i

Draft EPA-USGS Technical Report: Protecting 

Aquatic Life from Effects of Hydrologic Alteration 

EPA Report 822–P–15–002

USGS Scientific Investigations Report 2015–5160

U.S. Department of the Interior 

U.S. Geological Survey 

 

 

United States

Environmental Protection 

Agency
ii

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 Novak1, Jonathan G. Kennen2, Ralph W. Abele3, Carol F. Baschon4, Daren M. Carlisle5, Laura Dlugolecki6, Joe 

E. Flotermersch7, Peter Ford8, Jamie Fowler9, Rose Galer10, Lisa P. Gordon11, Susan N. Hansen12, Bruce Herbold13, 

Thomas E. Johnson14, John M. Johnston15, Christopher P. Konrad16, Beth Leamond17, and Paul W. Seelbach18. 

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

Office of Water, Office of Science and Technology, Washington, D.C.) 

2. U.S. Geological Survey (USGS), New Jersey Water Science Center, Lawrenceville, New Jersey 

3. EPA, Region 1, Office of Ecosystem Protection, Boston, Massachusetts 

4. EPA, Region 4, Office of Regional Counsel, Atlanta, Georgia 

5. USGS, Kansas Water Science Center, Lawrence, Kansas 

6. Former Oak Ridge Institute for Science and Education (ORISE) participant in EPA Office of Water, Office of 

Wetlands, Oceans and Watersheds, Washington, D.C. 

7. EPA, Office of Research and Development, National Exposure Research Lab, Cincinnati, Ohio 

8. EPA, Office of General Counsel, Washington, D.C. 

9. EPA, Office of Water, Office of Wetlands, Oceans and Watersheds, Washington, D.C. 

10. Former ORISE participant in EPA Office of Water, Office of Science and Technology Standards and Health 

Protection Program, Washington, D.C. 

11. EPA, Region 4, Water Quality Standards, Atlanta, Georgia 

12. EPA, Region 4, Office of Regional Counsel, Atlanta, Georgia 

13. EPA, Region 9 (retired), San Francisco, California 

14. EPA, Office of Research and Development, National Center for Environmental Assessment, Arlington, 

Virginia 

15. EPA, Office of Research and Development, National Exposure Research Lab, Athens, Georgia 

16. USGS Geological Survey, Washington Water Science Center, Tacoma, Washington 

17. EPA Office of Water (retired), Office of Science and Technology, Washington, D.C. 

18. USGS Geological Survey, Great Lakes Science Center, Ann Arbor, Michigan 

Jointly prepared by the U.S. Environmental Protection Agency and U.S. Department of the Interior, U.S. 

Geological Survey 

EPA Report 822–P–15–002

USGS Scientific Investigations Report 2015–5160

U.S. Department of the Interior 

U.S. Geological Survey 

 United States

Environmental Protection 

Agency 

 

 
iv 

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 (m2) 0.00025 Acre

square kilometer (km2) 0.3861 square mile (mi2)

hectare (ha) 2.4710 Acre

Volume

cubic meter (m3) 35.3147 cubic foot (ft3)

cubic meter (m3) 0.00026 million gallon (gal)

Flow rate

cubic meter per second per square kilometer 

[(m3/s)/km2]

91.47 cubic foot per second per square mile [(ft3/s)/mi2]

cubic meter per second (m3/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 Best Management Practice

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 integrated reporting

MS4 Municipal Separate Storm Sewer System

NPDES National Pollutant Discharge Elimination System

TMDL Total Maximum Daily Load

USDA U.S. Department of Agriculture

USGS U.S. Geological Survey

WQS water quality standards
1 

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)........................................................................................ 28
2 

4.3.6 Climate Change .................................................................................................................... 30

4.4 Physical and Chemical Effects of Flow Alteration ................................................................... 34

4.4.1 Effects on Geomorphology .................................................................................................. 34

4.4.2 Effects on Connectivity ........................................................................................................ 35

4.4.3 Effects on Water Temperature and Chemistry .................................................................... 36

4.5 Biological Responses to Flow Alteration ................................................................................. 37

5 Examples of State and Federal Actions to Protect Aquatic Life from Altered Flows ...................... 39

5.1 Narrative Criteria in State and Tribal Water Quality Standards ............................................ 42

5.2 Monitoring, Assessing, and Identifying Waters Impaired as a Result of Flow Alteration ...... 49

5.3 Development of Total Maximum Daily Loads......................................................................... 55

5.4 Consideration of Flow Alteration in Issuing 401 Certifications .............................................. 56

5.5 Consideration of Flow Alteration in Issuing 404 Permits ....................................................... 57

5.6 Consideration of Flow Alteration in Issuing National Pollutant Discharge Elimination System 

(402) Permits ........................................................................................................................... 59

5.7 Further considerations ............................................................................................................ 63

6 Framework for Quantifying Flow Targets to Protect Aquatic Life ................................................... 65

6.1 Link Narrative Criteria to Biological Goals and Assessment Endpoints .................................. 68

6.2 Identify Target Streams........................................................................................................... 69

6.3 Conduct Literature Review ..................................................................................................... 71

6.4 Develop Conceptual Models ................................................................................................... 72
3 

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. ................................. 12
4 

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).. ........................................................................................................... 73
5 

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.149
6 

Boxes 

Box A. Goals of the Clean Water Act ........................................................................................................ 10

Box B. Ecological Risk Assessment ............................................................................................................ 15

Box C. Addressing Flow Regime Components .......................................................................................... 48

Box D. Procedures for Capturing Flow Information in the State of Texas ................................................ 52

Box E. Vermont Addresses Hydrologically Altered Waters ...................................................................... 55

Box F. 401 Certifications, Sufficient Flow, and Water quality Standards ................................................. 57

Box G. Stormwater and West Virginia Department of Environmental Protection (DEP) Municipal 

Separate Storm Sewer Systems (MS4) Permit Language ................................................................... 63

Box H. Fundamentals of Stream Classification ......................................................................................... 70

Box I. Components of Climate-Change Vulnerability ............................................................................. 140

Box J. California’s Climate-Change Vulnerability Index .......................................................................... 142

Box K. Addressing Regional Climate-Change Effects on Salmon Habitat in the Pacific Northwest: 

Examples for Prioritizing Restoration Activities ............................................................................... 145
7 

1 Abstract 

The U.S. Congress enacted the Clean Water Act (CWA) in 1972 to "restore and maintain the chemical, physical 

and biological integrity of the Nation’s waters" (Section 101(a)). The natural flow regime, defined as the 

characteristic pattern of flow magnitude, timing, duration, frequency, and rate of change, plays a critical role 

in supporting the chemical, physical, and biological integrity of streams and rivers and the services they 

provide. Human-induced alteration of the natural flow regime can degrade a stream’s physical and chemical 

properties, leading to loss of aquatic life and reduced aquatic biodiversity. Protecting aquatic life from the 

effects of flow alteration involves maintaining multiple components of the flow regime within their typical 

range of variation. This report was developed to serve as a source of information for states, tribes, and 

territories on (1) the natural flow regime and potential effects of flow alteration on aquatic life; (2) CWA 

programs that can be used to support the natural flow regime and maintain the health of aquatic biota; and 

(3) a flexible, nonprescriptive framework to quantify targets for flow regime components that are protective 

of aquatic life. 

Anthropogenic landscape change and water management activities are modifying flood flows, base flows, 

peak-flow timing, and other flow characteristics in streams and rivers throughout the United States. Under 

natural conditions, a stream’s flow regime is determined by hydrologic properties at two scales, the upstream 

drainage area (catchment) and the local, reach scale. At the catchment scale, climate determines patterns of 

water and energy input over time, whereas physical characteristics like soils, geology, and topography 

determine pathways, rates of runoff, and routing through the stream network. Reach-scale factors such as 

local groundwater dynamics further influence natural flow regime characteristics. Human activities that alter 

the natural flow regime also occur at both the catchment and reach scales and include impoundments, 

channelization, diversions, groundwater pumping, wastewater discharges, urban development, thermoelectric 

power generation, and agricultural practices. Many of these activities alter hydrologic processes like 
8 

infiltration, groundwater recharge, channel storage, or routing and lead to flow conditions outside the natural 

range of variation. Others directly add or remove water from a stream such that flows are uncommonly high 

or low over long periods of time. Occurring in conjunction with these activities is climate change. Climate 

trends observed in recent decades and future projections (for example, rising ambient air temperatures, 

increasing frequency of heavy precipitation events, reductions in the thickness of snow pack and ice) may 

magnify the effects of other anthropogenic processes on the natural flow regime. 

Alteration of the natural flow regime can have cascading effects on the physical, chemical, and biological 

properties of riverine ecosystems. Effects on physical properties include altered channel geomorphology 

(channel incision, widening, bed armoring, etc.), reduced (or augmented) riparian and flood-plain connectivity, 

and reduced (or augmented) longitudinal (upstream-downstream) and vertical (surface water/groundwater) 

connectivity. Effects on water quality can also result from altered flow magnitudes. For example, salinity, 

sedimentation, and water temperature can increase when flow volumes are reduced, whereas erosion and 

sediment transport can increase with amplified flow volumes. These changes to a stream can in turn lead to 

the degradation of aquatic life as a result of the loss and disconnection of high-quality habitat. Furthermore, 

altered flows can fail to provide the cues needed for aquatic species to complete their life cycles and can 

encourage the invasion and establishment of non-native aquatic species. The ability of a water body to 

support aquatic life is tied to the maintenance of key flow-regime components. 

CWA programs can incorporate strategies to protect water quality and aquatic life from the potentially 

harmful effects of flow alteration. Water quality standards programs can adopt criteria for flow to protect 

aquatic life designated uses. As of 2014, 10 states and several tribes had adopted a narrative form of flow 

criteria in their water quality standards. Water quality monitoring and assessment programs can collect flow 

data and develop methods to evaluate whether flow alteration is contributing to water quality impairments. 

National Pollutant Discharge Elimination System (NPDES) permitting programs can incorporate hydrologic and 
9 

flow regime considerations into permit conditions. For example, several states and the U.S. Environmental 

Protection Agency (EPA) have defined numeric post-construction standards in permits for municipal separate 

storm sewer systems (MS4s) that require the treatment or retention of a specified volume of runoff to be 

managed on site. In addition, CWA Section 404 permit programs, which authorize activities such as dam 

construction, can consider whether a proposed project would alter the natural flow regime and adversely 

affect aquatic life. These activities are subject to CWA Section 401 certification, in which a state verifies that a 

project requiring a Federal license or permit will not violate State water quality standards. A state can include 

flow as a condition for Section 401 certification even if flow criteria are not yet adopted in State water quality 

standards. 

Efforts to implement strategies to protect aquatic life from flow alteration will be most effective if numeric 

targets are identified for flow-regime components that equate to intact and healthy aquatic communities. This 

report presents a flexible framework to quantify flow targets that incorporates EPA Guidelines for Ecological 

Risk Assessment (ERA) and concepts from contemporary environmental flow literature. The framework 

consists of eight steps that begins with identifying biological goals and assessment endpoints and ends with an 

evaluation of effects to aquatic life under varying degrees of flow alteration. The framework does not 

prescribe any particular analytical approach (for example, statistical or mechanistic modeling methodology), 

but rather focuses on the process and information needed to evaluate relations between flow and aquatic life 

and to select numeric flow targets. 

2 Introduction 

Healthy aquatic ecosystems provide an array of services to individuals and society, including clean drinking 

water, irrigation supplies, and recreational opportunities (U.S. Environmental Protection Agency, 2012c). 

Sound and sustainable management of aquatic ecosystems is an integral part of managing water resources to 

meet the needs of society and the goals of the Clean Water Act (CWA) (see Box A). 
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 chemical, physical and biological integrity of the Nation’s waters" (Section

101(a)). In addition, the CWA establishes as an interim goal "water quality which provides for the protection 

and propagation of fish, shellfish and wildlife and provides for recreation in and on the water," wherever 

attainable (Section 101(a)(2)).

Freshwater aquatic ecosystems are the most altered ecosystems globally; they exhibit declines in biodiversity 

that far outpace those of terrestrial or marine ecosystems (Dudgeon and others, 2006; Strayer and Dudgeon, 

2010). Although discharge of contaminants ranks as a top threat to aquatic biodiversity, other important 

sources of stress include urbanization, agriculture practices, and engineered structures used for 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). 

Today’s water-resource managers face a universal challenge: balancing the needs of a growing human 

population with the protection of natural hydrologic regimes to support aquatic life, ecosystem health, and 

services of crucial importance to society (Annear and others, 2004; Postel and Richter, 2003). Further 

complicating this challenge are expected changes to historic hydrologic conditions as a result of climate 

change, which add complexity to the task of estimating acceptable levels of hydrologic variation (Milly and 

others, 2008). 

The natural flow regime, defined as the characteristic pattern of flow magnitude, timing, duration, frequency, 

and rate of change, plays a critical role in supporting the ecological integrity of streams and rivers and the 

services they provide (Figure 1). Human-induced alteration of the natural flow regime can degrade the 

physical, chemical, and biological properties of a water body (Annear and others, 2004; Bunn and Arthington,
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 from decreased dilution, increased temperatures, or a 

decrease in dissolved-oxygen concentration. Lower flows can reduce sensitive taxa diversity and abundance, 

alter life cycles, cause mortality in aquatic life, and promote the expansion of invasive plants and animals 

(Bunn and Arthington, 2002; Poff and Zimmerman, 2010). 

Flow alteration can be a primary contributor to the impairment of water bodies that are designated to support 

aquatic life. Addressing flow conditions by using CWA mechanisms such as water quality standards (WQS) can 

contribute to a comprehensive approach to managing and protecting water quality, improving aquatic 

restoration efforts, maintaining designated uses (for example, aquatic life, cold-water or warm-water fisheries, 

economically or recreationally important aquatic species), and satisfying antidegradation requirements. As the 

science of flow ecology has uncovered aquatic life needs across the full spectrum of the flow regime (base 

flows, high flows, etc.), water-resource managers are starting to recognize that protecting aquatic life from the 

adverse effects of flow alteration involves maintaining multiple components of the flow regime within their 

typical range of variation. This perspective requires an understanding of natural flow variability over space and 

time and the many ways in which biota respond to varied flow conditions. 
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 such as recreation or 

drinking water, although they also can be affected by hydrologic alteration and can benefit from measures to 

maintain hydrologic conditions. 

This report was developed by the U.S. Environmental Protection Agency (EPA) in collaboration with the U.S. 

Geological Survey (USGS) in response to evidence that flow alteration has adversely affected the biological 

integrity of water bodies throughout the United States (Bunn and Arthington, 2002; Carlisle and others, 2010; 

Poff and Zimmerman, 2010). The information presented is drawn from the Guidelines for Ecological Risk 

Assessment (ERA) (U.S. Environmental Protection Agency, 1998), relevant environmental flows literature (for 

example, Bunn and Arthington, 2002; Petts, 2009; Poff and Zimmerman, 2010), and the experience of states 

and tribes that have adopted narrative flow criteria to protect aquatic life uses in their waters. 

3.2 Overview 

Section 4 is a summary of available scientific information about the effects of flow alteration on ecosystems, 

including the role of climate change, which can exacerbate the stresses that result from flow alteration. 

Section 5 is an overview of CWA programs that are applicable to maintaining hydrologic conditions that 

protect aquatic life. It provides state and tribal examples of flow considerations and management approaches 

that promote the sustainability of aquatic ecosystems, including a review of existing state and tribal narrative 
14

flow criteria. Section 6 presents concepts, tools, and examples that may be useful for translating narrative flow 

criteria into quantitative flow targets. It includes examples of quantification to support states, authorized 

tribes, and territories (hereinafter, “states”) that wish to adopt flow criteria to protect aquatic life designated 

uses in their WQS regulations. It also describes the potential role of narrative criteria as a tool to manage flow 

to restore and maintain aquatic ecosystems. Appendix A is general review of the CWA and WQS, and Appendix 

B provides a brief overview of the legal background and relevant case law relating to flow protection for 

support of aquatic life designated uses. 

Climate change is one category among a range of stressors that is likely to increase the vulnerability of rivers 

and streams to flow alteration and affect the ecosystem services they provide (see Section 4.3.6). Given the 

inherent difficulties associated with climate change assessment, many natural-resource management agencies 

will likely encounter increasing challenges as they work to protect and restore the health of aquatic 

ecosystems. Appendix C provides examples of vulnerability assessments of freshwater aquatic life and 

environmental flows related to climate change. 

3.3 Who Can Use This Information? 

This report presents scientific information that can help water-resource managers improve the protection of 

flow for aquatic life uses. Additionally, it serves as a source of information for a broad stakeholder audience 

involved in water-resource management and aquatic life protection. It does not establish any new authorities 

or impose any additional requirements on states, tribes, or territories. Under the CWA, any state or authorized 

tribe may protect aquatic life or use the CWA state programs to address flow (see Section 5) and develop 

numeric flow targets by following a flexible, nonprescriptive framework described in this report (see Section 6) 

to protect aquatic life. 
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 (Box B, below), a conceptual model consists of a written description and diagram 

of the relations and pathways between human activities (sources), stressors, and direct and indirect effects on 

ecological entities (U.S. Environmental Protection Agency, 1998). A conceptual model links one or more 

stressors to ecological assessment endpoints that are important for achieving management goals. Under the 

CWA, management goals are established by states as designated uses of waters (for example, to support 

aquatic life) and criteria to protect those uses. 

Box B. Ecological Risk Assessment

Ecological Risk Assessment (ERA) provides a framework for evaluating the likelihood that adverse ecological 

effects may occur or are occurring as a result of exposure to one or more stressors (U.S. Environmental 

Protection Agency, 1998). It can apply to a range of environmental problems associated with chemical, 

physical, and biological stressors, including evaluating the risk posed to aquatic life by flow alteration. A key 

step in the first phase of the ERA process, problem formulation, is the development of a conceptual model 

that explicitly demonstrates the hypothesized relations between ecological entities and the stressors to which 

they may be exposed.

The conceptual model (Figure 2) describes in a general way how various stressors can alter the natural flow 

regime, how flow alteration affects the chemical and physical conditions of an aquatic ecosystem, and how 
16

those changes may ultimately reduce the ability of a stream to support aquatic life. The general model is 

intended only to provide a foundation for detailed regional or catchment models; for a specific area, specific 

types of flow alteration and biological responses should be identified. 

The general conceptual model of the biological effects of flow alteration presented in this report (Figure 2) is a 

broad framework relating streamflow alteration and its sources to degraded aquatic life. The model is 

constructed around the following concepts and relations: 

 A stream’s natural flow regime is primarily a function of climate and physical catchment-scale properties, 

and is further affected by local, reach-scale conditions. 

 The natural flow regime supports the integrity of aquatic life by maintaining habitat of sufficient size, 

character, diversity, and connectivity by supporting natural sediment, water-temperature, and 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 lead to the reduction, elimination, or disconnection of 

optimal habitat for aquatic biota. 

 Biological responses to flow-mediated changes in stream chemistry and physical habitat can have 

cascading effects across trophic levels and aquatic communities, which may result in degraded aquatic life 

as determined by measures of effect (for example, survival, growth, and reproduction of aquatic biota).

The following sections describe the components of the general conceptual model. A detailed conceptual 

model of flow alteration with explicit directional relations is provided in Section 6.4. For detailed conceptual 
17

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 (catchment1). Climate determines patterns of water and energy input over time, 

whereas physical catchment characteristics such as soils, geology, and topography determine infiltration 

pathways (surface or subsurface) and rates of runoff and routing of streamflow through the drainage network. 

For example, a large proportion of rainfall in a catchment dominated by steep slopes and poorly-permeable 

soils will be converted to surface runoff that is quickly routed through the channel network. The flow regime 

of a stream in such a catchment would be characterized by high peak flows relative to average conditions, high 

rates of streamflow change during and after storm events, and relatively low dry-weather flows. In contrast, in 

 

1 The term “catchment” throughout this report refers specifically to the unique drainage area upstream from a stream reach of 

interest. Although the term “watershed” also fits this definition, catchment is used in this report because managers use the term 

“watershed” to describe larger geographic or planning units within a state or region. 
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 twofold 
20

increase in the likelihood of effects on fish and macroinvertebrate communities 2 (Carlisle and others, 2011). 

Sources of such effects may include groundwater and surface-water withdrawals, new and existing dams, 

impoundments and reservoirs, interbasin transfers, channelization, impervious cover, and water diversions. 

Human adaptations to increased drought, including expansion of surface- and groundwater uses, may 

compound these effects by decreasing the magnitude of low flows and increasing the frequency and duration 

of low flows in streams and rivers. Alterations in high flows can affect use; for instance, an increase in 

impervious surface area may cause an increase in flow, resulting in deleterious alterations to habitat or the 

biological community. The following sections describe potential stressors in more detail. 

4.3.1 Dams and Impoundments 

Dams and impoundments (for example, reservoirs) are designed to control and store streamflow for various 

purposes and can provide multiple societal benefits through increased recreation opportunities, flood 

attenuation, hydroelectric power, irrigation, public water supply, and transportation. However, dams are also 

a cause of flow alteration throughout the United States, as only about 40 large rivers (defined as longer than 

200 kilometers) remain free-flowing (Benke, 1990). At a national scale, when interregional flow variation 

before and after dam construction is compared, streams below dams can be subject to reduced high flows, 

augmented low flows, reduced seasonal variation, and other changes relative to predam conditions, resulting 

in a regional homogenization of the flow regime (Poff and others, 2007). At a finer scale, however, within a 

more homogenous hydroclimatic region, dams can create new flow regimes (McManamay and others, 2012). 

 

2

 Carlisle and others (2011) use the term “impairment” to describe this effect on the aquatic community, defining it as occurring when 

the value of the ratio of the observed condition to the expected reference condition (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 were represented in the U.S. National Inventory of Dams (NID) (U.S. Army 

Corps of Engineers, 2013). Not included in this total are small impoundments for farm ponds, fishing ponds, 

community amenities that fragment stream networks (for example, impoundments less than 2 meters [m] 

high), and larger dams that have not yet been included in the national database. New geographic information 

system (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 Basin in the southeastern United States identified the presence of more than 25,362 impoundments 

(Ignatius and Stallins, 2011), whereas the NID database recognized 1,415 (fewer than 6 percent of the 

reported total) in the same basin. The extensive presence of dams with impoundment heights greater than 2 

m on United States waterways in the NID (U.S. Army Corps of Engineers, 2013) is shown in Figure 3. Estimates 

made by Poff and Hart (2002), identify more than 2,000,000 dams across the country which includes small and 

large sized dams. 

Studies have shown that dam reregulation (when operational guidelines for the dam are modified to address 

environmental management concerns about downstream fisheries, riparian habitats, recreation, flow, etc.) 

has the potential to restore ecological function downstream of dams. Although the ability to modify 

operations varies on the basis of the type and purpose of the dam (that is, hydropower, flood control, 

irrigation, etc.), virtually all dams, regardless of size, have the potential to be modified (Arthington, 2012). 

Since 2000, large-scale flow experiments have become an important component of water-management 

planning, with considerably more than 100 large-scale flow experiments documented worldwide, including 56 
22

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. Groundwater 

is also a major source of water for irrigation, public water supplies, and industrial use. Groundwater 

withdrawals can lower the water table, resulting in reduced discharge to streams (Reeves and others, 2009; 
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 spikes at times of the year when adequate flows are needed to 

support important biological behaviors and processes (for example, in summer when certain fish migrate and 

reproduce). 

4.3.4 Effluents and Other Artificial Inputs (Discharges) 

In contrast to diversions, surface- and groundwater withdrawals, and other human activities that remove 

water from streams, discharge (effluent) from industrial and municipal wastewater-treatment facilities and tile 

drainage systems add water to streams and can alter natural flow patterns. For example, the effects on 

streamflow are amplified when artificial discharges consist of water that is not part of the natural water 

budget of the stream, such as deep groundwater or water derived from other basins, as in the case of 

interbasin transfers (Jackson and others, 2001). Such exogenous contributions shift the hydrograph upward 

and may be especially noticeable during natural low-flow periods as well as during flood flows resulting from 

storm events (Figure 6). This flow augmentation distorts the flow-sediment balance characteristic of 

undisturbed catchments, leading to effects such as channel downcutting and bank erosion as the stream 

strives to attain a new balance between water and sediment flux (as discussed in Section 4.4.1). In many arid 

environments, streamflow during dry seasons is composed almost entirely of treated effluent from 
28

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 as 

other 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 of 
29

precipitation to enter stream channels through surface runoff, rather than infiltrate into the ground or 

evaporate. Moreover, engineered drainage systems (for example, municipal stormwater systems) and road 

networks can directly route runoff to receiving waters, increasing the rate of change to streamflow during a 

storm event. As a result, streams in developed areas exhibit extreme flashiness, characterized by a rapid rise in 

flow during storm events to a high peak-flow rate followed by rapid recession of flow after precipitation 

ceases (Dunne and Leopold, 1978; Walsh and others, 2005a, 2005b). 

In addition, impervious surfaces reduce base flow in the days or weeks after a storm event as a result of 

reduced infiltration and groundwater recharge. In agricultural areas, the opposite effect is observed with 

subsurface drainage structures (or tile drains), which discharge groundwater that would otherwise be held in 

storage or lost through evapotranspiration. However, agricultural drainage systems can reduce base flow, 

particularly when drainage lowers the water table and decreases groundwater recharge (Blann and others, 

2009). During prolonged drought, differences in low-flow conditions between developed and natural streams 

generally are less pronounced than during average or high-flow conditions because developed areas tend to 

have a smaller effect on the deep groundwater recharge that supports flow during drought conditions than on 

the shallow groundwater and runoff that contribute water to a stream when precipitation is more plentiful 

(Konrad and Booth, 2005). 

Urban and agricultural land uses can accompany water-use and management practices such as interbasin 

transfers, irrigation and other surface-water withdrawals, on-site wastewater disposal, impoundment, and 

groundwater pumping. Each of these practices affects the direction and magnitude of flow alteration in urban 

and agricultural streams and can compound hydrologic effects, as discussed previously. 

The effects of surface mining on streamflow are highly localized and depend on the catchment characteristics 

and vegetative cover, the geology of the mine and degree of valley fills, the extent of underground mines and 

sediment ponds, and the amount of soil compaction and infiltration. Mining has been found to increase peak 
30

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 landscape 
31

effects vary across the United States, with some regions exhibiting a trend of decreasing low flows (longer dry 

spells) and others trending toward higher low flows (Figure 7) (U.S. Environmental Protection Agency, 2014b). 

Anthropogenic alterations that reduce streamflow may be further exacerbated by this climate-change trend. 

In areas where flow regimes are strongly affected by snowmelt, observations show a trend toward earlier 

timing of spring high flows (Figure 8) that corresponds to declines in the spring snowpack and earlier 

snowmelt (Melillo and others, 2014). These examples demonstrate the exposure of aquatic ecosystems to 

climate-driven flow alteration. Exposure analysis is an essential part of an assessment of the vulnerability of 

aquatic life to climate change. Additional discussion and examples of climate-change vulnerability assessments 

related to altered flow and aquatic life are included in Appendix C. 

Climate change is occurring in conjunction with other anthropogenic stressors related to population increase 

and land-use change and may magnify the hydrologic and biological effects of those existing stressors 

(Intergovernmental Panel on Climate Change, 2007; Karl and others, 2009; Kundzewicz and others, 2008; 

Palmer and others, 2009; Pittock and Finlayson, 2011). For example, the combination of earlier spring 

snowmelt and increased water withdrawals can reduce summer flows to levels that would not otherwise 

occur in response to either stressor alone and that reduce the survival of aquatic biota. An additional example 

is the compounding effect of increased storm intensity on flood frequency in areas where impervious cover 

already drives flood flows at a frequency that degrades stream habitat (Intergovernmental Panel on Climate 

Change, 2007). These and other changes to the flow regime may further benefit invasive species to the 

detriment of native species (Rahel and Olden, 2008). 

Adaptive capacity, or the ability of a stream ecosystem to withstand climate-driven stresses, may be seen in 

rivers whose flow patterns more closely resemble the natural flow regime. These rivers may be buffered from 

the harmful effects of climate-related disturbances on aquatic life (Palmer, 2009; Pittock and Finlayson, 2011). 
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 minimally 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. Channel geometry, bed 

substrate, and the presence of geomorphic features such as oxbow lakes, point bars, or riffle-pool sequences 

vary according to the frequency of bankfull flows, the magnitude of floods, and other flow characteristics 

(Trush and others, 2000). Research has uncovered a variety of geomorphic responses to flow alteration, with 

specific effects depending on the type and severity of streamflow change. These effects can include channel 

incision, narrowing, or widening; increased deposition of fine sediment or bed armoring (coarsening); and 

reduced channel migration (Poff and others, 1997). 

A primary mechanism for geomorphic change is a shift in energy and sediment dynamics following flow 

alteration. For example, increased peak flows resulting from urban land use can increase bed erosion and 

drive channel incision or widening. In contrast, reduced flooding as a result of dam regulation can lower the 

distribution of nutrient-bearing sediments to flood plains, starve downstream channel and coastal areas of 

needed sediment, and increase sedimentation upstream from the dam (Syvitski and others, 2005). These 

processes can lead to simplified channels that are disconnected from their natural flood plains. Natural 
35

mosaics of geomorphic features serve as important habitats for a range of aquatic and flood-plain species, and 

the loss of habitat diversity following hydrologic alteration can have adverse effects on the health of biological 

communities. 

4.4.2 Effects on Connectivity 

Hydrologic connectivity is the water-mediated transfer of matter, energy, and (or) organisms within or 

between elements of a hydrologic system (Pringle, 2003). In aquatic ecosystems, it encompasses longitudinal 

connectivity of the stream network and specific habitat types, as well as lateral connectivity among stream 

channels, riparian zones, flood plains, and wetlands. The vertical connection between surface water and 

groundwater is a third dimension of connectivity along the various flow paths that connect points of recharge 

(beginning at the water table) to points of discharge (for example, a river or stream) (Ward, 1989). 

Longitudinal, lateral, and vertical connectivity naturally vary spatially and temporally with climate, 

geomorphology, groundwater dynamics, and other factors. Longitudinal connectivity, for example, may be 

continuous from headwaters to lower reaches in one catchment but interrupted by intermittent or ephemeral 

reaches in another (Larned and others, 2010a, 2010b, 2011). Lateral connectivity is restricted to 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, 1986; U.S. Environmental Protection Agency, 2015). 

Flow alteration can affect connectivity in several ways. Longitudinal connectivity of the stream network is 

disrupted by dams, weirs, diversions, and other manmade structures that obstruct upstream-downstream 

passage by fish and other organisms. Longitudinal connectivity is also disrupted by fragmentation of aquatic 

habitat without manmade barriers. For example, an increase in the frequency of zero-flow conditions in a 
36

stream reach as a result of water withdrawals can cause the disconnection of upstream areas from the rest of 

the stream network (U.S. Environmental Protection Agency, 2015). Lateral connectivity among the stream 

channel, riparian areas, flood plains, and wetlands is reduced as a result of the decreased frequency of high 

flows and floods caused by geomorphic change (for example, channel incision) or of direct modification of 

stream channels (channelization, levee construction, etc.). Vertical connectivity is altered directly and 

indirectly through practices that alter infiltration and runoff (for example, irrigation return flow), which can 

affect recharge to groundwater and outflow to surface water. Other activities (for example, drainage) can alter 

surface-runoff rates and potentially reduce recharge and contribute to flooding. Other practices may cause a 

rise in the water table and, subsequently, the base level of a stream (for example, reservoirs) (Winter and 

others, 1998). For systems characterized by an absence of connectivity, flow alterations such as stream 

channelization, irrigation, and impervious surface area can increase flashiness and increase connectivity (U.S. 

Environmental Protection Agency, 2015). 

4.4.3 Effects on Water Temperature and Chemistry 

The water quality effects of flow alteration are varied and can include changes in water temperature, salinity 

(which is measured by specific conductance), dissolved-oxygen concentration, pH, nutrient concentrations, 

and other parameters. For example, dilution of dissolved salts or toxic contaminants are reduced because of a 

decrease in flow magnitude when water is diverted or groundwater is pumped (Caruso, 2002; Olden and 

Naiman, 2010; Sheng and Devere, 2005). Stream temperature is also closely linked to flow magnitude (Cassie,

2006; Gu and Li, 2002; Wehrly and others, 2006); artificially low flows can result in increased water 

temperatures as a result of reduced depths and (or) reduced input of cool groundwater. Low flows also 

increase the likelihood of stagnant water with a low dissolved-oxygen concentration. In contrast, dam 

tailwaters can become supersaturated with gases and harm aquatic life (Weitkamp and Katz, 1980). 

Additionally, dam tailwaters, particularly those drawing water from the depths of stratified reservoirs, show 
37

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, 2004; Morgan and Good, 1988; Mulholland and others, 

2008; Paul and Meyer, 2001). Effects may differ among water-body types (for example, lentic and lotic 

waters). 

4.5 Biological Responses to Flow Alteration 

The combined physical and chemical effects of flow alteration (summarized in the previous section) may result 

in the degradation, loss, and disconnection of ecological integrity within a stream system. Moreover, flow 

modification can eliminate hydrologic cues needed to stimulate spawning or flow volume and timing needed 

to aid seed dispersal, resulting in a mismatch between flow and species’ life-history needs, and can encourage 

the invasion and establishment of non-native species (Bunn and Arthington, 2002). The ability of a water body 

to support healthy aquatic life is therefore tied to the maintenance of key flow-regime components. 

Specific biological effects of a given type of flow alteration vary by location and degree of alteration; however, 

some generalities can be made. Literature summarizing biological responses to altered flows, compiled and 

reviewed by Bunn and Arthington (2002) and Poff and Zimmerman (2010), includes studies showing overall 

reductions in the abundance and diversity of fish and macroinvertebrates, excessive growth of aquatic 
38

macrophytes, reduced growth of riparian vegetation, and shifts in aquatic and riparian species composition. 

These changes are tied to altered habitat. For example, the stabilization of flow downstream of dams tends to 

reduce habitat diversity and, therefore, species diversity. Reduced longitudinal connectivity of habitat types 

can reduce the survival of migratory fish species, and reduced lateral connectivity between stream channels 

and flood-plain wetlands limits access to important reproduction and feeding areas, refugia, and rearing 

habitat for native and resident fishes. Reduced lateral connectivity can reduce habitat needed for aquatic life 

stages of macroinvertebrates and amphibians, and can reduce the potential for gene flow (mixing individuals 

from different locations). Fish spawning is disrupted by changes to the natural seasonal pattern of flow. For 

some fish species, spawning is triggered by rising flows in the spring; therefore, a shift in the timing of high 

flows can result in aseasonal reproduction during periods when conditions for larval survival are suboptimal. 

In addition, changes in species abundance and richness, ecosystem functions such as contaminant removal 

and nutrient cycling rates, can degrade in the environment due to flow alteration (Palmer and Febria, 2012; 

Poff and others, 1997). 

The relations among variables such as flow, temperature, habitat features, and biology are key in controlling 

species distribution (for example, Zorn and others, 2008). Water temperature is an associated hydrologic 

characteristic and has a particularly strong effect on aquatic organisms in summer months, when streamflows 

are lowest and temperatures are highest (Brett, 1979; Elliot, 1981; Wehrly and others, 2003). Increases in 

water temperature that result from alterations such as withdrawals, especially during critical summer 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 and 
39

Jones, 2002). Dam releases in the winter result in warmer water temperatures, which may eliminate 

developmental cues and increase growth, leading to earlier aquatic insect emergence. These changes in 

temperature can create a mismatch between life-history stages and environmental conditions that may 

increase mortality as a result of high-flow events, predation, reduction in resource availability earlier in the 

season, and other stresses (Olden and Naiman, 2010; Vannote and others, 1980; Ward and Stanford, 1982). 

The result of these hydrologic alterations may be impairment of a water body due to the physical, chemical, or 

biological effects discussed above. The most severe of alterations, the complete dewatering of a perennial 

stream or river, will result in complete extirpation of aquatic species in those water bodies. In addition to 

directly contributing to impairments through ecologically deleterious physical changes (that is, hydrologic, 

geomorphic, and connectivity change), hydrologic alteration may also be the underlying source of other 

impairments such as low dissolved oxygen, modified thermal regimes, increased concentrations of sediment, 

anoxic byproducts (such as downstream of dams), and nutrients or toxic contaminants. While the focus of this 

report is primarily on those direct physical factors (for example, geomorphic and hydrologic) that can affect 

biological communities, addressing these hydrologic alterations may also help to mitigate the effects of 

contaminants such as those mentioned above. 

The following section (Section 5) provides some examples of State actions within a CWA framework to protect 

aquatic life from flow alteration. 

5 Examples of State and Federal Actions to Protect Aquatic Life from Altered Flows 

States have CWA tools and other tools that can address the effects of altered flows on aquatic life. This section 

briefly discusses those programs that are within the CWA. The CWA was intended to protect the chemical, 

physical, and biological integrity of the Nation’s waters (see Box A). The two sections of the CWA related to 

the development of the information presented in this report are CWA Sections 304(a)(2) and 304(f). CWA 

Section 304(a)(2) generally requires EPA to develop and publish information on the factors necessary to 
40

restore and maintain the chemical, physical, and biological integrity of navigable waters. Section 304(a)(2) also 

allows EPA to provide information on the conditions necessary for the protection and propagation of shellfish, 

fish, and wildlife in receiving waters and for allowing recreational activities in and on the water3. CWA Section 

304(f) requires EPA to issue information to control pollution resulting from, among other things, “changes in 

the movement, flow, or circulation of any navigable waters.”

CWA case law has affirmed that the distinction between water quantity and water quality is artificial and that 

sufficient water quantity may be necessary in order to protect designated uses and meet antidegradation 

requirements. Public Utility District No. 1 of Jefferson County v. Washington Department of Ecology, 511 U.S. 

700, 719-721 (1994); S.D. Warren Co. v. Maine Board of Environmental Protection, 547 U.S. 370 (2006). 

Additionally, the U.S. Supreme Court cited provisions in the CWA (Section 502(19)) recognizing that a 

reduction in streamflow can constitute water pollution, including the CWA’s definition of “pollution” as the 

manmade or man-induced alteration of the chemical, physical, biological, and radiological integrity of water. 

PUD No.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. (An exhaustive 

discussion of these CWA programs is beyond the scope of this document; readers can learn more by accessing

available EPA resources as noted below5.) Water quality standards (WQS) play a central role in the other CWA 

programs mentioned (see Figure 9) and therefore are discussed first. Additional information on WQS is found 

in Appendix A. 

 

4

 The responsibility for administering and enforcing CWA Section 404 is shared by the U.S. Army Corps of Engineers and the U.S. EPA 

except in two states, Michigan and New Jersey, that have assumed CWA Section 404 responsibilities. 

5

 See Water Quality Standards Academy (http://water.epa.gov/learn/training/standardsacademy/index.cfm) and Watershed Academy 

Water Law Modules (http://cfpub.epa.gov/watertrain/index.cfm). 
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 Nation’s waters (see CWA sections 101 and 303(c); see also Title 40 of the Code of 

Federal Regulations (40 CFR) part 131.11(b)). This section presents examples of existing narrative flow criteria 
43

for states interested in developing or revising their own and some considerations for developing narrative 

language. 

As of 2014, 10 states had adopted narrative flow criteria in their WQS: New Hampshire, Rhode Island, 

Vermont, New York, Virginia, Kentucky, Tennessee, Louisiana, Missouri, and Oregon. Also as of 2014, six tribes 

with Treatment in a Manner Similar to a State (TAS) had adopted narrative flow criteria in their WQS. (Many 

other authorized tribes have adopted wetland flow criteria.) As of 2015, no United States territories have yet 

adopted flow criteria in their WQS. Table 1 contains example language for State and Tribal flow criteria.6

 

6

 For the full text of State water quality standards, please see the following U.S. Environmental Protection Agency Web site for links to 

the most up-to-date information: http://water.epa.gov/scitech/swguidance/standards/wqslibrary/index.cfm. 
44

Table 1. Excerpts from narrative flow criteria for selected states and tribes. 

[Key terms are shown in bold for emphasis; see U.S. Environmental Protection Agency (2014e) for complete text of individual criteria; %, percent; 7Q10, 

the 7-day, 10-year annual low-flow statistic; WMT, Water Management Type; ] 

State/Tribe Water Quality Standard description of protected resource and corresponding goal

New Hampshire “surface water quantity shall be maintained at levels adequate to protect existing and designated uses”

“These rules shall apply to any person who causes point or nonpoint source discharge(s) of pollutants to surface waters, or who undertakes hydrologic 

modifications, such as dam construction or water withdrawals, or who undertakes any other activity that affects the beneficial uses or the level of water 

quality of surface waters.”

Rhode Island “quantity for protection of... fish and wildlife...adequate to protect designated uses” 

“For activities that will likely cause or contribute to flow alterations, streamflow conditions must be adequate to support existing and designated uses.”

Vermont Class A(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 regime shall provide for maintenance of flow characteristics 

that ensure the full support of uses and comply with the applicable water quality criteria.”

New York Class N fresh surface waters ... “There shall be no alteration to flow that will impair the waters for their best usages.”

Virginia “Man-made alterations in stream flow shall not contravene designated uses including protection of the propagation and growth of aquatic life.”

Kentucky Section 4. “Aquatic Life. (1) Warm water aquatic habitat. The following parameters and associated criteria shall apply for the protection of productive 
45

State/Tribe Water Quality Standard description of protected resource and corresponding goal

warm water aquatic communities, fowl, animal wildlife, arboreous growth, agricultural, and industrial uses:...(c) Flow shall not be altered to a degree which 

will adversely affect the aquatic community.”

Tennessee Rule 0400-40-03-.03, Criteria for Water Uses: Section (3) The criteria for the use of Fish and Aquatic Life are the following, subsection (n) Habitat—“The 

quality of stream habitat shall provide for the development of a diverse aquatic community that meets regionally-based biological integrity goals. Types of 

habitat loss include, but are not limited to: channel and substrate alterations....stream flow changes....for wadeable streams, the instream habitat within 

each subecoregion shall be generally similar to that found at reference streams. However, streams shall not be assessed as impacted by habitat loss if it 

has been demonstrated that the biological integrity goal has been met.” Subsection (o) Flow—“Stream or other waterbody flows shall support the fish and 

aquatic life criteria.”

“Section (4) The criteria for the use of Recreation are the following: Subsection (m) Flow—Stream flows shall support recreational uses.”

Missouri “Waters shall be free from physical, chemical, or hydrologic changes that would impair the natural biological community.”

Seminole Tribe 

of Florida

“Class 2-A waters shall be free from activities....that....impair the biological community as it naturally occurs....due to....hydrologic changes.”

Bad River Band 

of the Lake 

Superior Tribe 

of Chippewa 

Indians

“Water quantity and quality that may limit the growth and propagation of, or otherwise cause or contribute to an adverse effect to wild rice, wildlife, and 

other flora and fauna of cultural importance to the Tribe shall be prohibited.”

“Natural hydrological conditions supportive of the natural biological community, including all flora and fauna, and physical characteristics naturally 

present in the waterbody shall be protected to prevent any adverse effects.”

“Pollutants or human-induced changes to Tribal waters, the sediments of Tribal waters, or area hydrology that results in changes to the natural biological 

communities and wildlife habitat shall be prohibited. The migration 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 Agency, 2014d).

More complete examples from New Hampshire and Rhode Island narrative flow criteria are as follows and 

illustrate additional attributes these states chose to emphasize, such as broad applicability across all surface 

waters: 

“Unless flows are caused by naturally occurring conditions, surface water quantity shall be maintained at 

levels adequate to protect existing and designated uses.” (New Hampshire Code of Administrative Rules EnvWq 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) within the bounds of the natural flow 

regime to support the ecological structure and function of streams and rivers. However, alterations in low or 

high flows that are human-induced, affect and can control many ecosystem patterns, such as habitat extent 

and condition, water quality, connectivity, and material and energy exchange. These patterns can in turn 

affect many ecosystem processes, including biological composition, distribution, recruitment of biota, and 

ecosystem production (Rolls and others, 2012). 

Although low flows serve a critical role in ecosystem function, current scientific research indicates that flow 

criteria ideally should support the natural flow regime as a whole, and that criteria for minimum flow alone 

(that is, a single minimum discharge value or a minimum passing flow) are not sufficient for maintaining 

ecosystem integrity (Annear and others, 2004; Bunn and Arthington, 2002; Poff and others, 1997). Minimum 

flow criteria do not address the full range of seasonal and interannual variability of the natural flow regime in 

most rivers and streams. 

The natural fluctuation of water volume and levels in rivers and streams is critical for maintaining aquatic 

ecosystems because aquatic biota have developed life-history strategies in response to these fluctuations (Hill 

and others, 1991; Lytle and Poff, 2004; Mims and Olden, 2012, 2013; Postel and Richter, 2003; Stalnaker,

1990). Comprehensive flow criteria not only identify flow needs (that is, magnitude) but may also address the 

rate, frequency, timing, and duration of streamflow required to support ecosystem health (Poff and others,

2010). The Instream Flow Council (a non-profit organization working to improve the effectiveness of instream 

flow programs and activities: http://www.instreamflowcouncil.org/) recommends developing criteria that 

incorporate natural patterns of intra- and interannual variability in a manner that maintains and (or) restores 

riverine form and function to effectively maintain ecological integrity (Annear and others, 2004). Therefore, 

narrative hydrologic criteria and their implementation ideally should address several flow-regime components 
49

(frequency, duration, timing, rate of change) in addition to flow magnitude. The components necessary are 

determined on a case-by-case basis, depending on which values are most ecologically relevant.

Minimum flow statistics such as the 7Q10 design flow (the minimum 7-day average flow likely to occur in a 10-

year period) are recommended by the U.S. Environmental Protection Agency for the derivation of water 

quality-based effluent limits in the National Pollutant Discharge Elimination System permitting program, but,

although they include magnitude, duration, and frequency components, they were not derived to support the 

hydrologic requirements of aquatic ecosystems (Annear and others, 2004). The main purpose of these design 

flows is to determine pollutant discharge values (or limits) rather than to support the flow requirements of 

aquatic ecosystems (see U.S. Environmental Protection Agency, 1991).

5.2 Monitoring, Assessing, and Identifying Waters Impaired as a Result of Flow Alteration 

Once WQS are adopted, states ensure they are met through monitoring to assess use attainment status, 

reporting on use attainment and identifying impaired waters, and implementing appropriate restoration 

measures. Waters are classified and states report on their condition to support use attainment decisions 

under Sections 303(d) and 305(b). States use their monitoring and assessment programs to identify and report 

to the public those waters that have impairments from pollution, defined under the CWA as “the man-made 

or man-induced alteration of the chemical, physical, biological, and radiological integrity of water” (Section 

502(19)), including the effects of altered flow regimes or hydromodification (U.S. Environmental Protection 

Agency, 1997, 2003, 2005). Attainment of designated uses is evaluated through monitoring and assessment of 

indicators that reflect State WQS, including narrative or numeric criteria, or evaluating other data or 

information (U.S. Environmental Protection Agency, 1991). Accurately identifying the impairment status of 

these waters allows states to engage stakeholders on appropriate restoration strategies. The state of the

science for restoring waters impaired by hydrologic alteration has evolved considerably, including, for 

instance, dam reregulation and improved methods for surface- or groundwater withdrawals. 
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, 2002, 

Chapters 8 and 10). In order to accurately assess flow conditions over time, states evaluate monitoring data 

and information relating to the flow regime. 

States can record and evaluate flow information even when routine monitoring cannot occur as a result of 

extreme (high or low) flow conditions. This evaluation could include desktop analyses sources such as USGS 

StreamStats (a Web application that provides users with access to stream network tools for water-resources 

planning purposes: http://water.usgs.gov/osw/streamstats/) or qualitative visual observations of streams. 

Such data or information could be used for making attainment decisions. For instance, the absence of water 

from a perennial stream could demonstrate that the aquatic life designated use is not being attained, and a 

state may conclude that the designated use is impaired. Texas provides an example: for each visit to nontidally 

influenced freshwater streams or rivers, the Texas Commission on Environmental Quality (TCEQ) monitoring 

procedures require that a “flow-severity” field (with a value of no flow, low flow, normal flow, flood flow, high 

flow, or dry) be recorded, even if it is not possible to quantitatively measure flow or conduct sampling during a 

visit (see Box D).

States and tribes can use these data and information to classify the water-body segments into one of five of 

the 303(d) and 305(b) Integrated Reporting (IR) categories7

 (U.S. Environmental Protection Agency, 2005). 

 

7

 The listing categories are as follows: Category 1—All designated uses are supported, no use is threatened; Category 2—Available 

data and (or) information indicate that some, but not all, of the designated uses are supported; Category 3—There is insufficient 

available data and (or) information to make a use support determination; Category 4 (includes subcategories)—Available data and (or) 

information indicate that at least one designated use is not being supported or is threatened, but a Total Maximum Daily Load (TMDL) 
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 water body is 

characterized by entrenchment, bank destabilization, or channelization. Where the specific pollutant causing 

the impairment has not been identified (for example, for biological impairments), EPA recommends that states 

list those waters in Category 5 (the 303[d] list, impaired by a pollutant and requiring a TMDL), unless they can 

demonstrate that the impairment is solely attributable to a nonpollutant (for example, flow) (U.S. 

Environmental Protection Agency, 2003; 2005). Additionally, EPA’s guidance has noted that assessment 

categories are not mutually exclusive, and waters may be placed in more than one category (for example, 

categories 4c and 5) (U.S. Environmental Protection Agency, 2005).

The integrated reporting format provides transparency in reporting the status of all assessed waters and, 

therefore, is one way to acknowledge the important role of flow in contributing to water-body impairments. 

An example of a reporting option that helps clearly delineate and address waters impaired as a result of 

streamflow alteration is described in Box E, which illustrates the use of Category 4F in Vermont. 

 

is not needed; Category 5— Available data and (or) information indicate that at least one designated use is not being supported or is 

threatened, and a TMDL is needed. For more information on Integrated Reporting categories, see 

http://water.epa.gov/lawsregs/lawsguidance/cwa/tmdl/upload/2006irg-report.pdf. 
52

Box D. Procedures for Capturing Flow Information in the State of Texas

The publication “Surface water quality monitoring procedures, Volume 1: Physical and chemical monitoring 

methods” (Texas Commission on Environmental Quality [TCEQ], 2012) describes how Texas monitors all flow 

conditions and captures flow information in its State database. Parameter codes for data uploads to the U.S. 

Environmental Protection Agency (EPA) Storage and Retrieval Data Warehouse (STORET), a repository for 

water monitoring data, are provided for each type of data collected. In addition to describing methods for 

capturing quantitative flow information, the document describes how to capture qualitative flow information 

with the “flow-severity” field:

 “Record a flow-severity value for each visit to freshwater streams or rivers (nontidally influenced) and 

report the value to the TCEQ central office. Do not report flow severity for reservoirs, lakes, bays, or tidal 

streams. It should be recorded even if it was not possible to measure flow on a specific sampling visit. See 

the Surface water quality monitoring data management reference guide for detailed information on data 

reporting.“ (Texas Commission on Environmental Quality, 2013)

 “No numerical guidelines are associated with flow severity, an observational measurement that is highly 

dependent on the water body and the knowledge of monitoring personnel. It is a simple but useful piece 

of information when assessing water quality data. For example, a bacteria value of 10,000 with a flow 

severity of 1 would represent something entirely different than the same value with a flow severity of 5.”

Table 3.2 of Texas Commission on Environmental Quality (2012) provides photographs of each “flow-severity” 

category and the following descriptions, which can be found at

https://www.tceq.texas.gov/assets/public/comm_exec/pubs/rg/rg415/rg-415_chapter3.pdf (accessed 

February 4, 2016):
53

 “No Flow. When a flow severity of 1 is recorded for a sampling visit, record a flow value of 0 ft3/s (using 

parameter code 00061) for that sampling visit. A flow severity of 1 describes situations where the stream 

has water visible in isolated pools. There should be no obvious shallow subsurface flow in sand or gravel 

beds between isolated pools. ―No flow not only applies to streams with pools, but also to long reaches of 

streams that have water from bank to bank but no detectable flow.”

 “Low Flow. When streamflow is considered low, record a flow-severity value of 2 for the visit, along with 

the corresponding flow measurement (parameter code 00061). In streams too shallow for a flow 

measurement where water movement is detected, record a value of < 0.10 ft3/s. In general, at low flow 

the stream would be characterized by flows that don‘t fill the normal stream channel. Water would not 

reach the base of both banks. Portions of the stream channel might be dry. Flow might be confined to one 

side of the stream channel.” 

 “Normal Flow. When streamflow is considered normal, record a flow severity value of 3 for the visit, along 

with the corresponding flow measurement (parameter code 00061). What is normal is highly dependent 

on the stream. Normality is characterized by flow that stays within the confines of the normal stream 

channel. Water generally reaches the base of each bank.”

 “Flood Flow. Flow-severity values for high and flood flows have long been established by the EPA and are 

not sequential. Flood flow is reported as a flow severity of 4. Flood flows are those that leave the confines 

of the normal stream channel and move out onto the floodplain (either side of the stream).”

 “High Flow. High flows are reported as a flow severity of 5. High flow would be characterized by flows that 

leave the normal stream channel but stay within the stream banks.”
54

 “Dry. When the stream is dry, record a flow-severity value of 6 for the sampling visit. In this case the flow 

(parameter code 00061) is not reported, indicating that the stream is completely dry with no visible 

pools.”
55

Box E. Vermont Addresses Hydrologically Altered Waters

Vermont first adopted narrative criteria into its water quality standards (WQS) for Clean Water Act purposes 

for flow or hydrologic condition in 1973 (for full text, see http://www2.epa.gov/sites/production/files/2014-

12/documents/vtwqs.pdf [accessed February 4, 2016] or Vt. Code R. 12 004 052, 

http://www.vtwaterquality.org/wrprules/wsmd_wqs.pdf [accessed February 4, 2016]). Although hydrologic 

alteration is listed under integrated reporting guidance as Category 4c (impairments due to pollution not 

requiring a Total Maximum Daily Load), Vermont does address flow-related exceedance of the WQS through 

the Vermont Priority Waters List. This list includes waters assessed as “altered” using the state’s assessment 

methodology (Vermont Department of Environmental Conservation, 2014: 

http://www.vtwaterquality.org/mapp/docs/mp_assessmethod.pdf [accessed February 4, 2016]). Part F of the 

Priority Waters List is water bodies that do not support one or more designated uses as a result of alteration 

by flow regulation (primarily from hydroelectric facilities, other dam operations, or industrial, municipal, or 

snowmaking water withdrawals). This list includes a description of the problem, current status or control 

activity, and the projected year the water-body segment will come into compliance with WQS. Creating a new 

category for hydrologic alteration helps separate it from other causes of pollution effects that would be 

reported in Category 4.

5.3 Development of Total Maximum Daily Loads 

When waters are placed into Category 5, a TMDL must be developed to address the pollutant(s) causing the 

impairment. A TMDL is a calculation of the maximum amount of a pollutant that a water body can receive and 

still meet WQS, and an allocation of that load among the various sources of those pollutants. Quantity of flow 

and variation in flow regimes are important factors in transporting pollutants (for example, sediment, 

pathogens, and metals) for which there may be WQS, and therefore flow is considered when calculating 

TMDLs. In addition, EPA regulations require that seasonal variations, critical conditions, and a margin of safety, 
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 new 

water 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 Utility 
57

District No. 1 of Jefferson City v. Washington Department of Ecology, 511 U.S. 700, 719-721 (1994), described 

in Box F. A State narrative criterion describing desired hydrologic conditions would provide a state with a basis 

to identify conditions for inclusion in a Federal permit or license that might have beneficial effects on aquatic 

life designated uses that would otherwise be harmed by altered hydrologic conditions (see two examples in 

Box F). 

Identification of flow impairments can aid in the 401 certification process. For example, a 4C identification or 

other related category developed by a state (for example, the 4F category described in Box E) might help the 

state recognize the potential for flow-related impairments caused by proposed projects. Such adverse effects 

can be addressed through CWA 401 certification for operating conditions for a Section 404 permit (see Section 

5.5), or as part of the Federal Energy Regulatory Commission permitting process for hydroelectric power 

generation, for example. 

Box F. 401 Certifications, Sufficient Flow, and Water Quality Standards

South Carolina Board of Health and Environmental Control Denied Certification

In 2009, South Carolina denied a 401 certification of a hydroelectric project license renewal (involving 11 

dams), stating, “[t]he Board finds that the WQ Certification does not provide sufficient flow to protect 

classified uses, the endangered shortnose sturgeon and adequate downstream flow....to provide reasonable 

assurance....that WQS will be met.” As a result of that action, negotiations were held that resulted in an 

agreement in 2014 and granting of the 401 certification. The agreement conditions committed the energy 

company to operating its dams to improve conditions for the sturgeon, protect flow conditions during 

spawning periods, and provide periodic flood-plain inundation mimicking ecologically important natural floods 

and recessions. 

Public Utility District No. 1 of Jefferson County v. Washington Department of Ecology , 511 U.S. 700, 719–721 

(1994), addressed the question of whether flow may be linked to WQS and whether a state may include 
58

specific flow requirements in a Clean Water Act Section 401 certification. The challenge was related to the 

State of Washington’s inclusion of minimum-flow requirements in a 401 certification for a Federal Energy 

Regulatory Commission relicensing of a hydropower plant. The Court held that the State of Washington was 

authorized to require the plant to maintain certain streamflows as a condition of a Section 401 certification. In 

this case, the State of Washington did not have explicit narrative or numeric criteria related to flow, but the 

certification was conditioned to address flow in order to protect the designated use and meet antidegradation 

requirements.

5.5 Consideration of Flow Alteration in Issuing 404 Permits 

Reviews conducted pursuant to CWA Section 404 also take into account potential effects on aquatic life uses 

caused by hydrologic alteration associated with the discharge of dredged or fill material (for example, dams or 

other impoundments). CWA Section 404 regulates8

 discharge of dredged or fill material into waters of the 

United States, and some proposed projects may result in loss of the conditions necessary for survival of 

aquatic life, including, for example, lotic species (species that depend on flowing water for survival). As a 

result, such projects could result in the inability to meet WQS, including protecting for the designated use, 

narrative and numeric criteria (that is, dissolved oxygen, temperature, or biological narratives), and 

antidegradation. Potential effects on the ability of a water body to meet WQS are a required consideration 

when evaluating whether to issue a Section 404 permit [see 40 CFR 230.10(b)]. The Section 404 review entails 

evaluating efforts to avoid the adverse effects on aquatic resources, minimizing effects if they cannot be 

avoided, and mitigating any unavoidable adverse effects that remain. For example, avoidance could include 

water conservation and efficiency programs and (or) use of an existing impoundment in lieu of creating a new 

 

8

 The responsibility for administering and enforcing CWA Section 404 is shared by the U.S. Army Corps of Engineers and the U.S. 

Environmental Protection Agency. For more information on these responsibilities, see http://www.epa.gov/cwa-404/laws-regulationsexecutive-orders and http://www.epa.gov/cwa-404/policy-and-guidance 
59

water-supply reservoir; minimizing could include reducing the scope of effects associated with a proposed 

impoundment; and compensatory mitigation to offset the effects of a project could include hydrologic 

restoration of waters through dam removal. 

Examples of projects involving discharge of dredged or fill material that affect hydrology include the 

construction of new water withdrawal or storage systems (for example, reservoirs); expansion of existing 

withdrawal or storage systems; diversions and construction of projects such as drinking-water or flood-control 

reservoirs, impoundments for energy generation, and fishing reservoirs or amenity ponds (an impoundment 

developed for recreation and (or) aesthetic purposes). Impoundments alter streamflows, and operation of 

dams to manage releases largely determines how closely downstream flows resemble the natural hydrograph. 

State review of such proposed activities ideally would consider whether the proposed project would adversely 

affect the designated use (aquatic life) or result in nonattainment of narrative or numeric WQS. Activities 

proposed for Section 404 permits (issued by the U.S. Army Corps of Engineers) are reviewed by resource 

agencies (Federal and State) and are subject to Section 401 certification. Permits issued by a state that has 

assumed the Section 404 program (as of 2015, only Michigan and New Jersey have approved Section 404 

programs), or issued by a state or tribe implementing a programmatic general permit issued by the U.S. Army 

Corps of Engineers, must also consider the potential effects of a project on attainment of WQS, including 

antidegradation requirements. A State program must be at least as stringent as the CWA requirements. 

5.6 Consideration of Flow Alteration in Issuing National Pollutant Discharge Elimination System (402) 

Permits 

The National Pollutant Discharge Elimination System (NPDES) is another CWA program that can play a role in 

protecting aquatic life from the effects of hydrologic alteration. NPDES permits are generally required for 

point-source discharges of pollutants. 
60

Many NPDES permits depend on streamflow data for pollutant discharge limit calculations. Permits issued 

under CWA Section 402 use critical low-flow values such as the 7Q10 (7-day, 10-year annual low-flow statistic) 

or regulated low flows to calculate a permittee’s discharge limits so that permitted values will be protective of 

aquatic life under the most critical conditions. Many rivers and streams across the United States have 

experienced trends in low flows since the 1940’s–with increases generally in the Northeast and Midwest, and 

decreases (streams carrying less water) in the Southeast and the Pacific Northwest (Figure 7). Permit writers 

use the most up-to-date critical low-flow information for the receiving water and, where historical flow data 

are no longer representative, use current low-flow data to calculate effluent permit limits to protect for the 

new critical low flow (see the EPA Water Quality Standards Handbook [U.S. Environmental Protection Agency,

1994, Chapter 5.2]). 

As states issue permits for new surface-water intakes or other surface- or groundwater withdrawals that will 

alter the existing low flow of a stream, NPDES permits may need to be re-evaluated to ensure that the new 

low flow is incorporated into effluent limit calculations and updated as needed. Safeguarding protective 

instream flows from anthropogenic alteration will help maintain streamflow for existing NPDES permits, 

reducing the need to modify them to meet new low-flow conditions. The protection of flow levels would 

prevent additional treatment requirements for those permittees. 

Among NPDES permits are those generally required for stormwater discharges from three sources: Municipal 

Separate Storm Sewer Systems (MS4) identified in EPA regulations, construction activities that disturb one or 

more acres, and industrial activities. MS4 regulations require that the permitted MS4, including storm-sewer 

systems serving populations of 100,000 or more and systems serving populations located within the 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 minimize 
61

effects on water quality. The post-construction program allows states to help protect aquatic life in receiving 

waters from flow alteration as development occurs. 

A substantial portion of the Nation’s impervious cover was created since the 1950’s, and the conversion of 

land types, including forest, meadow, prairie, and agriculture, to impervious cover is expected to continue. An 

increase in impervious cover increases runoff and affects NPDES permitting. According to the U.S. Department 

of Agriculture (USDA) National Resources Inventory, developed land area increased almost 600 percent, from 

18.6 to 111 million acres (7.5 to 44.9 million hectares), in the contiguous United States from 1954 to 2007 

(U.S. Department of Agriculture, 1997; U.S. Environmental Protection Agency, 2013c). From 1982 to 2007, 

more than 40 million acres of land—more than one-third of all land that has ever been developed in the 

contiguous United States—was newly developed (U.S. Department of Agriculture, 2009). Approximately 25 

percent of the land that has been developed in the United States is considered to be impervious (Elvidge and 

others, 2004; U.S. Department of Agriculture, 2009). Impervious surface area in the United States is projected 

to increase 14.2 percent from 2010 to 2040 (U.S. Environmental Protection Agency, 2009, 2010a). 

An increase in impervious surface cover will increase the amount of runoff. Substantial effects of runoff 

generally take one of two forms. The first is caused by an increase in the type and quantity of pollutants in 

stormwater runoff. These pollutants can become suspended in runoff and are carried to receiving waters, such 

as lakes, ponds, and streams, and can impair the aquatic life uses of these waters (see Section 4.4.3 for more 

information). The second kind of runoff effect occurs by increasing the quantity of water delivered to the 

water body as a result of storms. Increased impervious surface area (for example, parking lots, driveways, and 

rooftops) interrupts the natural process of gradual percolation of water through vegetation and soil, and the 

water that would percolate under natural conditions may instead be discharged through an MS4. The effects 

of this alteration include streambank scouring and downstream flooding, which can affect aquatic life and 

damage property (see Section 4.3.5 for more information). 
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 

rainfall from a 24-hour rain event (see Box G). This proactive approach using prior planning and design for the 

minimization of contaminant concentrations and erosive flows is a cost-effective approach to stormwater 

management. 
63

Box G. Stormwater and West Virginia Department of Environmental Protection (DEP) Municipal Separate 

Storm Sewer Systems (MS4) Permit Language

The West Virginia DEP issued a small MS4 permit including the language below for new and redevelopment 

projects to reduce effects from stormwater runoff at permitted sites:

“Performance Standards. The permittee must implement and enforce via ordinance and/or other enforceable 

mechanism(s) the following requirements for new and redevelopment: [....]”

“Site design standards for all new and redevelopment that require, in combination or alone, management 

measures that keep and manage on site the first one inch of rainfall from a 24-hour storm preceded by 48 

hours of no measurable precipitation. Runoff volume reduction is achieved by canopy interception, soil 

amendments, evaporation, rainfall harvesting, engineered infiltration, extended filtration, and/or 

evapotranspiration and any combination of the aforementioned practices. This first one inch of rainfall must 

be 100% managed with no discharge to surface waters.”

For a full compendium of this and other examples, see U.S. Environmental Protection Agency (2014c).

For additional examples of stormwater-related permits and their analysis, see U.S. Environmental Protection 

Agency (2012b).

5.7 Further considerations 

The discussion above is not meant to be a comprehensive assessment of all Federal CWA programs that may 

address flow and the protection of aquatic life uses. In addition to the approaches mentioned above, other 

non-CWA mechanisms exist that may protect aquatic ecosystems from alteration of flow. Although many of 

these programs may provide a method to specifically address these altered-flow effects, others may lack 

specified frameworks and (or) established methods to quantify targets to address the impacts of flow on

aquatic life uses, allowing room for supplemental considerations or the application of methods considered the 
64

“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. (The term “quantitative translation” encompasses the qualitative 

approaches described further in this section.) 

A fundamental goal of any effort to translate narrative flow criteria is to establish scientifically sound, 

quantitative flow targets that are readily implemented in State water quality management programs. This 

section describes a framework (illustrated in Figure 10) for developing quantitative flow targets for protection 

of aquatic life uses that incorporates elements of the EPA Guidelines for Ecological Risk Assessment (ERA) (U.S. 

Environmental Protection Agency, 1998), recent environmental flow literature (Arthington, 2012; Kendy and 

others, 2012; Poff and others, 2010), and procedures outlined in EPA guidance documents (U.S. Environmental 

Protection Agency 2000a, 2000b, 2001, 2008, 2010b). The framework is intended to be flexible; decisions 

regarding whether and how each step is applied depend on project-specific goals and resources. 

The framework presented in this section is organized into eight discrete steps that integrate science and policy 

(Figure 10). Steps 1 through 4 correspond to the “problem formulation phase” of the EPA ERA framework; 
66

Steps 5 through 7 represent the “analysis phase”; and Step 8 incorporates concepts from the “risk 

characterization” phase as an “effects characterization”. Throughout the process, opportunities for public and 

stakeholder involvement should be considered. Certain steps within this framework are particularly well 

suited for public participation (see discussion of Steps 1 and 8). The benefits of public involvement are 

twofold. First, public input can help strengthen the study design by incorporating suggested methods or 

addressing deficiencies identified in proposed approaches. Second, public involvement can foster a sense of 

support and ownership in the resulting flow targets, leading to streamlined implementation (Annear and 

others, 2004; Locke and others, 2008). 
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 used to evaluate 

whether goals are met. If, for example, a biological goal was to “maintain a cold-water fishery,” assessment 

endpoints could include spawning success rate and adult abundance for one or more cold-water fish species. 

Assessment endpoints use “neutral phrasing” in that they do not call for any desired level of achievement. The 

EPA document “Guidelines for Ecological Risk Assessment” (U.S. Environmental Protection Agency, 1998) 

outlines three main criteria for selecting assessment endpoints: (1) ecological relevance; (2) susceptibility to 

known or potential stressors; and (3) relevance to management goals. Selection of assessment endpoints can 
69

take into consideration available methods for measuring biological conditions, although endpoints without 

standard measurement protocols may be selected. Additional discussion of biological measures for 

quantitative analysis is provided in Section 6.6, and example endpoints are listed in Table 2. 

Biological goals and assessment endpoints defined during this step may be shared with the public for 

comment. Soliciting feedback at this step can improve public awareness of a state’s intent to quantitatively 

translate narrative flow criteria and promote transparency at the onset of the process, both of which are

crucial to the successful development and implementation of flow targets. 

6.2 Identify Target Streams 

Flow targets are quantified for a single stream, all streams within a geographic area (for example, a catchment 

or a state), or a subset of streams that satisfy a set of selection criteria. The second step in the framework for 

quantifying flow targets is to clearly define the spatial extent of the project and the target stream population. 

When multiple streams over a large area are the subject of study, it is advantageous to classify target streams 

according to their natural flow, geomorphic properties, temperature regimes, and other attributes. The 

purpose of stream classification is to identify groups of streams with similar characteristics so that data for 

each group are aggregated and extrapolated (Archfield and others, 2013; Arthington and others, 2006; Olden 

and others, 2011; Poff and others, 2010; Wagener and others, 2007). It is a key step described in EPA’s 

“Biological assessment program review” (U.S. Environmental Protection Agency, 2013a), the EPA technical 

guidance for developing numeric nutrient criteria for streams (U.S. Environmental Protection Agency, 2000a) 

and the Ecological Limits of Hydrologic Alteration (ELOHA) framework for developing regional flow standards 

outlined in Poff and others (2010). Stream classification based on flow, geomorphology, or other attributes 

should not be confused with the definition of stream condition classes that may serve as the basis of tiered 

biological thresholds or effects levels [see Section 6.8]. Additionally, although stream classification offers 
70

several benefits (Box H), it is not a requirement for successful development of quantitative flow targets (Kendy 

and others, 2012). 

Box H. Fundamentals of Stream Classification

Stream classification is the grouping of multiple streams into a smaller number of classes on the basis of 

shared hydrologic, physical, chemical, and (or) biological attributes. Stream classification is a valuable tool for 

quantifying flow targets because (1) data from multiple streams are pooled for analysis, and (2) conclusions 

drawn for a given class are reasonably applied to all streams in that class. A general goal of stream 

classification is to systematically arrange streams of the study area into groups that are unique in key 

attributes for environmental flow research and management (for example, catchment size and temperature 

regime, as in example Scenario A described in Section 6.9). The process requires compiling observed and

modeled data for the streams of interest, identifying metrics to serve as the basis of classification, and 

determining appropriate breakpoints for these metrics. Statistical methods such as correlation analysis, 

principal component analysis, regression, and cluster analysis are used to select metrics for classification and 

determine stream groupings. Important considerations include the types of data and attributes such as the 

number of classes, analytical methods, approaches to data gaps and uncertainty, and methods for evaluating 

results. As an example, a simple classification scheme may reflect the dependence of flow characteristics on 

catchment size and would require a database of stream drainage areas and the definition of drainage-area 

breakpoints for stream-size classes (for example—small, less than 50 square miles [mi2]; medium, 50–100 mi2;

large, greater than 100 mi2). A comprehensive review of stream classification to support environmental flow 

management is provided in Olden and others (2011) and Melles and others (2012). Example approaches are 

found in Seelbach and others (2006), Kennard and others (2010b), Kennen and others (2007), Reidy Liermann 

and others (2012), Melles and others (2012), and Archfield and others (2013).
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, historical 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 flow-regime component is believed to drive one or more biological responses. The 

pathways leading to indirect biological responses to flow alteration (that is, those mediated by habitat or 

water quality change) are clearly depicted. Conceptual models developed as part of this process are therefore 

much more detailed than the general model presented in Section 4 (Figure 2). 

The EPA Causal Analysis/Diagnosis Decision Information System (CADDIS) Web site includes a conceptual 

diagram of potential biological responses to several types of flow alteration (Figure 11) that may serve as a 

useful starting point for conceptual model development; other existing conceptual diagrams can be 

considered. Although this example does not include climate change as a source of flow alteration, climate 

effects on flow and biota can be conceptualized to more accurately reflect climate as a dynamic component of 

the ecosystem. Relations among climate, flow, and aquatic life might already be apparent from past studies, 

particularly if a state has undertaken a climate-change vulnerability assessment. (See Appendix C for 

additional discussion and examples of climate-change vulnerability and assessments.) Where information on 

climate change effects does not already exist, available climate, hydrologic, and biological literature may be 

synthesized to infer potential types of flow alteration and potential biological responses. 

The conceptual models resulting from this step of the framework are used to guide subsequent analysis of 

flow targets, including the selection of biological and flow variables and analysis methods. In general, 

conceptual models created for flow target development contain a similar structure, but focus on stressors and 
73

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 Partnership9, or state agencies. Sampling methods, 

including the attributes measured, timing, equipment used, habitat type sampled, and taxonomic 

classification, are reviewed for each biological dataset. These and other sampling protocols are important for 

evaluating whether and how data from multiple sources are synthesized. A thorough discussion of potential 

data compatibility issues is provided in Cao and Hawkins (2011) and Maas-Hebner and others (2015). 

The literature and data review will likely reveal information gaps that hinder the quantification of flow targets. 

Common issues include a lack of biological data for streams with long-term flow data or a lack of reference 

biological or flow data with which to evaluate alteration. Depending on the scope of the effort, additional 

monitoring or modeling may be required to fill such gaps. 

 

9

 The National Fish Habitat Partnership has created data for every stream reach and catchment in the United States, available at 

http://www.tandfonline.com/doi/full/10.1080/03632415.2011.607075#.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 analyze the relations between flow 

alteration and biological response (termed “flow-ecology” relations). Flow indicators correspond to “measures 

of exposure” in the EPA ERA framework, whereas biological indicators correspond to “measures of effect.” 

Biological indicators reflect narrative flow criteria and can include various measures of the diversity, 

abundance, or specific life-history traits of fish, macroinvertebrates, and aquatic vegetation. Many flow 

indicators have been proposed to characterize the flow regime; these indicators describe the magnitude, 

timing, frequency, duration, and rate of change of various flow conditions. They are calculated from long-term 

daily flow datasets, and software tools are available to automate this process (for example, Henriksen and 

others, 2006; The Nature Conservancy, 2009; and the USGS EflowStats “R” package which is available at 

https://github.com/USGS-R/EflowStats). Example flow and biological indicators that have been used in past 

studies of flow-ecology relations are listed in Table 2. These examples are only a small subset of the full 

universe of indicators that could be considered for a target-setting effort. 

The biological indicators selected for analysis ideally are consistent with narrative flow criteria and the 

biological goals and assessment endpoints developed under Step 1 of this framework. Ideally, the biological 

indicators selected directly reflect the biological attributes of concern described by assessment endpoints (for 

example, fish diversity). In cases where assessment endpoints cannot be directly measured or have limited 

observational data for flow-ecology modeling, surrogate biological indicators are linked to assessment 

endpoints through additional analysis. For example, if an assessment endpoint involves a rare fish species with 

few monitoring records, a surrogate biological indicator is selected by identifying a data-rich species with 

similar life-history traits. (See Merritt and others [2010] or Mims and Olden [2012, 2013] for examples of 

methods for grouping biota by life-history strategies.) 
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 

component

Flow indicators (measures of exposure) Biological 

component

Biological

indicators (measures of effect)

Reference

Magnitude Mean June–July flow;

Mean August flow

Fish Fish density;

Fish abundance

Peterson and Kwak (1999);

Zorn and others (2008)

Magnitude Spring maximum flow;

Summer median flow

Fish Fish abundance;

Fish-assemblage composition

Freeman and others (2001)

Magnitude Magnitude of 10-year low-flow event Fish Fish Index of Biotic Integrity;

Fish-species richness

Freeman and Marcinek (2006)

Magnitude Mean annual flow; 

Base-flow index

Macroinvertebrates Macroinvertebrate abundance; 

Macroinvertebrate assemblage;

composition

Kennen and others (2014)

Castella and others (1995)

Magnitude Maximum flow; 

Ratio of maximum to minimum flow

Macroinvertebrates Macroinvertebrate Index of Biotic 

Integrity;

Macroinvertebrate species richness

Morley and Karr (2002)

Magnitude Magnitude of 1-, 2-, 5-, 10-, and 20-year flood 

events

Macroinvertebrates Macroinvertebrate O/E (ratio between 

the observed and expected) scores; 

Macroinvertebrate-assemblage

composition

Nichols and others (2006)
78

Flow 

component

Flow indicators (measures of exposure) Biological 

component

Biological

indicators (measures of effect)

Reference

Magnitude Summer diversion magnitude Macroinvertebrates Macroinvertebrate abundance Wills and others (2006)

Timing Date of annual maximum flow;

Date of annual minimum flow

Fish Fish abundance; 

Fish-assemblage composition

Koel and Sparks (2002)

Frequency Number of days above mean annual flow; 

Number of events above 75% exceedance flow 

value

Macroinvertebrates Macroinvertebrate Index of Biotic 

Integrity

Macroinvertebrate richness

Booth and others (2004)

Kennen and others (2010)

Frequency Number of flood events; 

Number of low-flow events

Riparian

vegetation

Riparian tree abundance

Lytle and Merritt (2004)

Duration Duration of high-flow events; 

Duration of low-flow events

Fish Fish abundance; 

Fish-assemblage composition

Koel and Sparks (2002)

Rate of change Mean rise rate; 

Mean fall rate

Fish Fish abundance; 

Fish-assemblage composition

Koel and Sparks (2002)
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, 

2010b). 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, 2010b). Where feasible, 

confounding variables should be factored into the development of quantitative flow-ecology models. In 
81

practice, researchers have dealt with this issue by explicitly including possible confounding variables in 

preliminary models (for example, Carlisle and others,. 2010), by using modeling approaches that implicitly 

assume the presence of other confounding factors (for example, Konrad and others, 2008; Kennen and others, 

2010), or, at a minimum, acknowledging that potential confounding factors were not included in modeling 

efforts, but that other evidence indicates that their influence likely was minimal (for example, Merritt and 

Poff, 2010). 

Available data may be insufficient to support quantitative flow-ecology modeling, or that data or analytical 

limitations result in quantitative relations with a low level of statistical significance. In such cases, qualitative 

flow-ecology modeling is a practical alternative. Qualitative modeling does not attempt to uncover precise 

numerical relations between flow and biological indicators. Rather, the objective is to describe relations 

between variables based on hypothesized cause-effect associations using any available evidence. Qualitative 

modeling can help identify the direction of flow-ecology relations, and possible thresholds for degraded 

conditions, in data-limited environments. 

The conceptual models discussed in Sections 4.1 and 6.4 are examples of qualitative models; however, it may 

be useful to reformulate conceptual models in terms of the flow and biological indicators selected for analysis. 

Qualitative models can incorporate numerical flow alteration and biological response thresholds reported in 

relevant literature, and (or) available data on reference flow and biological conditions. Such models are 

sometimes referred to as semiquantitative because they include numeric values but, unlike quantitative 

models, do not allow for precise predictions across the full spectrum of flow alteration. Qualitative modeling 

can incorporate a set of decision rules for combining and weighting conclusions from existing studies that used 

inconsistent study designs and data (Webb and others, 2013). An example approach to flow-target 

development using qualitative modeling is described in Section 6.9 (see Table 3 and Figure 14).
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 evaluated and adjusted to ensure that the desired goals are achieved. 

The adaptive management approach is continually informed and updated by results of monitoring, research, 

and experimentation to address specific uncertainties. (See Richter and others [2003] and Konrad and others 

[2011] for specific examples.) 
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 represents one potential application of the framework discussed in 

this section (Section 6) to quantitatively translate the following narrative flow criterion: Changes to the natural 

flow regime shall not impair the ability of a stream to support characteristic fish populations. The two 

scenarios differ in their approach to several framework steps. These scenarios are not intended to convey 

recommended methods, but rather describe example approaches for each step and demonstrate the 

adaptability of the framework to project-specific goals and available resources. 

Scenario A is a case in which a state incorporates existing numeric biological condition criteria and an ample 

hydrologic and biological dataset for quantitative flow-ecology modeling, in which the resulting flow-ecology 

curves are used as a focal point for estimating effects, identifying acceptable effects levels, and selecting 

numeric flow targets. In Step 1, biological goals and assessment endpoints are selected from state WQS, which 

define minimum acceptable values 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 state’s WQS do not include biological criteria that establish assessment endpoints defining biological 

goals, so the state takes appropriate actions, and includes stakeholder input, to identify specific biological 

goals that are consistent with its designated aquatic life uses. This effort identifies specific fish species and 

functional groups that are key to ensuring attainment of the state’s designated aquatic life uses and, in turn,

establishes the goals for interpreting the state’s narrative flow criteria. In Step 2, the decision is made to 

include all streams in the state in the effort and opt not to address stream classification until after the 

literature review of flow-ecology relations is complete. Literature reviewed in Step 3 demonstrates clear links 

between fish health and a broad range of flow components. Because documented relations are consistent 

across stream size and ecoregion, stream classification is not pursued. The conceptual models developed in 

Step 4 summarize known and hypothesized flow needs of fish, organized by fish species/functional group, 

season, and flow characteristic. Data compiled in Step 5 focus on streamflow, with long-term records used to 

calculate reference and affected values of more than 50 flow metrics to evaluate the sensitivity of each metric 

to anthropogenic sources of flow alteration. On the basis of this analysis and evidence for biological sensitivity, 

a subset of flow metrics is selected in Step 6. A lack of biological data is determined to prohibit quantitative 

flow-ecology modeling; therefore, qualitative modeling is undertaken in Step 7 to reframe conceptual models 

in terms of the subset of flow indicators identified during Step 6. In Step 8, participating agencies review 

available evidence to estimate effects associated with increasing levels of hydrologic change and, with public 
86

input, use effects estimates to set targets that express the maximum allowable deviation from reference 

conditions for each flow indicator. 

Although the examples in Scenarios A and B are largely hypothetical, components were drawn from real-world 

examples. Many more case studies of flow-target quantification can be found in Colorado Division of Water 

Resources and Colorado Water Conservation Board (2009), Cummins and others (2010), DePhilip and Moberg 

(2010), Kendy and others (2012), Kennen and others (2013), Richardson (2005), and Zorn and others (2008).
87

Table 3. Example applications of the framework to quantitatively translate the following narrative flow criterion: “Changes to the natural flow regime 

shall not impair the ability of a stream to support characteristic fish populations.” 

Framework Step Scenario A: Quantitative Example Scenario B: Qualitative Example 

(1) Link narrative 

criteria to biological 

goals and assessment 

endpoints

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: to maintain the abundance of riffle obligate species.

(2) Define scope of 

action: identify target 

streams 

Statewide stream classification is undertaken that builds on prior stream 

mapping and fish-ecology research. Individual stream segments are 

assigned to one of 10 stream classes according to catchment size and 

water-temperature regime, characteristics known to affect fish 

distributions. Example stream class: cold headwater.

All streams in the state are included in the effort to develop flow targets. 

As a result of data and resource constraints, the need for stream 

classification following the literature review is evaluated.

(3) Conduct literature 

review

Literature is reviewed to identify flow-regime changes that most affect

the condition of fish communities. Relevant literature points to summer 

base-flow depletion as a key factor in reduced fish diversity and 

abundance throughout the state. 

Literature is reviewed to highlight flow-dependent life history and habitat 

traits of fish species/functional groups referenced in Step 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. On the basis of these findings, 

a systematic stream classification is not needed. 
88

Framework Step Scenario A: Quantitative Example Scenario B: Qualitative Example 

(4) Develop 

conceptual models

Conceptual models depict pathways between anthropogenic sources of 

summer base-flow depletion and effects on fish populations. Important 

relations include reduced food availability for both benthic and watercolumn taxa as a result of reduced wetted-channel perimeter and water 

depth.

Conceptual models summarize known and hypothesized flow needs of fish, 

organized by fish species/functional group, season, and flow characteristic. 

(5) Conduct data 

inventory

A database of existing flow and fish-survey records is prepared. Observed 

data are augmented with predictions from previous hydrologic modeling 

efforts. Modeled data include reference and present-day values of 

median monthly streamflow for every stream segment in the state.

Long-term daily flow records, land-use information, and water-use data are 

compiled. Reference streams (those with minimal flow alteration) and 

affected streams are identified. Flow records for these sites are used to 

calculate reference and affected values of 50 or more flow metrics. The 

sensitivity of each flow metric to anthropogenic sources flow alteration is 

quantified by comparing reference and affected values. 

(6) Identify flow and 

biological indicators

to serve as measures 

of exposure and 

effect

Two indicators are selected for quantitative flow-ecology modeling: fish 

Index of Biotic Integrity score and the percent reduction in August 

median flow (relative to reference conditions).

A subset of the flow metrics quantified in Step 5 is selected for flow-target 

development. Metrics are evaluated according to their sensitivity to 

anthropogenic sources flow alteration and evidence of biological 

relevance. Flow indicators describe magnitude and frequency 

characteristics of high/flood flows, seasonal/average flows, and 

low/drought flows.

(7) Develop flowecology models Regression modeling is undertaken by using monitoring and modeling 

data from sites with paired flow and biological data. Final models 

Qualitative flow-ecology models are developed by reframing conceptual 

models in terms of the flow indicators selected in Step 6 (Figure 14). 
89

Framework Step Scenario A: Quantitative Example Scenario B: Qualitative Example 

(termed “fish response curves”; see Figure 13) quantify the relation 

between fish IBI scores and reduced August median flow. Fish response 

curves are generated for each of the 10 stream classes defined in Step 2. 

(8) Estimate effects

and identify 

acceptable levels

Fish response curves are divided into high, medium, and low effects

levels and shared with stakeholders to guide discussion of acceptable 

levels. Because of model uncertainty, participating agencies and 

stakeholders add a 5-percent margin of safety to fish IBI thresholds 

defined in Step 1 and agree that flow alteration resulting in IBI scores 

below this threshold present an unacceptable effects to fish 

communities. Flow targets determined from fish response curves and 

acceptable effects levels are selected for each stream class. Targets are 

expressed as a maximum allowable percentage reduction in August 

median flow by stream type.

Participating agencies review available evidence to estimate effects 

associated with increasing levels of hydrologic change. For some flow 

indicators, past studies indicate the likelihood of high effect of biological 

degradation under any magnitude of flow change. For others, healthy 

biotic communities are observed under moderate flow change and are 

determined to pose a lower effect if altered. This information is shared 

with stakeholders to further refine effects estimates and levels of flow 

alteration presenting unacceptable effects to stream biota. The outcome 

of these discussions is a set of targets expressing the maximum allowable 

deviation from reference conditions for each flow indicator that will 

protect the aquatic life use.

Follow-up and 

adaptive 

management

Participating agencies continue to collect flow and fish-community data. 

A plan is developed to assess flow targets every 5 years by analyzing new 

and historic data for evidence of their effectiveness. 

Participating agencies continue to collect flow and fish-community data. A 

plan is developed to assess flow targets every 5 years by analyzing new and 

historic data for evidence of their effectiveness. 
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

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Appendix A. Overview of the Clean Water Act and Water Quality Standards Relevant to the 

Development and Use of Criteria for Hydrologic Condition 

In 1972, with the objective of protecting lakes, rivers, streams, estuaries, wetlands, coastal waters, the ocean, 

and other water bodies, the U.S. Congress enacted comprehensive amendments to the Federal Water 

Pollution Control Act, now commonly known as the Clean Water Act (CWA). The overall objective of the CWA 

is to "restore and maintain the chemical, physical and biological integrity of the Nation’s waters" (Section 

101(a)). In addition, the CWA establishes as an interim goal "water quality which provides for the protection 

and propagation 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). 
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A1. Designated Uses and Existing Uses 

EPA’s regulatory provisions regarding designated uses are defined in 40 CFR Section 131.10. Designated uses 

are those uses specified in the state’s WQS for each water body or segment regardless of whether or not 

those uses are actually being attained. Designated uses are a state’s concise statements of its management 

objectives and expectations for each of the individual surface waters under its jurisdiction and may include 

(but are not limited to) propagation of fish, shellfish and wildlife (including protection of human health when 

consuming aquatic life), recreation, agricultural uses, industrial uses, navigation, and (or) public water supply. 

Water quality criteria are adopted to protect the designated uses. When designating uses and adopting 

criteria, states and tribes must consider the WQS of downstream waters, and ensure that the designated uses 

and criteria provide for the attainment and maintenance of the WQS of downstream waters (40 CFR Section 

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: 
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





Historical/current water quality; 

Historical/current biological condition; and 

Historical pattern, frequency, and type of use. 

Once a use has been designated for a particular water body or segment that designated use may be removed 

under specific conditions. If a designated use is an existing use for a particular water body or segment, 

however, it cannot be removed unless a use requiring more stringent criteria is added. As described in 40 CFR 

Section 131.10(g), when removing a use for those uses specified in CWA Section 101(a)(2) or subcategories of 

such a use, the state or authorized tribe must demonstrate through a Use Attainability Analysis (UAA) that 

attaining the use is not feasible because of one the six factors provided in the regulation. Additionally, if the 

state or authorized tribe adopts a new or revised water quality standard based on a required UAA, they must 

also adopt the highest attainable use (defined at 40 CFR Section 131.3(m)). If a state or authorized tribe wishes 

to remove or revise a designated use that is a unrelated to the protection and propagation 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; and 
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 Include sufficient parameters (at acceptable concentrations and levels) to support protection of the 

designated uses of a particular water body, including the most sensitive use. 

States adopting numeric criteria may either adopt the recommended criteria that EPA publishes into their 

WQS, modify the EPA criteria to reflect site-specific conditions, or use other scientifically defensible methods 

(40 CFR Section 131.11(b)(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 and EPA regulations 

in 131.12(a) (40 CFR Section 131.12(b)). The state’s or authorized tribe’s antidegradation policy must ensure 

the maintenance and protection of existing uses of a water body and the level of water quality necessary to 

protect those existing uses (Tier 1); maintain and protect water quality where the quality exceeds the levels 

necessary to support propagation of fish, shellfish, and wildlife and recreation in and on the water, unless the 

state or authorized tribe finds that allowing lower water quality is necessary to accommodate important 

economic or social development in the area where the waters are located (Tier 2); and provide for the 

maintenance and protection of water quality in outstanding national resource waters identified by the state or 

authorized tribe (Tier 3). The state or tribal antidegradation policy and implementation methods must be 

consistent with EPA regulations, although states may adopt antidegradation statements that are more 

protective than those prescribed by EPA. 
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

Appendix B. Legal Background and Relevant Case Law

The U.S. Environmental Protection Agency (EPA) notes that it has been argued “that the Clean Water Act is 

only concerned with water ‘quality,’ and does not allow the regulation of water ‘quantity.’” Public Utility 

District No. 1 of Jefferson County v. Washington Department of Ecology (“PUD No.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’ concern with the physical and biological 

integrity of water – refutes petitioners’ assertion that the Act draws a sharp distinction between the 

regulation of water ‘quantity’ and water ‘quality’.” 511 U.S. 719. 

The Court held that the State of Washington had authority to impose minimum flow conditions on a 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

In S.D. Warren Co. v. Maine Board of Environmental Protection (“S.D.Warren”) 547 U.S. 370, 385 (2006), the 

Supreme Court held that “Congress passed the Clean Water Act to ‘restore and maintain the chemical, 

physical, and biological integrity of the Nation’s waters,’....the ‘national goal’ being to achieve ‘water quality 

which provides for the protection and propagation 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-induced alteration of 

the chemical, physical, biological, and radiological integrity of water.” Id. “The alteration of water quality as 

thus defined is a risk inherent in limiting flow and releasing water through turbines. Warren itself admits that 

its dams “can cause changes in the movement, flow and circulation of a river .... caus[ing] a river to absorb less 

oxygen and to be less passable by boaters and fish...” Id. “Changes in the river like these fall within a State’s 

legitimate legislative business, and the Clean Water Act provides for a system that respects the State’s 

concerns.” 547 U.S. at 386. The Court upheld the State of Maine’s CWA Section 401 certification requiring 

minimum flows to protect the designated fishing and recreational uses of an affected water body for which 

Maine did not have an explicit flow criterion. 

The Supreme Court, in PUD No.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 Energy 
137

Regulatory Commission (FERC), 495 U.S. 490, 498 (1990), construing an analogous provision of the Federal 

Power Act, where the Court explained that “minimum stream flow requirements neither reflect nor establish 

proprietary rights” to water. 511 U.S. at 720. 

In reaching its decision upholding the State’s authority to require minimum streamflow requirements 

necessary to protect state water quality standards, the Court noted that its view was reinforced by the 1977 

amendments to the CWA adding Section 101(g). The Court quoted from the Library of Congress, Congressional 

Research Service, Environmental Policy Division (1978): “The requirements [of the Act] may incidentally affect 

individual water rights....It is not the purpose of this amendment to prohibit those incidental effects. It is the 

purpose of this amendment to [e]nsure that State allocation systems are not subverted, and that effects on 

individual rights, if any, are prompted by legitimate and necessary water quality considerations.” 511 U.S. at 

721.
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 not 
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only a way to protect and restore rivers and streams from anthropogenic stressors, but it may also be a means 

of adapting to climate-change. 

Not all rivers and streams are equally vulnerable to the effects of climate change. An assessment of 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).
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Box I. Components of Climate-Change Vulnerability

The paragraphs that follow briefly describe the primary components of climate-change vulnerability that may 

be included in climate vulnerability assessments: exposure, sensitivity, and adaptive capacity. An in-depth 

discussion of these components is available in Glick and others (2011) and Poff and others (2012). Generalized 

case examples available in Glick and others (2011) demonstrate assessment approaches for climate 

vulnerability assessments across various ecosystems and species, both aquatic and terrestrial. Examples that 

focus on watershed vulnerability and aquatic resources are included in Furniss and others (2013). An 

additional resource (U.S. Environmental Protection Agency, 2014a) is a workbook for organizations managing 

environmental resources that provides a two-part process to carry out vulnerability assessments and develop 

effects-based adaptation plans for strategic climate-change plans. 

Exposure: Exposure generally refers to the character, magnitude, and rate of climatic changes (Glick and 

others, 2011). Results of climate model simulations such as regional climate projections or downscaled climate 

projections, though accompanied by uncertainty, can help to estimate the range and location of potential 

climate change. Identifying sources of increased past variability may also be helpful (for example, paleoclimate 

records of tree-rings). Those changes that are ecologically significant (for example, those that affect an 

assessment endpoint) are considered as exposure metrics (for example, snowpack vulnerability, winter water 

temperature, aridity index, monthly precipitation, winter peak flows, freeze and thaw days, etc.) Additional

examples of exposure metrics used in case studies are given in Furniss and others (2013). 

Sensitivity: Climate sensitivity is the degree to which a system, habitat, or species is (or is likely to be) altered

by or responsive to a given amount of climate change (in this case, climate-induced hydrologic changes in 

particular) (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. For 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 watershed (see the Beechie and others [2013] example in Box K). Many of the intrinsic 

attributes at the landscape level (for example, geology, soil, topography) affect the sensitivity of the aquatic 

ecosystem to any stressor. For example, the rate at which shifts in stream temperature can occur is driven by 

variables such as stream slope and interannual variability—so the rate at which temperature gradients shift 

are variable, even within a given basin, and statistically significant signals may not be detected for decades

(Isaak and Reiman, 2013). The intrinsic factors that affect sensitivity at the population scale may include 

environmental tolerance range (for example, thermal tolerances), mobility, genetic adaptation, and range or 

population size.

Adaptive Capacity: Adaptive capacity is the ability of a species or system to cope with or adjust to climatechange effects with minimal disruption (Glick and others, 2011). It is also a subset of system resilience and can 

help managers assess vulnerability for use in decision making. Ecosystems and aquatic organisms can cope 

with climate change in different ways; for example, they may migrate, shift to more suitable microhabitats, or 

persist in place (for example, phenotypic plasticity) (Dawson and others, 2011). On a landscape scale, some 

vulnerability assessment approaches include landscape/river connectivity under this component. Many 

adaptive capacity factors may be those pre-existing conditions that future management conditions can 

address (for example, reducing fragmentation of a water body, thereby preventing mobility to more suitable 

conditions, such as cooler temperatures) (Glick and others, 2011). The Pacific Northwest salmon restoration 

case study (Box K) provides some examples of restoration practices Beechie and others (2013) identified as 

adaptive activities that may ameliorate some of the expected climate changes and increase habitat diversity 

and salmon population resilience.
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Box J. California’s Climate-Change Vulnerability Index

The goal of the California Integrated Assessment of Watershed Health (U.S. Environmental Protection Agency,

2013b) was to identify and better protect healthy watersheds by integrating data and making them available 

to planning agencies for improved coordination of monitoring and prioritization of protection efforts. The 

primary partners included the U.S. Environmental Protection Agency (EPA) and the Healthy Streams 

Partnership (HSP), an interagency workgroup of the California Water Monitoring Council. The assessment 

partners identified and integrated 23 indicators of watershed health, stream condition, and watershed 

vulnerability to characterize relative watershed health and vulnerability across California. The indicators used 

in this assessment reflect the reality that multiple ecological attributes and anthropogenic effects play a role in

watershed and stream health, and need to be considered together. 

The integrated watershed vulnerability index used in the assessment of watershed health is a composite of 

four vulnerability indices that may change from 2010 to 2050 (land cover, wildfire severity, water use, and 

climate change). The composite climate-change vulnerability index, in turn, is composed of seven component 

metrics of estimated climate-change parameters using projections from Cal-Adapt, a collaboration of several 

institutions that modeled downscaled hydrologic response across California by using temperature and 

precipitation projections produced from global general circulation models (GCMs). The interagency partners 

used the modeled outputs to evaluate the relative response of watersheds in California to future climate 

change, but the models did not explicitly simulate effects on ecosystem health or watershed processes 

(although they are certainly related to the modeled inputs), nor was the sensitivity of those watersheds to 

such changes a focus of this screening-level assessment. Rather, the vulnerability index is meant to be 

assessed with the composite indices of stream health and watershed condition to help prioritize protection 

opportunities.
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The HSP used annual precipitation, mean base flow, mean surface runoff, and snowpack (as snow water 

equivalent) as the hydrologic responses to projected climate change because they were identified as the 

primary indicators affecting stream hydrology. It also identified annual temperature maximum, minimum, and 

mean as climate variables that may affect future watershed vulnerability. The interagency partners calculated 

the percent difference between projected values of these indicators (that is, component metrics of exposure) 

from 2050 and 2010.

The composite results of the vulnerability assessment (Figure C-1) illustrate the climate exposure primarily in 

terms of its effects on temperature and hydrology-related parameters in this example. Overall, the climate 

vulnerability component of this assessment identified the greatest vulnerability for northern California as a 

result of a combination of expected temperature increases and changes in snowpack, surface runoff, and base

flow. 

This screening-level assessment is an instructive example that may help inform the protection of healthy 

watersheds based on climate-change vulnerability. However, the assessment combined other vulnerability 

indices—land cover, water use, and fire-regime class (which can affect surface erosion, sediment deposition, 

and stream temperature)—with climate change as characteristics that could modify (exacerbate or 

ameliorate) overall vulnerability. Additionally, this assessment not only sought to develop priorities based on 

ecosystem vulnerability, but also a comprehensive understanding of the overall status of the aquatic 

ecosystem. For the entire assessment, stream condition, watershed health, and vulnerability were considered. 

For more information, see U.S. Environmental Protection Agency (2013b)

(http://www.epa.gov/sites/production/files/2015-11/documents/ca_hw_report_111213_0.pdf ).
144

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. (Additional component metrics including projected 

change in precipitation, mean temperature, maximum temperature, and baseflow are shown in U.S. 

Environmental Protection Agency [2013b], available at

http://water.epa.gov/polwaste/nps/watershed/integrative_assessments.cfm.) 
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Box K. Addressing Regional Climate-Change Effects on Salmon Habitat in the Pacific Northwest: Examples 

for Prioritizing Restoration Activities

Salmon habitat restoration is a prominent issue in the Pacific Northwest; however, a need exists to better 

understand whether current restoration activities and priorities will be effective under future climate 

conditions. Beechie and others (2013) sought to address this issue by providing insight into ways in which a 

restoration plan might be altered under various climate-change scenarios. 

The authors developed a decision support system to adapt salmon recovery plans to address climatemediated stream temperature and flow changes in order to both ameliorate climate effects and increase 

salmon resilience. To guide the effort, the researchers mapped scenarios of future stream temperature and 

flow and performed a literature review of current restoration practices.

The authors modeled stream temperature and flow from a multimodel average of daily gridded precipitation 

and air temperature. By using the variable infiltration capacity (VIC) model, the inputs were used to predict 

daily runoff, runoff routing, and stream temperature and flow. (Additional information on the specifics of the 

development of these parameters are found in Beechie and others [2013].) The scenario mapping exercise 

compared historical baseline (1970–99) water temperature and flow conditions to those projected for the 

periods 2000–29, 2030–69, and 2070–99. The researchers modeled mean monthly flows, calculating the 

change in magnitude and timing of maximum monthly flows between the future period and the historical 

baseline for each stream cell. They modeled and mapped stream temperature directly. The results indicated 

lower summer flows (35–75 percent lower), higher monthly maximum flows (10–60 percent higher), and 

higher air and stream temperatures (maximum weekly mean temperature 2–6 oC [degrees Celsius] higher). 

Snowmelt-dominated hydrologic regimes across the region almost entirely disappeared by the 2070–99 time 

period, and transitional (rain-snow mix) hydrologic regimes contracted substantially as well. By the final 2070–
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 known thermal thresholds and seasonal flows 

needed during different salmonid life stages (Figure C-2). 

Beechie and others (2013) carried out a literature review to identify restoration practices that could 

ameliorate expected changes in streamflow (base-flow decrease and peak-flow increase) and stream 

temperature, and increase habitat diversity and population resilience. The primary activities most likely to do 

so include restoring flood-plain connectivity, restoring streamflow regimes, and reaggrading incised stream 

channels. 

This Pacific Northwest salmonid restoration example combines projected climate-exposure information and 

known ecological sensitivities of salmonid species to improve understanding of potential vulnerability to 

climate change. This knowledge can help inform management plans to prioritize restoration practices that are 

more likely to be effective under projected climate scenarios.
147

.

Figure C- 2. Diagram showing effect of climate change on life stages of salmonids through time, by season. 

(Modified from Beechie and others, 2013; white rectangles represent the freshwater life-history stage of 

salmonids, gray boxes represent the ocean stage, and stippled lines indicate an alternate life-history)

The science of incorporating climate change into environmental flow assessments is young and complex. 

Considerations for incorporating climate change into the framework for developing flow targets to protect 

aquatic life discussed in Section 6 and illustrated in Figure 10 are presented below. This information can help 

identify which ecologically significant flow indicators may be most affected by climate change (as determined 

from the observed trends and projections). These examples can help elucidate relative climate effects (that is, 

vulnerability) related to flow targets and the aquatic life uses they are designed to protect. States and tribes 
148

can more effectively prioritize limited resources and identify new management actions more strategically to 

increase aquatic-ecosystem resilience. This framework is meant to be a qualitative assessment to rank relative 

effects, which may help in identifying and ranking adaptive management actions in later steps. In a 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. 
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Table C1. Incorporating climate-change considerations into the framework for quantifying flow targets. 

 

Framework component Potential climate-change considerations 

(1) Formally link narrative 

criteria to biological goals 

May not be applicable to Step 1 unless climate changes affect biological expectations. 

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

(3) Conduct literature 

review 

Consider all potential climate-change-related effects that could eventually threaten the target 

streams. Identify available climate-change reports relevant to the region or state water resources. 

Identify potential changes in ecologically relevant flow components from both observed trends and 

projected changes. It may be helpful to create broad categories of effects and list specific stressors 

by type for consideration in conceptual model development. 

(4) Develop conceptual 

models

Include climate change in development of conceptual models. Consider how climate-related 

stressors can affect biological goals from various pathways, building on the findings obtained from 

the literature review. The level of detail should be commensurate with the level of detail for 

planning or screening. 

(5) Inventory data Identify which of the available observed hydrologic, climatic, and biological data may be affected by 

climate-related stress identified in preceding steps. Consider observed data/projected information 

to identify the already or potentially affected biological indicators and (or) flow indicators/flowregime components. Rate them considering the following qualitative categories: consequences 

(low, medium, high); likelihood (low, medium, high); spatial extent (site, watershed, region); time 

until problem begins (decades, within next 15 to 30 years, already occurring/likely occurring).

Consider sensitivity: Do some characteristics of the catchment increase or decrease sensitivity to 

these climate stressors (for example, north-facing aspect or high elevations may reduce sensitivity 

of snowmelt or water temperature to increased air temperature, whereas south-facing aspect or

low elevations may increase sensitivity).
150

Framework component Potential climate-change considerations 

(6) Identify biological and 

flow indicators

Identify which biological and flow indicators may be most affected by climate change. Rate them by 

considering the qualitative categories previously mentioned (consequence, likelihood, spatial 

extent, time until problem begins). 

(7) Develop qualitative or 

quantitative flow-ecology 

models 

Climate change considerations may not be applicable to Step 7.

(8) Identify acceptable 

biological condition 

goals/effects levels

Compare range of potential likely climate changes to the potential flow targets.

(9) Select candidate flow 

targets

Compare range of potential likely changes to the actual selected flow target. 

Identify management adaptation actions and determine which of them are most appropriate given 

the likely effect to flow targets/biological goals.

(10) Monitor, evaluate, and 

periodically refine flow 

targets

Assess observed climate and hydrologic data for any emerging climate-change related trends in 

variability of magnitude, frequency, duration, timing, and rate of change of flow. Identify and assess 

new or updated climate-change projections. Are the updated projections consistent with observed 

trends and (or) other existing projected information? How are the updated projections ecologically 

significant? Do the updated climate change projections merit reassessment of acceptable effects

levels and the ability to meet environmental flow targets under current management practices? 

As discussed in this appendix, climate change may challenge the management of aquatic resources because 

past variability is no longer a reliable assumption for the future. However, protection of environmental flows 

can serve as an adaptation tool, increasing resilience so that a system is more likely to recover from the effects 
151

of 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, whereas the 

Pacific Northwest example (Box K) additionally accounts for potential effects of climate exposure on

assessment endpoints, in large part on the basis of the sensitivity of the biota and their life stages. The 

information developed during a climate-change vulnerability assessment can help managers identify 

differential effects to aquatic resources and understand the reasons that their resources are at risk so they can 

set priorities and develop appropriate management responses. 

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