i 

# Draft EPA-USGS Technical Report: Protecting Aquatic Life from Effects of Hydrologic Alteration

EPA Report 822

– P

– 15

– 002 USGS Scientific Investigations Report 2015

– 5 160 U.S. Department of the Interior U.S. Geological Survey United States Environmental Protection Agencyii 

## 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., MC 4304T 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)iii 

# Draft: EPA-USGS Technical Report: Protecting Aquatic Life from Effects of Hydrologic Alteration By Rachael Novak 1 , Jonathan G. Kennen 2 , Ra lph W. Abele 3 , Carol F. Baschon 4 , Daren M. Carlisle 5 , Laura Dlugolecki 6 , Joe E. Flotermersch 7 , Peter Ford 8 , Jamie Fowler 9 , Rose Galer 10 , Lisa P. Gordon 11 , Susan N. Hansen 12 , Bruce Herbold 13 , Thomas E. Johnson 14 , John M. Johnston 15 , Christopher P. Konrad 16 , Beth Leamond 17 , and Paul W. Seelbach 18

. 1. Bureau of Indian Affairs, Washington, D.C. (Formerly with U.S. Environmental Protection Agency (EPA), Of fice 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 

## EP A Report 822

– P

– 15

– 002 USGS Scientific Investigations Report 2015

– 5 160 U .S. Department of the Interior U.S. Geological Survey United States Environmental Protection Agencyiv 

### 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 /

or call 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, T.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 lifeambient-water quality-criteria

.v 

### 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.vi 

### 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.vii 

## Conversion Factors
International System of Units to Inch/Pound

Multiply By To obtain Length centimeter (cm) 0.3937 inch (in.) meter (km) 3.2808 foot (ft) kilometer (km) 0.6213 mile (mi) Area square meter (m 2 ) 0.00025 A cre square kilometer (km 2 ) 0.3861 square mile (mi 2 ) hectare (ha) 2.4710 A cre Volume cubic meter (m 3 ) 35.3147 cubic foot (ft 3 ) cubic meter (m 3 ) 0.00026 million gallon (gal) Flow rate cubic meter per second per square kilometer [(m 3 /s)/km 2 ] 91.47 cubic foot per second per square mile [(ft 3 /s)/mi 2 ] cubic meter per second (m 3 /s) 22.8244 million gallons per day (Mgal /d) Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as °F = (1.8 × °C) + 32.viii 

### Acronyms
Acronym /Abbreviation Definition BMP B est M anagement P ractice CADDIS Causal Analysis/Diagnosis Decision Information System CFR Code of Federal Regulations CWA Clean Water Act ELOHA Ecological Limits of Hydrologic Alteration EPA U.S. Environmental Protection Agency ERA Ecological Risk Assessment FERC Federal Energy Regulatory Commission GCM General Circulation Model IBI Index of Biotic Integrity IFC Instream Flow Council IPCC Intergovernmental Panel on Climate Change IR i ntegrated r eporting MS4 Municipal Separate Storm Sewer System NPDES Nati onal Pollutant Discharge Elimination System TMDL Total Maximum Daily Load USDA U

. S

. Department of Agriculture USGS U

. S

. Geological Survey WQS water quality s tandards1 

## 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 Groundwater Withdrawals
.................................................................................................. 26
4.3.4 Effluents and Other Artificial Inputs (Discharges)
............................................................... 27 4.3.5 Land-Cover Alteration (Land Use)
........................................................................................ 282

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
................................................................................................... 723

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 A1. 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.
................................ . 124 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 under the 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)..
........................................................................................................... 735 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 of fish and other aquatic biota by season in major tributaries of the Susquehanna River Basin, northeastern United States.
.............. 91 Figure C-1. (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 C1. Incorporating climate-change considerations into the framework for quantifying flow targets. 1496 

## 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: Ex amples for Prioritizing Restoration Activities
............................................................................... 1457 

### 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 like8 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 and9 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 fl ow 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).10 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 che mical, physical and biological integrity of the Nation’s waters " ( S ection 101(a)). In addition, the CWA establishes as an interim goal " water quality which provides for the protection and propagation of fish, shellfish and wildlife and provides for recreat ion in and on the water ," wherever attainable ( S ection 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 importantsources of stress include urbanization, agriculture practices, and engineered structures used for waterresource development (Vörösmarty 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). T oday’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,11 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 fr om 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.12

Figure 1 . Schematic diagram depicting the interaction between the natural flow regime, natural watershed conditions and the many ecosystem services it helps to maintain.13 

### 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 su ch as recreation or drinking water, al though 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 narrative14 flow criteria. Section 6 presents concepts, tools, and examples that may be useful for translating narrative flow criteria into quantitative flow targets. It includ es 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.15 

### 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 (B ox 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 Asse ssment 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. E nvironmental P rotection A gency, 1998). It can appl y 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 devel opment 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 how16 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 (Figu re 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 catchme nt -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 waterchemistry 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 l ead 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 conceptual17 models developed for the EPA Causal Analysis/Diagnosis Decision Information System (CADDIS), see U.S. Environmental Protection Agency (2012a)

Figure 2 . Schematic diagram illustrating a generalized conceptual model of the biological effects of flow alteration.18 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 (catchment 1 ). Climate determines patterns of water and energy input over time, wh ereas 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.19 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 twofold20 increase in the likelihood of effects on fish and macroinvertebrate communities 2 (Carlisle and others, 201 1). 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 n ew 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 (O/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 O/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.21 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 we re 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 (GIS) 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 B asin 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 5622 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).23 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.24 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.25 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.26 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. Groundwate r 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;27 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 spik es 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 from28 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.

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 asother important processes and characteristics (for example, sediment dynamics, temperature). Such landcover 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 of29 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, 200 9). 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 previous ly. 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 peak30 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 (Harr and 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 landscape31 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, 2014 b). 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 (I ntergovernmental 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).32 Understanding and enhancing adaptive capacity, along with an assessment of climate-change vulnerability, is a key part of climate-change adaptation planning.

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 minimal ly affected by changes in land use and water use . Modified from U.S. Environmental Protection Agency, 2014b)33 Figure 8 . Map showing trends in the timing of winter-spring runoff in the United States, 1940-2009. (Streamflow trends are 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).34 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. C hannel 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. Natural35 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 ephemeralreaches in another (Larned and others, 2010a, 2010b, 2011). Lateral connectivity is restricted to shortduration 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, 198 6; 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 a36 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 fr equency 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 co ntribute 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, show37 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; Vörösmarty 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, 2 004 ; 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 aquatic38 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 reduc e habitat diversity and, th erefore, 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 ( fo r example, Zorn and others, 2008). Water temperature is an associated hydrologic characteristic and ha s 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 inwater temperature that result from alterations such as withdrawals, especially during critical summer lowflow 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 and39 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 discuss es 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 to40 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 water 3 . 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. PU D No.1, 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)(1), 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.”41 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. (A n exhaustive discussion of these CWA programs is beyond the scope of this document; readers can learn more by accessing available EPA resources as noted below 5 .) 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 )

.42 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 N ation’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 criteria43 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) ha d 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 W eb site for links to the most up- to -date information: http://water.epa.gov/scitech/swguidance/standards/wqslibrary/index.cfm

.44 Table 1 . Excerpts from n arrative flow criteria f or select ed states and tribes
. [K ey terms are shown in bold for emphasis ; s ee U.S. E nvironmental P rotection A gency (2014 e ) for complete text of individual criteria ; %, percent; 7Q10, the 7

- day, 10

- year annual low

- flow statistic ; WMT, Water Management Type; ] State/Tribe W ater Q uality S tandard description of p rotected resource and corresponding goal
N ew H ampshire “ 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.”
R hode I sland “ 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. ”
V ermont Class A( 1)
— “ 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 r egime shall provide for maintenance of flow characteristics that ensure the full support of uses and comply with the applicable water quality criteria. ”
N ew Y ork Class N fresh surface waters ... “There shall be no alteration to flow that will impair the wat ers for their best usages .”
V irginia “ Man - made alterations in stream flow shall not contravene designated uses including protection of the propagation and growth of aquatic life .”
K entucky Section 4. “Aquatic Life. (1) Warm water aquatic habitat. The following parameters and associated criteria shall apply for the protectio n of productive45

State/Tribe W ater Q uality S tandard description of p rotected resource and corresponding goal

warm water aquatic communities, fowl, animal wildlife, arboreous growth, agricultural, and industrial uses:...(c) Flo w shall not be altered to a degree which will adversely affect the aquatic community.”
T ennessee 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
.... f or 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 integrit y 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.”
M issouri “Waters shall be free from physical, chemical, or hydrologic changes that would impair the natural biological community.” Seminole Tribe of F lorida “Class 2

- A waters shall be free from activities...
. that
. ... i mpair 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 ric e, 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 of fish 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.”46 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 Agen cy, 2014d ). More complete examples from New Hampshire and Rhode Island narrative flow criteria are as follows and illustrate additional attributes the se 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)).47 “ 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)(1)(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.48 Box C . Addressing Flow Regime Components It is critically important to maintain extremes (floods and droughts) with in the bounds of the natural flow regime to support the ecological structure and function of streams and rivers. However, a lteration s in low or h igh 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 bio logical 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). Comprehensi ve 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 organizati on 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 components49 (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. E nvironmental P rotection A gency for the derivation of water quality

- based effluent limits in the N ational P ollut ant D ischarge E limination S ystem 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. E nvironmental P rotection A gency, 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.50 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, 2 002 , 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 (s ee 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) categories 7 (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)51 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 wat er 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 solel y 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

.52 Box D . Procedures for Capturing Flow Information in the State of Texas The publication “ Surface w ater q uality m onitoring p rocedures, V olume 1: Physical and c hemical m onitoring

m ethods ” (T exas C ommission on E nvironmental Q uality [TCEQ] , 2012) describes how Texas monitors all flow conditions and captures flow information in its S tate database. Parameter codes for dat a 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 fl ow information, th e document describes how to capture qualitative flow information with the “flow

- severity” field:

 “ Record a flow

- severit y 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 w ater q uality m onitoring d ata m anagement r eference g uide 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 T exas C ommission on E nvironmental Q uality (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 ):53  “ N o Flow. When a flow severity of 1 is recorded for a sampling visit, record a flow value of 0 ft 3 /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 be tween 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 n o detectable flow. ”

 “ Low F low. 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 d etected, 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 t he stream. Normality is characterized by flow that stays within the confines of the normal stream channel. Water generally reaches the base of each bank. ”

 “ Flo od 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). ”

 “ H igh Flow. High flows are reported as a flow seve rity of 5. High flow would be characterized by flows that leave the normal stream channel but stay within the stream banks. ”54  “ D ry. 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. ”55 Box E . Vermont Addresses Hydrologically Altered Waters Vermont first adopted narrative criteria into its w ater q uality s tandards (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 L oad), Vermont does address flow-related exceedance of the WQS through the Vermont Priority Waters List. This list includes waters assessed as “altered” usi ng 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 D aily 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,56 which are likely to be influenced by flow regimes, also be taken into account when developing a TMDL (40 CFR §130.7(c)(1)). 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 newwater intake that alters the water quantity on which the TMDL was based), states ideally would consider reevaluating 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)(1)). 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 Utility57 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 Q uality Standards South Carolina Board of H ealth and Environmental Control Denied Certificati on 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 condition s 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.
Publi c 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 include58 specific flow requirements in a Clean Water Act Sec tion 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 Wash ington 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 c onditioned 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 regulates 8 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-regulationsexecutive-orders and http://www.epa.gov/cwa-404/policy- and -guidance59 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 D ischarge Elimination System (402) P ermits 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.60 Ma ny 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 perm ittee’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-sewersystems serving populations of 100,000 or more and systems serving populations located within the censusdefined 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 minimize61 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 N ation’s impervious cover was created since the 195 0’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, 20 13 c). 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, 200 9). 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 (s ee 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).62 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 postconstruction 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 rai nfall from a 24-h ou r 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.63 Box G . Stormwater and West Vir ginia 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 stormwate r 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 redevelo pment 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% m anaged 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 Age ncy ( 2012 b ).

5.7 Further considerations Th e 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 the64 “best available science
. ” Section 6 below presents a framework for quantifying flow targets to protect aquatic life.65 

### 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. (T he term “q uantitative translation” encompass es 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 E RA framework;66 Steps 5 through 7 represent the “analysis phase” ; and Step 8 incorporat es 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).67 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/2014-11/documents/eco_risk_assessment1998.pdf)68 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 us ed 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 can69 take into consideration available methods for measuring biological conditions, although endpoints withou t 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 offers70 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) d ata 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 sys tematically 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 S cenario A described in S ection 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 co mponent 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 o f drainage

- area breakpoints for stream

- size classes ( for example
— small , less than 50 sq uare miles [mi2]; medium , 50
– 100 mi2; large , greater than 100 mi 2 ). A comprehensive review of stream classification to support environmental flow management is provided in Olden and others (2011) and Melles and others (2012)
. E xample approaches are found in Seelbach and others (2006), Kennard and others (2010 b ), Kennen and others (2007), Re idy Liermann and others (2012), Melles and others (2012) , and Archfield and others (2013)
.71 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, historic al and projected trends in climate variables (precipitation, temperature, etc.) may be used to model flow regime changes for a state.72 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 fl ow -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) W eb 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 and73 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.

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 ).74 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 (GIS) 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/type/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 Partnership 9 , 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/10.1080/03632415.2011.607075#.VPc9VGjF- 4I . The fish data are available at http://ecosystems.usgs.gov/fishhabitat/data_viewer.jsp

.75 6.6 Identify Flow and Biological Indicators Streamflow and biological indicators are specific measures that are used to analy ze the relations between flow alteration and biological response (termed “ flow-ecology ” relations). Flow indicators correspond to “measures of exposure” in the EPA E RA framework, wh ereas 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 of fish, macroinvertebrates, and aquatic vegetation. Many flow indicators have been proposed to characterize the flow regime; th ese indicators describe the magnitude, timing, frequency, duration, and rate of change of various flow conditions. T he y 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.)76 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).77 Table 2
. Example flow and biological indicators used to evaluate relations between streamflow characteristics and aquatic assemblage response.
Flow

c omponent Flow i ndicators ( m easures of e xposure) Biological

c omponent Biological

i ndicato rs ( m easures of e ffect) Reference

Magnitude Mean June
– July f low;

Mean August f low Fish Fish d ensity ; Fish a bundance Peterson and Kwak (1999) ; Zorn and others ( 2008 ) Magnitude Spring m aximum f low;

Summer m edian f low Fish Fish a bundance; Fish

- a ssemblage c omposition Freeman and others (2001)

Magnitude Magnitude of 10

- y ear l ow - f low e vent Fish Fish Index of Bio tic Integrity; Fish

- s pecies r ichness Freeman and Marcinek (2006)
Magnitude Mean a nnual f low;

Base

- flow i ndex Macroinvertebrates Macroinvertebrate a bundance; Macroinvertebrate a ssemblage ;
c omposition Kennen and others (2014) Castella and others (1995)
Magnitude Maximum f low;

Ratio of m aximum to m inimum f low Macro i nvertebrates Macroinvertebrate Index of Biotic Integrity ; Macroinvertebrate s pecies r ichness Morley and Karr (2002)

Magnitude Magnitude of 1

- , 2

- , 5

- , 10

- , and 20

- y ear f lood

e vents Macro i nvertebrates Macroinvertebrate O/E (ratio between the observed and expected) s cores; Macroinvertebrate

- a ssemblage

c omposition Nichols and others (2006)78

Flow

c omponent Flow i ndicators ( m easures of e xposure) Biological

c omponent Biological

i ndicato rs ( m easures of e ffect) Reference

Magnitude Summer d iversion m agnitude Macro i nvertebrates Macroinvertebrate a bundance Wills and others (2006) Timing Date of a nnual m aximum f low;

Date of a nnual m inimum f low Fish Fish a bundance; Fish

- a ssemblage c omposition Koel and Sparks (2002)
Frequency Number of d ays a bove m ean a nnual f low;

Number of e vents a bove 7 5% e xceedance f low

v alue Macro i nvertebrates Macroinvertebrate Index of Biotic Integrity Macroinvertebrate r ichness Booth and others (2004) Kennen and others (2010)
Frequency Number of f lood e vents;

Number of l ow - f low e vents Riparian

v egetation Riparian t ree a bundance Lytle and Merritt (2004)

Duration Duration of h igh

- f low e vents;

Duration of l ow - f low e vents Fish Fish a bundance; Fish

- a ssemblage c omposition Koel and Sparks (2002)

Rate of c hange Mean r ise r ate;

Mean f all r ate Fish Fish a bundance; Fish

- a ssemblage c omposition Koel and Sparks (2002)79 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, 2010 b). An example approach to flow-target development using quantitative modeling is described in Section 6.9 (see Table 3 and Figure 13).80 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, 2010 b). Where feasible, confounding variables should be factored into the development of quantitative flow-ecology models. In81 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- ef fect 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, 20 13). An example approach to flow-target development using qualitative modeling is described in Section 6.9 (see Table 3 and Figure 14 ).82 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 flowecology 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).83 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 evaluat ed and adjust ed 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.)84 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 re presents 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 i s 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 of fish 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.85 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 s tate’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 S tep 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 co mplete. 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. O n 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 public86 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 W ater Resources and Colorado W ate r 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 ).87 Table 3 . Example applications of the framework to quantitatively translate the following narrative flow criterion: “ C hanges to the natural flow regime shall not impair the ability of a stream to support characteristic fish populations
. ”
Framework S tep Scenario A: Q uantitative E xample Scen ario B: Q ualitative E xample ( 1) Link n arrative

c riteria to b iological g oals and a ssessment

e ndpoints Numeric biological goals are defined from existing biological condition criteria, expressed as minimum acceptable values of fish Index of Biotic Integrity (IBI) scores. 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: t o maintain the abundance of riffle obligate species
.

( 2) Define s cope of

a ction: i dentify t arget

s treams 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: c old h eadwater
. All streams in the state are included in the effort to develop flow targets. A s a result of data and resource constraints, the need for stream classification following the literature review is evaluated
.

( 3) Conduct l iterature

r eview Literature is reviewed to identify flow

- regime changes that most affect

the condition of fish commu nities. 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 of fish species/f unctional groups referenced in S tep 1 . Relevant literature demonstrates the importance of a wide range of flow conditions on the health of fish communities in the state, with consistent relations identified across stream size and ecoregion. O n the basis of these fin dings, a systematic stream classification is not needed
.88

Framework S tep Scenario A: Q uantitative E xample Scen ario B: Q ualitative E xample ( 4) Develop

c onceptual m odels 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 of fish, organize d by fish species/functional group, season, and flow characteristic.

( 5) Conduct d ata i nventory 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 altera tion) 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 f low and b iological i ndicators
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 A ugust median flow (relative to reference conditions). A subset of the flow metrics quantified in S tep 5 is selected for flow

- target development. Metrics are evaluated according to their sensitivity to anthropogenic sources flow alteration and evidence of b iological relevance. Flow indicators describe magnitude and frequency characteristics of high/flood flows, seasonal/average flows, and low/drought flows. ( 7) Develop f low

e cology m odels Regression modeling is undertaken by using monitoring and modeling d ata from sites with paired flow and biological data. Final models Qualitative flow

- ecology models are developed by reframing conceptual models in terms of t he flow indicators selected in S tep 6 ( Figure 1 4 ).89

Framework S tep Scenario A: Q uantitative E xample Scen ario B: Q ualitative E xample

(termed “ fish response curves ” ; see F igure 1 3 ) quantify the relation between fish IBI scores and reduced August median flow. Fish response curves are generated for each of th e 10 stream classes defined in S tep 2
. ( 8) Estimate effects and i dentify

a cceptable l evels 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 i n S tep 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 . Ta rgets are expressed as a maximum allowable percentage reduction in August median flow by stream type. Participating agencies review available evidence to estimate effect s associated with increasing levels of hydrologic change. For some flow indicators, pas t 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 informa tion 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 referen ce 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 evide nce of their effectiveness.90 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)91 Figure 14 . Conceptual diagram illustrating hypothesized flow needs of fish 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)92 

### 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.93 

### 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_al2005a.pdf .] 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.esajournals.org/doi/pdf/10.1890/0012-9658(1998)079%5B0911%3ALVRIOL%5D2.0.CO%3B2 .] 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 .] 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 .] 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/ .]94 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/ .] 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 .] Arthington, A.H., 2012, Environmental flows
— Saving rivers in the third millennium: Berkeley and Los Angeles, Calif., University of California Press. Arthington, A.H., Bunn, S.E., Poff, N.L., and Naiman, R.J., 2006, The challenge of providing environmental flow rules to sustain river ecosystems: Ecological Applications, v. 16, p. 1,311
– 1,318. [Also available at http://dx.doi.org/10.1890/1051-0761(2006)016[1311:TCOPEF]2.0.CO;2 ] Baron, J.S., Poff, N.L., Angermeier, P.L., Dahm, C.N., Gleick, P.H., Hariston, N.G., Jr., Jackson, R.B., Johnston, C.A., Richter, B.D., and Steinman, A.D., 2002, Meeting ecological and societal needs for freshwater: The Ecological Society of America, Ecological Applications, v. 12, no. 5, p. 1247
– 1260. [Also available at http://dx.doi.org/10.1890/1051-0761(2002)012[1247:MEASNF]2.0.CO;2 .] Beechie, T, Imaki, H., Greene, J., Wade, A., Wu, H., Pess, G., Roni, P., Kimball, J., Stanford, J., Kiffney, P., and Mantua, N., 2013, Restoring salmon habitat for a changing climate: River and Research Applications, v. 29, no. 8, p. 939
– 960. [Also available at http://dx.doi.org/10.1002/rra.2590 .] Benke, A.C., 1990, A perspective on America's vanishing streams: Journal of the North American Benthological Society, v. 9, no. 1, p. 77
– 88. [Also available at http://dx.doi.org/10.2307/1467936 .]95 Blann K.L., Anderson, J.L., Sands, G.R., and Vondracek, Bruce, 2009, Effects of agricultural drainage on aquatic ecosystems — A review: Critical Reviews in Environmental Science and Technology, v. 39, no. 11, p. 909
– 1001. [Also available at http://dx.doi.org/10.1080/10643380801977966 .] Bolke, E.L., and Waddell, K.M., 1975, Chemical quality and temperature of water in Flaming Gorge Reservoir,Wyoming and Utah, and the effect of the reservoir on the Green River: U.S. Geological Survey WaterSupply Paper 2039
– A, 26 p. [Also available at http://pubs.er.usgs.gov/publication/wsp2039A .] Booth, D.B., Karr, J.R., Schauman, Sally, Konrad, C.P., Morley, S.A., Larson, M.G., and Burger, S.J., 2004, Reviving urban streams
— Land use, hydrology, biology, and human behavior: Journal of the American Water Resources Association, v. 40, no. 5, p. 1351
– 1364. [Also available at http://dx.doi.org/10.1111/j.1752-1688.2004.tb01591.x .] Boulton, A.J., 2003, Parallels and contrasts in the effects of drought on stream macroinvertebrate assemblages: Freshwater Biology, v. 48, no. 7, p. 1173
– 1185. [Also available at http://dx.doi.org/10.1046/j.1365-2427.2003.01084.x .] Bradford, M.J., and Heinonen, J.S., 2008, Low flows, instream needs and fish ecology in small streams: Canadian Water Resources Journal, v. 33, no. 2, p. 165
– 180. [Also available at http://dx.doi.org/10.4296/cwrj3302165 .] Brenden, T.O., Wang, Lizhu, Seelbach, P.W., Clark, R.D., Jr., Wiley, M.J., and Sparks-Jackson, B.L., 2008, A spatially constrained clustering program for river valley segment delineation from GIS digital river networks: Environmental Modeling and Software, v. 23, no. 5, p. 638
– 649. [Also available at http://dx.doi.org/10.1016/j.envsoft.2007.09.004 .] Brett, J.R., 1979, Environmental factors and growth, in Hoar, W.S., Randall, D.J., and Brett, J.R., eds., Fish physiology: New York, Academic Press, Bioenergetics and Growth, v. VIII, p. 599
– 675.96 Brooks, B.W., Riley, T.M., and Taylor, R.D., 2006, Water quality of effluent-dominated ecosystems
— Ecotoxological, hydrological, and management considerations: Hydrobiologia, v. 556, no. 1, p. 365
– 379. [Also available at http://dx.doi.org/10.1007/s10750-004-0189-7 .] Bunn, S.E., and Arthington, A.H., 2002, Basic principles and ecological consequences of altered flow regimes for aquatic biodiversity: Environmental Management, v. 30, no. 4, p. 492
– 507. [Also available at http://dx.doi.org/10.1007/s00267- 002 -2737-0 .] Cao, Yong, and Hawkins, C.P., 2011, The comparability of bioassessments
— A review of conceptual and methodological issues: The Society for Freshwater Science, Journal of the North American Benthological Society, v. 30, no. 3, p, 680
– 701. [Also available at http://dx.doi.org/10.1899/10-067.1 .] Carlisle, D.M., Meador, M.R., Short, T.M., Tate, C.M., Gurtz, M.E., Bryant, W.L., Falcone, J.A., and Woodside, M.D., 2013, The quality of our Nation’s waters—Ecological health in the Nation’s streams, 1993– 2005: U.S. Geological Survey Circular 1391, 120 p. [Also available at http://pubs.usgs.gov/circ/1391/ .] Carlisle, D.M., Nelson, S.M., and Eng, K., 2012, Macroinvertebrate community condition associated with the severity of streamflow alteration: River Research and Applications, v. 30, no. 1, p. 29
– 39. [Also available at http://dx.doi.org/10.1002/rra.2626 .] Carlisle, D.M., Wolock, D.M., and Meador, M.R., 2011, Alteration of streamflow magnitudes and potential ecological consequences
— A multiregional assessment: The Ecological Society of America, Frontiers in Ecology and the Environment, v. 9, no. 5, p. 264
– 270. [Also available at http://dx.doi.org/10.1890/100053 .] Caruso, B.S., 2002, Temporal and spatial patterns of extreme low flows and effects on stream ecosystems in Otago, New Zealand: Journal of Hydrology, v. 257, no. 1
– 4, p. 115
– 133. [Also available at http://dx.doi.org/10.1016/S0022-1694(01)00546-7 .]97 Cassie, D., 2006, The thermal regime of rivers
— A review: Freshwater Biology, v. 51, no. 8, p. 1389
– 1406. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2006.01597.x .] Castella, E., Bickerton, M., Armitage, P.D., and Petts, G.E., 1995, The effects of water abstractions on the invertebrate communities in U.K. streams: Hydrobiologia, v. 308, no. 3, p. 167
– 182. [Also available at http://dx.doi.org/10.1007/BF00006869 .] Chessman, B.C., Royal, M.J., and Muschal, Monika, 2011, The challenge of monitoring impacts of water abstraction on macroinvertebrate assemblages in unregulated streams: River Research and Applications, v. 27, no. 1, p. 76
– 86. [Also available at http://dx.doi.org/10.1002/rra.1340 .] Collier, Michael, Webb, R.H., and Schmidt, J.C., 1996, Dams and rivers
— A primer on the downstream effects of dams: U.S. Geological Survey Circular 1126, 94 p. [Also available at http://pubs.er.usgs.gov/publication/cir1126 .] Colorado Division of Water Resources, and Colorado Water Conservation Board, 2008, State of Colorado’s water supply model (StateMod) version 12: Denver, Colo., Colorado Division of Water Resources and Colorado Water Conservation Board. [Also available at ftp://dwrftp.state.co.us/cdss/projects/StateMod/ .] Crisp, D.T., 1977, Some physical and chemical effects of the Cow Green (Upper Teesdale) impoundment: Freshwater Biology, v. 7, no. 2, p. 109
– 120. [Also available at http://dx.doi.org/10.1111/j.1365- 2427.1977.tb01662.x .] Cummins, James, Buchanan, Claire, Haywood, Carlton, Moltz, Heidi, Griggs, Adam, Jones, R.C., Kraus, Richard, Hitt, N.P., and Bumgardner, R.V., 2010, Potomac basin large river environmental flow needs: Rockville, Md., Interstate Commission on the Potomac River Basin, ICRPRB Report 10
– 3. [Also available at http://www.potomacriver.org/wp-content/uploads/2015/02/ICPRB10-3.pdf .]98 Davies, S.P., and Jackson, S.K., 2006, The biological condition gradient
— A descriptive model for interpreting change in aquatic ecosystems: Ecological Applications, v. 16, no. 4, p. 1251
– 1266. [Also available at http://www.esajournals.org/doi/pdf/10.1890/1051- 0761(2006)016%5B1251%3ATBCGAD%5D2.0.CO%3B2 .] Dawson, T.P., Jackson, S.T., House, J.I., Prentice, I.C., and Macde, G.M., 2011, Beyond predictions
— Biodiversity conservation in a changing climate: Science, v. 332, no. 53, p. 53
– 58. [Also available at http://dx.doi.org/10.1126/science.1200303 .] De Jalon, D.G., Sanchez, Pablo, and Camargo, J.A., 1994, Downstream effects of a new hydropower impoundment on macrophyte, macroinvertebrate and fish communities: Regulated Rivers Research and Management, v. 9, no. 4, p. 253
– 261. [Also available at http://dx.doi.org/10.1002/rrr.3450090406 .] DePhilip, Michele, and Moberg, Tara, 2010, Ecosystem flow recommendations for the Susquehanna River Basin: Harrisburg, Pa., The Nature Conservancy, Report to the Susquehanna River Basin Commission and U.S. Army Corps of Engineers, 95 p., plus 9 appendices. [Also available at http://www.nature.org/media/pa/tnc-final-susquehanna-river-ecosystem-flows-study-report.pdf .] Dudgeon, David, Arthington, A.H., Gessner, M.O., Kawabata, Zen-Ichiro, Knowler, D.J., Lévêque, Christian, Naiman, R.J., Prieur-Richard, Anne-Hélène, Soto, Doris, Stiassny, M.L.J., and Sullivan, C.A., 2006, Freshwater biodiversity
— Importance, threats, status and conservation challenges: Biological Reviews, v. 81, no. 2, p. 163
– 182. [Also available at http://dx.doi.org/10.1017/S1464793105006950 .] Dunne, Thomas, and Leopold, L.B., 1978, Water in environmental planning: San Francisco, Calif., Freeman and Company, 818 p.99 Dynesius, Mats, and Nilsson, Christer, 1994, Fragmentation and flow regulation of the river systems in the northern third of the world: Science, v. 266, no. 5186, p. 753
– 762. [Also available at http://dx.doi.org/10.1126/science.266.5186.753 .] Elliott, J.M., 1981, Some aspects of thermal stress on freshwater teleosts, in Pickering, A.D., ed., Stress and Fish: New York, Academic Press, p. 209
– 245. Elvidge, C.D., Milesi, Cristina, Dietz, J.B., Tuttle, B.T., Sutton, P.C., Nemani, Ramakrishna, and Vogelmann, J.E., 2004, U.S. constructed area approaches the size of Ohio: EOS, Transactions, American Geophysical Union, v. 85, no. 24, p. 233
– 240. [Also available at http://dx.doi.org/10.1029/2004EO240001 .] Environmental Policy Division of the Congressional Research Service of the Library of Congress, 1978, A legislative history of the Clean Water Act of 1977
— A continuation of the legislative history of the Federal Water Pollution Control Act: 95th Congress, 2d session, January 19
– October 15, 1978, Printed for the use of the Committee on Environmental and Public Works, Serial no. 95
– 1 4. Falcone, J.A., 2011, Gages- II
— Geospatial attributes of gages for evaluating streamflow: U.S. Geological Survey, digital spatial dataset. [Also available at http://water.usgs.gov/GIS/metadata/usgswrd/XML/gagesII_Sept2011.xml .] Falcone, J.A., Carlisle, D.M., Wolock, D.M., and Meador, M.R., 2010, Gages
— A stream gage database for evaluating natural and altered flow conditions in the conterminous United States: The Ecological Society of America, Ecology, v. 91, no. 2, p. 621. [Also available at http://dx.doi.org/10.1890/09-0889.1 .] Field, C.B., Barros, V.R., Doken, D.J., Mach, K.J., Mastrandrea, M.D., Bilir, T.E., Chatterjee, Monalisa, Ebi, K.L., Estrada, Y.O., Genova, R.C., Girma, Betlhelm, Kissel, E.S., Levy, A.N., MacCracken, Sandy, Mastrandrea, P.R., and White, L.L., eds., 2014, Climate change 2014 impacts, adaptation, and vulnerability
— Part A
— Global and sectoral aspects
— Working group II contribution to the fifth assessment report of the100

Intergovernmental Panel on Climate Change: Cambridge, United Kingdom, and New York, Cambridge University Press, 1,132 p. [Also available at https://ipcc-wg2.gov/AR5/images/uploads/WGIIAR5- PartA_FINAL.pdf .] Freeman, M.C., Bowen, Z.H., Bovee, K.D., and Irwin, E.R., 2001, Flow and habitat effects on juvenile fish abundance in natural and altered flow regimes: The Ecological Society of America, Ecological Applications, v. 11, no. 1, p. 179
– 190. [Also available at http://dx.doi.org/10.2307/3061065 .] Freeman, M.C., and Marcinek, P.A., 2006, Fish assemblage responses to water withdrawals and water supply in reservoirs in Piedmont streams: Environmental Management, v. 38, no. 3, p. 435
– 450. [Also available at http://dx.doi.org/10.1007/s00267- 005 -0169-3 .] Frissell, C.A., Liss, W.J., Warren, C.E., and Hurley, M.D., 1986, A hierarchical framework for stream habitat classification
— Viewing streams in a watershed context: Environmental Management, v. 10, no. 2, p. 199
– 214. [Also available at http://dx.doi.org/10.1007/BF01867358 .] Furniss, M.J., Roby, K.B., Cenderelli, Dan, Chatel, John, Clifton, C.F., Clingenpeel, Alan, Hays, P.E., Higgins, Dale, Hodges, Ken, Howe, Carol, Jungst, Laura, Louie, Joan, Mai, Christine, Martinez, Ralph, Overton, Kerry, Staab, B.P., Steinke, Rory, and Weinhold, Mark, 2013, Assessing the vulnerability of watersheds to climate change
— Results of national forest watershed vulnerability pilot assessments: Portland, Oreg., General Technical Report PNW
– GTR
– 884, U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 32 p., plus appendix. [Also available at http://www.treesearch.fs.fed.us/pubs/43898 .] Gao, Yongxuan, Vogel, R.M., Kroll, C.N., Poff, N.L., and Olden, J.D., 2009, Development of representative indicators of hydrologic alteration: Journal of Hydrology, v. 374, no. 1
– 2, p. 136
– 147. [Also available at http://dx.doi.org/10.1016/j.jhydrol.2009.06.009 .]101 Gende, S.M., Edwards, R.T., Willson, M.F., and Wipfli, M.S., 2002, Pacific salmon in aquatic and terrestrial ecosystems: BioScience, v. 52, no. 10, p. 917
– 928. [Also available at http://dx.doi.org/10.1641/0006- 3568(2002)052[0917:PSIAAT]2.0.CO;2 .] Georgakakos, Aris, Fleming, Paul, Dettinger, Michael, Peters-Lidard, Christa, Richmond, T.C., Reckhow, Ken, White, Kathleen, and Yates, David, 2014, Chapter 3 water resources, in Melillo, J.M., Richmond, T.C., and Yohe, G.W., Climate change impacts in the United States: The Third National Climate Assessment, U.S. Global Change Research Program, p. 69
– 112. [Also available at http://nca2014.globalchange.gov/report/sectors/water .]Gido, K.B., Dodds, W.K., and Eberle, M.E., 2010, Retrospective analysis of fish community change during a halfcentury of landuse and streamflow changes: Journal of the North American Benthological Society, v. 29, no. 3, p. 970
– 987. [Also available at http://dx.doi.org/10.1899/09-116.1 .] Glick, Patty, Stein, B.A., and Edelson, N.A., eds., 2011, Scanning the conservation horizon
— A guide to climate change vulnerability assessment: Washington, National Wildlife Federation, 168 p. [Also available athttp://www.nwf.org/~/media/pdfs/global-warming/climate-smartconservation/nwfscanningtheconservationhorizonfinal92311.ashx .] Graf, W.L., 1999, Dam nation
— A geographic census of American dams and their large-scale hydrologic impacts: Water Resources Research, v. 35, no. 4, p. 1305
– 1311. [Also available at http://dx.doi.org/10.1029/1999WR900016 .] Grimm, N.B., Sheibley, R.W., Crenshaw, C.L., Dahm, C.N., Roach, W.J., and Zeglin, L.H., 2005, N retention and transformation in urban streams: The Society of Freshwater Science, Journal of the North American Benthological Society, v. 24, no. 3, p. 626
– 642. [Also available at http://dx.doi.org/10.1899/04-027.1 .]102 Gu, R.R., and Li, Yitian, 2002, River temperature sensitivity to hydraulic and meteorological parameters: Journal of Environmental Management, v. 66, no. 1, p. 43
– 56. [Also available at http://dx.doi.org/10.1006/jema.2002.0565 .] Hamilton, D.A., and Seelbach, P.W., 2011, Michigan’s water withdrawal assessment process and internet screening tool: State of Michigan Department of Natural Resources, Fisheries Special Report 55. [Also available at http://www.michigandnr.com/PUBLICATIONS/PDFS/ifr/ifrlibra/special/reports/sr55/SR55_Abstract.pdf .] Hannan, H.H., and Young, W.J., 1974, The influence of a deep-storage reservoir on the physicochemical limnology of a central Texas River: Hydrobiologia, v. 44, no. 2
– 3, p. 177
– 207. [Also available at http://dx.doi.org/10.1007/BF00187269 .] Harr, R.D., Levno, Al, and Mersereau, Roswell, 1982, Streamflow changes after logging 130-year old Douglas fir in two small watersheds: Water Resources Research, v. 18, no. 3, p. 637
– 644. [Also available at http://dx.doi.org/10.1029/WR018i003p00637 .] Hartman, K.J., Kaller, M.D., Howell, J.W., and Sweka, J.A., 2005, How much do valley fills influence headwater streams?: Hydrobiologia, v. 532, no. 1
– 3, p. 91
– 102. [Also available at http://dx.doi.org/10.1007/s10750- 004 -9019-1 .] Hatt, B.E., Fletcher, T.D., Walsh, C.J., and Taylor, S.L., 2004, The influence of urban density and drainage infrastructure on the concentrations and loads of pollutants in small streams: Environmental Management, v. 34, no. 1, p. 112
– 124. [Also available at http://dx.doi.org/10.1007/s00267- 004 -0221-8 .] Helms, B.S., Schoonover, J.E., and Feminella, J.W., 2009, Assessing influences of hydrology, physicochemistry, and habitat on stream fish assemblages across a changing landscape: Journal of the American Water103

Resources Association, v. 45, no. 1, p. 157
– 169. [Also available at http://dx.doi.org/10.1111/j.1752- 1688.2008.00267.x .] Henriksen, J.A., Heasley, John, Kennen, J.G., and Nieswand, Steven, 2006, Users’ manual for the hydroecological integrity assessment process software (including the New Jersey Assessment Tools): U.S. Geological Survey Open-File Report 2006
– 1093, 71 p. [Also available at https://www.fort.usgs.gov/sites/default/files/products/publications/21598/21598.pdf .] Hewlett, J.D., and Hibbert, A.R., 1961, Increases in water yield after several types of forest cutting: Hydrological Sciences Journal, v. 6, no. 3, p. 5
– 17. [Also available at http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.513.5979&rep=rep1&type=pdf .] Hill, M.T., Platts, W.S., and Beschta, R.L., 1991, Ecological and geomorphological concepts for instream and
out- of -channel flow requirements: Rivers, v. 2, no. 3, p. 198
– 210. [Also available at http://www.nativefishlab.net/library/textpdf/20402.pdf .] Hitt, N.P., Eyler, Sheila, and Wofford, J.E.B., 2012, Dam removal increases American Eel abundance in distant headwater streams: Transactions of the American Fisheries Society, v. 141, no. 5, p. 1171
– 1179. [Also available at http://dx.doi.org/10.1080/00028487.2012.675918 .] Holtschlag, D.J., 2009, Application guide for AFINCH (analysis of flows in networks of channels) described by NHDPlus: U.S. Geological Survey Scientific Investigations Report 2009
– 5188, 106 p. [Also available at http://pubs.usgs.gov/sir/2009/5188/ .] Ignatius, Amber, and Stallins, J.A., 2011, Assessing spatial hydrological data integration to characterize geographic trends in small reservoirs in the Apalachicola-Chattahoochee-Flint River Basin: Southeastern Geographer, v. 51, no. 3, p. 371
– 393. [Also available at http://dx.doi.org/10.1353/sgo.2011.0028 .]104 Intergovernmental Task Force on Monitoring Water Quality, The, 1995, Technical appendix D
— Indicators for meeting management objectives
— Summary and rationale matrices, in The Intergovernmental Task Force on Monitoring Water Quality, The strategy for improving water quality monitoring in the United States: U.S. Geological Survey Open-File Report 95
– 742, p. 17
– 26. [Also available at http://pubs.usgs.gov/of/1995/0742/report.pdf .] Intergovernmental Panel on Climate Change, 2007, Climate change 2007
— Synthesis report. Contribution of working groups I, II and III to the fourth assessment report of the Intergovernmental Panel on Climate Change (Core Writing Team, Pachauri, R.K., and Reisinger, Andy, eds.): Geneva, Switzerland, Intergovernmental Panel on Climate Change, 104 p. [Also available at http://www.ipcc.ch/pdf/assessmentreport/ar4/syr/ar4_syr_full_report.pdf .] Isaak, D J., and Rieman, B.E., 2013, Stream isotherm shifts from climate change and implications for distributions of ectothermic organisms: Global Change Biology, v. 19, no. 3, p. 742
– 751, http://dx.doi.org/10.1111/gcb.12073

. Jackson, R.B., Carpenter, S.R., Dahm, C.N., McKnight D.M., Naiman, R.J., Postel, S.L., and Running, S.W., 2001, Water in a changing world: Ecological Applications, v. 11, no. 4, p. 1027
– 1045. [Also available at http://dx.doi.org/10.1890/1051-0761(2001)011[1027:WIACW]2.0.CO;2 .] Johnson, P.T.J., Olden, J.D., and Vander Zanden, M.J., 2008, Dam invaders
— Impoundments facilitate biological invasions into freshwaters: Frontiers in Ecology and the Environment, v. 6, no. 7, p. 357
– 363. [Also available at http://dx.doi.org/10.1890/070156 .] Junk, W.J., Bayley, P.B., and Sparks, R.E., 1989, The flood pulse concept in river- fl oodplain systems, in Dodge, D.P., ed., Proceedings of the International Large River Symposium (LARS): Canadian Special Publication of Fisheries and Aquatic Sciences 106, p. 110
– 127. [Also available at http://www.dfompo.gc.ca/Library/111846.pdf .]105 Karl, T.R., Melillo, J.M., and Peterson, T.C., eds., 2009, Global climate change impacts in the United States: New York, Cambridge University Press. [Also available at http://downloads.globalchange.gov/usimpacts/pdfs/climate-impacts-report.pdf .] Kendy, Eloise, Apse, Colin, Blann, K.L., Smith, M.P., and Richardsome, Alisa, 2012, A practical guide to environmental flows for policy and planning
— With nine case studies in the United States: The Nature Conservancy. [Also available at http://www.oregon.gov/owrd/docs/SB839/2012_9_Case_Studies_Practical_Guide.pdf .] Kennard, M.J., Mackay, S.J., Pusey, B.J., Olden, J.D., and Marsh, Nick, 2010a, Quantifying uncertainty in estimation of hydrologic metrics for ecohydrological studies: River Research and Applications, v. 26, no. 2, p. 137
– 15 6. [Also available at http://dx.doi.org/10.1002/rra.1249 .] Kennard, M.J., Pusey, B.J., Olden, J.D., Mackay, S.J., Stein, J.L., and Marsh, Nick, 2010b, Classification of natural flow regimes in Australia to support environmental flow management: Freshwater biology, v. 55, no. 1, p. 171
– 193. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2009.02307.x .] Kennen, J.G., Henriksen, J.A., and Nieswand, S.P., 2007, Development of the hydroecological integrity assessment process for determining environmental flows for New Jersey streams: U.S. Geological Survey Scientific Investigations Report 2007
– 5206, 55 p. [Also available at http://pubs.usgs.gov/sir/2007/5206/pdf/sir2007- 5206 -508.pdf .] Kennen, J.G., Riskin, M.L., and Charles, E.G., 2014, Effects of streamflow reductions on aquatic macroinvertebrates
— Linking groundwater withdrawals and assemblage response in southern New Jersey streams, USA: Hydrological Sciences Journal, v. 59, no. 3
– 4, p. 545
– 561. [Also available at http://dx.doi.org/10.1080/02626667.2013.877139 .]106 Kennen, J.G., Riskin, M.L., Reilly, P.A., and Colarullo, S.J., 2013, Method to support Total Maximum Daily Load development using hydrologic alteration as a surrogate to address aquatic life impairment in New Jersey streams: U.S. Geological Survey Scientific Investigations Report 2013
– 5089, 86 p. [Also Available at http://pubs.usgs.gov/sir/2013/5089/pdf/sir2013-5089.pdf ] Kennen, J.G., Riva-Murray, Karen, and Beaulieu, K.M., 2010, Determining hydrologic factors that influence stream macroinvertebrate assemblages in the northeastern US: Ecohydrology, v. 3, no. 1, p. 88
– 106. [Also available at http://dx.doi.org/10.1002/eco.99 .] Koel, T.M., and Sparks, R.E., 2002, Historical patterns of river stage and fish communities as criteria for operations of dams on the Illinois River: River Research and Applications, v. 18, no. 1, p. 3
– 19. [Also available at http://dx.doi.org/10.1002/rra.630 .] Konikow, L.F., 2013, Groundwater depletion in the United States (1900−2008): U.S. Geological Survey Scientific Investigations Report 2013−5079, 63 p. [Also available at http://pubs.usgs.gov/sir/2013/5079 .] Konrad, C.P., and Booth, D.B., 2005, Hydrologic changes in urban streams and their ecological significance, in Brown, L.R., Gray, R.H., Hughes, R.M., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: Bethesda, Md., American Fisheries Society Symposium, p. 157
– 177. [Also available at http://faculty.washington.edu/dbooth/Konrad%20and%20Booth%20AFS.pdf .] Konrad, C.P., Brasher, A.M.D., and May, J.T., 2008, Assessing streamflow characteristics as limiting factors on benthic invertebrate assemblages in streams across the western United States: Freshwater Biology, v. 53, no. 10, p. 1983
– 1998, http://dx.doi.org/10.1111/j.1365-2427.2008.02024.x

. Konrad, C.P., Olden, J.D., Lytle, D.A., Melis, T.S., Schmidt, J.C., Bray, E.N., Freeman, M.C., Gido, K.B., Hemphill, N.P., Kennard, M.J., McMullen, L.E., Mims, M.C., Pyron, Mark, Robinson, C.T., and Williams, J.G., 2011,107

Large-scale flow experiments for managing rivers systems: Bioscience, v. 61, no. 12, p. 948
– 959. [Also available at http://dx.doi.org/10.1525/bio.2011.61.12.5 .] Kundzewicz, Z.W., Mata, L.J., Arnell, N.W., Döll, P., Jimenez, B., Miller, K., Oki, T., Şen, Z., and Shiklomanov, I., 2008, The implications of projected climate change for freshwater resources and their management: Hydrological Sciences Journal, v. 53, no. 1, p. 3
– 10. [Also available at http://dx.doi.org/10.1623/hysj.53.1.3 .] Larned, S.T., Arscott, D.B., Schmidt, Jochen, and Diettrich, J.C., 2010a, A framework for analyzing longitudinal and temporal variation in river flow and developing flow-ecology relationships: Journal of the American Water Resources Association, v. 46, no. 3, p. 541
– 553. [Also available at http://dx.doi.org/10.1111/j.1752- 1688.2010.00433.x .]Larned, S.T., Datry, Thibault, Arscott, D.B., and Tockner, Klement, 2010b, Emerging concepts in temporaryriver 5 ecology: Freshwater Biology, v. 55, no. 4, p. 717
– 738. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2009.02322.x .] Larned, S.T., Schmidt, Jochen, Datry, Thibault, Konrad, C.P., Dumas, J.K., and Diettrich, J.C., 2011, Longitudinal river ecohydrology
— Flow variation down the lengths of alluvial rivers: Ecohydrology, v. 4, no. 4, p. 532
– 548. [Also available at http://dx.doi.org/ 10.1002/eco.126 .] Lieb, D.A., and Carline, R.F., 2000, Effects of urban runoff from a detention pond on water quality, temperature and caged Gammarus minus (Say) (Amphipoda) in a headwater stream: Hydrobiologia, v. 441, no. 1, p. 107
– 116. [Also available at http://dx.doi.org/10.1023/A:1017550321076 .] Locke, Allan, Stalnaker, C.B., Zellmer, Sandra, Williams, Kathleen, Beecher, Hal, Richards, Todd, Robertson, Cindy, Wald, Alan, Paul, Andrew, and Annear, Tom, 2008, Integrated approaches to riverine resource management — Case studies, science, law, people, and policy: Cheyenne, Wyo., Instream Flow Council.108 Lytle, D.A., and Merritt, D.M., 2004, Hydrologic regimes and riparian forests
— A structured population model for cottonwood: Ecology, v. 85, no. 9, p. 2493
– 2503. [Also available at http://dx.doi.org/10.1890/04-0282 .] Lytle, D.A., and Poff, N.L., 2004, Adaptation to natural flow regimes: Trends in Ecology and Evolution, v. 19, no. 2, p. 94
– 100. [Also available at http://dx.doi.org/10.1016/j.tree.2003.10.002 .] Maas-Hebner, K.G., Harte, M.J., Molina, N., Hughes, R.M., Schreck, C., 2015, Combining and aggregating environmental data for status and trend assessments: challenges and approaches: Environmental Monitoring and Assessment, v. 187, no 5. [Also available at http://dx.doi.org/10.1007/s10661- 015

- 4504 -8 ] Magilligan, F.J., and Nislow, K.H., 2005, Changes in hydrologic regime by dams: Geomorphology, v. 71, no. 1
– 2, p. 61
– 78. [Also available at http://dx.doi.org/10.1016/j.geomorph.2004.08.017 .] Maxwell, J.R., Edwards, C.J., Jensen, M.E., Paustian, S.J., Parrott, Harry, and Hill, D.M., 1995, A hierarchical framework of aquatic ecological units in North America (Nearctic Zone): St. Paul, Minn.,U.S. Department of Agriculture, Forest Service, North Central Forest Experiment Station, General Technical Report NC
– 176, 72 p. [Also available at http://www.treesearch.fs.fed.us/pubs/10240 .] McCartney, M.P., 2009, Living with dams
— Managing the environmental impacts: IWA Publishing, Water Policy, v. 11, no. 1, p. 121
– 139. [Also available at http://dx.doi.org/10.2166/wp.2009.108 .] McManamay,R.A., Orth, D.J., and Dolloff, C.A., 2012, Revisiting the homogenization of dammed rivers in the southeastern US: Journal of Hydrology, v. 424
– 425, p. 217
– 237. [Also available at http://dx.doi.org/10.1016/j.jhydrol.2012.01.003 .] McManamay, R.A., Orth, D.J., Kauffman, John, and Davis, M.M., 2013, A database and meta-analysis of ecological responses to stream flow in the South Atlantic region: Eagle Hill Institute, Southeastern Naturalist, v. 12, no. 5, p. 1
– 36. [Also available at http://www.bioone.org/doi/full/10.1656/058.012.m501 .]109 McMullen, L.E., and Lytle, D.A., 2012, Quantifying invertebrate resistance to floods
— A global-scale metaanalysis: Ecological Applications, v. 22, no. 8, p. 2164
– 2175. [Also available at http://dx.doi.org/10.1890/11-1650.1 .] Melillo, J.M., Richmond, T.C., and Yohe, G.W., eds., 2014, Climate change impacts in the United States
— Highlights
— The third National climate assessment: Washington, U.S. Government Printing Office, U.S. National Climate Assessment, U.S. Global Change Research Program, 148 p. [Also available at http://s3.amazonaws.com/nca2014/low/NCA3_Highlights_LowRes.pdf?download=1 .] Melles, S.J., Jones, N.E., and Schmidt, B., 2012, Review of theoretical developments in stream ecology and their influence on stream classification and conservation planning: Freshwater Biology, v. 57, no. 3, p. 415
– 434. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2011.02716.x .] Merritt, D.M., and Poff, N.L., 2010, Shifting dominance of riparian Populus and Tamarix along gradients of flow alteration in western North American rivers: Ecological Applications, v. 20, no. 1, p. 135
– 152. [Also available at http://dx.doi.org/10.1890/08-2251.1 .] Merritt, D.M., Scott, M.L., Poff, N.L., Auble, G.T., and Lytle, D.A., 2010, Theory, methods and tools for determining environmental flows for riparian vegetation
— Riparian vegetation-flow response guilds: Freshwater Biology, v. 55, no. 1, p. 206
– 225. [Also available at http://dx.doi.org/10.1111/j.1365- 2427.2009.02206.x .] Messinger, Terence, 2003, Comparison of storm response of streams in small, unmined and valley-filled watersheds, 1999-2001, Ballard Fork, West Virginia: U.S. Geological Survey Water-Resources Investigations Report 02
– 4303, 22 p. [Also available at http://pubs.usgs.gov/wri/wri024303/ .]110 Milly, P.C.D., Betancourt, Julio, Falkenmark, Malin, Hirsch, R.M., Kundzewicz, Z.W., Lettenmaier, D.P., and Stouffer, R.J., 2008, Stationarity is dead
— Wither water management?: Science, v. 319, no. 5863, p. 573
– 574. [Also available at http://dx.doi.org/10.1126/science.1151915 .] Mims, M.C., and Olden, J.D., 2012, Life history theory predicts fish assemblage response to hydrologic regimes: Ecology, v. 93, no. 1, p. 35
– 45. [Also available at http://dx.doi.org/10.1890/11-0370.1 .] Mims, M.C., and Olden, J.D., 2013, Fish assemblages respond to altered flow regimes via ecological filtering of life history strategies: Freshwater Biology, v. 58, no. 1, p. 50
– 62. [Also available at http://dx.doi.org/10.1111/fwb.12037 .] Montgomery, D.R., 1999, Process domains and the river continuum: Journal of the American Water Resources Association, v. 35, no. 2, p. 397
– 410. [Also available at http://dx.doi.org/10.1111/j.1752- 1688.1999.tb03598.x .] Morgan, M.D., and Good, R.E., 1988, Stream chemistry in the New Jersey pinelands
— The influence of precipitation and watershed disturbance: Water Resources Research, v. 24, no. 7, p. 1091
– 1100. [Also available at http://dx.doi.org/10.1029/WR024i007p01091 .] Morley, S.A., and Karr, J.R., 2002, Assessing and restoring the health of urban streams in the Puget Sound Basin: Conservation Biology, v. 16, no. 6, p. 1498
– 1509. [Also available at http://online.sfsu.edu/jerry/geo_642/refs/MorleyandKarr2002.pdf .]
Mul holland, P.J., Helton, A.M., Poole, G.C., Hall, R.O., Hamilton, S.K., Peterson, B.J., Tank, J.L., Ashkenas, L.R., Cooper, L.W., Dahm, C.N., Dodds, W.K., Findlay, S.E.G., Gregory, S.V., Grimm, N.B., Johson, S.L., McDowell, W.H., Meyer, J.L., Valett, H.M., Webster, J.R., Arango, C.P., Beaulieu, J.J., Bernot, M.J., Burgin, A.J., Crenshaw, C.L., Johson, L.T., Niederlehner, B.R., O’Brien, J.M., Potter, J.D., Sheibley, R.W., Sobota, D.J., and111

Thomas, S.M., 2008, Stream denitrification across biomes and its response to anthropogenic nitrate loading: Nature, v. 452, no. 7184, p. 202
– 205. [Also available at http://dx.doi.org/10.1038/nature06686 .] Naiman, R.J., Bunn, S.E., Nilsson, Christer, Petts, G.E., Pinnay, Gilles, and Thompson, L.C., 2002, Legitimizing fluvial ecosystems as users of water
— An overview: Environmental Management, v. 30, no. 4, p. 455
– 467. [Also available at http://dx.doi.org/10.1007/s002 67 -002-2734-3 .] Nature Conservancy, The, 2009, Indicators of hydrologic alteration
— Version 7.1 —User’s manual: The Nature Conservancy, 76 p. [Also available at https://www.conservationgateway.org/Documents/IHAV7.pdf .] Nichols, Susan, Norris, Richard, Maher, William, and Thoms, Martin, 2006, Ecological effects of serial impoundment on the Cotter River, Australia: Hydrobiologia, v. 572, no. 1, p. 255
– 273. [Also available at http://dx.doi.org/10.1007/s10750- 005 -0995-6 .] Olden, J.D., 2004, Fish fauna homogenization of the United States, life-history correlates of native extinction and nonnative invasions in the American Southwest, and the bidirectional impacts of dams in the American Southeast: Fort Collins, Colo., Colorado State University, Ph.D. dissertation. Olden, J.D., Kennard, M.J., and Pusey, B.J., 2011, A framework for hydrologic classification with a review of methodologies and applications in ecohydrology: Ecohydrology, v. 5, no. 4, p. 503
– 518. [Also available at http://dx.doi.org/10.1002/eco.251 .] Olden, J.D., Konrad, C.P., Melis, T.S., Kennard, M.J., Freeman, M.C., Mims, M.C., Bray, E.N., Gido, K.B., Hemphill, N.P., Lytle, D.A., McMullen, L.E., Pyron, Mark, Robinson, C.T., Schmidt, J.C., and Williams, J.G., 2014, Are large-scale flow experiments informing the science and management of freshwater ecosystems?: Frontiers in Ecology and the Environment, v. 12, no. 3, p. 176
– 185. [Also available at http://dx.doi.org/10.1890/130076 .]112 Olden, J.D., and Naiman, R.J., 2010, Incorporating thermal regimes into environmental flows assessments
— Modifying dam operations to restore freshwater ecosystem integrity: Freshwater Biology, v. 55, no. 1, p. 86
– 107. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2009.02179.x .]
Ol den, J.D., and Poff, N.L., 2003, Redundancy and the choice of hydrologic indices for characterizing streamflow regimes: River Research and Applications, v. 19, no. 1, p. 101
– 121. [Also available at http://dx.doi.org/10.1002/rra.700 .] Olivera, Francisco, and DeFee, B.B., 2007, Urbanization and its effect on runoff in the Whiteoak Bayou Watershed, Texas: Journal of the American Water Resources Association, v. 43, no. 1, p. 170
– 182. [Also available at http://dx.doi.org/10.1111/j.1752-1688.2007.00014.x .] Osborne, L.L., and Wiley, M.J., 1992, Influence of tributary spatial position on the structure of warmwater fish communities: Canadian Journal of Fisheries and Aquatic Sciences, v. 49, no. 4, p. 671
– 681. [Also available
at http://dx.doi.org/10.1139/f92-076 .] Palmer, M.A., and Febria, C.M., 2012, The heartbeat of ecosystems: Science, v. 336, no. 6087, p. 1393
– 1394. [Also available at http://dx.doi.org/10.1126/science.1223250 .] Palmer, M.A., Lettenmaier, D.P., Poff, N.L., Postel, S.L., Richter, B.D., and Warner, Richard, 2009, Climate change and river ecosystems
— Protection and adaptation options: Environmental Management, v. 44, no. 6, p. 1053
– 1068. [Also available at http://dx.doi.org/10.1007/s00267- 009

- 9329 -1 .] Palmer, M.A., Reidy Liermann, C.A., Nilsson, Christer, Florke, Martina, Alcamo, Joseph, Land, P.S., and Bond, Nick, 2008, Climate change and the world’s river basins— Anticipating management options: Frontiers in Ecology and the Environment, v. 6, no. 2, p. 81
– 89. [Also available at http://dx.doi.org/10.1890/060148 .] Paul, M.J., and Meyer, J.L., 2001, Streams in the urban landscape: Annual Review of Ecology and Systematics, v. 32, p. 333
– 365. [Also available at http://dx.doi.org/10.1146/annurev.ecolsys.32.081501.114040 .]113 Peterson, J.T., and Kwak, T.J., 1999, Modeling the effects of land use and climate change on riverine smallmouth bass: Ecological Applications, v. 9, no. 4, p. 1391
– 1404. [Also available at http://dx.doi.org/10.1890/1051-0761(1999)009[1391:MTEOLU]2.0.CO;2 .] Petts, G.E., 2009, Instream flow science for sustainable river management: Journal of the American Water Resources Association, v. 45, no. 5, p. 1071
– 1086. [Also available at http://dx.doi.org/10.1111/j.1752- 1688.2009.00360.x .] Pittock, Jamie, and Finlayson, C.M., 2011, Australia’s Murray -Darling Basin
— Freshwater ecosystem conservation options in an era of climate change: Marine and Freshwater Research, v. 62, no. 3, p. 232
– 243. [Also available at http://dx.doi.org/10.1071/MF09319 .] Poff, N.L., Allan, J.D., Bain, M.B., Karr, J.R., Prestegaard, K.L., Richter, B.D., Sparks, R.E., and Stromberg, J.C., 1997, The natural flow regime
— A paradigm for river conservation and restoration: Bioscience, v. 47, no. 11, p. 769
– 784. [Also available at http://www.americanrivers.org/assets/pdfs/water-supply/the-naturalflow-regime.pdf?bf5c96 .] Poff, N.L., Bledsoe, B.P., and Cuhaciyan, C.O., 2006, Hydrologic variation with land use across the contiguous United States
— Geomorphic and ecological consequences for stream ecosystems: Geomorphology, v. 79, no. 3
– 4, p. 264
– 285. [Also available at http://dx.doi.org/10.1016/j.geomorph.2006.06.032 .] Poff, N.L., and Hart, D.D., 2002, How dams vary and why it matters for the emerging science of dam removal: BioScience, v. 52, no. 8, p. 659
– 66 8. [Also available at http://dx.doi.org/10.1641/0006- 3568(2002)052[0659:HDVAWI]2.0.CO;2 .] Poff, N.L., Olden, J.D., Merritt, D.M., and Pepin, D.M., 2007, Homogenization of regional river dynamics by dams and global biodiversity implications: Proceedings of the National Academy of Sciences of the United114

States of America, v. 104, no. 14, p. 5732
– 5737. [Also available at http://dx.doi.org/10.1073/pnas.0609812104 .] Poff, N.L., Olden, J.D., and Strayer, D.L., 2012, Climate change and freshwater fauna extinction risk, chap. 17 of Hannah, Lee, ed., 2012, Saving a million species
— Extinction risk from climate change: Washington, Island Press, p. 309
– 336. Poff, L.N., Richter, B.D., Arthington, A.H., Bunn, S.E., Naiman, R.J., Kendy, Eloise, Acreman, Mike, Apse, Colin, Bledsoe, B.P., Freeman, M.C., Henriksen, J.A., Jacobson, R.B., Kennen, J.G., Merritt, D.M., O’Keeffe, J.H., Olden, J.D., Rogers, Kevin, Tharme, R.E., and Warner, Andrew, 2010, The ecological limits of hydrologic alteration (ELOHA)
— A new framework for developing regional environmental flow standards: Freshwater Biology, v. 55, no. 1, p. 147
– 170. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2009.02204.x .] Poff, N.L., and Zimmerman, J.K.H., 2010, Ecological responses to altered flow regimes
— A literature review to inform the science and management of environmental flows: Freshwater Biology, v. 55, no. 1, p. 194
– 205. [Also available at http://dx.doi.org/10.1111/j.1365-2427.2009.02272.x .] Postel, S.L., and Richter, B.D., 2003, Rivers for life
— Managing water for people and nature: Washington, Island Press, 220 p. Pozo, Jesús, Orive, Emma, Fraile, Henar, and Basaguren, A., 1997, Effects of the Cernadilla-Valparaiso reservoir system on the River Tera: Regulated Rivers
— Research and Management, v. 13, no. 1, p. 57
– 73. [Also available at http://dx.doi.org/10.1002/(SICI)1099-1646(199701)13:1<57::AID-RRR427>3.0.CO;2-W .] Preece, R.M., and Jones, H.A., 2002, The effect of Keepit Dam on the temperature regime of the Namoi River, Australia: River Research and Applications, v. 18, no. 4, p. 397
– 414. [Also available at http://dx.doi.org/10.1002/rra.686 .]115 Pringle, Catherine, 2003, What is hydrologic connectivity and why is it ecologically important?: Hydrological Processes, v. 17, no. 13, p. 2685
– 2689. [Also available at http://dx.doi.org/10.1002/hyp.5145 .] Rahel, F.J., and Olden, J.D., 2008, Assessing the effects of climate change on aquatic invasive species: Conservation Biology, v. 22, no. 3, p. 521
– 533. [Also available at http://dx.doi.org/10.1111/j.1523- 1739.2008.00950.x .] Reeves, H.W., Hamilton, D.A., Seelbach, P.W., and Asher, A.J., 2009, Ground-water-withdrawal component of the Michigan water-withdrawal screening tool: U.S. Geological Survey Scientific Investigations Report 2009
– 5003, 36 p. [Also available at http://pubs.usgs.gov/sir/2009/5003/ .] Reidy Liermann, C.A., Olden, J.D., Beechie, T.J., Kennard, M.J., Skidmore, P.B., Konrad, C.P., and Imaki, H., 2012, Hydrogeomorphic classification of Washington State rivers to support emerging environmental flow management strategies: River Research and Applications, v. 28, no. 9, p. 1340
– 1358. [Also available at http://dx.doi.org/10.1002/rra.1541 .] Richardson, A.R., 2005, Modified aquatic base flow (RI-ABF) for Rhode Island: Providence, R.I., Rhode Island Department of Environmental Management, Office of Water Resources, 33 p. [Also available at http://www.dem.ri.gov/programs/benviron/water/withdraw/pdf/riabf.pdf .] Richter, B.D., 2010, Re-thinking environmental flows
— From allocations and reserves to sustainability boundaries: River Research and Applications, v. 28, no. 8, p. 1052
– 1063. [Also available at http://dx.doi.org/10.1002/rra.1320 .] Richter, B.D., Mathews, Ruth, Harrison, D.L., and Wigington, Robert, 2003, Ecologically sustainable water management — Managing river flows for ecological integrity: Ecological Applications, v. 13, no. 1, p. 206
– 224. [Also available at http://dx.doi.org/10.1890/1051-0761(2003)013[0206:ESWMMR]2.0.CO;2 .]116 Richter, B.D., and Thomas, G.A., 2007, Restoring environmental flows by modifying dam operations: Ecology and Society, v. 12, no. 1, 26 p. [Also available at http://www.ecologyandsociety.org/vol12/iss1/art12/ .] Richter, B.D., Warner, A.T., Meyer, J.L., and Lutz, Kim, 2006, A collaborative and adaptive process for developing environmental flow recommendations: River Research and Applications, v. 22, no. 3, p. 297
– 318. [Also available at http://dx.doi.org/10.1002/rra.892 .] Rolls, R.J., Leigh, Catherine, and Sheldon, Fran, 2012, Mechanistic effects of low-flow hydrology on riverine ecosystems — Ecological principles and consequences of alteration: Freshwater Science, v. 31, no. 4, p. 1163
– 1186. [Also available at http://dx.doi.org/10.1899/12-002.1 .] Roy, A.H., Freeman, M.C., Freeman, B.J., Wenger, S.J., Ensign, W.E., and Meyer, J.L., 2005, Investigating hydrologic alteration as a mechanism of fish assemblage shifts in urbanizing streams: Journal of the North American Benthological Society, v. 24, no. 3, p. 656
– 678. [Also available at http://dx.doi.org/10.1899/04- 022.1 .] Roy, A.H., Purcell, A.H., Walsh, C.J., and Wenger, S.J., 2009, Urbanization and stream ecology
— Five years later: Journal of the North American Benthological Society, v. 28, no. 4, p. 908
– 910. [Also available at http://dx.doi.org/10.1899/08-185.1 .] Sanborn, S.C., and Bledsoe, B.P., 2006, Predicting streamflow regime metrics for ungauged streams in Colorado, Washington, and Oregon: Journal of Hydrology, v. 325, no. 1, p. 241
– 261. [Also available at http://dx.doi.org/10.1016/j.jhydrol.2005.10.018 .] Seelbach, P.W., Wiley, M.J., Baker, M.E., and Wehrly, K.E., 2006, Initial classification of river valley segments across Michigan’s Lower Peninsula, chap. 1 of Hughes, R.M., Wang, Lizhu, and Seelbach, P.W., eds., Landscape influences on stream habitats and biological assemblages
— Proceedings of the symposium on Influences of Landscape on Stream Habitat and Biological Communities held in Madison, Wisconsin, USA,117

25
– 26 August 2004: American Fisheries Society, Volume 48 of American Fisheries Society symposium, p. 25
– 39. Sheng, Zhuping, and Devere, Jeff, 2005, Understanding and managing the stressed Mexico-USA transboundary Hueco Bolson aquifer in the El Paso del Norte region as a complex system: Hydrogeology Journal, v. 13, no. 5
– 6, p. 813
– 825. [Also available at http://dx.doi.org/10.1007/s10040- 005

- 0451 -8 .] Sherman, Bradford, Todd, C.R., Koehn, J.D., and Ryan, Tom, 2007, Modelling the impact and potential mitigation of cold water pollution on Murray cod populations downstream of Hume Dam, Australia: River Research and Applications, v. 23, no. 4, p. 377
– 389. [Also available at http://dx.doi.org/10.1002/rra.994 .] Smith, M.P., Schiff, Roy, Olivero, Arlene, and MacBroom, J.G., 2008, The active river area
— A conservation framework for protecting rivers and streams: Boston, Mass., The Nature Conservancy, Eastern U.S. Freshwater Program, 59 p. [Also available at http://www.floods.org/PDF/ASFPM_TNC_Active_River_%20Area.pdf .] Stalnaker, C.B., 1990, Minimum flow is a myth [abs.], in Bain, M.B., Ecology and assessment of warmwater
streams — Workshop synopsis: Washington, U.S. Fish and Wildlife Service, Biological Report, v. 90, no. 5, p. 31
– 33. [Also available at https://www.fort.usgs.gov/sites/default/files/products/publications/4/4.pdf .] Strayer, D.L., and Dudgeon, David, 2010, Freshwater biodiversity conservation
— Recent progress and future challenges: Journal of North American Benthological Society, v. 29, no. 1, p. 344
– 358. [Also available at http://dx.doi.org/10.1899/08-171.1 .] Stuckey, M.H., Koerkle, E.H., and Ulrich, J.E., 2012, Estimation of baseline daily mean streamflows for ungaged locations on Pennsylvania streams, water years 1960
– 2008: U.S. Geological Survey Scientific Investigations Report 2012
– 5142, 61 p. [Also available at http://pubs.usgs.gov/sir/2012/5142/ .]118 Syvitski, J.P.M., Vorosmarty, C.J., Kettner, A.J., and Green, Pamela, 2005, Impact of humans on the flux of terrestrial sediment to the global coastal ocean: Science, v. 308, no. 5720, p. 376
– 380. [Also available at http://dx.doi.org/10.1126/science.1109454 .] Texas Commission on Environmental Quality, 2012, Surface water quality monitoring procedures, volume 1
— Physical and chemical monitoring methods: Austin, Tex., Texas Commission of Environmental Quality, RG
– 415, [variously paged]. [Also available at https://www.tceq.texas.gov/publications/rg/rg- 415 .] Texas Commission on Environmental Quality, 2013, Surface water quality monitoring data management reference guide: Austin, Tex., Texas Commission on Environmental Quality, 133 p. [Also available at http://www.tceq.state.tx.us/assets/public/compliance/monops/water/wdma/dmrg/dmrg_complete.pdf .] Thompson, J.R., Taylor, M.P., Fryirs, K.A., and Brierley, G.J., 2001, A geomorphological framework for river characterization and habitat assessment: Aquatic Conservation
— Marine and Freshwater Ecosystems, v. 11, no. 5, p. 373
– 389. [Also available at http://dx.doi.org/10.1002.aqc.467 .] Trush, W.J., McBain, S.M., and Leopold, L.B., 2000, Attributes of an alluvial river and their relation to water policy and management: Proceedings of the National Academy of Sciences of the United States of America, v. 97, no. 22, p. 11858
– 11863. [Also available at http://dx.doi.org/10.1073/pnas.97.22.11858 .] Turner, B.L., II, Kasperson, R.E., Matson, P.A., McCarthy, J.J., Corell, R.W., Christensen, Lindsey, Eckley, Noelle, Kasperson, J.X., Luers, Amy, Martello, M.L., Polsky, Collin, Pulsipher, Alexander, and Schiller, Andrew, 2003, A framework for vulnerability analysis in sustainability science: Proceedings of the National Academy of Sciences of the United States of America, v. 100, no. 14, p. 8074
– 8079. [Also available at http://dx.doi.org/10.1073/pnas.1231335100 .] U.S. Army Corps of Engineers, 2013, CorpsMap
— National inventory of dams: U.S. Army Corps of Engineers, accessed August 2014 at http://geo.usace.army.mil/pgis/f?p=397:1:0::NO

.119 U.S. Army Corps of Engineers, The Nature Conservancy, and Interstate Commission on the Potomac River Basin, 2013, Middle Potomac River Watershed assessment
— Potomac River sustainable flow and water resources analysis: Final Report, 144 p., 10 appendices. [Also available at http://www.potomacriver.org/wp-content/uploads/2015/01/MPRWA_FINAL_April_2013.pdf .] U.S. Department of Agriculture, 1997, Agricultural resources and environmental indicators, 1996
– 97: U.S. Department of Agriculture, Economic Research Service Report, Agricultural Handbook no. 712. U.S. Department of Agriculture, 2009, Summary report
— 2007 National Resources Inventory: Washington and Ames, Iowa, National Resources Conservation Service and Iowa State University, Center for Statistics and Methodology, 123 p. [Also available at http://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb1041379.pdf .] U.S. Environmental Protection Agency, 1991, Technical support document for water quality-based toxics control: Washington, U.S. Environmental Protection Agency, EPA/505/2

– 90
– 001, PB91
– 127415. [Also available at http://water.epa.gov/scitech/datait/models/upload/2002_10_25_npdes_pubs_owm0264.pdf .] U.S. Environmental Protection Agency, 1994, Water quality standards handbook (2d ed.): Washington, U.S. Environmental Protection Agency, EPA
– 823
– B
– 94
– 005a. [Also available at http://nepis.epa.gov/Exe/ZyPDF.cgi/20003QXV.PDF?Dockey=20003QXV.PDF .] U.S. Environmental Protection Agency, 1997, Guidelines for preparation of the comprehensive state water quality assessments (305(b) reports) and electronic updates: Washington, U.S. Environmental Protection Agency, EPA841
– B- 97
– 002A. [Also available at http://water.epa.gov/type/watersheds/monitoring/guidelines.cfm .]120 U.S. Environmental Protection Agency, 1998, Guidelines for ecological risk assessment: Washington, U.S. Environmental Protection Agency, EPA/630/R

– 95/002F, [variously paged]. [Also available at http://www.epa.gov/raf/publications/pdfs/ECOTXTBX.PDF .] U.S. Environmental Protection Agency, 1999, Protocol for developing sediment TMDLs (1st ed.): Washington, U.S. Environmental Protection Agency, EPA/841/B

– 99/004, 132 p. [Also available at http://www.epa.gov/owow/tmdl/sediment/pdf/sediment.pdf .] U.S. Environmental Protection Agency, 2000a, Nutrient criteria technical guidance manual
— Lakes and reservoirs (1st ed.): Washington, U.S. Environmental Protection Agency, EPA
– 822
– B00
– 001, [variously paged]. [Also available at http://www2.epa.gov/sites/production/files/documents/guidance_lakes.pdf .] U.S. Environmental Protection Agency, 2000b, Nutrient criteria technical guidance manual
— Rivers and Streams: Washington, U.S. Environmental Protection Agency, EPA
– 822
– B00
– 002, [variously paged]. [Also available at http://www2.epa.gov/sites/production/files/documents/guidance_rivers.pdf .] U.S. Environmental Protection Agency, 2000c, Risk characterization handbook: Washington, U.S. Environmental Protection Agency, Office of Science Policy, Office of Research and Development, EPA 100
– B
– 00
– 002, [variously paged]. [Also available at https://cluin.org/download/contaminantfocus/sediments/risk-characterization-handbook.pdf .] U.S. Environmental Protection Agency, 2001, Nutrient criteria technical guidance manual
— Estuarine and coastal marine waters: Washington, U.S. Environmental Protection Agency, Office of Water 4304, EPA
– 822
– B
– 01
– 003, [variously paged]. [Also available at http://www2.epa.gov/nutrient-policy-data/nutrientcriteria-technical-guidance-manual-estuarine-and-coastal-waters .] U.S. Environmental Protection Agency, 2002, Consolidated assessment and listing methodology
— Toward a compendium of best practices: U.S. Environmental Protection Agency, Office of Water, Office of Wetlands,121

Oceans, and Watersheds, [variously paged]. [Also available at http://water.epa.gov/type/watersheds/monitoring/calm.cfm .] U.S. Environmental Protection Agency, 2003, Guidance for 2004 assessment, listing and reporting requirements pursuant to Sections 303(d) and 305(b) of the Clean Water Act: U.S. Environmental Protection Agency, Office of Water, Office of Wetlands, Oceans, and Watersheds, Assessment and Watershed Protection Division, Watershed Branch, TMDL
– 01
– 03, 32 p. [Also available at http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/tmdl0103_index.cfm .] U.S. Environmental Protection Agency, 2005, Guidance for 2006 assessment, listing and reporting requirements pursuant to Sections 303(d), 305(b) and 314 of the Clean Water Act: U.S. Environmental Protection Agency, Office of Water, Office of Wetlands, Oceans, and Watersheds, Assessment and Watershed Protection Division, Watershed Branch, 89 p. [Also available at http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/upload/2006irg-report.pdf .] U.S. Environmental Protection Agency, 2007, An approach for using load duration curves in development of TMDLs: Washington, U.S. Environmental Protection Agency, Office of Water, Office of Wetlands, Oceans, and Watersheds, Assessment and Watershed Protection Division, Watershed Branch (4503T), EPA 841
– B
– 07
– 006. [Also available at http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/upload/2007_08_23_tmdl_duration_curve_guide _aug2007.pdf .] U.S. Environmental Protection Agency, 2008, Nutrient criteria technical guidance manual
— Wetlands: Washington, U.S. Environmental Protection Agency, Office of Water 4304T, EPA
– 822
– B
– 08
– 001 , [variously paged]. [Also available at http://water.epa.gov/scitech/swguidance/standards/upload/2008_11_24_criteria_nutrient_guidance_wet lands_wetlands-full.pdf .]122 U.S. Environmental Protection Agency, 2009, Economic analysis of final effluent limitation guidelines and standards for the construction and development industry: Washington, U.S. Environmental Protection Agenc y, Office of Water (4304T), [variously paged]. [Also available at http://water.epa.gov/scitech/wastetech/guide/construction/upload/2009_12_8_guide_construction_files _economic.pdf .] U.S. Environmental Protection Agency, 2010a, ICLUS v1.3 estimated percent impervious surface for the conterminous USA: Washington, U.S. Environmental Protection Agency, Office of Research and Development, National Center for Environmental Assessment , Global Change Research Program. U.S. Environmental Protection Agency, 2010b, Using stressor-response relationships to derive numeric nutrient criteria: Washington, U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, EPA
– 820
– S
– 10
– 001, 80 p. [Also available athttp://water.epa.gov/scitech/swguidance/standards/criteria/nutrients/upload/Using-Stressor-responseRelationships- to -Derive-Numeric-Nutrient-Criteria-PDF.pdf .] Environmental Protection Agency, 2012a, CADDIS volume 2: Sources, stressors & responses: accessed August 12, 2015, at http://www.epa.gov/caddis/ssr_flow_int.html. U.S. Environmental Protection Agency, 2012b, Stormwater: U.S. Environmental Protection Agency, Green Infrastructure Permitting and Enforcement Series, Factsheet 4, EPA 832F12015, 7 p. [Also available at http://water.epa.gov/infrastructure/greeninfrastructure/upload/EPA-Green-Infrastructure-Factsheet-4- 061212 -PJ.pdf .] U.S. Environmental Protection Agency, 2012c, The economic benefits of protecting healthy watersheds: U.S. Environmental Protection Agency, EPA 841
– N
– 12
– 004, 4 p. [Also available at http://water.epa.gov/polwaste/nps/watershed/upload/economic_benefits_factsheet3.pdf .]123 U.S. Environmental Protection Agency, 2013a, Biological assessment program review
— Assessing level of technical rigor to support water quality management: U.S. Environmental Protection Agency, Office of Water, Office of Science and Technology, EPA 820
– R
– 13
– 001, 144 p. [Also available at http://water.epa.gov/scitech/swguidance/standards/criteria/aqlife/biocriteria/upload/2013biological_ass essment.pdf .] U.S. Environmental Protection Agency, 2013b, California integrated assessment of watershed health
— A report on the status of vulnerability of watershed health in California: Washington, Prepared by The Cadmus Group, Inc. for the U.S. Environmental Protection Agency, Office of Water, Office of Wetlands, Oceans, and Watersheds, EPA 841
– R
– 14
– 003, 110 p. [Also available at http://www.epa.gov/sites/production/files/2015-11/documents/ca_hw_report_111213_0.pdf .] U.S. Environmental Protection Agency, 2013c, Our built and natural environments
— A technical review of the interactions among land use, transportation, and environmental quality: Washington, U.S. Environmental Protection Agency, Office of Sustainable Communities, EPA 231
– K
– 13
– 001. [Also available at http://www.epa.gov/smartgrowth/pdf/b-and-n/b-and-n-EPA-231K13001.pdf .] U.S. Environmental Protection Agency, 2014a, Being prepared for climate change
— A workbook for developing risk-based adaptation plans: U.S. Environmental Protection Agency, Office of Water, Climate Ready Estuaries, EPA 842
– K
– 14
– 002, 120 p. [Also available at http://www2.epa.gov/sites/production/files/2014- 09/documents/being_prepared_workbook_508.pdf .] U.S. Environmental Protection Agency, 2014b, Climate change indicators in the United States, 2014 (3d ed.): U.S. Environmental Protection Agency, EPA 430
– R
– 14
– 004, 107 p. [Also available at http://www.epa.gov/climatechange/pdfs/climateindicators-full-2014.pdf .]124U.S. Environmental Protection Agency, 2014c, Post-construction performance standards and water qualitybased requirements
— A compendium of permitting approaches: U.S. Environmental Protection Agency, Office of Water, Water Permits Division, Municipal Separate Storm Sewer Permits, EPA 833
– R
– 14
– 003, 36 p. [Also available at http://water.epa.gov/polwaste/npdes/stormwater/upload/sw_ms4_compendium.pdf .] U.S. Environmental Protection Agency, 2014d, Protection of downstream waters in water quality standards
— Frequently asked questions: U.S. Environmental Protection Agency, Office of Water, EPA
– 820
– F
– 14
– 001, 12 p. [Also available at http://water.epa.gov/scitech/swguidance/standards/library/upload/downstreamfaqs.pdf .] U.S. Environmental Protection Agency, 2014e, State, tribal, and territorial standards: accessed October 5, 2015, at http://water.epa.gov/scitech/swguidance/standards/wqslibrary/index.cfm

. U.S. Environmental Protection Agency, 2015, Connectivity of streams and wetlands to downstream waters
— A review and synthesis of the scientific evidence: Washington, U.S. Environmental Protection Agency, Office of Research and Development, EPA/600/R

– 14/475F, [variously paged]. [Also available at http://cfpub.epa.gov/ncea/cfm/recordisplay.cfm?deid=296414#Download .] U.S. Geological Survey, 2012, National hydrography dataset: U.S. Geological Survey, The National Map, accessed March 18, 2012 at http://nhd.usgs.gov/

. Vannote, R.L., Minshall, G.W., Cummins, K.W., Sedell, J.R., and Cushing, C.E., 1980, The river continuum concept: Canadian Journal of Fisheries and Aquatic Sciences, v. 37, no. 1, p. 130
– 137. [Also available at http://dx.doi.org/10.1139/f80-017 .] Vermont Department of Environmental Conservation, 2014, Vermont surface water assessment and listing methodology: Montpelier, Vt., Vermont Department of Environmental Conservation, Watershe d125

Management Division, 32 p. [Also available at http://www.vtwaterquality.org/mapp/docs/mp_assessmethod.pdf .] Vliet, M.T.H. van, and Zwolsman, J.J.G., 2008, Impact of summer droughts on the water quality of the Meuse River: Journal of Hydrology, v. 353, no. 1
– 2, p. 1
– 17. [Also available at http://dx.doi.org/10.1016/j.jhydrol.2008.01.001 .] Vörösmarty, C.J., McIntyre, P.B., Gessner, M.O., Dudgeon, David, Prusevich, A., Green, P., Glidden, S., Bunn, S.E., Sullivan, C.A., Reidy Liermann, C.A., and Davies, P.M., 2010, Global threats to human water security and river biodiversity: Nature v. 467, no. 7315, p. 555
– 561. [Also available at http://dx.doi.org/10.1038/nature09440 .] Vörösmarty, C. J., Meybeck, Michel, Fekete, Balázs, Sharma, Keshav, Green, Pamela, and Syvitski, J.P.M., 2003, Anthropogenic sediment retention
— Major global impact from registered river impoundments: Global and Planetary Change, v. 39, no. 1
– 2, p. 169
– 190. [Also available at http://dx.doi.org/10.1016/S0921- 8181(03)00023-7 .] Walker, Brian, Holling, C.S., Carpenter, S.R., and Kinzig, Ann, 2004, Resilience, adaptability and transformability in social-ecological systems: Ecology and Society, v. 9, no. 2, 9 p. [Also available at ht tp://www.ecologyandsociety.org/vol9/iss2/art5/ .] Walsh, C.J., Fletcher, T.D., and Ladson, A.R., 2005a, Stream restoration in urban catchments through redesigning stormwater systems
— Looking to the catchment to save the stream: Journal of the North American Benthological Society, v. 24, no. 3, p. 690
– 705. [Also available at http://dx.doi.org/10.1899/04- 020.1 .]126 Walsh, C.J., Roy, A.H., Feminella, J.W., Cottingham, P.D., Groffman, P.M., and Morgan, R.P., II, 2005b, The urban stream syndrome
— Current knowledge and the search for a cure: Journal of the North American Benthological Society, v. 24, no. 3, p. 706
– 723. [Also available at http://dx.doi.org/10.1899/04- 028 .1 .] Wang, Lizhu, Infante, Dana, Lyons, John, Stewart, Jana, and Cooper, Arthur, 2011, Effects of dams in river networks on fish assemblages in non-impoundment sections of rivers in Michigan and Wisconsin, USA: River Research and Applications, v. 27, no. 4, p. 473
– 487. [Also available at http://dx.doi.org/10.1002.rra.1356 .] Wang, Lizhu, Seelbach, P.W., and Hughes, R.M., 2006, Introduction to landscape influences on stream habitats and biological assemblages: American Fisheries Society Symposium, v. 48, p. 1
– 23. [Also available at http://www.researchgate.net/publication/228879323_Landscape_Influences_on_Stream_Habitats_and_B iological_Assemblages .] Ward, J.V., 1989, The four-dimensional nature of lotic ecosystems: Journal of the North American Benthological Society, v. 8, no. 1, p. 2
– 8. [Also available at http://www.jstor.org/stable/1467397 .] Ward, J.V., and Stanford, J.A., 1982, Thermal responses in the evolutionary ecology of aquatic insects: Annual Review of Entomology, v. 27, no. 1, p. 97
– 117. [Also available at http://dx.doi.org/10.1146/annurev.en.27.010182.000525 .] Ward J.V., and Stanford, J.A., 1987, The ecology of regulated streams
— Past accomplishments and directions for future research, section V of Craig, J.F., and Kemper, J.B., Regulated streams
— Advances in ecology: New York, Plenum Press, p. 391
– 409. [Also available at http://dx.doi.org/10.1007/978-1-4684-5392-8_28 .] Ward, J.V., and Stanford, J.A., 1995, The serial discontinuity concept
— Extending the model to floodplain rivers: Regulated Rivers
— Research and Management, v. 10, no. 2
– 4, p. 159
– 168. [Also available at http://dx.doi.org/10.1002/rrr.3450100211 .]127 Watts, R.J., Richter, B.D., Opperman, J.J., and Bowmer, K.H., 2011, Dam reoperation in an era of climate change: Marine and Freshwater Research, v. 62, no. 3, p. 321
– 327. [Also available at http://dx.doi.org/10.1071/MF10047 .] Webb, J.A., Miller, K.A., King, E.L., Little, S.C. de, Stewardson, M.J., Zimmerman, J.K.H., and Poff, N.L., 2013, Squeezing the most out of existing literature
— A systematic re-analysis of published evidence on ecological responses to altered flows: Freshwater Biology, v. 58, no 12, p. 2439
– 2451. [Also available at http://dx.doi.org/10.1111/fwb.12234 .] Wagener, T., Sivapalan, M., Troch, P., Woods R., 2007, Catchment classification and hydrologic similarity: Geography Compass, v. 1, no. 4, p. 901
– 931. [Also available at http://dx.doi.org/10.1111/j.1749- 8198.2007.00039.x ] Wehrly, K.E., Wiley, M.J., and Seelbach, P.W., 2003, Classifying regional variation in thermal regime based on stream fish community patterns: Transactions of the American Fisheries Society, v. 132, no. 1, p. 18
– 38. [Also available at http://dx.doi.org/10.1577/1548-8659(2003)132<0018:CRVITR>2.0.CO;2 .] Wehrly, K.E., Wiley, M.J., and Seelbach, P.W., 2006, Influence of landscape features on summer water temperatures in lower Michigan streams, in Hughes, R.M., Wang, Lizhu, and Seelbach, P.W., Landscape influences on stream habitats and biological assemblages
— Proceedings of the symposium on Influences of Landscape on Stream Habitat and Biological Communities held in Madison, Wisconsin, USA, 25
– 26 August 2004: American Fisheries Society, Volume 48 of American Fisheries Society symposium, p. 113
– 127. Weitkamp, D.E., and Katz, Max, 1980, A review of dissolved gas supersaturation literature: Transactions of the American Fisheries Society, v. 109, no. 6, p. 659
– 702. [Also available at http://dx.doi.org/10.1577/1548- 86 59(1980)109%3C659:ARODGS%3E2.0.CO;2 .]128 Wenger, S.J., Peterson, J.T., Freeman, M.C., Freeman, B.J., and Homans, D.D., 2008, Stream fish occurrence in response to impervious cover, historic land use, and hydrogeomorphic factors: Canadian Journal of Fisheries and Aquatic Sciences, v. 65, no. 7, p. 1250
– 1264. [Also available at http://dx.doi.org/10.1139/F08-046 .] Wiley, M.J., Kohler, S.L., and Seelbach, P.W., 1997, Reconciling landscape and local views of aquatic communities
— Lessons from Michigan trout streams: Freshwater Biology, v. 37, no. 1, p. 133
– 148. [Also available at http://dx.doi.org/10.1046/j.1365-2427.1997.00152.x .] Wills, T.C., Baker, E.A., Nuhfer, A.J., and Zorn, T.G., 2006, Response of the benthic macroinvertebrate community in a northern Michigan stream to reduced summer streamflows: River Research and Applications, v. 22, no. 7, p. 819
– 836. [Also available at http://dx.doi.org/10.1002/rra.938 .] Winter, T.C., Harvey, J.W., Franke, O.L., and Alley, W.M., 1998, Ground water and surface water a single resource: U.S. Geological Survey Circular 1139, 79 p. [Also available at http://pubs.usgs.gov/circ/circ1139/ .] Zarriello, P.J., and Ries, K.G., III, 2000, A precipitation runoff model for analysis of the effects of waterwithdrawals on streamflow, Ipswich River Basin, Massachusetts: U.S. Geological Survey Water ResourcesInvestigations Report 00
– 4029, 107 p. [Also available at http://pubs.usgs.gov/wri/wri004029/ .] Zimmerman, J.K.H, Letcher, B.H., Nislow, K.H., Lutz, K.A., and Magilligan, F.J., 2010, Determining the effects of dams on subdaily variation in river flows at a whole-basin scale: River Research and Applications, v. 26, no. 10, p. 1246
– 1260. [Also available at http://dx.doi.org/10.1002/rra.1324 .] Zorn, T.G., Seelbach, P.W., Rutherford, E.S., Wills, T.C., Cheng, Su-Ting, and Wiley, M.J., 2008, A regional-scale habitat suitability model to assess the effects of flow reduction on fish assemblages in Michigan streams: Ann Arbor, Mich., State of Michigan Department of Natural Resources, Fisheries Division Research Report129

2089, accessed January 2011 at http://www.michigandnr.com/PUBLICATIONS/PDFS/ifr/ifrlibra/Research/reports/2089/RR2089.pdf

. Zorn, T.G., Seelbach, P.W., and Rutherford, E.S., 2012, A regional-scale habitat suitability model to assess the effects of flow reduction on fish assemblages in Michigan streams: Journal of the American Water Resources Association, v. 48, no. 5, p. 871
– 895. [Also available at http://dx.doi.org/10.1111/j.1752- 1688.2012.00656.x .] Zwolsman, J.J.G., and Bokhoven, A.J. van, 2007, Impact of summer droughts on water quality of the Rhine River
— A preview of climate change?: IWA Publishing, Water Science and Technology, v. 56, no. 4, p. 45
– 55. [Also available at http://dx.doi.org/10.2166/wst.2007.535 .]130 

### 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 chemi cal, 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 of fish, shellfish and wildlife and provides for recreation in and on the water , " wherever attainable (Section 101(a)(2)). Section 303(c)(1) 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).131 A1. Designated Uses and Existing Uses EPA’s regulatory provisions regardi ng 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 s tatements 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 131.10(b)). 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:132 



 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 of fish, 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; and133  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)(1)). 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 a nd 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.134 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.135 

### App endix B. Legal Background and Relevant Case L aw 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.1”) , 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.1 , 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’ conce rn 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 FERClicensed 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.136 I n S.D. Warren Co. v. Maine Board of Environmental Protection (“S.D.Warren”) 547 U.S. 370, 385 (2006), the Supreme Cour t 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 of fish, 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- in duced 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.1, 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 Energy137 Regulatory Commission (FERC), 495 U.S. 490, 498 (1990), construing an analogous provision of the Federal Power Act, where the Court ex plained 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 721.138 

### 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 not139 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 climatechange 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 ).140 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 assessmen ts: exposure, sensitivity, and adaptive capacity. A n in

- depth discussion of these components is available in Glick and others (2011) and Poff and others (2012). Generalized case examples available in Glick and others (2011) demonstrate assessment approache s for climate vulnerability assessments across various ecosystems and species, both aquatic and terrestrial. E xamples that focus on watershed vulnerability and aquatic resources are included in Furniss and others (2013) . An additional resource ( U.S. E nvironmental P rotection A gency , 2014 a ) 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 (Glick and others, 2011). Results of c limate model simulations such as regional climate projections or downscaled climate projections, though accompanied by unce rtainty, 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
- ring s ). 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 o f 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) (Glick 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. Fo r example, the hydrology in a snowmelt

- dominated watershed (and the ecosystem that is adapted to this hydrologic regime)141 may be more sensitive to climate changes that reduce the proportion of precipitation from snow than that in a rainfall

- dominated waters hed (see the Beechie and others [ 2013 ] example in B ox 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 detect ed 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 (Glick and others, 2011). It is also a subset of system resilience and can help managers assess vulnerability for u se 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 , reduc ing fragmentation of a water body , thereby prevent ing mobility to more suitable conditions , such as cooler temperatures) (Glick and others, 2011). The Pacific Northwest salmon restoration case study ( B ox 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
.142 Box J . California’s Climate - Change Vulnerability Index The goal of the C alifornia Integrated Assessment of Watershed Health (U.S. E nvironmental P rotection A gency, 2013b) was to identify and better protect healthy watersheds by integrating data and making them available to planning agencies for improved coordination of monitori ng and prioritization of protection efforts. The primary partners included the U.S. E nvironmental P rotection A gency (EPA) and the Healthy Streams Partnership (HSP), an interagency workgroup of the California Water Monitoring Council. The assessment partner s 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 mult iple 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 i s a composite of four vulnerabili ty 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, i s composed of seven component metrics of estimated climate

- change parameters using proj ections 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 partner s 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 pri oritize protection opportunities.143 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

- 1) illustrate the climate exposure primarily in terms of its effects on temperature and hydrolog y - 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, surfa ce runoff, and base flow.
Th is screening

- level assessment is an instructive example that may help inform the protect ion of healthy watersheds based on climate

- change vulnerability. However, the assessment combined other vulnerability indices
— land cover, w ater 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 no t onl y sought to develop priorities based on ecosystem vulnerability, but also a comprehensive understanding of the overall status of the aquatic ecosystem. For t he entire assessment , stream condition, watershed health, and vulnerability were considered
. For more information, see U.S. E nvironmental P rotection A gency ( 2013b ) ( http://www.epa.gov/sites/production/files/2015-11/documents/ca_hw_report_111213_0.pdf ).144 Figure C - 1 . (a) C omposite results of the vulnerability assessment illustrat ing the combined changes in the seven component metrics of projected climate - change parameters , three of which a re shown : (b) surface runoff, (c) minimum temperature , and (d) snowpack. ( A dditional component metrics including projected change in precipitation, mean temperature, maximum temperature, and baseflow are shown in U.S. E nvironmental P rotection A gency [ 2013b ] , available at http://water.epa.gov/polwaste/nps/watershed/integrative_assessments.cfm .)145 Box K . Addressing Regional Climate - Change Effects on Salmon Habitat in the Pacific Northwest : E xamples 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 clima te 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 recov ery 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 u sing the variable infiltration capacity (VIC) model, the inputs were use d 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 an d 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 temperat u re 2
– 6 o C [ degrees Celsius ] higher ). Snowmelt

- dominated hydrologic regimes across the region almost entirely disappeared by the 2070
– 99 time period , and transition al (rain

- snow mix) hydrologic regime s contracted substantially as well. B y the final 2070
–146 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 k nown 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

- fl ow 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 understand ing of potential vulnerability to climate change. Thi s knowledge can help inform management plans to prioritize restoration practices that are more likely to be effective under projected climate scenarios.147 . Figure C - 2 . Diagram showing e ffect of c limate 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). Th ese 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 tribes148 ca n 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 relativeeffects, which may help in identifying and ranking adaptive management actions in later steps. In a resourceconstrained 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.149

Table C1. Incorporating climate-change considerations in to the framework for quantifying flow targets.
Framework c omponent Potential c limate - c hange c onsiderations ( 1) Formally l ink n arrative

c riteria to b iological g oals May not be applicable to S tep 1 unless climate changes affect biological expectations.

( 2) Identify t arget s treams Consider which elements, if any, in the classification of target streams are climate dependent.

( 3) Conduct l iterature

r eview Consider all potential climate

- change

- related effect s 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 com ponents 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 c onceptual

m odels Include climate change i n 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

- r elated 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: c onsequences (low, med ium , high) ; likelihood (low, med ium , high) ; spatial extent (site, watershed, region) ; time until problem begins (decades, within next 15 to 30 years, already occurring/likely occurring ).

Consider s ensitivity: 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 , wh ereas south

- facing asp ect or low elevations may increase sensitivity)
.150

Framework c omponent Potential c limate - c hange c onsiderations

( 6) Identify b iological and f low i ndicators Identify which biological and flow indicators may be most affected by climate change . Rate them by considering the qualitative categories previously mentioned (c onsequence, likelihood, spatial extent, time until problem begins). ( 7) Develop q ualitative or q uantitative f low

- e cology

m odels Climate change considerations may not be applicable to S tep 7.

( 8) Identify a cceptable b iological c ondition g oals/ effects l evels Compare range of potential likely climate changes to the potential flow targets.

( 9) Select c andidate f low
t argets 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, e valuate, and p eriodically r efine f low
t argets 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 inform ation? 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 effects151of climate change. Climate-change vulnerability assessments can help managers strategically address waterresource 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, wh ereas 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.



### Refe rences Cited

B eechie, T.J., Imaki, H., Greene, J., Wade, A., Wu, H., Pess, G., Roni, P., Kimball, J., Stanford, J., Kiffney, P., and Mantua, N., 2013, Restoring salmon habitat for a changing climate: River and Research Applications, v. 29, no. 8, p. 939
– 960. [Also available at http://dx.doi.org/10.1002/rra.2590 .] Dawson, T.P., Jackson, S.T., House, J.I., Prentice, I.C., and Macde, G.M., 2011, Beyond predictions
— Biodiversity conservation in a changing climate: Science, v. 332, no. 53, p. 53
– 58. [Also available at http://dx.doi.org/10.1126/science.1200303 .] Dudgeon, David, Arthington, A.H., Gessner, M.O., Kawabata, Zen-Ichiro, Knowler, D.J., Lévêque, Christian, Naiman, R.J., Prieur-Richard, Anne-Hélène, Soto, Doris, Stiassny, M.L.J., and Sullivan, C.A., 2006, Freshwater biodiversity
— Importance, threats, status and conservation challenges: Biological Reviews, v. 81, no. 2, p. 163
– 182. [Also available at http://dx.doi.org/10.1017/S1464793105006950 .]152 Field, C.B., Barros, V.R., Doken, D.J., Mach, K.J., Mastrandrea, M.D., Bilir, T.E., Chatterjee, Monalisa, Ebi, K.L., Estrada, Y.O., Genova, R.C., Girma, Betlhelm, Kissel, E.S., Levy, A.N., MacCracken, Sandy, Mastrandrea, P.R., and White, L.L., eds., 2014, Climate change 2014 impacts, adaptation, and vulnerability
— Part A
— Global and sectoral aspects
— Working group II contribution to the fifth assessment report of the Intergovernmental Panel on Climate Change: Cambridge, United Kingdom, and New York, Cambridge University Press, 1,132 p. [Also available at https://ipcc-wg2.gov/AR5/images/uploads/WGIIAR5- PartA_FINAL.pdf .] Furniss, M.J., Roby, K.B., Cenderelli, Dan, Chatel, John, Clifton, C.F., Clingenpeel, Alan, Hays, P.E., Higgins, Dale, Hodges, Ken, Howe, Carol, Jungst, Laura, Louie, Joan, Mai, Christine, Martinez, Ralph, Overton, Kerry, Staab, B.P., Steinke, Rory, and Weinhold, Mark, 2013, Assessing the vulnerability of watersheds to climate change
— Results of national forest watershed vulnerability pilot assessments: Portland, Oreg., General Technical Report PNW
– GTR
– 884, U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 32 p., plus appendix. [Also available at http://www.treesearch.fs.fed.us/pubs/43898 .] Georgakakos, Aris, Fleming, Paul, Dettinger, Michael, Peters-Lidard, Christa, Richmond, T.C., Reckhow, Ken, White, Kathleen, and Yates, David, 2014, Chapter 3 water resources, in Melillo, J.M., Richmond, T.C., and Yohe, G.W., Climate change impacts in the United States: The Third National Climate Assessment, U.S. Global Change Research Program, p. 69
– 112. [Also available at http://nca2014.globalchange.gov/report/sectors/water .] Glick, Patty, Stein, B.A., and Edelson, N.A., eds., 2011, Scanning the conservation horizon
— A guide to climate change vulnerability assessment: Washington, National Wildlife Federation, 168 p. [Also available athttp://www.nwf.org/~/media/pdfs/global-warming/climate-smartconservation/nwfscanningtheconservationhorizonfinal92311.ashx .]153 Intergovernmental Panel on Climate Change, 2007, Climate change 2007
— Synthesis report. Contribution of working groups I, II and III to the fourth assessment report of the Intergovernmental Panel on Climate Change (Core Writing Team, Pachauri, R.K., and Reisinger, Andy, eds.): Geneva, Switzerland, Intergovernmental Panel on Climate Change, 104 p. [Also available at http://www.ipcc.ch/pdf/assessmentreport/ar4/syr/ar4_syr_full_report.pdf .] Isaak, D J., and Rieman, B.E., 2013, Stream isotherm shifts from climate change and implications for distributions of ectothermic organisms: Global Change Biology, v. 19, no. 3, p. 742
– 751, http://dx.doi.org/10.1111/gcb.12073

. Karl, T.R., Melillo, J.M., and Peterson, T.C., eds., 2009, Global climate change impacts in the United States: New York, Cambridge University Press. [Also available at http://downloads.globalchange.gov/usimpacts/pdfs/climate-impacts-report.pdf .] Milly, P.C.D., Betancourt, Julio, Falkenmark, Malin, Hirsch, R.M., Kundzewicz, Z.W., Lettenmaier, D.P., and Stouffer, R.J., 2008, Stationarity is dead
— Wither water management?: Science, v. 319, no. 5863, p. 573
– 574. [Also available at http://dx.doi.org/10.1126/science.1151915 .] Palmer, M.A., and Febria, C.M., 2012, The heartbeat of ecosystems: Science, v. 336, no. 6087, p. 1393
– 1394. [Also available at http://dx.doi.org/10.1126/science.1223250 .] Palmer, M.A., Lettenmaier, D.P., Poff, N.L., Postel, S.L., Richter, B.D., and Warner, Richard, 2009, Climate change and river ecosystems
— Protection and adaptation options: Environmental Management, v. 44, no. 6, p. 1053
– 1068. [Also available at http://dx.doi.org/10.1007/s00267- 009

- 932 9-1 .] Palmer, M.A., Reidy Liermann, C.A., Nilsson, Christer, Florke, Martina, Alcamo, Joseph, Land, P.S., and Bond, Nick, 2008, Climate change and the world’s river basins— Anticipating management options: Frontiers in Ecology and the Environment, v. 6, no. 2, p. 81
– 89. [Also available at http://dx.doi.org/10.1890/060148 .]154 Pittock, Jamie, and Finlayson, C.M., 2011, Australia’s Murray

- Darling Basin
— Freshwater ecosystem conservation options in an era of climate change: Marine and Freshwater Research, v. 62, no. 3, p. 232
– 243. [Also available at http://dx.doi.org/10.1071/MF09319 .] Poff, N.L., Olden, J.D., and Strayer, D.L., 2012, Climate change and freshwater fauna extinction risk, chap. 17 of Hannah, Lee, ed., 2012, Saving a million species
— Extinction risk from climate change: Washington, Island Press, p. 309
– 336. Turner, B.L., II, Kasperson, R.E., Matson, P.A., McCarthy, J.J., Corell, R.W., Christensen, Lindsey, E ckley, Noelle, Kasperson, J.X., Luers, Amy, Martello, M.L., Polsky, Collin, Pulsipher, Alexander, and Schiller, Andrew, 2003, A framework for vulnerability analysis in sustainability science: Proceedings of the National Academy of Sciences of the United St ates of America, v. 100, no. 14, p. 8074
– 8079. [Also available at http://dx.doi.org/10.1073/pnas.1231335100 .] U.S. Environmental Protection Agency, 2013b, California integrated assessment of watershed health
— A report on the status of vulnerability of watershed health in California: Washington, Prepared by The Cadmus Group, Inc. for the U.S. Environmental Protectio n Agency, Office of Water, Office of Wetlands, Oceans, and Watersheds, EPA 841
– R
– 14
– 003, 110 p. [Also available at http://www.epa.gov/sites/production/fil es/2015

- 11/documents/ca_hw_report_111213_0.pdf .] U.S. Environmental Protection Agency, 2014a, Being prepared for climate change
— A workbook for developing risk

- based adaptation plans: U.S. Environmental Protection Agency, Office of Water, Climate Ready Est uaries, EPA 842
– K
– 14
– 002, 120 p. [Also available at http://www2.epa.gov/sites/production/files/2014

- 09/documents/being_prepared_workbook_508.pdf .] U.S. Environmental Protection Agency, 2014b, Climate change indicators in the United States, 2014 (3d ed.): U.S. Environmental Protection Agency, EPA 430
– R
– 14
– 004, 107 p. [Also available at http://www.epa.gov/climatechange/pdfs/climateindicators

- full

- 2014.pdf .]155 Walker, Brian, Holling, C.S., Carpenter, S.R., and Kinzig, Ann, 2004, Resilience, adaptability and transformability in social

- ecological systems: Ecology and Societ y, v. 9, no. 2, 9 p. [Also available at http://www.ecologyandsociety.org/vol9/iss2/art5/ .]