&EPA
United States
Environmental Protection
Agency
Draft EPA-USGS Technical Report: Protecting
Aquatic Life from Effects of Hydrologic Alteration
EPA Report 822-P-15-002
USGS Scientific Investigations Report 2015-5160
U.S. Department of the Interior
U.S. Geological Survey
United States
Environmental Protection
Agency
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For more information concerning this document contact:
U.S. Environmental Protection Agency
Diana M. Eignor
EPA, Office of Water, Office of Science and Technology
1200 Pennsylvania Ave., N.W., MC4304T
Washington, DC 20460
Phone: (202) 566-1143, Fax: (202) 566-1140
Email: Eignor.Diana@epa.gov
U.S. Geological Survey
Jonathan G. Kennen
New Jersey Water Science Center
3450 Princeton Pike, Suite 110
Lawrenceville, NJ 08648
Phone: (609) 771-3948, Fax (609) 771-3915
Email: jgkennen@usgs.gov
Cover. Redfish Lake Creek, Stanley, Idaho. (Photo by Daniel Hart, U.S. Environmental Protection Agency)
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Draft: EPA-USGS Technical Report: Protecting Aquatic Life
from Effects of Hydrologic Alteration
By Rachael Novak1, Jonathan G. Kennen2, Ralph W. Abele3, Carol F. Baschon4, Daren M. Carlisle5, Laura Dlugolecki6, Joe
E. Flotermersch7, Peter Ford8, Jamie Fowler9, Rose Galer10, Lisa P. Gordon11, Susan N. Hansen12, Bruce Herbold13,
Thomas E. Johnson14, John M. Johnston15, Christopher P. Konrad16, Beth Leamond17, and Paul W. Seelbach18.
1. Bureau of Indian Affairs, Washington, D.C. (Formerly with U.S. Environmental Protection Agency (EPA),
Office of Water, Office of Science and Technology, Washington, D.C.)
2. U.S. Geological Survey (USGS), New Jersey Water Science Center, Lawrenceville, New Jersey
3. EPA, Region 1, Office of Ecosystem Protection, Boston, Massachusetts
4. EPA, Region 4, Office of Regional Counsel, Atlanta, Georgia
5. USGS, Kansas Water Science Center, Lawrence, Kansas
6. Former Oak Ridge Institute for Science and Education (ORISE) participant in EPA Office of Water, Office of
Wetlands, Oceans and Watersheds, Washington, D.C.
7. EPA, Office of Research and Development, National Exposure Research Lab, Cincinnati, Ohio
8. EPA, Office of General Counsel, Washington, D.C.
9. EPA, Office of Water, Office of Wetlands, Oceans and Watersheds, Washington, D.C.
10. Former ORISE participant in EPA Office of Water, Office of Science and Technology Standards and Health
Protection Program, Washington, D.C.
11. EPA, Region 4, Water Quality Standards, Atlanta, Georgia
12. EPA, Region 4, Office of Regional Counsel, Atlanta, Georgia
13. EPA, Region 9 (retired), San Francisco, California
14. EPA, Office of Research and Development, National Center for Environmental Assessment, Arlington,
Virginia
15. EPA, Office of Research and Development, National Exposure Research Lab, Athens, Georgia
16. USGS Geological Survey, Washington Water Science Center, Tacoma, Washington
17. EPA Office of Water (retired), Office of Science and Technology, Washington, D.C.
18. USGS Geological Survey, Great Lakes Science Center, Ann Arbor, Michigan
Jointly prepared by the U.S. Environmental Protection Agency and U.S. Department of the Interior, U.S.
Geological Survey
EPA Report 822-P-15-002
USGS Scientific Investigations Report 2015-5160
U.S. Department of the Interior United States
U.S. Geological Survey Environmental Protection
Agency
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U.S. Department of the Interior
SALLY JEWELL, Secretary
U.S. Geological Survey
Suzette M. Kimball, Director
U.S. Environmental Protection Agency
GINA MCCARTHY, Administrator
Office of Water
Joel Beauvais, Deputy Assistant
Administrator
U.S. Geological Survey, Reston, Virginia: 2015
U.S. EPA, Washington, DC: 2015
For more information on the USGS—the Federal source for science about the Earth,
its natural and living resources, natural hazards, and the environment—visit
http://www.usgs.gov/orcall 1-888-ASK-USGS (1-888-275-8747).
For an overview of USGS information products, including maps, imagery, and publications,
visit http://www.usgs.gov/pubprod/.
For more information on the EPA and our mission to protect human health and the environment—visit
http://www3.epa.gov/.
For an overview of EPA publications, visit http://www2.epa.gov/nscep
Any use of trade, firm, or product names is for descriptive purposes only and does not imply
endorsement by the U.S. Government.
Although this information product, for the most part, is in the public domain, it also may
contain copyrighted materials as noted in the text. Permission to reproduce copyrighted items
must be secured from the copyright owner.
Suggested citation:
Novak, Rachael, Kennen, J.G., Abele, R.W., Baschon, C.F., Carlisle, D.M., Dlugolecki, Laura, Flotermersch, J.E., Ford, Peter,
Fowler, Jamie, Galer, Rose, Gordon, L.P., Hansen, S.N., Herbold, Bruce, Johnson, I.E., Johnston, J.M., Konrad, C.P.,
Leamond, Beth, and Seelbach, P.W, 2015, Draft: EPA-USGS Technical Report: Protecting Aquatic Life from Effects of
Hydrologic Alteration: U.S. Geological Survey Scientific Investigations Report 2015-5160, U.S. Environmental Protection
Agency EPA Report 822-P-15-002, XX p., http://pubs.usgs.gov/sir/2015/5160/ and http://www2.epa.gov/wqc/aquatic life-
ambient-water quality-criteria
IV
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Disclaimer
This report provides technical support and examples to advance the protection of aquatic life use from
adverse effects of hydrologic alterations in streams and rivers. The provisions in the Clean Water Act (CWA)
and in the U.S. Environmental Protection Agency (EPA) regulations described in this document contain legally
binding requirements; however, this document is not a law itself, nor does it change or substitute for those
requirements. It does not impose legally binding requirements on EPA, states, tribes, or the regulatory
community. This document does not confer legal rights or impose legal obligations on any member of the
public.
Although the U.S. Geological Survey (USGS) and EPA have made every effort to ensure the accuracy of the
discussion in this document, the obligations of the regulated community are determined by statutes,
regulations, and other legally binding requirements. In the event of a conflict between the discussion in this
document and any statute or regulation, this document will not be controlling.
Depending on individual circumstances, the general descriptions provided here may not apply to a given
situation. Interested parties are free to raise questions and objections about the substance of this document
and the appropriateness of the application of the information presented to a specific situation. This document
does not make any judgment regarding any specific data collected or determinations made as part of a state
or tribal water quality program. State and tribal decision makers retain the discretion to adopt approaches on
a case-by-case basis that differ from the approaches described in this report.
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Acknowledgments
The authors thank LeRoy Poff (Colorado State University), Julian Olden (University of Washington), Mark Rains
(University of South Florida), Larry Brown (USGS, California Water Science Center) and Eric Stein (Southern
California Coastal Water Research Project) for providing timely and thoughtful reviews that greatly improved
the draft version of this report. We graciously thank Robie Anson, Cheryl Atkinson, Bill Beckwith, Betsy Behl,
Renee Bellew, Britta Bierwagen, David Bylsma (former ORISE Fellow), Valentina Cabrera-Stagnos, Leah Ettema,
Colleen Flaherty, Brian Fontenot, Laura Gabanski, Kathryn Gallagher, Tom Hagler, Rosemary Hall, Wayne
Jackson, Ann Lavaty, Christine Mazzarella, Stephen Maurano, Brenda Rashleigh, Susan Spielberger, Michele
Wetherington, and Ann Williams of the EPA for their constructive comments and suggestions. The authors
thank Jerry Diamond, Anna Hamilton, Maggie Craig, and Shann Stringer (Tetra Tech, Inc.), and Andrew Somor,
Corey Godfrey, and Karen Sklenar (The Cadmus Group, Inc.) for their technical support throughout the
development and publication of this report. Editorial, graphical, and publishing support from Dale Simmons
and Denis Sun, respectively, of the USGS West Trenton Publishing Service Center, was greatly appreciated.
VI
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Conversion Factors
International System of Units to Inch/Pound
Multiply
By
To obtain
Length
centimeter (cm)
meter (km)
kilometer (km)
0.3937
3.2808
0.6213
inch (in.)
foot (ft)
mile (mi)
Area
square meter (m2)
square kilometer (km2)
hectare (ha)
0.00025
0.3861
2.4710
Acre
square mile (mi2)
Acre
Volume
cubic meter (m3)
cubic meter (m3)
35.3147
0.00026
cubic foot (ft3)
million gallon (gal)
Flow rate
cubic meter per second per square kilometer
[(m3/s)/km2]
cubic meter per second (m3/s)
91.47
22.8244
cubic foot per second per square mile [(ft3/s)/mi2]
million gallons per day (Mgal/d)
Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as °F = (1.8 x °C) + 32.
VII
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Acronyms
Acronym/Abbreviation Definition
BMP
CADDIS
CFR
CWA
ELOHA
EPA
ERA
FERC
GCM
IBI
IFC
IPCC
IR
MS4
NPDES
TMDL
USDA
USGS
WQS
Best Management Practice
Causal Analysis/Diagnosis Decision Information System
Code of Federal Regulations
Clean Water Act
Ecological Limits of Hydrologic Alteration
U.S. Environmental Protection Agency
Ecological Risk Assessment
Federal Energy Regulatory Commission
General Circulation Model
Index of Biotic Integrity
Instream Flow Council
Intergovernmental Panel on Climate Change
integrated reporting
Municipal Separate Storm Sewer System
National Pollutant Discharge Elimination System
Total Maximum Daily Load
U.S. Department of Agriculture
U.S. Geological Survey
water quality standards
VIM
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Contents
Disclaimer v
Acknowledgments vi
Acronyms viii
1 Abstract 7
2 Introduction 9
3 Purpose, Scope, and Overview 13
3.1 Purpose and Scope 13
3.2 Overview 13
3.3 Who Can Use This Information? 14
4 Effects of Altered Flow on Aquatic Life 15
4.1 Conceptual Model of the Biological Effects of Flow Alteration 15
4.2 Drivers of the Natural Flow Regime 18
4.3 Sources of Flow Alteration 19
4.3.1 Dams and Impoundments 20
4.3.2 Diversions 24
4.3.3 Ground water Withdrawals 26
4.3.4 Effluents and Other Artificial Inputs (Discharges) 27
4.3.5 Land-Cover Alteration (Land Use) 28
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4.3.6 Climate Change 30
4.4 Physical and Chemical Effects of Flow Alteration 34
4.4.1 Effects on Geomorphology 34
4.4.2 Effects on Connectivity 35
4.4.3 Effects on Water Temperature and Chemistry 36
4.5 Biological Responses to Flow Alteration 37
5 Examples of State and Federal Actions to Protect Aquatic Life from Altered Flows 39
5.1 Narrative Criteria in State and Tribal Water Quality Standards 42
5.2 Monitoring, Assessing, and Identifying Waters Impaired as a Result of Flow Alteration 49
5.3 Development of Total Maximum Daily Loads 55
5.4 Consideration of Flow Alteration in Issuing 401 Certifications 56
5.5 Consideration of Flow Alteration in Issuing 404 Permits 57
5.6 Consideration of Flow Alteration in Issuing National Pollutant Discharge Elimination System
(402) Permits 59
5.7 Further considerations 63
6 Framework for Quantifying Flow Targets to Protect Aquatic Life 65
6.1 Link Narrative Criteria to Biological Goals and Assessment Endpoints 68
6.2 Identify Target Streams 69
6.3 Conduct Literature Review 71
6.4 Develop Conceptual Models 72
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6.5 Perform Data Inventory 74
6.6 Identify Flow and Biological Indicators 75
6.7 Develop Qualitative or Quantitative Flow-Ecology Models 79
6.8 Estimate Effects and Identify Acceptable Levels 82
6.9 Example Applications of the Flow-Target Framework 84
7 Conclusions 92
8 Selected References 93
Appendix A. Overview of the Clean Water Act and Water Quality Standards Relevant to the
Development and Use of Criteria for Hydrologic Condition 130
Al. Designated Uses and Existing Uses 131
A2. Water quality Criteria 132
A3. Antidegradation 133
A4. Using Narrative Criteria 134
Appendix B. Legal Background and Relevant Case Law 135
Appendix C. Climate-Change Vulnerability and the Flow Regime 138
References Cited 151
Figures
Figure 1. Schematic diagram depicting the interaction between the natural flow regime, natural
watershed conditions and the many ecosystem services it helps to maintain 12
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Figure 2. Schematic diagram illustrating a generalized conceptual model of the biological effects of flow
alteration 17
Figure 3. Map showing dams in the conterminous United States listed in the National Inventory of
Dams (NID) (U.S. Army Corps of Engineers, 2013) 23
Figure 4. Map showing location of water-conveyance structures in the medium-resolution National
Hydrography Dataset (NHD) (U.S. Geological Survey, 2012), illustrating the widespread extent of
canals, ditches, and pipelines in the conterminous United States 25
Figure 5. Graph showing streamflow at Halfmoon Creek, Colorado (U.S. Geological Survey station
number 7083000), May-September, 2010 26
Figure 6. Graph showing artificially augmented daily streamflow at Sixth Water Creek, Utah (U.S.
Geological Survey station number 10149000), January-December, 2000 28
Figure 7. Map showing trends in the magnitude of 7-day low streamflows in the United States, 1940-
2009 32
Figure 8. Map showing trends in the timing of winter-spring runoff in the United States, 1940-2009.. 33
Figure 9. Schematic diagram illustrating water quality management programs based on water quality
standards underthe Clean Water Act 42
Figure 10. Flow diagram illustrating a framework for quantifying flow targets to protect aquatic life. 67
Figure 11. Example conceptual diagram illustrating the ecological effects of human-induced flow
alteration from the U.S. Environmental Protection Agency Causal Analysis/Diagnosis Decision
Information System (CADDIS) 73
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Figure 12. Example flow-ecology curves illustrating quantitative relations between flow and biological
indicators 80
Figure 13. Example fish response curve from Scenario A generated through regression modeling 90
Figure 14. Conceptual diagram illustrating hypothesized flow needs offish and other aquatic biota by
season in major tributaries of the Susquehanna River Basin, northeastern United States 91
Figure C-l. (a) Composite results of the vulnerability assessment illustrating the combined changes in
the seven component metrics of projected climate-change parameters, three of which are shown:
(b) surface runoff, (c) minimum temperature, and (d) snowpack 144
Figure C- 2. Diagram showing effect of climate change on life stages of salmonids through time, by
season 147
Tables
Table 1. Excerpts from narrative flow criteria for selected states and tribes 44
Table 2. Example flow and biological indicators used to evaluate relations between streamflow
characteristics and aquatic assemblage response 77
Table 3. Example applications of the framework to quantitatively translate the following narrative flow
criterion: "Changes to the natural flow regime shall not impair the ability of a stream to support
characteristic fish populations." 87
Table Cl. Incorporating climate-change considerations into the framework for quantifying flow targets.149
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Boxes
Box A. Goals of the Clean Water Act 10
Box B. Ecological Risk Assessment 15
Box C. Addressing Flow Regime Components 48
Box D. Procedures for Capturing Flow Information in the State of Texas 52
Box E. Vermont Addresses Hydrologically Altered Waters 55
Box F. 401 Certifications, Sufficient Flow, and Water quality Standards 57
Box G. Stormwater and West Virginia Department of Environmental Protection (DEP) Municipal
Separate Storm Sewer Systems (MS4) Permit Language 63
Box H. Fundamentals of Stream Classification 70
Box I. Components of Climate-Change Vulnerability 140
Box J. California's Climate-Change Vulnerability Index 142
Box K. Addressing Regional Climate-Change Effects on Salmon Habitat in the Pacific Northwest:
Examples for Prioritizing Restoration Activities 145
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1 Abstract
The U.S. Congress enacted the Clean Water Act (CWA) in 1972 to "restore and maintain the chemical, physical
and biological integrity of the Nation's waters" (Section 101(a)). The natural flow regime, defined as the
characteristic pattern of flow magnitude, timing, duration, frequency, and rate of change, plays a critical role
in supporting the chemical, physical, and biological integrity of streams and rivers and the services they
provide. Human-induced alteration of the natural flow regime can degrade a stream's physical and chemical
properties, leading to loss of aquatic life and reduced aquatic biodiversity. Protecting aquatic life from the
effects of flow alteration involves maintaining multiple components of the flow regime within their typical
range of variation. This report was developed to serve as a source of information for states, tribes, and
territories on (1) the natural flow regime and potential effects of flow alteration on aquatic life; (2) CWA
programs that can be used to support the natural flow regime and maintain the health of aquatic biota; and
(3) a flexible, nonprescriptive framework to quantify targets for flow regime components that are protective
of aquatic life.
Anthropogenic landscape change and water management activities are modifying flood flows, base flows,
peak-flow timing, and other flow characteristics in streams and rivers throughout the United States. Under
natural conditions, a stream's flow regime is determined by hydrologic properties at two scales, the upstream
drainage area (catchment) and the local, reach scale. At the catchment scale, climate determines patterns of
water and energy input over time, whereas physical characteristics like soils, geology, and topography
determine pathways, rates of runoff, and routing through the stream network. Reach-scale factors such as
local groundwater dynamics further influence natural flow regime characteristics. Human activities that alter
the natural flow regime also occur at both the catchment and reach scales and include impoundments,
channelization, diversions, groundwater pumping, wastewater discharges, urban development, thermoelectric
power generation, and agricultural practices. Many of these activities alter hydrologic processes like
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infiltration, groundwater recharge, channel storage, or routing and lead to flow conditions outside the natural
range of variation. Others directly add or remove water from a stream such that flows are uncommonly high
or low over long periods of time. Occurring in conjunction with these activities is climate change. Climate
trends observed in recent decades and future projections (for example, rising ambient air temperatures,
increasing frequency of heavy precipitation events, reductions in the thickness of snow pack and ice) may
magnify the effects of other anthropogenic processes on the natural flow regime.
Alteration of the natural flow regime can have cascading effects on the physical, chemical, and biological
properties of riverine ecosystems. Effects on physical properties include altered channel geomorphology
(channel incision, widening, bed armoring, etc.), reduced (or augmented) riparian and flood-plain connectivity,
and reduced (or augmented) longitudinal (upstream-downstream) and vertical (surface water/groundwater)
connectivity. Effects on water quality can also result from altered flow magnitudes. For example, salinity,
sedimentation, and water temperature can increase when flow volumes are reduced, whereas erosion and
sediment transport can increase with amplified flow volumes. These changes to a stream can in turn lead to
the degradation of aquatic life as a result of the loss and disconnection of high-quality habitat. Furthermore,
altered flows can fail to provide the cues needed for aquatic species to complete their life cycles and can
encourage the invasion and establishment of non-native aquatic species. The ability of a water body to
support aquatic life is tied to the maintenance of key flow-regime components.
CWA programs can incorporate strategies to protect water quality and aquatic life from the potentially
harmful effects of flow alteration. Water quality standards programs can adopt criteria for flow to protect
aquatic life designated uses. As of 2014, 10 states and several tribes had adopted a narrative form of flow
criteria in their water quality standards. Water quality monitoring and assessment programs can collect flow
data and develop methods to evaluate whether flow alteration is contributing to water quality impairments.
National Pollutant Discharge Elimination System (NPDES) permitting programs can incorporate hydrologic and
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flow regime considerations into permit conditions. For example, several states and the U.S. Environmental
Protection Agency (EPA) have defined numeric post-construction standards in permits for municipal separate
storm sewer systems (MS4s) that require the treatment or retention of a specified volume of runoff to be
managed on site. In addition, CWA Section 404 permit programs, which authorize activities such as dam
construction, can consider whether a proposed project would alter the natural flow regime and adversely
affect aquatic life. These activities are subject to CWA Section 401 certification, in which a state verifies that a
project requiring a Federal license or permit will not violate State water quality standards. A state can include
flow as a condition for Section 401 certification even if flow criteria are not yet adopted in State water quality
standards.
Efforts to implement strategies to protect aquatic life from flow alteration will be most effective if numeric
targets are identified for flow-regime components that equate to intact and healthy aquatic communities. This
report presents a flexible framework to quantify flow targets that incorporates EPA Guidelines for Ecological
Risk Assessment (ERA) and concepts from contemporary environmental flow literature. The framework
consists of eight steps that begins with identifying biological goals and assessment endpoints and ends with an
evaluation of effects to aquatic life under varying degrees of flow alteration. The framework does not
prescribe any particular analytical approach (for example, statistical or mechanistic modeling methodology),
but rather focuses on the process and information needed to evaluate relations between flow and aquatic life
and to select numeric flow targets.
2 Introduction
Healthy aquatic ecosystems provide an array of services to individuals and society, including clean drinking
water, irrigation supplies, and recreational opportunities (U.S. Environmental Protection Agency, 2012c).
Sound and sustainable management of aquatic ecosystems is an integral part of managing water resources to
meet the needs of society and the goals of the Clean Water Act (CWA) (see Box A).
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Box A. Goals of the Clean Water Act
In 1972, with the objective of protecting lakes, rivers, streams, estuaries, wetlands, coastal waters, oceans,
and other water bodies, the U.S. Congress enacted the Clean Water Act (CWA). The overall objective of the
CWA is to "restore and maintain the chemical, physical and biological integrity of the Nation's waters" (Section
101(a)). In addition, the CWA establishes as an interim goal "water quality which provides for the protection
and propagation offish, shellfish and wildlife and provides for recreation in and on the water," wherever
attainable (Section 101(a)(2)).
Freshwater aquatic ecosystems are the most altered ecosystems globally; they exhibit declines in biodiversity
that far outpace those of terrestrial or marine ecosystems (Dudgeon and others, 2006; Strayer and Dudgeon,
2010). Although discharge of contaminants ranks as a top threat to aquatic biodiversity, other important
sources of stress include urbanization, agriculture practices, and engineered structures used for water-
resource development (Vorosmarty and others, 2010). These factors directly and indirectly alter the natural
hydrology of a catchment and can have cascading effects on aquatic organisms (Poff and others, 1997).
Today's water-resource managers face a universal challenge: balancing the needs of a growing human
population with the protection of natural hydrologic regimes to support aquatic life, ecosystem health, and
services of crucial importance to society (Annear and others, 2004; Postel and Richter, 2003). Further
complicating this challenge are expected changes to historic hydrologic conditions as a result of climate
change, which add complexity to the task of estimating acceptable levels of hydrologic variation (Milly and
others, 2008).
The natural flow regime, defined as the characteristic pattern of flow magnitude, timing, duration, frequency,
and rate of change, plays a critical role in supporting the ecological integrity of streams and rivers and the
services they provide (Figure 1). Human-induced alteration of the natural flow regime can degrade the
physical, chemical, and biological properties of a water body (Annear and others, 2004; Bunn and Arthington,
10
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2002; Naiman and others, 2002; Poff and others, 1997; Poff and Zimmerman, 2010; and many others). For
example, an increase in the duration and frequency of high flows can degrade aquatic habitat through
scouring and streambank erosion. More frequent low-flow conditions can degrade water quality through
elevated concentrations of toxic contaminants resulting from decreased dilution, increased temperatures, or a
decrease in dissolved-oxygen concentration. Lower flows can reduce sensitive taxa diversity and abundance,
alter life cycles, cause mortality in aquatic life, and promote the expansion of invasive plants and animals
(Bunn and Arthington, 2002; Poff and Zimmerman, 2010).
Flow alteration can be a primary contributor to the impairment of water bodies that are designated to support
aquatic life. Addressing flow conditions by using CWA mechanisms such as water quality standards (WQS) can
contribute to a comprehensive approach to managing and protecting water quality, improving aquatic
restoration efforts, maintaining designated uses (for example, aquatic life, cold-water or warm-water fisheries,
economically or recreationally important aquatic species), and satisfying antidegradation requirements. As the
science of flow ecology has uncovered aquatic life needs across the full spectrum of the flow regime (base
flows, high flows, etc.), water-resource managers are starting to recognize that protecting aquatic life from the
adverse effects of flow alteration involves maintaining multiple components of the flow regime within their
typical range of variation. This perspective requires an understanding of natural flow variability over space and
time and the many ways in which biota respond to varied flow conditions.
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Natural watershed conditions
(Climate, soils, physiography, etc.)
Natural flow regime
(Magnitude, frequency, duration, timing, rate of change)
I
Maintenance of ecosystem services
(Recreation, fisheries, water supply, navigation, etc.)
Figure 1. Schematic diagram depicting the interaction between the natural flow regime, natural
watershed conditions and the many ecosystem services it helps to maintain.
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3 Purpose, Scope, and Overview
3.1 Purpose and Scope
The purpose of this report is threefold. First, it describes the effects of flow alteration on aquatic life
designated uses in streams, rivers, and other natural flowing water bodies. Second, it shows how CWA
mechanisms address hydrology or flow alterations through state and tribal examples. Third, it provides a
flexible, nonprescriptive framework to quantify flow targets to protect aquatic life from the effects associated
with flow alteration. Nonflowing waters (lakes or wetlands, for example) and nonfreshwater systems
(estuaries, tidal waters) are not discussed in this report, nor are other designated uses such as recreation or
drinking water, although they also can be affected by hydrologic alteration and can benefit from measures to
maintain hydrologic conditions.
This report was developed by the U.S. Environmental Protection Agency (EPA) in collaboration with the U.S.
Geological Survey (USGS) in response to evidence that flow alteration has adversely affected the biological
integrity of water bodies throughout the United States (Bunn and Arthington, 2002; Carlisle and others, 2010;
Poff and Zimmerman, 2010). The information presented is drawn from the Guidelines for Ecological Risk
Assessment (ERA) (U.S. Environmental Protection Agency, 1998), relevant environmental flows literature (for
example, Bunn and Arthington, 2002; Petts, 2009; Poff and Zimmerman, 2010), and the experience of states
and tribes that have adopted narrative flow criteria to protect aquatic life uses in their waters.
3.2 Overview
Section 4 is a summary of available scientific information about the effects of flow alteration on ecosystems,
including the role of climate change, which can exacerbate the stresses that result from flow alteration.
Section 5 is an overview of CWA programs that are applicable to maintaining hydrologic conditions that
protect aquatic life. It provides state and tribal examples of flow considerations and management approaches
that promote the sustainability of aquatic ecosystems, including a review of existing state and tribal narrative
13
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flow criteria. Section 6 presents concepts, tools, and examples that may be useful for translating narrative flow
criteria into quantitative flow targets. It includes examples of quantification to support states, authorized
tribes, and territories (hereinafter, "states") that wish to adopt flow criteria to protect aquatic life designated
uses in their WQS regulations. It also describes the potential role of narrative criteria as a tool to manage flow
to restore and maintain aquatic ecosystems. Appendix A is general review of the CWA and WQS, and Appendix
B provides a brief overview of the legal background and relevant case law relating to flow protection for
support of aquatic life designated uses.
Climate change is one category among a range of stressors that is likely to increase the vulnerability of rivers
and streams to flow alteration and affect the ecosystem services they provide (see Section 4.3.6). Given the
inherent difficulties associated with climate change assessment, many natural-resource management agencies
will likely encounter increasing challenges as they work to protect and restore the health of aquatic
ecosystems. Appendix C provides examples of vulnerability assessments of freshwater aquatic life and
environmental flows related to climate change.
3.3 Who Can Use This Information?
This report presents scientific information that can help water-resource managers improve the protection of
flow for aquatic life uses. Additionally, it serves as a source of information for a broad stakeholder audience
involved in water-resource management and aquatic life protection. It does not establish any new authorities
or impose any additional requirements on states, tribes, or territories. Under the CWA, any state or authorized
tribe may protect aquatic life or use the CWA state programs to address flow (see Section 5) and develop
numeric flow targets by following a flexible, nonprescriptive framework described in this report (see Section 6)
to protect aquatic life.
14
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4 Effects of Altered Flow on Aquatic Life
This section describes the scientific principles of the natural flow regime, hydrologic alteration, and ecological
responses to altered flows and presents a general conceptual model of the effects of flow alteration on
aquatic life. Potential causes of various types of streamflow change are outlined and pathways to degraded
biological conditions are discussed.
4.1 Conceptual Model of the Biological Effects of Flow Alteration
In ecological risk assessment (Box B, below), a conceptual model consists of a written description and diagram
of the relations and pathways between human activities (sources), stressors, and direct and indirect effects on
ecological entities (U.S. Environmental Protection Agency, 1998). A conceptual model links one or more
stressors to ecological assessment endpoints that are important for achieving management goals. Under the
CWA, management goals are established by states as designated uses of waters (for example, to support
aquatic life) and criteria to protect those uses.
Box B. Ecological Risk Assessment
Ecological Risk Assessment (ERA) provides a framework for evaluating the likelihood that adverse ecological
effects may occur or are occurring as a result of exposure to one or more stressors (U.S. Environmental
Protection Agency, 1998). It can apply to a range of environmental problems associated with chemical,
physical, and biological stressors, including evaluating the risk posed to aquatic life by flow alteration. A key
step in the first phase of the ERA process, problem formulation, is the development of a conceptual model
that explicitly demonstrates the hypothesized relations between ecological entities and the stressors to which
they may be exposed.
The conceptual model (Figure 2) describes in a general way how various stressors can alter the natural flow
regime, how flow alteration affects the chemical and physical conditions of an aquatic ecosystem, and how
15
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those changes may ultimately reduce the ability of a stream to support aquatic life. The general model is
intended only to provide a foundation for detailed regional or catchment models; for a specific area, specific
types of flow alteration and biological responses should be identified.
The general conceptual model of the biological effects of flow alteration presented in this report (Figure 2) is a
broad framework relating streamflow alteration and its sources to degraded aquatic life. The model is
constructed around the following concepts and relations:
« A stream's natural flow regime is primarily a function of climate and physical catchment-scale properties,
and is further affected by local, reach-scale conditions.
• The natural flow regime supports the integrity of aquatic life by maintaining habitat of sufficient size,
character, diversity, and connectivity by supporting natural sediment, water-temperature, and water-
chemistry regimes and by providing cues for spawning, migration, and other life-history strategies.
« A variety of human activities that change pathways and rates of runoff, modify channel storage and
dimensions, or directly add water to or remove water from streams can alter the natural flow regime.
« Alteration of the natural flow regime leads to changes in water temperature and chemistry and (or) the
physical properties of streams and adjacent riparian areas and flood plains. Feedback between altered
flow and altered physical properties can further modify flow characteristics. Changes to stream chemical
and physical condition following flow alteration can lead to the reduction, elimination, or disconnection of
optimal habitat for aquatic biota.
• Biological responses to flow-mediated changes in stream chemistry and physical habitat can have
cascading effects across trophic levels and aquatic communities, which may result in degraded aquatic life
as determined by measures of effect (for example, survival, growth, and reproduction of aquatic biota).
The following sections describe the components of the general conceptual model. A detailed conceptual
model of flow alteration with explicit directional relations is provided in Section 6.4. For detailed conceptual
16
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models developed for the EPA Causal Analysis/Diagnosis Decision Information System (CADDIS), see U.S.
Environmental Protection Agency (2012a)
|
Natural hydroloqic regime
Climate
Topography
Soil texture
(Catchment scale)
Position in river network
Channel and valley morphology
Groundwater dynamics
(Local scale)
Altered flow magnitude, timing, duration, frequency, and rate of change
Landusa Discharges Dam sand impoundments
Climate change Levees/channelization Impervious surfaces
Divarsions/interbasin transfers Surface- and groundwaterwithdrawals
Sediment and turbidity
Salinity, dissolved oxygen, and temperature
Nutrients and toxics
(Change in malar quality)
Depth, width, slope, and sinuosity
Substrata texture and stability
Velocity and residence time
IChange in physical properties!1
Adverse effects on survival, growth, and reproduction of aquatic life
Change in reproductive success and timing
Change in food availability
Change in competition and predation
Change in physiology and behavior
Figure 2. Schematic diagram illustrating a generalized conceptual model of the biological effects of
flow alteration.
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4.2 Drivers of the Natural Flow Regime
The natural flow regime is the characteristic pattern of flow in a stream under natural conditions. Poff and
others (1997) present five components of the natural flow regime that are critical to aquatic ecosystems:
• the magnitude of flow over a given time interval (for example, average flow rate [reported in either cubic
feet per second or cubic meters per second] during the month of April, or the spring season);
« the frequency with which flow is above or below a threshold value (for example, the number of times that
flow exceeds the long-term average in one year);
• the duration of a flow condition over a given time interval (for example, the number days in a year during
which the flow exceeds some value);
• the timing of a flow condition (for example, the date of the annual peak flow); and
« the rate of change of flow (for example, how rapidly flow increases during a storm event).
A stream's natural flow regime is largely a function of the climate and physical properties of its unique
upstream drainage area (catchment1). Climate determines patterns of water and energy input over time,
whereas physical catchment characteristics such as soils, geology, and topography determine infiltration
pathways (surface or subsurface) and rates of runoff and routing of streamflow through the drainage network.
For example, a large proportion of rainfall in a catchment dominated by steep slopes and poorly-permeable
soils will be converted to surface runoff that is quickly routed through the channel network. The flow regime
of a stream in such a catchment would be characterized by high peak flows relative to average conditions, high
rates of streamflow change during and after storm events, and relatively low dry-weather flows. In contrast, in
1 The term "catchment" throughout this report refers specifically to the unique drainage area upstream from a stream reach of
interest. Although the term "watershed" also fits this definition, catchment is used in this report because managers use the term
"watershed" to describe larger geographic or planning units within a state or region.
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a catchment dominated by well-drained soils, peak flows would more closely match average flows as a result
of higher rates of infiltration and groundwater routing to the stream channel.
Although the natural flow regime is driven primarily by catchment-scale properties, flow characteristics are
also affected by local-scale drivers specific to individual stream reaches and the location of the reach within
the river network. Heterogeneity of local topography and geology, for example, can result in variable
groundwater inputs among reaches with similar catchment-scale properties. Other potential local-scale drivers
of the natural flow regime include channel morphology and riparian vegetation, although such characteristics
are themselves affected by the flow regime.
4.3 Sources of Flow Alteration
The natural flow regime is driven by both catchment and local properties; human activities that alter the
natural flow regime also occur at both of these scales. Changes to water quantity (flow volume) may result in
loss of the designated use, such as when perennial streams or rivers are anthropogenically dewatered or
intermittent streams are dewatered permanently or well beyond their natural variability. This section
describes the major potential sources of flow alteration and their typical effects on the natural flow regime.
Other sources of flow alteration (for example, artificial perennialization of intermittent streams [see Section
4.3.4]) may need to be considered depending on local or regional circumstances.
Recent assessments indicate that streamflow alteration is pervasive in the Nation's streams and rivers. In a
national assessment, the USGS found that human alteration of waterways has affected the magnitude of
minimum and maximum streamflows in more than 86 percent of monitored streams (Carlisle and others,
2013). In addition, human-caused depletion of minimum and maximum flows was associated with a twofold
19
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increase in the likelihood of effects on fish and macroinvertebrate communities 2 (Carlisle and others, 2011).
Sources of such effects may include groundwater and surface-water withdrawals, new and existing dams,
impoundments and reservoirs, interbasin transfers, channelization, impervious cover, and water diversions.
Human adaptations to increased drought, including expansion of surface- and groundwater uses, may
compound these effects by decreasing the magnitude of low flows and increasing the frequency and duration
of low flows in streams and rivers. Alterations in high flows can affect use; for instance, an increase in
impervious surface area may cause an increase in flow, resulting in deleterious alterations to habitat or the
biological community. The following sections describe potential stressors in more detail.
4.3.1 Dams and Impoundments
Dams and impoundments (for example, reservoirs) are designed to control and store streamflow for various
purposes and can provide multiple societal benefits through increased recreation opportunities, flood
attenuation, hydroelectric power, irrigation, public water supply, and transportation. However, dams are also
a cause of flow alteration throughout the United States, as only about 40 large rivers (defined as longer than
200 kilometers) remain free-flowing (Benke, 1990). At a national scale, when interregional flow variation
before and after dam construction is compared, streams below dams can be subject to reduced high flows,
augmented low flows, reduced seasonal variation, and other changes relative to predam conditions, resulting
in a regional homogenization of the flow regime (Poff and others, 2007). At a finer scale, however, within a
more homogenous hydroclimatic region, dams can create new flow regimes (McManamay and others, 2012).
2 Carlisle and others (2011) use the term "impairment" to describe this effect on the aquatic community, defining it as occurring when
the value of the ratio of the observed condition to the expected reference condition (0/E) was less than that at 90 percent of
reference sites within the same region. The aquatic community at a site was considered "unimpaired" when the 0/E did not meet this
condition. Although the term "impairment" is used in the original publication, the term "affected" is used for the purposes of this
report to avoid confusion with the specific use of the term "impaired" in CWA programs.
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The ecological costs of controlling natural flows can have wide-ranging effects on the chemical, physical, and
biological integrity of streams and rivers (Collier and others, 1996; Dynesius and Nilsson, 1994; Magilligan and
Nislow; 2005; Poff and others, 2007; Wang and others, 2011; Zimmerman and others, 2010). The various types
of effects are highly dependent on dam purpose, size, and release operations (Poff and Hart, 2002).
As of 2013, more than 87,000 dams were represented in the U.S. National Inventory of Dams (NID) (U.S. Army
Corps of Engineers, 2013). Not included in this total are small impoundments for farm ponds, fishing ponds,
community amenities that fragment stream networks (for example, impoundments less than 2 meters [m]
high), and larger dams that have not yet been included in the national database. New geographic information
system (CIS) and remote-sensing tools are used to identify the extent and number of small impoundments,
which may be in the tens of thousands per state. For example, a study in the Apalachicola-Chattahoochee-Flint
River Basin in the southeastern United States identified the presence of more than 25,362 impoundments
(Ignatius and Stallins, 2011), whereas the NID database recognized 1,415 (fewer than 6 percent of the
reported total) in the same basin. The extensive presence of dams with impoundment heights greater than 2
m on United States waterways in the NID (U.S. Army Corps of Engineers, 2013) is shown in Figure 3. Estimates
made by Poff and Hart (2002), identify more than 2,000,000 dams across the country which includes small and
large sized dams.
Studies have shown that dam reregulation (when operational guidelines for the dam are modified to address
environmental management concerns about downstream fisheries, riparian habitats, recreation, flow, etc.)
has the potential to restore ecological function downstream of dams. Although the ability to modify
operations varies on the basis of the type and purpose of the dam (that is, hydropower, flood control,
irrigation, etc.), virtually all dams, regardless of size, have the potential to be modified (Arthington, 2012).
Since 2000, large-scale flow experiments have become an important component of water-management
planning, with considerably more than 100 large-scale flow experiments documented worldwide, including 56
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in the United States alone (Olden and others, 2014). Alterations to dam operations, including changes in the
magnitude, frequency, and duration of high-flow events; changes to minimum releases; and alteration of
reservoir drawdown regimes or restoration of flows to bypassed reaches; can result in ecological benefits,
including recovery of fish and shellfish, improved water quality, reactivation of flood-plain storage, and
suppression of non-native species (Konrad and others, 2011; Olden and others, 2014; Richter and Thomas,
2007). Key components of successful dam reregulation include clearly articulating objectives and expectations
prior to beginning reregulation, inclusion of a process to monitor or model the short -and long-term effects of
proposed release operations, and the ability to adaptively manage the dam operations (Konrad and others,
2011; Richter and Thomas, 2007).
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EXPLANATION
Dam with impoundment height
greater than 2 meters
0 250 500 KILOMETERS
Base from U.S. Census Bureau cartographic boundary file, 2013,1:500,000
Albers Equal-Area Conic projection
Standard parallels 29°30'N and 45°30'N
Central meridian 96°00'W
Figure 3. Map showing dams in the conterminous United States listed in the National Inventory of Dams
(NID) (U.S. Army Corps of Engineers, 2013). The NID database contains the most comprehensive set of dam
information in the United States and lists dams with an impoundment height greater than 2 meters.
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4.3.2 Diversions
In contrast to dams and reservoirs that store water and sustain releases, diversions remove a specified volume
of flow from a stream channel as needed. Diversions include permanent or temporary structures and water
pumps designed to divert water to ditches, canals, or storage structures. Diverted waters are used for
hydropower, irrigation, municipal, and (or) industrial purposes. Permanent infrastructure to convey diverted
waters (pipelines, canals, ditches, etc.) exists throughout the United States; a large number of these structures
are found in certain areas of the country (Figure 4).
The effects of diversions on the flow regime depend on the quantity and timing of the diversion (for example,
see Figure 5) (Bradford and Heinonen, 2008). Although the largest diversions by volume occur during storm
events, a greater proportion of flow is generally removed during low-flow periods, when plants and wildlife
are already under stress. Although diversions result in an immediate decrease in downstream flow magnitude,
some of the diverted water may eventually return to the stream as irrigation return flow or point-source
discharge (see Section 4.3.4). This is not the case, however, for interbasin water transfers, a distinct class of
diversion in which water is transported out of one basin and used in another. Regardless of the fate of the
water, the quantity and timing of the diversion can alter the natural flow regime.
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EXPLANATION
Water-conveyance structure
Canal or ditch
Pipeline
0 250 500 KILOMETERS
Base from U.S. Census Bureau cartograpriic boundary file, 2013,1:500,000
Alters Equal-Area Conic projection
Standard parallels 29>30'N and 45°3Q'N
Central meridian 96COQ'W
Figure 4. Map showing location of water-conveyance structures in the medium-resolution National
Hydrography Dataset (NHD) (U.S. Geological Survey, 2012), illustrating the widespread extent of canals,
ditches, and pipelines in the conterminous United States.
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350
300
250
- ISO
ICC
50'
EXPLANATION
— Upstream of diversion
Downstream of diversion
May
June
July
2010
August
September
Figure 5. Graph showing streamflow at Halfmoon Creek, Colorado (U.S. Geological Survey station number
7083000), May-September, 2010. (Streamgages are located upstream and immediately downstream from
the diversion structure. Diverted water is stored in a nearby reservoir for irrigation.)
4.3.3 Groundwater Withdrawals
Most surface-water features interact with shallow groundwater, serving as points of discharge or recharge to
local and regional aquifers. In many parts of the United States, groundwater contributes to streamflow and is
the primary natural source of water during periods without substantial precipitation and runoff. Groundwater
is also a major source of water for irrigation, public water supplies, and industrial use. Groundwater
withdrawals can lower the water table, resulting in reduced discharge to streams (Reeves and others, 2009;
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Winter and others, 1998; Zarriello and Ries, 2000; Zorn and others, 2008). Once thought to be limited to the
arid west, groundwater depletion has been identified throughout the United States. The rate of groundwater
depletion continues to increase and has been recognized globally as a threat to sustainability of water supplies
(Konikow, 2013). Groundwater withdrawals for irrigation increase during drought, when the only source of
streamflow may be base flows from groundwater. The ecological effects of reduced groundwater
contributions to streamflow, like those of other reductions in stream base flows, include the desiccation of
aquatic and riparian habitat, reduced velocities and increased sedimentation, increased water temperature,
and reduced connectivity of the stream network (discussed in Sections 4.4 and 4.5). These effects are
exacerbated by groundwater demand, which spikes at times of the year when adequate flows are needed to
support important biological behaviors and processes (for example, in summer when certain fish migrate and
reproduce).
4.3.4 Effluents and Other Artificial Inputs (Discharges)
In contrast to diversions, surface- and groundwater withdrawals, and other human activities that remove
water from streams, discharge (effluent) from industrial and municipal wastewater-treatment facilities and tile
drainage systems add water to streams and can alter natural flow patterns. For example, the effects on
streamflow are amplified when artificial discharges consist of water that is not part of the natural water
budget of the stream, such as deep groundwater or water derived from other basins, as in the case of
interbasin transfers (Jackson and others, 2001). Such exogenous contributions shift the hydrograph upward
and may be especially noticeable during natural low-flow periods as well as during flood flows resulting from
storm events (Figure 6). This flow augmentation distorts the flow-sediment balance characteristic of
undisturbed catchments, leading to effects such as channel downcutting and bank erosion as the stream
strives to attain a new balance between water and sediment flux (as discussed in Section 4.4.1). In many arid
environments, streamflow during dry seasons is composed almost entirely of treated effluent from
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wastewater-treatment facilities (Brooks and others, 2006). These inputs can cause a change in the stability of
natural systems by artificially raising the water level during low-flow periods.
1.6
a
I 1.4
U
S 1-0
0.8
I 0-6
0.4
8 0.2
EXPLANATION
Sixth Water Creek
Reference stream
Jan. Feb. Mar. Apr. May June July
Aug. Sept.
Oct
Nov.
Dec.
Figure 6. Graph showing artificially augmented daily streamflow at Sixth Water Creek, Utah (U.S. Geological
Survey station number 10149000), January-December, 2000.
4.3.5 Land-Cover Alteration (Land Use)
The alteration of natural land cover for agricultural, forestry, industrial, mining, or urban use can modify
several hydrologic processes that govern the amount and timing of runoff from the land surface, as well as
other important processes and characteristics (for example, sediment dynamics, temperature). Such land-
cover alterations may involve the removal of or change in vegetation cover, construction of impervious
surfaces (for example, parking lots and rooftops), land grading, stream-channel alteration, or construction of
engineered drainage systems. These changes reduce the potential for precipitation to be stored in shallow
depressions and soils (Blann and others, 2009; Konrad and Booth, 2005) and allow a greater fraction of
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precipitation to enter stream channels through surface runoff, rather than infiltrate into the ground or
evaporate. Moreover, engineered drainage systems (for example, municipal stormwater systems) and road
networks can directly route runoff to receiving waters, increasing the rate of change to streamflow during a
storm event. As a result, streams in developed areas exhibit extreme flashiness, characterized by a rapid rise in
flow during storm events to a high peak-flow rate followed by rapid recession of flow after precipitation
ceases (Dunne and Leopold, 1978; Walsh and others, 2005a, 2005b).
In addition, impervious surfaces reduce base flow in the days or weeks after a storm event as a result of
reduced infiltration and groundwater recharge. In agricultural areas, the opposite effect is observed with
subsurface drainage structures (or tile drains), which discharge groundwater that would otherwise be held in
storage or lost through evapotranspiration. However, agricultural drainage systems can reduce base flow,
particularly when drainage lowers the water table and decreases groundwater recharge (Blann and others,
2009). During prolonged drought, differences in low-flow conditions between developed and natural streams
generally are less pronounced than during average or high-flow conditions because developed areas tend to
have a smaller effect on the deep groundwater recharge that supports flow during drought conditions than on
the shallow groundwater and runoff that contribute water to a stream when precipitation is more plentiful
(Konrad and Booth, 2005).
Urban and agricultural land uses can accompany water-use and management practices such as interbasin
transfers, irrigation and other surface-water withdrawals, on-site wastewater disposal, impoundment, and
groundwater pumping. Each of these practices affects the direction and magnitude of flow alteration in urban
and agricultural streams and can compound hydrologic effects, as discussed previously.
The effects of surface mining on streamflow are highly localized and depend on the catchment characteristics
and vegetative cover, the geology of the mine and degree of valley fills, the extent of underground mines and
sediment ponds, and the amount of soil compaction and infiltration. Mining has been found to increase peak
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flows, unless other transport pathways, such as substantial connections to underground mines, intercept the
stormwater discharges to streams (Messinger, 2003).
Finally, management activities in natural areas can cause flow alteration. Timber harvesting in forested areas
generally increases peak flows and base flows as a result of decreased evapotranspiration and increased
snowpack resulting from decreased canopy interception (Harrand others, 1982; Hewlett and Hibbert, 1961).
These effects are temporary and are dependent on the size and type of harvest and the rate of vegetation
regeneration.
4.3.6 Climate Change
Climate change is an important and complex source of flow alteration because of the broad geographic extent
of its effects and the lack of management options for direct mitigation at the watershed scale. Recent climate
trends have included rising ambient air and water temperatures, increased frequency of extreme weather
such as heavy precipitation events, increased intensity of droughts, longer growing seasons, and reductions in
snow and ice, all of which are expected to continue in the coming years and decades (Karl and others, 2009).
Some of these changes have occurred or are projected to occur throughout the United States, such as
increases in the frequency of very heavy precipitation events during the 20th century (Melillo and others,
2014). Other changes have been or are projected to be limited to certain regions, such as a projected increase
in winter and spring precipitation in the northern United States and a decrease in winter and spring
precipitation in the southwestern United States (Melillo and others, 2014).
Each of these aspects of climate change can substantially alter historic flow patterns. Projected nationwide
increases in the frequency of heavy storm events and summer droughts have the potential to result in more
frequent flooding and extreme low flows in streams and rivers across the United States. Specific effects on
streamflows, however, will vary by region on the basis of regional climate change and hydrologic regimes. For
example, observed trends in the magnitude of 7-day low flows at streamgauges with minimal landscape
30
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effects vary across the United States, with some regions exhibiting a trend of decreasing low flows (longer dry
spells) and others trending toward higher low flows (Figure 7) (U.S. Environmental Protection Agency, 2014b).
Anthropogenic alterations that reduce streamflow may be further exacerbated by this climate-change trend.
In areas where flow regimes are strongly affected by snowmelt, observations show a trend toward earlier
timing of spring high flows (Figure 8) that corresponds to declines in the spring snowpack and earlier
snowmelt (Melillo and others, 2014). These examples demonstrate the exposure of aquatic ecosystems to
climate-driven flow alteration. Exposure analysis is an essential part of an assessment of the vulnerability of
aquatic life to climate change. Additional discussion and examples of climate-change vulnerability assessments
related to altered flow and aquatic life are included in Appendix C.
Climate change is occurring in conjunction with other anthropogenic stressors related to population increase
and land-use change and may magnify the hydrologic and biological effects of those existing stressors
(Intergovernmental Panel on Climate Change, 2007; Karl and others, 2009; Kundzewicz and others, 2008;
Palmer and others, 2009; Pittock and Finlayson, 2011). For example, the combination of earlier spring
snowmelt and increased water withdrawals can reduce summer flows to levels that would not otherwise
occur in response to either stressor alone and that reduce the survival of aquatic biota. An additional example
is the compounding effect of increased storm intensity on flood frequency in areas where impervious cover
already drives flood flows at a frequency that degrades stream habitat (Intergovernmental Panel on Climate
Change, 2007). These and other changes to the flow regime may further benefit invasive species to the
detriment of native species (Rahel and Olden, 2008).
Adaptive capacity, or the ability of a stream ecosystem to withstand climate-driven stresses, may be seen in
rivers whose flow patterns more closely resemble the natural flow regime. These rivers may be buffered from
the harmful effects of climate-related disturbances on aquatic life (Palmer, 2009; Pittock and Finlayson, 2011).
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Understanding and enhancing adaptive capacity, along with an assessment of climate-change vulnerability, is
a key part of climate-change adaptation planning.
EXPLANATION
Decrease greater than 50 percent
V Decrease greater than 20 percent
but less than 60 percent
o Decrease less than 20 percent
or increase less than 20 percent
A Increase greater than 20 percent
but less than 50 percent
/\ Increase greater than 50 percent
0 250 500 KILOMETERS
Base from U.S. Census Bureau cartographic boundary file. 2013,1:500,01)0
Albers Equal-Area Conic projection
Standard parallels 29r30'N and 45°30'N
Central meridian 96'WW
Figure 7. Map showing trends in the magnitude of 7-day low streamflows in the United States, 1940-2009.
(Minimum streamflow is based on data from 193 long-term U.S. Geological Survey streamgages over the 70-
year period whose drainage basins are only minimally affected by changes in land use and water use.
Modified from U.S. Environmental Protection Agency, 2014b)
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EXPLANATION
Timing of winter-spring runoff,
in number of days earlier
o Less than or equal to 2
T Greater than 2 to 5
V Greater than 5 to 10
Greater than 10
i r
0 250 500 KILOMETERS
Base from U.S. Census Bureau cartographic boundary file, 2013,1:500,000
Albers Equal-Area Cunic projection
Standard parallels 29P3Q'N and 45^30'N
Central meridian 96
-------
4.4 Physical and Chemical Effects of Flow Alteration
Changes to the natural flow regime resulting from land-use and water-management practices can affect
physical and chemical properties of riverine ecosystems, including geomorphology, connectivity, and water
quality (Annear and others, 2004). This section provides an overview of the effects of flow alteration on each
of these properties.
4.4.1 Effects on Geomorphology
The geomorphology of stream channels and flood plains is shaped largely by natural flow patterns.
Geomorphology is the expression of the balance between flow strength (for example, flow magnitude, slope)
and flow resistance and sediment supply (for example, grain size, vegetation, sediment load), with a tendency
toward channel erosion and degradation when flow strength increases and a tendency toward channel
deposition and aggradation when flow resistance and sediment supply increase. Channel geometry, bed
substrate, and the presence of geomorphic features such as oxbow lakes, point bars, or riffle-pool sequences
vary according to the frequency of bankfull flows, the magnitude of floods, and other flow characteristics
(Trush and others, 2000). Research has uncovered a variety of geomorphic responses to flow alteration, with
specific effects depending on the type and severity of streamflow change. These effects can include channel
incision, narrowing, or widening; increased deposition of fine sediment or bed armoring (coarsening); and
reduced channel migration (Poff and others, 1997).
A primary mechanism for geomorphic change is a shift in energy and sediment dynamics following flow
alteration. For example, increased peak flows resulting from urban land use can increase bed erosion and
drive channel incision or widening. In contrast, reduced flooding as a result of dam regulation can lower the
distribution of nutrient-bearing sediments to flood plains, starve downstream channel and coastal areas of
needed sediment, and increase sedimentation upstream from the dam (Syvitski and others, 2005). These
processes can lead to simplified channels that are disconnected from their natural flood plains. Natural
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mosaics of geomorphic features serve as important habitats for a range of aquatic and flood-plain species, and
the loss of habitat diversity following hydrologic alteration can have adverse effects on the health of biological
communities.
4.4.2 Effects on Connectivity
Hydrologic connectivity is the water-mediated transfer of matter, energy, and (or) organisms within or
between elements of a hydrologic system (Pringle, 2003). In aquatic ecosystems, it encompasses longitudinal
connectivity of the stream network and specific habitat types, as well as lateral connectivity among stream
channels, riparian zones, flood plains, and wetlands. The vertical connection between surface water and
groundwater is a third dimension of connectivity along the various flow paths that connect points of recharge
(beginning at the water table) to points of discharge (for example, a river or stream) (Ward, 1989).
Longitudinal, lateral, and vertical connectivity naturally vary spatially and temporally with climate,
geomorphology, groundwater dynamics, and other factors. Longitudinal connectivity, for example, may be
continuous from headwaters to lower reaches in one catchment but interrupted by intermittent or ephemeral
reaches in another (Larned and others, 2010a, 2010b, 2011). Lateral connectivity is restricted to short-
duration flooding of narrow riparian areas in headwater reaches, whereas meandering and braided lower
reaches are subject to longer periods of inundation over broader flood plains (Ward and Stanford, 1995).
Aquatic biota have adapted to connectivity patterns through space and time, with life-history traits such as
migration and spawning closely linked to the timing, frequency, and duration of upstream-downstream and
channel/flood-plain connections (Junk and others, 1986; U.S. Environmental Protection Agency, 2015).
Flow alteration can affect connectivity in several ways. Longitudinal connectivity of the stream network is
disrupted by dams, weirs, diversions, and other manmade structures that obstruct upstream-downstream
passage by fish and other organisms. Longitudinal connectivity is also disrupted by fragmentation of aquatic
habitat without manmade barriers. For example, an increase in the frequency of zero-flow conditions in a
35
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stream reach as a result of water withdrawals can cause the disconnection of upstream areas from the rest of
the stream network (U.S. Environmental Protection Agency, 2015). Lateral connectivity among the stream
channel, riparian areas, flood plains, and wetlands is reduced as a result of the decreased frequency of high
flows and floods caused by geomorphic change (for example, channel incision) or of direct modification of
stream channels (channelization, levee construction, etc.). Vertical connectivity is altered directly and
indirectly through practices that alter infiltration and runoff (for example, irrigation return flow), which can
affect recharge to groundwater and outflow to surface water. Other activities (for example, drainage) can alter
surface-runoff rates and potentially reduce recharge and contribute to flooding. Other practices may cause a
rise in the water table and, subsequently, the base level of a stream (for example, reservoirs) (Winter and
others, 1998). For systems characterized by an absence of connectivity, flow alterations such as stream
channelization, irrigation, and impervious surface area can increase flashiness and increase connectivity (U.S.
Environmental Protection Agency, 2015).
4.4.3 Effects on Water Temperature and Chemistry
The water quality effects of flow alteration are varied and can include changes in water temperature, salinity
(which is measured by specific conductance), dissolved-oxygen concentration, pH, nutrient concentrations,
and other parameters. For example, dilution of dissolved salts or toxic contaminants are reduced because of a
decrease in flow magnitude when water is diverted or groundwater is pumped (Caruso, 2002; Olden and
Naiman, 2010; Sheng and Devere, 2005). Stream temperature is also closely linked to flow magnitude (Cassie,
2006; Gu and Li, 2002; Wehrly and others, 2006); artificially low flows can result in increased water
temperatures as a result of reduced depths and (or) reduced input of cool groundwater. Low flows also
increase the likelihood of stagnant water with a low dissolved-oxygen concentration. In contrast, dam
tailwaters can become supersaturated with gases and harm aquatic life (Weitkamp and Katz, 1980).
Additionally, dam tailwaters, particularly those drawing water from the depths of stratified reservoirs, show
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elevated levels of nutrients and metals, low dissolved-oxygen concentrations, and altered temperature
relative to downstream waters (Arnwine, 2006; De Jalon and others, 1994; McCartney, 2009; Olden and
Naiman, 2010; Poff and Hart, 2002; Preece and Jones, 2002; Sherman and others, 2007; Vorosmarty and
others, 2003). Thermal regime modifications can include an increase in temperatures when warm water is
released from the reservoir surface (common in smaller dams and diversions), or lower temperatures when
water is released from beneath a reservoir's thermocline (Olden and Naiman, 2010). In urban areas, stream
temperatures are elevated during high-flow conditions (constituting an increase in the rate of change) as a
result of the input of runoff that has come in contact with warm impervious surfaces. Moreover, runoff from
developed lands can transport nutrients, organic matter, sediment, bacteria, metals, and other contaminants
to streams (Grimm and others, 2005; Hatt and others, 2004; Morgan and Good, 1988; Mulholland and others,
2008; Paul and Meyer, 2001). Effects may differ among water-body types (for example, lentic and lotic
waters).
4.5 Biological Responses to Flow Alteration
The combined physical and chemical effects of flow alteration (summarized in the previous section) may result
in the degradation, loss, and disconnection of ecological integrity within a stream system. Moreover, flow
modification can eliminate hydrologic cues needed to stimulate spawning or flow volume and timing needed
to aid seed dispersal, resulting in a mismatch between flow and species' life-history needs, and can encourage
the invasion and establishment of non-native species (Bunn and Arthington, 2002). The ability of a water body
to support healthy aquatic life is therefore tied to the maintenance of key flow-regime components.
Specific biological effects of a given type of flow alteration vary by location and degree of alteration; however,
some generalities can be made. Literature summarizing biological responses to altered flows, compiled and
reviewed by Bunn and Arthington (2002) and Poff and Zimmerman (2010), includes studies showing overall
reductions in the abundance and diversity of fish and macroinvertebrates, excessive growth of aquatic
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macrophytes, reduced growth of riparian vegetation, and shifts in aquatic and riparian species composition.
These changes are tied to altered habitat. For example, the stabilization of flow downstream of dams tends to
reduce habitat diversity and, therefore, species diversity. Reduced longitudinal connectivity of habitat types
can reduce the survival of migratory fish species, and reduced lateral connectivity between stream channels
and flood-plain wetlands limits access to important reproduction and feeding areas, refugia, and rearing
habitat for native and resident fishes. Reduced lateral connectivity can reduce habitat needed for aquatic life
stages of macroinvertebrates and amphibians, and can reduce the potential for gene flow (mixing individuals
from different locations). Fish spawning is disrupted by changes to the natural seasonal pattern of flow. For
some fish species, spawning is triggered by rising flows in the spring; therefore, a shift in the timing of high
flows can result in aseasonal reproduction during periods when conditions for larval survival are suboptimal.
In addition, changes in species abundance and richness, ecosystem functions such as contaminant removal
and nutrient cycling rates, can degrade in the environment due to flow alteration (Palmer and Febria, 2012;
Poff and others, 1997).
The relations among variables such as flow, temperature, habitat features, and biology are key in controlling
species distribution (for example, Zorn and others, 2008). Water temperature is an associated hydrologic
characteristic and has a particularly strong effect on aquatic organisms in summer months, when streamflows
are lowest and temperatures are highest (Brett, 1979; Elliot, 1981; Wehrly and others, 2003). Increases in
water temperature that result from alterations such as withdrawals, especially during critical summer low-
flow periods, have detrimental biological effects. Dam operations can have diverse effects on biology through
modifying the thermal regime, and these modifications depend on the size, purpose, and release operations of
the dam. For example, depressed spring and summer temperatures due to dam releases from the deep, cool
layer in a stratified reservoir, may result in delayed or reduced spawning of fish species or extirpation of native
warm-water biological communities in favor of cool- and cold-water assemblages (Olden, 2004; Preece and
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Jones, 2002). Dam releases in the winter result in warmer water temperatures, which may eliminate
developmental cues and increase growth, leading to earlier aquatic insect emergence. These changes in
temperature can create a mismatch between life-history stages and environmental conditions that may
increase mortality as a result of high-flow events, predation, reduction in resource availability earlier in the
season, and other stresses (Olden and Naiman, 2010; Vannote and others, 1980; Ward and Stanford, 1982).
The result of these hydrologic alterations may be impairment of a water body due to the physical, chemical, or
biological effects discussed above. The most severe of alterations, the complete dewatering of a perennial
stream or river, will result in complete extirpation of aquatic species in those water bodies. In addition to
directly contributing to impairments through ecologically deleterious physical changes (that is, hydrologic,
geomorphic, and connectivity change), hydrologic alteration may also be the underlying source of other
impairments such as low dissolved oxygen, modified thermal regimes, increased concentrations of sediment,
anoxic byproducts (such as downstream of dams), and nutrients or toxic contaminants. While the focus of this
report is primarily on those direct physical factors (for example, geomorphic and hydrologic) that can affect
biological communities, addressing these hydrologic alterations may also help to mitigate the effects of
contaminants such as those mentioned above.
The following section (Section 5) provides some examples of State actions within a CWA framework to protect
aquatic life from flow alteration.
5 Examples of State and Federal Actions to Protect Aquatic Life from Altered Flows
States have CWA tools and other tools that can address the effects of altered flows on aquatic life. This section
briefly discusses those programs that are within the CWA. The CWA was intended to protect the chemical,
physical, and biological integrity of the Nation's waters (see Box A). The two sections of the CWA related to
the development of the information presented in this report are CWA Sections 304(a)(2) and 304(f). CWA
Section 304(a)(2) generally requires EPA to develop and publish information on the factors necessary to
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restore and maintain the chemical, physical, and biological integrity of navigable waters. Section 304(a)(2) also
allows EPA to provide information on the conditions necessary for the protection and propagation of shellfish,
fish, and wildlife in receiving waters and for allowing recreational activities in and on the water3. CWA Section
304(f) requires EPA to issue information to control pollution resulting from, among other things, "changes in
the movement, flow, or circulation of any navigable waters."
CWA case law has affirmed that the distinction between water quantity and water quality is artificial and that
sufficient water quantity may be necessary in order to protect designated uses and meet antidegradation
requirements. Public Utility District No. 1 of Jefferson County v. Washington Department of Ecology, 511 U.S.
700, 719-721 (1994); S.D. Warren Co. v. Maine Board of Environmental Protection, 547 U.S. 370 (2006).
Additionally, the U.S. Supreme Court cited provisions in the CWA (Section 502(19)) recognizing that a
reduction in streamflow can constitute water pollution, including the CWA's definition of "pollution" as the
manmade or man-induced alteration of the chemical, physical, biological, and radiological integrity of water.
PUD No.l, 511 U.S. at 719. The Supreme Court held that this broad definition of pollution addresses the U.S.
Congress's concern regarding the physical and biological integrity of water, and refutes the distinction
between water quantity and quality. Appendix B provides additional discussion of the legal background and
relevant case law.
3 EPA notes that CWA Section 304(a)(2) is distinct from CWA Section 304(a)(l), which requires EPA to "develop and publish....criteria
for water quality accurately reflecting the latest scientific knowledge (A) on the kind and extent of all identifiable effects on health and
welfare including, but not limited to, plankton, fish, shellfish, wildlife, plant life, shorelines, beaches, esthetics, and recreation which
may be expected from the presence of pollutants in any body of water, including groundwater; (B) on the concentration and dispersal
of pollutants, or their byproducts, through biological, physical, and chemical processes; and (C) on the effects of pollutants on
biological community, diversity, productivity, and stability, including information on the factors affecting rates of eutrophication and
rates of organic and inorganic sedimentation for varying types of receiving waters."
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This section describes CWA programs that are used to address flow issues for aquatic life protection.
It provides illustrative case examples from states using the following six programs:
• Water quality standards (WQS) (Section 5.1),
• Monitoring and assessment of water bodies (Section 5.2),
• Total maximum daily load (TMDL) development (Section 5.3),
• Clean Water Act (CWA) 401 certifications (Section 5.4),
• CWA Section 404 permits (Section 5.5)4, and
• CWA Section 402 National Pollutant Elimination Discharge System (NPDES) permits (Section 5.6).
This section describes how these programs consider flow alteration to protect aquatic life. (An exhaustive
discussion of these CWA programs is beyond the scope of this document; readers can learn more by accessing
available EPA resources as noted below5.) Water quality standards (WQS) play a central role in the other CWA
programs mentioned (see Figure 9) and therefore are discussed first. Additional information on WQS is found
in Appendix A.
4 The responsibility for administering and enforcing CWA Section 404 is shared by the U.S. Army Corps of Engineers and the U.S. EPA
except in two states, Michigan and New Jersey, that have assumed CWA Section 404 responsibilities.
5 See Water Quality Standards Academy (http://water.epa.gov/learn/training/standardsacademy/index.cfm) and Watershed Academy
Water Law Modules (http://cfpub.epa.gov/watertrain/index.cfm).
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Point-source
discharge permitting
Targets for cleanup
actions under
the Superfund program
Listing of
impaired waters
Nonpoint-source
assessments
Basis for certification of
and conditions for
Federal permits/licenses
-quality
standards
Targets for total
maximum daily load
Wet weather discharge
(combined sewer
overflows, stormwater)
Area-wide waste
treatment plans
Reporting of condition
of waters
Figure 9. Schematic diagram illustrating water quality management programs based on water quality
standards under the Clean Water Act.
5.1 Narrative Criteria in State and Tribal Water Quality Standards
One set of CWA tools that states use to address the effects of hydrologic alteration on aquatic life is WQS,
which include designated uses, criteria, and antidegradation requirements. (A WQS overview is provided in
Appendix A.) The goals and provisions of the CWA and corresponding EPA regulations provide for states to
adopt narrative and (or) numeric chemical-specific criteria, as well as criteria that address the physical and
biological integrity of the Nation's waters (see CWA sections 101 and 303(c); see also Title 40 of the Code of
Federal Regulations (40 CFR) part 131.11(b)). This section presents examples of existing narrative flow criteria
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for states interested in developing or revising their own and some considerations for developing narrative
language.
As of 2014, 10 states had adopted narrative flow criteria in their WQS: New Hampshire, Rhode Island,
Vermont, New York, Virginia, Kentucky, Tennessee, Louisiana, Missouri, and Oregon. Also as of 2014, six tribes
with Treatment in a Manner Similar to a State (TAS) had adopted narrative flow criteria in their WQS. (Many
other authorized tribes have adopted wetland flow criteria.) As of 2015, no United States territories have yet
adopted flow criteria in their WQS. Table 1 contains example language for State and Tribal flow criteria.6
6 For the full text of State water quality standards, please see the following U.S. Environmental Protection Agency Web site for links to
the most up-to-date information: http://water.epa.gov/scitech/swguidance/standards/wqslibrary/index.cfm.
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Table 1. Excerpts from narrative flow criteria for selected states and tribes.
[Key terms are shown in bold for emphasis; see U.S. Environmental Protection Agency (2014e) for complete text of individual criteria; %, percent; 7Q10,
the 7-day, 10-year annual low-flow statistic; WMT, Water Management Type; 1
State/Tribe
New Hampshire
Water Quality Standard description of protected resource and corresponding goal
"surface water quantity shall be maintained at levels adequate to protect existing and designated uses"
"These rules shall apply to any person who causes point or nonpoint source discharge(s) of pollutants to surface waters, or who undertakes hydrologic
modifications, such as dam construction or water withdrawals, or who undertakes any other activity that affects the beneficial uses or the level of water
quality of surface waters."
Rhode Island
"quantity for protection of... fish and wildlife...adequate to protect designated uses"
"For activities that will likely cause or contribute to flow alterations, streamflow conditions must be adequate to support existing and designated uses."
Vermont
Class A(l)—"Changes from natural flow regime shall not cause the natural flow regime to be diminished, in aggregate, by more than 5% of 7Q10 at any
time;"
Class B WMT 1 Waters—"Changes from the natural flow regime, in aggregate, shall not result in natural flows being diminished by more than a minimal
amount provided that all uses are fully supported; and when flows are equal to or less than 7Q10, by not more than 5% of 7Q10."
Class A(2) Waters and Class B Waters other than WMT1—"Any change from the natural flow regime shall provide for maintenance of flow characteristics
that ensure the full support of uses and comply with the applicable water quality criteria."
New York
Class N fresh surface waters ... 'There shall be no alteration to flow that will impair the waters for their best usages."
Virginia
"Man-made alterations in stream flow shall not contravene designated uses including protection of the propagation and growth of aquatic life."
Kentucky
Section 4. "Aquatic Life. (1) Warm water aquatic habitat. The following parameters and associated criteria shall apply for the protection of productive
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State/Tribe
warm water aquatic communities, fowl, animal wildlife, arboreous growth, agricultural, and industrial uses:...(c) Flow shall not be altered to a degree which
will adversely affect the aquatic community."
Tennessee
Rule 0400-40-03-.03, Criteria for Water Uses: Section (3) The criteria for the use of Fish and Aquatic Life are the following, subsection (n) Habitat—'The
quality of stream habitat shall provide for the development of a diverse aquatic community that meets regionally-based biological integrity goals. Types of
habitat loss include, but are not limited to: channel and substrate alterations....stream flow changes....for wadeable streams, the instream habitat within
each subecoregion shall be generally similar to that found at reference streams. However, streams shall not be assessed as impacted by habitat loss if it
has been demonstrated that the biological integrity goal has been met." Subsection (o) Flow—"Stream or other waterbody flows shall support the fish and
aquatic life criteria."
"Section (4) The criteria for the use of Recreation are the following: Subsection (m) Flow—Stream flows shall support recreational uses."
Missouri
"Waters shall be free from physical, chemical, or hydrologic changes that would impair the natural biological community."
Seminole Tribe
of Florida
"Class 2-A waters shall be free from activities....that....impair the biological community as it naturally occurs....due to....hydrologic changes."
Bad River Band
of the Lake
Superior Tribe
of Chippewa
Indians
"Water quantity and quality that may limit the growth and propagation of, or otherwise cause or contribute to an adverse effect to wild rice, wildlife, and
other flora and fauna of cultural importance to the Tribe shall be prohibited."
"Natural hydrological conditions supportive of the natural biological community, including all flora and fauna, and physical characteristics naturally
present in the waterbody shall be protected to prevent any adverse effects."
"Pollutants or human-induced changes to Tribal waters, the sediments of Tribal waters, or area hydrology that results in changes to the natural biological
communities and wildlife habitat shall be prohibited. The migration offish and other aquatic biota normally present shall not be hindered. Natural daily
and seasonal fluctuations of flow (including naturally occurring seiche), level, stage, dissolved oxygen, pH, and temperature shall be maintained."
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Table 1 demonstrates that narrative flow criteria are written in various ways. However, the language
commonly addresses two general components: (1) a description of the resource or attribute to be protected
and (or) protection goal; and (2) one or more statements describing the hydrologic condition needed to be
maintained to achieve the protection goal. The resource to be protected generally is an explicit reference to
aquatic life designated uses or general language that targets the protection of a suite of designated and (or)
existing uses (for example, "propagation and growth of aquatic life," "biological community as it naturally
occurs," "diverse aquatic community," etc.). For most existing narrative flow criteria, the flow condition to be
maintained is written in general terms (for example, "There shall be no alteration to flow....," "natural daily
and seasonal fluctuations in flow," etc.). The addition of language that references specific aquatic life
endpoints, such as migration or other life-cycle events, may serve as important reminders of biological goals to
guide the selection of assessment endpoints, measures of effect (biological and flow indicators), and flow
targets to meet aquatic life needs. These concepts are discussed in detail in Section 6. Additionally, EPA
recently reiterated that WQS (designated uses and criteria) must ensure attainment and maintenance of
downstream WQS, including the hydrologic condition (U.S. Environmental Protection Agency, 2014d).
More complete examples from New Hampshire and Rhode Island narrative flow criteria are as follows and
illustrate additional attributes these states chose to emphasize, such as broad applicability across all surface
waters:
"Unless flows are caused by naturally occurring conditions, surface water quantity shall be maintained at
levels adequate to protect existing and designated uses." (New Hampshire Code of Administrative Rules Env-
Wq 1703.01 (d)). "These rules shall apply to any person who causes point or nonpoint source discharge(s) of
pollutants to surface waters, or who undertakes hydrologic modifications, such as dam construction or water
withdrawals, or who undertakes any other activity that affects the beneficial uses or the level of water quality
of surface waters." (New Hampshire Code of Administrative Rules Env-Wq 1701.02 (b)).
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"General Criteria—The following minimum criteria are applicable to all waters of the State, unless criteria
specified for individual classes are more stringent:....(h). For activities that will likely cause or contribute to
flow alterations, streamflow conditions must be adequate to support existing and designated uses." (Rhode
Island Department of Environmental Management Water Quality Regulations (2010) Rule 8(D)(l)(h)).
Although the narrative examples in Table 1 may be useful tools to help states make informed decisions about
their water resources, they do not explicitly describe the specific components of the natural flow regime (that
is, magnitude, duration, frequency, rate of change, and timing) to be maintained to protect aquatic life uses.
The framework presented in Section 6 can help guide a state through a process to determine which of these
components are most important to protect the designated use. Box C describes the physical and biological
importance of considering the specific components of the natural flow regime in the development of
environmental flow targets rather than relying on a more general minimum flow magnitude to protect aquatic
life.
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Box C. Addressing Flow Regime Components
It is critically important to maintain extremes (floods and droughts) within the bounds of the natural flow
regime to support the ecological structure and function of streams and rivers. However, alterations in low or
high flows that are human-induced, affect and can control many ecosystem patterns, such as habitat extent
and condition, water quality, connectivity, and material and energy exchange. These patterns can in turn
affect many ecosystem processes, including biological composition, distribution, recruitment of biota, and
ecosystem production (Rolls and others, 2012).
Although low flows serve a critical role in ecosystem function, current scientific research indicates that flow
criteria ideally should support the natural flow regime as a whole, and that criteria for minimum flow alone
(that is, a single minimum discharge value or a minimum passing flow) are not sufficient for maintaining
ecosystem integrity (Annear and others, 2004; Bunn and Arthington, 2002; Poff and others, 1997). Minimum
flow criteria do not address the full range of seasonal and interannual variability of the natural flow regime in
most rivers and streams.
The natural fluctuation of water volume and levels in rivers and streams is critical for maintaining aquatic
ecosystems because aquatic biota have developed life-history strategies in response to these fluctuations (Hill
and others, 1991; Lytle and Poff, 2004; Mims and Olden, 2012, 2013; Postel and Richter, 2003; Stalnaker,
1990). Comprehensive flow criteria not only identify flow needs (that is, magnitude) but may also address the
rate, frequency, timing, and duration of streamflow required to support ecosystem health (Poff and others,
2010). The Instream Flow Council (a non-profit organization working to improve the effectiveness of instream
flow programs and activities: http://www.instreamflowcouncil.org/) recommends developing criteria that
incorporate natural patterns of intra- and interannual variability in a manner that maintains and (or) restores
riverine form and function to effectively maintain ecological integrity (Annear and others, 2004). Therefore,
narrative hydrologic criteria and their implementation ideally should address several flow-regime components
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(frequency, duration, timing, rate of change) in addition to flow magnitude. The components necessary are
determined on a case-by-case basis, depending on which values are most ecologically relevant.
Minimum flow statistics such as the 7Q10 design flow (the minimum 7-day average flow likely to occur in a 10-
year period) are recommended by the U.S. Environmental Protection Agency for the derivation of water
quality-based effluent limits in the National Pollutant Discharge Elimination System permitting program, but,
although they include magnitude, duration, and frequency components, they were not derived to support the
hydrologic requirements of aquatic ecosystems (Annear and others, 2004). The main purpose of these design
flows is to determine pollutant discharge values (or limits) rather than to support the flow requirements of
aquatic ecosystems (see U.S. Environmental Protection Agency, 1991).
5.2 Monitoring, Assessing, and Identifying Waters Impaired as a Result of Flow Alteration
Once WQS are adopted, states ensure they are met through monitoring to assess use attainment status,
reporting on use attainment and identifying impaired waters, and implementing appropriate restoration
measures. Waters are classified and states report on their condition to support use attainment decisions
under Sections 303(d) and 305(b). States use their monitoring and assessment programs to identify and report
to the public those waters that have impairments from pollution, defined under the CWA as "the man-made
or man-induced alteration of the chemical, physical, biological, and radiological integrity of water" (Section
502(19)), including the effects of altered flow regimes or hydromodification (U.S. Environmental Protection
Agency, 1997, 2003, 2005). Attainment of designated uses is evaluated through monitoring and assessment of
indicators that reflect State WQS, including narrative or numeric criteria, or evaluating other data or
information (U.S. Environmental Protection Agency, 1991). Accurately identifying the impairment status of
these waters allows states to engage stakeholders on appropriate restoration strategies. The state of the
science for restoring waters impaired by hydrologic alteration has evolved considerably, including, for
instance, dam reregulation and improved methods for surface- or groundwater withdrawals.
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In the Consolidated Assessment and Listing Methodology guidance (U.S. Environmental Protection Agency,
2002), EPA recommends that the flow regime be a "core" water quality indicator for general designated uses
in the following categories: aquatic life and wildlife, recreation, and drinking water. As a core indicator, states
ideally would incorporate flow into their monitoring designs (U.S. Environmental Protection Agency, 2002,
Chapters 8 and 10). In order to accurately assess flow conditions over time, states evaluate monitoring data
and information relating to the flow regime.
States can record and evaluate flow information even when routine monitoring cannot occur as a result of
extreme (high or low) flow conditions. This evaluation could include desktop analyses sources such as USGS
StreamStats (a Web application that provides users with access to stream network tools for water-resources
planning purposes: http://water.usgs.gov/osw/streamstats/) or qualitative visual observations of streams.
Such data or information could be used for making attainment decisions. For instance, the absence of water
from a perennial stream could demonstrate that the aquatic life designated use is not being attained, and a
state may conclude that the designated use is impaired. Texas provides an example: for each visit to nontidally
influenced freshwater streams or rivers, the Texas Commission on Environmental Quality (TCEQ) monitoring
procedures require that a "flow-severity" field (with a value of no flow, low flow, normal flow, flood flow, high
flow, or dry) be recorded, even if it is not possible to quantitatively measure flow or conduct sampling during a
visit (see Box D).
States and tribes can use these data and information to classify the water-body segments into one of five of
the 303(d) and 305(b) Integrated Reporting (IR) categories7 (U.S. Environmental Protection Agency, 2005).
7 The listing categories are as follows: Category 1—All designated uses are supported, no use is threatened; Category 2—Available
data and (or) information indicate that some, but not all, of the designated uses are supported; Category 3—There is insufficient
available data and (or) information to make a use support determination; Category 4 (includes subcategories)—Available data and (or)
information indicate that at least one designated use is not being supported or is threatened, but a Total Maximum Daily Load (TMDL)
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Water-body segments where an applicable WQS for a pollutant is not met and a total maximum daily load
(TMDL) is required are placed on the 303(d) list of impaired waters, also known as IR Category 5 (U.S.
Environmental Protection Agency, 2005).
Where there is no associated pollutant, EPA recommends reporting impairments due to hydrologic alteration
in Category 4c, which are those impairments due to pollution not requiring a TMDL (U.S. Environmental
Protection Agency, 2005). Examples of hydrologic alteration may include the following: a perennial water body
is dry, no longer has flow, has low flow, has stand-alone pools, or has extreme high flows; or there is altered
frequency, magnitude, duration, or rate of change of natural flows in a water body; or a water body is
characterized by entrenchment, bank destabilization, or channelization. Where the specific pollutant causing
the impairment has not been identified (for example, for biological impairments), EPA recommends that states
list those waters in Category 5 (the 303[d] list, impaired by a pollutant and requiring a TMDL), unless they can
demonstrate that the impairment is solely attributable to a nonpollutant (for example, flow) (U.S.
Environmental Protection Agency, 2003; 2005). Additionally, EPA's guidance has noted that assessment
categories are not mutually exclusive, and waters may be placed in more than one category (for example,
categories 4c and 5) (U.S. Environmental Protection Agency, 2005).
The integrated reporting format provides transparency in reporting the status of all assessed waters and,
therefore, is one way to acknowledge the important role of flow in contributing to water-body impairments.
An example of a reporting option that helps clearly delineate and address waters impaired as a result of
streamflow alteration is described in Box E, which illustrates the use of Category 4F in Vermont.
is not needed; Category 5— Available data and (or) information indicate that at least one designated use is not being supported or is
threatened, and a TMDL is needed. For more information on Integrated Reporting categories, see
http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/upload/2006irg-report.pdf.
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Box D. Procedures for Capturing Flow Information in the State of Texas
The publication "Surface water quality monitoring procedures, Volume 1: Physical and chemical monitoring
methods" (Texas Commission on Environmental Quality [TCEQ], 2012) describes how Texas monitors all flow
conditions and captures flow information in its State database. Parameter codes for data uploads to the U.S.
Environmental Protection Agency (EPA) Storage and Retrieval Data Warehouse (STORET), a repository for
water monitoring data, are provided for each type of data collected. In addition to describing methods for
capturing quantitative flow information, the document describes how to capture qualitative flow information
with the "flow-severity" field:
• "Record a flow-severity value for each visit to freshwater streams or rivers (nontidally influenced) and
report the value to the TCEQ central office. Do not report flow severity for reservoirs, lakes, bays, or tidal
streams. It should be recorded even if it was not possible to measure flow on a specific sampling visit. See
the Surface water quality monitoring data management reference guide for detailed information on data
reporting." (Texas Commission on Environmental Quality, 2013)
• "No numerical guidelines are associated with flow severity, an observational measurement that is highly
dependent on the water body and the knowledge of monitoring personnel. It is a simple but useful piece
of information when assessing water quality data. For example, a bacteria value of 10,000 with a flow
severity of 1 would represent something entirely different than the same value with a flow severity of 5."
Table 3.2 of Texas Commission on Environmental Quality (2012) provides photographs of each "flow-severity"
category and the following descriptions, which can be found at
https://www.tceq.texas.gov/assets/public/comm exec/pubs/rg/rg415/rg-415 chapter3.pdf (accessed
February 4, 2016):
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• "No Flow. When a flow severity of 1 is recorded for a sampling visit, record a flow value of 0 ft3/s (using
parameter code 00061) for that sampling visit. A flow severity of 1 describes situations where the stream
has water visible in isolated pools. There should be no obvious shallow subsurface flow in sand or gravel
beds between isolated pools. —No flow not only applies to streams with pools, but also to long reaches of
streams that have water from bank to bank but no detectable flow."
• "Low Flow. When streamflow is considered low, record a flow-severity value of 2 for the visit, along with
the corresponding flow measurement (parameter code 00061). In streams too shallow for a flow
measurement where water movement is detected, record a value of < 0.10 ft3/s. In general, at low flow
the stream would be characterized by flows that don't fill the normal stream channel. Water would not
reach the base of both banks. Portions of the stream channel might be dry. Flow might be confined to one
side of the stream channel."
• "Normal Flow. When streamflow is considered normal, record a flow severity value of 3 for the visit, along
with the corresponding flow measurement (parameter code 00061). What is normal is highly dependent
on the stream. Normality is characterized by flow that stays within the confines of the normal stream
channel. Water generally reaches the base of each bank."
• "Flood Flow. Flow-severity values for high and flood flows have long been established by the EPA and are
not sequential. Flood flow is reported as a flow severity of 4. Flood flows are those that leave the confines
of the normal stream channel and move out onto the floodplain (either side of the stream)."
• "High Flow. High flows are reported as a flow severity of 5. High flow would be characterized by flows that
leave the normal stream channel but stay within the stream banks."
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"Dry. When the stream is dry, record a flow-severity value of 6 for the sampling visit. In this case the flow
(parameter code 00061) is not reported, indicating that the stream is completely dry with no visible
pools."
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Box E. Vermont Addresses Hydrologically Altered Waters
Vermont first adopted narrative criteria into its water quality standards (WQS) for Clean Water Act purposes
for flow or hydrologic condition in 1973 (for full text, see http://www2.epa.gov/sites/production/files/2014-
12/documents/vtwqs.pdf [accessed February 4, 2016] or Vt. Code R. 12 004 052,
http://www.vtwaterquality.org/wrprules/wsmd wqs.pdf [accessed February 4, 2016]). Although hydrologic
alteration is listed under integrated reporting guidance as Category 4c (impairments due to pollution not
requiring a Total Maximum Daily Load), Vermont does address flow-related exceedance of the WQS through
the Vermont Priority Waters List. This list includes waters assessed as "altered" using the state's assessment
methodology (Vermont Department of Environmental Conservation, 2014:
http://www.vtwaterquality.org/mapp/docs/mp assessmethod.pdf [accessed February 4, 2016]). Part F of the
Priority Waters List is water bodies that do not support one or more designated uses as a result of alteration
by flow regulation (primarily from hydroelectric facilities, other dam operations, or industrial, municipal, or
snowmaking water withdrawals). This list includes a description of the problem, current status or control
activity, and the projected year the water-body segment will come into compliance with WQS. Creating a new
category for hydrologic alteration helps separate it from other causes of pollution effects that would be
reported in Category 4.
5.3 Development of Total Maximum Daily Loads
When waters are placed into Category 5, a TMDL must be developed to address the pollutant(s) causing the
impairment. A TMDL is a calculation of the maximum amount of a pollutant that a water body can receive and
still meet WQS, and an allocation of that load among the various sources of those pollutants. Quantity of flow
and variation in flow regimes are important factors in transporting pollutants (for example, sediment,
pathogens, and metals) for which there may be WQS, and therefore flow is considered when calculating
TMDLs. In addition, EPA regulations require that seasonal variations, critical conditions, and a margin of safety,
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which are likely to be influenced by flow regimes, also be taken into account when developing a TMDL (40 CFR
§130.7(c)(l)). Flow conditions are used to help establish the cause-and-effect relation between the numeric
TMDL target and the identified pollutant sources using a water quality model. Understanding flow regimes
and how they transport the pollutant of concern can help identify actions needed to meet WQS. Flow patterns
play a major role when considering loading capacities in TMDL development and, therefore, states are
encouraged to consider the most up-to-date flow information available when developing TMDLs. Similarly,
when hydrologic alteration occurs after the completion of a TMDL (for example, the construction of a new
water intake that alters the water quantity on which the TMDL was based), states ideally would consider re-
evaluating the TMDL and, if necessary, revise it. A common source of streamflow data is the USGS National
Water Information System. Several EPA TMDL technical documents discuss the role of flow in the context of
methods and models to develop loadings and load and waste-load allocations. These include the EPA
document on developing TMDLs based on the load-duration curve approach (U.S. Environmental Protection
Agency, 2007) and the EPA protocol for developing sediment TMDLs (U.S. Environmental Protection Agency,
1999).
5.4 Consideration of Flow Alteration in Issuing 401 Certifications
An additional CWA program that can address protection of aquatic life from flow alteration is the CWA Section
401 water quality certification process. This certification process gives states the authority to grant, condition,
or deny a Federal permit or license (see CWA Section 401(a)(l)). Before issuing a CWA Section 401
certification, the state would ensure that any discharge to United States waters from the activity to be
permitted or licensed will be consistent with, among other things, the state's WQS and any other appropriate
requirement of State law including provisions relating to hydrologic conditions. See S. D. Warren Co. v. Maine
Board of Environmental Protection, 547 U.S. 370 (2006). The state can include flow as a condition for a Federal
401 permit or license, even if flow criteria are not explicitly included in the state's WQS. See Public Utility
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District No. 1 of Jefferson City v. Washington Department of Ecology, 511 U.S. 700, 719-721 (1994), described
in Box F. A State narrative criterion describing desired hydrologic conditions would provide a state with a basis
to identify conditions for inclusion in a Federal permit or license that might have beneficial effects on aquatic
life designated uses that would otherwise be harmed by altered hydrologic conditions (see two examples in
Box F).
Identification of flow impairments can aid in the 401 certification process. For example, a 4C identification or
other related category developed by a state (for example, the 4F category described in Box E) might help the
state recognize the potential for flow-related impairments caused by proposed projects. Such adverse effects
can be addressed through CWA 401 certification for operating conditions for a Section 404 permit (see Section
5.5), or as part of the Federal Energy Regulatory Commission permitting process for hydroelectric power
generation, for example.
Box F. 401 Certifications, Sufficient Flow, and Water Quality Standards
South Carolina Board of Health and Environmental Control Denied Certification
In 2009, South Carolina denied a 401 certification of a hydroelectric project license renewal (involving 11
dams), stating, "[t]he Board finds that the WQ Certification does not provide sufficient flow to protect
classified uses, the endangered shortnose sturgeon and adequate downstream flow....to provide reasonable
assurance....that WQS will be met." As a result of that action, negotiations were held that resulted in an
agreement in 2014 and granting of the 401 certification. The agreement conditions committed the energy
company to operating its dams to improve conditions for the sturgeon, protect flow conditions during
spawning periods, and provide periodic flood-plain inundation mimicking ecologically important natural floods
and recessions.
Public Utility District No. 1 of Jefferson County v. Washington Department of Ecology , 511 U.S. 700, 719-721
(1994), addressed the question of whether flow may be linked to WQS and whether a state may include
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specific flow requirements in a Clean Water Act Section 401 certification. The challenge was related to the
State of Washington's inclusion of minimum-flow requirements in a 401 certification for a Federal Energy
Regulatory Commission relicensing of a hydropower plant. The Court held that the State of Washington was
authorized to require the plant to maintain certain streamflows as a condition of a Section 401 certification. In
this case, the State of Washington did not have explicit narrative or numeric criteria related to flow, but the
certification was conditioned to address flow in order to protect the designated use and meet antidegradation
requirements.
5.5 Consideration of Flow Alteration in Issuing 404 Permits
Reviews conducted pursuant to CWA Section 404 also take into account potential effects on aquatic life uses
caused by hydrologic alteration associated with the discharge of dredged or fill material (for example, dams or
other impoundments). CWA Section 404 regulates8 discharge of dredged or fill material into waters of the
United States, and some proposed projects may result in loss of the conditions necessary for survival of
aquatic life, including, for example, lotic species (species that depend on flowing water for survival). As a
result, such projects could result in the inability to meet WQS, including protecting for the designated use,
narrative and numeric criteria (that is, dissolved oxygen, temperature, or biological narratives), and
antidegradation. Potential effects on the ability of a water body to meet WQS are a required consideration
when evaluating whether to issue a Section 404 permit [see 40 CFR 230.10(b)]. The Section 404 review entails
evaluating efforts to avoid the adverse effects on aquatic resources, minimizing effects if they cannot be
avoided, and mitigating any unavoidable adverse effects that remain. For example, avoidance could include
water conservation and efficiency programs and (or) use of an existing impoundment in lieu of creating a new
8 The responsibility for administering and enforcing CWA Section 404 is shared by the U.S. Army Corps of Engineers and the U.S.
Environmental Protection Agency. For more information on these responsibilities, see http://www.epa.gov/cwa-404/laws-regulations-
executive-orders and http://www.epa.gov/cwa-404/policy-and-guidance
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water-supply reservoir; minimizing could include reducing the scope of effects associated with a proposed
impoundment; and compensatory mitigation to offset the effects of a project could include hydrologic
restoration of waters through dam removal.
Examples of projects involving discharge of dredged or fill material that affect hydrology include the
construction of new water withdrawal or storage systems (for example, reservoirs); expansion of existing
withdrawal or storage systems; diversions and construction of projects such as drinking-water or flood-control
reservoirs, impoundments for energy generation, and fishing reservoirs or amenity ponds (an impoundment
developed for recreation and (or) aesthetic purposes). Impoundments alter streamflows, and operation of
dams to manage releases largely determines how closely downstream flows resemble the natural hydrograph.
State review of such proposed activities ideally would consider whether the proposed project would adversely
affect the designated use (aquatic life) or result in nonattainment of narrative or numeric WQS. Activities
proposed for Section 404 permits (issued by the U.S. Army Corps of Engineers) are reviewed by resource
agencies (Federal and State) and are subject to Section 401 certification. Permits issued by a state that has
assumed the Section 404 program (as of 2015, only Michigan and New Jersey have approved Section 404
programs), or issued by a state or tribe implementing a programmatic general permit issued by the U.S. Army
Corps of Engineers, must also consider the potential effects of a project on attainment of WQS, including
antidegradation requirements. A State program must be at least as stringent as the CWA requirements.
5.6 Consideration of Flow Alteration in Issuing National Pollutant Discharge Elimination System (402)
Permits
The National Pollutant Discharge Elimination System (NPDES) is another CWA program that can play a role in
protecting aquatic life from the effects of hydrologic alteration. NPDES permits are generally required for
point-source discharges of pollutants.
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Many NPDES permits depend on streamflow data for pollutant discharge limit calculations. Permits issued
under CWA Section 402 use critical low-flow values such as the 7Q10 (7-day, 10-year annual low-flow statistic)
or regulated low flows to calculate a permittee's discharge limits so that permitted values will be protective of
aquatic life under the most critical conditions. Many rivers and streams across the United States have
experienced trends in low flows since the 1940's-with increases generally in the Northeast and Midwest, and
decreases (streams carrying less water) in the Southeast and the Pacific Northwest (Figure 7). Permit writers
use the most up-to-date critical low-flow information for the receiving water and, where historical flow data
are no longer representative, use current low-flow data to calculate effluent permit limits to protect for the
new critical low flow (see the EPA Water Quality Standards Handbook [U.S. Environmental Protection Agency,
1994, Chapter 5.2]).
As states issue permits for new surface-water intakes or other surface- or groundwater withdrawals that will
alter the existing low flow of a stream, NPDES permits may need to be re-evaluated to ensure that the new
low flow is incorporated into effluent limit calculations and updated as needed. Safeguarding protective
instream flows from anthropogenic alteration will help maintain streamflow for existing NPDES permits,
reducing the need to modify them to meet new low-flow conditions. The protection of flow levels would
prevent additional treatment requirements for those permittees.
Among NPDES permits are those generally required for stormwater discharges from three sources: Municipal
Separate Storm Sewer Systems (MS4) identified in EPA regulations, construction activities that disturb one or
more acres, and industrial activities. MS4 regulations require that the permitted MS4, including storm-sewer
systems serving populations of 100,000 or more and systems serving populations located within the census-
defined urbanized area, develop a post-construction program to address stormwater runoff from new
development and redevelopment projects to reduce the discharge of pollutants and prevent or minimize
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effects on water quality. The post-construction program allows states to help protect aquatic life in receiving
waters from flow alteration as development occurs.
A substantial portion of the Nation's impervious cover was created since the 1950's, and the conversion of
land types, including forest, meadow, prairie, and agriculture, to impervious cover is expected to continue. An
increase in impervious cover increases runoff and affects NPDES permitting. According to the U.S. Department
of Agriculture (USDA) National Resources Inventory, developed land area increased almost 600 percent, from
18.6 to 111 million acres (7.5 to 44.9 million hectares), in the contiguous United States from 1954 to 2007
(U.S. Department of Agriculture, 1997; U.S. Environmental Protection Agency, 2013c). From 1982 to 2007,
more than 40 million acres of land —more than one-third of all land that has ever been developed in the
contiguous United States—was newly developed (U.S. Department of Agriculture, 2009). Approximately 25
percent of the land that has been developed in the United States is considered to be impervious (Elvidge and
others, 2004; U.S. Department of Agriculture, 2009). Impervious surface area in the United States is projected
to increase 14.2 percent from 2010 to 2040 (U.S. Environmental Protection Agency, 2009, 2010a).
An increase in impervious surface cover will increase the amount of runoff. Substantial effects of runoff
generally take one of two forms. The first is caused by an increase in the type and quantity of pollutants in
stormwater runoff. These pollutants can become suspended in runoff and are carried to receiving waters, such
as lakes, ponds, and streams, and can impair the aquatic life uses of these waters (see Section 4.4.3 for more
information). The second kind of runoff effect occurs by increasing the quantity of water delivered to the
water body as a result of storms. Increased impervious surface area (for example, parking lots, driveways, and
rooftops) interrupts the natural process of gradual percolation of water through vegetation and soil, and the
water that would percolate under natural conditions may instead be discharged through an MS4. The effects
of this alteration include streambank scouring and downstream flooding, which can affect aquatic life and
damage property (see Section 4.3.5 for more information).
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EPA requires that municipalities with permitted MS4s develop an implementation strategy that includes a
combination of structural and (or) nonstructural best management practices (BMPs) to control post-
construction discharges. EPA recommends that the BMPs chosen attempt to maintain predevelopment runoff
conditions (40 CFR 122.34(b)(5) http://www.epa.gov/npdes/npdes-stormwater-program ). Some states and
the EPA have included measurable post-construction requirements in their MS4 permits, such as requirements
for the treatment or retention of a specified volume of runoff to be managed on site. These requirements
clearly specify the expectations for controlling discharges from new development and redevelopment in order
to protect the aquatic life uses in the receiving water. An example of a post-construction volume retention
requirement is West Virginia's requirement to keep and maintain on site the first 1 inch (2.54 centimeters) of
rainfall from a 24-hour rain event (see Box G). This proactive approach using prior planning and design for the
minimization of contaminant concentrations and erosive flows is a cost-effective approach to stormwater
management.
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Box G. Stormwater and West Virginia Department of Environmental Protection (DEP) Municipal Separate
Storm Sewer Systems (MS4) Permit Language
The West Virginia DEP issued a small MS4 permit including the language below for new and redevelopment
projects to reduce effects from stormwater runoff at permitted sites:
"Performance Standards. The permittee must implement and enforce via ordinance and/or other enforceable
mechanism(s) the following requirements for new and redevelopment: [....]"
"Site design standards for all new and redevelopment that require, in combination or alone, management
measures that keep and manage on site the first one inch of rainfall from a 24-hour storm preceded by 48
hours of no measurable precipitation. Runoff volume reduction is achieved by canopy interception, soil
amendments, evaporation, rainfall harvesting, engineered infiltration, extended filtration, and/or
evapotranspiration and any combination of the aforementioned practices. This first one inch of rainfall must
be 100% managed with no discharge to surface waters."
For a full compendium of this and other examples, see U.S. Environmental Protection Agency (2014c).
For additional examples of stormwater-related permits and their analysis, see U.S. Environmental Protection
Agency (2012b).
5.7 Further considerations
The discussion above is not meant to be a comprehensive assessment of all Federal CWA programs that may
address flow and the protection of aquatic life uses. In addition to the approaches mentioned above, other
non-CWA mechanisms exist that may protect aquatic ecosystems from alteration of flow. Although many of
these programs may provide a method to specifically address these altered-flow effects, others may lack
specified frameworks and (or) established methods to quantify targets to address the impacts of flow on
aquatic life uses, allowing room for supplemental considerations or the application of methods considered the
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"best available science." Section 6 below presents a framework for quantifying flow targets to protect aquatic
life.
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6 Framework for Quantifying Flow Targets to Protect Aquatic Life
The adoption of narrative flow criteria in WQS is a mechanism to address the effect of flow alteration on
aquatic life. Narrative criteria are qualitative statements that describe the desired water quality condition
needed to protect a specified designated use (for example, aquatic life uses). The adoption of explicit narrative
flow criteria allows for a clear link between the natural flow regime and the protection of designated uses.
Moreover, the adoption of narrative flow criteria ensures that flow conditions are considered under various
other CWA programs (for example, CWA Section 401 certifications, monitoring and assessment, and
permitting under CWA Sections 402 and 404).
The effectiveness of narrative flow criteria depends, in part, on the establishment of scientifically defensible
methods to quantitatively translate and implement the narrative. Quantitative translation of narrative flow
criteria requires an understanding of the principles of the natural flow regime, hydrologic alteration, and
ecological responses to altered flows. (The term "quantitative translation" encompasses the qualitative
approaches described further in this section.)
A fundamental goal of any effort to translate narrative flow criteria is to establish scientifically sound,
quantitative flow targets that are readily implemented in State water quality management programs. This
section describes a framework (illustrated in Figure 10) for developing quantitative flow targets for protection
of aquatic life uses that incorporates elements of the EPA Guidelines for Ecological Risk Assessment (ERA) (U.S.
Environmental Protection Agency, 1998), recent environmental flow literature (Arthington, 2012; Kendy and
others, 2012; Poff and others, 2010), and procedures outlined in EPA guidance documents (U.S. Environmental
Protection Agency 2000a, 2000b, 2001, 2008, 2010b). The framework is intended to be flexible; decisions
regarding whether and how each step is applied depend on project-specific goals and resources.
The framework presented in this section is organized into eight discrete steps that integrate science and policy
(Figure 10). Steps 1 through 4 correspond to the "problem formulation phase" of the EPA ERA framework;
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Steps 5 through 7 represent the "analysis phase"; and Step 8 incorporates concepts from the "risk
characterization" phase as an "effects characterization". Throughout the process, opportunities for public and
stakeholder involvement should be considered. Certain steps within this framework are particularly well
suited for public participation (see discussion of Steps 1 and 8). The benefits of public involvement are
twofold. First, public input can help strengthen the study design by incorporating suggested methods or
addressing deficiencies identified in proposed approaches. Second, public involvement can foster a sense of
support and ownership in the resulting flow targets, leading to streamlined implementation (Annear and
others, 2004; Locke and others, 2008).
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Phase
Step
Problem formulation
..., Link narrative criteria to biological goals
and assessment endpoints
4
(2) Define scope of action
i
(3) Conduct literature review
I
(4) Develop conceptual models
Analysis
^
(5) Data inventory
i
(6) Identify measures of
exposure and effect
i
.... Develop qualtative and (or)
quantitative flow-ecology models
Risk characterization
i
Estimate risk and identify
acceptable risk levels
Figure 10. Flow diagram illustrating a framework for quantifying flow targets to protect aquatic life.
(Adapted from EPA Guidelines for Ecological Risk Assessment;
http://www.epa.gov/sites/production/files/2014-ll/documents/eco_risk_assessmentl998.pdf)
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6.1 Link Narrative Criteria to Biological Goals and Assessment Endpoints
As described in Section 4, narrative flow criteria (see Table 1) are generally composed of (1) a description of
the resource to be protected and the protection goal, and (2) statements describing the flow condition needed
to be maintained to achieve the protection goal.
The first step in the framework for quantifying flow targets is to link narrative flow criteria to biological goals
and assessment endpoints for the purpose of directing subsequent steps. A biological goal is a specific type of
management goal that focuses on the biological characteristics of an aquatic system, such as fish or
macroinvertebrate populations. Biological goals clearly state the desired condition of biological attributes
relevant to flow target development (for example, "restore and maintain cold-water fisheries"). In most cases,
a narrative flow criterion will already provide or suggest biological goals for a particular community or species
that are tied to aquatic life designated uses. For narrative criteria worded in general terms, biological goals are
derived through interpretation of narrative statements or are based on existing biological criteria to protect
aquatic life designated uses. Examples of linking narrative flow criteria to biological goals are provided in
Section 6.9.
Assessment endpoints are "explicit expressions of the actual environmental value that is to be protected"
(U.S. Environmental Protection Agency, 1998). Whereas biological goals describe the desired condition of
aquatic biota and communities, assessment endpoints specify which biological attributes are used to evaluate
whether goals are met. If, for example, a biological goal was to "maintain a cold-water fishery," assessment
endpoints could include spawning success rate and adult abundance for one or more cold-water fish species.
Assessment endpoints use "neutral phrasing" in that they do not call for any desired level of achievement. The
EPA document "Guidelines for Ecological Risk Assessment" (U.S. Environmental Protection Agency, 1998)
outlines three main criteria for selecting assessment endpoints: (1) ecological relevance; (2) susceptibility to
known or potential stressors; and (3) relevance to management goals. Selection of assessment endpoints can
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take into consideration available methods for measuring biological conditions, although endpoints without
standard measurement protocols may be selected. Additional discussion of biological measures for
quantitative analysis is provided in Section 6.6, and example endpoints are listed in Table 2.
Biological goals and assessment endpoints defined during this step may be shared with the public for
comment. Soliciting feedback at this step can improve public awareness of a state's intent to quantitatively
translate narrative flow criteria and promote transparency at the onset of the process, both of which are
crucial to the successful development and implementation of flow targets.
6.2 Identify Target Streams
Flow targets are quantified for a single stream, all streams within a geographic area (for example, a catchment
or a state), or a subset of streams that satisfy a set of selection criteria. The second step in the framework for
quantifying flow targets is to clearly define the spatial extent of the project and the target stream population.
When multiple streams over a large area are the subject of study, it is advantageous to classify target streams
according to their natural flow, geomorphic properties, temperature regimes, and other attributes. The
purpose of stream classification is to identify groups of streams with similar characteristics so that data for
each group are aggregated and extrapolated (Archfield and others, 2013; Arthington and others, 2006; Olden
and others, 2011; Poff and others, 2010; Wagener and others, 2007). It is a key step described in EPA's
"Biological assessment program review" (U.S. Environmental Protection Agency, 2013a), the EPA technical
guidance for developing numeric nutrient criteria for streams (U.S. Environmental Protection Agency, 2000a)
and the Ecological Limits of Hydrologic Alteration (ELOHA) framework for developing regional flow standards
outlined in Poff and others (2010). Stream classification based on flow, geomorphology, or other attributes
should not be confused with the definition of stream condition classes that may serve as the basis of tiered
biological thresholds or effects levels [see Section 6.8]. Additionally, although stream classification offers
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several benefits (Box H), it is not a requirement for successful development of quantitative flow targets (Kendy
and others, 2012).
Box H. Fundamentals of Stream Classification
Stream classification is the grouping of multiple streams into a smaller number of classes on the basis of
shared hydrologic, physical, chemical, and (or) biological attributes. Stream classification is a valuable tool for
quantifying flow targets because (1) data from multiple streams are pooled for analysis, and (2) conclusions
drawn for a given class are reasonably applied to all streams in that class. A general goal of stream
classification is to systematically arrange streams of the study area into groups that are unique in key
attributes for environmental flow research and management (for example, catchment size and temperature
regime, as in example Scenario A described in Section 6.9). The process requires compiling observed and
modeled data for the streams of interest, identifying metrics to serve as the basis of classification, and
determining appropriate breakpoints for these metrics. Statistical methods such as correlation analysis,
principal component analysis, regression, and cluster analysis are used to select metrics for classification and
determine stream groupings. Important considerations include the types of data and attributes such as the
number of classes, analytical methods, approaches to data gaps and uncertainty, and methods for evaluating
results. As an example, a simple classification scheme may reflect the dependence of flow characteristics on
catchment size and would require a database of stream drainage areas and the definition of drainage-area
breakpoints for stream-size classes (for example—small, less than 50 square miles [mi2]; medium, 50-100 mi2;
large, greater than 100 mi2). A comprehensive review of stream classification to support environmental flow
management is provided in Olden and others (2011) and Melles and others (2012). Example approaches are
found in Seelbach and others (2006), Kennard and others (2010b), Kennen and others (2007), Reidy Liermann
and others (2012), Melles and others (2012), and Archfield and others (2013).
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6.3 Conduct Literature Review
A review of existing literature provides a foundation for understanding how the natural flow regime supports
aquatic life and the biological effects of flow alteration in target streams. The literature review can include any
published or unpublished journal articles, reports, presentations, and other documents that are relevant to
the target streams. The literature review ideally should identify the most important aspects of flow regimes
that are vital to support aquatic life and include both direct and indirect connections between flow variables
and ecological response (Richter and others, 2006). Studies that characterize natural flow and biological
conditions are valuable even if they do not specifically address flow alteration (Mims and Olden, 2012;
McMullen and Lytle, 2012; Rolls and others, 2012). For example, studies of the historical and current biological
condition of target streams, the physical and chemical conditions that support aquatic life, and the life-history
strategies of aquatic species are all relevant for subsequent analysis steps. Literature reviews are aided by
existing databases of flow-ecology literature for the region of interest (for example, McManamay and others,
2013). Global-scale literature reviews, such as Bunn and Arthington (2002) or Poff and Zimmerman (2010),
may also help to identify candidate sources of flow alteration, and the relevance of these potential effects are
evaluated on the basis of local information.
The literature review can help to identify data gaps that could be filled through subsequent studies. It can
provide a set of references for characterizing the types and sources of flow alteration in target streams. Past
studies may provide detailed descriptions of observed flow modifications below dams and diversions or in
urbanized catchments. Studies of observed and projected climate change may be reviewed, particularly those
conducted at the state or regional scale. Information on climate-mediated changes in flow will be most
valuable for subsequent steps; however, historical and projected trends in climate variables (precipitation,
temperature, etc.) may be used to model flow regime changes for a state.
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6.4 Develop Conceptual Models
The literature review is used to guide the development of one or more conceptual models that depict
hypothesized relations between biological conditions and flow alteration in target streams. A conceptual
model consists of a diagram and accompanying narrative describing hypothesized cause-and-effect relations.
Poff and others (2010) recommend that these hypotheses focus on process-based relations between a
particular flow-regime component and ecological change. The conceptual models, therefore, ideally depict
how a specific change in a flow-regime component is believed to drive one or more biological responses. The
pathways leading to indirect biological responses to flow alteration (that is, those mediated by habitat or
water quality change) are clearly depicted. Conceptual models developed as part of this process are therefore
much more detailed than the general model presented in Section 4 (Figure 2).
The EPA Causal Analysis/Diagnosis Decision Information System (CADDIS) Web site includes a conceptual
diagram of potential biological responses to several types of flow alteration (Figure 11) that may serve as a
useful starting point for conceptual model development; other existing conceptual diagrams can be
considered. Although this example does not include climate change as a source of flow alteration, climate
effects on flow and biota can be conceptualized to more accurately reflect climate as a dynamic component of
the ecosystem. Relations among climate, flow, and aquatic life might already be apparent from past studies,
particularly if a state has undertaken a climate-change vulnerability assessment. (See Appendix C for
additional discussion and examples of climate-change vulnerability and assessments.) Where information on
climate change effects does not already exist, available climate, hydrologic, and biological literature may be
synthesized to infer potential types of flow alteration and potential biological responses.
The conceptual models resulting from this step of the framework are used to guide subsequent analysis of
flow targets, including the selection of biological and flow variables and analysis methods. In general,
conceptual models created for flow target development contain a similar structure, but focus on stressors and
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responses specific to the streams of study. Biological responses to flow-mediated changes in water chemistry
and temperature can be included which are not explicitly depicted in Figure 11. A detailed conceptual model
may also identify alternative pathways (that is, other than flow alteration) to a given biological response. This
approach also facilitates identification of potential confounding variables for consideration in flow-ecology
modeling. The topic of confounding variables is discussed further in Section 6.6.
Wnterstied
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Figure 11. Example conceptual diagram illustrating the ecological effects of human-induced flow alteration
from the U.S. Environmental Protection Agency Causal Analysis/Diagnosis Decision Information System
(CADDIS). (Modified from CADDIS Volume 2: Sources, Stressors and Responses,
http://www3.epa.gov/caddis/ssr_flow4s.html).
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6.5 Perform Data Inventory
Existing streamflow and ecological data from target streams ideally are compiled, inventoried, and reviewed
for use in quantifying flow targets. A common source of streamflow data is the USGS National Water
Information System database (http://waterdata.usgs.gov/nwis), in which catchment attributes for many
streams monitored by the USGS have been compiled in geographic information system (CIS) datasets (Falcone
and others, 2010; Falcone, 2011). Existing mechanistic or statistical models of streamflow can provide
continuous flow estimates, estimates of historical summary statistics, or estimates of flow under projected
future climate scenarios (for example, Archfield and others, 2010; Holtschlag, 2009; Stuckey and others, 2012).
Potential sources of biological data include the EPA Wadeable Streams Assessment program
(http://water.epa.gov/tvpe/rsl/monitoring/streamsurvey/web data.cfm), the USGS BioData retrieval system
(https://aquatic.biodata.usgs.gov/landing.action), and databases maintained by the U.S. Forest Service, the
Bureau of Land Management, the National Fish Habitat Partnership9, or state agencies. Sampling methods,
including the attributes measured, timing, equipment used, habitat type sampled, and taxonomic
classification, are reviewed for each biological dataset. These and other sampling protocols are important for
evaluating whether and how data from multiple sources are synthesized. A thorough discussion of potential
data compatibility issues is provided in Cao and Hawkins (2011) and Maas-Hebner and others (2015).
The literature and data review will likely reveal information gaps that hinder the quantification of flow targets.
Common issues include a lack of biological data for streams with long-term flow data or a lack of reference
biological or flow data with which to evaluate alteration. Depending on the scope of the effort, additional
monitoring or modeling may be required to fill such gaps.
9 The National Fish Habitat Partnership has created data for every stream reach and catchment in the United States, available at
http://www.tandfonline.com/doi/full/10.1080/03632415.2011.607075tf.VPc9VGiF-4l. The fish data are available at
http://ecosystems.usRS.Rov/fishhabitat/data viewer.jsp.
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6.6 Identify Flow and Biological Indicators
Streamflow and biological indicators are specific measures that are used to analyze the relations between flow
alteration and biological response (termed "flow-ecology" relations). Flow indicators correspond to "measures
of exposure" in the EPA ERA framework, whereas biological indicators correspond to "measures of effect."
Biological indicators reflect narrative flow criteria and can include various measures of the diversity,
abundance, or specific life-history traits offish, macroinvertebrates, and aquatic vegetation. Many flow
indicators have been proposed to characterize the flow regime; these indicators describe the magnitude,
timing, frequency, duration, and rate of change of various flow conditions. They are calculated from long-term
daily flow datasets, and software tools are available to automate this process (for example, Henriksen and
others, 2006; The Nature Conservancy, 2009; and the USGS EflowStats "R" package which is available at
https://github.com/USGS-R/EflowStats). Example flow and biological indicators that have been used in past
studies of flow-ecology relations are listed in Table 2. These examples are only a small subset of the full
universe of indicators that could be considered for a target-setting effort.
The biological indicators selected for analysis ideally are consistent with narrative flow criteria and the
biological goals and assessment endpoints developed under Step 1 of this framework. Ideally, the biological
indicators selected directly reflect the biological attributes of concern described by assessment endpoints (for
example, fish diversity). In cases where assessment endpoints cannot be directly measured or have limited
observational data for flow-ecology modeling, surrogate biological indicators are linked to assessment
endpoints through additional analysis. For example, if an assessment endpoint involves a rare fish species with
few monitoring records, a surrogate biological indicator is selected by identifying a data-rich species with
similar life-history traits. (See Merritt and others [2010] or Mims and Olden [2012, 2013] for examples of
methods for grouping biota by life-history strategies.)
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The flow and biological indicators selected for analysis should be consistent with the conceptual models
developed as part of Step 4 of this framework. Biological indicators (that is, measures of effect) may include
measurements along the scales of ecological organization, but they should be quantitatively related to
survival, reproduction, or growth, as indicated in the general conceptual model presented in Figure 2. In most
cases, the ability to analyze each and every hypothesized relation will be prohibited by data limitations and
the project schedule and resources. Moreover, multiple flow indicators may be relevant to a particular
relation. For example, analysis of a hypothesized relation between peak flow magnitude and fish-species
diversity could use one of several peak-flow indicators (peak daily flow, peak 7-day flow, etc.). It may therefore
be beneficial to establish a set of guidelines for flow indicator selection. Guidelines proposed in Apse and
others (2008) include the use of flow indicators that are readily calculated, replicated, and communicated.
Also recommended by Apse and others (2008) is the use of nonredundant flow indicators (that is, those that
are not strongly correlated with one another). Olden and Poff (2003) and Gao and others (2009) describe the
use of principal component analysis to identify nonredundant indicators and Archfield and others (2013) used
a subset of fundamental daily streamflow statistics to capture the stochastic properties of the streamflow
signal while minimizing the potential for redundancy. Other studies have addressed redundancy by
investigating the correlation between pairs of potential flow indicators and discarding one indicator from
highly correlated pairs (U.S. Army Corps of Engineers and others, 2013). The uncertainty associated with
potential flow indicators and attempt to select indicators with low measurement uncertainty can be
considered (Kennard and others, 2010a). Finally, identification of flow indicators that are most sensitive to
sources of flow alteration can be attempted. For example, if climate change is considered to be an important
source of flow alteration, available climate-vulnerability information to identify flow indicators that are
sensitive to observed and projected climate trends and that are amenable to management changes can be
evaluated (See Appendix C for additional discussion of climate-change vulnerability).
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Table 2. Example flow and biological indicators used to evaluate relations between streamflow characteristics and aquatic assemblage response.
component
Magnitude
Flow indicators (measures of exposure)
Mean June-July flow;
Mean August flow
Biological
component
Fish
Biological
indicators (measures of effect)
Fish density;
Fish abundance
Reference
Peterson and Kwak (1999);
Zorn and others (2008)
Magnitude
Spring maximum flow;
Summer median flow
Fish
Fish abundance;
Fish-assemblage composition
Freeman and others (2001)
Magnitude
Magnitude of 10-year low-flow event
Fish
Fish Index of Biotic Integrity;
Fish-species richness
Freeman and Marcinek (2006)
Magnitude
Mean annual flow;
Base-flow index
Macroinvertebrates
Macroinvertebrate abundance;
Macroinvertebrate assemblage;
composition
Kennen and others (2014)
Castella and others (1995)
Magnitude
Maximum flow;
Ratio of maximum to minimum flow
Macroinvertebrates
Macroinvertebrate Index of Biotic
Integrity;
Macroinvertebrate species richness
Morley and Karr (2002)
Magnitude
Magnitude of 1-, 2-, 5-, 10-, and 20-year flood
events
Macroinvertebrates
Macroinvertebrate O/E (ratio between
the observed and expected) scores;
Macroinvertebrate-assemblage
composition
Nichols and others (2006)
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Biological
Biological
Reference
component
Magnitude
Summer diversion magnitude
component
Macroinvertebrates
indicators (measures of effect)
Macroinvertebrate abundance
Wills and others (2006)
Timing
Date of annual maximum flow;
Date of annual minimum flow
Fish
Fish abundance;
Fish-assemblage composition
Koel and Sparks (2002)
Frequency
Number of days above mean annual flow;
Number of events above 75% exceedance flow
value
Macroinvertebrates
Macroinvertebrate Index of Biotic
Integrity
Macroinvertebrate richness
Booth and others (2004)
Kennen and others (2010)
Frequency
Number of flood events;
Number of low-flow events
Riparian
vegetation
Riparian tree abundance
Lytle and Merritt (2004)
Duration
Duration of high-flow events;
Duration of low-flow events
Fish
Fish abundance;
Fish-assemblage composition
Koel and Sparks (2002)
Rate of change
Mean rise rate;
Mean fall rate
Fish
Fish abundance;
Fish-assemblage composition
Koel and Sparks (2002)
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6.7 Develop Qualitative or Quantitative Flow-Ecology Models
A flow-ecology model is a specific type of stressor-response model that describes the relation between a flow
indicator and a biological indicator in absolute terms (for example, fish diversity as a function of annual peak
flow magnitude) or relative to reference conditions (for example, the percent change in fish diversity as a
function of the percent change in annual peak flow magnitude).
Guided by the conceptual model, quantitative flow-ecology models are developed by using statistical methods
and used to predict the value of a biological indicator under a variety of flow conditions (Figure 12).
Quantitative flow-ecology models take the form of linear or nonlinear regression equations, but other
approaches, such as regression tree analysis or change point analysis, also are available. Their development is
guided by a variety of exploratory data-analysis techniques to characterize individual indicator datasets (their
range, average, distribution, etc.), evaluate potential relations, and determine appropriate modeling methods.
A thorough review of statistical methods to employ for stressor-response modeling is provided in the report
"Using stressor-response relations to derive numeric nutrient criteria" (U.S. Environmental Protection Agency,
2010b). An example approach to flow-target development using quantitative modeling is described in Section
6.9 (see Table 3 and Figure 13).
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15 E
O3 CO
O
to
_0
O
CD
J3 S
-a =
o, =
-a E
2 E
O} O
Gray bands along curves indicate
the degree of uncertainty
Curve B
Natural flow
conditions
Flow indicator
Highly altered
flow
Figure 12. Example flow-ecology curves illustrating quantitative relations between flow and biological
indicators. (Quantitative models provide continuous predictions of biological responses to flow alteration.
Curve A depicts a flow-ecology relation with higher sensitivity but greater uncertainty than those associated
with Curve B.)
As introduced in Section 4.5, confounding variables are associated with alternative stressors and pathways
(that is, other than flow alteration) to a given biological response. The presence of confounding variables at
biological monitoring sites can limit the strength of causal inferences about the association between altered
streamflow and biological indicators (U.S. Environmental Protection Agency, 2010b). Where feasible,
confounding variables should be factored into the development of quantitative flow-ecology models. In
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practice, researchers have dealt with this issue by explicitly including possible confounding variables in
preliminary models (for example, Carlisle and others,. 2010), by using modeling approaches that implicitly
assume the presence of other confounding factors (for example, Konrad and others, 2008; Kennen and others,
2010), or, at a minimum, acknowledging that potential confounding factors were not included in modeling
efforts, but that other evidence indicates that their influence likely was minimal (for example, Merritt and
Poff, 2010).
Available data may be insufficient to support quantitative flow-ecology modeling, or that data or analytical
limitations result in quantitative relations with a low level of statistical significance. In such cases, qualitative
flow-ecology modeling is a practical alternative. Qualitative modeling does not attempt to uncover precise
numerical relations between flow and biological indicators. Rather, the objective is to describe relations
between variables based on hypothesized cause-effect associations using any available evidence. Qualitative
modeling can help identify the direction of flow-ecology relations, and possible thresholds for degraded
conditions, in data-limited environments.
The conceptual models discussed in Sections 4.1 and 6.4 are examples of qualitative models; however, it may
be useful to reformulate conceptual models in terms of the flow and biological indicators selected for analysis.
Qualitative models can incorporate numerical flow alteration and biological response thresholds reported in
relevant literature, and (or) available data on reference flow and biological conditions. Such models are
sometimes referred to as semiquantitative because they include numeric values but, unlike quantitative
models, do not allow for precise predictions across the full spectrum of flow alteration. Qualitative modeling
can incorporate a set of decision rules for combining and weighting conclusions from existing studies that used
inconsistent study designs and data (Webb and others, 2013). An example approach to flow-target
development using qualitative modeling is described in Section 6.9 (see Table 3 and Figure 14).
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6.8 Estimate Effects and Identify Acceptable Levels
After modeling flow-ecology relations, dividing lines between acceptable and unacceptable flow alteration to
select numeric flow targets can be determined. Effects characterization can guide this process. In general,
effects characterization involves estimating effects levels that correspond to increasing magnitudes of a
stressor. Effects characterization can define the likelihood that biological goals will not be achieved given a
certain magnitude of flow alteration. Effects estimates are categorical (low, medium, high) or numeric (the
probability of not meeting a certain biological condition). Effects estimation integrates quantitative or
qualitative flow-ecology models, biological goals, and other available evidence.
In cases where quantitative flow-ecology models are available, effects estimation may be centered on the
numerical relations between flow and biological indicators and their uncertainty. For example, descriptive
effects levels are assigned to incremental flow-indicator values on the basis of predicted effects on stream
biota and the degree of uncertainty associated with those predictions (for example, narrative effects
statements based on the Biological Condition Gradient [Davies and Jackson, 2006] may provide useful
examples). When quantitative models are not available, effects estimates are generated from qualitative flow-
ecology models, results of past observational studies, information on current and expected levels of flow
alteration, and any other lines of evidence. For more detailed information on characterization and estimation,
see, "Guidelines for Ecological Risk Assessment" (U.S. Environmental Protection Agency, 1998) and "Risk
Characterization Handbook" (U.S. Environmental Protection Agency, 2000c).
Effects estimation can be guided by threshold values or range of biological indicators, concentration of the
stressor magnitude response, etc. that correspond to attainment or non-attainment of biological goals. For
some biological indicators, point thresholds may be readily apparent from past studies or known reference
conditions, or may be defined by existing biological criteria (for example, Index of Biotic Integrity = 90).
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Alternatively, available evidence may point to a range of biological-indicator values as a suitable threshold (for
example, Index of Biotic Integrity between 80 and 90).
After generating effects estimates, numeric flow targets are determined by identifying acceptable levels
toward attainment of biological goals. For example, if flow-indicator values are divided into high, medium, or
low effects ranges, the decision to set the flow target to the high-medium effects breakpoint, the low-medium
breakpoint, or some alternative level is made. The process of identifying acceptable effects levels offers an
opportunity to further incorporate uncertainty (for example, uncertainty caused by natural temporal and
spatial variability of biological and hydrologic processes, sampling, etc.) in flow-ecology models and is helpful
for soliciting and incorporating feedback from stakeholders and the public. The utility of feedback received at
this step will likely be maximized if stakeholders have been kept informed and involved throughout the
completion of prior steps. Decisions on whether and how to act on suggested modifications to acceptable
effects levels and proposed numeric flow targets are weighed according to the strength of scientific support
for the change and implications for meeting biological goals.
After acceptable effects levels have been identified and flow targets have been quantified, planning for
implementation is enhanced by several key activities. Peer review can be used to evaluate the strength of
flow-target values and highlight areas for improvement. Targeted monitoring or modeling can support
validation of the ability of flow targets to achieve desired goals. Finally, an adaptive management approach
allows flow targets to be periodically evaluated and adjusted to ensure that the desired goals are achieved.
The adaptive management approach is continually informed and updated by results of monitoring, research,
and experimentation to address specific uncertainties. (See Richter and others [2003] and Konrad and others
[2011] for specific examples.)
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6.9 Example Applications of the Flow-Target Framework
Two hypothetical efforts to quantify flow targets to protect aquatic life (referred to as Scenario A and Scenario
B) are described in Table 3. Each scenario represents one potential application of the framework discussed in
this section (Section 6) to quantitatively translate the following narrative flow criterion: Changes to the natural
flow regime shall not impair the ability of a stream to support characteristic fish populations. The two
scenarios differ in their approach to several framework steps. These scenarios are not intended to convey
recommended methods, but rather describe example approaches for each step and demonstrate the
adaptability of the framework to project-specific goals and available resources.
Scenario A is a case in which a state incorporates existing numeric biological condition criteria and an ample
hydrologic and biological dataset for quantitative flow-ecology modeling, in which the resulting flow-ecology
curves are used as a focal point for estimating effects, identifying acceptable effects levels, and selecting
numeric flow targets. In Step 1, biological goals and assessment endpoints are selected from state WQS, which
define minimum acceptable values offish Index of Biotic Integrity (IBI) scores for attaining designated uses. In
Step 2, statewide stream classification is undertaken to assign stream segments to one of 10 classes on the
basis of catchment size and temperature regime (cold headwater, warm large river, etc.). In Step 3, the
literature review uncovers extensive evidence for the effect of summer base-flow depletion on fish diversity
and abundance. Conceptual models are developed in Step 4 to demonstrate pathways between
anthropogenic sources of summer base-flow depletion and effects on fish populations. Data compiled in Step
5 include fish-survey results, flow-monitoring records, and modeled streamflow data for ungaged stream
segments. In Step 6, fish IBI score and the percent reduction in August median flow are determined to be
appropriate indicators for flow-ecology modeling because they reflect biological goals and sufficient data are
available for analysis. Regression modeling is undertaken in Step 7 by using paired biological and flow data to
generate response curves that quantify relations between fish IBI score and reduced August median flow.
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Separate response curves are developed for each of the 10 stream classes defined for the project so that
selected targets are transferable between stream segments within each class. In Step 8, fish response curves
are used to guide discussions with stakeholders of acceptable effects levels to fish populations and to identify
appropriate targets for August median flow.
In Scenario B, qualitative flow-ecology models are generated and integrated with other lines of evidence to
identify a set of flow indicators that, if altered, present an unacceptable effect to aquatic communities. In Step
1, the state's WQS do not include biological criteria that establish assessment endpoints defining biological
goals, so the state takes appropriate actions, and includes stakeholder input, to identify specific biological
goals that are consistent with its designated aquatic life uses. This effort identifies specific fish species and
functional groups that are key to ensuring attainment of the state's designated aquatic life uses and, in turn,
establishes the goals for interpreting the state's narrative flow criteria. In Step 2, the decision is made to
include all streams in the state in the effort and opt not to address stream classification until after the
literature review of flow-ecology relations is complete. Literature reviewed in Step 3 demonstrates clear links
between fish health and a broad range of flow components. Because documented relations are consistent
across stream size and ecoregion, stream classification is not pursued. The conceptual models developed in
Step 4 summarize known and hypothesized flow needs of fish, organized by fish species/functional group,
season, and flow characteristic. Data compiled in Step 5 focus on streamflow, with long-term records used to
calculate reference and affected values of more than 50 flow metrics to evaluate the sensitivity of each metric
to anthropogenic sources of flow alteration. On the basis of this analysis and evidence for biological sensitivity,
a subset of flow metrics is selected in Step 6. A lack of biological data is determined to prohibit quantitative
flow-ecology modeling; therefore, qualitative modeling is undertaken in Step 7 to reframe conceptual models
in terms of the subset of flow indicators identified during Step 6. In Step 8, participating agencies review
available evidence to estimate effects associated with increasing levels of hydrologic change and, with public
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input, use effects estimates to set targets that express the maximum allowable deviation from reference
conditions for each flow indicator.
Although the examples in Scenarios A and B are largely hypothetical, components were drawn from real-world
examples. Many more case studies of flow-target quantification can be found in Colorado Division of Water
Resources and Colorado Water Conservation Board (2009), Cummins and others (2010), DePhilip and Moberg
(2010), Kendy and others (2012), Kennen and others (2013), Richardson (2005), and Zorn and others (2008).
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Table 3. Example applications of the framework to quantitatively translate the following narrative flow criterion: "Changes to the natural flow regime
shall not impair the ability of a stream to support characteristic fish populations."
Framework Step
(1) Link narrative
criteria to biological
goals and assessment
endpoints
Scenario A: Quantitative Example
Numeric biological goals are defined from existing biological condition
criteria, expressed as minimum acceptable values offish Index of Biotic
Integrity (IBI) scores.
Scenario B: Qualitative Example
Narrative biological goals are defined through interpretation of the
narrative flow criterion and stakeholder input. Each biological goal
identifies a specific fish species or functional group to protect. Example
biological goal: to maintain the abundance of riffle obligate species.
(2) Define scope of
action: identify target
streams
Statewide stream classification is undertaken that builds on prior stream
mapping and fish-ecology research. Individual stream segments are
assigned to one of 10 stream classes according to catchment size and
water-temperature regime, characteristics known to affect fish
distributions. Example stream class: cold headwater.
All streams in the state are included in the effort to develop flow targets.
As a result of data and resource constraints, the need for stream
classification following the literature review is evaluated.
(3) Conduct literature
review
Literature is reviewed to identify flow-regime changes that most affect
the condition offish communities. Relevant literature points to summer
base-flow depletion as a key factor in reduced fish diversity and
abundance throughout the state.
Literature is reviewed to highlight flow-dependent life history and habitat
traits offish species/functional groups referenced in Step 1. Relevant
literature demonstrates the importance of a wide range of flow conditions
on the health offish communities in the state, with consistent relations
identified across stream size and ecoregion. On the basis of these findings,
a systematic stream classification is not needed.
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Framework Step
(4) Develop
conceptual models
Conceptual models depict pathways between anthropogenic sources of
summer base-flow depletion and effects on fish populations. Important
relations include reduced food availability for both benthic and water-
column taxa as a result of reduced wetted-channel perimeter and water
depth.
Conceptual models summarize known and hypothesized flow needs offish,
organized by fish species/functional group, season, and flow characteristic.
(5) Conduct data
inventory
A database of existing flow and fish-survey records is prepared. Observed
data are augmented with predictions from previous hydrologic modeling
efforts. Modeled data include reference and present-day values of
median monthly streamflow for every stream segment in the state.
Long-term daily flow records, land-use information, and water-use data are
compiled. Reference streams (those with minimal flow alteration) and
affected streams are identified. Flow records for these sites are used to
calculate reference and affected values of 50 or more flow metrics. The
sensitivity of each flow metric to anthropogenic sources flow alteration is
quantified by comparing reference and affected values.
(6) Identify flow and
biological indicators
to serve as measures
of exposure and
effect
Two indicators are selected for quantitative flow-ecology modeling: fish
Index of Biotic Integrity score and the percent reduction in August
median flow (relative to reference conditions).
A subset of the flow metrics quantified in Step 5 is selected for flow-target
development. Metrics are evaluated according to their sensitivity to
anthropogenic sources flow alteration and evidence of biological
relevance. Flow indicators describe magnitude and frequency
characteristics of high/flood flows, seasonal/average flows, and
low/drought flows.
(7) Develop flow-
ecology models
Regression modeling is undertaken by using monitoring and modeling
data from sites with paired flow and biological data. Final models
Qualitative flow-ecology models are developed by reframing conceptual
models in terms of the flow indicators selected in Step 6 (Figure 14).
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Framework Step
(termed "fish response curves"; see Figure 13) quantify the relation
between fish IBI scores and reduced August median flow. Fish response
curves are generated for each of the 10 stream classes defined in Step 2.
(8) Estimate effects
and identify
acceptable levels
Fish response curves are divided into high, medium, and low effects
levels and shared with stakeholders to guide discussion of acceptable
levels. Because of model uncertainty, participating agencies and
stakeholders add a 5-percent margin of safety to fish IBI thresholds
defined in Step 1 and agree that flow alteration resulting in IBI scores
below this threshold present an unacceptable effects to fish
communities. Flow targets determined from fish response curves and
acceptable effects levels are selected for each stream class. Targets are
expressed as a maximum allowable percentage reduction in August
median flow by stream type.
Participating agencies review available evidence to estimate effects
associated with increasing levels of hydrologic change. For some flow
indicators, past studies indicate the likelihood of high effect of biological
degradation under any magnitude of flow change. For others, healthy
biotic communities are observed under moderate flow change and are
determined to pose a lower effect if altered. This information is shared
with stakeholders to further refine effects estimates and levels of flow
alteration presenting unacceptable effects to stream biota. The outcome
of these discussions is a set of targets expressing the maximum allowable
deviation from reference conditions for each flow indicator that will
protect the aquatic life use.
Follow-up and
adaptive
management
Participating agencies continue to collect flow and fish-community data.
A plan is developed to assess flow targets every 5 years by analyzing new
and historic data for evidence of their effectiveness.
Participating agencies continue to collect flow and fish-community data. A
plan is developed to assess flow targets every 5 years by analyzing new and
historic data for evidence of their effectiveness.
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o
•D
Vt
CD
JBI_goal_defined_
in step S
IBI goal defined
in step 1
I
Percent change in August median flow
Figure 13. Example fish response curve from Scenario A generated through regression modeling. (In this
scenario, fish response curves depict the relation between altered August median flow and fish-community
condition; IBI, Index of Biotic Integrity)
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Flow Components and Needs: Major Tributaries
10000
Example: 01543500 Sinnemahoning Creek at Sinnemahoning, PA (585 s
" • High Flow-related needs
• Seasonal Flow needs
• Low Flow-related needs
5000
4000
Flow Component (Daily Exceedance Probability )
High Flow Events (Q. .toQ,,)
Seasonal Flow (QJ= toQ. ,)
H Low Flow (Q. to Q....)
•S Minimum to 0,5
FALL
t
WINTER
Cue diadromous
2000 fish emigration
Ul
• Maintain stable
hibernation habitats
* Maintain ke scour
events and floodplain
connectivity
Support winter
•mergence of aquatic
Insects and maintain
overwinter habitat for
macroinvertebrates
• Maintain overwinter
habitats for resident fish
RING
Maintain channel
morphology. Island formation,
and Roodplain habitat
Cue alosid spawning
migration and promote egg and
larval development
Support spring emergence of
aquatic insects and maintain
habitats for mating and, egg
laving
• Support resident fish
spav
SUMMER
• Transport organic matter and fine
sediment
• *• Promote vegetation growth
M
• Cue and direct immigration of juvenile
American Eel
* Provide abundant food resources and
nesting and feeding habitats for birds
and mammals
•• Support development and growth of
all fishes, reptiles, and amphibians
•• Maintain connectivity between
habitats and refugia for resident and
diadromous fishes
• • Support mussel spawning, glochidia
release, and growth
• Promote macroinvertebrate growth
» Maintain water quality
• Maintain hyporhek habitat
I
i of
Figure 14. Conceptual diagram illustrating hypothesized flow needs offish and other aquatic biota by
season in major tributaries of the Susquehanna River Basin, northeastern United States. (Example
hydrograph shown is from U.S. Geological Survey station 01543500, Sinnemahoning Creek at
Sinnemahoning, Pennsylvania [drainage basin 685 square miles]; as described in Scenario B, conceptual
diagrams are used in conjunction with information on natural flow variability, flow alteration, and biological
response thresholds to quantify candidate flow targets.) (From DePhilip and Moberg, 2010)
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7 Conclusions
The flow regime plays a central role in supporting healthy aquatic ecosystems and the ecological services they
provide to society. A stream's natural flow regime is determined by climate and other catchment and reach
scale properties that affect hydrologic processes such as infiltration, groundwater recharge, or channel
storage. Human activities can alter the flow regime by modifying streamflow-generation processes (for
example, infiltration, overland flow, etc.), altering the physical properties of stream channels (for example,
channelization), or through direct manipulation of surface water and groundwater (dams or water
withdrawals). Climate change effects on patterns of water and energy inputs to streams may further
exacerbate these effects of flow on aquatic ecosystems.
Alterations to the natural flow regime can contribute to the degradation of biological communities by reducing
habitat quality, extent, and connectivity and by failing to provide cues needed for aquatic species to complete
their life cycles. Flow alteration can prevent water bodies from supporting aquatic life designated uses defined
by state water quality standards. Water quality programs implemented to address the Clean Water Act (CWA)
objective of restoring and maintaining the chemical, physical and biological integrity of waters ideally consider
strategies to maintain key components of the natural flow regime. This report was cooperatively developed to
serve as a source of information for states, tribes, and territories that may want to proactively protect aquatic
life from the adverse effects of flow alteration. It provides background information on the natural flow regime
and potential effects of flow alteration on aquatic life, a summary of CWA programs that can be used to
support the natural flow regime, and a flexible, nonprescriptive framework to quantify targets for flow regime
components that are protective of aquatic life.
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8 Selected References
Ahearn, D.S., Sheibley, R.W., and Dahlgren, R.A., 2005, Effects of river regulation on water quality in the lower
Mokelumne River, California: River Research and Applications, v. 21, no. 6, p. 651-670. [Also available at
https://watershed.ucdavis.edu/pdf/crg/reports/pubs/ahearn et a!2005a.pdf.1
Angermeier, P.L., and Winston, M.R., 1998, Local vs. regional influences on local diversity in stream fish
communities of Virginia: Ecology, v. 79, no. 3, p. 911-927. [Also available at
http://www.esaiournals.org/doi/pdf/10.1890/0012-9658(1998)079%5B0911%3ALVRIOL%5D2.0.CO%3B2.1
Annear, Tom, Beecher, Hal, and Instream Flow Council, 2004, Instream flows—For riverine resource
stewardship, revised edition: Cheyenne, Wyo., Instream Flow Council.
Apse, Colin, DePhilip, Michele, Zimmerman, J.K.H., and Smith, M.P., 2008, Developing instream flow criteria to
support ecologically sustainable water resource planning and management: Harrisburg, Pa., The Nature
Conservancy, final report to the Pennsylvania Instream Flow Technical Advisory Committee. [Also available
at http://www.portal.state.pa.us/portal/server.pt/document/440033/pa instream flow report-
tnc growing greener- final.pdf.1
Archfield, S.A., Kennen, J.G., Carlisle, D.M., and Wolock, D.M., 2013, An objective and parsimonious approach
for classifying natural flow regimes at a continental scale: River Research and Applications, v. 30, no. 9, p.
1166-1183. [Also available to http://dx.doi.Org/10.1002/rra.2710.1
Archfield, S.A., Vogel, R.M., Steeves, P.A., 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. [Also available at http://pubs.usgs.gOV/sir/2009/5227/.1
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Armstrong, D.S., Richards, T.A., and Levin, S.B., 2011, Factors influencing riverine fish assemblages in
Massachusetts: U.S. Geological Survey Scientific Investigations Report 2011-5193, 58 p. [Also available at
http://pubs.usgs.gOV/sir/2011/5193/.1
Arnwine, D.H., Sparks, K.J., and James, R.R., 2006, Probabilistic monitoring of streams below small
impoundments in Tennessee: Nashville, Tenn., Tennessee Department of Environment and Conservation,
Division of Water Pollution Control Report. [Also available at
https://www.tn.gov/assets/entities/environment/attachments/isp report.pdf.1
Arthington, A.M., 2012, Environmental flows—Saving rivers in the third millennium: Berkeley and Los Angeles,
Calif., University of California Press.
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Appendix A. Overview of the Clean Water Act and Water Quality Standards Relevant to the
Development and Use of Criteria for Hydrologic Condition
In 1972, with the objective of protecting lakes, rivers, streams, estuaries, wetlands, coastal waters, the ocean,
and other water bodies, the U.S. Congress enacted comprehensive amendments to the Federal Water
Pollution Control Act, now commonly known as the Clean Water Act (CWA). The overall objective of the CWA
is to "restore and maintain the chemical, physical and biological integrity of the Nation's waters" (Section
101(a)). In addition, the CWA establishes as an interim goal "water quality which provides for the protection
and propagation offish, shellfish and wildlife and provides for recreation in and on the water/' wherever
attainable (Section 101(a)(2)). Section 303(c)(l) of the CWA provides that states must review, and revise as
appropriate, their water quality standards (WQS) at least once every 3 years. Section 303(c)(3) requires the
U.S. Environmental Protection Agency (EPA) to review and approve or disapprove such new or revised WQS.
Specific requirements and procedures for developing, reviewing, revising, and approving WQS are outlined in
the Code of Federal Regulations, Chapter I, Subchapter D, part 131 (40 CFR Part 131)
(http://www.ecfr.gov/cgi-bin/text-idx?node=pt40.22.131&rgn=div5).
Generally speaking, WQS define the water quality goals for a water body, or part of a water body, by (1)
designating the use or uses of the water; (2) setting criteria sufficient to protect those designated uses; and (3)
preserving water quality that exceeds the levels necessary to support propagation of fish, shellfish, and
wildlife and recreation in and on the water, as well as existing uses, through antidegradation provisions. States
adopt WQS to protect public health or welfare, enhance the quality of water, and serve the purposes of the
CWA. WQS serve as the regulatory basis for establishing water quality-based treatment controls and
strategies, such as National Pollutant Discharge Elimination System (NPDES) permits and Total Maximum Daily
Loads(TMDLs).
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Al. Designated Uses and Existing Uses
EPA's regulatory provisions regarding designated uses are defined in 40 CFR Section 131.10. Designated uses
are those uses specified in the state's WQS for each water body or segment regardless of whether or not
those uses are actually being attained. Designated uses are a state's concise statements of its management
objectives and expectations for each of the individual surface waters under its jurisdiction and may include
(but are not limited to) propagation of fish, shellfish and wildlife (including protection of human health when
consuming aquatic life), recreation, agricultural uses, industrial uses, navigation, and (or) public water supply.
Water quality criteria are adopted to protect the designated uses. When designating uses and adopting
criteria, states and tribes must consider the WQS of downstream waters, and ensure that the designated uses
and criteria provide for the attainment and maintenance of the WQS of downstream waters (40 CFR Section
Existing uses are defined in 40 CFR Section 131. 3(e) as uses that have been "actually attained" in a water body
on or after November 28, 1975. Existing uses are known to have been "actually attained" when the use has
actually occurred and the water quality necessary to support the use has been attained. The EPA recognizes,
however, that all necessary data may not be available to determine whether the use actually occurred or the
water quality to support the use has been attained. When determining an existing use, EPA provides
substantial flexibility to states and authorized tribes to evaluate the strength of the available data and
information where data may be limited, inconclusive, or insufficient regarding whether the use has occurred
and the water quality necessary to support the use has been attained. In this instance, states and authorized
tribes may decide that based on such information, the use is indeed existing (Water Quality Standards
Regulatory Revisions; Final Rule; 80 FR 51027; August 21, 2015). Determination of existing uses that actually
have been attained in a water body is done on a site-specific basis and may involve evaluating data on the
following:
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• Historical/current water quality;
• Historical/current biological condition; and
• Historical pattern, frequency, and type of use.
Once a use has been designated for a particular water body or segment that designated use may be removed
under specific conditions. If a designated use is an existing use for a particular water body or segment,
however, it cannot be removed unless a use requiring more stringent criteria is added. As described in 40 CFR
Section 131.10(g), when removing a use for those uses specified in CWA Section 101(a)(2) or subcategories of
such a use, the state or authorized tribe must demonstrate through a Use Attainability Analysis (UAA) that
attaining the use is not feasible because of one the six factors provided in the regulation. Additionally, if the
state or authorized tribe adopts a new or revised water quality standard based on a required UAA, they must
also adopt the highest attainable use (defined at 40 CFR Section 131.3(m)). If a state or authorized tribe wishes
to remove or revise a designated use that is a unrelated to the protection and propagation offish, shellfish,
wildlife or recreation in or on the water (i.e., a "non-101(a)(2) use"), the state or authorized tribe must submit
documentation justifying how its consideration of the use and value of water for the use appropriately
supports the state's or authorized tribe's action (see 40 CFR Sections 131.10(a) and 131.10(k)(3)).
A2. Water quality Criteria
Water quality criteria are defined in 40 CFR Section 131.3(b) as constituent concentrations, levels, or narrative
statements representing a quality of water that supports a particular use, such as propagation of fish and
wildlife, recreation, and public water supply. EPA develops recommendations for many water quality criteria
under the authority of CWA Section 304(a). Consistent with EPA WQS regulation at 40 CFR Section 131.11, the
criteria that states adopt must meet the following requirements:
• Be based on a sound scientific rationale; and
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« Include sufficient parameters (at acceptable concentrations and levels) to support protection of the
designated uses of a particular water body, including the most sensitive use.
States adopting numeric criteria may either adopt the recommended criteria that EPA publishes into their
WQS, modify the EPA criteria to reflect site-specific conditions, or use other scientifically defensible methods
(40 CFR Section 131.11(b)(l)). States may also adopt narrative criteria or criteria based on biomonitoring
methods (40 CFR Section 131(b)(2)).
A3. Antidegradation
Antidegradation is an integral component of a comprehensive approach to protect and maintain water quality.
EPA antidegradation regulations are specified in 40 CFR Section 131.12. Each state and authorized tribe must
develop and adopt a statewide antidegradation policy (40 CFR Section 131.12(a)) and develop methods for
implementing the antidegradation policy that are, at minimum, consistent with the policy and EPA regulations
in 131.12(a) (40 CFR Section 131.12(b)). The state's or authorized tribe's antidegradation policy must ensure
the maintenance and protection of existing uses of a water body and the level of water quality necessary to
protect those existing uses (Tier 1); maintain and protect water quality where the quality exceeds the levels
necessary to support propagation of fish, shellfish, and wildlife and recreation in and on the water, unless the
state or authorized tribe finds that allowing lower water quality is necessary to accommodate important
economic or social development in the area where the waters are located (Tier 2); and provide for the
maintenance and protection of water quality in outstanding national resource waters identified by the state or
authorized tribe (Tier 3). The state or tribal antidegradation policy and implementation methods must be
consistent with EPA regulations, although states may adopt antidegradation statements that are more
protective than those prescribed by EPA.
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A4. Using Narrative Criteria
Narrative water quality criteria are qualitative statements that describe the desired water quality condition
sufficient to protect applicable designated uses—for example, "no toxic compounds in toxic concentrations."
Many states have adopted narrative criteria. Where narrative criteria are in place, they may serve as the basis
for limiting the discharge of contaminants from permitted discharges when there is reasonable potential that
a specific contaminant will cause or contributes to an exceedance of the narrative criteria, regardless of
whether numeric criteria are in place to address the contaminant. EPA's regulatory provisions for satisfying
narrative criteria in NPDES permits are specified in Section 40 CFR 122.44. Where a state or authorized tribe
adopts narrative criteria for toxic pollutants to protect designated uses, the state or authorized tribe must
provide information identifying the method by which they intend to translate the narrative for use in
development of NPDES permit limits (40 CFR Section 131.11(a)(2)). For other pollutants, states and authorized
tribes may include a procedure to translate narrative criteria in their WQS to facilitate the development of
NPDES permit limits and other quantitative targets.
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Appendix B. Legal Background and Relevant Case Law
The U.S. Environmental Protection Agency (EPA) notes that it has been argued "that the Clean Water Act is
only concerned with water 'quality/ and does not allow the regulation of water 'quantity.'" Public Utility
District No. 1 of Jefferson County v. Washington Department of Ecology ("PUD No.l"), 511 U.S. 700, 719-
(1994). In PUD No. 1, the U.S. Supreme Court, however, found that the distinction between water quality and
water quantity is "artificial," explaining that "[i]n many cases, water quantity is closely related to water
quality; a sufficient lowering of the water quantity in a body of water could destroy all of its designated uses,
be it for drinking water, recreation, navigation or....as a fishery." Id.
The Court, in PUD No.l, cited various provisions of the CWA that recognize that "reduced stream flow, I.e.,
diminishment of water quantity, can constitute water pollution," including the Act's definition of "pollution"
as "the man-made or man-induced alteration of the chemical, physical, biological, and radiological integrity of
water" in Section 502(19). 511 U.S. at 719-720. The Supreme Court held in that case that "[t]his broad
conception of pollution - one which expressly evinces Congress' concern with the physical and biological
integrity of water - refutes petitioners' assertion that the Act draws a sharp distinction between the
regulation of water 'quantity' and water 'quality'." 511 U.S. 719.
The Court held that the State of Washington had authority to impose minimum flow conditions on a FERC-
licensed project through Section 401 of the CWA to protect designated uses and comply with the State's
antidegradation policy. Despite the fact that the State of Washington did not have specific flow criteria, the
State had determined that the project and license at issue and as proposed would not comply with one of the
designated uses for the water body at issue, Class AA (fish rearing, spawning, and harvesting). The Court held
that CWA Section 401 certifications may include conditions to ensure compliance with not only criteria, but
also designated uses and antidegradation requirements.
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In S.D. Warren Co. v. Maine Board of Environmental Protection ("S.D.Warren") 547 U.S. 370, 385 (2006), the
Supreme Court held that "Congress passed the Clean Water Act to 'restore and maintain the chemical,
physical, and biological integrity of the Nation's waters,'....the 'national goal' being to achieve 'water quality
which provides for the protection and propagation offish, shellfish, and wildlife and provides for recreation in
and on the water,'...." To do this, the Act does not stop at controlling the 'addition of pollutants,' but deals
with 'pollution' generally ...., which Congress defined to mean 'the man-made or man-induced alteration of
the chemical, physical, biological, and radiological integrity of water." Id. "The alteration of water quality as
thus defined is a risk inherent in limiting flow and releasing water through turbines. Warren itself admits that
its dams "can cause changes in the movement, flow and circulation of a river.... caus[ing] a river to absorb less
oxygen and to be less passable by boaters and fish..." Id. "Changes in the river like these fall within a State's
legitimate legislative business, and the Clean Water Act provides for a system that respects the State's
concerns." 547 U.S. at 386. The Court upheld the State of Maine's CWA Section 401 certification requiring
minimum flows to protect the designated fishing and recreational uses of an affected water body for which
Maine did not have an explicit flow criterion.
The Supreme Court, in PUD No.l, also addressed arguments raised by the petitioners that Sections 101(g) and
510(2) of the CWA exclude the regulation of water quantity from the coverage of the CWA, specifically arguing
that "these provisions exclude 'water quantity issues from direct regulation under the federally controlled
water quality standards in § 303." 511 U.S. at 720. The Supreme Court noted the peculiarity of the petitioners'
argument that these provisions (which give the states authority to allocate water rights) prevent states from
regulating streamflow. The Court went on to address the meaning of these provisions and found that
"[s]ections 101(g) and 510(2) preserve the authority of each State to allocate water quantity as between users;
they do not limit the scope of water pollution controls that may be imposed on users who have obtained,
pursuant to state law, a water allocation." Id. The Court cited its decision in California v. Federal Energy
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Regulatory Commission (FERC), 495 U.S. 490, 498 (1990), construing an analogous provision of the Federal
Power Act, where the Court explained that "minimum stream flow requirements neither reflect nor establish
proprietary rights" to water. 511 U.S. at 720.
In reaching its decision upholding the State's authority to require minimum streamflow requirements
necessary to protect state water quality standards, the Court noted that its view was reinforced by the 1977
amendments to the CWA adding Section 101(g). The Court quoted from the Library of Congress, Congressional
Research Service, Environmental Policy Division (1978): "The requirements [of the Act] may incidentally affect
individual water rights....It is not the purpose of this amendment to prohibit those incidental effects. It is the
purpose of this amendment to [e]nsure that State allocation systems are not subverted, and that effects on
individual rights, if any, are prompted by legitimate and necessary water quality considerations." 511 U.S. at
721.
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Appendix C. Climate-Change Vulnerability and the Flow Regime
Climate change is one category of stressors among many (see Section 4.3) that increase the vulnerability of
rivers and streams to flow alteration and affect the ecosystem services they provide. Changes in global
temperature and shifts in precipitation are superimposed on local stressors such as water contamination,
habitat degradation, exotic species, and flow modification (Dudgeon and others, 2006). Given the challenges
posed by climate change, many natural-resource management agencies likely will find protecting and
restoring the health of aquatic ecosystems increasingly challenging. For example, projected changes in
temperature and precipitation due to climate change are expected to increase the departures from historic
conditions. This means that using the past envelope of variability as a guide for the future is no longer a
reliable assumption in water-resources management (Milly and others, 2008). Observed streamflow trends
since about 1940 indicate regional changes in low flows, high flows, and timing of winter/spring runoff (U.S.
Environmental Protection Agency, 2014b). However, there is much uncertainty about the future effect of
climatically driven changes on streamflow. Even though knowledge of national and regional climate-change
effects are useful at a coarse scale, water scientists need to move from generalizations of climate-change
effects to more regional and (or) place-based effects to develop approaches relevant to the scale of
management (Palmer and others, 2009). Global, national, and regional effects are described comprehensively
elsewhere (Intergovernmental Panel on Climate Change, 2007; Field and others, 2014; Georgakakos and
others, 2014; Karl and others, 2009).
Resilience is the ability of a system to recover after disturbance and the capacity of that system to maintain its
functions in spite of the disturbance (Turner and others, 2003; Walker and others, 2004). Restoring or
maintaining a natural flow regime can increase system resilience to climate-change effects and help avoid or
reduce intensification of historical stresses (Beechie and others, 2013; Palmer and others, 2008, 2009; Pittock
and Finlayson, 2011; Poff and others, 2012). Therefore, defining and protecting environmental flows is not
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only a way to protect and restore rivers and streams from anthropogenic stressors, but it may also be a means
of adapting to climate-change.
Not all rivers and streams are equally vulnerable to the effects of climate change. An assessment of climate-
change vulnerability can help identify locations and hydrologic and ecological attributes that are most
vulnerable to altered climate conditions. A climate-change vulnerability assessment, at a minimum, will supply
specific information on the type of climate change expected across the assessed area. Depending on the scope
of the effort, a climate-change vulnerability assessment may also translate projected changes in climate into
effects on flow and (or) aquatic biota. This information is valuable for planning and implementation of Clean
Water Act program strategies to support the resilience of aquatic life to a changing climate. Furthermore, flow
and biological projections are incorporated into efforts to quantify flow targets that are protective of aquatic
life under both historic and projected future climate conditions.
Approaches for assessing climate-change vulnerability are evolving and becoming more robust (Dawson and
others, 2011). This appendix describes the components of vulnerability (Box I) and presents two examples
from studies in California (Box J) and the Pacific Northwest (Box K) that illustrate the ways in which regional
climate-change effects are being incorporated into vulnerability studies of the flow regime and the potential
resulting effects on aquatic life (Box J).
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Box I. Components of Climate-Change Vulnerability
The paragraphs that follow briefly describe the primary components of climate-change vulnerability that may
be included in climate vulnerability assessments: exposure, sensitivity, and adaptive capacity. An in-depth
discussion of these components is available in Click and others (2011) and Poff and others (2012). Generalized
case examples available in Click and others (2011) demonstrate assessment approaches for climate
vulnerability assessments across various ecosystems and species, both aquatic and terrestrial. Examples that
focus on watershed vulnerability and aquatic resources are included in Furniss and others (2013). An
additional resource (U.S. Environmental Protection Agency, 2014a) is a workbook for organizations managing
environmental resources that provides a two-part process to carry out vulnerability assessments and develop
effects-based adaptation plans for strategic climate-change plans.
Exposure: Exposure generally refers to the character, magnitude, and rate of climatic changes (Click and
others, 2011). Results of climate model simulations such as regional climate projections or downscaled climate
projections, though accompanied by uncertainty, can help to estimate the range and location of potential
climate change. Identifying sources of increased past variability may also be helpful (for example, paleoclimate
records of tree-rings). Those changes that are ecologically significant (for example, those that affect an
assessment endpoint) are considered as exposure metrics (for example, snowpack vulnerability, winter water
temperature, aridity index, monthly precipitation, winter peak flows, freeze and thaw days, etc.) Additional
examples of exposure metrics used in case studies are given in Furniss and others (2013).
Sensitivity: Climate sensitivity is the degree to which a system, habitat, or species is (or is likely to be) altered
by or responsive to a given amount of climate change (in this case, climate-induced hydrologic changes in
particular) (Click and others, 2011). Sensitivity factors can include intrinsic attributes of a watershed, aquatic
ecosystem, or organism, as well as the existing condition owing to anthropogenic factors. For example, the
hydrology in a snowmelt-dominated watershed (and the ecosystem that is adapted to this hydrologic regime)
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may be more sensitive to climate changes that reduce the proportion of precipitation from snow than that in a
rainfall-dominated watershed (see the Beechie and others [2013] example in Box K). Many of the intrinsic
attributes at the landscape level (for example, geology, soil, topography) affect the sensitivity of the aquatic
ecosystem to any stressor. For example, the rate at which shifts in stream temperature can occur is driven by
variables such as stream slope and interannual variability—so the rate at which temperature gradients shift
are variable, even within a given basin, and statistically significant signals may not be detected for decades
(Isaak and Reiman, 2013). The intrinsic factors that affect sensitivity at the population scale may include
environmental tolerance range (for example, thermal tolerances), mobility, genetic adaptation, and range or
population size.
Adaptive Capacity: Adaptive capacity is the ability of a species or system to cope with or adjust to climate-
change effects with minimal disruption (Click and others, 2011). It is also a subset of system resilience and can
help managers assess vulnerability for use in decision making. Ecosystems and aquatic organisms can cope
with climate change in different ways; for example, they may migrate, shift to more suitable microhabitats, or
persist in place (for example, phenotypic plasticity) (Dawson and others, 2011). On a landscape scale, some
vulnerability assessment approaches include landscape/river connectivity under this component. Many
adaptive capacity factors may be those pre-existing conditions that future management conditions can
address (for example, reducing fragmentation of a water body, thereby preventing mobility to more suitable
conditions, such as cooler temperatures) (Click and others, 2011). The Pacific Northwest salmon restoration
case study (Box K) provides some examples of restoration practices Beechie and others (2013) identified as
adaptive activities that may ameliorate some of the expected climate changes and increase habitat diversity
and salmon population resilience.
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Box J. California's Climate-Change Vulnerability Index
The goal of the California Integrated Assessment of Watershed Health (U.S. Environmental Protection Agency,
2013b) was to identify and better protect healthy watersheds by integrating data and making them available
to planning agencies for improved coordination of monitoring and prioritization of protection efforts. The
primary partners included the U.S. Environmental Protection Agency (EPA) and the Healthy Streams
Partnership (HSP), an interagency workgroup of the California Water Monitoring Council. The assessment
partners identified and integrated 23 indicators of watershed health, stream condition, and watershed
vulnerability to characterize relative watershed health and vulnerability across California. The indicators used
in this assessment reflect the reality that multiple ecological attributes and anthropogenic effects play a role in
watershed and stream health, and need to be considered together.
The integrated watershed vulnerability index used in the assessment of watershed health is a composite of
four vulnerability indices that may change from 2010 to 2050 (land cover, wildfire severity, water use, and
climate change). The composite climate-change vulnerability index, in turn, is composed of seven component
metrics of estimated climate-change parameters using projections from Cal-Adapt, a collaboration of several
institutions that modeled downscaled hydrologic response across California by using temperature and
precipitation projections produced from global general circulation models (GCMs). The interagency partners
used the modeled outputs to evaluate the relative response of watersheds in California to future climate
change, but the models did not explicitly simulate effects on ecosystem health or watershed processes
(although they are certainly related to the modeled inputs), nor was the sensitivity of those watersheds to
such changes a focus of this screening-level assessment. Rather, the vulnerability index is meant to be
assessed with the composite indices of stream health and watershed condition to help prioritize protection
opportunities.
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The HSP used annual precipitation, mean base flow, mean surface runoff, and snowpack (as snow water
equivalent) as the hydrologic responses to projected climate change because they were identified as the
primary indicators affecting stream hydrology. It also identified annual temperature maximum, minimum, and
mean as climate variables that may affect future watershed vulnerability. The interagency partners calculated
the percent difference between projected values of these indicators (that is, component metrics of exposure)
from 2050 and 2010.
The composite results of the vulnerability assessment (Figure C-l) illustrate the climate exposure primarily in
terms of its effects on temperature and hydrology-related parameters in this example. Overall, the climate
vulnerability component of this assessment identified the greatest vulnerability for northern California as a
result of a combination of expected temperature increases and changes in snowpack, surface runoff, and base
flow.
This screening-level assessment is an instructive example that may help inform the protection of healthy
watersheds based on climate-change vulnerability. However, the assessment combined other vulnerability
indices—land cover, water use, and fire-regime class (which can affect surface erosion, sediment deposition,
and stream temperature)—with climate change as characteristics that could modify (exacerbate or
ameliorate) overall vulnerability. Additionally, this assessment not only sought to develop priorities based on
ecosystem vulnerability, but also a comprehensive understanding of the overall status of the aquatic
ecosystem. For the entire assessment, stream condition, watershed health, and vulnerability were considered.
For more information, see U.S. Environmental Protection Agency (2013b)
(http://www.epa.gov/sites/production/files/2015-ll/documents/ca hw report 111213 O.pdf).
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Figure C-l. (a) Composite results of the vulnerability assessment illustrating the combined changes in the
seven component metrics of projected climate-change parameters, three of which are shown: (b) surface
runoff, (c) minimum temperature, and (d) snowpack. (Additional component metrics including projected
change in precipitation, mean temperature, maximum temperature, and baseflow are shown in U.S.
Environmental Protection Agency [2013b], available at
http://water.epa.gov/polwaste/nps/watershed/integrative_assessments.cfm.)
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Box K. Addressing Regional Climate-Change Effects on Salmon Habitat in the Pacific Northwest: Examples
for Prioritizing Restoration Activities
Salmon habitat restoration is a prominent issue in the Pacific Northwest; however, a need exists to better
understand whether current restoration activities and priorities will be effective under future climate
conditions. Beechie and others (2013) sought to address this issue by providing insight into ways in which a
restoration plan might be altered under various climate-change scenarios.
The authors developed a decision support system to adapt salmon recovery plans to address climate-
mediated stream temperature and flow changes in order to both ameliorate climate effects and increase
salmon resilience. To guide the effort, the researchers mapped scenarios of future stream temperature and
flow and performed a literature review of current restoration practices.
The authors modeled stream temperature and flow from a multimodel average of daily gridded precipitation
and air temperature. By using the variable infiltration capacity (VIC) model, the inputs were used to predict
daily runoff, runoff routing, and stream temperature and flow. (Additional information on the specifics of the
development of these parameters are found in Beechie and others [2013].) The scenario mapping exercise
compared historical baseline (1970-99) water temperature and flow conditions to those projected for the
periods 2000-29, 2030-69, and 2070-99. The researchers modeled mean monthly flows, calculating the
change in magnitude and timing of maximum monthly flows between the future period and the historical
baseline for each stream cell. They modeled and mapped stream temperature directly. The results indicated
lower summer flows (35-75 percent lower), higher monthly maximum flows (10-60 percent higher), and
higher air and stream temperatures (maximum weekly mean temperature 2-6 9C [degrees Celsius] higher).
Snowmelt-dominated hydrologic regimes across the region almost entirely disappeared by the 2070-99 time
period, and transitional (rain-snow mix) hydrologic regimes contracted substantially as well. By the final 2070-
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99 time period, most of the region was characterized by a rainfall-dominated hydrologic regime. The authors
compared the projected stream-temperature changes to the known thermal thresholds and seasonal flows
needed during different salmonid life stages (Figure C-2).
Beechie and others (2013) carried out a literature review to identify restoration practices that could
ameliorate expected changes in streamflow (base-flow decrease and peak-flow increase) and stream
temperature, and increase habitat diversity and population resilience. The primary activities most likely to do
so include restoring flood-plain connectivity, restoring streamflow regimes, and reaggrading incised stream
channels.
This Pacific Northwest salmonid restoration example combines projected climate-exposure information and
known ecological sensitivities of salmonid species to improve understanding of potential vulnerability to
climate change. This knowledge can help inform management plans to prioritize restoration practices that are
more likely to be effective under projected climate scenarios.
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Sep Dec Mar Jun Sep Dec Mar Jun Sep Dec Mar Jun
Spawn KEmergeW Rearing
• Increased summer temperature may decrease growth or kill juvenile salmon where temperatures are already
high, but may increase growth where temperatures are low. May also decrease spawning fecundity (e.g., Chum).
D Decreased summer low flow may contribute to increased temperatures, decrease rearing habitat capacity for
juvenile salmonids, and decrease access to or availability of spawning areas.
• Increased winter floods may increase scour of eggs from the gravel, or increase mortality of rearing juveniles
where flood refugia are not available.
DLoss of spring snowmelt may decrease or eliminate spawning opportunities for spring spawners, and may alter
survival of eggs or emergent fry for fall-spawning species.
Figure C- 2. Diagram showing effect of climate change on life stages of salmonids through time, by season.
(Modified from Beechie and others, 2013; white rectangles represent the freshwater life-history stage of
salmonids, gray boxes represent the ocean stage, and stippled lines indicate an alternate life-history)
The science of incorporating climate change into environmental flow assessments is young and complex.
Considerations for incorporating climate change into the framework for developing flow targets to protect
aquatic life discussed in Section 6 and illustrated in Figure 10 are presented below. This information can help
identify which ecologically significant flow indicators may be most affected by climate change (as determined
from the observed trends and projections). These examples can help elucidate relative climate effects (that is,
vulnerability) related to flow targets and the aquatic life uses they are designed to protect. States and tribes
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can more effectively prioritize limited resources and identify new management actions more strategically to
increase aquatic-ecosystem resilience. This framework is meant to be a qualitative assessment to rank relative
effects, which may help in identifying and ranking adaptive management actions in later steps. In a resource-
constrained environment, managers also need to evaluate the importance of projected climate change on key
hydrologic variables compared to that of hydrologic alteration from other anthropogenic sources. The ranking
of effects below can assist in this process to optimize management of limited resources.
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Table Cl. Incorporating climate-change considerations into the framework for quantifying flow targets.
Framework component
(1) Formally link narrative
criteria to biological goals
Potential climate-change considerations
May not be applicable to Step 1 unless climate changes affect biological expectations.
(2) Identify target streams
Consider which elements, if any, in the classification of target streams are climate dependent.
(3) Conduct literature
review
Consider all potential climate-change-related effects that could eventually threaten the target
streams. Identify available climate-change reports relevant to the region or state water resources.
Identify potential changes in ecologically relevant flow components from both observed trends and
projected changes. It may be helpful to create broad categories of effects and list specific stressors
by type for consideration in conceptual model development.
(4) Develop conceptual
models
Include climate change in development of conceptual models. Consider how climate-related
stressors can affect biological goals from various pathways, building on the findings obtained from
the literature review. The level of detail should be commensurate with the level of detail for
planning or screening.
(5) Inventory data
Identify which of the available observed hydrologic, climatic, and biological data may be affected by
climate-related stress identified in preceding steps. Consider observed data/projected information
to identify the already or potentially affected biological indicators and (or) flow indicators/flow-
regime components. Rate them considering the following qualitative categories: consequences
(low, medium, high); likelihood (low, medium, high); spatial extent (site, watershed, region); time
until problem begins (decades, within next 15 to 30 years, already occurring/likely occurring).
Consider sensitivity: Do some characteristics of the catchment increase or decrease sensitivity to
these climate stressors (for example, north-facing aspect or high elevations may reduce sensitivity
of snowmelt or water temperature to increased air temperature, whereas south-facing aspect or
low elevations may increase sensitivity).
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Framework component
Potential climate-change considerations
(6) Identify biological and
flow indicators
Identify which biological and flow indicators may be most affected by climate change. Rate them by
considering the qualitative categories previously mentioned (consequence, likelihood, spatial
extent, time until problem begins).
(7) Develop qualitative or
quantitative flow-ecology
models
Climate change considerations may not be applicable to Step 7.
(8) Identify acceptable
biological condition
goals/effects levels
Compare range of potential likely climate changes to the potential flow targets.
(9) Select candidate flow
targets
Compare range of potential likely changes to the actual selected flow target.
Identify management adaptation actions and determine which of them are most appropriate given
the likely effect to flow targets/biological goals.
(10) Monitor, evaluate, and
periodically refine flow
targets
Assess observed climate and hydrologic data for any emerging climate-change related trends in
variability of magnitude, frequency, duration, timing, and rate of change of flow. Identify and assess
new or updated climate-change projections. Are the updated projections consistent with observed
trends and (or) other existing projected information? How are the updated projections ecologically
significant? Do the updated climate change projections merit reassessment of acceptable effects
levels and the ability to meet environmental flow targets under current management practices?
As discussed in this appendix, climate change may challenge the management of aquatic resources because
past variability is no longer a reliable assumption for the future. However, protection of environmental flows
can serve as an adaptation tool, increasing resilience so that a system is more likely to recover from the effects
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of climate change. Climate-change vulnerability assessments can help managers strategically address water-
resource protection in spite of uncertainty. Climate-change vulnerability assessment approaches are highly
diverse; the two presented here illustrate only two of the many possible approaches. The California example
(Box J) describes a screening-level assessment in which climate-change exposure is the focus, whereas the
Pacific Northwest example (Box K) additionally accounts for potential effects of climate exposure on
assessment endpoints, in large part on the basis of the sensitivity of the biota and their life stages. The
information developed during a climate-change vulnerability assessment can help managers identify
differential effects to aquatic resources and understand the reasons that their resources are at risk so they can
set priorities and develop appropriate management responses.
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