaticslntro.aspx

The Pennsylvania Aquatic Community Classification was conducted for the State of Pennsylvania to identify
stream community types and habitat types for freshwater mussels, macroinvertebrates, and fish. A condition
assessment was  then conducted to identify the least  disturbed  streams  and set watershed  conservation,
restoration, and enhancement priorities. Various conservation planning and watershed management projects
are already applying this classification system throughout Pennsylvania.

One of the  objectives identified in  Pennsylvania's Comprehensive Wildlife Conservation Strategy (Wildlife
Habitat Action  Plan)  is the development of a standardized  community/habitat classification  system (The
Pennsylvania Game  Commission  and Pennsylvania Fish and Boat Commission, 2005). In  addition, the
Pennsylvania Department of Conservation and Natural Resource's Biodiversity Workgroup Report and State
Forest Resource Management Plan also identify a standardized classification system as a priority. In response
to this need, the  Pennsylvania  Natural Heritage Program  created the Aquatic  Community Classification.
Classification of aquatic community types and the physical habitat upon which they depend is important for
assessing the condition of freshwater ecosystems. Through a common classification system, reference conditions
can be determined for similar community types. The degree of a disturbance can then be assessed through an
evaluation of disturbance indicators. In addition to Pennsylvania's Wildlife Habitat Action Plan, The Nature
Conservancy's Lower New England Ecoregional Plan was a key resource in the development of the  project, as
the classification procedure is very similar to TNC's macrohabitat  classification approach. The National Fish
Habitat Assessment also uses a similar approach, and Pennsylvania plans on incorporating their results into
such national and regional scale classifications.

The primary steps in the analysis are as follows:

    •   Develop a study approach.
    •   Mine and manage data.
    •   Create  biological classifications.
    •   Associate  environmental data with communities and develop a physical stream
        classification.
    •   Evaluate and refine biological classifications.
    •   Model  community habitats.
    •   Identify high quality streams and watersheds.
    •   Select poor quality watersheds for restoration prioritization.

Multivariate ordination and cluster analysis were used to classify biological communities. This  classification
was then refined through an expert review and indicator species  analysis. The classification resulted  in  13
mussel communities, 11 fish communities,  12  macro invertebrate communities at the genus level, and eight
macroinvertebrate communities at  the family level. Watershed, stream channel, and water chemistry data were
then used to describe  community habitats, and a model of physical stream types was  developed  to predict
community occurrence based on these channel and watershed attributes. Watershed and riparian land  cover,
mines and point sources, stream crossings, and dams were used to assess the condition of each  stream  reach.
Least disturbed streams were identified and prioritized for watershed conservation actions (Figure 4-23), and
the results are being used in a variety of conservation and watershed management projects in Pennsylvania.
                                                                                                         4-43

-------
Identifying and Protecting Healthy Watersheds
         The  results  of the  least  disturbed streams analysis were combined with fish, mussel, and  macroinvertebrate
         data to prioritize streams  based on  their ecological  integrity. Tier 1 streams  are of the highest quality (>90th
         percentile, or the best  10%)  and are the highest priority for conservation, Tier 2 streams are still high quality
         (80th—90th percentile) and  considered for conservation, and streams that do not contain high quality biological
         communities (<80th percentile)  are  considered a non-priority for conservation. The  analysis  was completed
         region-wide and for specific unique areas including large rivers, watersheds with calcareous geology, and specific
         physiographic provinces. Figure 4-24 shows the watershed conservation priorities in Pennsylvania.
                                                                                                             Pennsylvania

                                                                                                         Aquatic Community

                                                                                                             Classification

                                                                                                              Penim Kiinia's
                                                                                                           I i-iisl-DiMirlii-tl MIV.MII
                                                                                                              (LDS) Rt-iichfs

                                                                                                        I t.i-l-,li-unliol stream (U)S) reaches
                                                                                                        ueie dm.vi.-ii ID iilemir'y areas; for aiaser-
                                                                                                        vation protection. LDS reaches can
                                                                                                        also be used to select aquatic habitats
                                                                                                        that can senv V • i  Im < !  for restor-
                                                                                                        ation of degraded streams. HKSC high
                                                                                                        t|ii;ihtv stream s^niertts rcleaUy have
                                                                                                        , . I  'l H'l '. '.I. !|.. II !l> II I I lllllllcltCL'S
                                                                                                        .irtil AB&Mtt&9t9 n;illlral ccolocical
                                                                                                        [uncliulk

                                                                                                        Stream null  lor Ittc analysis are the
                                                                                                        stream scgincnk itelmetl by EPA Reach
                                                                                                        Ftics I ^ ers inn 3.0). Each stream reach
                                                                                                        uas assi^ncd iiilorniation about its
                                                                                                        position in Ihc watershed, local cnyif(>n~
                                                                                                        mental characteristics and landscape
                                                                                                        infomiation >ib(nil  the uaicrshed tli.n
                                                                                                        diain^ to theixaeh, tire\ streams arc

                                                                                                                             oknin
                                                                                                        l.uul use JilLl. These streams M ere
                                                                                                        ili :  '"i. oniittcil troni the LDS .m, I
                                                                                                           ".HP     LegenU

                                                                                                           i f.r.t DiNiiM i>.->] Stream
                                                                                                               Sizrl   -»»—SS»J



                                                                                                               Olhtr Hlvira & Slrrumi
                                                                                                           !  ^J rrnnsylvaniii Ai *'o«ntic»
                                                                                                           |    | Iliinlrrlnt! Stalw
          Figure 4-23 Map of Pennsylvania's least disturbed streams (Walsh, Deeds, & Nightingale, 2007).
4-44

-------
                                                                                                                : Healthy Watersheds Integrated Assessments
                                                                                                                          Pennsylvania
                                                                                                                     Aquatic Community
                                                                                                                          Classification
                                                                                                                    Priority Cotisen sitiim Areas
                                                                                                                            'il :in.J hhto(uf k"iil Jiiia were used
                                                                                                                  i. • -eKx t w.ikTsheds nnd m-cr readies tiia( MC
                                                                                                                  n!" grtulest consm'nltuu priority in the region
                                                                                                                  Although difci xv ere used fn>m the emtre stud\
                                                                                                                  area, this anaksis ccm«n,tralcs miia|>- on
                                                                                                                  pennsj- Iv aniiVs rjvt'FsajiJ
                                                                                                                  metric set-res M fie iists.1 1,-. Jelcrmnn: sedinns
                                                                                                                             wn tcrslicJs xviCh high quality
                                                                                                                   -• iili .ihii'li'iriciil J;iUi which rchlcJ jnlonniilhi
                                                                                                                   ,)Kiii Urulsciipe lI(im$jlUBtfXDttQB in c.K'h
                                                                                                                   ivalcrshcJ B\ L'xunnnjng Knh hioli-gic^l and
                                                                                                                   ithu'lojjittfil inii >mialii m. we were aWc l<-
                                                                                                                   Jctcrminc W!IK-!I watersheds he LI high, ijiulitv
                                                                                                                   h.»hi:its bigh levels oflnokigieal dimsA)  unJ
                                                                                                                   low levels iiMuuniin Jtsliaiiiincc See U-\l  |uf
                                                                                                                           i 'I iUt;i uscj iiinl GOtcutttKWI mclh-
                                                                                                                                 ' compaimon 
                                                                                                                               Legend
                                                                                                                             n Prinritj I
                                                                                                                           tiun Prinrity Rivi-r

                                                                                                                            fYrnch C'n-tfc

                                                                                                                            Lirge River Tier 1 Se

                                                                                                                                     'Non-lViurih,'
                                                                                                                      f-i Frenrli Cm-k \Yutcrthnl
                                                                                                                      2-^ (.x»'r I mull < m'k Miipl

                                                                                                                     |     | IVnmylviinia & Cnunlit*
                                                                                                                     czi«
Figure 4-24 Watershed  conservation priorities in Pennsylvania (Walsh, Deeds, & Nightingale,  2007).
                                                                                                                                                           4-45

-------
Identifying and Protecting Healthy Watersheds
          Connecticut Least Disturbed Watersheds
          Author or Lead Agency: Connecticut Department of Environmental Protection
          More Information: http://www.ct.gov/dep/lib/dep/water/water quality management/ic studies/least disturbed
            rpt.pdf
        Using GIS to evaluate watershed characteristics for the State of Connecticut, the Department of Environmental
        Protection identified the 30 watersheds considered least disturbed based on Stoddard's (2006)  definition of
        "best  available  physical,  chemical,  and biological habitat conditions  given  today's state of the landscape."
        This analysis  expands upon the Connecticut Impervious Cover (1C) Model that was developed for use in the
        TMDL program (Figure 4-25)- Macroinvertebrates and fish were sampled in the 30 least disturbed watersheds,
        as identified by the 1C model and other watershed stressors.

        The negative effects  of 1C on  aquatic biota  are numerous (Schueler,  1994) and include altered hydrology,
        increased erosion, and degraded water quality, all of which impact the biological communities present in these
        urban watersheds. Connecticut has modeled the aggregate effects of 1C on  macroinvertebrate communities
        in the state and uses this 1C Model in its TMDL program. The  low end of the 1C gradient in this  model
        (<4%) was used to identify small watersheds with streams that fall into the "best"  stream class. Locations of
        dams, diversions, and salmonid fry stocking were used  to further refine the selection of these least  disturbed
        watersheds. Table 4-7 describes these parameters and the thresholds used.

        Table 4-7 Parameters and criteria used to identify least disturbed watersheds in Connecticut
                     Parameter
         Impervious cover
         Natural land cover
         Developed land
         Diversions
         Reservoirs/large Class C dams
         Sample site distance below a dam
         Streams stocked with salmonid fry
         Watershed size
         Criterion
          > 80%
          < 10%
           None
           None
> 0.5 mile downstream from dam
     No known stocking
       > 1 square mile
        Macroinvertebrates and fish were then sampled at the identified least disturbed sites to determine the health of
        the biological community. An IBI approach, borrowed from Vermont, was used to evaluate the fish community
        at all sites. A macroinvertebrate multimetric index (MMI) score was also calculated for each site based on the
        following seven metrics:
            •   Ephemeroptera taxa.
            •   Plecoptera taxa.
            •   Percent Sensitive EPT.
            •   Trichoptera taxa.
 Scraper Taxa.
 BCG Taxa Biotic Index.
 Percent Dominant Genus.
        Temperature, water chemistry, and nutrient samples were also collected at each site. Results from the biological
        and water quality sampling confirmed minimally impacted  conditions in all but one of the 30 watersheds
        identified through the GIS-based screening process. This suggests that the 1C Model is able to predict  the
        locations of the "best" stream classes that should be prioritized for "preservation" strategies. Figure 4-26 shows
        the results of the statewide assessment of least disturbed watersheds.
        Applications of the Connecticut Least Disturbed watersheds assessment include refinement of Tiered Aquatic
        Life Uses (TALUs) based on a new  BCG  for  fish species,  identification of BCG Level 1  sites, providing
        information to local land use planners on locations of sensitive areas, development of nutrient criteria, and
        development of minimum stream flow regulations.
4-46

-------
                                                                      : Healthy Watersheds Integrated Assessments
                  Poor
                       Low
                                         Stream Classes
                                        Medium
High
                 Excellent
                                    Management Strategies
                  Poor
                       Low
                                        Medium

                                    Watershed Percent Impervious Cover
High
      Figure 4-25 Conceptual model of the effect of impervious cover on stream quality.
      Watershed percent impervious cover is used to identify stream classes (top) and
      potential management strategies (bottom) (Bellucci, Beauchene, & Becker, 2009).
                                                     l.cgcnd

                                                     H Best-Preservation

                                                     IB Streams of Hope-Active Management

                                                        | Urban-Mitigation
Figure 4-26 Map of Connecticut showing stream classes and management classes by watershed
(Bellucci, Beauchene, & Becker, 2009).
                                                                                                   4-47

-------
Identifying and Protecting Healthy Watersheds
          Kansas Least Disturbed Watersheds Approach
          Author or Lead Agency: Kansas Department of Health and Environment
          More Information: http://www.kdheks.gov/befs/download/bibliography/Kansas reference stream report.pdf

        The streams selected to represent reference condition, the highest attainable quality in a given environment,
        are an important factor in stream water quality assessments. Reference streams are used to characterize baseline
        conditions, establish surface water quality criteria, identify impaired streams, interpret the findings of statewide
        water quality assessments, and set restoration goals. Because stream ecosystems are dynamic and the interactions
        between their biological, chemical, and physical components are poorly understood, reference streams provide
        the  context needed for determining when stream ecosystem conditions  are healthy or unhealthy. The types
        of streams chosen  to  represent reference  conditions are often  found in healthy watersheds. Recognizing
        the  influence that the  reference stream selection process has on its  state water quality program, the Kansas
        Department of Health and Environment (KDHE) has begun to assess how a set of reference streams can be
        best selected and protected.

        KDHE began this assessment by compiling a database of geospatial watershed data. NHDPlus data were used to
        delineate stream reaches, allocated and accumulated watersheds, and 90-meter riparian corridors. An allocated
        watershed in the NHDPlus is the immediate drainage area to a single stream reach whereas an accumulated
        watershed is the entire upstream drainage area for that stream reach. Watershed attributes, such as land cover
        composition, can be tracked as allocated or accumulated  values. Annual average flow was also estimated for
        each reach using the unit runoff method in NHDPlus.  In order to ensure that the set of candidate reference
        streams identified was  representative of the variety of environments found in Kansas, all streams were  first
        sorted into ecoregions.  Principal components analysis (PCA) and non-hierarchical clustering analysis were used
        to group watersheds by ecoregion (Figure 4-27). Scores for the first three principal components, pertaining
        largely to elevation and climate, topographical relief, and soil water retention capacity, were converted  to  a
        color intensity scale, and average values were calculated and mapped for each ecoregion.

        Once environmental variability had  been  analyzed,  KDHE incorporated variability in human disturbance
        levels into the  assessment. Arithmetic means were calculated and normalized to a zero to one scale for twenty
        variable measures of landscape alteration for all watersheds (Table 4-8). A PCA was performed on the watershed
        disturbance data,  and principal components accounting for most of the  variability in the data were retained
        for further analysis. Component scores were converted to absolute values and used as weighting coefficients for
        their respective disturbance indicators. The weighted sum  of all indicators was calculated for each component
        and the  average of these weighted  sums was  used  as  an integrated  disturbance  index to sort watersheds
        into seven equally-sized groups (septiles) of watersheds.  Groups were mapped in  colors corresponding to
        their integrated disturbance index scores, in a  spectrum ranging from green  (low disturbance) to red (high
        disturbance). A summation of the normalized means  of landscape alteration variables for each watershed was
        used to check the watersheds' integrated disturbance classifications.
4-48

-------
                                                                            : Healthy Watersheds Integrated Assessments
        r.-fi-
         .     •  ..
                                                                      « •:
                                                                           ;£
                                                               \ 4
                        ER1

                                                                                   >
                        ER3
                                                                       ER4
                        ER5
Statewide
  Figure 4-27 Location of least disturbed watersheds within individual quantitative ecoregions (ER) (k = 5)
  (Angelo, Knight, Olson, & Stiles, 2010). Rankings are based on the disturbance index derived via principal
  components analysis. Highlighted watersheds rank in the lowest (best) 10th percentile within their
  respective ecoregions. The statewide (10th percentile) map is shown for comparison.
Table 4-8 Landscape alteration variables used in KDHE's reference stream assessment (Angelo et al., 2010).
Density of:
Active and inactive Superfund sites
Active and inactive permitted landfills
Active and inactive permitted mines and quarries
Confined livestock (animal units)
Grazing cattle
Human residents
Permitted ground water diversions
Permitted surface water diversions
Registered active and inactive oil and natural gas wells
Registered and unregistered dams
Stream/industrial pipeline intersections
Stream/railroad intersections
Stream/road intersections
Ratio of:
Cropland area to total land area
Cropland area to total land area within 90-meter riparian corridor
Inundated land area to total land area
Urban area to total land area
Urban area to total land area within 90-meter riparian corridor


Combined annual application rate for all pesticides
Total permitted wastewater output divided by catchment area




                                                                                                          4-49

-------
Identifying and Protecting Healthy Watersheds
        KDHE also  evaluated the association  between  human disturbance  level and  an important indicator  of
        watershed health: stream taxonomic richness. Richness data were drawn from state-sponsored biological surveys
        of native fish species,  freshwater mussel species, and aquatic insects of the EPT orders conducted between
        1990 and 2007- Taxonomic richness data were then merged with  the  integrated disturbance  index dataset.
        Separate models were developed for each ecoregion and for the  state overall, incorporating  all five ecoregions.
        The ability to accurately predict responses to new observations,  as measured by the predicted R2 statistic, was
        used to select the final  models.

        Governmental planning documents, statistical abstracts, permit applications,  unpublished databases, and
        various reports were reviewed to evaluate potential future  threats to candidate  reference streams  in Kansas.
        Data pertaining to the following potential sources of degradation were extracted from these resources: urban
        and residential sprawl; transportation and utility infrastructure development; mineral resource development;
        development of new dams and reservoirs; growing anthropogenic water demand; conversion of grassland to
        other uses; industrialization of livestock  production;  and  introduction and spread of non-native species. This
        literature review was used to identify the most serious threats to stream integrity and the regions of the state
        most vulnerable to those threats.

        KDHE intends to sort  watersheds in the  tenth  percentile by ecoregion and  stream flow and assess  them
        with computer-assisted  desktop  reconnaissance.  Final  reference stream  selections will be based on four
        primary factors: watershed disturbance score, field assessment results, site accessibility (i.e., permission from
        the landowner), and perceived future disturbance risk. The physical habitat, water chemistry, and biological
        communities of the selected reference streams will be monitored every four to eight years. As a database of
        reference stream conditions is developed over time, it can be used to inform regulatory,  incentive-based, and
        interagency efforts to protect reference streams and their watersheds from degradation.
4-50

-------
Case   Study
 National Fish Habitat  Assessment
 More Information: Esselman et al., 2011
 Similar to the way in which KDHE used NHDPlus
 and an integrated index of human  disturbance to
 analyze watershed condition, scientists working on the
 National Fish Habitat Assessment (NFHA) have also
 assessed landscape disturbance for stream catchments
 using NHDPlus (Figure 4-28). The NFHA cumulative
 disturbance index uses five environmental variables
 and 15 human  disturbance  variables quantified at
 local and network catchment levels to assess landscape
 disturbance.  The  local   and network  catchments
 are  comparable  to  the  allocated and  accumulated
 watersheds that KDHE used in their analysis. Means
 for  elevation, slope,  and  soil permeability  were
 calculated for each network catchment. Mean annual
 precipitation and  air  temperature were calculated
 for  each  local  catchment.  Human   disturbance
 variables were calculated  for both catchment types.
 Catchment  means  were  calculated  for  water use
 estimates and cattle density. Catchment percentages
 were generated for each land use type: low, medium,
 and high intensity  development; impervious cover;
 pasture; and cultivated crops.  Catchment densities
 were calculated for point  data (road crossings, dams,
 mines,  superfund sites, toxic release inventory sites,
 and national pollutant discharge elimination system
sites), and road densities were represented as total
road length per square kilometer of catchment area.

Using principal components analysis,  the human
disturbance variables were  combined  into  a  few
composite disturbance axes  that describe  most of
the variation in these variables at the stream reach
level. Individual disturbance axes were then weighted
according  to  their  influence on freshwater  fishes
using canonical correlation analysis and summed into
indices of local and network catchment disturbance.
Local  and  network   disturbance   indices   were
weighted using canonical  correspondence analysis
to reflect the different impacts disturbances have on
communities in streams  of different sizes. They were
then combined to  determine a cumulative landscape
disturbance index  score  for each stream reach.  The
cumulative disturbance index was scaled from zero to
100 with high  scores indicating greater disturbance.
A national fish community dataset was  used to
calibrate the landscape disturbance index. The NFHA
team identified vulnerability to future threats as an
information gap in their landscape disturbance  index,
a factor that KDHE found a way to address in concert
with its integrated human disturbance index.
                     | 5 Best Condition
                     | 36001-49999
                      2 3334 - 3 6000
                      1.00Q1 -23333
                     | 1 Powest Condition
                      Unscored Reach
               Figure 4-28 Reach cumulative landscape disturbance scores summarized by
               local catchments for the United States. Scores are presented in five percentile
               categories, each containing 20% of the reaches (Esselman et al., 2011).
                                                                                                 4-51

-------
Identifying and Protecting Healthy Watersheds
          Recovery Potential Screening
          Author or Lead Agency: U.S. Environmental Protection Agency, Office of Water
          More Information: www.epa.gov/recoverypotential/ and http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/
            upload/recovery empub-2.pdf

        The Recovery Potential Screening method provides a systematic approach for comparing waters or watersheds
        and identifying differences in how well they may respond to restoration. Recovery potential is defined as the
        likelihood of an impaired water to attain water quality standards or other valued attributes given its ecological
        capacity to regain function,  its exposure to  stressors, and the social context affecting efforts to improve its
        condition.

        Although originally  developed as a  tool to help states set restoration  priorities among the impaired waters
        on their CWA Section 303(d) lists,  this method can also be used to assess healthy waters or watersheds for
        protection  (Norton, Wickham, Wade, Kunert, Thomas, & Zeph,  2009; Wickham & Norton, 2008). The
        screening process is based on  ecological, stressor, or social indicators measured from a wide variety of landscape
        datasets, impaired waters attributes reported by states to EPA, and monitoring data sources. The  user's control
        over assessment purpose and  selection  of relevant indicators and weights makes this flexible method adaptable
        to numerous uses and differences in  locality.  The method  prioritizes watersheds for restoration through  a
        transparent and consistent comparison process.

        Examples of the  130 indicators developed for use in the recovery potential screening are provided  in Table
        4-9. Five to eight metrics in each of three different classes are chosen for an individual assessment. Ecological
        capacity,  stressor  exposure, and social  context  represent  three gradients, or axes, along which watersheds are
        rated  using the selected indicators. The user's  objective  is to choose indicators that  collectively estimate the
        influence of each of the three classes on a watershed's overall recovery potential. Within each class, raw scores
        for each selected indicator are normalized to a maximum score of one, weighted if desired,  then compiled into
        a summary score normalized to 100 across all the scored watersheds.  Higher ecological and  social  scores signify
        better recovery potential, and higher stressor scores imply lower recovery potential.

        Scoring the three classes of metrics ensures that ecological condition,  stressor scenarios, and the influence of
        social factors are all addressed, and they can be considered together  or separately.  It is particularly valuable to
        distinguish the influence of social variables from the influence of watershed condition, as social variables are
        often the dominant variable determining restoration success. Although it is useful to distinguish the ecological,
        stressor, and social summary scores of each watershed, it is also desirable  to have the scores in an integrated
        form. This is accomplished in two ways. If a single score per  watershed is desired  (e.g., for rank ordering,
        or developing a mapped representation of watersheds color-coded by relative recovery potential scores), the
        formula is as follows:

                                  (Ecological summary score + Social summary score)
                                                Stressor summary score

        A second method for integrating the three summary scores uses three-dimensional "bubble-plotting" (Figure
        4-29). In this approach,  the X and Y axes  represent the stressor and  ecological summary scores,  and this
        determines the position of each watershed bubble on the graph. The social summary score determines the size
        of the bubble (the larger the better). While more a visualization than quantitative method, this display method
        is effective at producing 'at a glance' understanding of the basic differences among a population of watersheds
        considering all three classes. As a starting point, the watersheds that fall in the upper left quadrant of the bubble
        plot have higher ecological summary scores  and lower stressor summary scores, and are initially assumed  to
        have high recovery potential. The user, however, may choose to elevate the importance of ecological score  in
        both  upper quadrants to  select priorities, or may consider social score as the primary factor.  This  flexibility
        allows expert judgment to play a more interactive role. For example, a watershed with moderate ecological and
        stressor scores but an exceptionally strong social score could be prioritized along with watersheds that meet the
        initial high-ecological and low-stressor scoring criterion.
4-52

-------
                                                                             : Healthy Watersheds Integrated Assessments
Table 4-9 Example Recovery Potential Indicators. The user selects five to eight minimally correlated metrics from
each class that are most relevant to the place and purpose of the screening, selects the measurement technique
for each metric given available data, and weights the indicators if desired before calculating ecological, stressor,
and  social summary  scores. Yellow-highlighted metrics are potentially appropriate for  healthy  watersheds
protection and priority-setting as well as restoration planning.
Ecological Capacity Metrics Stressor Exposure Metrics Social Context Metrics
Natural channel form
Recolonization access
Strahler stream order
Rare taxa presence
Historical species occurrence
Species range factor
Elevation
Corridor % forest
Corridor % woody vegetation
Corridor slope
Bank stability/soils
Bank stability/woody vegetation
Watershed shape
Watershed size
Watershed % forest
Proximity to green infrastructure hub
Contiguity w/green infrastructure corridor
Biotic community integrity
Soil resilience properties
Invasive species risk
Channelization
Hydrologic alteration
Aquatic barriers
Corridor road crossings
Corridor road density
Corridor % u-index
Corridor % agriculture
Corridor % urban
Corridor % impervious surface
Watershed % u-index
Watershed road density
Watershed % agriculture
Watershed % tile-drained cropland
Watershed % urban
Watershed % impervious surface
Severity of 303(d) listed causes
Severity of loading
Land use change trajectory
Watershed % protected land
Applicable regulation
Funding eligibility
303(d) schedule priority
Estimated restoration cost
Certainty of causal linkages
Plan existence
University proximity
Certainty of restoration practices
Watershed organizational leadership
Watershed collaboration
Large watershed management potential
Government agency involvement
Local socio-economic stress
Landownership complexity
Jurisdictional complexity
Valued ecological attribute
Human health and safety
Recreational resource
                U)
                £
                o
                u
                w
                I
                w
                o
                S
                ^o
                c
                (B
                U
                'ro
                _o
                o
                u
                UJ
                                     Stressor Indicator Summary Scores

 Figure 4-29 Three-dimensional bubble plot comparing recovery potential  among subwatersheds. Dots
 represent subwatersheds plotted by summary score relative to the ecological and stressor axes. Social context
 scores (higher = better) are incorporated as dot size and color. Median values for ecological and stressor
 scores statewide (dashed lines) are added to enable a coarse sorting by quadrant that initially targets high
 ecological/low stressor subwatersheds (upper left, shaded), with selected subwatersheds (arrows) added where
 special information warrants. This example screening flagged 11 of 30 subwatersheds as more restorable
 (Norton et al., 2009). Reprinted with  permission of Springer Science and  Business Media B.V.
                                                                                                          4-53

-------
Identifying and Protecting Healthy Watersheds
        The recovery potential  screening data formats contain  flexibility for  further  analyses.  Indicator scores  are
        managed in spreadsheets and, once completed, alternate combinations or weights of indicators can be selected
        and plotted to verify consistency of high-scoring watersheds under alternate scoring approaches.  Large (e.g.,
        statewide) datasets can often be re-assessed in a matter of hours. The "R" script used for bubble plotting (Figure
        4-30) also allows for varying color assignment based on any attribute in  the spreadsheet.

        Recovery potential  screening in Maryland  demonstrates how a restoration-oriented screening can easily be
        adapted for protection screening purposes. The goal was to identify which impaired watersheds are the strongest
        prospects for successful  restoration, but all of the state's healthy watersheds were also screened with the same
        indicators (Table  4-10).  Despite  the  main focus  on impaired watersheds, the screening secondarily revealed
        many patterns about the healthy watersheds that may also  be  relevant to their  management. For example,
        the watersheds that passed bioassessment but still show elevated stressor scores may be at risk.  Further, wide
        differences in social  score imply that some of the healthy watersheds have far better social context for continued
        protection than others. In addition, several  of the  impaired watersheds that  scored as well  as the  healthy
        watersheds (see upper left quadrant,  Figure 4-30) may be  strong prospects  for protection in time. Assessing
        watersheds specifically for protection purposes is feasible given the many protection-relevant metrics  that can
        be considered (Table 4-10) or developed.
        Table 4-10 Recovery potential indicators used to screen Maryland watersheds.
             Ecological Metrics (5)
        Stressor Metrics (5)
                                               Social Metrics (5)
         Biotic condition: benthic IBI score     Proportion of degraded sites per watershed   Protected landownership % by watershed

         Biotic condition: fish IBI score        Corridor % impervious cover per watershed   *°P°r!io" °f feam mileS With StreSS°r
         Recolonization: density of
         confluences
         Bank stability: MBSS buffer
         vegetation
                                     Attributed Risk

Watershed % cropland and pasture         Complexity: watershed # of local jurisdictions

                                     Tier 2 waters % per watershed
Housing counts per corridor length in
watershed
         Natural channel form and condition   Watershed 2006* of impairment causes     Watershed % targeted by DNRfor protection
                               £•    O  _
                               E
                               E
                               £2
                               3
                               &
                               -
                               T3
                                    10  ~
o
o ^^
Qp ^ Q. .
o
o o
0
0
O c

STATEWIDE
O
00° °

O ®
o ef op
o° OP

0
I i 1 i i
10 20 30 40 50
Pass
Fan

0
O

i
60
                                               Stressor Indicators Summary Score
                                  Circle size increases with Social Context summary score value

         Figure 4-30 Bubble plot of recovery potential screening of 94 non-tidal watersheds in Maryland. Colors
         signify whether watersheds passed the state's watershed bio-assessment. Although indicators were selected to
         compare recovery potential of impaired waters, the output also contrasts healthy watershed differences (e.g.,
         social context and stressor levels) that have implications for protection priority-setting.
4-54

-------
                                                                                    : Healthy Watersheds Integrated Assessments
         Classification Systems and Indicators Used in Integrated Assessments
              Indicator
 Hydrologic Unit Code                    •1 mi2

  >2,000 mi2

 Biological Communities

  Mussels

  Fish

  Macroinvertebrates

 Ecological Classification System
 Subsections

  Climate

  Geology

  Topography

  Soils

  Hydrology

  Vegetation

VA WIM: Virginia Watershed Integrity Model
MN WAT: Minnesota's Watershed Assessment Tool
OR WAM: Oregon Watershed Assessment Manual
CA WAM: California Watershed Assessment Manual
PA ACC: Pennsylvania Aquatic Community Classification
CT LDW: Connecticut Least Disturbed Watersheds
KS LDW: Kansas Least Disturbed Watersheds
EPA RPST: EPA Recovery Potential Screening Tool
 MN      OR      CA
WAT    WAM    WAM
 CT      KS      EPA
LOW    LOW    RPST
                              r                          r
                                                 V
                                       v'

                                       v'
                                                                                                                    4-55

-------
Identifying and Protecting Healthy Watersheds
                            Landscape Indicators Used in Integrated Assessments
                          ..                        VA       MN       OR      CA      PA      CT       KS      EPA
                       indicator                  WIM     WAT    WAM    WAM    ACC    LDW    LDW    RpST
         Index of Terrestrial Integrity
           % Watershed Natural Land Cover
           >80% Natural Land Cover
           % River Corridor Natural
           Land  Cover
           Proportion of habitat fragmentation due
           to roads
           % Impervious Cover
           <4% Impervious Cover
         Catchment % Forested (>75%)
         Watershed % Developed Land
           <10% Developed
         Catchment % Urbanization (<1.5%)
         Ratio of urban land area to total land
         area
         Watershed % Urban
         Watershed % Forestry
         Watershed % Agriculture/Rangeland
         Density of Confined Livestock
         Density of Grazing Cattle
         Ratio of Cropland to Total Land Area
         Annual Pesticide Application Rate
         Catchment Non Row Crop Agriculture
         Catchment Row Crop Agriculture <3.5%
         Corridor % Impervious Surface
         Corridor % Urban
        VA WIM: Virginia Watershed Integrity Model
        MN WAT: Minnesota's Watershed Assessment Tool
        OR WAM: Oregon Watershed Assessment Manual
        CA WAM: California Watershed Assessment Manual
        PA ACC: Pennsylvania Aquatic Community Classification
        CT LDW: Connecticut Least Disturbed Watersheds
        KS LDW: Kansas Least Disturbed Watersheds
        EPA RPST: EPA Recovery Potential Screening Tool
4-56

-------
                                                                                     : Healthy Watersheds Integrated Assessments
               Landscape Indicators Used in Integrated Assessments (cont.)
               Indicator
 VA      MN      OR       CA       PA      CT      KS      EPA
WIM     WAT     WAM    WAM    ACC     LDW    LDW   RPST
 Stream Crossings
   < 11,500 for watersheds larger than
   2,000 mi2
 # Road Stream Crossings (all streams
 and first order streams)
 Density of Stream/ Pipeline Intersections
 Density of Stream/ Railroad Intersections
 Corridor Road Density
 Corridor % Agriculture
 Corridor % Woody Vegetation
 Location of FEMA Floodplain
 Locations of Headwaters                    •/
   Steep Slopes                              •/
 Green Infrastructure (GI)                    V
   Watershed % Forested
   Locations of Ecological Cores                V
   Contiguity with GI Corridors
   Proximity to GI Hub
   Locations of Riparian Areas                  •/
 Locations of Source Water Protection         >
 Zones
 Remaining High Quality Native Plant
 Communities
 Wetland Locations
 Wetland Attributes (size, connectivity,
 buffer, watershed position)
 Locations of Fires
 Fire Regime Condition Class
VA WIM: Virginia Watershed Integrity Model
MN WAT: Minnesota's Watershed Assessment Tool
OR WAM: Oregon Watershed Assessment Manual
CA WAM: California Watershed Assessment Manual
PA ACC: Pennsylvania Aquatic Community Classification
CT LDW: Connecticut Least Disturbed Watersheds
KS LDW: Kansas Least Disturbed Watersheds
EPA RPST: EPA Recovery Potential Screening Tool
                                                          V       *
                                                                                                                      4-57

-------
Identifying and Protecting Healthy Watersheds
                               Habitat Indicators Used in Integrated Assessments
                         Indicator
 VA      MN      OR      CA      PA      CT      KS      EPA
WIM    WAT    WAM   WAM    ACC    LOW    LOW    RPST
          Designated Trout Streams
          Karst Features
           Springs
           Stream Sink
           Sinkhole
          Species Range Factor
          Domestic Predators
          Habitat Diversity
          RTE Species Habitat
          Stream Crossing Density
          Recolonization Access
          Migration Barriers
           Culverts Passable
           Water Velocity <2 fps
           Outlet perching <6 in.
           Flow Depth >12 in.
           Outlet Drop less than 6 in.
           Slope <0.5%
           Diameter >0.5 X bankful channel width
           Length < 100 feet
           Substrate Complexity and Embeddedness
          Riffles with >35% Gravel
          Riffles with <8% Silt, Sand, Organics
          Ratio of Fine Sediment Volume In Pools To
          Total Pool Volume
          Large Woody Debris Recruitment Potential
           >20 Pieces of Large Woody Debris per 100
           Meters
           Expected Riparian Vegetation by Ecoregion
          Stream Shading by Riparian Vegetation
          Shade > 70% of reach
          Pool Area > 35% of stream area
          Pool Frequency (every 5-8 channel widths)
          >300 Conifers within 30 M of Stream per
          1,000 ft
          Corridor % Woody Vegetation
         VA WIM: Virginia Watershed Integrity Model
         MN WAT: Minnesota's Watershed Assessment Tool
         OR WAM: Oregon Watershed Assessment Manual
         CA WAM: California Watershed Assessment Manual
         PA ACC: Pennsylvania Aquatic Community Classification
         CT LDW: Connecticut Least Disturbed Watersheds
         KS LDW: Kansas Least Disturbed Watersheds
         EPA RPST: EPA Recovery Potential Screening Tool
4-58

-------
                                                                                   : Healthy Watersheds Integrated Assessments
                   Hydrologic Indicators Used in Integrated Assessments
               Indicator
 VA      MN      OR      CA       PA
WIM    WAT    WAM    WAM     ACC
 CT      KS      EPA
LOW    LOW    RPST
 Average Annual Precipitation
 Precipitation Type that Causes Peak
 Flows
  Rain
  Rain on Snow
  Spring Snowmelt
 Discharge
 Peak Flow
 Dams and Impoundments
  No Reservoirs
  <160 for watersheds >2,000 mi2
  No large Class C Dams
 < 11,500 Road Crossings for Watersheds
 >2,000 mi2
 Water Use Permits (> 10,000 GPD)
 Consumptive Use
 No Diversions
 Number of Permitted Water Diversions
 Permitted Wastewater Relative to
 Catchment Size
 Dry Season Artificial Discharges
 Average Annual Ground Water Recharge
 Well Index
 Floodplain Connection
 Hydrologic Alteration
VA WIM: Virginia Watershed Integrity Model
MN WAT: Minnesota's Watershed Assessment Tool
OR WAM: Oregon Watershed Assessment Manual
CA WAM: California Watershed Assessment Manual
PA ACC: Pennsylvania Aquatic Community Classification
CT LDW: Connecticut Least Disturbed Watersheds
KS LDW: Kansas Least Disturbed Watersheds
EPA RPST: EPA Recovery Potential Screening Tool
                                                                                                                   4-59

-------
Identifying and Protecting Healthy Watersheds
                         Geomorphology Indicators Used in Integrated Assessments
          Roads Next to Streams                                        V
          Locations of Stream Bank Protection                            *
          (riprap)
          Channelization                                                                                              •/"
          Bank Erosion                                                          i^
          Bank Stability/Soils                                                                                         -/
          Bank Stability/Woody Vegetation                                                                             •/
          Soil Resilience Properties                                                                                    V
          Locations of Debris Flows                                     J
          Locations of Landslides                                       •/*
          Sand or Gravel Mining Locations                               -f
          Sinuosity                                                             •2%)                                                                    •/
          Watershed Size                                                                  •/
           Headwaters (0-2 mi2)                                                            •/
           Small (3-10 mi2)                                                                 -/
           Mid-Reach (11-100 mi2)                                                          V
           Large (> 100 mi2)                                                                •/
         VA WIM: Virginia Watershed Integrity Model
         MN WAT: Minnesota's Watershed Assessment Tool
         OR WAM: Oregon Watershed Assessment Manual
         CA WAM: California Watershed Assessment Manual
         PA ACC: Pennsylvania Aquatic Community Classification
         CT LDW: Connecticut Least Disturbed Watersheds
         KS LDW: Kansas Least Disturbed Watersheds
         EPA RPST: EPA Recovery Potential Screening Tool
4-60

-------
                                                                                    : Healthy Watersheds Integrated Assessments
                 Water Quality Indicators Used in Integrated Assessments
                 Indicator
 VA     MN      OR      CA      PA      CT      KS      EPA
WIM    WAT    WAM   WAM    ACC    LOW    LOW   RPST
 Locations of Unimpaired Streams
 Potential Contaminant Sites (e.g., Superfund,
 landfills, mines, oil or gas wells, etc.)
 Point Sources
   <200 for watersheds >2,000 mi2
 Dissolved Organic Carbon
   Dissolved Organic Carbon Export Downstream
 Bromide Reactive Compounds
 Temperature
   Daily Maximum of64°F
 Dissolved Oxygen
   8.0 mg/l
   >7.0 mg/l for coldwater streams
   >3.5 mg/l for warm water streams
 Nitrogen
 Nitrate
   0.30 mg/l
 Total Phosphorus
   0.05 mg/l
 Suspended Solids
 Turbidity
   50 ntu  maximum above background
 Conductivity
   Between 150 and 500 ^mhos/cm
 pH
   6.5 to 8.5 units
 Chloride
 Hardness
 Alkalinity
VA WIM: Virginia Watershed Integrity Model
MN WAT: Minnesota's Watershed Assessment Tool
OR WAM: Oregon Watershed Assessment Manual
CA WAM: California Watershed Assessment Manual
PA ACC: Pennsylvania Aquatic Community Classification
CT LDW:  Connecticut Least Disturbed Watersheds
KS LDW: Kansas Least Disturbed Watersheds
EPA RPST: EPA Recovery Potential Screening Tool
                            s
                            s
                            V
                            V
                                                                                                                    4-61

-------
Identifying and Protecting Healthy Watersheds
                              Biological Indicators Used in Integrated Assessments
                               ..                            VA      MN      OR      CA     PA    CT      KS     EPA
                            indicator                     WIM    WAT   WAM   WAM   ACC   LDW   LDW    RpST
          Observed/Expected
          Modified Index of Biotic Integrity
           Number of Intolerant Species
           Species Richness
           Number of RTE Species
           Number of Non-Indigenous Species
           Number of Critical/Significant Species
           Number of Tolerant Species
          Mussel Catch per Unit Effort
          Areas of Biodiversity Significance
          Rare Taxa Presence
          Biotic Community Integrity
          Fish State or Federally Listed as Endangered
          Fish Stocking History
           Streams Stocked with Salmonid Fry (No Known
           Stocking)
          Fish Species Distribution
           Salmonid Species Distribution, Abundance, and
           Population Status
           Brook Trout Density
           Fluvial  Specialists
           Fluvial  Dependants
           Macrohabitat Generalists
         VA WIM: Virginia Watershed Integrity Model
         MN WAT: Minnesota's Watershed Assessment Tool
         OR WAM: Oregon Watershed Assessment Manual
         CA WAM: California Watershed Assessment Manual
         PA ACC: Pennsylvania Aquatic Community Classification
         CT LDW:  Connecticut Least Disturbed Watersheds
         KS LDW: Kansas Least Disturbed Watersheds
         EPA RPST: EPA Recovery Potential Screening Tool
4-62

-------
                                                                                    : Healthy Watersheds Integrated Assessments
               Biological Indicators Used in Integrated Assessments (cont.)
                    ..                         VA      MN      OR       CA       PA      CT      KS     EPA
                 indicator                  ^^    WA].    WAM    WAM    ACC    LDW    LDW   RpST
 Periphyton Dry Biomass
   <5 mg/cm2
 Periphyton Chl-a Mass
   Between 2 and 6 \ig chl-a/cm2
 Periphyton Community Succession
 Periphyton % Cover
 Shannon Diversity Index for Diatoms
 Pollution Tolerance Index for Diatoms
 Percent Sensitive Diatoms
 Abundance Achnanthes minutissima (<25%)
 Taxa Richness (Total # of Taxa)
   # Intolerant Taxa
   # Tolerant Taxa
   Native Taxa
   Non-Native Taxa
   Darter + Perch
   Minnow
   Sucker
   Sunfish
   % Similarity to Reference Reach (of fish taxa
   metrics above)
 EPT Index (Total # of Ephemeroptera,
 Plecoptera, Trichoptera Taxa)
 % Sensitive EPT
 % Collector
 % Filterers
 % Scrapers
 % Predators
 % Shredders
 % Dominant Taxa
VA WIM: Virginia Watershed Integrity Model
MN WAT: Minnesota's Watershed Assessment Tool
OR WAM: Oregon Watershed Assessment Manual
CA WAM: California Watershed Assessment Manual
PA ACC: Pennsylvania Aquatic Community Classification
CT LDW: Connecticut Least Disturbed Watersheds
KS LDW: Kansas Least Disturbed Watersheds
EPA RPST: EPA Recovery Potential Screening Tool
                                                                                                                     4-63

-------
Identifying and Protecting Healthy Watersheds
                          Vulnerability Indicators Used in Integrated Assessments
                    Indicator
 VA      MN      OR      CA
WIM    WAT    WAM    WAM
 CT      KS      EPA
LDW    LDW    RPST
          Population Density

          Change in Population

          Modeled Erosion Potential

          Land Use Trajectory

          Watershed % Protected Land

          Location of Public Lands or
          Protected Areas

          Expanding Transportation and
          Utility Infrastructure

          Escalating Mineral Resource
          Extraction
          Proliferation of Dams and
          Reservoirs
          Industrialization of Livestock
          Industry
          Growing Anthropogenic Demand
          for Water
          Introduction and Spread of
          Nonnative Species

         VA WIM: Virginia Watershed Integrity Model
         MN WAT: Minnesota's Watershed Assessment Tool
         OR WAM: Oregon Watershed Assessment Manual
         CA WAM: California Watershed Assessment Manual
         PA ACC: Pennsylvania Aquatic Community Classification
         CT LDW: Connecticut Least Disturbed Watersheds
         KS LDW: Kansas Least Disturbed Watersheds
         EPA RPST: EPA Recovery Potential Screening Tool
4-64

-------
5.   Management  Approaches
                         Introduction
                          This chapter introduces the Healthy Watersheds Initiative, discusses the
                          characteristics of a healthy watershed, and reviews the benefits of protecting
                          healthy watersheds. This chapter also describes the purpose, target audience, and
                          intended use of this document.
                         Overview of Key Concepts
                          This chapter describes the healthy watersheds conceptual framework. It then
                          discusses, in detail, each of the six assessment components- landscape condition,
                          habitat, hydrology, geomorphology, water quality, and biological condition.
                          A sound understanding of these concepts is necessary for the appropriate
                          application of the methods described in later chapters. This chapter concludes
                          with a discussion of watershed resilience.
                         Examples of Assessment Approaches

                          This chapter summarizes a range of assessment approaches currently being used
                          to assess the health of watersheds. This is not meant to be an exhaustive list of all
                          possible approaches, nor is this a critical review of the approaches included. These
                          are provided solely as examples of different assessment methods that can be used
                          as part of a healthy watersheds integrated assessment. Discussions of how the
                          assessments were applied are provided for some approaches. Table 3-1 lists all of
                          the assessment approaches included in this chapter.
                                                                                        —'

                         Healthy Watersheds Integrated Assessments

                          This chapter presents two examples for conducting screening level healthy
                          watersheds integrated assessments. The first example relies on the results of a
                          national assessment. The second example demonstrates a methodology using
                          state-specific data for Vermont. This chapter also includes examples of state
                          efforts to move towards integrated assessments.
                         Management Approaches
                          This chapter includes examples of state healthy watersheds programs and
                          summarizes a variety of management approaches for protecting healthy
                          watersheds at different geographic scales. The chapter also includes a brief
                          discussion of restoration strategies, with focus on targeting restoration towards
                          degraded systems that have high ecological capacity for recovery. The results of
                          healthy watersheds integrated assessments can be used to guide decisions on
                          protection strategies and inform priorities for restoration.
                                                                                              5-1

-------
Identifying and Protecting Healthy Watersheds
         Table 5-1 Management approaches and case studies summarized in Chapter 5.
          The Nature Conservancy: Setting Freshwater Conservation Priorities
          Wild and Scenic Rivers
          Wildlife Action Plans
          The National Flood Insurance Program
          The U.S. Forest Service's Forest Legacy Program
          The Trust for Public Land's Center for Land and Water
          State/Interstate
          Minnesota Healthy Watersheds Program
          Virginia Healthy Waters Program
          California Healthy Streams Partnership
          NatureServe's Conservation Priorities for Freshwater Biodiversity in the Upper Mississippi River Basin
          Antidegradation
          Instream Flow Protection
          Using Antidegradation to Protect Instream Flows in Tennessee
          Source Water Protection
          Growth Management
          State River and Habitat Protection Programs
          Minnesota Department of Natural Resources' Fen Protection Program
          Delaware River Basin Commission's Use of Antidegradation
          Washington's Critical Areas Growth Management Act
          Michigan's Water Withdrawal Assessment
          Vermont Agency of Natural Resources River Corridor Protection Program
          Michigan's Natural Rivers Program
          Wyoming Wetlands Conservation Strategy
          Maryland's GreenPrint Program
          Enabling Source Water Protection in Maine
 5-5
 5-9
 5-9
5-10
5-10
5-10
s
 5-3
 5-4
 5-4
 5-7
5-12
5-12
5-14
5-14
5-15
5-15
5-15
5-16
5-18
5-19
5-21
5-23
5-24
5-25
5-27
          National Wild and Scenic Rivers: Lumber River, North Carolina
          Land Protection
          The Central Texas Greenprint for Growth: A Regional Action Plan for Conservation and Economic Opportunity
          Land Protection and Climate Change
          Land Use Planning
          Green Infrastructure and Master Plans Alachua County, Florida
          Watershed-Based Zoning in James City County, Virginia
          River Corridor and Headwaters Protection
          Headwaters: A Collaborative Conservation Plan for the Town of Sanford, Maine
          Lower Meramec Drinking Water Source Protection Project
          Cecil County, Maryland Green Infrastructure Plan
          Sustainable Agriculture
          Sustainable Forestry
          Invasive Species Control
          Ground Water Protection
5-11
5-28
5-28
5-28
5-29
5-29
5-31
5-32
5-33
5-35
5-37
5-39
5-39
5-40
5-40
5-2

-------
                                                                                       5 Management Approaches
5.1   Implementing  Healthy Watersheds  Programs in States

A number of states are making protection  of healthy  watersheds, especially using a systems approach,
an important part of their state programs. The restoration of impaired water bodies has  long been a focus
of many state water quality programs. This  is due to the fact that 40-50% of the  nation's assessed waters
are listed as  impaired  (U.S. Environmental Protection  Agency, 2008a).  However, successful restoration
and protection efforts work hand in hand. As important as restoration of impaired  water bodies is, success
in restoring ecological  integrity will largely depend on pollution prevention and the protection of healthy
aquatic ecosystems that provide the ecological infrastructure that supports restoration.  The goal of the Healthy
Watersheds Initiative is to help interested states and other partners identify and protect this critical natural
infrastructure and inform restoration priorities, and increase awareness of how these states and other partners
are using these approaches and techniques to improve aquatic ecosystems.

Interested states are now using Healthy Watershed Programs that complement the traditional focus on single
problem management  by utilizing a systems-based approach  to meet  the  cross-disciplinary,  cross-agency
demands and challenges of aquatic ecosystem  protection. This  integrated approach to protecting aquatic
ecosystems can help to achieve environmental results quickly and cost-effectively. This technical document and
the complementary Healthy Watersheds Initiative website  (www.epa.gov/healthywatersheds) are two resources
that EPA has  developed to help states accomplish this.

The following are examples of the efforts that three states  (Minnesota, Virginia, and California) are taking to
develop and implement state-specific Healthy Watersheds Programs.

Minnesota Healthy Watersheds Program

" What happens on our lands impacts our waters; what happens to our waters impacts our habitats, ecosystems, and
biodiversity."

Recognizing  the  need to connect management  of the  state's  land and water resources, the Minnesota
Department of Natural Resources (DNR) made a significant change to their organizational structure, which
transformed their programs, operations, and research in order to increase focus  on, and enhance support for,
healthy watersheds throughout the state. Specifically, Minnesota DNR created  a new Division of Ecological
and Water Resources by integrating its former Division of Ecological Resources and  Division of Waters.
Integration of the two divisions into one will  foster and accelerate the development of integrated approaches
for improving the health of Minnesota's land  and water at local, watershed, and landscape scales. Minnesota
DNR  recognizes  that  an  integrated approach to resource  management  is necessary to  effectively address
multiple resource issues at multiple scales. This new division will  better position Minnesota DNR to address
the multiple pressures facing the state's land, water, fish and wildlife, and ecological  resources, by leveraging
existing systems of analysis and frameworks in complementary, rather than competing ways.

The new Division of Ecological and Water Resources is not just a merger of the work by the  former Division
of Ecological Resources and Division of Waters. Minnesota DNR's intention from the onset was to use this
new division to facilitate "systems-oriented natural resources management" throughout the entire department.
To initiate this department-wide transformation toward systems management, the new division is focusing its
attention on their most threatened natural resources: water, biodiversity, and ecosystem services. By focusing
their work around  the central vision of "Healthy Watersheds," DNR believes it can deliver  even stronger
protections for biodiversity and water resources (both ground and surface) than they were previously structured
to provide. With this new division, Minnesota DNR will be able to better shape their management goals and
strategies around protection and maintenance of vital ecosystem services—the natural processes that provide
benefits to humans, such as water purification, biodiversity maintenance, flood mitigation, and soil fertility.

More information: http://files.dnr.state.mn.us/aboutdnr/reports/legislative/2010  healthy  watersheds.pdf
                                                                                                         5-3

-------
Identifying and Protecting Healthy Watersheds
        Virginia Healthy Waters Program

        "At a time when so much of the news about the environment is negative, some biologists have been wading through
        Virginia's  streams in search of some positive information. What they've found suggests that there is another very
        important story."

        Virginia's  Healthy Waters  Initiative was designed to  raise  awareness about the need to maintain ecological
        balance and protect the state's critical healthy waters before they become impaired. Healthy Waters broadens
        existing conservation efforts to include the nearly 200 ecologically healthy streams, creeks, and rivers identified
        throughout the state thus far, as well  as the many more expected to be identified in the future (streams
        throughout the state will continue to be assessed and added to the list as resources become available).

        Healthy waters in Virginia are generally defined as those having the following characteristics:  high number
        of native  species and a broad diversity of species; few or no non-native species;  few generalist species that
        are tolerant of degraded water quality; high number of native predators; migratory species whose presence
        indicates that river or stream systems are not blocked by dams or other  impediments; low incidence of disease
        or parasites; and intact buffers of vegetation in the riparian zone. The current list of about 200 healthy waters
        in Virginia were identified and ranked  (as  "exceptionally healthy," "healthy," or  "restoration candidate")
        based on  these and other characteristics, using a stream ecological integrity assessment method  known  as the
        Interactive Stream Assessment Resource, or InSTAR (see Section 3-6).

        The Healthy Waters Initiative expands the existing water quality programs' focus on restoring degraded water
        quality to protecting everything from aquatic insect larvae and bugs hidden in gravelly stream bottoms, to
        fish and amphibians, to forested buffers alongside streams, to natural  stream flow, to the water that people
        drink. The identification and protection of healthy waters is expected to reduce the number of waters that will
        become degraded in the future.

        More information: www.dcr.virginia.gov/healthywaters

        California Healthy Streams Partnership

        Led by the  California  State Water  Board's Surface Water Ambient Monitoring  Program,   the Healthy
        Streams Partnership seeks to promote improved ecological conditions of California's streams by encouraging
        a paradigm shift from concern  about impaired  streams to an understanding of healthy stream systems and
        their ecological characteristics.  By expanding this understanding, the Healthy Streams Partnership hopes to
        contribute to a change in perspective  and thinking about natural resource management. With a strong focus
        on  connecting science and policy, the Healthy Streams Partnership supports hypothesis driven data collection,
        analysis, and reporting to provide more  useful and more integrated information to decision makers.

        The Healthy Streams Partnership consists of representatives from the State and Regional Water Boards, the
        Department  of Fish and Game, the State and Federal  Contractors Water  Agency, and  the Coast Keeper
        Alliance.  Coordination among these water quality data generating organizations is  expected to increase the
        rigor of the state's assessment capacity and to  provide more contextual information to managers  and decision-
        makers who  may have an impact on stream conditions. They are currently working to gather various data
        sources into a "web portal" and online application for developing indices that translate various data types into
        a report card format that provides an  assessment of overall stream condition. The effort focuses on including
        and synchronizing as many monitoring efforts as possible, striving for compatibility and comparability, and
        emphasizing  the need for monitoring to be hypothesis driven, in support of statewide adaptive management
        effectiveness.

        More  information:  http://www.swrcb.ca.gov/mywaterquality/monitoring council/meetings/2011iun/hsp
        outreach.pdf
5-4

-------
                                                                                         5 Management Approaches
5.2   Protection Programs

The following are examples of some of the many programs  and strategies available for protecting healthy
watersheds.  The strategies and programs are identified as national, regional, state, or local scale approaches.
These categories should not be considered rigid or constraining. They merely serve to organize the diversity of
techniques that can be used to maintain and improve watershed health at different geographic scales.

5.2.1  National

Freshwater  Conservation Priorities

Creating a set of freshwater conservation priorities helps to develop a common vision for galvanizing partners
and stakeholders to  implement  a wide  range  of  strategies  in many  places,  allowing those with specific
capacities, expertise, geographic, and programmatic  responsibilities to contribute to that vision of success. The
Nature Conservancy works with  others to develop  and implement approaches  and tools to identify regional
and basin-wide freshwater conservation priorities (Higgins J. V., 2003;  Higgins, Bryer, Khoury, & Fitzhugh,
2005; Higgins & Esselman, 2006). These and similar approaches and tools have been applied across parts of
five continents (Nel et al., 2009), including the vast majority of the United States (Higgins & Duigan, 2009).
Examples from the United States include Smith et al. (2003), Weitzell et al. (2003), and Khoury et al. (2010)
(see http://www.conservationgateway.org/content/ecoregional-reports for access to  all currently available
reports and  data).

The Nature  Conservancy has generally used a six-step conservation planning process to  identify priorities for
conserving the full range of freshwater habitats, processes, and  biodiversity in a given region or basin. The first
step is to define the assessment region. The region is defined using units  that delineate environmental patterns
and processes that result in freshwater ecological patterns. The region may be a collection of catchments within
an ongoing  terrestrial-focused assessment, a freshwater ecoregion, or a basin of a large freshwater system. Abell
et al. (2008) provide  a global coverage of freshwater ecoregions for conservation planning that is useful for
defining assessment regions, or subregions within very large assessment regions.

The second  step is to  define and  spatially represent the variety of biodiversity elements or ecosystems, which
characterize  environmental patterns, processes, and habitats that support the broad range of biodiversity in the
region of interest. A subset of species and natural communities that require focused attention to  ensure that
rare, endangered, declining, keystone, and migratory species are appropriately represented in the plan are also
identified in this step.  Ecosystems are defined and mapped using a freshwater ecosystem classification approach
(Appendix A).

Goals are set for defining  the numerical redundancy and environmental stratification of elements  thought to
be necessary to maintain ecological and evolutionary potential across the region of interest. Most regions that
are evaluated are large and contain subregions that differ in broad patterns of environmental characteristics
(e.g., climate, geology, drainage density, presence of lakes) and species composition. Therefore, subregions are
often delineated,  and  goals are set for each subregion using additional criteria such as conservation status and
range of elements. Often, different sets of goals are created, generating  different risk scenarios for sustaining
biodiversity, where higher numerical goals represent  lower risks to extirpation.

All of the occurrences of the biodiversity elements are then  evaluated  for their relative condition/integrity.
Condition is assessed  using best available  information,  commonly  using abundance, density,  or spatial extent
of freshwater species,  and the condition of the ecosystems, including: the intactness of species composition,
ecological processes, physical processes, habitat  ratings, and landscape context (includes but not  limited to:
degree  of connectivity of habitats, locations and densities of dams, stream  crossings,  catchment and local
contributing area, patterns of current and future land use/cover, and protected and managed areas).
                                                                                                           5-5

-------
Identifying and Protecting Healthy Watersheds
        Through working with partners and stakeholders to review and refine analytical products, priority catchments
        and connectivity corridors are selected to  represent the areas of biodiversity significance  (the best examples
        of each type of biodiversity element in each stratification unit) to best achieve goals in a comprehensive, yet
        efficient solution. Connectivity is especially important in aquatic systems, where connectivity of habitats  is
        vital to maintain many ecological processes, species, and ecosystem services. The Active River Area approach
        described in Chapter 4 explicitly identifies areas important  for processes  and sources of water and material
        inputs for freshwater ecosystems.  These areas include headwaters, riparian corridors, and floodplain wetlands.
        The Active River Area approach has been applied to many areas in the northeastern and southeastern United
        States  (Contact  The Nature Conservancy's Freshwater program for more information: http://www.nature.
        org/ourinitiatives/habitats/riverslakes/index.htm).  Additional  criteria  considered  in  assessments include
        existing conservation  opportunities, potential return on investments, ecosystem services, and climate change
        adaptation.

        The last step of the conservation  planning  process defines the major threats that occur regionally and in each
        of those  areas of significance, and develops strategies  to address them. This process can be conducted on a
        regional scale and/or at  the scale of each area. Regional strategy development is becoming more common, and
        defining strategies to address large scale threats and opportunities to leverage successful interventions requires
        a regional perspective. The selection of a subset  of high priority areas  based on  risks of conditional change,
        opportunities to implement strategies, or leverage efforts to broaden their impact is recommended. Strategies
        can include managing dams for  environmental flows  and other water resource  management activities, best
        management practices (BMPs), purchasing and/or reconnecting floodplain habitats to rivers, protection and
        rehabilitation of natural land cover, etc. Using this framework, The Nature Conservancy and its partners have
        developed regional freshwater conservation plans  that cover the majority of the United States. Many GIS tools
        are available to use to  define a suite of priorities. Priorities exist for the majority of the United States, and these
        provide a good place to  start (http://www.conservationgateway.org/topic/setting-freshwater-priorities).
5-6

-------
Conservation  Priorities for  Freshwater
Biodiversity in  the  Upper Mississippi  River
Basin
More Information: Weitzell, Khoury, Gagnon, Schreurs, Grossman, & Higgins, 2003 (http://
www.natureserve.org/library/uppermsriverbasin.pdf)
The  Upper  Mississippi  River Basin  (UMRB)  is
home to approximately 25% of the freshwater fish
species in the United States and 20% of the mussel
species found  in  the United  States  and  Canada.
NatureServe ranks 69 of these species as at-risk. Using
the  freshwater  ecosystem  classification  approach
described in Appendix A,  the  UMRB was divided
into  22  subregions  (Ecological  Drainage  Units).
There were 153 species  and 36 ecological systems
defined and mapped as conservation elements. Goals
were set for each species based on  its proportional
range representation  and spatial  distribution. The
minimum goal for aquatic ecological systems was to
conserve at least one of each unique system type in
each ecological drainage unit it occurred in.

Relative   condition/ecological  integrity   of  the
ecosystems  was  evaluated  using   land  cover/use,
impervious cover,  road  density,  stream   crossing
density,  dams, point sources,  mines,  and  impaired
stream designations.  Local  scientists  and  resource
managers  were consulted  to  provide additional
information for use in the assessment  and  to review
and  adapt the examples that were chosen to best
represent each biodiversity element.

The  network  of Areas  of  Biodiversity Significance
was  then  constructed  (Figure  5-1).  Priority  for
inclusion was given to those ecological systems that
captured species elements,  had the highest relative
ecological  integrity,  and  were expert recommended
and/or included  in  already  existing  conservation
plans. Inclusion of additional ecological systems and
connectivity  to  support environmental  processes
was conducted by including all headwater ecological
systems upstream of areas of biodiversity significance
in the network.  The medium rivers  immediately
downstream of each selected small river system were
also  included  in  the network. Finally, ecological
system types  that had not yet been included were
added to ensure representation of all types. Goals were
met for all ecological system types. The areas that were
selected included representation of 102 of the species
elements.  Goals were met  or  exceeded for 45%  of
these species elements, including for 71% of the fish
species and 55% of the mussel species. A subset of 47
areas that overlapped with terrestrial priorities were
mapped to identify areas where conservation resources
may be used more efficiently and outcomes may  be
more  effective through cooperative and synergistic
freshwater and terrestrial conservation actions.

A variety of strategies are being implemented across
the UMRB by a range of partners and  stakeholders.
These strategies include demonstrations  of floodplain
protection   and   restoration,   flow/water  level
management,  alternative  land  use management and
agricultural BMPs, restoring natural wetlands and
creating artificial wetlands for  processing land-based
sources of nutrients,  and retiling agricultural lands
to manage soil  moisture and  nutrient  applications,
among others.

                              Continued on page 5-8
                                                                                                    5-7

-------
                      Expert or ecoregion priority

                Big River

                      ABS

                      Stale Line
                CX3
                C3
Upper Mississippi River Basin  ?t,
(Region 7>             22 O"*'1"'*'
Ecoiogical Drainage Unit (EDO)
                Figure 5-1 Areas of Freshwater Biodiversity Significance in the Upper Mississippi River Basin
                (Weitzell et al., 2003).
5-8

-------
                                                                                          5 Management Approaches
Wild and Scenic Rivers

Enacted in 1968, the Wild and Scenic Rivers Act protects free-flowing rivers from new hydropower projects,
federal water resource development projects, and other federally assisted water resource projects (Interagency
Wild and Scenic Rivers Council, 2009)- Among other factors, to qualify for designation, a river must be free-
flowing and have one or more "outstandingly remarkable" values. Outstandingly remarkable values are defined
loosely, but typically include scenic, recreational,  geologic, fish and wildlife, historic, cultural, or other similar
values (Interagency Wild and  Scenic  Rivers Council, 2009)- Rivers have traditionally been designated  as a
wild, scenic, or recreational river area through congressional designation. However, Section 2(a)(ii) of the Wild
and Scenic Rivers Act authorizes the Secretary of the Interior to include a river already protected by a state
river protection program in the National System upon the request of that state's governor. Many states already
have their own river protection programs in place. Inclusion in the National Wild and Scenic Rivers System
ensures that (American Rivers,  2009b):

     •   A river's "outstandingly remarkable" values and free-flowing character are protected.
     •   Existing uses of the river are protected.
     •   Federally licensed dams and  any other federally assisted water resource  projects  are
        prohibited if they would negatively impact the river's outstanding values.
     •   A quarter mile protected corridor on both sides of the river is established.
     •   A cooperative river management plan that addresses resource protection, development
        of lands and facilities, user capacities, etc. is developed.

Outside of federal lands, the federal government has little or no control over certain river resource threats, such
as land use. Thus, it is critical  that state and local organizations have a clear and effective plan for managing
the  protected river area.  Floodplain  zoning  and wetlands protection  laws are  examples of state  and local
management actions that  can be used to protect designated river areas.

Wildlife Action Plans

Two programs created by Congress in 2000, the  Wildlife Conservation  and Restoration Program and the
State Wildlife Grants Program, require the development of Wildlife Action Plans for all 50 states. These plans
are meant to protect states' wildlife before  it  becomes endangered or threatened. The  plans evaluate wildlife
habitat at the landscape level and target conservation actions at the local level. Many  of these plans include
aquatic resource protection. The plans are being implemented in all 50 states and receive funding from the
U.S. Fish and Wildlife Service. Information  from these plans can  be used  in the development of strategies
to protect  healthy watersheds. Partnerships with the many organizations involved in  the development  and
implementation of wildlife action plans can be formed to the mutual benefit of both programs. Wildlife action
plans can be used by local land use agencies and  sewer and water utilities in facility siting determinations (to
prevent habitat loss), land maintenance (to prevent  the spread of invasive species), and  other infrastructure
decisions, including water withdrawal and discharge decisions  (to prevent pollution) (Environmental Law
Institute, 2007b).  Some strategies that utilities have pursued include acquiring land to  protect water recharge
areas, putting land  into  conservation easements,  initiating  stream clean-ups,  carrying out  environmental
education, and conducting biological research (Environmental Law Institute, 2007b).
                                                                                                            5-9

-------
Identifying and Protecting Healthy Watersheds
        The National Flood Insurance Program

        The National  Flood Insurance  Program  (NFIP)  can contribute  significantly toward  protecting healthy
        watersheds. The program is  intended primarily to  protect  human life and property through  requiring
        participating  communities  to adopt  certain standards in their floodplain  development  ordinances.  By
        participating in the program and  complying with the  standards,  the  communities  receive insurance and
        assistance for flood-related disasters. The minimum requirements of the NFIP serve the purpose of protecting
        human life and property. However, through the Community Rating System, communities can implement
        floodplain management policies that  exceed the NFIP minimum  requirements  and receive  a  significant
        discount in their flood insurance premiums. Many strategies using the No Adverse Impact approach promoted
        by the Association of State Floodplain Mangers qualify for credit under the Community Rating System.
        Adverse impacts can be defined as  increases in flood  stages, velocity, or flows, the potential for erosion and
        sedimentation, degradation of water quality, or increased cost  of public services (Vermont Law School  Land
        Use Institute,  2009).  The No  Adverse Impact  approach extends development management beyond the
        floodplain to include managing development in any area within the watershed that may have an adverse impact
        on downstream property owners. For example, it promotes limiting the amount of impervious surfaces allowed
        on new development sites or requiring mitigation strategies such  as infiltration basins to capture the increased
        runoff from new  impervious surfaces. Another example is the Vermont Stream Geomorphic Assessments
        discussed in Chapter 3, through which a fluvial erosion hazard (FEH) zone is defined. Using this approach,
        the state has begun assisting communities in developing and implementing FEH districts, which have qualified
        under the Community Rating System program for providing additional protections not provided for in the
        NFIP minimum requirements, which do not address fluvial erosion.

        The U.S.  Forest Service's Forest Legacy Program

        The U.S.  Forest Service's Forest  Legacy Program purchases conservation easements to  protect tracts of forest
        lands greater than  100 acres that are vulnerable to development and growth pressures. Thirty seven state forest
        legacy programs have identified water quality, wetland, and riparian buffer protection  as goals of their program.
        The program is administered in cooperation with state partners. For example, the Forest Service worked with
        the State  of Montana and a number of other partners to protect nearly 8,000 acres  in the North Swan  River
        Valley,  the most intact biological ecosystem remaining in the lower 48 states. Forest  Legacy Program funding
        was leveraged with other funding to complete the protection of 66,000 acres in Swan Valley. Landowners must
        prepare a multiple resource management plan with project costs of which at least 25% must be  funded by
        private, state, or local sources. Landowners benefit from the sale of the property rights and also from reduced
        taxes on the preserved open space once the sale is complete.

        The Trust for Public Land's Center for Land and Water

        The Trust for Public Land's Center for Land  and Water works in partnership with communities across the
        nation to identify  and protect the most critical watershed lands for maintaining healthy aquatic resources. The
        Center protects these lands by designing networks of conservation lands, facilitating conservation transactions,
        and supporting funding and  legislation for  land protection.  Much of the Center's efforts are focused on
        protecting lands surrounding drinking water sources. By assisting with land acquisition  or  conservation
        easements in the watersheds of source waters, the Center helps to minimize nonpoint sources of pollution that
        can threaten water supplies. The  Enabling  Source Water Protection in Maine and Lower Meramec Drinking
        Water Source Protection Project case studies at the end of this section describe specific examples of the Center's
        work.
5-10

-------
Case   Study
 Wild  and  Scenic  Rivers: Lumber  River,  North
 Carolina
 More Information: http://www.rivers.gov/wsr-lumber.html
 The Lumber River is located in south-central North
 Carolina, and  although  most of the river corridor
 is in private ownership, it is virtually unmodified.
 In 1996, North  Carolina's governor petitioned the
 Secretary of the Interior to add 115 miles of the river
 to the National Wild and Scenic Rivers System. The
 river had previously received protection under the
 North Carolina Natural  and Scenic Rivers Act, and
 a State Park Master Plan had recently been developed
 for the river corridor. This plan outlined a strategy for
 the state to work with local governments  on future
 land use and zoning regulations and acquire riparian
 lands through  fee simple purchase and conservation
 easements.
As part  of the national designation process,  an
examination of existing  zoning was  conducted to
determine if the river would receive adequate local
protection while the master plan strategy was being
implemented. The City of Lumberton amended
its land use ordinance by adding the Lumber River
Protection Overlay District  to ensure that the river
received designation as a National Wild and Scenic
River, a source of pride for the community. The river
was successfully designated as a result of local river
protection interests, key  political leaders, scientists,
and the  National  Park  Service working  together
throughout the process.
                The Lumber River, North Carolina (The Lumber River Conservancy, 2009).
                                                                                        5-11

-------
Identifying and Protecting Healthy Watersheds
        5.2.2  State and Interstate

        Antidegradation

        In addition to defining designated uses and identifying water quality criteria, states and authorized tribes are
        required to develop and adopt statewide antidegradation policies that protect and maintain: existing instream
        uses and their associated water quality; high quality waters, unless the state or tribe finds that allowing lower
        water quality is necessary to accomodate important economic or social development; and outstanding national
        resource waters (ONRW), as designated by the state or tribe. They are also required to identify implementation
        methods for the antidegradation policy These implementation methods typically define how the high quality
        waters will be identified, what activities will trigger the antidegradation review process, and the components of
        an antidegradation review. All waters of a state should be categorized into one of three protection Tiers. Tier 1
        is the minimum baseline of protection afforded to all waters of a state and requires that existing uses and their
        associated water quality be maintained and protected. Tier 2, high quality waters, are those  waters that exceed
        the minimum quality necessary to support the CWA's "fishable/swimmable" goals and can only have their
        water quality lowered when the state or tribe finds the lowering to be "necessary to accommodate important
        economic or social development," as determined through the antidegradation review process. No degradation
        is allowed  in Tier 3 waters, ONRWs, except on a short-term, temporary basis,  as identified by the state's or
        tribe's policies and procedures. Antidegradation applies when an activity lowers water quality and is, therefore,
        an attractive option for states or tribes to pursue in the protection of healthy watersheds. Healthy watersheds
        assessments can help strengthen and inform Tier 2 and Tier 3 designations.

        Instream Flow Protection

        With the  ever increasing  demands that humans place on freshwater  resources for drinking water, power
        generation, and industrial and agricultural uses, aquatic biota are experiencing not only lower flows, but a loss
        of the natural variability in flows. Historical methods for determining instream  flow needs focused on single
        species, often leading to decreased health of the larger ecosystem (Poff N., 2009).  Scientists now understand
        that the natural  flow regime  must be maintained to ensure aquatic ecological integrity. This understanding
        is beginning to be integrated into flow management by the U.S.  Army Corps of Engineers, who have been
        working with The Nature Conservancy on pilot projects like those  on the Savannah River in Georgia (Richter,
        Warner, Meyer, & Lutz, 2006), and utilities like the Rivanna Water and Sewer Authority,  also working with
        The  Nature Conservancy on developing  environmental flow management  practices (Richter B., 2007).
        Both projects defined flow prescriptions for a river segment by evaluating ecological and social  needs. More
        information on managing instream flows  for humans  and ecosystems  can be found in Postel and Richter
        (2003).

        Some states, such as Washington, Massachusetts, Connecticut, South  Carolina, and Michigan have begun
        developing flow management and water allocation policies to ensure protection of instream flows. For example,
        Michigan  uses its Water Withdrawal Assessment  Tool, described in Chapter 3, to  develop flow  alteration-
        ecological  response curves  for various classes of rivers, and the effects of proposed surface  water and ground
        water withdrawals can be  estimated with  an  online  user  interface. Use of this tool is required for all new
        > 100,000  gallons per day withdrawal applications as part of the implementation  of a variety of Michigan
        water allocation policies intended to protect and restore instream flows.  Similarly, Connecticut has developed
        draft stream flow regulations based on expert consensus  and best available science to set flow standards for
        six seasonal bioperiods. The regulations  apply  to surface  water withdrawals and reservoir releases.  The
        Massachusetts Water Policy is a comprehensive approach to water management that seeks to maintain sufficient
        quantity and quality of water for aquatic life and human use. It  leverages the benefits of Smart Growth to
        "keep water local" by: allowing  for infiltration of precipitation onsite, instead of sending it across impervious
        surfaces and down storm drains; encouraging municipalities to live within their water budgets and not import
        water from other basins; and increasing treated wastewater recharge and reuse. These actions help to maintain
        natural river flow conditions. South Carolina passed the Surface Water Withdrawal and Reporting Act in 2010
5-12

-------
                                                                                        5 Management Approaches
that sets water-permitting requirements for withdrawals greater than 3 million gallons per month; establishes
statewide, seasonally variable minimum flows to protect aquatic life, recreation, and water supply; and requires
new users to have contingency plans so that they can cease their consumptive use of water when stream flows
get too low.
The Columbia Basin Water Transactions Program uses a variety of mechanisms to ensure sufficient instream
flows  throughout the basin in Washington, Oregon,  Montana, and  Idaho. Some of the tools used include
(National Fish and Wildlife Foundation; Bonneville Power Administration, 2004):
    •   Water Acquisitions:
            o   Short and long-term leases.
            o   Permanent purchase.
            o   Split Season — A portion of a water right is used for irrigation in the spring
                and the remainder is left instream in late summer/fall.
            o   Dry  Year Option  — An opportunity  to lease  a  water right  during  a
                particularly dry year.
            o   Forbearance agreement.
            o   Diversion reduction agreement.
    •   Boosting Efficiency:
            o   Switching from a flood to sprinkler irrigation system.
            o   Modernizing headgates.
            o   Improving ditch efficiency.
    •   Conserving Habitat:
            o   Protecting/restoring stream habitat and changing a portion of the associated
                water right.
    •   Rethinking the Source:
            o   Changing the point of diversion from a tributary to a main stem in order to
                improve stream flows.
            o   Switching from surface to ground water source.
    •   Pools:
            o   Rotational pool — A group of irrigators take turns leaving a portion of their
                water in stream.
    •   Banks:
            o   Water Banking — Producers in an irrigation district  "bank" water they may
                not need so it can be available for other uses.
                                                                                                         5-13

-------
Identifying and Protecting Healthy Watersheds
                               Using Antidegradation to Protect Instream Flows
         The Tennessee Division of Water Pollution Control regulates water withdrawals that can lower water quality or affect
         designated  use support in waters of the state. Most regulated water withdrawals in the state are for public water
         supply. Tennessee's permit process  under antidegradation  requires an alternatives analysis, which includes social,
         economic, and environmental considerations. Regional water supply  planning conducted by the community is an
         important tool to help identify water supply alternatives that avoid or minimize degradation. From the regulatory
         perspective, an environmental review  should  seek to  avoid and minimize  degradation.  From the community's
         perspective, an environmental  review  should  include  the  affected public  and  represent their  interests.  The
         alternatives  analysis helps encourage avoidance and minimization, while the intergovernmental coordination and
         public participation provisions help  ensure that the community has  input on potentially important economic or
         social development.

         The alternatives analysis process has led to the development of regional, coordinated  water supply planning to
         address permit application requirements and the Division of Water Pollution Control has assisted in the completion
         of two  such pilot efforts. In one case, the regional plan showed that the raising of an existing dam would serve
         as a regional  supply for the stated  planning horizon and was therefore justified under  antidegradation;  and  that
         other water supply development proposals within  the region were therefore not justified. In the other case, the
         impoundment and lowering of water quality of a tier two stream was shown to be unjustified; and that purchase of
         treated water from a nearby utility who obtained their raw water from the Cumberland River was feasible.

         Other innovations in water supply planning are occurring throughout Tennessee. For example, the Huntsville utility
         district operates an existing withdrawal on a tier two stream, the New River, a tributary of the Big South Fork National
         Recreational River. The Huntsville utility district has recently applied for a permit to increase their withdrawal  rate
         and volume from the  New River. However, they propose to change their operation to harvest water based on the
         amount of flow in the river and subsequently withdraw no more than  5% of the flow at any time. This minimization
         of impact was driven, in part, by Tennessee's de-minimis flow reduction standard, serving as a presumptive flow
         standard.
        Source Water Protection

        The Safe Drinking Water Act (SDWA) Amendments of 1996 require states to develop and implement source
        water assessment programs (SWAPs) to analyze existing and potential threats to the safety of public drinking
        water sources throughout the state. States have completed source water assessments for virtually every public
        water system in the nation, from major metropolitan areas to the smallest towns. A source water assessment
        is a water system-specific study and report that  provides  basic information about the source water used to
        provide drinking water. Many of the biggest threats to  source waters identified in SWAPs are related to land
        use practices. These include stormwater and nonpoint  source runoff (e.g., from  fertilized crop lands), septic
        systems, and chemical storage tanks at commercial and  industrial sites. Drawing from resources such as EPA's
        Drinking Water State Revolving Fund (DWSRF)  and Clean Water State Revolving Fund (CWSRF), states can
        assist local water suppliers with source water protection  measures, including a variety of land use management
        tools, to  address the threats identified  in the SWAP These two  EPA financing programs are administered by
        each of the states and may provide funding to projects  that support compliance  with SDWA drinking water
        standards (DWSRF) or protect,  enhance, or restore water quality (CWSRF). The  interest rates on loans under
        these programs are typically well below market rates and have flexible repayment terms  that can be extended
        up to 20 years.

        Land trusts have also taken advantage  of both the DWSRF and CWSRF for land acquisition. Aligning State
        Land  Use and Water Protection Programs is an EPA-funded initiative  that will have  strategies and  lessons
        learned to share with other states. Initiative  partners (The Trust for Public Land, Smart Growth Leadership
        Institute, River Network, and the Association of State Drinking Water Administrators) are working with a
        small group of states to identify opportunities to work across political and  programmatic boundaries to better
        align planning, economic development, regulation, and conservation to protect drinking water sources at the
        local and watershed level (see www.landuseandwater.org).
5-14

-------
                                                                                         5 Management Approaches
Growth Management

Some states have growth management laws, which typically provide more specific guidance  to localities in
the development of land use plans than do the more  typical land use planning enabling laws. In addition to
providing specific guidance and requirements, growth management laws also sometimes include a state land use
plan to guide local land use planning (Environmental Law Institute; Defenders of Wildlife, 2003)- However,
the primary authority to regulate land use remains with the local government. Some growth management laws
establish mechanisms for adjoining jurisdictions to coordinate their planning activities (Environmental Law
Institute; Defenders of Wildlife, 2003)- The State of Washington is protecting "critical  areas" through the use
of its Growth Management Act (see case study at end of section).

State River and Habitat Protection Programs

Many state agencies maintain habitat protection programs  and river protection programs that  seek to protect
riparian areas  and  river  corridors.  Some examples include: Vermont's integrated river corridor protection
program, which is used to protect riverine and riparian habitat, in addition to protecting human infrastructure
from flood and fluvial erosion hazards; Michigan's  Natural  Rivers Program that protects riverine and riparian
habitats; Wyoming's statewide planning process to protect wetland-associated habitats; Maryland's GreenPrint
Program; and Minnesota's state  legislation for fen protection.

Both voluntary and regulatory techniques are frequently used to implement these programs, and collaboration
with local  governments and organizations is key to their  success. For example,  the New Hampshire River
Management and Protection Program is administered by the New Hampshire Department of Environmental
Services  and  a statewide River Management Advisory  Committee. However, protection hinges upon
partnerships between the state and  local municipalities. Local individuals or organizations nominate rivers
when sufficient local support is  demonstrated. Once approved by the state, designated rivers receive protection
from potential threats according to the classification they were given at the time  of designation:  natural,
rural, rural community, or community. Protection  measures consider channel alterations, dams, hydroelectric
energy facilities, interbasin water transfers, protected instream flows, siting of solid  and hazardous waste
facilities, recreational  river use, and water quality. A local advisory committee consisting of representatives
from all riverfront municipalities develops and implements a management plan for the designated river with
assistance from  the Department of Environmental  Services.  Local  advisory  committees also comment on
activities requiring state or federal permits that may impact  the river. The intent of the River Management and
Protection Program is to balance competing demands for river resources for the benefit of present and future
generations.
The Massachusetts Rivers Protection Act takes a somewhat different approach  to river protection.  The Act
protects the 200 feet of land adjacent to either
bank of every perennial river, stream, or brook,
with
      a few  exceptions  in densely  populated
urban areas, where only 25 feet on either side of
the perennially flowing water body is protected.
These  tracts  of land,  referred to as riverfront
areas, are protected from any new development
unless the developer  can prove  to the  local
conservation commission or the Massachusetts
Department   of   Environmental   Protection
that there  is no practicable alternative for the
development or that the development will not
have a significant  adverse  impact on the river.
As  a  result, the Rivers Protection Act protects
a seamless network of the  state's  perennially
flowing water bodies.
    Minnesota Fen Protection
i://www.dnr.state.mn.us/eco/wetlands/index.l
                                                Calcareous Tens are a wetiana type cnaraaenzea oy a non-
                                                acidic peat substrate and dependent on a constant supply of
                                                cold, oxygen-rich ground water with high concentrations of
                                                calcium and  magnesium bicarbonates. Calcareous  fens  are
                                                some of the rarest natural communities in the United States
                                                and  are highly susceptible to disturbance.  The Minnesota
                                                Wetlands  Conservation Act protects calcareous seepage fens
                                                from being "filled, drained, or otherwise degraded, wholly or
                                                partially, by any activity, unless the commissioner of natural
                                                resources,  under an approved  management  plan, decides
                                                some alteration is  necessary"  (Minnesota  Department of
                                                Natural Resources, 2008).  In addition,  any state-threatened
                                                plants occurring on a calcareous fen  are  protected  under
                                                Minnesota's endangered species law.
                                                                                                          5-15

-------
                                          Case   Study
                   Antidegradation: Delaware River Basin
                   Commission Special Protection  Waters
                   More Information: http://www.state.ni.us/drbc/spw.htm
       The Delaware River  Basin  Commission  adopted
       Special Protection Waters regulations in 1992, 1994,
       and 2005  to protect existing high quality waters in
       areas of the Delaware  River Basin deemed  "to have
       exceptionally high scenic, recreational, ecological and/
       or water supply values."

       The Special  Protection Waters  regulations  adopted
       in  1992 and 1994 initially applied to a 121-mile
       stretch of the  Delaware River  from Hancock,  NY
       downstream  to the Delaware Water Gap, and  its
       drainage area. This corridor includes the two sections
       of the river federally designated as "Wild and Scenic"
       in 1978, as well as an eight-mile reach between Milrift
       and Milford, PA which is not federally designated.

       In  2000,  federal  legislation was  enacted  adding
       key segments of the  Lower Delaware and selected
       tributaries  to  the National Wild and Scenic Rivers
       System. This  designation  was followed in April
       2001 with a petition from the Delaware Riverkeeper
       Network to the Delaware River Basin Commission
       to classify the Lower Delaware as a Special Protection
       Water.  Extensive water quality data were collected
       from 2000 through 2004 at over 26 tributary and
       main-stem Delaware River locations. The resulting
       water  quality  data confirmed  that existing  water
       quality in  this stretch of river  exceeded most state
       and federal standards,  making it a worthy candidate
       for the Delaware  River Basin  Commission's  anti-
       degradation program.
Based in part  upon these findings,  in  2008 the
Delaware River Basin Commission permanently
designated the 76-mile stretch of the non-tidal lower
Delaware River between the Delaware Water Gap and
the head of tide at Trenton, NJ as Special Protection
Waters  (Figure  5-2). The entire 197-mile non-tidal
Delaware River is now protected by Special Protection
Waters anti-degradation regulations.

The primary focus for  the Special Protection Waters
Program is to ensure that the existing high quality
waters are not  measurably changed as a  result of
point source discharges and to mitigate the impacts
of nonpoint source pollution from new service areas.
In order to evaluate point source discharge projects
for conformance with the  Special Protection Waters
Program, Commission staff prioritized water quality
model development  in those watersheds  that have
a high  number of existing point source discharges
as well as in those watersheds that were expected to
have new growth and associated wastewater discharge
needs.

The water quality models are used to predict changes
to water quality as all  of the  existing  and proposed
point source  discharges reach their permitted flow/
loads. These  cumulative impact models  are then
utilized to identify effluent limitations for the point
source  discharges to prevent a  measurable water
quality change to Special Protection Waters.
5-16

-------
                                                    Neversink River
                                                      Watershed
   Brodhead Creek
     Watershed
  Lower Lehigh
 River Watershed
                                  ,>-*5DelawareTWater Gap
                                                   Lower
                                              Delaware River
                                                & Tributaries
    PENNSYLVANIA
                                           NEW JERSEY ,4
                                 Delaware

                          Miford
   DRB Basin Outline

Q3 Water Quality Modd Watershed
Q DRBC - SPW

                E~2
                         '  DELAWARE
                                                    1   '  ioL.  '   '
Figure 5-2 The Delaware River Basin Commission (DRBC) permanently designated
the entire 197-mile non-tidal Delaware River as a Special Protection Water (SPW)
subject to anti-degradation regulations (image courtesy of Robert Tudor, DRBC).
                                                                                       5-17

-------
                                            Case   Study
                    Washington  Critical Areas Growth
                    Management Act
                    More Information: http://www.commerce.wa.aov/site/418/default.aspx
       The  State  of Washington  adopted  its  Growth
       Management Act  (GMA) in 1990  in response to
       rapid, uncoordinated, and unplanned growth that was
       threatening the environment, sustainable economic
       development, and the health, safety, and high quality
       of life afforded to its citizens. The Act requires all
       Washington  counties  and  cities to  designate  and
       protect critical areas and natural resource areas. Critical
       areas include wetlands,  fish and wildlife  habitat
       conservation areas, aquifer recharge areas, frequently
       flooded  areas,  and  geologically  hazardous  areas.
       Natural  resource  areas include  forest, agricultural,
       and mineral lands. The Act has 14 goals that include
       reducing sprawl by focusing growth  in urban areas,
       maintenance of natural resource based industries and
       encouragement of sustainable economic development,
       and protection of the environment by retaining open
       space and habitat areas. Based on county population
       and growth rate, some counties (and  all cities within
       them) are  required to fully plan under the GMA,
       while others can choose to  plan. However,  all  cities
       and counties are  required to designate and protect
       critical areas.

       Although each city and county is required to designate
       and protect critical areas, functions, and values under
       the GMA, they are given wide latitude in how they
       do so. The State  of Washington provides guidance
       and technical assistance, including example codes and
       ordinances, but continues the tradition of  allowing
       local government to control its own land use decisions
       by allowing them  to choose the particular strategies
       and tools  they will use.  However, designation and
       protection  of critical  areas  must include the  "best
       available science" and must give special consideration
       to protection of anadromous fish habitat. A variety of
regulatory and non-regulatory tools are available to
communities for protection of critical areas, including
zoning,  subdivision codes,  clearing   and grading
ordinances, critical areas  regulations,  conservation
easements,  public  education,   and  transfer  of
development rights. The focus  is  on  performance
measures designed to  protect  the  functions  and
values of each critical  area.  Although  critical  areas
can be protected with a number of regulations, many
communities in Washington include a separate critical
areas chapter in their development  regulations.  The
State Environmental Policy  Act, Shoreline  Master
Program, Storm Water Management, and Clearing
and Grading Ordinances are also useful for protecting
critical areas, and any critical  areas regulations should
be consistent with these programs.

In  2008,   Snohomish  County  conducted   an
effectiveness  monitoring  study  to  determine  how
well it  was protecting  the functions and values of
critical  areas.  The  county uses regulatory (critical
areas regulations),  non-regulatory (best  management
practices), and monitoring and adaptive management
to protect its critical areas. The critical areas regulations
have science-based standards for techniques  such
as buffer  widths   around  wetlands  and  streams.
Alternative and innovative approaches are permitted
when they can be shown to achieve the same level
of protection  as  the  regulations.  A  combination
of permit tracking,  enhancement project tracking,
remote sensing, shoreline inventories, and intensive
catchment studies  are being  used to determine the
impacts of development on critical areas, with a focus
on fish and wildlife habitat  (Haas,  Ahn, Rustay, &
Dittbrenner, 2009).
5-18

-------
Case   Study
 Michigan Water Withdrawal  Assessment
 Process
 More Information: http://web2.msue.msu.edu/bulletins/Bulletin/PDF/W060.pdf
 In  response  to  the Great Lakes  — St. Lawrence
 River Basin  Water  Resources  Compact of 2005,
 the Michigan State Legislature enacted new laws to
 manage large-quantity  water withdrawals based  on
 hydroecological principles. Public Act 179 of 2008
 defines a large-quantity water withdrawal as an average
 of 100,000 gpd over any consecutive 30 day period.
 Using a process that parallels the Ecological Limits of
 Hydrologic Alteration,  Michigan has classified river
 segments, determined flow-ecology relationships, and
 identified environmental flow targets based on socially
 acceptable ecological  conditions.  To  implement
 its  policy, Michigan has created a statewide water
 withdrawal assessment tool (Chapter 3).
                         The water withdrawal assessment  tool  uses "fish
                         response curves" to evaluate the impact  of a water
                         withdrawal on fish populations in the 11 different
                         stream  types  defined  for  Michigan (Figure 5-3).
                         The stream types are defined based  on  habitat
                         characteristics such as catchment size, base flow yield,
                         and July mean water temperature. The fish response
                         curves were developed using fish abundance and
                         stream flow data to determine relationships between
                         flow reduction and change in fish  populations  for
                         all  11 stream types.  Using the  water withdrawal
                         assessment tool,   the  user inputs  the proposed
                         location  and quantity  of their withdrawal, and  the
                         tool estimates the level of impact. Depending on  the

                                                   Continued on page 5-20
               Zone A      Zone B
   ~  0.4
   !
               Increasing user involvement
                                           Adverse Resource Impact
and responsibility
                              Proportion of index now removed

    Figure 5-3 Example fish response curves. The dark curve represents "thriving species still thriving" at
    incremental reductions in index flow. The light curve represents "characteristic species still present and
    abundant." (TroyZorn, MI DNR, Personal Communication).
                                                                                         5-19

-------
        proportion of the index flow removed for  a  given
        stream type, the  proportion of the fish population
        remaining can  be determined  through the use  of
        the fish response curves. Four zones  of index flow
        reduction  have been defined for  each stream  type.
        These  zones  represent  different  policy  actions  as
        shown in Figure 5-4.

        The water withdrawal assessment  tool  is considered
        a  screening tool. When appropriate, site-specific
analyses  can   be  conducted   to   determine  the
appropriate  zone  and  consequent  action.  A new
Water  Resources  Conservation  Advisory Council
was  created  to  evaluate  and  oversee  the  state's
water management programs,  including the Water
Withdrawal Assessment Process. The council ensures
that the process is inclusive and collaborative and that
it is based on the best available science.
            User
            Can
            Enter.
            Either
Process Component Process Result
-1
Screening
Tool

And possibly

1
1 Zones C&D
• And p ^ssibly Zone B
J *
1
1
I
1
1
I
L
Site
Specific
Analysis
1


X,™, 1
r *•
j J
7oner^
V /7
^ * K
User Group
or
Legal Options
                                                                            Action
                  Withdrawal authorized

                  Undetermined; some increased
                  degree of engagement &
                  responsibility is intended
                                                                             Withdrawal authorized
                                                                            Undetermined; some increased
                                                                            degree of engagement &
                                                                            responsibility is intended
                                                                        •*.   Withdrawal denied
                                                                             New site-specific analysis
                                                                             MDEQ Administrative decision
                                                                             Judicial decision
            Figure 5-4 Illustration of the water withdrawal assessment process and resulting actions. (Troy Zorn, MI
            DNR, Personal Communication).
5-20

-------
Case   Study
 Vermont  River  Corridor  Protection Program
 More Information: Kline, 2010 (http://www.anr.state.vt.us/dec/waterq/rivers/htm/rv
 restoration.htm)
 The Vermont River Corridor Protection Program
 is a program of the Department of Environmental
 Conservation,  within   the   Agency  of  Natural
 Resources (ANR), that seeks to restore and protect the
 natural values of rivers and minimize flood damage.
 Achieving natural stream stability over time through a
 reduction in riparian infrastructure can minimize cost
 from flood damage and improve aquatic and riparian
 ecological integrity. Vermont ANR provides technical
 assistance to communities throughout  the  state  to
 help  delineate  river corridors,  develop  municipal
 fluvial erosion hazard zoning districts, and implement
 river  corridor easements.  Delineation  of the river
 corridor is carried out using the stream geomorphic
 assessment protocols described in Chapter 3- The
 primary purpose of this  delineation, with respect to
 river  corridor planning, is to capture the meander
 belt and other active areas of the river that are likely
 to  be  inundated or erode  under flooding flows. As
 part of the stream geomorphic assessment, a stream
 sensitivity rating is  assigned to each reach based on
 existing stream type and geomorphic condition.

 Based on the river corridor delineations, Vermont
 ANR  works with  communities to develop river
 corridor plans that analyze geomorphic  condition,
 identify   stressors   and  constraints   to   stream
 equilibrium,  and prioritize management strategies
 such as:
    •   Protecting river corridors.
    •   Planting stream buffers.
    •   Stabilizing stream banks.
    •   Arresting head cuts and nick points.
    •   Removing berms and other constraints
        to flood and sediment load attenuation.
    •   Removing/replacing/retrofitting
        structures   (e.g.,  undersized  culverts,
        constrictions, low dams).
    •   Restoring incised reaches.
    •   Restoring aggraded reaches.
By focusing on  "key attenuation assets," flood and
fluvial erosion  hazards,  water  quality, and habitat
are improved  at minimum cost. Attenuation areas
are  captured  in  the  corridor  delineation process
and include Active  River Area components such as
floodplains, wetlands, and  riparian vegetation that
store flood flows and sediments and reduce watershed
nutrient and organic matter inputs.

The  river corridor plans  are  incorporated  into
existing watershed plans, and ANR also works with
municipalities to develop Fluvial Erosion Hazard Area
Districts in their bylaws or zoning ordinances. A River
Corridor Easement Program has also been established
to purchase river channel management rights (Figure
5-5). This prevents  land owners from dredging and
armoring  the channel and gives the easement holder
the right  to establish vegetated  buffers in the river
corridor.

The Town of Hinesburg, Vermont developed a stream
corridor plan for the LaPlatte River in 2007 to take
advantage of the stream geomorphic assessments that
had already been completed  and to develop river
corridor protection  projects. The plan  development
process began with outreach and education activities
including landowner contact through direct mailing
of informative letters followed up by telephone calls
to each landowner. Meetings  were scheduled with
each  landowner to discuss the planning process and
reach condition  details specific to each landowner's
parcel.  Presentations were also  given to  the  Select
Board,  Conservation  Commission, and  Planning
Commission at the beginning and end of the planning
process.
                             Continued on page 5-22
                                                                                                 5-21

-------
         The LaPlatte Watershed Partnership used the stream
         geomorphic   assessment   results   and  conducted
         a  stressor,  departure,  and  sensitivity analysis  to
         prioritize planning and  management strategies for
         each reach. They identified strategies such as properly
         sizing  stream crossings (i.e.,  bridges  and culverts)
         when  these  structures  are  up  for  replacements
         or  repairs,  implementation  of a Water  Resources
         Overlay  District  (which encompasses  the  FEH
zone),  planting  of stream buffers, and  restoration
of incised reaches. The Town of Hinesburg adopted
stream  buffers  and  setback  requirements  in  its
zoning regulations that prevent encroachment into
the stream  corridor,  protecting  property and  the
ecological integrity of the LaPlatte River.
           Figure 5-5 Map and orthophoto depicting the meander belt width-based river corridor being considered
           for protection in the Town of Cabot, Vermont to help restore water quality, aquatic habitat, and natural
           channel stability of the Winooski River. The belt width corridor is designed to accommodate the
           geomorphology and fluvial processes associated with the river's dynamic equilibrium condition (Mike
           Kline, Vermont Agency of Natural Resources, Personal Communication).
5-22

-------
Case   Study
 Michigan's  Natural Rivers  Program
 More Information: http://www.michiaan.aov/dnr/0,1607,7-153-30301 31431 31442-.00.html
 The State  of Michigan's Natural Rivers Act, passed
 in 1970, established The Natural Rivers Program as
 part of the Habitat Management Unit in the Fisheries
 Division  of  the  state's  Department  of  Natural
 Resources (DNR). Since the program's establishment,
 2,091  miles on 16 rivers have been designated as part
 of Michigan's  Natural Rivers  System.  The  system
 serves  to  preserve and enhance a variety of values
 each river provides for current and future generations,
 including:    aesthetics,    free-flowing   condition,
 recreation, boating, historic value, water conservation,
 floodplain, ecological, fisheries and other aquatic life,
 and wildlife habitat. In this way, the Program focuses
 on protecting natural river ecosystem conditions so
 that rivers can continue to provide ecosystem services
 to their local communities  for many years to come.

 In order  to be considered for designation  in  the
 program,   stakeholders  must   form  an  advisory
 group   to  develop a  comprehensive  management
 plan for a river. Management plans include  baseline
 data describing the  river's condition,  defined river
 segments  proposed for  designation,  and proposed
 standards for land development in the river's Natural
 River District, defined as the land area extending 400
 feet from  either side of the river's edge.  Standards
 typically include structural and septic system setbacks
 (100-200 feet from the water's edge), natural riparian
 buffers (25-100 feet from the water's edge), minimum
 lot size and frontage requirements (one acre with 100-
 200 feet of frontage), and prohibitions on filling or
 building in the 100-year floodplain or wetlands. The
 standards also restrict use of the Natural River District
 to residential development and limit timber harvest,
 oil  and gas  activity, bank stabilization  activities,
 intensive habitat management of fisheries and public
 lands,  and public  access. Because  the Natural River
District  applies to both public and private lands, a
river's designation  into Michigan's Natural  Rivers
System incorporates uniform standards across all land
ownerships  and multiple  jurisdictions,  resulting in
a seamlessly protected green infrastructure corridor
along the river's banks.

Once a river has been designated as part of the Natural
Rivers System, a permit process is  used to oversee
development in the Natural River District. Property
owners wishing to conduct activities in Natural River
Districts  apply  for  Natural  River  zoning permits
from the Program administrators for their districts.
Program staff conduct site inspections with applicants
and issue permits once  it  has been determined that
the applicant's activity  complies with development
standards.  The  Zoning Review Board,  a  seven-
member  board  consisting of representatives  from
each affected County and Township, NRCS, local
citizens,  and the DNR may grant variances in cases
where standards cannot be met.  Local governments
may become Natural Rivers Program administrators
on private  lands  in their  jurisdictions by adopting
Natural River zoning standards into  a county or town
ordinance. Natural Rivers Program staff support local
government program administrators by  reviewing
ordinance language  amendments,  commenting on
variance requests, and monitoring to ensure uniform
Program administration  within each river system. In
addition  to local governments,  watershed councils,
Resource Conservation and Development  programs,
the U.S. Forest Service, Trout  Unlimited chapters,
canoe livery owners, and the Michigan  Department
of Environmental Quality have also collaborated with
the DNR to contribute  to the success of Michigan's
Natural Rivers Program.
                                                                                                   5-23

-------
                                            Case   Study
                     Wyoming Wetlands Conservation Strategy
                     More Information: http://gf.state.wy.us/habitat/WetlandConservation/Wyoming%20
                     Wetlands%20Conservation%20Strateav%20September%207.%202010.pdf
       The Wyoming Joint  Ventures Steering  Committee
       has developed  a statewide wetlands conservation
       strategy to meet  seven goals: 1) delineate important
       wetland and riparian habitat areas and  assess their
       condition,  2)  identify  threats  to  the  functional
       integrity of wetlands and  riparian habitats, 3)  set
       state and regional conservation goals and priorities,
       4) develop  conservation  and management strategies
       for wetlands  and riparian habitats, 5)  promote
       partnerships among existing conservation initiatives,
       6) connect with non-conservation-based funding and
       planning resources, and  7) build technical support
       for the  wetland  component of the Wyoming State
       Wildlife Action Plan.  The Committee identified nine
       wetland complexes to be prioritized for conservation
       in the next 10-year planning  horizon. Six of these
       complexes were  selected for meeting two criteria:  1)
       a Shannon diversity rank no greater than  five, and 2)
       "high" project opportunity. The other three complexes
       were selected due to their ecological uniqueness and/
       or a high level of public interest. Data from a 1995
       Statewide   Comprehensive   Outdoor  Recreation
       Plan and an  assessment conducted  by The Nature
       Conservancy in 2010 support these selections.

       The  first step in implementing this conservation
       strategy is to build  the  state's capacity  to support
       wetlands conservation projects.  A pooled state agency
       and  non-governmental  organization  approach,   a
       state  wetlands  coordinator position, and/or  new
       funding sources  may be developed to provide needed
       technical resources that have been historically lacking
       to write grant proposals and plan, permit, and oversee
       projects.  Local and  regional wetlands and riparian
       habitat  conservation priorities  will   be identified
       in "step-down"  plans for the  following four areas:
       protection,  restoration,  creation and  enhancement,
       and recreation. Priority conservation projects for each
       of the four areas will be identified and made publicly
       known through a Wyoming Wetlands Web site.  In
       addition, the  "step-down" plans  will  be  used to set
       statewide objectives and priorities for the same four
areas. Protection priorities will focus on acquisitions
and conservation easements.

The state's highest conservation priority at this time
is to ensure "no  net loss" of existing  wetlands and
riparian habitats.  This  requires enforcing  existing
protections,  effective  mitigation  of  unavoidable
losses,  strategic use  of federal  financial incentives,
and negotiating land and water use rights to protect
high-risk areas. The committee  is  considering a
variety  of  approaches  to  foster land  and water
use  that is  protective of wetlands in the private
sphere. These approaches include: management and
stewardship  agreements,  property leases (including
water rights), managing  the timing of when water
rights  are  exercised,  temporary  water transfers,
rehabilitation and improvement of irrigation systems,
the  development of ground water wells to supply
constructed wetlands, and potentially  reintroducing
beaver populations. The establishment of minimum
stream flows that mimic natural hydrographs, removal
of barriers to stream connectivity, and discouraging
floodplain development are  other tactics that may
become a part of Wyoming's wetlands conservation
strategy. Lastly, the Committee also proposes that an
effort be made to incorporate wildlife habitat creation,
enhancement, maintenance or management into  the
state's legal  definition of beneficial uses of water to
expand the set of water sources that can potentially be
used to support wetlands.

Wyoming's     wetlands    conservation    strategy
incorporates several prioritization techniques that can
be similarly applied to prioritize healthy watersheds
for  protection. Wetlands identified  as conservation
priorities are likely to be found in healthy watersheds
that would  be identified as protection priorities. In
these  and other  ways,  wetlands  conservation  and
healthy watersheds  protection  strategies  can  be
developed synergistically to preserve the integrity of
healthy watersheds.
5-24

-------
Case    Stu
 Maryland's  GreenPrint  Program
 More Information: www.greenprint.maryland.gov

 The  State of Maryland has identified fragmentation
 and development of its natural and working lands as
 its biggest future conservation challenge. To address
 this  challenge,  Maryland's  Program  Open  Space
 developed a tool known as GreenPrint (Figure  5-6)
 to identify  the  state's  most  ecologically  valuable
 areas and track their conservation. The tool uses GIS
 data layers to identify  overlap between areas that are
 priorities for the  following  four  conservation  foci:
 green infrastructure, water quality  protection,  rare
                                               species habitat,  and  aquatic  biodiversity hotspots
                                               (Figure 5-7). Areas that are conservation priorities
                                               for several of these purposes are then  designated as
                                               targeted ecological areas (TEA). It is likely that there
                                               will be overlap between areas that should be protected
                                               as  healthy watersheds  and TEAs  because both are
                                               landscape-level approaches to protecting the integrity
                                               of freshwater systems.

                                                                              Continued on page 5-25
                                                                                           Unprotected Targeted
                                                                                           Ecological^feas
                                                                                           Lands Protected
                                                                                           from Development
                                                                                           Military Installations

                                                                                           Tributary Strategy
              GreenPrint
           Taraeted Ecoloaical Areas
     ; and watersheds of high ecological value that have
     identified as conservation priorities by the Maryland
          Department of Natural Resources.
                                                                                       Click on any county to gel
                                                                                        that county's statistics.
       How many acres have been identified as
        Targeted Ecological Areas, and how
            much is protected?
                        Since 2007, which state conservation
                        programs are protecting the Targeted
                             Ecological Areas?
                               2007-2010 Land Conservation in and
                                Out of Targeted Ecological Areas
Protected and Unprotected Targeted
     Ecological Areas
              in Ft,
              I I Unprotected
                Other
 I Program Open Space
| Rural Legacy
 I Maryland Environmental Trust Easements      Martin O'Malley
| Maryland ^rioultural Land Preservation Foundation    Governor
                         Anthony G. Browi
                           Lt. Governor
                                                                            0  5 10
                                                                                    20
                                                                                    1 Miles
                                                                                          r*

                                                                                        v-dfc-l
   Figure 5-6 Maryland's GreenPrint map of targeted ecological areas (Maryland Department of Natural
   Resources, 2011).
                                                                                                          5-25

-------
                 Green Infrastructure
                                                                                    Rare Species Habitats
                                                                /
               Water Quality Protection
                                                                                    Aquatic Life Hotspots
                                                  Targeted Ecological Areas

                                                       .
                                                       rtmrca*ie. .*
          Figure 5-7 Identification of targeted ecological areas (Maryland Department of Natural Resources, 2011).
        Maryland's Board of Public Works uses an ecological
        ranking protocol to measure how conservation projects
        contribute  to  the protection of TEAs.  The protocol
        requires that each conservation project be evaluated
        using  a  standard  scorecard.   The  scorecard  asks
        project managers to address the four aforementioned
        conservation priority areas used by GreenPrint in both
        a landscape score and a parcel ecological characteristic
        score.  Other  components  that contribute  to  the
        project's  final  score  include  recreational  or  cultural
        value,  restoration  value,  consistency  with  local
        land use, and provisions  for future management of
the land.  The Board of Public Works also  uses the
scorecards to track how many projects are located in
GreenPrint TEAs  as a key performance measure for
Program Open  Space.  The  goal  of the  GreenPrint
Program is  to channel  conservation  resources into
protecting TEAs, thus supporting  both the green and
blue infrastructure needed  to  maintain  a  complete
ecological network across the state.
5-26

-------
Case   Study
 Enabling Source Water Protection  in Maine
 More Information: http://www.landuseandwater.org/index.htm
 Maine's landscape is home to an abundance of lakes,
 ponds, and rivers. Many of these surface waters, and
 associated ground waters, serve as sources of drinking
 water for local residents. Unlike most states, utilities
 in Maine  are  often  able  to provide only minimal
 treatment to their source  waters before distribution
 to customers. This is due to the high quality of these
 source waters in their natural condition.  Although
 Maine has  already taken  a number of measures to
 ensure that its  aquifers and surface sources continue
 to provide clean drinking  water into the future, the
 state decided  to participate in the Enabling Source
 Water Protection initiative, an EPA-funded project to
 integrate state land and water programs. The project
 is  a  partnership among the Trust for Public Land,
 the Smart  Growth Leadership  Institute,  the River
 Network, and the Association of State Drinking Water
 Administrators. The Enabling Source Water Protection
 project assesses state programs to recommend the best
 opportunities for program alignment that will support
 local communities in their  source protection efforts.

 Working  with  a  diverse  group  of  state agency
 representatives,  public  water   systems,  non-profit
 organizations, and other interested stakeholders, the
 national project team identified key opportunities for
 improved collaboration in  the areas of smart growth,
 conservation,   and  water  quality. After  soliciting
 stakeholder input  and  feedback  on the  identified
 opportunities,  the  project  team  identified  successful
 implementation efforts from other states and created
 a draft action plan for Maine. Using an online survey,
 stakeholders were  asked  to read  the document to
 further refine  and prioritize action items. Those
 steps rated  as low  impact, high  investment and low
 chance of success were eliminated from consideration.
Developing a  dedicated statewide funding source
for  drinking water source protection  was identified
as the action  that would  have  the highest positive
impact,  but that would require long-term planning
and implementation. The final action plan focuses on
those action steps where the majority of respondents
rated  them as: having high  impact  on drinking
water  source protection; requiring low-to-moderate
investment  of public resources;  demanding  high
urgency  for  implementation;  having  a short-to-
medium  time  frame  for implementation; having a
moderate-to-high chance for implementation; and
requiring low-to-moderate (primarily administrative)
effort to implement.

In-depth analysis of existing programs and listening
sessions  with  representatives  from across the  state
revealed that three key short-term actions can  assist
with better synergy between land use  and drinking
water  source  protection:  1)  Employing the  State
of Maine's Quality of Place Investment  Strategy to
strengthen drinking water source protection,  using
the state's ability to direct  funding for infrastructure
and  economic  development.  2)  Continuing  a
phased  investment in  on-line mapping resources
and information sharing to provide critical  data to
local governments and developers so they can  make
more  informed land-use  decisions. 3) Developing
guidelines for compatible  recreational  opportunities
in and around sensitive protection areas to provide
greater access to conservation funding and a broader
constituency to preserve lands and waters important
for drinking water. Maine's Drinking Water Program
has initiated implementation  efforts in all of  these
areas.
                                                                                                   5-27

-------
Identifying and Protecting Healthy Watersheds
        5.2.3  Local

        Land Protection

        Land trusts are typically non-profit entities that coordinate the acquisition of land, or easements  that limit
        development  on land, for the purpose of protecting open space and conserving natural resources.  Land can
        be donated, sold at a discount, or sold at market price to local, state, or federal government, or to land trusts
        that will typically then serve as the stewards of that land or entrust stewardship to a local or state government
        agency. A conservation easement is a tool that allows the landowner to  maintain ownership of the land while
        entering into  a legal arrangement to limit the  uses of the land. For example, a farmer may own a large tract of
        land that can be sold on the private market and be developed, or they can work with a land trust to place an
        easement on the property whereby the land is permitted to remain in agricultural use or to remain idle but is
        not permitted to be developed. Organizations such as The Trust for Public Land, American Farmland Trust,
        and The Land Trust Alliance can provide information and assistance  on land protection issues. Conservation
        easements and other types of development restrictions can be pursued by state and local governments as well.
        Many states provide income or other tax credits to landowners who donate land or easements for conservation
        purposes. This can be a useful mechanism for increasing voluntary participation in conservation.
        Green  infrastructure  assessments,  such as
        those described in Chapter 3, are increasingly
        being used as an overarching  conservation
        framework in the comprehensive planning
        process  of  municipalities  and  counties.
        Some maintain their  approach within the
        strict  definition  of  green  infrastructure,
        while others have expanded their programs
        to   consider "working  lands"  such  as
        agricultural  areas,   historic  lands,   and
        cultural  resources.   Identification  of  a
        community's green  infrastructure  is  the
        first step in preserving it. The  community's
        zoning and comprehensive plan  (or master
        plan)  can  then  be  revised  to  plan for
        growth  around  the  green infrastructure
        (see sidebar). Chapter 3 contains additional
        examples of green infrastructure assessments
        and the role that they play in local land use
        planning.
     The Central Texas Greenprint for Growth:
     A Regional Action Plan for Conservation
         and Economic Opportunity, Texas
   http://envisioncentraltexas.ora/resources/GreenprintMkt.pdf
,
n
1998 after years  ot advocacy surrounding  watershed  protection
and parks. The most sensitive third of the region's land drains
into the Edwards  Aquifer in Texas. This area was designated as a
"Drinking Water Protection Zone" by the city's residents, and the
remaining two thirds were designated  a "Desired Development
Zone." Since then, Travis County and surrounding counties that are
part of the Austin metropolitan area have been growing quickly.
The Greenprint that the  Trust for Public Land, the Capitol  Area
Council  of Governments, and Envision  Central Texas  developed
in  partnership with Travis,  Hays, Bastrop,  and Caldwell County
residents suggests directing  development  towards  areas  with
existing  infrastructure and away from the sensitive lands draining
to  the  aquifers.   The Greenprint's  opportunity  maps identify
lands  that are most  important for regional water quality and
quantity protection for each of the counties. It includes maps for
conservation lands to  achieve other goals that residents identified
as  well.  Travis County, Hays County, and  City of Austin voters
have repeatedly  approved  tax  increases to  purchase  land and
development rights in order to protect critical lands in the region.
        The Protected Areas Database of the United
        States partnership  is creating a  national
        inventory of all public and private protected
        lands. The  draft data layer is available for download and online viewing and can be used to identify lands
        already in conservation easements  or some other kind  of protection status  (Protected Areas Database of the
        United States  Partnership, 2009). This resource can  be  helpful in further  prioritizing adjacent lands for
        protection or restoration.

        Land Protection and Climate Change

        Land protection and stewardship are critical components of protecting healthy watersheds. They are especially
        important in a changing climate.  EPA recently evaluated the decision-making strategies of land protection
        programs across the  country in the context of climate  change impacts.  Programs that focus on wildlife and
        watersheds were chosen for the evaluation due to the impacts that climate change is expected to have on these
        elements. The authors used the Trust for Public Land's LandVote database (2009), which compiles information
5-28

-------
                                                                                         5 Management Approaches
on land protection activities across the nation,  to analyze these management trends. The large majority of
land protection programs evaluated did not consider climate change in their decision making process (U.S.
Environmental Protection Agency, 2009b). However, the report identified strategies that might be useful for
land protection programs on how to  consider climate change in future transactions. These include  decision
support tools for advisory committees, promulgation of different land protection models (e.g., purchase, as
opposed to transfer, of development rights), and educational outreach for elected officials (U.S. Environmental
Protection Agency, 2009b).  Land protection strategies should consider both the mitigation potential of the
land through carbon sequestration and the adaptation potential of the  land for protecting water resources
and  wildlife  migration routes, as well as the potential to buffer infrastructure from storm events (U.S.
Environmental Protection Agency, 2009b).

Carbon markets are an emerging approach for mitigation of climate change and conservation of forested lands,
and may play an important role in land protection strategies in the coming years. Deforestation is responsible
for 20%  of all carbon emissions worldwide. Since forests  sequester large amounts of carbon,  protection of
these lands is a critical element in addressing climate change. Carbon markets provide a mechanism whereby
an emitter of carbon dioxide can purchase carbon credits from  sellers to offset their own emissions  below a
"cap," usually determined by a government or international body. The sellers must be emitting less than the
cap to have any credits to sell. Credits can also be determined through the use of a baseline, as opposed to a
government imposed cap. By helping to prevent deforestation, land protection can generate credits based on
the amount of carbon emissions avoided.

As the effects of climate change increasingly manifest themselves, adaptation strategies will become more and
more important. A certain amount of climate change will occur regardless of the actions taken to reduce future
greenhouse gas emissions.  Consequently, adaptation strategies  are an important component  to addressing
climate change. An important  component of these strategies can be  to protect  the remaining  natural areas.
Wetlands  and headwater streams, for example, regulate the downstream flow of water, retaining water in wet
conditions and releasing it in dry conditions. They thereby serve as important components  for protection
against both floods and droughts. Riparian vegetation protects  streams from the  effects of increased runoff
expected in many parts of the country due to increased intensity and frequency of extreme storm events. Also,
vegetated  riparian areas provide habitat and corridors for migration.
Land Use Planning

From  a big  picture  perspective,  protecting
healthy watersheds has a lot to do with land use,
sprawl, and development. River banks are often
armored to  "protect"  riparian development,
but this  practice typically  exacerbates erosion
downstream.  Increased  impervious  surfaces
associated  with  development  often increase
runoff volumes and  the build-up  and wash-
off of pollutants into surface  waters. Wildlife
habitat  and   valuable  plant   communities
are lost when  natural land cover is  removed
to  make  way  for new  development.  The
natural disturbance regime is  disrupted when
the natural  fire regime is suppressed, large
withdrawals are made from rivers  or ground
water,  or  dams  are  constructed to  generate
electricity to satisfy the ever increasing demands
of residential and industrial growth.
        Green Infrastructure and Master
          Plans Alachua County, Florida
              (Alachua County, 2008)
Alachua County, Florida updated their master plan in 2005 to
include specific policies that require or  incentivize protection
of wetlands, surface waters, floodplains,  listed species habitat,
significant geologic  features,  and the  highest  category  of
protection, "strategic ecosystems." Strategic  ecosystems  are
specific mapped areas in Alachua County that are the 47 most
significant natural communities, both  upland and  wetland,
remaining in  private  ownership.  Minimum  conservation
standards for this green infrastructure include protection of all
wetlands and surface waters, protection  of at least 50 percent
of all upland  within the strategic ecosystems, conservation
easements, management plans, and environmentally friendly
designs. Development rights are preserved through increased
allowable densities  on buildable  areas  or by transfer  of
development rights to other properties.
                                                                                                          5-29

-------
Identifying and Protecting Healthy Watersheds
        One of the greatest contributions to protecting healthy watersheds may come from ecologically-based land
        use planning. Land use regulation is primarily a local authority, with the state responsible for establishing the
        laws and regulations that enable local land use planning. These laws vary considerably from state to state, but
        generally provide guidance to localities (sometimes  mandatory, sometimes voluntary) in the development of
        comprehensive plans (sometimes referred to as master plans). Some state land  use planning laws require that
        natural resources are taken into account in comprehensive plans (Environmental Law Institute; Defenders of
        Wildlife, 2003). Others require provisions for protection of open space  or require consideration of wildlife
        habitat  (Environmental Law Institute;  Defenders  of Wildlife,  2003).  Some states may not  require these
        issues to be considered in the development of comprehensive plans, but may suggest it. Some state land use
        planning laws require  the state to develop a statewide land use plan or policy  (Environmental Law Institute;
        Defenders of Wildlife, 2003). Other states are authorized to provide support or assistance in the development
        or implementation of local land use plans (Environmental Law Institute; Defenders of Wildlife, 2003).

        In an evaluation of the role of conservation in land use planning, the Environmental Law Institute  (2007a)
        made six general recommendations for how to advance conservation planning:

            1.  Develop communications tools that convey the value of ecological knowledge and
                conservation planning to  decision makers.
            2.  Develop requirements and incentives for proactive conservation planning.
            3.  Measure  the   effectiveness of conservation planning  and  implement adaptive
                management where needed.
            4.  Find ways to overcome the disconnect between the different scales at which land use
                planning and conservation are carried out.
            5.  Define specific conservation thresholds  (e.g., minimum riparian buffer width) based
                on the best available science.
            6.  Provide a technical support infrastructure and interdisciplinary training for planners
                and conservation scientists.

        Smart Growth  is a land  use planning concept  that can  contribute significantly towards  protecting healthy
        watersheds. Smart Growth refers to a land use strategy to prevent sprawl and create communities with diverse
        transportation,  employment, and housing options. It focuses  on minimizing the development of  natural
        and rural areas  by directing growth within cities through rehabilitation and reuse of existing infrastructure,
        improving public transit  and bicycling or walking options, and making urban environments more desirable
        places to live. The Smart Growth Network (2009) identifies 10 principles of smart growth:

            1.  Create a range of housing opportunities and choices.
            2.  Create walkable neighborhoods.
            3.  Encourage community and stakeholder collaboration.
            4.  Foster distinctive, attractive communities with a strong sense of place.
            5.  Make development decisions predictable, fair, and cost effective.
            6.  Mix land uses.
            7-  Preserve open space, farmland, natural beauty, and critical environmental areas.
            8.  Provide a variety of transportation choices.
            9.  Strengthen and direct development towards existing communities.
            10.  Take advantage of compact building design.

        These principles have been adopted by numerous states in their own smart growth programs intended  to assist
        communities in developing local strategies to prevent sprawl and minimize the loss of remaining natural areas.
        Transportation and land use are two closely related issues. Traditional zoning practices encourage separation of
        land uses, requiring motorized transport for people  to travel to work, go grocery shopping, etc.  Public transit
5-30

-------
                                                                                         5 Management Approaches
options have virtually disappeared in all but the largest cities, leaving people with no choice but to purchase
automobiles, exacerbating the problem even further.
By encouraging mixed land uses, increasing public
transit and bicycling/walking options, and directing
development  towards  existing  communities,  the
pressures  that  create sprawl can be  reduced,  and
       of our  remaining  natural  places  can  be

                                                            Watershed-Based Zoning in
                                                            James City County, Virginia
                                                      http://www.jccegov.com/environmental/index.html

more
preserved.
Higher density  development  has  recently  been
recognized as  a strategy  that  can  help  prevent
the  spread  of  impervious  surfaces,  landscape
fragmentation, and  overall ecological degradation
(U.S.  Environmental Protection Agency,  2006b).
Although  high  density  development may  have
higher  proportions  of impervious  surfaces  per
acre,  it can  actually reduce the total amount of
impervious  surfaces  in  the  watershed.  This  is
partly because high  density development decreases
need  for  roads  and parking  lots.  High density
development is compatible with the 10 principles of
Smart Growth.
                                                   the  rapid development experienced in the previous two
                                                   decades,  the  county  decided  to  pursue a  watershed-
                                                   based zoning approach to protect its high quality streams
                                                   from future development impacts. An impervious cover
                                                   and  instream/riparian  habitat assessment  categorized
                                                   each of the county's subwatersheds as Excellent,  Good,
                                                   Fair, or Poor. Using a combination of innovative land use
                                                   planning  techniques, including transfer of development
                                                   rights, conservation development, rezoning, and resource
                                                   protection overlay districts, the county has directed growth
                                                   away from its most sensitive and ecologically valuable
                                                   subwatershed  and developed  strategies to  minimize
                                                   further  impacts   in  those  degraded  subwatersheds
                                                   designated  for  growth.  Each subwatershed was  also
                                                   targeted  for other specific management measures to
                                                   either conserve,  protect, or restore streams according to
                                                   the level of threat imposed on each.
Conservation  Development  (sometimes referred to as cluster  design) is a zoning  strategy that  decreases
residential  lot sizes  and clusters the  developed areas  together, protecting  the  remaining  areas as shared
open space. This prevents large lot development,  which has contributed to suburban sprawl and habitat
fragmentation. By clustering development together, whether in  rural cluster designs,  or by taking advantage
of infill development of cities, sprawl, and excessive spread of  impervious surfaces are reduced. Additional
information on conservation development can be found  in Arendt (1999).

Watershed-based zoning is a land use planning strategy  based  on the boundaries of small watersheds.  By
directing future  development towards  watersheds where it will  have the  least negative  impact, this strategy
can protect watersheds with high ecological integrity. This strategy involves significant collaboration between
adjacent municipalities, as watershed boundaries rarely coincide with political boundaries. A watershed-based
zoning approach should include the following nine steps (Schueler, 2000):

    1.  Conduct a comprehensive stream inventory.
    2.  Measure current levels of impervious cover.
    3.  Verify impervious cover/stream quality relationships.
    4.  Project future levels of impervious cover.
    5.  Classify  subwatersheds based on  stream  management "templates"  and current
        impervious cover.
    6.  Modify  master  plans/zoning   to  correspond   to  subwatershed  impervious  cover
        targets and  other management strategies identified  in  Subwatershed Management
        Templates.
    7-  Incorporate  management priorities from larger watershed management units such as
        river basins or larger watersheds.
    8.  Adopt specific watershed protection strategies for each subwatershed.
    9-  Conduct long-term monitoring over a prescribed cycle to assess watershed status.
                                                                                                          5-31

-------
Identifying and Protecting Healthy Watersheds
        Revision of zoning regulations and/or the use of transfer of development rights  are usually necessary in
        implementing watershed based zoning. Transfer of development rights is a technique that allows a land owner
        in an area designated as a priority for protection by local government to sell their development rights to another
        land owner in an area designated for higher density development.

        In addition to  zoning strategies, counties and municipalities have  the ability to create a variety  of other
        ordinances  that can serve to protect valuable natural resources. The Center for Watershed Protection (2008a)
        and EPA (2006a) both have web sites with model ordinances available  for communities to use in developing
        their own local ordinances to protect natural resources and ecologically valuable areas. These include ordinances
        to protect aquatic buffers, open space, wetlands, etc.

        Low Impact Development (LID) is a stormwater management approach that focuses on managing runoff at the
        source through  the use of design practices that allow for infiltration,  storage, and  evaporation. Rain gardens,
        pervious pavements, tree box planters, green roofs, and  disconnected  downspouts  are all examples of LID
        practices. These practices  have been shown to be less expensive and more environmentally friendly than more
        traditional  stormwater management  practices, such as conveyance systems (U.S.  Environmental  Protection
        Agency, 2007b). LID practices help  to reduce stormwater runoff from urban areas, which can improve water
        quality,  ground water recharge, and  the biological condition of stream habitats. However,  the potential for
        ground water contamination must also be considered, especially in areas with contaminated soils.

        River Corridor and Headwaters Protection

        As discussed in Chapter 2, natural river corridors are important
        for  maintaining dynamic  equilibrium of the river  channel,
        providing valuable wildlife habitat, and regulating floodwaters.
        When  designing river corridor protection  strategies,  it is
        important to remember that river channels can migrate laterally
        over time. When possible,  the entire river corridor should be
        protected from development through the use  of fluvial erosion
        hazard  area districts, river corridor easements, and other  local
        programs (Kline  & Dolan, 2009).  The  State of Vermont is
        in the  process  of implementing a statewide river corridor
        protection program. Using the results of their statewide stream
        geomorphic assessments  (Chapter 3), state  staff  are working
        with local  stakeholders to  identify  river  corridor protection
        options  such as easements  and  zoning overlay districts. These
        strategies are designed to protect the dynamic nature of the
        riparian area. Simple riparian buffer protection ordinances and
        overlay districts are certainly  beneficial for water quality and
        wildlife, yet they often fail to  address all  of the  requirements
        of the riverine system as it meanders over time and experiences
        flood events. River corridor protection benefits not only water
        quality and wildlife, but  also  public safety (Kline & Cahoon,
        2010).

        As described in the River Continuum Concept  (Vannote, Minshall, Cummins, Sedell, & Gushing,  1980),
        headwater streams contain  unique assemblages of organisms  that begin the processing of coarse particulate
        organic  matter, providing  the  energy required  by other assemblages of organisms downstream.  Healthy
        headwater stream areas provide valuable wildlife  habitat and corridors for migration of wildlife. They  also
        provide  sediment, nutrient, and flood control in  much the same way  that wetlands do.  Headwater streams
        also help to maintain base  flow in larger rivers downstream.  Fundamental to  a healthy watershed,  properly
        functioning headwater streams are one of the primary determinants  of downstream flow, water quality,  and
        biological communities. Protection  of these areas through land use  planning  and protection is  particularly
        important.
5-32

-------
Headwaters: A Collaborative Conservation
Plan for  the  Town  of Sanford,  Maine
More Information: http://swim.wellsreserve.org/results.php?article=828Conservation%20
Strategy%20September%207.%202010.pdf
The  Town  of Sanford, Maine is  located  at  the
headwaters  of five critically important watersheds
in southern Maine and New  Hampshire.  Using
community  input  and  science-based  conservation
principles  to  implement  the  conservation  goals
of its comprehensive plan,  the  town is  protecting
these  regional  resources. Over the  course of three
stakeholder workshops, and using innovative GIS and
keypad polling techniques, the community developed
the following core conservation values:

    •   Water quality protection.
    •   Conserving    productive   land   for
       agriculture.
    •   Conserving  significant wildlife  habitat
       and biodiversity.
    •   Protecting  human  health  and  safety
       through  conservation  of  floodplains,
       water supply buffers and wetlands.
    •   Conserving    scenic,    cultural    and
       recreational resources.
The  community recognizes that these values  are
provided  by Sanford's  green infrastructure. Using a
GIS software program called Community Viz  (www.
communityviz.com). the  community mapped  the
green infrastructure that is important for protecting
each  of  these  values  (Figure  5-8).  Once this
community-based assessment phase  was completed,
the town developed recommendations and strategies
for protecting  each of the five conservation values.
One of these strategies was to identify "focus  areas"
by considering the relative importance placed on each
conservation value by community members. Keypad
polling techniques,  which  use  electronic  keypads
(similar to television remote controls) to allow large
numbers of community members to place their vote
on which conservation values are most important to
them, were critical for ensuring participatory decision-
making without slowing down the process. The focus
areas were identified from the polling results, which
are automatically tallied by a computer and displayed
through a projector. These high-priority conservation
sites were evaluated for the amount of protected land
that they currently contain  and the  specific threats
posed to each focus area by human activities. These
focus areas are considered the priorities for action.

Outside of  the  focus  areas, there  are  additional
locations that  contain one or more  of  the  five
conservation values.  These   areas  were prioritized
for protection  based on a  ranking of land parcels
according  to their  relative  value. For  example,  a
parcel containing both exemplary wildlife habitat and
water  resources  would receive a higher  priority for
protection than a parcel that only contains wildlife
habitat.

The following strategies were identified as options to
implement the Sanford conservation plan:

   •    Fee simple purchase.
   •    Conservation easements.
   •    Conservation subdivisions.
   •    Current use program.
   •    Land use ordinances.
   •    Community education and outreach.
Responsibilities for implementation of the plan were
assigned to  each participating  stakeholder group,
funding sources were  identified, and a monitoring
and evaluation process was  put in place to ensure
effectiveness  of the plan.

                              Continued on page 5-34
                                                                                                   5-33

-------
                                  Conservation Resources:  Water
               Shapleigh
                                              Town of Sanford, Maine
             Legend
             j^l Water Supply Parcels
              |f National Wetlands Inventory
             Stream Buffers
                50-100 ft
             ^| 0 - 50 ft
                Highly erodible land
             Aquifers
              | 10 - 50 gpm
              | > 50 gpm
         Figure 5-8 Green infrastructure identified for water quality protection (Wells National Estuarine Research
         Reserve; Southern Maine Regional Planning Commission, 2009)
5-34

-------
Case    Stud
 Lower Meramec  Drinking  Water  Source
 Protection  Project
 More Information: http://cloud.tpl.ora/pubs/landwater-lowermer-swp-brochure.pdf
 The U.S. Forest Service and the Trust for Public Land
 (TPL) initiated the Lower Meramec Drinking Water
 Source Protection Project to expand the reach of forest
 protection projects  in drinking supply watersheds
 in the northeastern United States to the Midwest
 region. The Meramec River is a drinking water source
 for the City of St. Louis, Missouri and its suburbs.
 Although the  river's water is currently high-quality,
 the  watershed is highly susceptible to degradation
 due to development pressures.  Preserving the natural
 land that drains into  drinking water supplies is an
 ecosystem-level strategy for protecting water quality.
 In addition to providing drinking water, the Meramec
 River provides  wildlife  habitat and recreational
 opportunities.

 The Meramec  River Tributary Alliance, a partnership
 of more than 30 organizations interested in protecting
 the river, provided local knowledge over the course of
 the project. In the first phase of the project, the U.S.
 Forest Service, TPL, and the Meramec River Tributary
 Alliance refined the project area to focus on the Fox-
 Hamilton-Brush Creek watersheds.  GIS data  layers
 were used to score 30  meter landscape cells for their
 physical characteristics, such as  proximity to  water
 features, and current land use.  Raw scores were used
 to produce a conservation priority index map (Figure
 5-9)  and a restoration  priority index map.  Local
 units of government and real estate experts use these
 maps to identify opportunities for land protection,
 restoration, and  implementation  of stormwater
 best  management practices.  The  project steering
committee also developed a brochure describing the
project for local governments, water suppliers, and
conservation groups to use and distribute.

The project's second phase, referred to as the strategy
exchange, took place  over the  course of five days.
The strategy exchange was a discussion of drinking
water source education, stormwater best management
practices, septic  system  improvements,  and  land
conservation with state and local governments, as well
as other local actors. As an outcome of the exchange,
regional and national experts  contributed  strategy
recommendations to  a report addressing these four
topics.

In the project's third and final phase, subcommittees
of the Meramec River Tributary Alliance incorporated
the  exchange  team's  recommendations for  each  of
the  four topics into action plans for immediate
implementation that included  both voluntary and
regulatory or  enforcement tactics. Although  low-
budget tactics were identified, some tactics will require
additional funding  for implementation.  The  land
conservation subcommittee has started  to implement
recommendations from TPL's conservation finance
team to attract and retain funding for land acquisition.
Successful implementation of the action plans will
protect the ecological integrity of the Lower Meramec
so that it can provide not only clean drinking water,
but  also  all of the diverse services Meramec  River
Tributary Alliance member groups have individually
set out to protect.

                             Continued on page 5-36
                                                                                                 5-35

-------
        Lower Meramec Drinking Water Source Protection Project
                   Conservation Priority Index (CPI) Areas
              3 = Deciduous Forest, Evergreen
              Forest, Deciduous
              Woody/Herbaceous, Wood-
              Dominated Wetland, Herbaceous-
              Dominated Wetland
                                    May 5, 2009
                                                               Scotsdale
                 o
Legend
CPI 90th percentile
!• 13-21
CPI 70th percentile
• 12-21
collaboration with UMASS, USFS, and TPL

Protected Land
I 	 I Meramec River
^jCity Boundary
— i County Boundary
— Rivers and Streams

= Interstate
= Highway
	 Local Road
A
        Figure 5-9 Map of Lower Meramec Drinking Water Source Protection Project Conservation Priority Index
        Areas (Trust for Public Land, 2010).
5-36

-------
Cecil  County, Maryland Green Infrastructure
Plan
More Information: http://www.conservationfund.org/sites/default/files/
CecilCountv01.22.08.pdf
The  Conservation  Fund  is a national  organization
that  partners with  local communities to help them
fulfill their  conservation priorities. In  2007, The
Conservation Fund partnered with Cecil County,
Maryland to develop a green infrastructure plan. This
plan includes a green infrastructure network design,
water quality maintenance and enhancement analysis,
ecosystem services  assessment, and implementation
quilt  analysis.  As described  in Chapter 3, a  green
infrastructure   assessment   identifies   a  network
of lands,  composed  of  ecological core  areas and
corridors connecting  these hubs. The water quality
and  ecosystem  service  assessments  demonstrate the
importance  of protecting the green infrastructure
network. For  example, 81% of the value of the
county's  ecosystem services  ($1.7  billion/year) are
contained within the network. The implementation
quilt  analysis outlines  a comprehensive  approach to
protection  of Cecil  County's green infrastructure
network. Specific protection strategies were identified
to address the county's tremendous growth rate and
land use change and  the fact that only 23% of the
network is in some form of protected status.

Based on the assessment, a number of strategies for
protecting  water quality were identified. Sixteen
Conservation Focus Watersheds were identified where
existing land cover is  greater than 50% forest and
wetland (Figure 5-10). Natural  land cover in these
priority watersheds could  be maintained through
comprehensive  plan objectives, performance zoning
standards, and other land use planning programs. Ten
Reforestation Focus watersheds were also identified.
These watersheds have between 30-40% forest and
wetland cover and thus have high ecological capacity
for recovery.  Agricultural BMPs  such as riparian
fencing, nutrient management, reduced phosphorus
in animal feed,  and conservation tillage  were also
identified  as  management measures for improving
water  quality. A  comprehensive  zoning  program
using performance standards for site plan review was
recommended for improving development site design.
The performance zoning code would reward projects
using LID techniques.

In addition  to the management  strategies already
identified, the implementation quilt analysis identified
additional opportunities for protection. These include
use of  Program Open Space funds for acquisition of
high priority  properties in  the green infrastructure
network;  purchase   of  conservation   easements
through  the  Rural Legacy Program;  participation
in  the Maryland  Agricultural Land  Preservation
Foundation's   Agricultural   Preservation  District
program; donation of conservation easements through
the Maryland Environmental Trust program, which
provides tax credits and other  incentives to donors
of easements;  and a number  of federal programs.
The County also recently implemented a Transfer of
Development Rights and Purchase  of Development
Rights   program  to  protect  ecologically  valuable
lands from development.  The Conservation  Fund
specifically recommended that Cecil County enhance
its cluster development  option and  create a Green
Infrastructure Network  Overlay  with performance
standards in its zoning. The County is now using the
Green Infrastructure Plan as an advisory document in
its comprehensive planning process.

                             Continued on page 5-38
                                                                                                     5-37

-------
                             WESTERN
                             GATEWAY
                          Aberdeen Proving Ground
                A
               Cecil County Green Infrastructure Plan
                 December 2007 - The Conservation Fund

                       Conserved and Managed Lands
                          | Fed, DNR. Forest Legacy, MET/Co Parks, ESLC. Subdivision OS
                       Agricultural Easements
                          , MALPF, MET, PDR, Rural Legacy
                       Updated Green Infrastructure Network
                          • Hubs and Corridors
                                                                                                    1.200.000
Cecil County Watershed Boundaries
|    | 14-DigilHUCs
Reforestation Focus Watersheds (10)
  ^] 30-40% Forest/Wetland, <7% Impervious
Conservation Focus Watersheds (16)
   ~~| >AO% Forest/Wetland, <7% Impervious
              Figure 5-10 Map of Cecil County Green Infrastructure Plan (Will Allen, The Conservation Fund,
              Personal Communication).
5-38

-------
                                                                                          5 Management Approaches
5.2.4  Other Protection

Sustainable Agriculture

Agriculture   is   an   important
economic  and  cultural  activity
in  many  communities   across
the  United  States.  Similar  to
residential  development,  careful
management    of    agricultural
areas can ensure that the  aquatic
ecosystem   is    not   degraded
and  that  terrestrial  habitat  is
maintained.  Designing a green
infrastructure   network   is  one
method of identifying the most
critical  lands  to  protect  from
conversion to agriculture and can
also  include  certain  appropriate
agricultural   lands   as  cultural
protection priorities.  The  USDA
National    Organic   Program
develops    and     implements
standards for organic agricultural
products in the United States. Organic agriculture avoids the use of synthetic pesticides and fertilizers, both of
which impact water quality. It also reduces erosion and sequesters carbon dioxide in the soil. Individual growers
and producers can contact accredited certifying agents in their states  to become certified (U.S. Department of
Agriculture, 2009). Participation in certification programs can help to ensure that agricultural activities are
conducted in an ecologically sensitive manner.

Sustainable agricultural management practices include nutrient management,  which refers to the application
of fertilizers in appropriate amounts and at appropriate times; conservation tillage or continuous no-till; cover
crops to reduce erosion and keep nutrients in the field; and vegetative  buffers, which protect aquatic ecosystems
from agricultural runoff and provide wildlife habitat. The Conservation Effects Assessment Project is a multi-
agency effort to evaluate and quantify the effects  of these and other agricultural conservation techniques on the
environment. The USDA leads this effort, which focuses on watersheds, wetlands, and wildlife. The USDA
also leads the Environmental Quality Incentives Program, Conservation Reserve Program, Wetlands Reserve
Program, Wildlife  Habitat Incentives  Program, Conservation  Security  Program, and  Grassland  Reserve
Program, all of which are described  under Section 5-3-

Sustainable Forestry

Forestry is an important economic  and cultural activity in many parts of the  country. Organizations such as
the Forest Stewardship Council provide certification of sustainable forestry practices in the United States and
abroad. The Sustainable Forestry Initiative is an independent organization, originally developed as a program
of the American Forest and  Paper Association, which works to improve sustainable forest  management
practices through third-party certification audits. The principles of the Sustainable Forestry Initiative include
requirements for sustainable forestry practices, long-term forest health and productivity, prompt reforestation,
protection  of water  quality  and  the  promotion  of sustainable  forestry on private  nonindustrial  lands
(Barneycastle, 2001).
                                                                                                          5-39

-------
Identifying and Protecting Healthy Watersheds
        Invasive Species Control

        When a non-native species is introduced into an ecosystem, it can cause a tremendous amount of damage
        to native species. This is because the native species evolved over hundreds of thousands of years to compete
        with the unique combination of other species native to its ecosystem. When a non-native species is suddenly
        introduced (i.e., through human  intervention), the native species do  not  have time to evolve strategies to
        compete. Additionally, if ecosystems are degraded, it is easier for non-native species to take hold. Many such
        introductions  do not  cause  significant harm.  However,  a number of introduced  species become invasive,
        which means  that they  are directly harming or outcompeting native  species.  Invasive species  can decrease
        biodiversity and ecosystem resilience. Many of these species, such as Salt Cedar, replace native vegetation and
        form monocultures (stands of only one tree species). Salt Cedar specifically replaces  native riparian vegetation
        such as willows and cottonwoods and also uses a tremendous amount of water.  It uses so much water  in fact,
        that it can lower ground water levels to such a  degree that instream flows are affected and native vegetation is
        unable to reach the subsurface water for its own nourishment. The best strategy for controlling invasive species
        is prevention.  Education campaigns  about invasive species are key to prevention.  Even simple signs at public
        boat landings can help. Once an invasive species becomes established, it is difficult to eradicate. Early detection
        and action  is critical. Chemical, mechanical, and biological control techniques exist  for eradication. The most
        extreme cases  may require restoration actions,  such  as  controlled burning to remove the non-native species,
        followed by reintroduction of the native species.

        Ground Water Protection

        Any approach to healthy watershed management should incorporate ground water in addition to surface water
        components. In the case of ground water dependent ecosystems (GDE), direct  habitat protection,  ground
        water discharge to the GDE, and the temperature and chemistry requirements of ground water supplying the
        GDE must be considered. Specific management strategies can be identified to protect each of these attributes.
        GDE habitats can be protected by establishing buffer zones to separate  them  from resource extraction  and
        trampling.  Ground water discharge  to  GDEs  can be protected by establishing maximum limits for  ground
        water extraction or establishing minimum  distances from GDEs from which  ground water wells could be
        sited.  Ground water quality can be protected by limiting or eliminating land use activities in recharge zones
        that could impact water quality. To date, most ground water management in the United States has largely been
        developed and implemented with the objective of protecting ground water supplies  for human consumption.
        Additional  focus is needed to ensure protection for GDEs.
         In  many regions, focused discharge of ground water to the surface  supports critical biodiversity. On at least a
         seasonal basis, in the semi-arid western United States, these GDEs may have the only available water. When located
         on range land, the water and associated wetland vegetation make GDEs very inviting to livestock and can result in
         the damage or destruction of these features.

         In order to protect the integrity of GDEs on range land, the Forest Service and others have developed techniques
         to  limit the effects of grazing. Since the availability of water is critical to the success of ranching in many areas, any
         approach to protecting GDEs should address the need for livestock to access water. One approach the Forest Service
         has used with some success involves the development of a small-scale water diversion or withdrawal from the GDE,
         the siting of a stock tank or trough at  a  distance  outside the  GDE, and the development of  an exclosure fence
         surrounding the  GDE to exclude livestock from the GDE itself.

         This approach accomplishes several key range management goals, including: discouraging livestock use of the GDE
         by providing a consistent, readily available source of water away from the spring; allowing for a better distribution
         of  livestock across the allotment by reducing the incentive to congregate at the GDE; taking  pressure off of the
         sensitive soils and vegetation adjacent to the water and improving overall GDE conditions by limiting grazing effects;
         improving water quality  by improving soil  and  vegetation conditions within the GDE and eliminating livestock
         excrement from the water; and  improving water availability to wildlife.
5-40

-------
                                                                                         5 Management Approaches
5.3   Restoration Programs

Restoration strategies are an essential component of managing healthy watersheds. As development pressures
have expanded their reach to more and more pristine landscapes, entire healthy watersheds are less common. In
addition, even the watersheds that can be classified as healthy often have room for improvement. For example,
a healthy watershed may contain culverts. Replacing a dropped or undersized culvert with a larger,  open-
bottom culvert will enhance fish and wildlife passage along the stream. When planning restoration efforts, it
is generally helpful to consider the "protect the best first" strategy. This strategy prioritizes restoration  of the
systems that  are most likely to maintain their health post-restoration (as in improving healthy watersheds)
before investing resources in systems that may be degraded beyond their recovery potential.

Much of aquatic ecosystem restoration to  date  has focused on the symptoms, rather than the  causes, of
ecosystem degradation. Altered geomorphology, impaired water quality, and degraded biotic communities are
typically the  result of processes occurring in the watershed. Restoration of stream channel form must begin
at the watershed scale, focusing on processes such as watershed hydrology and sediment supply. Restoration of
water quality must focus on the landscape condition that is affected by the socioeconomic drivers of land use.
Restoration of biotic communities must focus on the natural flow regime necessary for the different life stages
of the aquatic biota,  the physical habitat determined by the geomorphic condition, and the water quality that
is largely determined by the landscape condition.

Ecological restoration is a new and growing field that, broadly defined, seeks to return degraded ecosystems to
a state closer to their original, natural conditions. EPA's Principles for the Ecological Restoration of Aquatic
Resources  (2007a)  emphasize, amongst other things, working within a watershed or landscape  context,
restoring ecological integrity based on a system's natural potential, and the use of passive restoration and natural
fixes.  A system's natural potential can be determined in a number of ways, including the use of appropriate
reference sites for the ecoregional setting. Passive restoration refers to a reduction or elimination in the sources
of degradation, as opposed to active approaches such as alum treatment. There are cases when active restoration
is necessary, but passive restoration  is often sufficient and more cost-effective. In addition, active restoration
can sometimes have unintended  and unforeseen effects on other system components.  A small sampling of
national, state, and local restoration programs are described below.

5.3.1  National

The National Fish Habitat Action Plan is a nationally linked, yet locally driven effort to improve fish habitat
across the country (www.fishhabitat.org). Fish habitat partnerships are formed voluntarily and collaborate to
protect, restore, and enhance fish habitat through, federal, state, and locally funded projects.

The National Fish Passage Program was initiated by the  USFWS to reconnect aquatic  species  with their
historic habitats.  Through the National  Fish  Passage Program USFWS leverages  federal funds to  secure
donations  from partners and provides technical assistance to  remove or bypass  artificial  barriers to fish
movement.

The Partners for  Fish and Wildlife Program provides technical and financial assistance to private landowners
and tribes who agree to work with the US Fish and Wildlife Service and other partners on a voluntary basis
to help  meet the  habitat needs of Federal Trust Species (migratory birds; threatened and endangered species;
inter-jurisdictional fish; certain marine mammals; and species of international concern).

The Restoration Center is the only office within the  National Oceanic and Atmospheric Administration
(NOAA) devoted solely to restoring the nation's  coastal, marine, and migratory fish habitat. They fund and
implement restoration projects to ensure healthy, productive,  sustainable fisheries;  employ technical staff to
help improve project design, ensure environmental compliance, and  advance  restoration techniques; engage
the local community and  encourage stewardship of the nation's coastal habitat; fund  projects that engage
local  people  and  resources, supporting the economy through  restoration activities, expertise, and materials;
collaborate with public,  private, and government partners to  prioritize projects and leverage resources; use
                                                                                                          5-41

-------
Identifying and Protecting Healthy Watersheds
        scientific monitoring to evaluate restoration project success and maximize the use of tax dollars; and conduct
        socioeconomic research that demonstrates the benefits of coastal restoration for community and environmental
        purposes.

        Total Maximum Daily Loads (TMDL) are a calculation of the maximum amount of a pollutant that a water
        body can receive and still meet water quality standards. They are watershed assessments that are conducted for
        impaired water bodies  as designated under section 303 (d)  of the Clean Water Act. TMDLs are required for all
        pollutant-impaired water bodies and can be considered the beginning of a watershed restoration plan focused
        on water quality. Most TMDLs now use a watershed approach for assessment and implementation. However,
        implementation of a TMDL and watershed restoration plan is critical if water quality is to be restored.

        The Nonpoint Source Management Program was established under section 319 of the Clean Water Act to
        support a variety of activities including technical assistance, financial assistance, education, training, technology
        transfer, demonstration projects, and monitoring to design and assess the success of nonpoint source programs
        and projects. In particular, the program provides funding  for the implementation of TMDLs and watershed
        management plans. The watershed management plans, though federally funded, are implemented at the state
        and local level, typically by county governments, conservation districts, and watershed councils.

        The Conservation Reserve Enhancement Program is a USDA program that protects ecologically sensitive
        land, wildlife habitat, and aquatic ecosystems through retirement of agricultural lands. The program provides
        payments to farmers and ranchers who agree to keep their land out of agricultural production for at least 10-
        15 years. The program has  been used to establish riparian buffers, restore wetlands, and create wildlife habitat
        through reforestation.

        The Wetlands Reserve Program, another US DA program, assists landowners in restoring agricultural wetlands.
        NRCS  may fund 75-100% of project costs on lands that are under a permanent conservation easement, and
        50-75% of restoration  costs on lands under temporary easements or cost-share agreements.

        The USDA Wildlife Habitat Incentives Program assists private landowners in creating and improving wildlife
        habitat through cost-share assistance up to 75% of project costs.

        The Environmental Quality Incentives  Program is a USDA program that  provides cost-share assistance
        to  farmers in implementing various  conservation measures including erosion control,  forest management,
        comprehensive nutrient management plans, etc.

        The USDA Conservation Security  Program provides technical  and financial assistance  for conservation
        purposes on working  lands, including cropland, grassland,  prairies, pasture and range land, and incidental
        forest lands on agricultural  properties.

        The Grasslands Reserve Program is a voluntary program to limit  future development and cropping uses on
        grazing lands to support protection of these areas. This USDA program establishes grazing management plans
        for all participants.

        5.3.2   State and  Interstate

        Restoration of Flow and Connectivity

        Historically, straightening  and  armoring of stream channels was a common practice to protect floodplain
        development from a meandering river and for navigation purposes. Unfortunately, this practice increases a
        stream's energy, which  is sent to a downstream reach where significant erosion of the stream channel can occur.
        Depending on the current riparian land  uses,  it may be possible  to remove the bank armoring and allow
        the stream channel to reclaim some of its original floodplain.  Similarly,  many dams have been built across
        the United States over the past 200 years. While many  of these dams are  essential for providing  drinking
        water, hydroelectric  power generation, and agricultural irrigation water, a large number of them have  been
5-42

-------
                           5 Management Approaches
 Meeting Urban Water Demands
While Protecting Rivers: Rivanna
 River, Virginia (Richter B., 2007)
workin
developed a  new water supply plan  that
meets growing water demands and improves
river ecosystem health. The new plan mimics
natural  flow  regimes  through  controlled
dam releases while ensuring adequate water
supplies during  drought. The  releases  are
calculated  as varying  percentages of  the
inflow to the reservoir.
decommissioned  or  abandoned.  These dams are  often  prime
candidates for removal to restore the natural flow regime and
improve aquatic  habitat connectivity. Dam  removal  projects
are a significant  undertaking and  involve physical, chemical,
hydrological, ecological,  social, and  economic considerations
(American Rivers, 2009a). Where it is not feasible to remove a
dam, reservoir release rules that mimic the natural flow regime
can improve the ecological function of the river (Richter et al.,
2006). However, when working in riverine ecosystems that have
been highly modified, managers must often rely on site-specific
flow-ecology relationships to inform restoration decisions. Some
possible  strategies identified  by The  Nature  Conservancy for
flow restoration include:

    •   Dam reoperation.
    •   Conjunctive ground-water/surface-water management.
    •   Drought management planning.
    •   Demand management (conservation).
    •   Water transactions (exchangeable water rights).
    •   Diversion point relocation.

Aquatic ecosystems are dependent on sufficient instream flows for maintaining their vitality. For example, Pacific
Salmon require specific gravels, water depths, and velocities during spawning to build their nests. Alteration
of the natural flow regime can change water depth, velocity, and the substrate on which the spawning salmon
depend. Anadromous fish, such as Pacific Salmon, also require stream connectivity for migration between the
headwaters streams, where they are born, to the ocean, where they live out most of their lives. Where dams and
other structures disrupt aquatic habitat connectivity and removal of these structures is not feasible or desirable,
fish ladders and other upstream or downstream passage facilities can be used to ensure  that fish retain access to
habitat  (U.S. Fish and Wildlife Service, 2009).  This is especially important for anadromous fish species (e.g.,
salmon, alewife).  States such as Oregon, Washington, and Pennsylvania have created fish passage rules that
require stream crossings and other artificial obstructions to allow for the passage of migratory fish.

5.3.3  Local

Greenways, discussed in Chapter 2, are recreational corridors of natural vegetation that can be fit into existing
developed areas to create or improve wildlife habitat, scenic and aesthetic values, and outdoor activities such as
walking, running, and cycling (American Trails, 2009).

Wetland construction and restoration is typically a site-based  restoration approach.  However, when viewed
in its landscape context, wetland restoration can improve wildlife habitat and connectivity, nutrient retention,
hydrologic regulation, and  pollutant removal.  The benefits of wetland  restoration are maximized  when
conducted in a landscape context (U.S. Environmental Protection Agency, 2007c).

Reforestation is a technique  that can be  conducted at a stand (site) or landscape scale and improves wildlife
habitat and  connectivity,  infiltration of rainfall, and regulation of surface temperatures. Riparian reforestation
can be especially  beneficial to aquatic ecosystems, as riparian forests are important components of the Active
River Area.  Riparian forests  in headwater catchments provide coarse particulate organic matter and large
woody debris that supply the unique assemblage of organisms  in headwater streams with the food  and habitat
they require. Organisms in lower reaches of the watershed depend on this  upstream supply of energy as well.
Floodplain forests in the lower reaches of the watershed provide valuable spawning grounds for some aquatic
species  during floods,  provide  habitat to terrestrial  and semi-aquatic species, serve  as  buffers to attenuate
nutrient delivery to the streams, and provide shading to the aquatic habitat which regulates water temperatures
(Center for Watershed Protection; U.S. Forest Service, 2008b).
                                           5-43

-------
Identifying and Protecting Healthy Watersheds
        5.4    Education, Outreach, and Collaboration

        Outreach and education are  two protection  strategies whose  importance cannot  be  overstated. Efforts  to
        protect healthy watersheds are more likely to  succeed if understood and supported by the local community.
        Communicating the results of healthy watersheds integrated assessments using plain language and graphical
        elements, such as watershed report cards or simple maps, facilitates the outreach and education process. Most
        community members will not be interested in fluvial geomorphology or flow duration curves. However, they
        will be interested in maintaining local fish populations and protecting their properties from flooding. Examples
        of outreach and education activities include:

            •    Presentations to local  governments and to the general public.
            •    Newspaper  articles describing  the benefits of protecting healthy watersheds,  and
                alerting the public to the sensitivity of healthy watersheds to degradation.
            •    Development and distribution of informative fact sheets or flyers.
            •    Development of a slide show and script for stakeholders to present with.
            •    Field trips (e.g., fishing, hiking, canoeing) that enable the public to see and appreciate
                examples of healthy watersheds firsthand.

        Reaching out to the local community and educating stakeholders early in the process can lead to increased
        support for environmental protection as a result of an increased understanding of the resource and threats,
        a sense  of shared responsibility for  maintaining the  resource, and cooperation in the implementation  of
        management measures.  Examples of actions that communities can take to protect healthy watersheds include
        integrating green infrastructure and habitat protection into comprehensive  plans, protecting the Active River
        Area from development through zoning, preventing landscape fragmentation through the use of conservation
        subdivisions, and many other  techniques discussed in this chapter. Collaborating with local watershed groups
        or land  trusts  can be an effective way to reach  community members and share resources  in  outreach and
        education campaigns. These groups also often have the  capacity and willingness to organize  volunteers  in
        performing field monitoring and assessment of water quality, biological condition, habitat condition, etc.

        Heal the Bay is a non-profit organization in  California that uses a  report card approach for communicating
        the health status of the  state's beaches, giving each beach a grade representing the relative risk of fecal coliform
        exposure posed to beachgoers (Heal the Bay, 2009). A report card approach is also used to communicate
        the health of the Chesapeake  Bay to stakeholders and watershed  residents and to increase their awareness  of
        aquatic ecological health (University of Maryland Center for Environmental Science; National Oceanic and
        Atmospheric Administration, 2009). The report card results are also displayed on a map (Figure 5-11). Another
        example is the Vermont Lake  Score Card that rates the condition  of Vermont's lakes with  regards to water
        quality, aquatic invasive species, atmospheric pollution, and shoreland and lake habitat. A similar technique
        can be used to rate watersheds across a state, county, or region.

        A report card, or another format for communicating monitoring  and assessment results, can  also  include
        information on how local land owners and other stakeholders can help protect or improve the health of their
        watershed. Providing stakeholders with the knowledge necessary for
        appreciating the importance of aquatic ecosystems and their watersheds,
        and tools for protecting those resources, is an important component
        of healthy  watersheds protection.  Establishing  a  local  volunteer
        monitoring network  is   another potential approach for getting more
        people involved and concerned about protecting these ecosystems. Such
        a network could involve training on, and participation in, shoreline
        monitoring surveys,  biomonitoring, water quality monitoring, etc.
        Annual  river  cleanups,  environmental education campaigns,  and
        meetings or presentations with local  communities can all help  to
        increase public awareness and understanding of healthy watersheds.
               e Score
Answers to lire Question "How are Vermont fakes doing?
5-44

-------
                                                                           5 Management Approaches
      Bay health scale
Very poor         Very good
  0  20 40 60 80100%
   J  D   C   B  A|
   Onsufficient data        M
                 Upper Bay (C+
     Upper Western
         Shore
Patapsco and
 Back Rivers
                          flower Western
                              Shore (MD) '
                   Potomac
                     River
 Upper Eastern
     Shore
             Rappahannock
                  River
            U«nt.r-.,!v or Maryland
            ClNTf It TOR ENVIRONMENTAL SCIENCE
                    Elizabeth
                      River
                                                                      Lower Eastern
                                                                      Shore (Tangier)
   Miles
0 ' 10   20
      Figure 5-11 Chesapeake Bay report card results for 2007 (University of Maryland Center for
      Environmental Science; National Oceanic and Atmospheric Administration, 2009).
                                                                                          5-45

-------
Identifying and Protecting Healthy Watersheds
        The various outreach and education options should not be viewed as mutually exclusive. Success in outreach
        campaigns can be determined by the number of people that hear your message and the number of times they
        hear it. Exposing people to your message through multiple types of media will help ensure that the message
        sticks. Tools such as EPA's Getting in Step: A Guide for Conducting Watershed Outreach Campaigns (U.S.
        Environmental  Protection Agency, 2003) and Ohio's Watershed Toolshed (Ohio Watershed Network, 2009)
        provide practitioners with the resources needed to get started on some of these approaches. The Conservation
        Campaign Toolkit (http://www.conservationcampaign.org/wizard/index.cfm?ID=125) provides a free online
        space for communities and citizen groups to organize their campaign to protect land and water resources.

        Millions  of Americans are outdoor enthusiasts, and many belong to organizations that  provide substantial
        protection to natural resources. Collaboration with  outdoor recreation organizations has  been shown to
        increase support for conservation time and time again. For example, Trout Unlimited is a national organization
        that supports the protection and restoration of coldwater fisheries and their supporting ecosystems. Members
        belong to local chapters and are often, though not always, recreational  anglers. By promoting responsible
        stewardship of the resource, Trout Unlimited and similar organizations provide recreational and educational
        opportunities for individuals to participate  in the protection of healthy aquatic ecosystems. Recreational use
        of ecologically intact aquatic systems and their watersheds is an important consideration in the management
        of healthy watersheds.  Encouraging compatible recreational uses  often enhances  public  acceptance  and
        understanding of the conservation process.

        Partnerships with less traditional groups can be just as rewarding as outreach  to groups that have historically
        supported environmental protection.  For example,  the community and public health benefits of protecting
        healthy watersheds are  often valued by groups such as community service clubs, chambers of commerce,
        religious  organizations, and  public health advocacy groups. These nontraditional partners can provide access
        to new audiences  and bring new resources  to watershed protection efforts.  Furthermore,  unconventional
        partnerships can be effective in garnering media attention. When individuals who do not necessarily align
        themselves with community organizations  see the breadth of interests represented by watershed protection
        efforts, they may be more likely to deem the efforts worthy of their individual  support as well. The greater the
        diversity  of groups that collaborate on these efforts, the less likely that the momentum will be lost.
5-46

-------
 References
Abell, R., Theime, M. L, Revenga, C.,  Bryer, M., Kottelat, M., Bogutskaya, N., et al. (2008). Freshwater
Ecoregions  of the World: A New Map  of Biogeographic Units for  Freshwater Biodiversity Conservation,
BioScience, 403-414.

Aber, J., Christensen, N.,  Fernandez, I., Franklin, J., Hidinger,  L., Hunter, M., et al. (2000). Applying
Ecological Principles to Management of the U.S. National Forests. Issues in Ecology, Number 6.

Alachua County. (2008). Alachua County Green Infrastructure Investment Program. Retrieved October 7,
2009, from http://www.alachuacounty.us/Pages/AlachuaCounty.aspx

Alley, W., Reilly, T,  & Franke, O. (1999). Sustainability of Ground Water Resources, USGS Circular 1186.
U.S. Government Printing Office.

Almendinger, J., &  Leete, J. (1998). Regional and local  hydrogeology of calcareous fens in the Minnesota
River basin. Wetlands, 184-202.

American Rivers. (2009a). Dams and  Dam Removal. Retrieved December 3, 2009,  from Restoring Rivers:
http://www.americanrivers.org/our-work/restoring-rivers/dams/

American Rivers. (2009b). What Does it Mean to be a Wild and Scenic River? Retrieved October 6, 2009,
from American Rivers: http://www.americanrivers.org/our-work/protecting-rivers/wild-and-scenic/

American Trails. (2009). Greenways and Community Trails. Retrieved December 3,  2009, from Resources:
http://www.americantrails.org/resources/greenways/index.html

Angelo, R., Knight, G., Olson,  K., & Stiles, T. (2010).  Kansas Reference Streams.  Kansas Department of
Health and the Environment.

Anne Arundel County. (2002). Anne Arundel County Greenways Master Plan. Anne Arundel County.

Annear, T,  Chisholm, L, Beecher, H.,  Locke, A, Aarrestad, P., Coomer, C., et al. (2004). Instream Flows for
Riverine Resource Stewardship. Instream  Flow Council.

Annis, G., Sowa, S.,  Diamond, D., Combes, M., Doisy, K., Garringer, A, & Hanberry, P. (2010). Developing
Synoptic Human Threat Indices for Assessing the Ecological Integrity of Freshwater Ecosystems in EPA Region
7- Missouri Resource Assessment  Partnership: http://morap.missouri.edu/Proiects.aspx?ProiectId=44

Archfield, S.A, Vogel, R.M., Steeves, PA, Brandt, S.L., Weiskel, P.K., and Garabedian,  S.P  (2010). The
Massachusetts Sustainable-Yield  Estimator:  A decision-support  tool to assess water  availability at ungaged
stream locations in Massachusetts: U.S. Geological Survey Scientific Investigations Report 2009—5227, 41 p.
plus CD-ROM.

Arendt, R. (1999). Growing Greener: Putting Conservation into Local Plans and Ordinances. Island Press.

Arthington,  A.  H., Bunn,  S. E., Poff,  N.  L.,  & Naiman,  R.  J.  (2006).  The Challenge  of Providing
Environmental Flow Rules to Sustain River Ecosystems. Ecological Applications, 1311-1318.

Association of Fish and Wildlife Agencies. (2006). The National Fish Habitat Action Plan. Washington D.C.:
Association of Fish and Wildlife Agencies.
                                                                                                     R-l

-------
Identifying and Protecting Healthy Watersheds
        Barneycastle, C. (2001). The Sustainable Forestry Initiative of the American Forest & Paper Association. U.S.
        Department of Agriculture, Forest Service.

        Baron, J. S., Poff, N. L, Angermeier, P. L, Dahm, C. N., Gleick, P. H., Hairston, N. G., et al. (2002). Meeting
        Ecological and Societal Needs for Freshwater. Ecological Applications, 1247-1260.

        Bayley, P.  B. (1995). Understanding Large River: Floodplain Ecosystems. BioScience, 153-158.

        Bedford, B. (1999). Cumulative effects on wetland landscapes: links to wetland restoration in the United States
        and southern Canada. Wetlands, 775-788.

        Bedford,  B., & Godwin, K. (2003). Fens of the  United States: distribution, characteristics, and scientific
        connection versus legal isolation. Wetlands, 608-629-

        Beechie, T., Sear, D., Olden, J.,  Pess, G., Buffington, J., Moir,  H., et al. (2010). Process-based Principles for
        Restoring River Ecosystems. BioScience, 209-222.

        Bellucci, C., Beauchene, M., & Becker, M. (2009). Physical,  Chemical, and Biological Attributes of Least
        Disturbed Watersheds in Connecticut. Connecticut Department of Environmental Protection.

        Benedict, M. A.,  & McMahon, E. T. (2002). Green Infrastructure: Smart Conservation for the 21st Century.
        Washington, D.C.: Sprawl Watch Clearinghouse.

        Benedict, M.  A., & McMahon, E. T. (2006). Green Infrastructure: Linking Landscapes and Communities.
        Washington D.C.: Island Press.

        Berkes, F. (2007). Understanding uncertainty and reducing vulnerability: lessons from resilience thinking. Nat
        Hazards, 41:283-295-

        Berkes, F.  &  Folke, C. (2000). Linking Social and Ecological Systems: Management Practices  and Social
        Mechanisms for Building Resilience. Cambridge: Cambridge University Press.

        Bierwagen, B., Theobald, D., Pyke, C., Choate, A., & Groth, P. (2010). National housing and impervious
        surface scenarios  for integrated climate impact assessments. Proceedings of the National Academy of Sciences
        of the United States of America.

        Brooks, J., Meinzer, F, Coulombe, R., & Gregg, J. (2002). Hydraulic redistribution of soil water during
        summer drought  in two contrasting Pacific Northwest coniferous forests. Tree Physiology, 1107-1117-

        Brown, J., Wyers, A., Aldous, A., & Bach, L. (2007). Groundwater and Biodiversity Conservation: A methods
        guide for integrating groundwater needs  of ecosystems and species into conservation plans in  the Pacific
        Northwest. The Nature Conservancy.

        Brown, J., Wyers, A., Bach, L., & Aldous, A. (2009a). Groundwater-Dependent Biodiversity and Associated
        Threats: A statewide screening methodology and spatial assessment of Oregon. The Nature Conservancy.

        Brown, J., Wyers, A., Bach, L., & Aldous, A. (2009b). Groundwater-Dependent Biodiversity and Associated
        Threats: Oregon Atlas. The Nature Conservancy.

        Brown, J., Bach, L., Aldous,  A., Wyers,  A.,  DeGagne,  J.  (2011). Groundwater-dependent  ecosystems in
        Oregon: an assessment of their distribution and associated threats. Frontiers in Ecology and the Environment
        9(2): 97-102.
R-2

-------
                                                                                                    References
Bunch, M. J., Morrison, K. E., Parkes, M. W, & Venema, H. D. (2011). Promoting health and well-being
by  managing  for social—ecological  resilience:  the  potential  of integrating ecohealth and water  resources
management approaches. Ecology and Society 16  (1): 6. [online] URL: http://www.ecologyandsociety.org/
voll6/issl/art6/

Bunn, S., & Arthington, A. H. (2002). Basic principles and consequences of altered hydrological regimes for
aquatic biodiversity. Environmental Management, 492-507-

Bureau of Land Management.  (1998). Riparian Area Management: Process for Assessing Proper Functioning
Condition. Denver, CO: U.S. Department of the Interior.

Carter, V. (1996).  Technical  Aspects  of Wetlands:  Wetland Hydrology, Water Quality, and Associated
Functions. In National Water Summary on Wetland Resources. U.S. Geological Survey.

Center for Watershed Protection. (2008a). Model Ordinances. Retrieved July 28, 2009, from Center for
Watershed   Protection:   http://www.cwp.org/index.php?option=com content&view=article&id=128:free-
downloads-intro&catid= 1 &Itemid= 116

Center for Watershed Protection; U.S. Forest Service. (2008b). Watershed Forestry Resource Guide. Retrieved
December 3, 2009, from Forests for Watersheds: http://www.forestsforwatersheds.org/

Center for Watershed Protection. (2008c). Wetlands and Watersheds. Retrieved January 23, 2009, from Center
for  Watershed  Protection:  http://www.cwp.org/index.php?option=com content&view=article&id=128:free-
downloads-intro&catid= 1 &Itemid= 116

Chicago   Wilderness.   (2009).  Chicago Wilderness. Retrieved  January  23,   2009,  from  http://www.
chicagowilderness.org/

Cohen, R. (1997). The Importance of Protecting Riparian Areas along Smaller Brooks and Streams. Retrieved
January 23, 2011,  from Massachusetts Department of Fish and Game: http://www.mass.gov/dfwele/der/
riverways/pdf/riparian factsheet 9.pdf

Collins, J., Stein, E.,  Sutula, M., Clark, R.,  Fetscher, A., Grenier, L., Grosso,  C, & Wiskind, A. (2008)
California Rapid Assessment Method (CRAM) for Wetlands and Riparian Areas (website), www.cramwetlands.
org

Collins, J., Stein, E.,  Sutula, M., Clark, R.,  Fetscher, A., Grenier, L., Grosso,  C., & Wiskind, A. (2008)
California Rapid Assessment Method (CRAM) for Wetlands, v. 5-0.2. 157 pp.

Committee on Hydrologic Impacts  of Forest Management, National  Research Council. (2008). Hydrologic
Effects of a Changing Forest Landscape. Washington D.C.: National Academies Press.

Copeland, H., Tessman, S., Girvetz, E.,  Roberts, L., Enquist, C., Orabona, A.,  et al. (2010).  A geospatial
assessment on the distribution, condition, and vulnerability  of Wyoming's wetlands. Ecological Indicators,
869-879-

Cox, K. M. (2006). Batten Kill Trout Management Plan. Vermont Agency of Natural Resources.

Daily, G.C., Alexander, S., Ehrlich, PR., Goulder, L., Lubchenco,  J., Matson, PA., Mooney, H.A., Postel,
S., Schneider, S.H., Tilman, D., Woodwell, G.M. (1997).  Ecosystem Services: Benefits Supplied to Human
Societies  by Natural Ecosystems. Issues in Ecology, Number 2.

Davies, S.P and S.K. Jackson. (2006). The Biological Condition Gradient: A descriptive model for interpreting
change in aquatic ecosystems. Ecological Applications and Ecological Archives 16(4)1251-1266.
                                                                                                        R-3

-------
Identifying and Protecting Healthy Watersheds
        Davies, S. and D. Courtemanch. (2012). A History of Biological Assessment and the Development ofTiered
        Aquatic Life Uses in  Maine. Maine  Department of Environmental  Protection, http://www.maine.gov/dep/
        water/monitoring/biomonitoring/material.htm

        Dingham, S. L. (2002). Physical Hydrology. Prentice Hall.

        Doppelt, B., Scurlock, M., Frissell, C., & Karr, J. (1993). Entering the Watershed: A New Approach to Save
        America's River Ecosystems. Washington D.C.: Island Press.

        Dunne, T., & Leopold,  L.  (1978). Water  in Environmental  Planning.  New York:  WH.  Freeman  and
        Company.

        Eamus, D. and R. Froend. (2006). Groundwater-Dependent ecosystems: The where, what and why of GDEs.
        Australian Journal of Botany, 54, 91-96.

        Environmental Law Institute; Defenders of Wildlife.  (2003). Planning for  Biodiversity: Authorities in State
        Land Use Laws. Washington D.C.: Environmental Law Institute.

        Environmental Law Institute. (2007a). Lasting Landscapes: Reflections on the Role of Conservation Science
        in Land Use Planning. Washington D.C.: The Environmental Law Institute.

        Environmental Law  Institute.  (2007b).  State Wildlife Action Plans  and Utilities: New  Conservation
        Opportunities for America's Wildlife.  Environmental Law Institute.

        Ernst, C. (2004). Protecting the Source: Land Conservation and the Future of America's Drinking Water. The
        Trust for Public Land.

        Esselman, P., Infante, D. M., Wang, L., Cooper, A.,  Taylor, W W, Tingley, R., et al. (2011). A landscape
        assessment of fish habitat  conditions in United States  rivers and  their watersheds. Retrieved  from www.
        fishhabitat.org

        Federal Interagency Stream Restoration Working  Group. (1998). Stream Corridor Restoration: Principles,
        Processes, and Practices.

        Frey, D. (1977). Biological Integrity of Water: An Historical Approach. The Integrity ofWater. Proceedings of
        a Symposium, March  10-12, 1975 (pp. 127-140). Washington D.C.: U.S. Environmental Protection Agency.

        Frissel, C.,  Poff, N. L.,  & Jensen, M.  (2001). Assessment of Biotic Patterns in Freshwater Ecosystems. In
        M. Jensen,  & P. Bourgeron, A Guidebook for Integrated Ecological Assessments (pp.  390-403). New York:
        Springer.

        Gao, Y, Vogel, R., Kroll, C., Poff, N., & Olden, J. (2009).  Development of Representative Indicators of
        Hydrologic Alteration. Journal of Hydrology,  136—147-

        GSA BBEST (Guadalupe, San Antonio, Mission, and  Aransas Rivers and Mission, Copano, Aransas, and San
        Antonio Bays Basin and Bay Expert Science Team). (2011).  Environmental Flows Recommendations Report
        Final Submission to the Guadalupe, San Antonio, Mission, and Aransas Rivers and Mission, Copano, Aransas,
        and San Antonio Bays Basin and Bay Area Stakeholder Committee, Environmental Flows Advisory Group,
        and Texas Commission on Environmental Quality.

        Gilbert, J.  (1996).  Do Ground Water Ecosystems Really Matter? Ground Water  and Land  Use Planning
        Conference. Perth: CSIRO Division of Water Resources Centre for Ground Water Studies.

        Gilbert, J., Danielopol, D., & Stanford, J. (1998). Groundwater Ecology. San Diego, CA: Academic Press.
R-4

-------
                                                                                                    References
Goldscheider, N., Hunkeler, D., Pronk, M., Rossi, P., Kozel, R., & Zopfi, J. (2007)- Heterogeneous aquifers as
habitats for microbial biocenoses. XXXV International Association of Hydrogeologists Congress Groundwater
and Ecosystems. Lisbon, Portugal: International Association of Hydrogeologists.

Grimm, N., Gergel, S., McDowell, W, Boyer, E., Dent, C., Groffman, P., et al.  (2003). Merging aquatic and
terrestrial perspectives of nutrient biogeochemistry. Oecologia, 485-501.

Groves, C., Klein, M., & Breden, T. (1995). Public-Private Partnerships for Biodiversity Conservation. Wildlife
Society Bulletin, 784-790.

H. John Heinz III Center for Science, Economics, and the Environment. (2008).  The State of the Nations
Ecosystems. Washington D.C.: Island Press.

Haas, A, Ahn, G.-C., Rustay, M., & Dittbrenner, B. (2009). Critical  Areas Monitoring 2008 Status Report.
Snohomish County Public Works.

Habich, E. E (2001). Ecological Site Inventory. Denver, Colorado: Bureau of Land Management.

Hancock,  P., Boulton, A, & Humphreys, W (2005). Aquifers and hyporheic zones: Towards an ecological
understanding of groundwater. Hydrogeology Journal, 98-111.

Hann, W, Shlisky, A., Havlina, D., Schon, K., Barrett, S., DeMeo, T., et al.  (2008). Interagency Fire Regime
Condition Class Guidebook. National Biological Information Infrastructure.

Hayashi, M., & Rosenberry,  D. (2002). Effects of groundwater exchange on the hydrology and ecology of
surface water. Ground Water, 309-316.

Heal the Bay.  (2009, October 27). Beach Report Card. Retrieved November 4, 2009, from Heal the Bay:
http://www.healthebay.org/brcv2/

Healy, R., Winter, T., LaBaugh, J., & Franke, O.  (2007). Water Budgets: Foundations for Effective Water
Resource and Environmental Management, USGS Circular 1308. U.S. Government Printing Office.

Henriksen, J., Heasley, J., Kennen, J., & Nieswand, S. (2006). Users' Manual for the Hydroecological Integrity
Assessment Process Software (including the New  Jersey Assessment Tools). Reston, VA: U.S. Geological
Survey.

Herlihy, A., Paulsen, S.,  Van  Sickle, J., Stoddard, J., Hawkins, C., Yuan, L. (2008). Striving for consistency in
a national assessment: the challenges of applying a reference-condition approach at a continental scale. Journal
of the North American Benthological Society, 860—877-

Higgins,  V. J.  (2003).  Maintaining the Ebbs and Flows of the Landscape -  Conservation Planning for
Freshwater Ecosystems. In C. R. Groves, Drafting a Conservation Blueprint: a Practitioner's Guide to Regional
Planning for Biodiversity. Washington D.C.: Island Press.

Higgins,  J., Bryer, M., Khoury,  M., &  Fitzhugh, T.  (2005). A Freshwater  Classification Approach for
Biodiversity Conservation Planning. Conservation Biology, 432-445-

Higgins, V. J.,  & Esselman,  R. (2006).  Ecoregional Assessment and Biodiversity Vision Toolbox. Retrieved
January 14, 2011, from The  Nature Conservancy:  http://conserveonline.org/workspaces/cbdgateway/era/
index html
                                                                                                        R-5

-------
Identifying and Protecting Healthy Watersheds
        Higgins, J. V., & Duigan, C.  (2009)- So Much to Do, So Little Time: Identifying Priorities for Freshwater
        Biodiversity Conservation in the United States and Britain.  In P. J. Boon, &  C.  M. Pringle, Assessing the
        Conservation Value of Freshwaters (pp. 61-90). New York, NY USA: Cambridge University Press.

        Hubert, W (2004). Ecological processes of riverine wetland habitats. In M. McKinstry, W Hubert, & S.
        Anderson, Wetland and Riparian Areas of the Intermountain West  (pp. 52—73). Austin, TX: University of
        Texas Press.

        Hugget, R. (2011). Fundamentals of Geomorphology New York, NY. Routledge.

        Humphreys, W (2006). Aquifers: The ultimate groundwater-dependent ecosystems. Australian Journal of
        Botany, 115-132.

        Interagency Wild and Scenic Rivers Council. (2009, October 6). Retrieved October 6, 2009, from National
        Wild and Scenic Rivers: www.rivers.gov

        IPCC (Intergovernmental Panel on Climate Change). (2007). Climate Change 2007: The Physical Science
        Basis.  Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on
        Climate Change [Solomon, S., D. Qin, M. Manning (eds.)].

        Jaquith, S., Kline,  M., Field, J., & Henderson, J. (2004). Phase 1 Geomorphic Assessment of the Batten Kill
        Main-Stem and Major Tributaries. Vermont Department of Environmental Conservation.

        Jelks, H.  L, Walsh, S. J., Burkhead, N. M., Contreras-Balderas, S.,  Diaz-Pardo, E., Hendrickson, D. A., et
        al.  (2008). Conservation Status of Imperiled North American Freshwater and Diadromous Fishes. Fisheries,
        33(8): 372-407-

        Jennings, M. (2000). Gap Analysis: Concepts, Methods, and Recent Results. Landscape Ecology,  15:5-20.

        Junk, W, & Wantzen, K. (2004). The Flood Pulse Concept: New Aspects, Approaches, and Applications.
        Max-Planck-Institute for Limnology, Working Group Tropical Ecology.

        Karr, J. R. (1981).  Assessment of Biotic Integrity Using Fish Communities. Fisheries, 6: 21-27-

        Karr, J., & Dudley, D. (1981). Ecological Perspectives on Water Quality Goals. Environmental Management,
        55-68.

        Karr, J. R., Fausch, K. D., Angermeier, P L., Yant, P. R., &  Schlosser, I. J. (1986). Assessment  of Biological
        Integrity in Running Waters: A Method and its Rationale. Champaign, Illinois: Illinois Natural History Survey
        Special Publication 5-

        Karr, J., & Yoder,  C. (2004). Biological assessment and criteria improve total maximum daily load decision
        making. Journal of Environmental Engineering, 594-604.

        Kenny, J.F., Barber, N.L., Hutson, S.S., Linsey, K.S., Lovelace, J.K., and Maupin, M.A. (2009). Estimated use
        of water in the United States in 2005: U.S. Geological Survey Circular 1344, 52  p.

        Khoury, M.,  Higgins, J., &  Weitzell,  R. (2010). A Freshwater Conservation Assessment of the Upper
        Mississippi River Basin Using a Coarse and Fine Filter Approach. Freshwater Biology, 1365-2427-

        Kidd, S., McFarlane, B., & Walberg, E. (2010). A Green Infrastructure Plan for the Hampton Roads Region.
        Chesapeake, VA: Hampton Roads Planning District Commission.

        King, R., Baker, M., Kazyak, P., Weller, D.  (2011). How novel is too novel? Stream community  thresholds at
        exceptionally low levels of catchment urbanization. Ecological Applications, 1659—1678.
R-6

-------
                                                                                                 References
King County Department of Natural Resources. (2000).  Literature Review and Recommended Sampling
Protocol for Bull Trout in King County . Seattle, WA: King County Department of Natural Resources.

Kline,  M., Alexander, C., Pytlik, S., Jaquith,  S., & Pomeroy,  S. (2009). Vermont Stream Geomorphic
Assessment Protocol Handbooks and Appendices. Waterbury, VT: Vermont Agency of Natural Resources.

Kline, M., & Dolan, K. (2009). River Corridor Protection Guide. Waterbury, VT: Vermont Agency of Natural
Resources.

Kline, M. (2010). VT ANR River Corridor Planning Guide:  to Identify and Develop River Corridor Protection
and Restoration Projects. Waterbury, VT: Vermont Agency of Natural Resources.

Kline, M.,  & Cahoon, B.  (2010). Protecting River Corridors in Vermont. Journal of the American Water
Resources Association , 227-236.

Komor, S. (1994). Geochemistry and  hydrology of a calcareous fen within the Savage fen wetlands complex,
Minnesota, U.S.A. Geochimica et Cosmochimica Acta, 3353-3367-

Kraemer, S. R., Schroer, K, Chesney, C.,  Bonds, J., Ryan, W, & Melgin, W  (2000).  Ground Water,
Watersheds and Environment. Unpublished US EPA Issue paper.

Leopold,  L., Wolman, M., & Miller, J.  (1964). Fluvial Processes in Geomorphology. WH. Freeman. San
Francisco,  CA.

Leopold, L. (1994). A View of the River. Cambridge, MA: Harvard University Press.

MacDonald, L. H.,  Smart, A. W, &  Wissmar, R. C.  (1991). Monitoring Guidelines to Evaluate Effects of
Forestry Activities on Streams in the  Pacific Northwest and Alaska. Seattle: U.S. Environmental Protection
Agency Region 10.

Mack, John J., Mick Micacchion, Lauren D. Augusta, and Gregg R. Sablak. 2000. Vegetation Indices of Bio tic
Integrity (VIBI) for Wetlands and Calibration of the Ohio Rapid Assessment Method for Wetlands v. 5-0.
Final Report to U.S. EPA Grant No. CD985276,  Interim Report to U.S. EPA Grant No. CD985875, Volume
1. Ohio Environmental  Protection Agency,  Division of Surface Water, Wetland Ecology Unit,  Columbus,
Ohio.

Mack, John J. 2001. Ohio Rapid Assessment Method for Wetlands, Manual for Using Version 5-0. Ohio EPA
Technical Bulletin Wetland/2001-1-1.  Ohio Environmental  Protection Agency, Division of Surface Water, 401
Wetland Ecology Unit, Columbus, Ohio.

Maryland  Department of Natural Resources.  (2003). A Physical Habitat Index for  Freshwater Wadeable
Streams in Maryland. Annapolis: Maryland Department of Natural Resources.

Maryland Department of Natural Resources.  (2011). GreenPrint.  Retrieved January 23, 2011, from Maryland
Department of Natural Resources: http://www.greenprint.maryland.gov/

Maryland Biological Stream Survey. (2005). Statewide and Basin Conditions 2000-2004. Annapolis: Maryland
Department of Natural Resources.

Massachusetts Department of Fish & Game and The Nature Conservancy. (2010). BioMap2: Conserving the
Biodiversity of Massachusetts in a Changing World. MA Department of Fish & Game.

Massachusetts Department of Fish & Game. (2011).  River Continuity Data Sheets. Retrieved January 11,
2011, from Division of Ecological Restoration:  http://www.mass.gov/dfwele/der/freshwater/rivercontinuity/
datasheets.htm
                                                                                                      R-7

-------
Identifying and Protecting Healthy Watersheds
        Matthews, R., & Richter, B. (2007)- Application of the Indicators of Hydrologic Alteration software in
        environmental flow-setting. Journal of the American Water Resources Association , 1400-1413-

        Maurer, E. P, Brekke, L., Pruitt, T., & Duffy, P. B. (2007)- Fine-resolution climate projections enhance regional
        climate change impact studies. Eos, Transactions, American Geophysical Union. 88(47), 504.

        Medalie, L.,  & Horn, M.A. (2010) Estimated water withdrawals and return flows in Vermont in 2005  and
        2020: U.S. Geological Survey Scientific Investigations Report 2010—5053- Available from: http://pubs.usgs.
        gov/sir/2010/5053

        Meyer, J. L., Wallace, J. B., Eggert, S. L., Helfman, G. S., & Leonard, N. E. (2007). The Contribution of
        Headwater Streams in Biodiversity Networks. Journal of the American Water Resources Association, 86-103-

        Millennium  Ecosystem  Assessment. (2005). Ecosystems and Human Well-Being. Washington D.C.: Island
        Press.

        Miller, W, Johnson, D., Loupe, T, Sedinger, J., Carroll, E., Murphy, J., et al. (2006).  Nutrients Flow From
        Runoff at Burned Forest Site in LakeTahoe Basin. Restoring Clarity, 65-71.

        Minnesota Department  of Natural Resources. (2008, February). What is a Calcareous Seepage Fen? Retrieved
        January 10, 2011, from  Wetlands: http://www.bwsr.state.mn.us/wetlands/Calc fen-factsheet.pdf

        Minnesota Department of Natural Resources. (2011). Watershed Assessment Tool. Retrieved November 29,
        2011, from http://www.dnr.state.mn.us/watershed tool/index.html

        Minnesota Pollution Control Agency. (2010). Minnesota National Lakes Assessment Project: An overview of
        water chemistry in Minnesota lakes. Environmental Analysis and Outcomes Division. Saint Paul, MN. Mitsch,
        W. J.,  & Gosselink, J. G. (2007). Wetlands.  Hoboken, NJ: John Wiley & Sons, Inc.

        Mitsch, W. J., & Gosselink, J. G. (2007). Wetlands. Hoboken, NJ: John Wiley & Sons, Inc.

        Moir-McClean, T, & DeKay, M. (2006). Beaver Creek Watershed Green  Infrastructure Plan. University of
        Tennessee  College of Architecture and Design.

        Montgomery, D. R., & Buffington, J.  M. (1998).  Channel Processes, Classification, and Response. River
        Ecology and  Management, 13-42.

        Murray, B., Hose, G., Eamus, D., & Licari,  D. (2006). Valuation of groundwater-dependent ecosystems: a
        functional methodology incorporating ecosystem services. Australian Journal of Botany , 221-229-

        National Fish and Wildlife Foundation; Bonneville Power Administration. (2004). Finding Balance. Retrieved
        July 24, 2009, from Columbia Basin Water Transactions Program: http://www.cbwtp.org/jsp/cbwtp/index.jsp

        National Fish Habitat Board. (2010). Through a Fish's Eye: The Status of Fish Habitats in the United States
        2010. Association of Fish and Wildlife Agencies, Washington D.C.

        NatureServe.  (2008). Natural Heritage Methodology. Retrieved May 21, 2009, from Products and Services:
        http://www.natureserve.org/prodServices/heritagemethodology.jsp

        Nel, J. L., Roux, D.  J., Cowling, R. M., Abell, R., Thieme, M., Higgins,  J. V,  et al. (2009). Progress  and
        Challenges in Freshwater Conservation Planning. Aquatic Conservation: Marine and  Freshwater Ecosystems,
        474-485.

        Nicholoff, S.  (2003). Wyoming Bird Conservation Plan, Version 2.0. Lander, WY: Wyoming Game and Fish
        Department.
R-8

-------
                                                                                                   References
Norton, D., Wickham, ]., Wade, T., Kunert, K., Thomas, J., & Zeph, a. P. (2009). A Method for Comparative
Analysis of Recovery Potential in Impaired Waters Restoration Planning. Environmental Management, 356-
368.

Noss, R. E, LaRoe III, E. T., & Scott, J. M. (1995). Endangered Ecosystems of the United States: A Preliminary
Assessment of Loss and Degradation. Washington D.C.: National Biological Service; U.S. Department of the
Interior.

Ohio Watershed Network. (2009). Watershed Toolshed. Retrieved July 28, 2009,  from Ohio Watersheds:
http://ohiowatersheds.osu.edu/

Oregon Department of Environmental Quality. (2008). Oregon Water Quality Index Summary Report Water
Years 1998-2007- Hillsboro, Oregon.

Oregon Institute for Natural Resources. (2009). Oregon Biodiversity Information Center. Retrieved September
24, 2011, from Oregon State: http://orbic.pdx.edu/

Perry, J. A, & Vanderklein, E. (1996). Water Quality: Management of a Natural Resource. Wiley-Blackwell.

Poff, N. L. (1996). A Hydrogeography of Unregulated Streams in  the United States and an Examination of
Scale Dependence in Some Hydrological Descriptors. Freshwater Biology, 71-91.

Poff, N. L., Allan, D. J., Bain, M. B., Karr, J. R., Prestegaard, K. L., Richter, B. D., et al. (1997). The Natural
Flow Regime: A Paradigm  for River Conservation and Restoration. BioScience, 47(11) 769-784.

Poff,  N.  (2009). Managing  for Variability  to Sustain Freshwater  Ecosystems.  Journal of Water  Resources
Planning and Management.

Poff,  N.  L., Richter, B.  D., Arthington, A. H., Bunn,  S. E., Naiman,  R. J., Kendy, E.,  et al. (2010). The
ecological limits of hydrologic alteration (ELOHA): A new framework for developing regional environmental
flow standards. Freshwater Biology, 147-170.

Poiani, K.,  Richter, B., Anderson, M., & Richter, H. (2000). Biodiversity Conservation at Multiple Scales.
BioScience, 133-146.

Postel, S., & Richter, B. (2003). Rivers for Life: Managing Water for People and Nature. Island Press.

Postel, S., & Thompson, B. (2005). Watershed protection: Capturing the benefits of nature's water supply
services. Natural  Resources Forum, 98-108.

Power, G.,  Brown, R., &  Imhof, J.  (1999). Groundwater and fish- insights from northern North America.
Hydrologic Processes, 401-422.

Protected Areas  Database  of the United  States Partnership.  (2009).  Retrieved November 11, 2009, from
Protected Lands: http://www.protectedlands.net/padus/

Reidy Liermann, C.A. Olden, J.D., Beechie, T.J., Kennard, M.J., Skidmore, P.B., Konrad, C.P  and H. Imaki.
(2011). Hydrogeomorphic classification of Washington  State rivers to support emerging environmental flow
management strategies. River Research and Applications, doi: 10.1002/rra. 1541

Richter, B. D., Baumgartner, J. V., Powell,  J., & Braun, D. P.  (1996).  A Method for Assessing Hydrologic
Alteration Within Ecosystems. Conservation Biology, 10(4) 1163-1174.
                                                                                                        R-9

-------
Identifying and Protecting Healthy Watersheds
        Richter, B., Mathews, R., Harrison, D., & Wigington, R. (2003)- Ecologically Sustainable Water Management:
        Managing River Flows for Ecological Integrity. Ecological Applications , 206-224.

        Richter, B., Warner, A., Meyer, J., & Lutz, K. (2006). A Collaborative and Adaptive Process for Developing
        Environmental Flow Recommendations. River Research and Applications, 297-318.

        Richter, B. (2007, June).  Meeting Urban Water Demands While Protecting Rivers: A Case Study from the
        Rivanna River in Georgia. Journal of the American Water Works Association, pp. 24-26.

        Riera, J.,  Magnuson, J., Kratz, T.,  & Webster, K. (2000). A geomorphic  template for  the analysis of lake
        districts applied to the Northern Highland Lake District. Freshwater Biology, 301-318.

        Roni, P.,  Beechie, T.J., Bilby, R.E., Leonetti, F.E., Pollock, M.M., & Pess, G.R.  (2002) A review of stream
        restoration techniques and a hierarchical strategy for prioritizing restoration in Pacific Northwest watersheds.
        North American Journal of Fisheries Management 22:1-20.

        Rosgen, D. (1994). A Classification of Natural Rivers. Catena, 169-199-

        Rosgen, D. (1996). Applied River Morphology. Pagosa Springs, CO: Wildland Hydrology Books.

        Sada,  D., Williams,  J.,  Silvey, J.,  Halford,  A,  Ramakka,  J.,  Summers, P., et  al. (2001). Riparian Area
        Management: A guide to managing, restoring, and conserving springs in the Western United States. Technical
        Reference 1737-17- Denver, Colorado: Bureau of Land Management.

        Schiff, R., Kline, M., & Clark, J. (2008). The Vermont  Reach Habitat Assessment Protocol. Waterbury, VT:
        Prepared by Milone and MacBroom, Inc. for the Vermont Agency of Natural Resources.

        Schueler, T. (1994). The Importance of Imperviousness. Watershed Protection Techniques, 100-111.

        Schueler,  T.  (2000).  The Tools of Watershed Protection. In T. Schueler,  & H. Holland, The Practice of
        Watershed Protection. Ellicott City, MD: Center for Watershed Protection.

        Schumm, S. A. (1977). The Fluvial System. New York, NY: John Wiley and Sons.

        Shilling, F. (2007). California Watershed Assessment Manual. Retrieved June 13, 2009, from  University of
        California Davis: http://cwam.ucdavis.edu/

        Simon, A., Doyle, M.,  Kondolf, M., Shields, F. J., Rhoads,  B., McPhillips, M.,  et  al.  (2007).  Critical
        Evaluation of How The Rosgen  Classification  and Associated "Natural Channel Design" Methods Fail to
        Integrate  And Quantify Fluvial Processes and Channel Response. Journal  of the  American Water Resources
        Association, 1117-1131-

        Smart Growth  Network. (2009).  Principles of Smart Growth. Retrieved July 27,  2009, from Smart Growth
        Online: http://www.smartgrowth.org/engine/index.php/principles/

        Smit,  B.,  & Wandel, J. (2006).  Adaptation, Adaptive Capacity and Vulnerability.  Global Environmental
        Change-Human and Policy Dimensions, 282-292.

        Smith, D. R., Ammann, A,  Bartoldus, C., and Brinson, M. M. (1995). An approach for assessing wetland
        functions using hydrogeomorphic classification, reference wetlands, and functional indices. Technical Report
        WRP-DE-9- U.S. Army Engineer Waterways Experiment Station. Vicksburg, MS.  NTIS No. AD A307 121.

        Smith, E., Tran, L., & O'Neill, R.  (2003). Regional Vulnerability Assessment  for the Mid-Atlantic Region:
        Evaluation of Integration Methods and Assessments Results. U.S. Environmental Protection Agency.
R-10

-------
                                                                                                   References
Smith, M.,  de Groot, D., Perrot-Maite, D., & Bergkamp, G.  (2006).  Pay — Establishing payments for
watershed services. Gland, Switzerland: IUCN.

Smith, M. P., Schiff, R., Olivero, A., & MacBroom,  J. (2008). The Active River Area:  A Conservation
Framework for Protecting Rivers and Streams. Boston: The Nature Conservancy.

Sowa, S., Annis, G., Morey, M., & Diamond, D. (2007). A GAP Analysis and Comprehensive Conservation
Strategy for Riverine Ecosystems of Missouri. Ecological Monographs, 301-334.

Springer, A, Stevens, L., Anderson, D., Parnell, R., Kreamer, D., & Flora,  S. (2008). A comprehensive springs
classification system:  integrating geomorphic, hydrogeochemical, and ecological criteria. In L. Stevens, & V.
Meretsky, Aridland Springs in North America:  Ecology and Conservation. Tucson, Arizona: University of
Arizona.

Stacey, P.B., A. Jones and J.  Catlin. (2007).  A User's Guide for the Rapid Assessment of the Functional
Condition of Stream-Riparian Ecosystems in the American Southwest. Wild Utah Project, Salt Lake City, UT.

Stalnaker, C.,  Lamb, B.,  Henriksen, J., Bovee, K., & Bartholow, J. (1995). The Instream Flow Incremental
Methodology. Washington D.C.: National Biological Service; U.S. Department of the Interior.

State of Ohio Environmental Protection Agency. (2009). Statewide Biological  and Water Quality Monitoring
& Assessment. Retrieved  September 24, 2009, from Monitoring and Assessment Section; Division of Surface
Water: http://www.epa.state.oh.us/dsw/bioassess/ohstrat.aspx

Stein, E., A. Fetscher, R. Clark, A. Wiskind, J. Grenier, M. Sutula, J. Collins, and C. Grosso. (2009). Validation
of a wetland rapid assessment method: use of EPA'S level 1-2-3 framework for method testing and refinement.
Wetlands, 29(2): 648-665-

Stevens, L.E.,  Stacey, PB., Jones, A.L., Duff, D., Gourley, C., and J.C. Catlin. (2005). A protocol for rapid
assessment of southwestern stream-riparian ecosystems.  Proceedings of the Seventh Biennial Conference of
Research on the Colorado Plateau titled The Colorado Plateau II, Biophysical, Socioeconomic, and Cultural
Research.  Charles van Riper III and David J. Mattsen Ed.s. pp. 397-420. Tucson, AZ: University of Arizona
Press.

Stoddard, J., Larsen,  D., Hawkins,  C., Johnson,  R., & Norris, R.  (2006). Setting Expectations  for the
Ecological Condition of Streams: The Concept of Reference Condition. Ecological Applications,  1267-1276.

Strager, J., Yuill, C.,  & Wood, P.  (2000). Landscape-based Riparian Habitat  Modeling for Amphibians and
Reptiles using ARC/INFO GRID and ArcView CIS. 2000 ESRI International User Conference. Redlands,
California: Environmental Systems Research Institute (ESRI).

Striegl, R. G., &  Michmerhuizen, C. M.  (1998).  Hydrologic  influence on methane and carbon  dioxide
dynamics  at two north-central Minnesota lakes. Limnology and Oceanography, 1519—1529-

Sundermann, A., Stoll, S., Haase, P.  (2011).  River restoration success depends on the  species pool of the
immediate surroundings.  Ecological Applications, 1962—1971.

Texas Commission on Environmental Quality; Texas Parks and Wildlife Department; Texas Water Development
Board. (2008). Texas Instream Flow Studies: Technical Overview. Texas Water Development Board. Report
369- Retrieved September 20, 2011, from Texas Commission on Environmental Quality: http://www.tceq.
texas.gov/assets/public/permitting/watersupply/water rights/eflows/resourcesisftechnicaloverview.pdf
                                                                                                       R-ll

-------
Identifying and Protecting Healthy Watersheds
       Tharme, R. (2003)- A global perspective on environmental flow assessment: emerging trends in the development
       and application of environmental flow methodologies for rivers. River Research and Applications, 397-441.

       The  Lumber   River   Conservancy.  (2009).   Retrieved   November   12,   2009,  from   http://www.
       lumberriverconservancy.org/lumber river.html

       The Nature Conservancy. (2003). Guidelines for Designing and Selecting Conservation Strategies. The Nature
       Conservancy.

       The Nature Conservancy. (201 la). Conservation by Design. Retrieved December 12, 2011, from The Nature
       Conservancy: http://www.nature.org/ourscience/conservationbydesign/index.htm

       The Nature Conservancy. (201 Ib). ELOHA Toolbox. Retrieved January 27, 2011, from ConserveOnline:
       http://www.conserveonline.org/workspaces/eloha/documents/hydrologic-foundation-0

       The Pennsylvania Game Commission and Pennsylvania Fish and  Boat Commission.  (2005). Pennsylvania
       Comprehensive Wildlife Conservation Strategy.

       Thorp, J., Thorns, M., & DeLong, M. (2006).  The Riverine Ecosystem  Synthesis:  Biocomplexity in River
       Networks Across Space and Time. River Research and Applications,  123-147-

       Thorp,  J., Thorns,  M.,  &  Delong,  M.  (2008).  The Riverine Ecosystem  Synthesis: Toward  Conceptual
       Cohesiveness in Riverine Science. Elsevier.

       Tiner, R.  (2004). Remotely Sensed Indicators for Monitoring the General  Condition of "Natural Habitat" in
       Watersheds: An Application for Delaware's Nanticoke River Watershed. Ecological Indicators,  227—243-

       Tomlinson, M., & Boulton, A.  (2008). Subsurface groundwater dependent ecosystems:  A review of their
       biodiversity, ecological processes and ecosystem services. Waterlines Occasional Paper Number 8.

       Trout Unlimited and Northstar Economics. (2008). The Economic Impact of Recreational Trout Angling in
       the Driftless Area. Trout Unlimited.

       Trust for Public Land. (2009). LandVote. Retrieved July 28, 2009, from LandVote: http://www.tpl.org/what-
       we-do/policy-legislation/landvote.html

       Trust for Public Land. (2010, January). Lower Meramec River Source Water Demonstration Project. Retrieved
       February  16,  2011,  from  Center  for Land  and Water:  http://www.tpl.org/tier3 cd.cfm?content item
       id=23278&folder id=1885

       U.S.  Department of Agriculture Economic Research Service. (2005, September 2). Rural-Urban Commuting
       Area  Codes.  Retrieved  December   11, 2009,  from  Measuring  Rurality:  http://www.ers.usda.gov/Data/
       Rural UrbanCommutingAreaCodes/

       U.S.  Department of Agriculture.  (2009, October 27). National Organic Program.  Retrieved  November 2,
       2009, from Agricultural Marketing Service: http://www.ams.usda.goV/AMSvl.0/NOP

       U.S. Department of Agriculture; U.S. Department of the Interior. (2009). LandFire. Retrieved May 21, 2009,
       from LandFire: http://www.landfire.gov

       U.S.  Environmental Protection Agency. (1987).  Handbook: Ground Water.  U.S. Environmental Protection
       Agency. EPA Number EPA/625/6-87/016.

       U.S.  Environmental Protection Agency. (1990).  Biological Criteria: National Program Guidance for  Surface
       Waters. Washington D.C.: U.S. Environmental Protection Agency. EPA Number EPA 440-5-90-004.
R-12

-------
                                                                                                 References
U.S. Environmental Protection Agency. (1995). America's Wetlands: Our Vital Link Between Land and Water.
U.S. Environmental Protection Agency. EPA Number 4502E

U.S. Environmental Protection Agency. (1997). The Index of Watershed Indicators. Washington D.C.: Office
of Water. EPA Number EPA-841-R-97-010.

U.S. Environmental Protection Agency. (2002). Summary of Biological Assessment Programs and Biocriteria
Development for States,  Tribes, Territories, and  Interstate Commissions:  Streams and Wadeable Rivers.
Washington D.C.: U.S. Environmental Protection Agency. EPA Number EPA-822-R-02-048.

U.S. Environmental Protection Agency. (2003). Getting in Step: A Guide for Conducting Watershed Outreach
Campaigns. Washington D.C.: U.S. Environmental Protection Agency.  EPA Number 841-B-03-002.

U.S. Environmental Protection Agency. (2006a, November 27). Model Ordinances to Protect Local Resources.
Retrieved July 28, 2009, from Nonpoint Source Pollution: http://www.epa.gov/owow/nps/ordinance/.

U.S.  Environmental   Protection  Agency.  (2006b).  Protecting  Water Resources  with Higher Density
Development. Washington D.C. EPA Number 231-R-06-001.

U.S. Environmental Protection Agency. (2006c). Wadeable Streams Assessment. Washington D.C.: Office of
Water. EPA Number 841-B-04-005-

U.S. Environmental Protection Agency.  (2007a, August 14). Principles for the Ecological Restoration of
Aquatic Resources.  Retrieved November 12, 2009, from Office of Wetlands Oceans and Watersheds: http://
www.epa.gov/owow/wetlands/restore/principles.html#l. EPA Number 841-F-00-003.

U.S.  Environmental   Protection  Agency. (2007b).  Reducing  Stormwater Costs  through Low  Impact
Development (LID) Strategies and Practices. Washington D.C.: U.S. Environmental Protection Agency. EPA
Number 841-F-07-006.

U.S. Environmental  Protection  Agency. (2007c, August 14). River Corridor and Wetland Restoration.
Retrieved December 3, 2009, from Wetlands, Oceans, and Watersheds: http://www.epa.gov/owow/wetlands/
restore/

U.S. Environmental Protection Agency. (2008a). Handbook for Developing Watershed Plans to Restore and
Protect Our Waters. Washington, DC: Office of Water. EPA Number 841-B-08-002.

U.S. Environmental Protection Agency. (2008b, December 19). National Aquatic Resource Surveys. Retrieved
January 23, 2009, from  Monitoring and Assessing Water  Quality:  http://water.epa.gov/type/watersheds/
monitoring/nationalsurveys.cfm

U.S. Environmental  Protection  Agency. (2008c, November 17).  The Wadeable  Streams  Assessment: A
Collaborative Survey  of the Nation's Streams. Retrieved January 20, 2010,  from Monitoring and Assessing
Water Quality:  http://water.epa.gov/type/rsl/monitoring/streamsurvey/index.cfm. EPA Number  841-B-06-
002.

U.S. Environmental Protection Agency.  (2009a). National Lakes Assessment: A Collaborative Survey of the
Nation's Lakes. Washington D.C.:  Office of Water and Office of Research and  Development. EPA Number
841-R-09-001.

U.S. Environmental Protection Agency. (2009b). An Assessment of Decision-Making Processes: The Feasibility
of Incorporating Climate Change Information into  Land Protection Planning. Global Change Research
Program, National Center  for  Environmental Assessment, Washington, DC;  EPA Number EPA/600/R-
09/142a.
                                                                                                    R-13

-------
Identifying and Protecting Healthy Watersheds
        U.S. Environmental Protection Agency. (2010). ICLUS VI.3 User's Manual: ARCGIS Tools for Modeling US
        Housing Density Growth. U.S. Environmental Protection Agency, Washington, DC; EPA Number EPA/600/
        R-09/143F. http://cfpub.epa.gov/ncea/global/recordisplay.cfm?deid=205305

        U.S. Environmental  Protection Agency.  (201 la). Inventory of U.S. Greenhouse Gas Emissions and Sinks:
        1990-2009- Washington D.C.; Office of Air. EPA Number 430-R-l 1-005-

        U.S. Environmental protection Agency (201 Ib). Biological assessments: Key Terms and Concepts. Washington
        D.C.; Office of Water. EPA Number EPA 820-F-l 1-006.

        U.S. Environmental protection Agency (201 Ic). A Primer on Using Biological Assessments to  Support Water
        Quality Management. Washington D.C.; Office of Water. EPA Number EPA 810-R-11-01.

        U.S.  Environmental  Protection Agency. (201 Id).  National  River  and Streams  Assessment  Fact Sheet.
        Washington D.C.; Office of Water. EPA Number EPA 941-F-l 1-001.

        U.S. Environmental  Protection Agency.  (201 le, February 15). Regional Vulnerability Assessment Program.
        Retrieved February 15, 2011, from www.epa.gov/reva

        U.S. EPA Science Advisory Board. (2002). A Framework for Assessing and Reporting on Ecological Condition.
        Washington D.C.: U.S. Environmental Protection Agency.

        U.S. Fish & Wildlife Service. (2002). Bull Trout (Salvelinus confluentus) Recovery Plan. U.S. Fish & Wildlife
        Service.

        U.S. Fish and Wildlife Service. (2009, September 4). National Fish Passage Program. Retrieved December 3,
        2009, from http://www.fws.gov/fisheries/fwco/fishpassage/

        U.S. Forest Service (2011). Watershed Condition Framework.  U.S. Department  of Agriculture.  Publication
        Number FS-977-

        U.S. Geological Survey. (1999). National Water Summary on Wetland Resources. U.S. Geological Survey.

        U.S.  Geological  Survey. (2006).  Ohio Aquatic  Gap  Analysis-An  Assessment  of the Biodiversity and
        Conservation Status  of Native Aquatic Animal Species.  Retrieved September 24, 2009, from  Publications
        Warehouse: http://pubs.er.usgs.gov/usgspubs/ofr/ofr20061385

        U.S. Geological  Survey.  (2009a, May 21).  National  Hydrologic Assessment Tool. Retrieved May 21, 2009,
        from Fort Collins Science Center: http://www.fort.usgs.gov/products/Software/NATHAT/

        U.S. Geological Survey. (2009b, May 21). National Water Information System. Retrieved May 21, 2009, from
        Water Resources: http://waterdata.usgs.gov/nwis

        U.S. Geological Survey. (2009c, April 19). National Water Quality Assessment Program (NAWQA). Retrieved
        April 26, 2009, from Water Resources of the United States: http://water.usgs.gov/nawqa/about.html

        U.S. Geological Survey. (2009d, April 17). SPARROW Surface Water Quality Modeling. Retrieved April 26,
        2009, from National Water Quality Assessment Program: http://water.usgs.gov/nawqa/sparrow/

        U.S. Geological  Survey.  (2009e, October  13). StreamStats. Retrieved December 1, 2009, from Office of
        Surface Water: http://water.usgs.gov/osw/streamstats/

        U.S. Government Printing Office. (1972). Report for the Committee on Public Works — Unites States House
        of Representatives with additional  and  supplemental views of H.R. 11896 to  amend  the  Federal Water
        Pollution Control Act. House Report 92-911. 92 Congress, 2nd Session, 11 March 1972, p. 149-
R-14

-------
                                                                                                   References
University of Connecticut Center for Land Use Education and Research. (2009)- Landscape Fragmentation
Tool. Retrieved October 26, 2009, from http://clear.uconn.edu/tools/lft/lft2/index.htm

University  of  Maryland  Center  for  Environmental  Science;  National  Oceanic  and  Atmospheric
Administration. (2009). EcoCheck. Retrieved October 28, 2009, from http://www.eco-check.org/reportcard/
chesapeake/2008/

Vannote, R. L,  Minshall, G. W., Cummins,  K. W.,  Sedell, J. R.,  &  Gushing, C. E.  (1980). The River
Continuum Concept. Canadian Journal of Fisheries and Aquatic Sciences, 37: 130-137-

Vermont Department of Environmental Conservation. (2007, July). Geomorphic Assessment. Retrieved April
27, 2009, from Water Quality Division: http://www.vtwaterquality.org/rivers/htm/rv  geoassess.htm

Vermont Law School  Land Use Institute. (2009). Preparing  for the Next  Flood: Vermont Floodplain
Management. Vermont Law School.

Virginia Commonwealth University. (2009, May 13). Center for Environmental Studies. Retrieved May 21,
2009, from Virginia Commonwealth University: http://www.vcu.edu/cesweb/

Virginia  Department of Conservation and  Recreation. (2008, July). Virginia Conservation Lands Needs
Assessment. Retrieved April 27, 2009, from Natural Heritage:  http://www.dcr.virginia.gov/natural  heritage/
vclna.shtml

Virginia Department of Conservation and Recreation.  (2009). Land Conservation Data Explorer. Retrieved
May 21, 2009, from Virginia Natural Heritage Program: http://www.vaconservedlands.org/gis.aspx

Vogel, R., Sieber, J., Archfield, S., Smith, M. A, & Huber-Lee, A. (2007). Relations Among Storage, Yield
and Instream Flow. Water Resources Research, 43-

Walsh, M., Deeds, J., & Nightingale, B.  (2007). User's Manual and Data Guide to the Pennsylvania Aquatic
Community Classification. Pennsylvania Natural Heritage Program.

Wang, X., & Yin, Z. (1997). Using GIS to Assess the Relationship Between Land Use and Water Quality at a
Watershed Level. Environment International, 103-114.

Watershed Professionals Network. (1999). Oregon Watershed Assessment Manual. Salem, Oregon: Governor's
Watershed Enhancement Board.

Weber, T (2003).  Maryland's Green Infrastructure Assessment. Annapolis, MD: Maryland Department of
Natural Resources.

Weitzell,  R. E., Khoury, M., Gagnon, P., Schreurs, B., Grossman, D., & Higgins,  J. (2003). Conservation
Priorities for  Freshwater Biodiversity in the Upper Mississippi River Basin. Nature Serve and The Nature
Conservancy.

Wells National  Estuarine Research  Reserve;   Southern  Maine  Regional Planning  Commission.  (2009).
Headwaters: A Collaborative Conservation Plan for the Town of Sanford.

Wheeler, B.,  Gowing,  D., Shaw,  S., Mountford, J., & Money, R. (2004). Ecohydrological guidelines for
lowland wetland plant communities. Environment Agency.

Wickham, J., & Norton, D. (2008).  Recovery Potential  as a Means of Prioritizing Restoration of Waters
Identified as Impaired Under the Clean Water Act . Water Practice, 1-11.
                                                                                                      R-15

-------
Identifying and Protecting Healthy Watersheds
        Wiens, J. A. (2002). Riverine Landscapes: Taking Landscape Ecology into the Water. Freshwater Biology, 501-
        515.

        Williams, D.,  & Williams, N. (1998). Invertebrate communities from freshwater springs: What can they
        contribute  to pure  and applied ecology? In L.Botosaneanu, Studies in Chrenobiology.  Leiden: Backhuys
        Publishers.

        Winter, T. (1978). Ground-water component  of lake  water  and  nutrient budgets. Verhandlungen des
        Internationalen Verein Limnologie, 438-444.

        Winter, T., Labaugh, J., & Rosenberry, D. (1988). The design and use of a hydraulic potentiomanometer for
        direct measurement of differences in hydraulic head between groundwater and surface water. Limnology and
        Oceanography, 1209-1214.

        Winter, T.  (1995).  Recent advances in  understanding the  interaction  of groundwater and surface  water.
        Reviews of Geophysics Supplement, 985-994.

        Winter, T, Harvey, J., Franke, O., & Alley, W (1998). Ground Water and Surface Water: A Single Resource.
        U.S. Geological Survey.

        Younger, P. (2006). Groundwater in the Environment. Blackwell Publishing.

        Zencich, S., & Froend, R.  (2001). Guidelines for identification and monitoring of terrestrial vegetation water
        requirements. Terrestrial Phreatophytic Vegetation Research Review Report Number 2001-16.

        Zganjar, C., Girvetz, E., & G., R. (2009). Retrieved October 28, 2009, from Climate Wizard: http://www.
        climatewizard. org/

        Zorn, T. G., Seelbach, P. W, Rutherford, E. S., Willis, T. C., Cheng, S. T, & Wiley, M. J. (2008). A Regional-
        scale Habitat Suitability Model to Assess the Effects  of Flow Reduction on Fish Assemblages  in Michigan
        Streams. Ann Arbor: Michigan Department of Natural Resources; Fisheries Division.
R-16

-------
Acronyms  &  Abbreviations
AES
ANR
BBASC
BBEST
BASINS
BCG
BMP
CADDIS
CRT
CRAM
CREP
CRP
CSP
CWA
CWAM
CWSRF
OCR
DEM
DEP
DEQ
DES
DNR
DWSRF
EDU
EEA
ELOHA
EMAP
EMDS
EPA
EPT
EQIP
ESRI
FDC
Aquatic Ecological System
Agency of Natural Resources
Basin and Bay Area Stakeholder Committee
Basin and Bay Expert Science Team
Better Assessment Science Integrating point & Nonpoint Sources
Biological Condition Gradient
Best Management Practice
Causal Analysis/Diagnosis Decision Information System
Channel Habitat Type
California Rapid Assessment Method
Conservation Reserve Enhancement Program
Conservation Reserve Program
Conservation Security Program
Clean Water Act
California Watershed Assessment Manual
Clean Water State Revolving Fund
Department of Conservation and Recreation
Department of Environmental Management or Digital Elevation Model
Department of Environmental Protection
Department of Environmental Quality
Department of Environmental Services
Department of Natural Resources
Drinking Water State Revolving Fund
Ecological Drainage Unit
Essential Ecological Attribute
Ecological Limits of Hydrologic Alteration
Environmental Monitoring and Assessment Program
Ecosystem Management Decision Support System
Environmental Protection Agency
Ephemeroptera, Plecoptera, Trichoptera
Environmental Quality Incentive Program
Environmental Systems Research Group
Flow Duration Curve
                                                                                      AA-1

-------
Identifying and Protecting Healthy Watersheds
       FEH
       FEMA
       FPZ
       FRCC
       FWS
       GAP
       GDE
       CIS
       GMA
       GPD
       GPS
       GRP
       HAT
       HEFR
       HHEI
       HIP
       HIT
       HSPF
       HUG
       IBI
       1C
       ICLUS
       IFIM
       IHA
       ILWIS
       INSTAR
       IIPCC
       ITI
       KDHE
       LID
       L-THIA
       MBSS
       mlBI
       MMI
       MRB
       NARS
       NAWQA
Fluvial Erosion Hazard
Federal Emergency Management Agency
Functional Process Zone
Fire Regime Condition Class
Fish and Wildlife Service
Gap Analysis Program
Ground water Dependent Ecosystem
Geographic Information System
Growth Management Act
Gallons Per Day
Global Positioning System
Grassland Reserve Program
Hydrologic Assessment Tool
Hydrology-based Environmental Flow Regimes
Headwaters Habitat Evaluation Index
Hydroecological Integrity Assessment Process
Hydrologic Index Tool
Hydrologic Simulation Program Fortran
Hydrologic Unit Code
Index of Biotic Integrity
Impervious Cover
Integrated Climate and Land Use Scenarios
Instream Flow Incremental Methodology
Indicators of Hydrologic Alteration
Integrated Land and Water Information System
Interactive Stream Assessment Resource
Intergovernmental Panel on Climate Change
Index of Terrestrial Integrity
Kansas Department of Health and the Environment
Low Impact Development
Long-Term Hydrologic Impact Assessment
Maryland Biological Stream Survey
Modified Index of Biotic Integrity
Macroinvertebrate Multimetric Index
Major River Basins
National Aquatic Resource Surveys
National Water Quality Assessment
AA-2

-------
                                                                                   Acronyms & Abbreviations
NCDC
NED
NEMO
NFHA
NFIP
NFPP
NHD
NLA
NLCD
NOAA
NPDES
NRCS
NRSA
NSPECT
NWI
NWIS
ONRW
ORAM
ORBIC
OWED
OWOW
PAD
PCA
PFC
PHI
PHWH
PRISM
RASCAL
RCC
RES
ReVA
RIVPACS
RPST
RPT
RSRA
RTE
SAB
National Climatic Data Center
National Elevation Dataset
Nonpoint Education for Municipal Officials
National Fish Habitat Assessment
National Flood Insurance Program
National Fish Passage Program
National Hydrography Dataset
National Lakes Assessment
National Land Cover Database
National Oceanic and Atmospheric Administration
National Pollutant Discharge Elimination System
Natural Resources Conservation Service
National Rivers and Streams Assessment
Nonpoint Source Pollution and Erosion Comparison Tool
National Wetlands Inventory
National Water Information System
Outstanding National Resource Water
Oregon Rapid Assessment Method
Oregon Biodiversity Information Center
Oregon Watershed Enhancement Board
Office of Wetlands, Oceans, and Watersheds
Protected Areas Database
Principal Components Analysis
Proper Functioning Condition
Physical Habitat Index
Primary Headwaters Habitat
Parameter-elevation Regressions on Independent Slopes Model
Rapid Assessment of Stream Conditions Along Length
River Continuum Concept
Riverine Ecosystem Synthesis
Regional Vulnerability Assessment
River Invertebrate Prediction and Classification System
Recovery Potential Screening Tool
Regime Prescription Tool
Rapid Stream and Riparian Assessment
Rare, Threatened, or Endangered
Science Advisory Board
                                                                                                  AA-3

-------
Identifying and Protecting Healthy Watersheds
       SABS
       SGA
       SDWA
       SPARROW
       SSURGO
       STORET
       SWAP
       SWMM
       SYE
       TCEQ
       TALU
       TDR
       TEA
       TIFP
       TMDL
       TNC
       TPL
       UMRB
       USA
       USDA
       USFWS
       USGS
       VCLNA
       VSP
       VST
       WAM
       WAT
       WATERS
       WHIP
       WQI
       WQS
       WQX
       WRP
       WSA
       WWF
Suspended and Bedded Sediments
Stream Geomorphic Assessment
Safe Drinking Water Act
Spatially Referenced Regressions On Watershed Attributes
Soil Survey Geographic Database
STOrage and RETrieval
Source Water Assessment Program
Storm Water Management Model
Sustainable Yield Estimator
Texas Commission on Environmental Quality
Tiered Aquatic Life Use
Transfer of Development Rights
Targeted Ecological Area
Texas Instream Flow Program
Total Maximum Daily Load
The Nature Conservancy
Trust for Public Land
Upper Mississippi River Basin
United States of America
United States Department of Agriculture
United States Fish & Wildlife Service
United States Geological Survey
Virginia Conservation Lands Needs Assessment
Visual Sample Plan
Valley Segment Types
Watershed Assessment Manual
Watershed Assessment Tool
Watershed Assessment, Tracking & Environmental ResultS
Wildlife Habitat Incentives Program
Water Quality Index
Water Quality Standards
Water Quality Exchange
Wetlands Reserve Program
Wadeable Streams Assessment
World Wildlife Fund
AA-4

-------
Appendix A.  Examples of
Assessment Tools
Classifying Freshwater Ecosystems
Developer: The Nature Conservancy
More Information: http://www.conservationgateway.org/topic/ecoregional-assessment
Freshwater systems are comprised of a variety of ecosystems that differ in geophysical, hydrological and
ecological  characteristics. Classifying and  mapping these distinctions is critical to defining the variety of
habitats and processes that comprise a large and complex freshwater system. Classification products are used
in biodiversity planning as "coarse-filter" conservation elements to "capture" many common, untracked, and
unknown species, and to identify the variety of environments and processes that support species and natural
communities across a region of interest. They can also be used to identify specific ecosystem attributes for
targeting strategies to protect and restore watershed health,  such as identifying areas  of high ground water
potential, or areas that provide high water yields from surface  runoff and are sensitive to a variety of land uses.
                                   a. On* Aquatic Zoogeography Urwl
                                           t>. Ecological Drainage Units within
                                            one Aquatic ZoogBograpnlc Unit
                                                 r Aquatic Ecological Systems wi:hr,
                                                  one Ecological Drainage Uffll
                                                        d. MacrofrtaMals wlhin one
                                                          Aquatic Ecological Syslem
              The Nature Conservancy's Freshwater Classification System (Weitzell et al., 2003).
                                                                                        A-l

-------
Identifying and Protecting Healthy Watersheds
        MapWindow
        Developer: Idaho State University Geospatial Software Lab
        More Information: http://www.mapwindow.org/
        The MapWindow application is a free GIS that can be used for the following:
            •   As an alternative desktop GIS.
            •   To distribute data to others.
            •   To develop and distribute custom spatial data analyses.
        MapWindow is free to use and redistribute to other users. Unlike other free tools, MapWindow is more than
        just a data viewer; it is an extensible geographic information system. This means that plug-ins can be created to
        add additional functionality (e.g., models, special viewers, hot-link handlers, data editors, etc.)  and these can
        be passed along to other users.
        ArcGIS
        Developer: Environmental Systems Research Institute (ESRI)
        More Information: http://www.esri.com/index.html
        ArcGIS is software for visualizing, managing, creating, and analyzing geographic data. Using ArcGIS, one can
        understand the geographic context of data, allowing the user to see relationships and identify patterns.
        IDRISI Taiga
        Developer: Clark Labs
        More Information: http://www.clarklabs.org/products/product-features.cfm
        IDRISI  Taiga is an integrated GIS and Image Processing software solution
        providing nearly 300 modules for the analysis and display of digital spatial
        information. IDRISI offers an extensive set of GIS and Image Processing tools
        in a single  package. With IDRISI, all analytical features come standard—
        there is no need to  buy add-ons to extend research capabilities.
        Integrated Land and Water Information System (ILWIS)
        Developer: World Institute for Conservation and Environment
        More Information: http://52north.org/
        ILWIS is free remote sensing and GIS software, which integrates image, vector, and thematic data in one unique
        and powerful desktop package. ILWIS delivers a wide range of features including import/export, digitizing,
        editing,  analysis and display of data, as well as production of quality maps. ILWIS software is renowned for its
        functionality,  user-friendliness and low cost, and has established a wide user community over the years of its
        development.


        Ecosystem Management Decision Support (EMDS)
        Developer: U.S.  Forest  Service, InfoHarvest,  Rules of Thumb, The  Redlands  Institute  (University of
        Redlands)
        More Information: http://www.institute.redlands.edu/emds/
        The EMDS system is an application framework  for  knowledge-based decision support of  environmental
        analysis  and planning at any geographic scale. EMDS integrates state-of-the-art GIS, as well  as knowledge-
        based reasoning and decision modeling technologies to provide decision support for the adaptive management
        process of ecosystem management.
A-2

-------
                                                                                                    Appendix A
NetMap
Developer: Earth Systems Institute
More Information: http://www.netmaptools.org/
NetMap is  a community  based  watershed science system  comprised  of a digital
watershed database, analysis  tools, and forums. The state-of-the-art desktop GIS analysis
tools, containing approximately 50 functions  and 60 parameters, address watershed  m.*    . • •
attributes and processes such as fluvial geomorphology, fish habitat, erosion, watershed  | NwllVlCtD
disturbance, road networks,  wildfire, hydrology, and large woody debris, among others.
NetMap is designed to integrate with ESRI ArcMap 9.2. Key features include:
    •   Decision support.  NetMap can inform fish habitat management, forestry, pre and
        post fire planning, restoration, monitoring, research, and education.
    •   Uniform data structure.  Channel segments (and tributary confluence nodes) are
        defined  as  the spatial relationship between  segments and hillsides. All watershed
        information is routed downstream revealing  patterns of watershed attributes at any
        spatial scale defined  by stream networks.
    •   Universal,  region-wide database. A large  and  expanding region-wide watershed
        database allows users easy access to hundreds of watersheds for rapid analyses and to
        facilitate comparative analyses across landscapes, states and regions.
    •   A new analysis paradigm and methods framework. In the context of watershed
        analysis, software tools  are distributed  with the  analysis  allowing stakeholders  to
        conduct custom analyses as new questions arise, as new data becomes available (or as
        more  accurate data  becomes available),  or as  watershed conditions change  (wildfires
        or land use activities).
    •   A "living analysis." NetMap watershed databases do not become dated over time
        because  "field link" tools allow rapid  validation  of predicted  attributes  and thus
        databases are made more accurate with use.
    •   NetMap is community based. As  new watershed databases are developed and new
        tools are created, they become immediately available to all users.


Analytical Tools Interface for Landscape Assessments (ATtlLA)
Developer: U.S. Environmental Protection Agency
More Information: http://www.epa.gov/esd/land-sci/attila/index.htm
ATtlLA  is an easy to  use ArcView extension that calculates  many commonly used landscape  metrics.  By
providing an intuitive interface, the extension provides the ability to generate landscape  metrics to a wide
audience, regardless of their  GIS knowledge level. ATtlLA is a robust, flexible program. It accepts data from a
broad range of sources  and is equally suitable for use across all landscapes, from deserts to rain forests to urban
areas, and may be used at local, regional, and national scales.


Impervious Surface Analysis Tool
Developer: NOAA  Coastal Services  Center and  the University of Connecticut  Nonpoint Education  for
Municipal Officials (NEMO) Program
More Information: http://www.csc.noaa.gov/digitalcoast/tools/isat/
The Impervious Surface Analysis Tool is  used to calculate  the percentage of impervious surface area of user-
selected geographic areas (e.g., watersheds,  municipalities, subdivisions). The tool is available as an ArcView
3.x, ArcGIS 8.x, or ArcGIS 9.x extension.
                                                                                                         A-3

-------
Identifying and Protecting Healthy Watersheds
        Land Change Modeler
        Developer: Clark Labs
        More Information: http://www.clarklabs.org/products/Land-Change-Modeler-Overview.cfm
        The Land Change Modeler is land cover change analysis and prediction software that also incorporates tools
        that allows one to analyze, measure, and project the impacts on habitat and biodiversity. Land Change Modeler
        includes a suite of tools that address the complexities of change analysis, resource management, and habitat
        assessment while maintaining a simple and automated workflow. The Land Change Modeler is included within
        the IDRISI GIS and Image Processing software and is  available as a software extension for use with ESRI's
        ArcGIS product.

        CommunityViz
        Developer: Placeways
        More Information: www.placeways.com/communityviz
        CommunityViz planning software is an extension for ArcGIS Desktop. Planners,  resource managers, local
        and regional  governments, and many others use CommunityViz to help  make planning decisions about
        development, land use, transportation, and conservation. A GIS-based decision-support tool, CommunityViz
        "shows" the implications of different plans and choices. Both flexible and robust, it supports scenario planning,
        sketch planning, 3-D visualization, suitability analysis, impact assessment, growth modeling, and other popular
        techniques. Its many layers of functionality make it useful for a wide range of skill levels and applications.
        NatureServe Vista
        Developer: NatureServe
        More Information: http://www.natureserve.org/prodServices/vista/overview.isp
        NatureServe Vista is a powerful, flexible, and free decision support system that helps users integrate conservation
        with land use and resource planning of all types. Planners, resource managers, scientists, and conservationists
        can use NatureServe Vista to:
            •   Conduct conservation planning and assessments.
            •   Integrate  conservation values with other planning and assessment activities, such as
                land use, transportation, energy, natural resource, and ecosystem-based management.
            •   Evaluate,  create, implement, and  monitor  land  use and  resource  management
                scenarios  designed to achieve conservation goals within  existing economic, social,
                and political contexts.
                                                          as  •
Version 2.5 of NatureServe Vista now integrates interoperability with NOAA's Nonpoint Source Pollution
and  Erosion Comparison  Tool  (NSPECT),  as  well
other hydrologic models to  support integrated land-water
assessment and planning. NatureServe Vista operates on
the ESRI ArcGIS  platform. NatureServe Vista supports
quantitative and defensible  planning approaches  that
incorporate science, expert opinion, community values,
and GIS. It works with a number of other useful software
tools to incorporate land use, economics, and ecological
and  geophysical modeling. The  flexible approach and
structure of Vista is suitable for planning and GIS  experts,
as well as those with minimal training and support.
A-4

-------
                                                                                                    Appendix A
Miradi
Developer: Conservation Measures Partnership
More Information: http://www.miradi.org
Miradi is a user-friendly program that allows nature conservation practitioners to design, manage, monitor, and
learn from their projects to more effectively meet their conservation goals. The program guides users through
a series of step-by-step interview wizards, based on the Open Standards for the  Practice of Conservation. As
practitioners go through these steps, Miradi helps them to define their project scope, and design conceptual
models and spatial maps of their project site. The software helps users to prioritize threats, develop objectives
and actions, and select monitoring indicators to assess the effectiveness of their strategies. Miradi also supports
the development  of workplans, budgets,  and other tools to  help practitioners implement and  manage their
project. Users  can export Miradi project data to reports or, in the future, to a central database to share their
information with other practitioners.


Habitat Priority Planner
Developer: National Oceanic and Atmospheric Administration (NOAA)
More Information: http://www.csc.noaa.gov/digitalcoast/tools/hpp/
The Habitat Priority Planner is a spatial decision-support tool (for  ArcGIS)  designed to assist  users  in
identifying high-priority areas in  the landscape or seascape for land use,  conservation, climate  change
adaptation, or  restoration action. The Habitat Priority Planner packages several landscape-based spatial analyses
for the intermediate GIS user. Scenarios can be easily displayed and changed, making this a helpful companion
tool when working with a group. In addition to the scenarios, the tool also generates reports, maps, and data
tables.


Causal Analysis/Diagnosis Decision Information System (CADDIS)
Developer: U.S. Environmental Protection Agency
More Information: http://cfpub.epa.gov/caddis/
CADDIS is an online application that  helps scientists  and  engineers find, access, organize, use,  and share
information to conduct causal evaluations in aquatic  systems. It  is based on  EPA's Stressor Identification
process, which is a formal method for identifying causes of impairments in aquatic systems.


Better Assessment Science Integrating Point and Nonpoint Sources (BASINS)
Developer: U.S. Environmental Protection Agency
More Information: http://water.epa.gov/scitech/datait/models/basins/index.cfm
BASINS is a desktop-based, multipurpose environmental analysis system designed for use by regional, state,
and local agencies in performing watershed and water  quality-based studies.  This system  makes it possible
to quickly assess large amounts of point source and nonpoint source data in a format that is easy to use and
understand.  BASINS allows the user to assess water quality  at selected stream sites or throughout  an entire
watershed. This tool integrates  environmental data,  analytical  tools,  and modeling programs to  support
development of cost-effective approaches to watershed management and environmental protection.


Visual Sample Pkn (VSP)
Developer: U.S. Department of Energy
More Information: http://vsp.pnl.gov/index.stm
VSP is  a software tool that supports the development of  a defensible sampling plan based  on statistical
sampling  theory  and the  statistical analysis of sample  results to support confident  decision making. VSP
couples visualization capabilities with optimal sampling design and statistical analysis strategies.
                                                                                                         A-5

-------
Identifying and Protecting Healthy Watersheds
        Nonpoint Source Pollution and Erosion Comparison Tool (NSPECT)
        Developer: National Oceanic and Atmospheric Administration (NOAA)
        More Information: http://www.csc.noaa.gov/digitalcoast/tools/nspect/
        NSPECT helps predict potential water quality  impacts to rivers and streams from nonpoint source pollution
        and erosion. Users first enter information about their study area (land cover, elevation, precipitation, and soil
        characteristics) to create the base data layer. They can then add different land cover change scenarios (such as
        a new developed area)  to obtain information about potential changes in surface water runoff, nonpoint source
        pollution, and erosion.


        Spatially Referenced Regressions On Watershed Attributes (SPARROW)
        Developer: U.S. Geological Survey                                      Monitoring Data    *+  Qe°9raPhlLD!taLjyer5
        More Information: http://water.usgs.gov/nawqa/sparrow/
Predpitat
                                                                            O£?^;vv
        SPARROW is a modeling tool for the regional interpretation of water
        quality  monitoring data. The model relates instream water quality
        measurements  to  spatially  referenced  characteristics  of  watersheds,
        including  contaminant sources and  factors  influencing terrestrial  and
        aquatic transport. SPARROW empirically estimates the origin and fate
        of contaminants in river networks and quantifies  uncertainties in model
        predictions.

        ArcHydro
        Developer: University of Texas at Austin Center for Research in Water Resources
        More Information: http://resources.arcgis.com/content/hydro-data-model
        The ArcHydro  Data Model  can be defined  as a geographic database containing a GIS representation  of a
        Hydrological Information System  under  a case-specific database design, which is extensible,  flexible,  and
        adaptable to user requirements. It takes advantage of the next generation of spatial data in Relational Database
        Management Systems, the geodatabase model. Conceptually, it is  a  combination of GIS objects enhanced
        with the capabilities of a relational database to allow for relationships, topologies, and geometric networks.
        ArcHydro facilitates  a variety of GIS-based hydrologic analyses including watershed delineation, stream
        network mapping, and watershed modeling.


        Indicators of Hydrologic Alteration
        Developer: The Nature Conservancy
        More Information: http://www.nature.org/initiatives/freshwater/conservationtools/artl7004.html
        IHA is a software program that provides useful  information  for those trying to understand the  hydrologic
        impacts of human  activities or trying to develop environmental flow recommendations for water managers.
        This software  program assesses 67 ecologically-relevant statistics derived  from daily hydrologic data.  For
        instance, IHA can calculate the timing and maximum flow  of each year's largest flood event or  lowest flows,
        then calculate the mean and variance of these values over a selected period of time. IHA's comparative analysis
        can then help statistically describe how these patterns have changed for a particular river or lake, due to abrupt
        impacts such as dam construction, or more gradual trends associated with  land and water use changes.
A-6

-------
                                                                                                 Appendix A
Water Budget Tools
A water budget is a conceptual model for understanding different water inflows and outflows of any given
system. It can be developed in order to evaluate the relative importance of surface water and ground water
inflows and outflows to a particular aquatic ecosystem or a conservation  area as a whole. The relationships
between the system and its inflows and outflows are depicted using a figure to represent the system and arrows
pointed toward or away from the figure and scaled in size to match their direction and magnitude, respectively.
Where flow values have not been measured,  estimates can  be developed from  sources such as local climate
stations, flow gaging stations, the Parameter-elevation Regressions  on Independent Slopes Model (PRISM),
or monthly average reference evapotranspiration values from the U.S. Bureau of Reclamation. In the case of
wetland water budgets, for example, there are four potential water inputs, each of which has a corresponding
potential output:
                                                       Surface water outflow (SWO).
                                                       Ground water outflow (GWO).
                                                       Tidal outflow (TO).
        Surface water inflow (SWI).
        Ground water inflow (GWI).
        Tidal inflow (TI).
        Precipitation (P).                            4.  Evapotranspiration (ET).
Although a water budget alone typically does not incorporate enough detail to form the basis for management
plans or policy decisions, a water budget can be a helpful tool for identifying data gaps and research needs and
planning future directions for resource management (Brown J., Wyers, Aldous, & Bach, 2007).
                                                                             High water
                                                                               table
 Components of the wetland water budget. (P+SWI+GWI=ET+SWO+GWO+AS, where P is precipitation, SWI is
 surface water inflow, SWO is surface water outflow, GWI is ground water inflow, GWO is ground water outflow,
 ET is evapotranspiration, and AS is change in storage (Carter, 1996).


Hydrologic Engineering Center Regime Prescription Tool (HEC-RPT)
Developer: The Nature Conservatory, U.S. Army Corps of Engineers
More Information: http://www.nature.org/initiatives/freshwater/conservationtools/hecrpt.html
HEC-RPT is a visualization tool that is designed to complement  existing software packages by facilitating
entry, viewing, and documentation of flow recommendations in real-time, public settings. The software was
developed in support of the Sustainable Rivers Project, a national partnership between the U.S. Army Corps of
Engineers and TNC to improve the health of rivers by changing the  operations of Corps dams.
                                                                                                       A-7

-------
Identifying and Protecting Healthy Watersheds
        Hydrologic Engineering Center Geospatial Hydrologic Modeling Extension (HEC-GeoHMS)
        Developer: Army Corps of Engineers
        More Information: http://www.hec.usace.army.mil/software/hec-geohms/
        The HEC-GeoHMS has been developed as a geospatial hydrology toolkit for engineers and hydrologists with
        limited GIS experience. HEC-GeoHMS uses ArcView and the Spatial Analyst extension to develop a number
        of hydrologic modeling inputs for the Hydrologic Engineering Center's Hydrologic Modeling System, HEC-
        HMS. Analyzing digital terrain data, HEC-GeoHMS transforms the drainage paths and watershed boundaries
        into a hydrologic data structure that represents the  drainage network. The program allows users  to visualize
        spatial information, document watershed characteristics, perform spatial analysis, and delineate subbasins and
        streams. HEC-GeoHMS' interfaces, menus, tools, buttons, and context-sensitive online help allow the user to
        expediently create hydrologic inputs for HEC-HMS.


        The Hydroecological Integrity Assessment Process (HIP) Tools
        Developer: U.S. Geological Survey
        More Information: http://www.fort.usgs.gov/Resources/Research Briefs/HIP.asp
        USGS scientists developed  the  HIP and  a suite  of tools for conducting a hydrologic classification of
        streams, addressing instream flow needs, and assessing past and proposed hydrologic alterations on stream
        flow and/or other ecosystem components. The HIP recognizes that stream flow is strongly related to many
        critical physiochemical components of rivers, such  as dissolved oxygen, channel geomorphology, and water
        temperature, and can be considered a "master variable"  that limits the disturbance, abundance, and diversity of
        many aquatic plant and animal species.
        The HIP is intended for use by any federal or state agency, institution, private firm, or nongovernmental entity
        that has responsibility for or interest in managing and/or regulating streams to  restore or maintain ecological
        integrity. In addition, the HIP can assist researchers by identifying ecologically relevant, stream-class-specific
        hydrologic indices that adequately characterize the  five major  components of the flow regime (magnitude,
        frequency, duration, timing, and rate of change) by using 10 nonredundant indices. The HIP is developed at a
        state or other large geographical area scale but is applied at the stream reach level.

        StreamStats
        Developer: U.S. Geological Survey
        More Information: http://water.usgs.gov/osw/streamstats/
        StreamStats  is  a web-based GIS that provides users  with access  to an  assortment of analytical  tools that are
        useful for  water resources planning and management, and for engineering design applications, such as the
        design of  bridges.  StreamStats allows users  to easily  obtain monthly stream flow statistics, drainage basin
        characteristics, and other information for user-selected  sites on streams. StreamStats users can choose locations
        of interest from an interactive map and obtain information for these locations. If a user selects the location of
        a USGS data collection station, the user will be provided with a list of previously published  information for
        the station. If a user selects a location where no data are available (an ungaged site), StreamStats will delineate
        the drainage basin boundary, measure basin characteristics and estimate monthly stream flow statistics for the
        site. These estimates assume natural flow conditions at  the site. StreamStats also allows users to identify stream
        reaches that are upstream or downstream from user-selected sites, and  to identify and obtain information for
        locations along the streams where activities that may  affect stream flow conditions are occurring.

-------
                                                                                                  Appendix A
Massachusetts Sustainable Yield Estimator
Developer: U.S. Geological Survey
More Information: http://pubs.usgs.gov/sir/2009/5227/pdf/sir2009-5227-508.pdf; http://ma.water.usgs.gov/
sarch/software/sye  mainpage.htm
The Massachusetts Sustainable-Yield Estimator is a decision-support tool  that calculates a screening-level
approximation of a basin's sustainable yield, defined as the difference between natural stream flow and the flow
regime required to support desired uses, such as aquatic habitat. A spatially-referenced database of permitted
surface water and  ground water withdrawals and discharges is used to calculate daily stream flows at ungaged
sites; however, impacts from septic-system discharge, impervious area, non-public water-supply withdrawals
less than 100,000 gpd, and impounded  surface water bodies are not accounted for  in  these stream flow
estimates.  Because this tool was developed with considerations specific to the hydrology of Massachusetts,
it can potentially  be  adapted for use in other New England states, but may not be applicable outside  this
geographic region.


Tools for Understanding Ground Water and Biodiversity
Developer: The Nature Conservancy
More Information: http://www.srnr.arizona.edu/nemo/WebDocs/Groundwater%20Methods%20Guide%20
TNC%201an08.pdf
This appendix offers a brief discussion of several tools that can be used with the assistance of experts in the field
to develop an understanding of the  relationship between ground water and biodiversity. The tools discussed
address the following topics: modeling recharge areas, seepage runs, base flow as a percentage of annual stream
flow, water table data, Forward Looking Infrared Remote Sensing, water chemistry analysis, and environmental
tracer analysis. Both motivations and data requirements for using  these tools as well as  the limitations  of the
tools are considered.

Long-Term Hydrologic Impact Assessment (L-THIA)
Developer: Local Government  Environmental Assistance Network
More Information: http://www.ecn.purdue.edu/runoff/lthianew/
The L-THIA model was developed as an online tool to support the assessment of land  use changes on water
quality.  Based on  community-specific climate  data,  L-THIA estimates  changes  in  recharge, runoff,  and
nonpoint source pollution resulting from past or proposed development. As a quick and  easy-to-use approach,
L-THIA's results can be used to  generate community awareness of potential long-term problems and to support
planning aimed at minimizing disturbance of critical areas. L-THIA assists in the evaluation of potential effects
of land use change and identifies the  best location of a particular land use so as to have minimum impact on a
community's natural environment.


Low Impact Development (LID) Urban Design Tools Web site
Developer: Low Impact Development Center (through a cooperative assistance agreement with EPA)
More Information: http://www.lid-stormwater.net/index.html
The LID Urban Design Tools  website was  developed  to provide guidance to  local governments, planners,
and engineers  for developing,  administering, and incorporating LID into their aquatic resource  protection
programs.  LID technology is an alternative comprehensive approach to stormwater management. It can be
used to address a wide range of wet weather flow issues, including combined sewer overflows, stormwater
runoff, and pollutant loading.
                                                                                                       A-9

-------
Identifying and Protecting Healthy Watersheds
        GeoTools
        Developer: Brian Bledsoe
        More Information: http://www.engr.colostate.edu/^bbledsoe/GeoTool/
        To improve watershed management  in the context of changing land uses,  GeoTools estimates  long-term
        changes in stream erosion potential, channel processes, and instream disturbance regime. The models include
        a suite of stream/land use management modules designed to operate with either continuous or single event
        hydrologic input in a variety of formats. The tools can also be used as a post-processor for the Storm Water
        Management Model (SWMM) and Hydrologic Simulation Program Fortran (HSPF) model (included in EPA's
        BASINS), as well as for any general time series of discharges. Based on the two input channel geometry and
        flow series,  the various modules can provide users with estimates of the following characteristics for pre and
        post  land use change  conditions: (1) the temporal distribution of hydraulic parameters including shear stress,
        specific stream power, and potential mobility of various particle sizes; (2)  effective discharge/sediment yield;
        (3) potential changes in sediment  transport and yield as  a result of altered flow and sedimentation regimes;
        (4) frequency, depth, and duration of bed scour; and (5) several geomorphically relevant  hydrologic metrics
        relating to channel  form, flow effectiveness, and "flashiness."


        Regional Vulnerability Assessment (ReVA) Environmental Decision Toolkit
        Developer: U.S. Environmental Protection Agency
        More Information: http://amethyst.epa.gov/revatoolkit/Welcome.isp
        EPA's ReVA program is designed to produce the methods needed  to  understand
        a region's environmental quality and  its spatial pattern. The objective is to assist
        decision makers in making better-informed decisions and in estimating the large-
        scale changes that might result from their actions.
A-10

-------
Appendix  B.  Sources  of  National
Data
Watershed Boundary Dataset
Source: U.S. Geological Survey and Natural Resources Conservation Service
More Information: http://www.ncgc.nrcs.usda.gov/products/datasets/watershed/
Watershed boundaries define the aerial extent of surface water drainage to a point. Hydrologic Unit Codes
(HUCs) are used to identify each hydrologic unit and are organized in a hierarchical fashion. The first level of
classification divides the nation into 21 major geographic areas, or regions. The second level of classification
divides the 21 regions into  221 subregions. The third  level of classification subdivides the subregions into
378 hydrologic accounting units. The fourth level of classification subdivides the hydrologic accounting units
into  2,264 cataloging units. The fifth level of classification subdivides these into watersheds  and the sixth
level subdivides watersheds into sub-watersheds. A hydrologic unit has a single flow  outlet except in  coastal
or lakefront areas.  However, multiple hydrologic units  must be combined to  represent the true hydrologic
watershed in many instances.


National Hydrography Dataset (NHD)
Source: U.S. Geological Survey
More Information: http://nhd.usgs.gov/
The NHD is a comprehensive set  of spatial data representing the  surface water
of the United States using common features such as lakes, ponds, streams,  rivers,
canals, and oceans. These data are designed to be used in general mapping and in £"""»"™™ro>™«ri»!*.,»„,»„re
the analysis of surface water systems using GIS.


National Elevation Dataset (NED)
Source: U.S. Geological Survey
More Information: http://ned.usgs.gov/
The NED  replaces Digital Elevation Models (DEMs) as  the primary elevation data product of the USGS.
The  NED is a seamless dataset with  the  best available raster elevation
data of the conterminous United States, Alaska, Hawaii, and territorial
islands. The NED  is updated on a nominal two month cycle to integrate
newly available, improved elevation source data. All NED data are public
domain. The NED is derived from diverse source data that are processed to
a common coordinate system and  unit of vertical measure. NED  data are
available nationally (except for Alaska) at resolutions of 1 arc-second (about
30 meters) and 1/3 arc-second (about 10 meters), and  in limited  areas at
1/9 arc-second (about 3 meters).


Soil Survey Geographic Database (SSURGO)
Source: Natural Resources Conservation Service
More Information: http://soils.usda.gov/survey/geography/ssurgo/
SSURGO is the most detailed level of soil mapping performed by  the NRCS. The soil maps  in SSURGO are
created using field mapping methods based on national standards. SSURGO digitizing duplicates the original
soil survey maps.  This level  of mapping is  designed for use by landowners, townships, and county natural
resource planning and management. The user should be knowledgeable of soils data and their characteristics.
                                                                                                B-l

-------
Identifying and Protecting Healthy Watersheds
        National Land Cover Database (NLCD)
        Source: Multi-Resolution Land Characteristics Consortium
        More Information: http://www.mrlc.gov/
        NLCD is a national land cover database with several independent data layers, which allow users a wide variety
        of potential applications. The data are provided at a resolution of 30 meters and include 21 classes of land
        cover, estimates of impervious cover, and tree canopy cover.


        Fire Regime Condition Class (FRCC)
        Source: U.S. Department of the Interior
        More Information: http://frcc.gov/
        LANDFIRE Rapid Assessment FRCC delineates  a standardized index to measure the departure of current
        conditions from reference conditions. FRCC is defined as a relative measure describing the degree of departure
        from the  reference fire regime. This  departure results in changes to one (or more) of the following ecological
        components: vegetation  characteristics; fuel  composition; fire  frequency, severity,  and  pattern; and other
        associated disturbances. These data can be downloaded for any region of the country to evaluate the degree of
        departure from the natural fire regime.


        National Climate Data Center (NCDC)
        Source: National Oceanic and Atmospheric Administration
        More Information: http://www.ncdc.noaa.gov/oa/ncdc.html
        NCDC is the world's largest  active archive of weather data. NCDC produces numerous climate publications
        and responds to data requests from all over the world. Accurate weather data are required by many watershed
        modeling programs and can be obtained from NCDC.


        Climate Wizard
        Source: The Nature Conservancy, University of Washington, University of Southern Mississippi
        More Information: http://www.climatewizard.org/
        ClimateWizard  enables  technical and non-technical audiences  alike  to  access  leading  climate  change
        information and visualize the impacts anywhere on Earth.  The first  generation of this web-based program
        allows the user to choose a state or country and both assess how climate has changed over time and to project
        what future changes are predicted to occur in a given area. ClimateWizard represents the first time  ever the full
        range of climate history and impacts for a landscape have been brought together in a user-friendly format.


        Integrated Climate and Land Use Scenarios (ICLUS)
        Source: U.S. Environmental Protection Agency
        More Information: http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=205305
        ICLUS is an ArcGIS extension that derives land use change projections that are consistent with Special Report
        on Emissions Scenarios (SRES)  driving global circulation models and other land-use change modeling efforts.
        The residential housing and impervious surface datasets provide a substantial first step toward comprehensive
        national land use/land cover scenarios, which have broad applicability for integrated  assessments as these data
        and tools  are publicly available.
B-2

-------
                                                                                                   Appendix B
Water Quality Exchange (WQX)
Source: U.S. Environmental Protection Agency
More Information: http://www.epa.gov/storet/wqx/index.html
EPA developed the National STOrage and RETrieval (STORET) Data Warehouse in 2001 to store and make
available water quality data collected by federal agencies, states, tribes, watershed organizations and universities.
A chief goal of the national  data warehouse has always been to encourage data sharing and to support national,
regional, and local analyses of water quality data collected around the country.  Until now, to upload water
quality data into STORET, users needed to operate the Oracle-based STORET database. This was cumbersome
and difficult for many users. The Water Quality Exchange (WQX)  is a new framework that makes it easier to
submit and share water quality monitoring data over the Internet. EPA will continue to maintain STORET
to ensure  that data of documented quality are  available across jurisdictional and organizational boundaries.
However,  with WQX, groups who collect water quality data no longer need to use STORET to submit their
information to  the National STORET Data Warehouse. Ease of use will encourage more groups to transfer
their data to the Warehouse, where it will be of value to federal, state, and local water quality managers  as well
as the public.


National Water Information System (NWIS)
Source: U.S. Geological Survey
More Information: http://waterdata.usgs.gov/nwis/help?nwisweb  overview
The USGS maintains a distributed network of computers and fileservers for the acquisition, processing, review,
dissemination,  and  long-term storage of water  data collected at  over 1.5  million sites  around  the country
and at some border and territorial sites. This distributed network  of computers is  called the National Water
Information System (NWIS). Many types  of data are stored in NWIS, including comprehensive information
for site characteristics,  well construction details, time-series data for gage height, stream flow, ground water
level, precipitation, and physical and chemical properties of water. Additionally, peak flows, chemical analyses
for discrete samples of water, sediment, and biological media are accessible within NWIS. NWISWeb provides
a framework to obtain data on the basis of category, such as surface water, ground water, or water quality, and
by geographic area.  Further refinement is possible by choosing specific site-selection criteria and by defining
the output desired. NWIS includes data from as  early as 1899 to present.


Distribution of Native U.S. Fishes by Watershed
Source: NatureServe
More Information: http://www.natureserve.org/getData/dataSets/watershedHucs/index.isp
NatureServe has compiled detailed data on the current and historic  distributions of the native freshwater fishes
of the  United States, excluding Alaska and Hawaii. Lists of the native fish species of each small watershed
(8-digit cataloging unit) are provided to facilitate biological assessments and interpretation.


Protected Areas Database of the United States (PAD-US)
Source: National Biological Information Infrastructure
More Information: http://www.protectedlands.net/padus/

The PAD-US is a national  database of federal and  state conservation lands. The protected areas included in
the PAD-US include lands  that are dedicated to the preservation of biological diversity and to other natural,
recreational and cultural uses, and managed for these purposes through legal or other effective means. These
lands  are  essential for conserving species  and  habitat. The lands in PAD-US  also include other  types of
publicly owned open space  areas, whether used for recreational, managed resource development, water quality
protection, or other uses.
                                                                                                         B-3

-------
Identifying and Protecting Healthy Watersheds:
       NatureServe Data
       Source: NatureServe
       More Information: http://www.natureserve.org/getData/index.isp
       NatureServe and its network of member programs are a leading source for reliable scientific information about
       species and ecosystems of the Western Hemisphere. This site serves as  a portal for accessing several types of
       publicly available biodiversity data including the Natural Heritage data for all states.


       The Nature Conservancy's Spatial Data Resources
       Source: The Nature Conservancy
       More Information: http://maps.tnc.org/
       Spatial data and related information plays a vital role in conservation at The Nature Conservancy. A wealth
       of data are generated across the  organization  throughout various parts of the process from setting priorities
       through ecoregional  assessments to developing strategies, taking action and  tracking results as  part of
       conservation projects to managing information on properties they purchase to protect. The primary purpose
       of this site is  to make this core conservation data publically available through easy-to-use web map viewers for
       non-GIS users, as well as in raw form via map  services for more experienced GIS professionals.


       FactFinder
       Source: United States Census Bureau
       More Information: http://factfinder.census.gov/home/saff/main.html? lang=en
       American FactFinder is an online source for population, housing, economic and geographic data that presents
       the results from four key data programs:
           •   Decennial Census of Housing and Population - 1990 and 2000.
           •   Economic Census 1997 and 2002.
           •   American Community Survey - 2005-2007-
           •   Population Estimates Program - July 1, 2003 to July 1, 2007-
       Results from each of these data  programs are provided in the  form of datasets, tables,  thematic maps,  and
       reference maps. These data can be useful for identifying threats to watershed ecosystems.


       Watershed Assessment, Tracking & Environmental ResultS (WATERS)
       Source: U.S. Environmental Protection Agency
       More Information: http://www.epa.gov/waters/
       WATERS is an integrated information system for the nation's surface waters. The EPA Office of Water manages
       numerous programs in support of the Agency's water quality efforts. Many of these programs collect and store
       water quality related data in databases. These databases are managed by the individual Water Programs  and
       this separation often inhibits the integrated application of the data they contain. Under WATERS, the Water
       Program databases are connected to a larger framework. This framework  is a digital network of surface water
       features, known as the National Hydrography Dataset (NHD). By linking to the NHD, one Water Program
       database can  reach another, and information can be shared across programs.
B-4

-------
                                                                                                 Appendix B
LandScope
Source: NatureServe, National Geographic
More Information: http://www.landscope.org/
LandScope America is an online resource for the land protection community and the public. By bringing
together maps, data, photos, and stories about America's natural places and open spaces, LandScope's goal is
to inform and inspire conservation of land and water.


National Adas
Source: U.S. Department of the Interior
More Information: http://www.nationalatlas.gov/index.html
The National Atlas is an online map  containing data layers available for viewing and download for the entire
United States. These data layers  include agricultural, biological, climate, political, economic, environmental,
geological,  historical, and other major categories. It  is a convenient source  of data  for many watershed
assessment applications.


National Fish Habitat Action Plan Spatial Framework               K^       NATIONAL
Source: National Fish Habitat Action Plan                              ^E 3    FISH HABITAT
More Information: http://fishhabitat.org                                ^J J-    ACTION  PLAN
The Science and Data Team of the  National Fish Habitat Action Plan    ^  ^
has developed a national spatial framework to facilitate summary and sharing of available national datasets in
support of conservation and management offish habitats in the conterminous United States. The framework
is based upon the National Hydrography Dataset Plus (NHDPlus), and data are summarized for local and
network catchments  of individual stream  reaches. Currently, 17 natural and  anthropogenic disturbance
variables have been attributed to local catchments and aggregated for network catchments and are available
across various geographic extents incorporated into the spatial framework.
                                                                                                       B-5

-------
Identifying and Protecting Healthy Watersheds:
B-6

-------
Appendix  C.  Cited  Assessment
and  Management  Examples
Assessment and Management Examples Organized Nationally and by State
   http://water.epa.gov/healthywatersheds
   Biological Condition Gradient and Tiered Aquatic Life Uses
   http://www.epa.gov/bioindicators/htm l/bcg.htm I
   Ecological Limits of Hydrologic Alteration
   http://www.conserveonline.org/workspaces/eloha
   Enabling Source Water Protection
   www.landuseandwater.org
   Index of Biotic Integrity (IBI)
   http://www.epa.gov/bioiwebl/htm l/ibi history.htm I
   Interagency Fire Regime Condition Class
   http://f ram es.nbii.gov/docu ments/frcc/documents/FRCC+Guidebook2008.10.30.pdf
   Process for Assessing Proper Functioning Condition
   ftp://ftp.blm.gov/pub/nstc/techrefs/Final%20TR%201737-9.pdf
   National Fish Habitat Assessment
   www.fishhabitat.org
   NatureServe's Natural Heritage Program Biodiversity Assessments
   http://www.natureserve.org/aboutUs/network.Jsp
   The Nature Conservancy's Approach to Setting Freshwater Conservation Priorities
   http://www.conservationgateway.org/topic/setting-freshwater-priorities
   Conservation Priorities for Freshwater Biodiversity in the Upper Mississippi River Basin
   http://www.natureserve.org/library/uppermsriverbasin.pdf
   The Nature Conservancy's Active River Area
   http://conserveonline.org/workspaces/freshwaterbooks/documents/active-river-area-a-conservation-framework-for/view.html
   The Nature Conservancy's Ground Water Dependent Ecosystem Assessment
   http://tinyurl.com/GDE-Workspace
   U.S. Environmental Protection Agency's National Lakes Assessment
   http://water.epa.gov/type/lakes/lakessurvey index.cfm
   U.S. Environmental Protection Agency's National Rivers and Streams Assessment (NRSA)
   http://water.epa.gov/type/rsl/monitoring/riverssurvey/riverssurvey index.cfm
   U.S. Environmental Protection Agency's Recovery Potential Screening Tools
   http://www.epa.gov/recoverypotential
   U.S. Environmental Protection Agency's Regional Vulnerability Assessment Program
   http://www.epa.gov/reva/
   U.S. Geological Survey's Aquatic GAP Analysis Program
   http://www.gap.uidaho.edu/projects/aquatic/default.htm
   U.S. Geological Survey's Regional and National Monitoring and Assessments of Streams and Rivers
   http://water.usgs.gov/nawqa/studies/mrb/
                                                                                                C-l

-------
Identifying and Protecting Healthy Watersheds
            California Healthy Streams Partnership
            http://www.swrcb.ca.gov/mywaterquality/monitoring  council/meetings/2011Jun/hsp outreach.pdf
            California Rapid Assessment Method
            http://www.cramwetlands.org/
            California Watershed Assessment Manual
            http://cwam.ucdavis.edu/
          Connecticut
            Connecticut Department of Environmental Protection's Least Disturbed Watersheds
            http://www.ct.gov/dep/lib/dep/water/water quality management/ic studies/least disturbed  rpt.pdf
           ^^^^H
            Delaware River Basin Commission's use of Antidegradation
            http://www.state.nj.us/drbc/spw.htm

            Kansas Department of Health and Environment's Least Disturbed Watersheds Approach
            http://www.kdheks.gov/befs/download/bibliography/Kansas reference stream report.pdf

            Enabling Source Water Protection in Maine
            http://www.landuseandwater.org/index.htm
            Headwaters: A Collaborative Conservation Plan for the Town of Sanford, Maine
            http://swim.wellsreserve.org/resu lts.php?article=828Conservation%20Strategy%20September%207,%202010.pdf
            Maine Department of Environmental Protection's Tiered Aquatic Life Uses
            http://www.maine.aov/dep/water/monitorina/biomonitorinq/index.html
          Maryland
            Anne Arundel County's Greenways Master Plan
            http://www.aacounty.org/PlanZone/MasterPlans/Greenways/Index.cfm
            Cecil County, Maryland Green Infrastructure Plan
            http://www.conservationfund.org/sites/default/files/CecilCounty01.22.08.pdf
            Maryland Department of Natural Resources Green Infrastructure Assessment
            http://www.greenprint.maryland.gov/
            Maryland Department of Natural Resources' Physical Habitat Index for Freshwater Wadeable Streams
            http://www.dnr.state.md.us/irc/docs/00014357.pdf
          Michigan
            Michigan's Natural Rivers Program
            http://www.rn ichigan.gov/dnr/0,1607,7-153-30301 31431 31442—.OO.html
            Michigan's Regional Scale Habitat Suitability Model to Assess the Effects of Flow Reduction on Fish Assemblages in Michigan
            Streams
            http://www.michigan.gov/documents/dnr/RR2089 268570 7.pdf
            Michigan's Water Withdrawal Assessment
            http://web2.msue.msu.edu/bulletins/Bulletin/PDF/WO60.pdf
C-2

-------
                                                                                                                   Appendix C
Minnesota
  Minnesota Department of Natural Resources' Fen Protection Program
  http://www.dnr.state.rn n.us/eco/wetlands/index.htm I
  Minnesota Department of Natural Resources Watershed Assessment Tool
  http://www.dnr.state.mn.us/watershed  tool/index.htm I
  Minnesota Healthy Watersheds Program
  http://files.dnr.state.mn.us/aboutdnr/reports/legislative/2010 healthy watersheds.pdf
  Minnesota National Lakes Assessment
  http://www.pca.state.mn.us/index.php/water/water-types-and-programs/surface-water/lakes/lake-water-quality/national-lakes-
  assessment-proiect-nlap.html?menuid = &redirect=l
  The U.S. Forest Service and Trust for Public Land's Lower Meramec Drinking Water Source Protection Project
  http://cloud.tpl.org/pubs/landwater-lowermer-swp-brochure.pdf
North Carolina
  National Wild and Scenic Rivers: Lumber River, North Carolina
  http://www.rivers.gov/wsr-lumber.html
 IM^^^|
  Ohio Environmental Protection Agency's Primary Headwaters Habitat Assessment
  http://www.epa.state.oh.us/dsw/wqs/headwaters/index.aspx
  Ohio Environmental Protection Agency's Statewide Biological and Water Quality Monitoring and Assessment
  http://www.epa.state.oh.us/dsw/bioassess/ohstrat.aspx
  Ohio Rapid Assessment Method
  http://www.epa.ohio.gov/dsw/wetlands/WetlandEcologySection.aspxffORAM
  U.S. Geological Survey's Ohio Aquatic GAP Analysis: An Assessment of the Biodiversity and Conservation Status of Native
  Aquatic Animal Species
  http://pubs.er.usqs.qov/usqspubs/ofr/ofr20061385
Oklahoma
  Oklahoma National Rivers and Streams Assessment
  http://www.owrb.ok.gov/studies/reports/reports pdf/REMAP-OKStream River ProbMonitorNetwork.pdf
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  Identifying GDEs and Characterizing their Ground Water Resources in the Whychus Creek Watershed
  http://tinyurl.com/GDE-Workspace
  Oregon Department of Environmental Quality's Oregon Water Quality Index
  http://www.deq.state.or.us/lab/wqm/wqimain.htm
  Oregon Natural Heritage Information Center
  http://orbic.pdx.edu/
  Oregon Watershed Enhancement Board's Oregon Watershed Assessment Manual
  http://www.oreaon.aov/OWEB/docs/pubs/OR wsassess manuals.shtml#OR Watershed Assessment Manual
Pennsylvania
  Pennsylvania Natural Heritage Program's Aquatic Community Classification and Watershed Conservation Prioritization
  http://www.naturalheritaae.state.pa.us/aauaticslntro.aspx
Tennessee
  Beaver Creek Green Infrastructure Plan (Knox County, TN)
  http://ww2.tdot.state.tn.us/sr475/library/bcgitdot.pdf
                                                                                                                          C-3

-------
Identifying and Protecting Healthy Watersheds
            San Antonio River Basin Instream Flow Assessment
            http://www.twdb.state.tx.us/instreamflows/sanantonioriverbasin.html
            Texas Instream Flow Program
            http://www.tceq.state.tx.us/permitting/water supply/water rights/eflows/resources.html
            The Central Texas Greenprint for Growth: A Regional Action Plan for Conservation and Economic Opportunity
            http://envisioncentraltexas.org/resources/GreenprintMkt.pdf

            Rapid Stream Riparian Assessment
            http://wildutahproject.org/files/images/rsra-ug2010v2 wcover.pdf

            Geomorphic Assessment and River Corridor Planning of the Batten Kill Main-Stem and Major Tributaries, Vermont
            http://www.anr.state.vt.us/dec/waterq/rivers/htm/rv geoassess.htm
            Vermont Agency of Natural Resources River Corridor Protection Program
            http://www.anr.state.vt.us/dec/waterq/rivers/htm/rv restoration.htm
            Vermont Agency of Natural Resources' Stream  Geomorphic and Reach Habitat Assessment Protocols
            http://www.vtwaterquality.org/rivers/htm/rv geoassess.htm
           ^Q^^^^^^^^^^^^^J
            Green Infrastructure in Hampton Roads, Virginia
            http://www.hrpdc.org/PEP/PEP Green InfraPlan2010.asp
            Virginia Conservation  Lands Needs Assessment Vulnerability Model
            http://www.dcr.virginia.gov/natural heritage/vclnavulnerable.shtm I
            Virginia Department of Conservation and Recreation's Healthy Waters Program
            www.dcr.virginia.gov/healthywaters
            Virginia Department of Conservation and Recreation's Interactive Stream Assessment Resource (INSTAR)
            http://instar.vcu.edu
            Virginia Department of Conservation and Recreation Natural Landscape Assessment
            http://www.dcr.virginia.gov/natural heritage/vclnavnla.shtml
            Virginia Department of Conservation and Recreation Watershed Integrity Model
            http://www.dcr.virginia.gov/natural heritage/vclnawater.shtml
            Virginia Land Conservation Data Explorer
            www.vaconservedlands.org
            Watershed-Based Zoning in James City County, Virginia
            http://www.jccegov.com/environmental/index.html
          Washington
            Washington's Critical Areas Growth Management Act
            http://www.commerce.wa.gov/site/418/default.aspx
          Wyoming
            Wyoming Department of Environmental Quality's Aquifer Sensitivity and Ground Water Vulnerability Assessment
            http://waterplan.state.wy.us/plan/green/techmemos/swquality.html
            The Wyoming Joint Ventures Steering Committee's Wetlands Conservation Strategy
            http://gf.state.w
            7,%202010.pdf
C-4

-------
                                                                                                                    Appendix C
Assessment Examples
 Landscape Condition
   Anne Arundel County's Greenways Master Plan
   http://www.aacounty.org/PlanZone/MasterPlans/Greenways/Index.cfm
   Beaver Creek Green Infrastructure Plan (Knox County, TN)
   http://ww2.tdot.state.tn.us/sr475/library/bcgitdot.pdf
   Green Infrastructure in Hampton Roads, Virginia
   http://www.hrpdc.org/PEP/PEP Green InfraPlan2010.asp
   Interagency Fire Regime Condition Class
   http://f ram es.nbii.gov/docu ments/frcc/documents/FRCC+Guidebook2008.10.30.pdf
   Maryland Department of Natural Resources Green Infrastructure Assessment
   http://www.greenprint.maryland.gov/
   The Nature Conservancy's Active River Area
   http://conserveonline.org/workspaces/freshwaterbooks/documents/active-river-area-a-conservation-framework-for/view.html
   Virginia Department of Conservation and Recreation's Natural Landscape Assessment
   http://www.dcr.virginia.gov/natural heritage/vclnavnla.shtm I
   Virginia Land Conservation Data Explorer
   www.vaconservedlands.org

   California Rapid Assessment Method
   http://www.cramwetlands.org/
   Maryland Department of Natural Resources' Physical Habitat Index for Freshwater Wadeable Streams
   http://www.dnr.state.md.us/irc/docs/00014357.pdf
   Ohio Environmental Protection Agency's Primary Headwaters Habitat Assessment
   http://www.epa.state.oh.us/dsw/wqs/headwaters/index.aspx
   Ohio Rapid Assessment Method
   http://www.epa.ohio.gov/dsw/wetlands/WetlandEcologySection.aspxffORAM
   Process for Assessing  Proper Functioning Condition
   ftp://ftp.blm.gov/pub/nstc/techrefs/Final%20TR%201737-9.pdf
   Rapid Stream Riparian Assessment
   http://wildutahproiect.ora/files/imaaes/rsra-ua2010v2 wcover.pdf
                                                                                                                          C-5

-------
Identifying and Protecting Healthy Watersheds
          Hydrology
            Ecological Limits of Hydrologic Alteration
            http://www.conserveonline.org/workspaces/eloha
            Identifying GDEs and Characterizing their Ground Water Resources in the Whychus Creek Watershed
            http://tinyurl.com/GDE-Workspace
            Michigan's Regional Scale Habitat Suitability Model to Assess the Effects of Flow Reduction on Fish Assemblages in Michigan
            Streams
            http://www.michigan.gov/documents/dnr/RR2089 268570 7.pdf
            San Antonio River Basin Instream Flow Assessment
            http://www.twdb.state.tx.us/instreamflows/sanantonioriverbasin.html
            Texas Instream Flow Program
            http://www.tceq.state.tx.us/permitting/water supply/water rights/eflows/resources.html
            The Nature Conservancy's Ground Water Dependent Ecosystem Assessment
            http://tinvurl.com/GDE-Workspace
          Geomorphology
            Vermont Agency of Natural Resources' Stream Geomorphic and Reach Habitat Assessment Protocols
            http://www.vtwaterquality.org/rivers/htm/rv geoassess.htm
            Geomorphic Assessment and River Corridor Planning of the Batten Kill Main-Stem and Major Tributaries, Vermont
            http://www.anr.state.vt.us/dec/waterq/rivers/docs/rv battenkillreport.pdf
          Water Quality
            Oregon Department of Environmental Quality's Oregon Water Quality Index
            http://www.dea.state.or.us/lab/wam/wgimain.htm
          Biological Condition
            Biological Condition Gradient and Tiered Aquatic Life Uses
            http://www.epa.gov/bioindicators/html/bcg.html
            Index of Biotic Integrity (IBI)
            http://www.epa.gov/bioiwebl/htm l/ibi history.htm I
            Maine Department of Environmental Protection's Tiered Aquatic Life Uses
            http://www.maine.gov/dep/water/monitoring/biomonitoring/index.html
            Natural Heritage Program Biodiversity Assessments
            http://www.natureserve.org/aboutUs/network.Jsp
            Ohio Environmental Protection Agency's Statewide Biological and Water Quality Monitoring and Assessment
            http://www.epa.state.oh.us/dsw/bioassess/ohstrat.aspx
            Oregon Natural Heritage Information Center
            http://orbic.pdx.edu/
            U.S. Geological Survey's Aquatic GAP Analysis Program
            http://www.gap.uidaho.edu/projects/aquatic/default.htm
            U.S. Geological Survey's Ohio Aquatic GAP Analysis: An Assessment of the Biodiversity and Conservation Status of Native
            Aquatic Animal Species
            http://pubs.er.usgs.gov/usgspubs/ofr/ofr20061385
            Virginia Department of Conservation and Recreation's Interactive Stream Assessment Resource (INSTAR)
            http://instar.vcu.edu
C-6

-------
                                                                                                                    Appendix C
National Aquatic Resource Assessments
  Minnesota National Lakes Assessment
  http://www.pca.state.mn.us/index.php/water/water-types-and-programs/surface-water/lakes/lake-water-quality/national-
  lakesassessm ent-proiect-nlap.htm l?menuid = &redirect=l
  Oklahoma National Rivers and Streams Assessment
  http://www.owrb.ok.gov/studies/reports/reports pdf/REMAP-OKStreamRiver ProbMonitorNetwork.pdf
  U.S. Environmental Protection Agency's National Lakes Assessment
  http://water.epa.gov/type/lakes/lakessurvey index.cfm
  U.S. Environmental Protection Agency's National River and Streams Assessment (NRSA)
  http://water.epa.gov/type/rsl/monitoring/riverssurvey/riverssurvey index.cfm
  U.S.Geological Survey's Regional and National Monitoring and Assessments of Streams and Rivers
  http://water.usgs.gov/nawqa/studies/mrb/
Integrated Assessments
  California Watershed Assessment Manual
  http://cwam.ucdavis.edu/
  Connecticut Department of Environmental Protection's Least Disturbed Watersheds
  http://www.ct.gov/dep/lib/dep/water/water  quality management/ic studies/least disturbed rpt.pdf
  U.S. Environmental Protection Agency's Recovery Potential Screening Tool
  www.epa.gov/recoverypotential/
  Kansas Department of Health and Environment's Least Disturbed Watersheds Approach
  http://www.kdheks.gov/befs/download/bibliography/Kansas reference stream  report.pdf
  Minnesota Department of Natural Resources' Watershed Assessment Tool
  http://www.dnr.state.mn.us/watershed tool/index.html
  National Fish Habitat Assessment
  http://fishhabitat.org/
  Oregon Watershed Enhancement Board's Watershed Assessment Manual
  http://www.oregon.gov/OWEB/docs/pubs/OR wassess manuals.shtml#OR Watershed  Assessment Manual
  Pennsylvania Natural Heritage Program's Aquatic Community Classification and Watershed Conservation Prioritization
  http://www.naturalheritage.state.pa.us/aquaticslntro.aspx
  Virginia Department of Conservation and Recreation's Watershed Integrity Model
  http://www.dcr.virainia.gov/natural heritage/vclnawater.shtml
Vulnerability
  U.S. Environmental Protection Agency's Regional Vulnerability Assessment Program
  http://www.epa.gov/reva/
  Virginia Conservation Lands Needs Assessment Vulnerability Model
  http://www.dcr.virginia.gov/natural heritage/vclnavulnerable.shtml
  Wyoming Department of Envrionmental Quality's Aquifer Sensitivity and Ground Water Vulnerability Assessment
  http://waterplan.state.wy.us/plan/green/techmemos/swquality.html
                                                                                                                          C-7

-------
Identifying and Protecting Healthy Watersheds
         Management Examples
            Enabling Drinking Water Source Protection
            http://www.landuseandwater.org/
            The Nature Conservancy's Approach to Setting Freshwater Conservation Priorities
            http://www.conservationgateway.org/topic/setting-freshwater-priorities
            U.S. Environmental Protection Agency's Healthy Watersheds Initiative Website
            http://water.epa.gov/healthvwatersheds
          State/Interstate
            California Healthy Streams Partnership
            http://www.swrcb.ca.gov/mywaterquality/monitoring council/meetings/2011Jun/hsp outreach.pdf
            Delaware River Basin Commission's use of Antidegradation
            http://www.state.nj.us/drbc/spw.htm
            Enabling Source Water Protection in Maine
            http://www.landuseandwater.org/maine.html
            Maryland's GreenPrint Program
            www.greenprint.maryland.gov
            Minnesota  Department of Natural Resources' Fen Protection Program
            http://www.dnr.state.mn.us/eco/wetlands/index.html
            Minnesota  Healthy Watersheds Program
            http://files.dnr.state.mn.us/aboutdnr/reports/legislative/2010 healthy watersheds.pdf
            NatureServe's Conservation  Priorities for Freshwater Biodiversity in the Upper Mississippi River Basin
            http://www.natureserve.org/library/uppermsriverbasin.pdf
            Michigan's  Natural Rivers Program
            http://www.rn ichigan.gov/dnr/0,1607,7-153-30301 31431  31442—.OO.htm I
            Michigan's  Water Withdrawal Assessment
            http://web2.msue.msu.edu/bulletins/Bulletin/PDF/WO60.pdf
            The Wyoming Joint Ventures Steering Committee's Wetlands Conservation Strategy
            http://gf.state.w
            7,%202010.pdf
            Vermont Agency of Natural  Resources River Corridor Protection Program
            http://www.anr.state.vt.us/dec/waterq/rivers/htm/rv restoration.htm
            Virginia Department of Conservation and Recreation's Healthy Waters Program
            www.dcr.virginia.gov/healthywaters
            Washington's Critical Areas Growth Management Act
            http://www.commerce.wa.gov/site/418/default.aspx

-------
                                                                                                                   Appendix C
Cecil County, Maryland Green Infrastructure Plan
http://www.conservationfund.org/sites/default/files/CecilCounty01.22.08.pdf
Headwaters: A Collaborative Conservation Plan for the Town of Sanford, Maine
http://www.wellsreserve.org/blog/63-headwaters a collaborative conservation plan  for the town of sanford
National Wild and Scenic Rivers: Lumber River, North Carolina
http://www.rivers.gov/wsr-lumber.html
The Central Texas Greenprint for Growth: A Regional Action Plan for Conservation and Economic Opportunity
http://envisioncentraltexas.org/resources/GreenprintMkt.pdf
The U.S. Forest Service and Trust for Public Land's Lower Meramec Drinking Water Source Protection Project
http://cloud.tpl.org/pubs/landwater-lowermer-swp-brochure.pdf
Watershed-Based Zoning in James City County, Virginia
http://www.icceaov.com/environmental/index.html
                                                                                                                          C-9

-------

-------

-------
  U.S. Environmental Protection Agency
Office of Wetlands, Oceans, and Watersheds
 1200 Pennsylvania Avenue, N.W (4503T)
      Washington, D.C. 20460
          Healthy
          Watersheds

-------