EPA/600/R-10/054 | July 2010 | www.epa.gov/ord 

Coral Reef Biological Criteria: Using the Clean 

Water Act to Protect a National Treasure
 

Office of Research and Development | National Health and Environmental Effects Research Laboratory
	

EPA/600/R-10/054 

July 2010 

www.epa.gov/ord 

Coral Reef Biological Criteria

Using the Clean Water Act 

to Protect a National Treasure
 

by 

Patricia Bradley Leska S. Fore Atlantic Ecology Division Statistical Design NHEERL, ORD 136 NW 40th St. 33 East Quay Road Seattle, WA 98107 Key West, FL 33040 

William Fisher Wayne Davis 

Gulf Ecology Division Environmental Analysis Division 

NHEERL, ORD Office of Environmental Information 

1 Sabine Island Drive 701 Mapes Road 

Gulf Breeze, FL 32561 Fort Meade, MD 20755 

Contract No. EP-C-06-033
 

Work Assignment 3-11
 

Great Lakes Environmental Center, Inc
 

Project Officer: Work Assignment Manager: 

Susan K. Jackson Wayne Davis 

Office of Water Office of Environmental Information 

Washington, DC 20460 Fort Meade, MD 20755 

National Health and Environmental Effects Research Laboratory 

Office of Research and Development 

Washington, DC 20460 

Printed on chlorine free 100% recycled paper with 

100% post-consumer fiber using vegetable-based ink. 
Notice and Disclaimer 
	

The U.S. Environmental Protection Agency through its Office of Research and Development, 

Office of Environmental Information, and Office of Water funded and collaborated in the 

research described here under Contract EP-C-06-033, Work Assignment 3-11, to Great Lakes 

Environmental Center, Inc. It has been subject to the Agency’s peer and administrative review and 

has been approved for publication as an EPA document. Mention of trade names or commercial 

products does not constitute endorsement or recommendation for use. 

This manual provides technical guidance to states, territories, and commonwealths to establish 

water quality criteria and standards under the Clean Water Act (CWA), to protect aquatic life 

from the effects of pollution. Under the CWA, states and territories are to establish water quality 

criteria to protect designated uses. State and territorial decision makers retain the discretion 

to adopt approaches on a case-by-case basis that differ from this guidance when appropriate 

and scientifically defensible. While this manual constitutes the U.S. Environmental Protection 

Agency’s (EPA) scientific recommendations regarding biological criteria to help protect coral reef 

ecosystem quality and aquatic life, it does not substitute for the CWA or EPA’s regulations; nor is 

it a regulation itself. Thus, it cannot impose legally binding requirements on EPA, states, territories 

or the regulated community, and might not apply to a particular situation or circumstance. EPA 

may change this guidance in the future. 

This is a contribution to the EPA Office of Research and Development’s Ecosystem Services 

Research Program, Coral Reefs Project. 

The appropriate citation for this report is: 

Bradley P, Fore L, Fisher W, and Davis W. 2010. Coral Reef Biological Criteria: Using the Clean 

Water Act to Protect a National Treasure. U.S. Environmental Protection Agency, Office of 

Research and Development, Narragansett, RI. EPA/600/R-10/054 July 2010. 

This document can be downloaded from EPA’s website for Biological Indicators of Watershed 

Health: http://www.epa.gov/bioindicators 

ii 
Preface
 

The Earth is a Blue Planet. 

Oceans cover about 70% of the globe. 

Coral reefs are the largest living structures on the planet. 

Coral reefs are one of the most threatened 

marine ecosystems. 

Intended Audience 

This manual has been written to support coral reef managers in United States jurisdictions (see 

map in Figure P-1), including: 

•		 Caribbean Basin (Commonwealth of Puerto Rico, U.S. Virgin Islands, and Navassa Island) 

•		 Gulf of Mexico (Flower Garden Banks) 

•		 Atlantic Ocean (southeast Florida and the Florida Keys) 

•		 Pacific Ocean (American Samoa, Commonwealth of the Northern Mariana Islands, Guam, 

Hawaii, Pacific Remote Island Areas) 

When the term “state” is used throughout the manual it is intended to represent any U.S. jurisdiction, 

which includes states, territories, tribes and commonwealths. In all jurisdictions with coral reefs, the 

Clean Water Act applies to marine and coastal systems within the 3-mile territorial waters. 

"State” in this document includes all states, territories, 

tribes, and commonwealths. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure iii 
Figure P-1. Map of United States 

Jurisdictions with Coral Reefs. 

Coral reef ecosystems are managed by a variety of federal and state agencies (Table P-1). 

Table P-1. Managers whose decisions potentially impact coral reef ecosystems. 

Types of Managers Role Scale 

Policy Makers Develop laws and regulations Federal/Regional/State 

Environmental Managers Implement and enforce federal/ 

state/territorial environmental 

laws and regulations 

Regional/State 

Natural Resource Managers Manage parks, sanctuaries, 

refuges, etc. 

Federal/Regional/State 

Local Government Managers Enforce land-use rules, permits 

and zoning 

Local 

iv 
Coral reef managers work for many different organizations both within government (at the 

federal, state, and local levels) and for non-profit organizations. While they all have a general 

responsibility to protect coral reefs, their authorities and roles can be quite varied, including: 

• Pollution prevention, including various permitting authorities 

• Coral reef protection 

• Coral reef restoration 

• Fisheries management 

• Park/sanctuary management 

This document uses the general term coral reef manager in reference to all of these roles. 

Coral Reef Managers work for many different 

organizations both within government (at the federal, 

state, and local levels) and for non-profit organizations. 

While they all have a general responsibility to protect 

coral reefs, their authorities and roles can be quite 

varied, including: pollution prevention, including various 

permitting authorities; coral reef protection; coral reef 

restoration; fisheries management; and park/sanctuary 

management. 

Reef managers and government scientists aren’t the only people interested in 

protecting coral reefs. All U.S. citizens are stakeholders. The Clean Water Act 

includes many opportunities for citizens and other stakeholders to comment, 

understand and influence regulatory decisions either during mandated public 

comment periods or through citizen lawsuits (USC33, §1365 and §505). 

Stakeholders include: 

• Residents of local communities adjacent to coral reefs 

• Tourists and the tourism industry 

• Fishermen and other marine-based industries 

• Land-based industries and commercial enterprises 

• Conservation and environmental groups 

• Research organizations 

• Educational institutions 

Citizen suit provisions USC33, 

§1365 and §505. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure v 
 

 

 

 

Why You Should Read This 

Coral reef managers have challenging jobs. This is truer now than ever before. First and foremost, 

coral reef ecosystems are declining, threatened by a variety of human activities including polluted 

runoff from agriculture and land-use practices, over-fishing, ship groundings, coastal development 

and climate change, as well as with natural stressors such as tropical storms, bleaching and 

disease that may also be increasing due to human actions. Second, coral reef managers are 

often faced with a lack of information, lack of resources, and lack of political will to take the actions 

necessary to protect or restore coral reef ecosystems. Finally, coral reef managers must navigate 

a complex web of federal, state, and local legislation—legislation that is too often duplicative, 

difficult to understand, and challenging to coordinate. 

If you are a coral reef manager, you are already aware Biological Criteria: A of many on-the-reef approaches to management. This description of the desired document will show you how to use the Clean Water Act natural aquatic community (CWA) and coral reef biological criteria (biocriteria) as part based on the numbers of a comprehensive framework to organize your protection and kinds of organisms efforts and make them more meaningful through enforceable expected to be present in coastal and watershed regulations. a water body and serve as 

the standard against which If you are a stakeholder, this document will show you how assessment results are the CWA and other management tools can be combined into compared. Biocriteria can a comprehensive watershed-based management approach also be used to determine for coral reefs and other coastal ecosystems. aquatic life use attainment 

and can be formally adopted The responsibility for implementing coral reef biocriteria lies 

with the state and federal coral reef managers. However, to into a state’s water quality 

standards (EPA 2002). be successful, their actions must be guided and informed by 

the knowledge, energy and resources of scientists and other 

stakeholders. 

How to Use This Manual 

Ask the Right Questions. This document is organized—in general—around broad questions that 

correspond to the needs of coral reef managers. The questions are part of the scientific and 

management discussion, and are topics with which most coral reef managers will be readily 

familiar. These questions are also essential to the development of scientifically sound coral reef 

biocriteria. 

• Why do we care about coral reefs? 

• What do we want to protect? 

• What should we measure? 

vi 
• How do we assess reef condition? 

• How are the reefs doing (are they getting better or worse)? 

• How do we account for reef variability? 

• What’s causing reefs to change? 

• What can we do to protect reefs? 

• Do our efforts protect reefs? 

These questions are the titles for chapters that describe the basis for biocriteria development 

under the CWA. Although the manual is intended as informational, rather than a “how-to” 

document, the issues related to these questions become a part of biocriteria development (Table 

P-2). 

Key Terms 

Where appropriate, this manual defines important terms in 

these text boxes. The first time a key term appears in the 

document, it will be both italicized and bolded. 

Important legislative citations are 

emphasized in these boxes 

Many states have incorporated biocriteria for freshwater and estuarine waterbodies. Examples 

of their development and application can be found at EPA’s Biocriteria Website (http://www.epa. 

gov/waterscience/biocriteria). Much of the information in this report draws from this combined 

experience. Information on planning, assessment and management needs for development of 

coral reef biocriteria are outlined. Table P-2 briefly summarizes some of the important steps, which 

are sometimes simultaneous and iterative, and where in this report these steps are discussed. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure vii 
Table P-2. Top ten steps for establishing a coral reef biocriteria program, who is usually responsible for completing 

those steps, and where in this report the steps are discussed. 

# Steps to Coral Reef Biocriteria Responsible Parties Chapters 

Planning 

1 

Establish aquatic life protection goals 

for state waterbodies and identify 

designated uses 

State water quality agency, coral reef 

managers and stakeholders through a 

public process 

1, 2, 3 

2 Develop an antidegradation policy 

and implementation procedures 

State water quality agency with public 

notification and participation 1 

3 

Develop a conceptual coral reef 

Biological Condition Gradient (BCG) 

to target potential decision points 

State water quality agency, reef 

scientists and managers 6 

Assessment 

4 

Develop indicators that are relevant, 

efficient and responsive to human 

disturbance 

State water quality agency and reef 

scientists 4 

5 

Characterize reference conditions 

(minimal human disturbance) and 

select decision thresholds (criteria) 

that support designated uses 

State water quality agency and reef 

scientists 6, 7 

6 

Initiate a long-term monitoring 

program to determine aquatic life use 

attainment 

State water quality agency and reef 

scientists 5 

Management Response 

7 

Report reef conditions and status of 

attainment for designated uses and 

aquatic life use goals 

State water quality agency 

1, 8 

8 Determine cause(s) of any impaired 

waterbodies 

State water quality agency and reef 

scientists 9 

9 

Implement management activities 

that restore the biological condition of 

impaired waterbodies 

State water quality agency, reef 

scientists, reef and watershed 

managers with notification of 

stakeholders 

9 

10 

Review aquatic life protection goals 

and the relationship to designated 

uses 

State water quality agency, reef and 

watershed managers with stakeholders 

through a public process 

1, 2, 3 

Additional material is provided in the Appendices, including a list of Acronyms and Abbreviations 

(A), a Glossary (B), a Bibliography (C), and Common Questions and Their Answers (D). 

viii 
Contents
 

Notice and Disclaimer.................................................................................................. ii
 

Preface........................................................................................................................... iii
 

Executive Summary ..................................................................................................... xiii
 

Acknowledgements...................................................................................................... xv
 

Chapter 1. The Clean Water Act: A Critical Asset..................................................... 1-1
 

1.1. The Clean Water Act: Integrity of the Nation’s Waters.............................................1-2
 

1.2. Water Quality Standards..........................................................................................1-5
 

1.2.1. Designated Uses .....................................................................................................1-6
 

1.2.2. Water Quality Criteria ..............................................................................................1-8
 

1.2.3. Antidegradation........................................................................................................1-10
 

1.3. Submittal and Approval of State Water Quality Standards ......................................1-11
 

1.4. Emergence of Biological Criteria .............................................................................1-12 

Chapter 2. Why Do We Care About Coral Reefs?..................................................... 2-1
 

Chapter 3. What Should Be Protected?..................................................................... 3-1
 

Chapter 4. What Should We Measure?...................................................................... 4-1
 

4.1. Selecting Indicators ..................................................................................................4-1
 

4.2. Evaluating Indicators ................................................................................................4-4
 

Chapter 5. How Do We Assess Reef Condition? ..................................................... 5-1
 

5.1. Probabilistic Sampling Design ..................................................................................5-2
 

5.2. Implementing a Probabilistic Survey.........................................................................5-6
 

5.3. Trend Detection ........................................................................................................5-8
 

5.4. Analyzing Data from a Probabilistic Survey..............................................................5-9
 

Chapter 6. How Are Reefs Doing? ............................................................................ 6-1
 

6.1. Impairment Thresholds .............................................................................................6-2
 

6.2. Application of Thresholds..........................................................................................6-5
 

6.3. Threshold Trends......................................................................................................6-7
 

Chapter 7. How Do We Account for Reef Variability? .............................................. 7-1
 

7.1. Spatial Variability ......................................................................................................7-1
 

7.2. Temporal Variability...................................................................................................7-3
 

7.3. Climate Change Variability........................................................................................7-5
 

Chapter 8. What Is Causing Reefs to Change? ....................................................... 8-1
 

Chapter 9. What Can We Do to Protect Reefs? ....................................................... 9-1
 

9.1. CWA and Existing Coral Reef Management Programs ............................................9-2
 

9.2. Biocriteria and Other CWA Programs .......................................................................9-6
 

9.3. Biocriteria Can Link CWA and CAA to Address Ocean Acidification.........................9-10
 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure ix 
Contents (con’t)
 

Chapter 10. Do Our Efforts Protect Reefs? .............................................................. 10-1
 

Appendices 

A. Acronyms and Abbreviations ......................................................................................A-1
 

B. Glossary .....................................................................................................................B-1
 

C. Bibliography ................................................................................................................C-1
 

D. Common Questions and Their Answers......................................................................D-1
 

E. DPSIR Framework ......................................................................................................E-1
 

F. Ocean Acidification ......................................................................................................F-1
 

G. CWA and Existing Coral Reef Management Programs ..............................................G-1
 

H. Biocriteria and Other CWA Programs .........................................................................H-1
 

x 
Figures 

Figure P-1. Map of United States jurisdictions with coral reefs ......................................iv
 

Figure 1-1. Components of Water Quality Standards ....................................................1-6
 

Figure 1-2. Five principal factors that influence and determine the integrity 

of surface water resources...........................................................................1-12
 

Figure 1-3. Biological assessments can sometimes detect impairment 

when chemical criteria do not ......................................................................1-13
 

Figure 1-4. Disagreement between biological and chemical assessments ....................1-16
 

Figure 2-1. Scuba diver enjoying coral reef....................................................................2-1
 

Figure 2-2. Victorian cameo brooch................................................................................2-1
 

Figure 2-3. Coral reefs provide important graphic and design elements........................2-2
 

Figure 2-4. State of Florida “Protect our Reefs” specialty license plate..........................2-5
 

Figure 4-1. Schematic diagram depicting proposed sampling along a 

gradient of human disturbance.....................................................................4-3
 

Figure 5-1. Contrasting survey designs for coral reefs around St. Croix, 

U.S. Virgin Islands........................................................................................5-4
 

Figure 5-2. Comparison of random and non-random sampling design ..........................5-5
 

Figure 6-1. The challenge of establishing thresholds ....................................................6-2
 

Figure 6-2. Biological Condition Gradient (BCG)............................................................6-3
 

Figure 6-3. Human Disturbance Gradient.......................................................................6-5
 

Figure 7-1. Scales and coral reef communities ..............................................................7-1
 

Figure 8-1. Conceptual model of stressors impacting a coral reef .................................8-2
 

Figure 9-1. Examples of coral reef management programs that may be 

supported by biocriteria................................................................................9-2
 

Figure 9-2. Managing tourism.........................................................................................9-4
 

Figure 9-3. The coastal watershed .................................................................................9-5
 

Figure E-1. Conceptual relationships among DPSIR sectors.........................................E-2
 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure xi 
 

Tables
	

Table P-1. Managers whose decisions potentially impact coral
 

reef ecosystems ............................................................................................iv
 

Table P-2. Top ten steps for establishing a coral reef biocriteria program, who is 

usually responsible for completing those steps, and where in this report 

the steps are discussed.................................................................................viii
 

Table 1-1. Biological diversity on coral reefs is evident from the number of species 

identified in two reports .................................................................................1-3
 

Table 2-1. Examples of goods and ecological services of coral 

reef ecosystems ............................................................................................2-4
 

Table 3-1. Relationship of designated use, ecosystem function, biological 

components, and ecosystem services ..........................................................3-1
 

Table 3-2. Examples of designated uses relevant to coral reefs ....................................3-2
 

Table 4-1. Stony coral metric testing...............................................................................4-5
 

Table 4-2. Types of measurements and examples of indicators for coral reef 

benthic communities .....................................................................................4-8
 

Table 6-1. Example of a rotating panel design for the U.S. Virgin Islands......................6-7
 

Table 7-1. Comparison of elements for characterizing reference condition....................7-4
 

Table 8-1. Examples of commonly observed biological responses characteristic 

for particular coral reef stressors...................................................................8-3
 

Table 9-1. Actions needed to protect coral reefs and whether they can 

be addressed under the authority of the U.S. Clean Water Act.....................9-3
 

xii 
Executive Summary 

The Clean Water Act (CWA) (33 U.S.C. § 1251 et seq. 1972) can be a powerful legal instrument 

for protecting water resources, including the biological inhabitants of coral reefs. The objective 

of the CWA is to restore and maintain the chemical, physical and biological integrity of water 

resources. The full intent of the CWA may be obscured by its name. Clean water is a goal partly 

because clean water supports biological communities; but the communities themselves are 

also protected. Biological integrity is a long-term objective of the CWA and, like its physical and 

chemical counterparts, biological standards and criteria can be defined to protect valued aquatic 

resources. The valued resources for coral reefs are the organisms that form the living reef 

community. Coral reef communities are, in fact, a national treasure. 

Biological criteria (biocriteria) are an important addition to existing management tools for coral 

reef ecosystems. Simply stated, biocriteria are expectations set by a jurisdiction for the quality 

and quantity of living aquatic resources in a defined waterbody. Biocriteria follow the same 

process and can draw on some of the same CWA authorities as the more familiar chemical and 

physical criteria. Biological criteria can be part of a state’s water quality standards which include 1) 

designated uses to reflect goals for the waterbody, 2) numeric or narrative criteria (thresholds) to 

protect and support the designated uses, and 3) antidegradation policies to help protect all waters 

from deterioration. The CWA requires that states have water quality standards, monitor conditions 

regularly, and submit reports summarizing water quality assessments, usually every two years. 

Reporting is a critical element: If criteria are not met, the waterbody is reported as impaired—this 

triggers a series of management actions to determine the cause of impairment and then restore 

the waterbody and its resident biota. 

Water quality standards for biological condition provide an opportunity to reverse the decline of 

coral reef condition. Although chemical and physical standards are intended to protect biota, they 

are not always sufficient. Biological standards, by tracking the condition of reef living systems, 

establish a direct process to determine whether a waterbody is achieving its biological goals. 

Biocriteria are complementary; they do not supersede or replace physical and chemical criteria. 

Biocriteria may be particularly important for coral reefs because bioassessments reflect the 

integrated effects of multiple and cumulative stressors, detect impairment that might be missed 

by physical and chemical criteria (e.g., overfishing or habitat loss), resonate with managers and 

stakeholders, and have been found (at least in freshwater systems) to be cost effective. 

Physical, chemical and biological criteria are intended to augment and support decision making 

and management through a defined regulatory process. Water quality standards must be 

scientifically sound, defensible to jurisdictional stakeholders (including the regulated community), 

and able to withstand legal challenge. Many states have implemented biological assessment 

programs for rivers, streams, estuaries and wetlands and are moving through the formal process 

to adopt biocriteria. A systematic and defensible approach has emerged from this process. This 

manual provides information and experience gained in these freshwater programs for application 

to development of coral reef biocriteria. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure xiii 
An extensive technical literature is available to connect readers to the legal and regulatory 

background developed for freshwater and estuarine resources. This document does not repeat 

or replace that literature, but provides a synopsis with focused application to coral reefs. It is 

intended to address questions often asked by coral reef managers, scientists, and stakeholders 

in the context of biocriteria. Included are approaches for determining what to protect, what 

to measure, reef assessments, thresholds, and response variability. Also included are brief 

descriptions of procedures for determining cause of waterbody impairment and gauging the 

success of management programs. 

Biocriteria are not a stand-alone proposition—they should build on existing programs to manage 

and protect coral reefs. In fact, biocriteria provide a framework that should help to link monitoring 

and reporting programs with regulatory and management decisions. Implementation of biocriteria 

should be viewed not so much as a new program but more as an opportunity to strengthen 

existing programs. Nine critical needs for coral reef conservation were summarized from the 2008 

International Coral Reef Symposium (Dodge et al. 2008): 

1. Cut CO2

 emissions by lowering our carbon footprint and ask our policy-makers to 

commit to low carbon economic growth.
 

2.	 Eliminate open access fisheries in coral reef ecosystems and instead establish and 

enforce regulations on user rights, total allowable catch, individual catch quotas, 

nondestructive gear, and other sustainable fisheries regulations. 

3.	 Protect coral reef herbivores, including parrotfish, by banning the harvesting of these 

species for sale and commercial consumption. 

4. Establish and strictly enforce networks of Marine Protected Areas that include No-Take 

Areas. 

5. Effectively manage the waters between Marine Protected Areas. 

6. Maintain connectivity between coral reefs and associated habitats; mangroves, sea 

grass beds, and lagoons contribute to the integrity of reef ecosystems and their 

continued production of ecosystem services. 

7. Report regularly and publicly on the health of local coral reefs. 

8. Recognize the links between what we do on land and how it affects the ocean. 

9. Bring local actors together—including members of industry, civil society, local 

government, and the scientific community—to develop a shared vision of healthy reefs 

and a road map for getting there. 

Biocriteria are worthy of this challenge. Within an integrated management approach, coral reef 

biocriteria can advance all nine needs (Fore et al. 2009). 

xiv 
 

Acknowledgements
	

This Coral Reefs report was prepared by the U.S. Environmental Protection Agency (EPA) Office 

of Research and Development (ORD). The principal authors for this report are: 

Patricia Bradley 

USEPA 

Office of Research and Development 

National Health and Environmental Effects 

Research Laboratory 

Atlantic Ecology Division 

c/o FKNMS 

33 East Quay Road 

Key West, FL 33040 

Leska Fore 

Statistical Design, Inc. 

3518 Fremont Ave. N #504 

Seattle, WA 98103 

William Fisher 

USEPA 

Office of Research and Development 

National Health and Environmental Effects 

Research Laboratory 

Gulf Ecology Division 

1 Sabine Island Drive 

Gulf Breeze, FL 32561 

Wayne Davis 

USEPA 

Office of Environmental Information 

Environmental Analysis Division 

701 Mapes Road 

Ft. Meade, Maryland 20755-5350 

EPA was supported in the development of this report by the Great Lakes Environmental Center, 

Inc., through contract EP-C-06-033, 

The production of this report would not have been possible without the participation of the people 

recognized below. 

Juanita Soto-Smith (Great Lakes Environmental Center) was responsible for document layout and 

design. 

Nancy Cunningham provided artwork. 

Photos from: Alan Humphrey (EPA ERT), Charles LoBue (EPA Region 2), Patricia Bradley 

(EPA ORD/NHEERL/AED), Wendy Wiltse (EPA Region 9), Jim Maragos (U.S. Fish and Wildlife 

Service), and Wayne Davis (EPA OEI). 

Many thanks to Key Accents and So Du Gallery in Key West for allowing us to photograph coral 

reef inspired decorative items and jewelry in their stores. 

The report was peer reviewed by Aaron Hutchins (The Nature Conservancy), Charles LoBue (U.S. 

Environmental Protection Agency), Ku-ulei Rodgers (University of Hawai’i, Hawai’i Institute of 

Marine Biology), James R. Karr (University of Washington), Russ Frydenborg (Florida Department 

of Environmental Protection), Cheryl Woodley (National Oceanic and Atmospheric Administration), 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure xv 
Virginia Engle (U.S. Environmental Protection Agency), Walt Galloway (U.S. Environmental 

Protection Agency), and Walter Berry (U.S. Environmental Protection Agency). Thanks to Virginia 

Houk (EPA ORD/NHEERL) for managing the external peer review. 

Additional technical reviews and information were provided by EPA Office of Water staff including: 

Joe Beaman, Thomas Gardner, John Lishman, Steve Sweeney, Bryan Goodwin, Gary Russo, 

Wade Lehmann, Sarah Lehmann, Susan Jackson, Holly Green, Joan Warren and Barbara Pace 

(EPA Office of General Counsel). 

Wayne Jackson and Charles LoBue (EPA Region 2), Carl Goldstein, Michael Mann, and Wendy 

Wiltse (Region 9), and Brian Keller (NOAA) provided information pertaining to jurisdictions. 

Key Words: 

biocriteria, biological criteria, coral reefs, coral, Biological Condition Gradient, BCG, Clean Water 

Act, water quality criteria 

We wish to also acknowledge the EPA Coral Reef Biocriteria Working Group, which has 

representatives from EPA Program and Regional Offices to foster development of coral reef 

biocriteria as specified in the Clean Water Act (CWA) through focused research, evaluation, and 

communication among Agency partners and interactive implementation with U.S. jurisdictions. 

This report is prepared for partial fulfillment of goals under ORD’s Water Quality and Ecosystem 

Services Research Programs. 

xvi 
1. The Clean Water Act: A Critical Asset
 

A thing is right when it tends to preserve the integrity, stability, and “ beauty of the biotic community. It is wrong when it tends otherwise. ” - Aldo Leopold, 1949 

Few can argue the beauty of coral reefs and the importance of preserving their integrity. Reefs 

worldwide are admired for the diversity of form, color, and movement. From solid massive corals 

to intricately branched gorgonians waving in the currents and brightly-colored fish darting among 

the crevices, a coral reef inspires the human imagination. And that’s not all. Benefits to humans 

from coral reefs are legion. Coral reefs provide edible fish and invertebrates, shoreline protection, 

construction material, pharmaceutical products, tourism opportunities, serve a host of ecological 

purposes, and are a source of cultural and social interactions. 

Despite the many natural benefits we receive from coral reefs, human actions threaten their 

existence. Stresses from air and water pollution, from food harvests, and from the physical 

presence of humans on and near reefs are creating environmental conditions that are detrimental 

to this vulnerable ecosystem. Concerted management, backed by strong community support, has 

made effective inroads toward protection of coral reefs and the valuable benefits they provide. Yet 

many reefs are still in decline and many are at increasing risk. 

One of the most influential mechanisms available for aquatic resource protection is the U.S. Clean 

Water Act (CWA). It was enacted to protect the integrity of the Nation’s waters, including biological 

components such as coral reefs. Many facets of the CWA are already employed in maintaining the 

high water quality imperative for coral reef persistence. However, the broad authority of the CWA 

is not being used to its full potential. 

States are tasked under the CWA to adopt water quality standards that include criteria for 

acceptable physical, chemical and biological condition. Biological criteria (biocriteria) are simply 

thresholds for biological condition that are adopted by states as part of water quality standards. 

Biological thresholds are no different than chemical thresholds (i.e., concentration limits) for toxic 

pollutants—both establish goals for condition of the waterbody. A potential strength of coral reef 

biocriteria is the capacity to integrate ongoing reef management activities into community-held 

goals for coral reef condition. 

The purpose of this manual is to describe procedures and concepts related to implementation of 

biocriteria for coral reefs. First, though, it is important to have a basic understanding of the CWA. 

The CWA represents the Nation’s commitment to protecting and restoring the Nation’s waters. 

While the CWA has traditionally been perceived and implemented to address end-of pipe chemical 

pollutants (Richmond et al. 2007), its mandate is much broader. The CWA is clearly intended to 

protect both water quality and biological resources, including coral reefs in territorial waters (Karr 

1991; Jameson et al. 2001). Moreover, the CWA provides an opportunity to integrate scientific 

knowledge with community goals for management of coral reef resources (Keller and Cavallaro 

2008; Fore et al. 2009). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-1
 
1.1 The Clean Water Act: Integrity of the Nation’s Waters 

The overall objective of the Clean Water Act (CWA) is to restore and maintain the chemical, 

physical and biological integrity of the Nation’s waters. To achieve this objective, the Act sets out 

several national goals, including the goal of section 101 (a) (2): Wherever attainable, an interim 

goal of water quality that provides for the protection and propagation of fish, shellfish and wildlife 

and recreation in and on the water. 

As one of several approaches to 

achieving these goals, Section 303 

of the Act tasks states with adopting 

water quality standards. Water 

quality standards are provisions 

of state law or regulation that: 

define the water quality goals of 

a water body, or segment thereof, 

by designating the use or uses to 

Federal Water Pollution Control Act
 

[As Amended Through P.L. 107-303, 

November 27, 2002] 33 U.S. Code 1251 et seq.
 

Also known as: The Clean Water Act 

Public Law 92-50033 U.S. Code 1251 et seq. 

be made of the water; set criteria 

necessary to protect the uses; 

and protect water quality through 

antidegradation provisions. 

While the CWA gives the 

Environmental Protection 

Agency (EPA) an important 

role in determining appropriate 

minimum levels of protection and 

providing national oversight, it 

also gives considerable flexibility 

and discretion to states to design 

their own programs and establish 

protective levels. States adopt 

water quality standards to protect 

public health or welfare, enhance 

the quality of water, and serve the purposes of the Act. “Serve the purposes of the Act” (as 

defined in Sections 101(a), 101(a)(2), and 303(c) of the Act) means that water quality standards 

should: (1) include provisions for restoring and maintaining chemical, physical, and biological 

integrity of state waters, (2) provide, wherever attainable, water quality for the protection and 

propagation of fish, shellfish, and wildlife and recreation in and on the water (fishable/swimmable 

where attainable), and (3) consider the use and value of state waters for public water supplies, 

propagation of fish and wildlife, recreation, agricultural and industrial purposes, and navigation. 

1-2 Chapter 1 — The Clean Water Act: A Critical Asset 
Integrity implies an intact condition, or the quality or state of being complete or undivided. 

Biological integrity means a natural, fully-functioning living system of organisms and 

communities plus the processes that generate and maintain them. The “living system” 

incorporates a variety of scales—from individuals to landscapes—and is embedded in a dynamic 

evolutionary and biogeographic context (Karr 2006). 

Biological Integrity: A balanced, integrated, adaptive community 

of organisms having a species composition, diversity, and 

functional organization comparable to that of the natural habitat of 

a region (Karr and Dudley 1981). 

Biological integrity also means that reef organisms (including those in Table 1-1) have a clean, 

healthy environment to support them, including habitats for propagation, nurseries, and refugia. In 

this context, a fully functioning coral reef ecosystem may include adjacent supporting ecosystems 

such as seagrasses and mangroves. 

Table 1-1. Biological diversity on coral reefs is evident from the number of species identified in two reports, 

one in Hawai’i (Eldredge and Miller 1995) and one in southern Gulf of Mexico (Tunnell et al. 2007). 

Even greater diversity may be found at other locations. Examples of different species morphologies are 

presented. 

Hawai’i Gulf of 

Mexico Examples 

“Algae” (Diatoms, red, green, 

blue-green and brown algae) 100’s 100’s 

Foraminiferans 

(Phylum Granuloreticulosa) 100’s >100 

Mangroves, sea grasses 

(Division Magnoliaphyta) 

Sponges ~100 ~25 (Phylum Porifera) 

Corals, anemones, jellies >200 ~80 (Phylum Cnidaria) 

Segmented worms, 

polychaetes 100’s ~40 

(Phylum Annelida) 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-3
 
Table 1-1 (con’t). Biological diversity on coral reefs is evident from the number of species identified in two 

reports, one in Hawai’i (Eldredge and Miller 1995) and one in southern Gulf of Mexico (Tunnell et al. 2007). 

Even greater diversity may be found at other locations. Examples of different species morphologies are 

presented. 

Hawai’i Gulf of 

Mexico Examples 

Ostracods, crabs, shrimp 

(Phylum Arthropoda) 100’s 100’s 

Bivalves, snails, octopus, 

mollusks, nudibranches 100’s 100’s 

(Phylum Mollusca) 

Stars, urchins 

(Phylum Echinodermata) >100 ~50 

Tunicates 

(Phylum Chordata) ~50 ~25 

Vertebrates 

(Subphylum Vertebrata) >1000 100’s 

Fishes, sharks, rays 100’s 100’s 

Turtles, snakes ~20 ~10 

Marine mammals ~25 ~10 

1-4 Chapter 1 — The Clean Water Act: A Critical Asset 
1.2 WaterQuality Standards 

Coral reef protection and restoration under the Clean Water Act begins with water quality 

standards. Water quality standards are provisions of state or federal law which consist of a 

designated use or uses for the waters of the United States and water quality criteria for such 

waters sufficient to protect such uses (Figure 1-1). Additionally, water quality standards contain 

an antidegradation policy and implementation procedures, which describe what will be done to 

protect existing water quality. Water quality standards are intended to protect the public health 

or welfare, enhance the quality of water and serve the purposes of the CWA. State water quality 

standards have two important functions: They establish the water quality goals for a waterbody, 

and they provide a regulatory basis for controls beyond the so-called “technology based” 

requirements that the Act talks about in Sections 301 and 306. 

Water Quality Standards: are provisions of state or federal law which consist 

of a designated use or uses for the waters of the United States and water 

quality criteria for such waters based upon such uses. Water quality standards 

are to protect public health or welfare, enhance the quality of the water and 

serve the purposes of the Act (EPA 1994). 

Water quality standards are the basis of a wide range of water quality management activities, 

including: (1) monitoring water quality to provide information to make decisions about whether 

or not a waterbody is attaining standards or is “impaired”, (2) calculating total maximum daily 

loads (TMDLs) for waters impaired by one or more pollutants, (3) developing state water quality 

management plans which prescribe the regulatory, construction, and management activities 

necessary to meet the water body goals, (4) calculating National Pollution Discharge Elimination 

System (NPDES) water quality-based effluent limitations for point sources, (6) preparing various 

reports and lists that document the condition of the state’s water quality, and (7) developing, 

revising, and implementing an effective control strategy for nonpoint sources of pollution (per CWA 

Section 319). 

States are required to establish water quality standards that define the goals and pollution limits 

for all waters within their jurisdictions, including waters of the territorial seas. The CWA identifies 

territorial seas as a belt of ocean waters extending three miles (or more in some states) from 

shore. In essence, water quality standards translate CWA goals into measurable objectives, such 

as the protection and propagation of fish, shellfish and wildlife, or recreation in and on the water 

(EPA 1994). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-5
 
 

Figure 1-1. Components of Water Quality Standards 

The responsibility for adopting water quality 

standards lies with state environmental 

agencies, but it is imperative that those 

affected by the standards are involved 

in the process. Designated uses, in 

particular, should represent the values 

of the community. People are more 

likely to support actions that protect the 

environmental resources they value. 

It is also important that states consult 

with the EPA Regional Office at an early 

stage of development because EPA must 

review the standards to ensure they meet 

the requirements of the CWA. EPA will 

approve state standards that meet the 

requirements, but will disapprove those 

that do not and could promulgate federal 

standards in their place. 

Designated Uses: Uses 

specified in Water Quality 1.2.1 Designated Uses Standards for each water 

The first step for developing water quality standards is to body or segment whether

or not they are being designate the purposes, or uses, to be protected for each 

waterbody. It is in designating uses that states establish attained (40 CFR 131.3f).

Designated uses are a the environmental goals for their water resources and are state’s concise statements of allowed to evaluate the attainability of those goals. its management objectives 

Designated uses are those uses specified in the water and expectations for each of 

quality standards for each water body or segment, the individual surface waters 

whether or not they are being attained (See 40 CFR 131.3 under its jurisdiction. 

and 40 CFR 131.10). The “use” of a water body is the 

most fundamental articulation of its role in the aquatic 

and human environments, and all of the water quality 

protections established by the CWA follow from the water’s designated use. 

The overall objective of the CWA is to restore and maintain the chemical, physical and biological 

integrity of the Nation’s waters. Biological integrity does not necessarily represent an aquatic 

system untouched by human influence, but does represent one that is balanced, adaptive and 

reflects natural evolutionary processes. Designated uses and criteria to protect those uses in state 

and tribal water quality standards programs provide one means of achieving biological integrity. 

1-6 Chapter 1 — The Clean Water Act: A Critical Asset 
Over the years, states have created many different use classification systems ranging from a 

straightforward replication of uses specifically listed in Section 303 of the Act to more complex 

systems that express designated uses in very specific terms or establish sub-classifications which 

identify different levels of protection. 

For coral reef ecosystems, instead of a 

generic aquatic life use or “protection of fish 

and shellfish” use, states may include in their 

water quality standards descriptions of goals 

(uses) and water quality criteria or conditions 

to protect those uses specifically tailored for 

coral reef viability or restoration. Aquatic life 

use is the designated use that is measured by 

biocriteria. 

States often weigh the environmental, social and economic consequences of their decisions 

in designating uses. Reaching a conclusion on the uses that appropriately reflect the potential 

for a water body, determining the attainability of those goals, and appropriately evaluating the 

consequences of a designation, however, can be a complicated task. Appropriate application of 

this process involves a balancing of environmental, scientific, technical, and economic and social 

considerations as well as public opinion. 

Section 131.10 of the CWA describes states’ responsibilities for designating and protecting uses. 

The regulation requires that states: specify the water uses to be achieved and protected; requires 

protection of downstream uses; allows for sub-category and seasonal uses, for instance, to 

differentiate between cold water and warm water fisheries; sets out minimum attainability criteria; 

lists six factors of which at least one must be satisfied to justify removal of designated uses which 

are not existing uses; prohibits removal of existing uses; establishes a mandatory upgrading of 

uses which are existing but not designated; and establishes conditions and requirements for 

conducting use attainability analyses. 

Aquatic Life Use (ALU): A beneficial use 

designation in which the waterbody provides 

suitable habitat for survival and reproduction 

of desirable fish, shellfish, and other aquatic 

organisms (EPA 2009a). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-7
 
 

These provisions make a distinction between existing and designated uses and set out specific 

requirements to ensure protection of these two broad use categories. Designated uses are defined 

as those uses specified in water quality standards for each water body or segment, whether or not 

they are being attained. EPA interprets existing uses as those uses actually attained in the water 

body on or after November 28, 1975 (the date of EPA’s initial water quality standards regulation), 

whether or not they are included in water quality standards. Designated uses focus on the desired 

or attainable condition while existing uses focus on the past or present condition. Section 131.10 

then links these two broad use categories in a manner which intends to ensure that States 

designate appropriate water uses, reflecting both the existing and attainable uses of each water 

body. 

The water quality standards regulation effectively establishes a “rebuttable presumption” that 

“protection and propagation/recreation in and on the water” uses of Section 101 (a) are indeed 

attainable, and therefore should apply to a water body unless it is affirmatively and credibly 

demonstrated that such uses are not attainable. This demonstration is often made through a “use 

attainability analysis”, discussed at 40 CFR 131.3 (g) and 40 CFR 131.10 (g), (j). 

Although a variety of approaches have evolved and become established in state programs, the 

current regulation is not specific about the level of precision states must achieve in designating 

uses. 

1.2.2 Water Quality Criteria 

The second step in developing water quality standards is to establish water quality criteria. 

To protect designated uses, states also adopt water quality criteria into their standards. 

Water quality criteria are elements of state water quality standards, expressed as constituent 

concentrations, levels or narrative statements, representing a level of water quality that supports 

a particular use. When criteria are met, water quality will generally protect the designated use (40 

CFR 131.3, 40 CFR 131.11). Criteria can either be narrative (e.g., “No toxics in toxic amounts.”) 

or numeric (e.g., “To protect aquatic life, the concentration of lead shall not exceed 65 ug/L as 1 

hour average more than once every three years.”). Most states typically have a mix of both as 

part of their standards (EPA 2002). When a water body is classified for more than one use, criteria 

necessary to protect the most sensitive use must be applied to the water body. 

To better address the integrity goal and more fully protect aquatic life uses, many states are 

incorporating bioassessments and biocriteria into their water quality standards and/or overall 

water quality management strategies. Biological assessments are used to evaluate the condition 

of a water body using direct measurements of the resident biota in surface waters. Biological 

assessments integrate the cumulative impacts of chemical, physical, and biological stressors on 

aquatic life. Biological criteria, derived from biological assessment information, can be used to 

define state water quality goals for aquatic life by directly characterizing the desired biological 

condition for an aquatic life use designation. Biological criteria are narrative descriptions or 

numerical values that describe the reference condition of the aquatic biota inhabiting waters of a 

specific designated aquatic life use (EPA 1990). Biological criteria are often based on integrated 

measures, or indices, of the composition, diversity, and functional organization of a reference 

1-8 Chapter 1 — The Clean Water Act: A Critical Asset 
aquatic community. The reference condition describes potential biological conditions for water 

body segments with common characteristics within the same biogeographic region. Biological 

criteria can play an important role in water quality programs and when properly implemented, 

complement and support other methods and criteria. 

For biological criteria, narrative criteria are 

statements that describe a desirable biological 

condition, such as “a balanced, healthy population Water Quality Criteria (WQC): 

of native aquatic life.” States can define narrative Elements of state water quality 

biological criteria early in program development standards, expressed as constituent 

without conducting biological assessments. concentrations, levels, or narrative 

To support the narrative criteria, a state needs statements, representing a quality of 

protocols that describe standardized procedures for water that supports a particular use. 

data collection, analysis and interpretation. Once When criteria are met, water quality 

vetted through a rigorous scientific process, these will generally protect the designated 

protocols provide the legal and programmatic basis use. 

for numeric criteria (EPA 1990; Karr 1991). Narrative criteria: Descriptions of 

Numeric criteria identify specific values for conditions necessary for the water 

measurements that are expected to support the body to attain its designated use. 

designated uses. For example, assuming protection 

of coral reef ecosystem is a designated use, 

numeric biological criteria might include a minimum 

percentage of coral cover, a minimum number of 

coral species in a defined region, or a maximum 

number of nonindigenous fish—at whatever levels 

are deemed necessary to support the designated 

Numeric criteria: Specific numeric 

values expressed as maximum 

acceptable chemical concentrations, 

an acceptable range of physical 

factors or acceptable condition of 

biological resources. 

use (EPA 2002). 

The Clean Water Act (§304(a)(1)) authorizes EPA 

to recommend criteria for water quality that accurately reflect the latest scientific knowledge. 

These criteria are based solely on data and scientific judgments on pollutant concentrations 

and environmental or human health effects. Criteria developed under Section 304 (a) do not 

reflect consideration of economic impacts or the technological feasibility of meeting the chemical 

concentration in ambient water. Section 304(a) also provides guidance to states and tribes in 

adopting water quality standards. Criteria are developed for the protection of aquatic life as well as 

for human health. 

In adopting water quality criteria to protect their waters, states may use EPA’s recommended 304 

(a) criteria, the 304(a) criteria modified to reflect site specific conditions, or they may use other 

scientifically defensible methods and develop their own. Site specific criteria may be appropriate in 

a number of instances, for example, if the species at the site are more or less sensitive than those 

in the data base used to develop EPA’s criteria, or the physical and/or chemical characteristics 

alter the biological availability and/or toxicity of the chemical. 

Currently, only a handful of states have numeric biological criteria as part of their standards, 

although many have developed quantitative protocols to determine whether waterbodies support 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-9
 
their narrative expressions for aquatic life uses. States often refer to these protocols as biocriteria 

even though they are not yet codified into state law as water quality standards. Many states are 

moving toward more specific aquatic life uses and numeric biocriteria at the urging of EPA and 

other scientific review panels (Davies and Jackson 2006; NRC 2001). 

1.2.3 Antidegradation 

The third component of a state water quality 

standards program is the antidegradation policy. 

Antidegradation: A policy designed 

to prevent deterioration of existing 

levels of good water quality. 

A state’s antidegradation policy (and implementation procedures) perform essential functions 

as part of the states’ water quality standards. Designated uses establish the water quality goals 

for the water body, water quality criteria define the conditions necessary to achieve the goals 

and an antidegradation policy specifies the framework to be used in making decisions regarding 

changes in water quality. The intent of an antidegradation policy is to ensure that in all cases, at 

a minimum, water quality necessary to support existing uses is maintained (40 CFR 131.12 (a) 

(1)), that where water quality is better than the minimum level necessary to support protection and 

propagation of fish, shellfish and wildlife, and recreation in and on the water, that water quality is 

also maintained and protected unless, through a public process, some lowering of water quality 

is deemed to be necessary to allow important economic or social development to occur (40 CFR 

131.12(2)), and to identify water bodies of exceptional recreational or ecological significance and 

maintain and protect water quality in such water bodies (so called Outstanding National Resource 

Waters, or ONRWs) (40 CFR 131.12 (3)). 

Antidegradation plays a critical role in helping states to maintain and protect the finite public 

resource of clean water and ensure that decisions to allow reductions in water quality are made in 

a public manner and serve the public good. 

High quality surface waters are an important and finite resource whose availability affects the 

health, welfare, and economic well-being of all the citizens of the United States. Antidegradation 

policies and procedures of states help ensure that water quality is conserved where possible and 

lowered only when necessary, and that those affected by the lowering of water quality have a 

say in the decision. As a result, antidegradation policies are well-suited to assist states and local 

communities in establishing and achieving goals for a particular waterbody. 

Sensitive or highly valued water bodies can be identified and protected from degradation 

through “Outstanding National Resource Water (ONRW)” or related designations. In other water 

bodies, where water quality is better than the minimum necessary to support fish and aquatic 

1-10 Chapter 1 — The Clean Water Act: A Critical Asset 
 

life and recreation, water quality should be maintained unless there is a demonstrated need to 

lower water quality. Consistent with a watershed approach, states’ antidegradation policies and 

procedures can be a basis for a systematic and accessible planning process that protects against 

development having negative impacts on water quality. Additional authorities exist at the local 

level beyond state, tribal and federal authorities which may allow additional protections to be put in 

place in accordance with the watershed management plan. 

Antidegradation requirements are typically triggered when a regulated activity is proposed that 

may affect existing water quality. Such activities are reviewed to determine, based on the level of 

antidegradation protection afforded to the affected water body segment, whether the proposed 

activity can be authorized. “Antidegradation reviews” should be documented and subjected to 

public review and comment (e.g., as part of the public review of the water quality certification, 

NPDES permit, or other regulatory action). 

Identifying the universe of activities that trigger antidegradation requirements is a fundamental 

and often controversial issue because of the number and variety of activities that can affect 

water quality. Clearly, a wide range of activities that affect water quality may be subject to 

antidegradation requirements, and states and tribes have considerable flexibility in applying 

antidegradation policies. 

It is important to remember, however, that the federal antidegradation requirements do not create, 

nor were they intended to create, state regulatory authority over otherwise unregulated activities. 

It is the position of EPA that, at a minimum, states must apply antidegradation requirements to 

activities that are “regulated” under state or federal law (i.e., any activity that requires a permit 

or a water quality certification pursuant to state or federal law) and any activity that is subject to 

state regulations that specify that water quality standards are applicable. Although states have 

discretion to apply antidegradation requirements more broadly than minimally required, application 

of antidegradation requirements to activities that are otherwise unregulated under state and 

federal water law is not required by the federal water quality standards regulation. 

Antidegradation policies are a powerful tool that states can use to maintain water quality and 

better plan economic and social development that might impact existing water quality. However, 

antidegradation policies are significantly underused by the states (63 Federal Register 129 1998). 

1.3 Submittal and Approval of State Water Quality Standards 

States are required to review their water quality standards at least once every three years, hold 

public hearings to review applicable water quality standards, and, if appropriate, adopt new and 

or revised standards. States can identify additions or revisions necessary to existing standards 

based on water quality reports, other available water monitoring data, previous water quality 

standards reviews, or requests from industry, environmental groups or the public. States are 

required to submit new or revised water quality standards (if any) to EPA for review and approval 

or disapproval. Finally, CWA section 303(c)(4)(B) authorizes the EPA Administrator to determine, 

even in the absence of a state submission, that a new or revised standard is needed to meet CWA 

requirements. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-11
 
 

While water quality standards have been used to protect inland, estuarine and coastal waters, to 

date states have not specifically protected coral reefs with their standards. Water quality standards 

present an opportunity to develop specific goals for reef water quality and biological condition, 

and to use other CWA programs (like assessment, NPDES permits, TMDLS, and nonpoint source 

management to help achieve those goals. 

Total Maximum Daily Load (TMDL): an example of a water quality 

improvement plan. A TMDL is the calculation of the maximum amount 

of a pollutant that a waterbody can receive and still meet water 

quality standards (Keller and Cavallero 2008; EPA 2009a). 

1.4 Emergence of Biological Criteria 

The CWA’s objective is that waterbodies maintain physical, chemical and biological integrity. 

Historically, however, regulatory agencies have attempted to attain biological integrity through 

chemical and physical criteria alone. This relies on a presumption that improvements in chemical 

and physical conditions will result in biological integrity (Yoder 1995) (Figure 1-2). 

Figure 1-2. Five principal factors that influence and determine the integrity 

of surface water resources. SOURCE: Yoder (1995) modified from Karr et 

al. (1986). 

1-12 Chapter 1 — The Clean Water Act: A Critical Asset 
Yet, some chemical pollutants are hard to measure and there are several physical factors critical 

to aquatic life, such as habitat structure, flow patterns, and energy sources that are altered by 

human activities and do not appear in state standards. Far and away the best means to evaluate 

and protect biological integrity is through biological assessment (Karr 2006 [see Appendix for 

other key biocriteria papers]; Figure 1-3). 

Biological Assessment (bioassessment): 

the evaluation of the biological condition of a 

waterbody using biological surveys and other 

direct measurements of resident biota in surface 

waters (EPA 2009a). 

Figure 1-3. Biological assessments can sometimes detect impairment 

when chemical criteria do not. Top panel shows phosphorus values for 

USVI well below the criterion. In contrast, bottom panel shows coral 

cover (gray bars) being replaced by macroalgae (blue bars) at a reef in 

St. John (Waddell and Clarke 2008). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-13
 
Biological assessments (bioassessments) are not intended to replace, but are a necessary 

complement to chemical and physical assessments. There are many advantages to biological 

assessments: 

• Biological indicators reflect the cumulative exposure to fluctuating water 

quality conditions over time. Chemical and physical monitoring provides 

only a snapshot of water quality condition at the moment of sampling. 

•		 Biological assessments reflect an integrated response of the system 

to multiple stressors. For example, coral reef organisms may be 

simultaneously exposed to elevated sea temperature, physical damage, 

and excess sediment loading, all of which are integrated into biological 

condition expressed at the level of individuals, populations and 

communities. Physical and chemical indicators are examined singly with 

little capacity for integrating effects of different stressors. 

•		 Finally, bioassessments are commonly employed in coral reef ecosystems 

(Adler 1995; Fisher 2007), perhaps even more often than physical and 

chemical monitoring. Although most coral reef monitoring programs are 

designed only to track changes in condition over time, the application 

of bioassessment procedures is a common foundation for biocriteria 

development. 

1-14 Chapter 1 — The Clean Water Act: A Critical Asset 
The underlying premise of the CWA is to maintain waterbodies in natural condition. Thus, 

biocriteria are expressed as either numeric values or narrative expressions that describe 

the expected natural biological condition of aquatic communities in the waterbody. Expected 

conditions are derived from reference locations where there has been no (or minimal) human 

disturbance. Values for the measurements that define reference condition become the 

thresholds for criteria. 

Reference condition: The chemical, physical and biological 

condition expected to be found in unimpaired waterbodies of 

a similar type. This can be determined by sampling at unimpaired or minimally impaired reference sites, from historical 

data and information, or through modeling and estimations. 

Many ongoing efforts of federal and state agencies are protecting coral reefs under the aegis of 

the CWA and other federal, state and local authorities. Watershed programs, pollutant discharge 

permitting, ocean discharge regulations, dumping regulations, fisheries regulations, coastal 

zone management (see Chapter 9)—all work to protect aquatic resources from adverse humangenerated effects. There is an opportunity to extend and set goals for coral reef protection through 

implementation of coral reef biocriteria. 

Because biocriteria are direct endpoints for determining aquatic life use attainment, they must 

be developed through a scientific process that is sufficiently meaningful to guide effective 

management and sufficiently rigorous to withstand possible legal challenge. There are obstacles 

to overcome—as those developing freshwater biocriteria can attest—but we can learn from the 

successes of ongoing biocriteria programs. 

There are many applications for bioassessment approaches and biocriteria. Some of these 

are iterated at the EPA Biocriteria Website (http://www.epa.gov/waterscience/biocriteria) and 

include support for enforcement and restorative assessments, setting protection priorities and 

restoration goals, assessment of water quality to identify impaired waters, contributing to stressor 

identification, supporting permit decisions, protecting watersheds and tracking restoration 

progress. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-15
 
Many aspects of biocriteria development were pioneered in Ohio. Prior to 1978, Ohio’s water 

quality standards reflected a single aquatic life designated use for all of the state’s waters. In 

1978, the standards were revised to account for the natural variability of aquatic ecosystems 

using a tiered classification scheme based on ecological components. It was recognized that 

environmental conditions for biological integrity varied for different populations and habitats. 

However, the water quality criteria linked to these classifications remained physical and chemical. 

In 1980, narrative biological criteria were developed for each ecological classification. These 

narrative biocriteria were the forerunners of the current numeric biocriteria adopted in state water 

quality standards in 1987 (Yoder and Rankin 1995; see Figure 1-4). 

Figure 1-4. Disagreement between biological and chemical 

assessments. Data from Oregon Department of Environmental Quality 

(DEQ) illustrate that 23% of stream miles that would pass for chemical 

criteria would fail for biological criteria and that 5% of stream miles had 

chemical impairment that was not detected by biological assessments. 

A typical example of the utility of bioassessments in a biocriteria program might be a fish kill 

experienced in Rock Creek Maryland in 2000 (Gerritsen et al. 2001). Investigation revealed a 

point-source pesticide spill as the likely cause. Biological assessments played a role in several 

aspects of the case. Routine biological monitoring provided historical data and a “before” picture 

of the integrity of the fish and macroinvertebrate communities. Standard methods recommended 

by EPA were used for all bioassessments. Sampling immediately after the event and then 

several months later provided legally defensible data for impact of the event and the degree of 

recovery. In 2001 the owner of a pesticide company pleaded guilty to federal CWA violations. The 

routine biological monitoring of this biocriteria program provided a powerful tool for documenting 

degradation from previous and historical condition and recovery. Data assisted enforcement 

agencies in assessing damage, levying fair and reasonable fines, and determining the rate of 

stream recovery. 

1-16 Chapter 1 — The Clean Water Act: A Critical Asset 
2. Why Do We Care About Coral Reefs?
	

Every one must be struck with astonishment, when he first “ beholds one of these vast rings of coral-rock, often many leagues 

in diameter, here and there surmounted by a low verdant island 

with dazzling white shores, bathed on the outside by the foaming 

breakers of the ocean, and on the inside surrounding a calm expanse 

of water, which, from reflection, is of a bright but pale green color. 

— Charles Darwin, 1842 ” 

The diverse communities that form coral reefs embody a natural beauty and mystique that have 

attracted people throughout the ages. Stony corals were once made into scarabs by ancient 

Egyptians, and Etruscans carved coral jewelry as early as 800 BC. The lure of coral reefs, 

particularly since the invention of SCUBA, now attracts millions of tourists annually to reef 

destinations and millions more enjoy reefs vicariously, reflecting on a healthy, diverse, interactive 

community of unique and colorful marine organisms (Figures 2-1 through 2-3). Coral reefs provide 

a source of food and shelter for a large variety of species including fish, shellfish, sponges, sea 

anemones, sea urchins, sea snakes, sea stars, worms, jellyfish, turtles, and snails. 

Figure 2-1. Scuba diver enjoying coral reef. Figure 2-2. Victorian cameo brooch 

made from coral. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 2-1
 
2-2 Chapter 2 — Why Do We Care About Coral Reefs? 

Figure 2-3. Coral reefs provide important graphic and design elements. 
Ecosystem structure: 

The physical and 

spatial aspects of 

an ecosystem that 

are contributed by 

the biotic and abiotic 

composition. 

Ecosystem function: 

Physical, chemical, 

and biological 

processes that occur in 

ecosystems. 

Ecosystem services: 

Benefits that human 

populations receive 

from functions that 

occur in ecosystems. 

But natural beauty and biological diversity are not the only values attributable to reefs. Coral 

reefs provide numerous benefits, including protecting coastlines from ocean storms and floods, 

providing sand for beaches and coral rock for construction material, supporting subsistence fishing 

and recreation, and providing a sense of place, tradition and culture. Non-residents benefit from 

tourism opportunities, food products, aquarium fish, jewelry and curios, and future pharmaceutical 

and cosmetic products. Coral reefs are important sources of new medicines that can be used to 

treat diseases and other health problems. 

Protection of these benefits and the ecosystems that provide them is an important objective for 

coral reef management. Human existence—certainly as we know it—would be at risk without 

functioning ecosystems. 

Coral reef ecosystems include items one can count (ecosystem 

structure) plus the processes (function) that generate and maintain 

them. The structure of the coral reef ecosystem includes: 

•		 The composition of the biological community including 

species, numbers, biomass, life history and distribution in 

space.
 

•		 The quantity and distribution of abiotic factors (non-living 

physical and chemical characteristics of the environment), 

including solar energy (amount of sun light), oxygen, CO2

, 

water, temperature, humidity, pH, and availability of nitrogen. 

• The conditions of existence such as temperature, light, etc. 

Coral reef ecosystem function includes: 

•		 The synthesis and storage of organic molecules during the 

growth and reproduction of photosynthetic organisms (primary 

productivity).
 

•		 The trophic interactions (the relationships between the feeding 

habits of organisms in the coral reef food chain)
 

•		 Flow (fluxes) of nutrients and energy throughout the 

ecosystem. 

Both structure and function are integral components of ecological integrity. The benefits we derive 

from ecosystems are characterized as ecosystem services (73 Federal Register 70 2008). This 

definition includes direct use services, such as food and material, which are sometimes referred to 

as “goods”. 

The concept of ecosystem services is receiving a lot of attention. A highly-collaborative, worldwide 

examination of ecosystems, the Millennium Ecosystem Assessment (MEA 2005), found that most 

ecosystems were in decline and that many life-sustaining benefits we receive from nature— 

such as clean air and water, fertile soil for crop production, pollination, and flood control—were 

becoming less and less available while the need for them was becoming greater and greater. 

Why more has not been done to stem the decline may lie in the relatively common perception that 

ecosystems are free and limitless, providing ample services into the foreseeable future at no real 

cost. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 2-3
 
Table 2-1. Examples of goods and ecological services of coral reef ecosystems (adapted from 

various sources, including Spurgeon 1992; Moberg and Folke 1999; Costanza et al. 1997; MEA 

2005). Direct use (goods)

Renewable 

Fisheries and 

pharmaceuticals 

Non-renewable 

Construction materials (coral blocks and 

sand) and decorative items (curios and 

jewelry) 

Indirect use

Physical 

Shoreline protection, 

land accretion, lagoon 

formation, beach sand 

Biological 

Ecosystem Integrity 

(biodiversity, genetic 

repository, ecosystem 

regulation, ecosystem 

resilience) 

Biogeochemical 

Nitrogen fixation, 

CO2

 regulation, 

primary production 

Non-use

Information 

Research, education, 

pollution record, climate 

record 

Social 

Tourism and recreation, aesthetics, artistic 

inspiration, folklore, tradition, religion 

There is evidence of this for coral reefs; many decisions and policies in coastal zones and 

watersheds (e.g., zoning and land-use permits) are implemented without knowledge or 

consideration of potential effects on reefs. Future protection of reefs may depend on reversing 

this perception. Research programs such as EPA’s Ecosystem Services Research Program (URL: 

www.EPA.gov/ORD/ESRP) are providing information and tools to transform the way we account for 

ecosystem services, including those provided by coral reefs (Table 2-1), so they can be routinely 

considered in environmental management decisions. Incorporation of ecosystem services requires 

a more holistic, systems approach to analyze human-coral reef interactions. EPA’s coral reef 

program is using a DPSIR framework which links Driving forces, Pressures, State, Impacts and 

Responses (See Appendix E). 

There is little doubt that 

Americans care about coral 

reefs—we support numerous 

actions, both governmental and 

non-governmental, to study and 

protect coral reefs. Although 

we don’t often think of reefs in 

economic terms, the following 

2-4 Chapter 2 — Why Do We Care About Coral Reefs? 
expenditures represent a valuation 

of the reef ecosystem: 

• The Nature Conservancy 

pledged $20 million in 

contributed funds to support 

“The Caribbean Challenge”, 

a commitment by Caribbean 

governments to protect 20 

percent of their marine and 

coastal habitats by 2020 (TNC 

2009a). 

• Since 2003, the State 

of Florida has offered a 

“Protect Our Reefs” specialty 

automobile license plate 

(Figure 2-4) at an additional 

cost of $25 each; in 2008 

alone, 43,985 coral reef plates 

were issued (Orlando Sentinel 

2008). 

Figure 2-4. State of Florida “Protect 

our Reefs” specialty license plate. 

• Elected representatives 

understand the public 

concern for the welfare of 

reefs: the U.S. Government 

has established and funded 

(over $200M yr-1) interagency 

programs (e.g., the Coral 

Reef Task Force), National 

Marine Sanctuaries, National 

Parks, and legislation (e.g., 

Coral Reef Conservation Act) 

specifically for protection of 

coral reefs. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 2-5
 

3. WhatShould Be Protected? 

In the end we will conserve only what we love; we will 

love only what we understand; and we will understand “ only what we are taught. ” — Baba Dioum, 1968 

Tourism, recreation, and fisheries are examples of ecosystem services that we care about. 

Protecting these services and the economic values derived from them means protecting the 

plants and animals, the biota, that provide them. The CWA protects these aquatic life uses as the 

“fishable/swimmable” goal, that is, the “protection and propagation of fish, shellfish, and wildlife 

and recreation in and on the water” (Section 101(a)(2)). Making the connections between the 

ecosystem services provided by the biota and protection of the aquatic life use helps stakeholders 

understand how protection of the biological parts and processes of natural ecosystems also 

provides valuable economic benefits to society (Table 3-1). Sustainable fisheries, for example, 

depend on ecosystem functions to support the persistence of large, abundant fish and 

invertebrates. Only an intact, functioning ecosystem can support the production of large fish and 

invertebrates. 

Although the aquatic life use goal is broadly protective, refined designated uses can make 

selection of indicators (Chapter 4) and establishing criteria (Chapter 5) more relevant to a 

particular waterbody and to stakeholders. Refined designated uses specifically describe the 

expected biological assemblage that the use depends on, for example “natural coral reef 

communities to support recreational diving,” “undisturbed fish nursery areas to support fisheries,” 

or “restricted spawning areas to support grouper propagation” specifically highlight the biological 

Table 3-1 Relationship of designated use, ecosystem function, biological components and ecosystem services. 

Designated 

Use 

Ecosystem 

Function 

Biological 

Components 

Ecosystem 

Services 

Coral reef 

communities 

Nutrient cycling; 

herbivory 

Rare and colorful fish and 

invertebrates; abundant herbivores 

such as urchins and parrotfish 

Tourism and 

Recreation 

Coral reef 

communities 

Calcification and 

skeletal growth; 

photosynthesis 

and water clarity 

Large, abundance scleractinian 

(stony) corals and crustose 

coralline algae to bind them 

Shoreline 

Protection 

Coral reef, 

seagrass, and 

mangrove 

communities 

Competition and 

predation 

Taxonomic diversity Pharmaceuticals 

Fish spawning, 

aggregation and 

nursery areas 

Complex trophic 

structure and food 

web dynamics 

Habitat and food provided by 

corals, seagrasses, and mangroves 

Fisheries 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 3-1
 
resources that are particularly important to stakeholders. The primary purpose of designated 

uses is to communicate the desired condition of water resources to water resource managers, 

the regulated community, and the stakeholders. The best designated uses translate easily 

into indicators that respond in predictable ways to degradation and can be assessed with data 

collected from the waterbody (EPA 2005). 

Designated uses can also directly include human use goals, but these are secondary to aquatic 

life uses. If a particular human use goal is needed, such as navigation for ships that may require a 

decline in integrity, then a Usability Attainment Analysis (UAA) with extensive public hearings may 

be required. Some existing designated uses are aquatic life use goals and some are human goals 

(Table 3-2). 

Table 3-2. Examples of designated uses relevant to coral reefs. 

Ecosystem Service Designated Use Used By 

Aquatic Habitat Coastal habitat protection and 

restoration 

U.S. Virgin Islands (USVI) 

Preservation of natural 

phenomena requiring special 

conditions (National Parks) 

USVI 

Biodiversity Propagation of shellfish and 

other marine life 

Commonwealth of the 

Northern Mariana Islands 

(CNMI), Hawaii 

Conservation of coral reefs 

and wilderness areas 

CNMI, Hawaii 

Fisheries Commercial, recreational and 

subsistence fishing 

American Samoa 

Support and propagation of 

shellfish 

American Samoa, Florida, 

Hawaii, USVI 

Industrial Industrial water supply American Samoa 

Research Scientific investigations and 

oceanic research 

CNMI, American Samoa 

Shoreline protection Coastal erosion and sediment 

control 

USVI 

Tourism and Recreation Primary contact recreation 

(swimming, snorkeling, scuba 

diving, etc.) 

American Samoa, CNMI, 

Hawaii, USVI 

Aesthetic enjoyment American Samoa, CNMI, 

Hawaii 

Transportation Boat launch and harbor American Samoa 

Commercial and recreational 

boating 

American Samoa 

3-2 Chapter 3 — What Should Be Protected? 
Not all state waterbodies are the same, and data collected from bioassessments, as part of a 

developing biocriteria program, may reveal unique and consistent differences among aquatic 

communities inhabiting different waters with the same designated use. Measurable biological 

attributes can be used to separate a waterbody use classification into two or more classes (EPA 

2009b). 

For example, if a state had an aquatic life use for protection of coral communities, there may also 

be unique aquatic communities found only in the higher quality waters that may need additional 

protection through more restrictive criteria (e.g., natural open water coral reef communities vs. 

shipping channel and harbor coral reef communities). These “refined aquatic life uses” can provide 

much great clarity of expectations as well as more specific criteria to better protect the use. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 3-3
 
3-4 Chapter 3 — What Should Be Protected? 
 

 

4. What Should We Measure? 

One of the most meaningful ways to answer basic questions about the quality of waters is to 

observe directly the communities of plants and animals that live in them. Because aquatic plants 

and animals are constantly exposed to the effects of various stressors, these communities reflect 

not only current conditions, but also stresses and changes in conditions over time and their 

cumulative impacts. Bioassessment data is invaluable for managing our aquatic resources and 

ecosystems. We can use it to set protection and restoration goals, to decide what to monitor and 

how to interpret what is found, to identify stresses to the waterbody and decide how they should 

be controlled, and to assess and report on the effectiveness of management actions. 

Understanding the purpose of bioassessments of the biological community of interest is 

essential, but it does little to narrow the list of possible measurements that could be made on 

coral reefs. Compendia of coral reef condition (e.g., Waddell and Clarke 2008) reveal a variety 

of measurements to characterize coral reefs and the stressors that threaten them. While there 

is no apparent limit to what might be measured, there is a limit on the time, cost and expertise 

needed to make the measurements. One solution is to select certain measurements or sets of 

measurements to serve as indicators. These 

are signs or signals that relay a complex 

message in a simplified, useful manner. 

An indicator can be a measure, an index of 

measures, or a model that characterizes some 

critical component of the system. 

Indicator: Information based on measured 

data used to represent a particular attribute, 

characteristic, or property of a system. 

4.1 Selecting Indicators 

There has been a long-standing 

interest in indicators both to 

characterize ecological condition 

(e.g., McKenzie et al. 1992; 

Cairns et al. 1993) and to inform 

regulatory applications and 

public decisions (e.g., Hunsacker 

and Carpenter 1990; Reams 

et al. 1992; Barber 1994; EPA 

1995; McElfish and Varnell 

2006). Different approaches for 

evaluating indicators are available, but most incorporate concepts similar to those presented 

by Jackson et al. (2000). Biocriteria require most of the same indicator characteristics. Indicator 

development for biocriteria entails an iterative process of review, testing, and analysis of candidate 

measurements. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-1
 
Relevance to purpose. Biological assessments serve a variety of different purposes, and 

the purpose influences the type of indicators that will be used. Some common purposes 

include characterizing the current condition of the resource, determining the effectiveness of 

various management actions, determining the cause of undesirable conditions, identifying 

the consequences of uncorrected problems, or simply improving the information available to 

managers and stakeholders (EPA 2006a). Some indicators may address more than one purpose. 

For biocriteria development, the principal purpose is characterizing the condition of the resource in 

relation to reference conditions. 

Relevance to ecosystem structure and function. Measuring ecosystem structure and function 

is critical to determining the biological condition of a waterbody. Biological integrity is expected 

in areas with little or no human influence; areas under human influence probably exhibit some 

departure from integrity. Many taxonomic assemblages could be assessed to characterize 

biological condition, including reef fish, stony corals, octocorals, sponges, invertebrates, 

zooplankton, phytoplankton, macrophytes, and foraminifera. Reef condition may even be related 

to the condition of associated ecosystems such as sea grasses and mangroves. Stony corals, 

because they form the complex three-dimensional structures that so many species depend upon, 

are often selected as an assessment target. This, however, does not mean that assessments 

should be limited to one assemblage. Early development of freshwater biocriteria focused on 

fishes (Karr 1981) and has expanded to include insects and algae (EPA 1995). 

Responsiveness to human influence. Perhaps one of the biggest challenges confronting coral reef 

managers is distinguishing effects of human activity. One way to evaluate responsiveness—at 

least local human activity—is to measure the responses of potential indicators across a gradient of 

human disturbance. 

Measurements are made at sampling locations within and progressively removed from an area 

affected by humans (Figure 4-1). If human influence is significant, it can alter the responses of 

indicators that are sensitive to the activity. Indicators that demonstrate a reliable and consistent 

association with human disturbance (typically referred to as “metrics”) provide the best candidates 

for biocriteria development (Karr and Chu 1999). Field testing along a human disturbance gradient 

not only identifies which indicators are responsive, but will have the added benefit of honing 

protocols, identifying levels of indicator sensitivity and clarifying the sampling effort required to 

detect a prescribed level of change. 

4-2 Chapter 4 — What Should We Measure? 
 

The primary challenge with field 

testing indicators is holding other 

confounding variables constant 

across the gradient of human 

disturbance. For example the natural 

influences of depth and wave action 

can have a significant effect on 

measures of coral reef condition. 

Other human influences such as 

fishing, trapping, or release of ballast 

water or sewage from passing 

ships may also influence coral reef 

condition. 

At this stage of indicator 

development, a consistent 

response to human disturbance 

must be documented in more than 

one setting to demonstrate that 

the indicator is reliable. Detailed 

information about the source 

of human influence may not be 

necessary, for example, changes 

in coral condition across a gradient 

of industrial land use can suffice. If 

connections can be made between 

certain types of human disturbance and specific biological indicators, this link can potentially 

identify causes of impairment and guide restoration plans; however a causal link is not necessary 

for indicator selection. 

Power to detect differences. Useful indicators have the statistical power to demonstrate change. 

This simply means that, for the number of stations that will be surveyed, measurement errors are 

smaller than natural variability across the stations. In some cases differences among stations 

(or over time) may be small so that high measurement precision (low measurement error) will 

be needed to detect significant differences. In other cases, differences among stations may be 

large and precision will be less critical; recognizing this can save valuable time and resources. 

Field tests across human disturbance gradients are a good means to characterize the ability of 

indicators to detect differences. Indicator values within a small spatial scale are generally more 

alike than from a larger regional area, but stations across a human disturbance gradient are more 

likely to provide a wide range of responses. 

Feasibility of implementation. The capacity of an agency to commit to long-term monitoring is 

sometimes overlooked in the early development of a biological assessment program. Resource 

assessment and trend detection generally require biological monitoring and reporting over many 

years; therefore, the indicators selected should represent measurements that can be expected to 

be sampled year after year given the available funds, equipment, expertise, and time. 

Area of disturbance ~100 m 

Industrial area 

Land 

Water 

Stations 

Replicates 

Different habitat 

Figure 4-1. Schematic diagram depicting proposed sampling along a 

gradient of human disturbance. Shown are an industrial point source, 

the area of disturbance, locations of 10 sampling stations along the 

gradient, 5 replicate stations in a similar habitat type, and 5 stations 

in a different habitat type. Data from the 10 primary stations would 

be used to test for a biological response to disturbance, replicates 

would be used to evaluate precision of the assessment protocol, and 

data from stations in a different habitat would test for consistency of 

the biological response across different habitat types. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-3
 
 

Interpretation and utility for management. Despite best intentions, it is possible to develop 

biological indicators that fulfill the above expectations but are not very useful as management 

tools. Some measurements may not be easily interpreted because interpretation requires 

additional information. Chemical and physical measurements, even those with clearly 

defined thresholds, don’t necessarily reflect the status of biota. Without additional (biological) 

measurements, it may be more difficult to quantify how much reducing contaminant levels 

improved coral reef communities. Sometimes, measurements simply may not reflect the things 

we care about and therefore have little influence with stakeholders and managers. Measurement 

of topographic complexity, for example, will likely not be as persuasive to stakeholders as 

measurements of fish abundance and diversity, which depend on that complexity. Sometimes 

measurements may not respond within the time scale that is needed or expected by a manager; 

live coral cover, for example, may change too quickly to assess long term trends in reef condition. 

4.2 Evaluating Indicators 

The issues described above emphasize the importance of iterative evaluation of bioindicators. 

Testing, evaluation and re-testing will, in the long run, save time, money, and generate a 

more successful bioassessment program. A first step for evaluating indicators is to determine 

the question(s) to be answered and the taxonomic assemblages that are important both for 

characterizing biological condition and communicating reef value to stakeholders. Exploring the 

literature with these concepts in mind will narrow the list of candidates. Results from previous 

studies can be examined in the context of published evaluation information (e.g., Jackson et 

al. 2000). This “desktop” analysis of indicators should distill the list even further, identifying 

measurements that are relevant, feasible, discriminating, interpretable and potentially useful for 

management. These are the measurements that should be taken to the field for testing. 

4-4 Chapter 4 — What Should We Measure? 
Field data have addressed a few of the important questions for biocriteria development in the U.S. 

Virgin Islands. Recent testing of candidate stony coral indicators found several measurements 

responded in a consistent and predictable manner to local human activity (Table 4-1). One 

gradient was selected along the south shore of St. Croix using an industrial ship channel as 

the center of a zone of human influence (Fisher et al. 2008). Another gradient was selected 

across the entrance to Charlotte Amalie, the major city of St. Thomas and a hub of cruise ship 

activity (unpublished). In both studies, a similar set of stony coral indicators showed a significant 

association with distance from the center of the zone of activity. However, disturbance gradient 

surveys may not always be as fruitful. For example, in the Florida Keys there is a small watershed 

and reefs occur relatively far offshore—what watershed influences there may be are likely diluted 

and more broadly distributed across the reefs. This does not mean that human activity doesn’t 

affect the reefs, only that the disturbance gradient is hard to detect. 

Table 4-1. Stony coral metric testing. Columns show the candidate metrics for stony coral, description of 

measurement, and whether the metric was significantly correlated with a gradient of human disturbance in 

St. Croix and St. Thomas, U.S. Virgin Islands (Fisher et al. 2008). Empty cells indicate that the metric did 

not correlate with disturbance. 

Candidate metric Measurement St. Croix St. Thomas 

Abundance and Composition 

Coral density Number of corals per m2 

Species richness Number of species Decrease 

Species frequency Number occurrences Depends 

on species 

Unique species Number of taxa that are rare, 

unique or protected 

Tolerant richness Number of taxa 

Intolerant richness Number of taxa 

Physical Stature 

Reef surface area Total 3D surface area (m2

) of corals Decrease Decrease 

Reef structure Total volume (m3

) of corals per m2 Decrease Decrease 

Community 

topographic complexity 

Coefficient of variation for coral 

colony surface area 

Decrease Decrease 

Biological Condition 

Reef percent live coral Average percent live coral for all 

colonies 

Reef live surface area Sum of live colony surface areas 

for all colonies 

Decrease Decrease 

Reef live to dead 

surface area 

Ratio of live to dead coral surface 

area for all colonies 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-5
 
Field surveys in U.S. Virgin Islands also demonstrated the feasibility of the bioassessment protocol 

and demonstrated that measurement error (differences among divers making measurements) 

was low enough that differences among stations were statistically significant (Fore et al. 2006c). 

Although stony corals were examined in these studies, other assemblages could also be tested. 

Field testing could examine the potential of several assemblages simultaneously. 

It may seem that the process for developing biological indicators is agonizing when answers 

for declining reef condition are needed quickly. However, biocriteria are legal thresholds and 

if precision, accuracy, measurement error, statistical design and protocol are not appropriate, 

carefully measured or documented, the stakeholders will (and should) actively oppose them. It 

is an iterative process that requires a rigorous approach and high quality, defensible procedures 

(Jackson et al. 2000; Fore et al. 2006b; Fore et al. 2006c). This should include development of 

Standard Operating Procedures with appropriate database management and documentation. It 

might also include intra- and extra-mural method validation/ variability studies and proficiency 

evaluations. 

Ultimately, indicators could be combined into a “multimetric index”. Each indicator may signal a 

different structural and functional aspect of the ecosystem, so aggregation provides a broader 

reflection of any changes in condition. Indicators that are sensitive to human disturbance should 

be used in a multimetric index. Indicator responses can be adjusted to account for habitat 

variability (if necessary), and compiled spatially to provide a regional assessment of condition (see 

text box for hypothetical example). 

A designated use to protect coral diversity, for example, can identify the assemblage (corals) 

and the purpose (diversity). An indicator for coral diversity might then include a measurement 

of the number of unique coral taxa found in a standardized reef area. Even so, field studies are 

still critical in characterizing responsiveness to human disturbance, to determine the power of 

the indicator to detect differences, and to generate feasible assessment methods (Table 4-2). 

Changes and re-evaluations should be considered a necessary part of this developmental 

process. The final suite of measurements that emerges still has to be incorporated into a survey 

design that meets logistical capabilities and the long-term commitment of the jurisdiction. 

A common question is whether coral reef indicators should be able to identify or characterize 

sources of impairment. Identification of causes may require a measurement response that is so 

typical of a particular stressor that it is considered “diagnostic”. While advantageous, indicators 

that identify causation are not necessary for biocriteria. Biocriteria determine whether a waterbody 

has or has not attained its biological expectations. Biocriteria assessments provide an alert to 

impaired conditions and a trigger for actions that will determine cause and help restore condition. 

Another question that often arises is whether biocriteria can trigger actions unrelated to the 

regulatory authority of the CWA. The answer is yes, because water quality standards are designed 

to determine attainment or impairment, not necessarily causation. Characterizing causation 

occurs after impairment is determined. Jurisdictions have all existing authorities available to 

them, including the CWA, to determine the cause(s) of impairment and take actions to restore 

4-6 Chapter 4 — What Should We Measure? 
an impaired waterbody (Fore et al. 2009). This is not unlike our approach to human health. If a 

routine checkup reveals a problem, e.g., an elevated white blood cell count, the doctor would 

order additional, related tests to determine the cause; but those tests would not be part of the 

routine screening. Chapter 9 provides a more complete discussion about responding to impaired 

waterbodies. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-7
 
 

Table 4-2. Types of measurements and examples of indicators for coral 

reef benthic communities (adapted from Jameson et al. 2001 and Cooper 

et al. 2009). 

Type of measure Example 

Organism • RNA/DNA ratio 

• Stress genes and proteins 

• Colony size 

• Disease and bleaching 

• Proportion of (live) tissue 

• Tissue thickness 

• Fecundity 

• Growth rate 

Population • Density 

• Size-frequency relationships 

• Larval supply 

• Recruitment 

Community • Taxa richness 

- stony corals 

- fish 

- soft corals (Gorgonians)

 - sponges 

- macro- and micro-benthos 

• Threatened and endangered taxa 

• Proportions of sensitive and tolerant taxa 

• Live coral cover; live coral surface area 

• Trophic interactions 

Ecosystem • Primary productivity 

• Calcification rates 

• Bioerosion rates 

Landscape • Stony coral (skeletal) surface area 

• Rugosity; topographic complexity 

• Connectivity 

4-8 Chapter 4 — What Should We Measure? 
5. How Do We Assess Reef Condition? 

The status of coral reefs in the U.S. has only recently been considered in terms of a formal, 

national assessment. Because coral monitoring and assessment is relatively new, there are no 

standardized monitoring programs, methods or data sets that can be used to compare across all 

U.S. jurisdictions. Nonetheless, scientific understanding and assessment of coral reef ecology has 

expanded dramatically during the past 15 years. The U.S. Coral Reef Task Force was convened 

in 1998 and three summaries of reef condition have been published since 2002 based on local 

monitoring programs and scientific studies (Turgeon et al. 2002; Waddell 2005; Waddell and 

Clarke 2008). In comparison, standardized methods for freshwater systems appeared only after 

about 30 years of monitoring (EPA 2006a). 

Coral reef monitoring is expensive, necessitating an 

efficient monitoring plan. 

A consensus among U.S. coral reef scientists and managers is that their current ability to monitor 

both coral reef condition and threats is inadequate for protection (Guerry et al. 2005). One 

limitation for coral reef assessment, compared with biological monitoring of streams and lakes, 

is the expense associated with data collection in the marine environment. Coral reef monitoring 

requires boats, SCUBA, and the staff to manage the gear. Thus, the need for an efficient 

monitoring plan is particularly acute. 

To assess coral reefs, we must first discover where they are. Stony coral and other reef-building 

organisms need hard substrate to settle and grow, and therefore occur in patterns across the sea 

floor where there is hardbottom substrate. When selecting locations for a coral survey design, 

time spent visiting locations with only sand and no hardbottom for corals translates into wasted 

time and resources. Until recently, little was known about the exact locations of coral reefs. Sonar 

mapping technology has now been used to create benthic habitat maps that accurately depict 

hardbottom substrate (Rohmann et al. 2005; NOAA 2009a), that is, areas that are potentially 

colonized by corals. These maps are useful because they identify limits and extent of potential 

coral reef areas and provide an essential tool to identify coral reef monitoring locations. In some 

cases, sonar mapping can detect hardbottom areas covered with sediment; corals may have 

previously inhabited these areas. 

The benthic maps of hardbottom substrate are an effective way to provide estimates of the 

nearshore area that supports designated uses. For example, “70% of hardbottom areas support 

their designated uses of coral reef habitat similar to reference condition.” To make this calculation, 

the area of hardbottom substrate is needed. Hardbottom is specified because it is not useful to 

report coral reef condition for areas, such as soft sediment, that are incapable of supporting reefs. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 5-1
 
 

 

 

 

 

Once the appropriate habitat type has been identified, e.g., hardbottom for coral reefs, a survey 

design may be used to select specific locations for data collection. The choice of survey design 

depends on the purpose of the survey. Typically, research studies are designed to answer specific 

questions about coral reef ecology; and a targeted sampling approach selects site locations 

according to scientific criteria. In contrast, for regional reporting of status and trends, selecting 

coral reef sites randomly provides an unbiased estimate of the condition of all coral reefs (Stevens 

1994; Olsen et al. 1999). 

Probability sampling allows estimates of aerial extent for: 

Status assessments: to characterize the condition of the 

resource and to address questions such as “what percentage of 

coral colonies in the nearshore environment have greater than 

50% living tissue?” 

Trend assessments: to detect change over time and address 

questions such as “has coral surface area decreased across the 

region?” 

Targeted sampling evaluates conditions and process at specific 

locations, and can be used to address questions such as “how does 

sediment affect coral survival?” 

5.1 Probabilistic Sampling Design 

As part of water resource monitoring, states should include a random survey design that is 

founded on random site selection. Why sample randomly? The key benefit is free information. 

If site selection is random, information from the sampled sites can be used to infer the condition 

of sites not sampled. Thus, results based on a random sample of sites can be scaled up to the 

entire population of sites within a region. The only other way to assess every site in a region would 

be to sample each one, i.e., take a census. Thus, random sampling is similar to polling in which 

the opinions from a random subset of households or individuals are used to predict an election 

outcome. 

When sites are selected using a simple random sampling design, they will often be clumped on 

the landscape. EPA scientists developed a probabilistic survey design that is still random, but 

uses a more sophisticated selection algorithm to spread sampling locations more evenly across 

the landscape (EPA 2008a). EPA’s probabilistic survey design is more efficient because sites are 

5-2 Chapter 5 — How Do We Assess Reef Condition? 
Census: Sampling every member of the population, i.e., every site on 

every coral reef. 

Random Sampling: Selects a subset of all coral reef sites to ensure that 

the sample is “representative” of all coral reefs and the estimate of condition 

is unbiased. 

Probabilistic Sampling: A type of random sampling that yields a spatially 

balanced subset of sites, and avoids the clumping associated with simple 

random sampling. 

far enough apart from each other that they contribute independent information about the condition 

of the resource. In other words, neighboring sites do not contribute redundant information about 

resource condition. The probabilistic survey design recommended by EPA for resource monitoring 

yields a more representative sample of resource condition while preserving random site selection 

and an unbiased sample. 

Probabilistic surveys can also support the regional reporting required under the CWA (Section 

305b) because they provide summary statistics for all areas included in the survey design, not just 

selected locations, segments or areas. The primary advantage of a probabilistic survey design 

for assessing coral reefs is that data from the sites sampled provide an unbiased estimate of 

biological condition for all coral reef areas. Furthermore, these regional estimates of coral reef 

condition can be compared through time (see also Section 6.3). 

Regional sampling of coral reefs in the U.S. Virgin Islands provides an example of the 

consequences of different agency mandates for coral protection. Regional, random sampling of 

coral and fish within Buck Island National Monument (St. Croix) has been extensive and long-term 

(Figure 5-1). Extensive long-term monitoring has also been conducted at St. John’s National Park. 

Although this sampling effort for federally-protected waters has been substantial, the data cannot 

be used to describe other segments of the USVI coastline that were not included in the survey 

design. 

In contrast, EPA’s probabilistic survey in USVI collected data from all coral reef areas in St. 

Croix because EPA’s mandate is to assess the condition of the entire water resource (Figure 

5-1). Although regionally more comprehensive for USVI’s nearshore areas, EPA’s survey was 

nonetheless restricted to coral reefs less than 12 m deep to minimize dive time. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 5-3
 
Figure 5-1. Contrasting survey designs for coral reefs around St. Croix, U.S. Virgin 

Islands. The top map shows sampling stations within Buck Island National Monument 

and limited sampling around the rest of the island (Waddell and Clarke 2008). The 

bottom map shows station locations for a probabilistic survey design conducted by 

EPA. Randomly selected locations are spread evenly across the hardbottom substrate 

(pink) occurring at <12m depth and within 1.5 km of shore. Data from this survey 

design represent the entire island. 

5-4 Chapter 5 — How Do We Assess Reef Condition? 
To assess status or trend, the primary advantage of random site selection is that any 

summary statistics derived from the sites sampled will be representative of the entire 

population, including all the sites that were not sampled (Figure 5-2). In contrast, data 

from a non-random site selection might only be representative of the sites sampled and 

their immediate surrounding area. 

sites

Figure 5-2 Comparison of random and non-random sampling design (Fore et al. 2006a). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 5-5
 
5.2 Implementing A Probabilistic Survey 

A probabilistic survey selects sampling locations such that the data collected at those sites can 

be used to estimate condition for the entire area of interest. The primary steps for implementing 

a probabilistic survey are summarized below, but EPA’s Aquatic Resource Monitoring Website 

should be consulted for greater detail on defining the target population and sampling units, 

selecting reef locations, and collecting and summarizing data (EPA 2008a). Because the 

probabilistic survey approach recommended by EPA is more complicated than a simple random 

survey, EPA has developed open source software that can be used to select sites from digital 

maps (shape files) and to properly calculate summary statistics and their confidence estimates. 

Define the target population. Although in biology the term Population: The “population” typically refers to a single group within a species, in entire aggregation statistics population refers to the complete set of whatever you are of items from which sampling. For example, the target population for coral reefs might samples can be be defined as “all hardbottom substrate within 1.5 km of shore to a 

drawn. Populations depth of 12 m.” Sonar mapping technology cannot reliably distinguish may be discrete between hardbottom with or without coral, nor can it discern whether (made up of separate the coral are living; therefore, the target habitat is typically referred individuals) or to collectively as hardbottom substrate. Different shapes and types continuous (without of hardbottom can be distinguished such as linear reef, spur and break or interruption). groove, or pavement. As a consequence, survey designs can 

selectively emphasize different types of reef.
 

Corals grow at a variety of depths, but if data collection requires 

SCUBA, restricting the depth of the dives makes a safer, less time-consuming monitoring program 

that may be easier to implement and sustain over time. In addition, monitoring in the more shallow 

reefs might detect the first effects of land-based pollution. Thus, the target population of coral 

reefs for a probabilistic survey may be defined in a variety of ways according to different depths, 

locations, or distances from shore; however, the key point is that the target population is explicitly 

defined before sampling begins so that when summary statements about reef condition are made, 

everyone understands which reefs are being described. 

5-6 Chapter 5 — How Do We Assess Reef Condition? 
Define the target sampling unit. Coral reefs are a continuous resource and do not array 

themselves into convenient patches of standard sizes; therefore, reefs need to be divided into 

discrete sampling units. For surveys of people, the sampling units are typically easier to define, 

such as a registered voter. For coral reefs the target population is continuous and must be broken 

into individual sampling units using some formula. 

For a probabilistic survey design, the sampling location is selected randomly, but we must also 

define the size of the sampling plot around the location. The plot area must be large enough to 

provide a reliable estimate of resource condition at that location but small enough to complete 

sampling within a reasonable amount of time. Thus, for a coral reef monitoring program, the size 

of the plot area should be the smallest area that yields consistent estimates of coral measures. To 

test whether the plot area was adequate for coral assessment in USVI, a 50 m2

 transect area was 

used (Fore et al. 2006a). All coral colonies within the transect area were identified and measured. 

During data collection, divers marked their data sheets for each quarter of the area, that is, for 

each ~12 m2. Coral indicators derived from the smallest areas (~12 m2) were highly variable and 

did not provide a consistent estimate of coral condition for the site. In contrast, moderate sized 

transects of 25 m2

 area provided estimates of coral condition that were nearly identical to estimate 

derived from the entire transect. Consequently, for subsequent surveys, a plot size of 25 m2

 was 

used. 

For a regional survey design, it is generally true that less information from more places provides 

a better estimate of resource condition than does more detailed information from a few places. 

Larger sample sizes yield greater confidence for the results of comparisons as well as tighter 

confidence intervals around any estimates of resource condition. 

Select a representative sample of reef sites. A probabilistic survey is intended to characterize the 

entire population of interest; therefore, the entire target population should be precisely defined and 

have an equal (or known) chance of being included in the sample. If coral reef sites are selected 

based on proximity to a harbor or accessibility from a pier, they cannot be used to accurately 

predict the condition of the entire resource. Similarly, if you polled only your neighbors about their 

political opinions, you are unlikely to obtain an unbiased prediction for the outcome of a national 

election. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 5-7
 
 

The probability of including every possible location does not need to be equal, but it should be 

specified, or known, for each location. For example, managers may be more interested in the 

condition of linear reefs because they are the source of the most tourism income; therefore, they 

might allocate 50% of their annual sampling effort to these habitat types even though linear reefs 

represent only 10% of the total coral reef area. 

Collect data from sample sites. Protocols for sites to visit and how to collect data need to be in 

place before field crews begin to collect data. If methods and locations are carefully defined, 

agencies can more easily form partnerships to collect the data for a probabilistic survey of coral 

reef condition. Other groups doing reef studies could collect data if they are near a selected site 

conducting their own field work. The Florida Reef Resilience Program (FRRP) is a good example 

of this type of agency cooperation: the standardized data collection protocols have facilitated four 

years of coral reef survey information from over 600 coral reef sites accomplished by volunteers 

and partners throughout the region (TNC 2009b). 

5.3 Trend Detection 

The data derived from a probabilistic survey design can be applied in three different ways to 

detect a trend in coral reef condition through time. First, reef sites can be randomly sampled 

each year and a biological measure, e.g., coral cover, compared from one year to the next year 

of sampling. In this case different sites are sampled each year. The advantage of this approach 

is that new sites are sampled and assessed each year. A second approach also selects new 

sites each year, but rather than comparing the raw indicator values from the sites, thresholds 

from biocriteria are applied to the data from each site and the percentage of sites supporting their 

designated uses is calculated for each year and compared through time. The advantage of this 

approach is that it accommodates measures of coral condition that are highly variable. In this 

case, translating indicator values into a binomial response variable (i.e., supports/fails to support) 

limits the variance and simplifies reporting and comparisons. 

For the third approach, a probabilistic design is used to randomly select sites only during the first 

year. Subsequent years of sampling return to the same sites and the trend analysis compares 

coral condition at each site to itself through time. The primary advantage of this last approach 

is that revisiting the same sites through time is the most sensitive design for detecting temporal 

change in reef condition. 

5-8 Chapter 5 — How Do We Assess Reef Condition? 
5.4 Analyzing Data From A Probabilistic Survey 

The methods used to calculate summary statistics from a probabilistic survey need to match the 

survey design used to collect the data. In other words, the survey design and analysis method 

must be derived from the same statistical mode. The probabilistic survey design recommended 

by EPA is somewhat complex because 1) the sites are selected from a continuous resource 

rather than discrete sampling units such as households, and 2) the algorithm used to select 

sites introduces complexity into the calculations to obtain a more even spread of sites across the 

landscape. To support states, EPA has developed open source software that can be downloaded 

from Aquatic Resources Monitoring Website to calculate summary statistics such as the mean and 

confidence limits for estimates of biological measures (EPA 2008a). 

A primary objective of a probabilistic survey is to obtain a representative and unbiased estimate 

of reef condition and to compare estimates through time to detect trend; but the data derived from 

a probabilistic survey can be used in a variety of ways, such as, to make regional comparisons of 

reef condition, to test for correlation between coral reef condition and independent measures of 

disturbance, or identify unique areas with coral reefs of exceptional quality. If sites are selected 

for inclusion in a probabilistic survey design with approximately equal probability, most of these 

analyses do not require any special statistical methods or EPA’s analysis software. However, if 

some areas are surveyed with a much higher intensity, then a subset of sites from these regions 

should be used for regional analysis and comparisons to avoid biasing the analysis with too many 

sites from one area. In contrast, estimates of regional condition and trend detection do require 

some special considerations for statistical analysis. 

A clear description of the target population should accompany any summary statistics when 

results are reported. For example, if a 3% decline in coral cover were observed for the target 

coral reef population described above, this result would only apply to reefs within 12 m of the 

surface and within 1.5 km of shore. Conclusions should not be extended to deeper reefs or reefs 

further off shore. The survey data, with confidence limits to provide an estimate of the uncertainty 

associated with the statistics and thresholds for biocriteria can be used in determining what 

percentage of the coral reef waters are supporting their designated uses. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 5-9
 

 

 

6. How Are Reefs Doing?
	

Coral Biocriteria 

Monitoring Programs 

Coral 

Monitoring Programs 

Are coral reefs improving or 

declining? 

Are coral reefs improving or 

declining below acceptable levels? 

Once indicators are selected for monitoring reef condition and data have been collected using 

an appropriate statistical design, decisions need to be made. Results of monitoring guide the 

next steps of action. What actions should be taken depend on the data. Are the reefs healthy or 

degraded? If degraded, is the level of degradation acceptable or is restoration needed? 

One purpose of biocriteria is to support decisions and actions by U.S. jurisdictions. If the 

waterbody attains its uses, no action other than reporting is necessary. But if the waterbody is 

impaired (fails to support its designated uses), the cause of impairment should be determined 

and restorative actions taken. Simply stated, biocriteria programs use biological monitoring to 

inform resource managers and stakeholders whether the waterbody is meeting its expectations. 

Biological information may be useful in distinguishing between different types of impairment. 

To make this determination requires standards for comparison. Thresholds must be established to 

reflect expectations for the waterbody. These thresholds, or criteria, guide decision-making. 

Numeric biological criteria are derived from measures of biological condition observed at reference 

locations. These values become the thresholds for criteria. Numeric criteria are expressed 

as values of the biological community related to the extent, numbers and kinds of organisms 

expected in a waterbody. For example, a numeric biological criterion might be expressed as a 

minimum percentage of coral cover, a minimum number of coral species in a defined region, or a 

maximum number of nonindigenous fish. 

Many challenges remain for insightful definition of impairment thresholds. One is that declining 

environmental condition (Figure 6-1) is not usually characterized by conspicuous breaks or jumps 

in indicator values, discontinuities that would clearly identify good and degraded condition. So how 

do we determine what amount of degradation is too much? Where do we draw the line? 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 6-1
 
 

Figure 6-1. The challenge 

of establishing thresholds. 

How much degradation is 

too much? Where do we 

draw the line? 

6.1 Impairment Thresholds 

EPA recommends a reference site approach for setting thresholds that define whether sites in 

a region support aquatic life uses (EPA 1990). This approach identifies a set of reference sites 

intended to reflect attainable conditions within the region to describe the biological condition 

expected for ecologically similar sites (EPA 2006a; EPA 2006b). Sites are selected based on 

minimal or no human influence within their watershed and coastal zone. If indicator values from 

other sites fall within an acceptable range of the distribution of reference sites (typically scores 

above a chosen percentile) then these sites attain their aquatic life designated uses. Other sites 

that fall below this percentile do not have the same or better condition and likely do not attain their 

designated uses; these are listed as impaired. 

Typically, reference condition is derived from samples collected from a set of regional 

locations, or reference sites, with minimal human influence. The set of reference sites is used to 

approximate the natural condition of a region (EPA 2006; Hughes 1995; Stoddard et al. 2006). To 

avoid circularity, reference sites are selected based on objective and independent measures of 

site condition and human influence, not measures of biological condition. 

In some areas minimally disturbed reference conditions no longer exist and may not be 

achievable. In these situations, states have defined an acceptable condition using “least 

disturbed sites” that establish a desired condition based on the best quality sites available. In 

these cases (least disturbed), a demonstration that the existing biological community structure and 

function is representative of a sustainable, natural system is necessary. If not, a Use Attainability 

Analysis (UAA) needs to be conducted to determine whether such a community is achievable 

under CWA provisions or a lower use is proposed that does not meet the minimum requirements 

for the CWA. 

6-2 Chapter 6 — How Are Reefs Doing? 
In heavily disturbed landscapes states may choose a “best potential” condition to establish as 

restoration goals which may be identified from “the best of what’s left”. Other approaches have 

used historical data sets to reconstruct a description of biological condition and empirical modeling 

to extrapolate from existing sites (Hughes 1995). 

Measurements of biological condition at reference sites will generate a range of values for each 

indicator. EPA recommends a state agency define biocriteria for an upper and lower percentile of 

this distribution of values, e.g., the 75th and 25th percentile. The selection of the upper percentile 

is intended to protect higher quality aquatic communities and the lower percentile the minimum 

level to protect the aquatic life use. States may select the upper percentile of this reference site 

distribution to reflect a refined aquatic life use, such as an exceptional quality use. The specific 

percentile selected depends on the relative confidence associated with the selection of reference 

sites. Reference sites can also vary through time; see Chapter 7 for a discussion of the effects of 

spatial and temporal variability on reference sites. 

Reference condition: Areas that are Least disturbed condition: Areas with 

undisturbed or minimally disturbed by the least amount of disturbance in altered 

human activity landscapes 

Minimally disturbed condition: Biological condition gradient (BCG): A 

Areas with a minimal amount of human scientific model that describes biological 

disturbance response to increasing levels of stressors. 

A useful tool to visualize where the reference sites and decision points lay on a scale from pristine 

to severely degraded is the biological condition gradient (BCG), which illustrates a range of 

biological responses that can result from human disturbance (EPA 2005 and Davies and Jackson 

2006). The condition of aquatic biological communities typically degrades with increases in the 

level of human disturbances. 

One advantage of the BCG approach is 

its capacity to incorporate historical and 

regional data, especially in cases where 

existing reference sites may already have 

declined below the conditions desired by 

the community. The BCG is a conceptual 

model that assigns the relative health 

of aquatic communities into one of six 

categories (Figure 6-2, EPA 2005a), 

which attempt to characterize what we 

would expect at a reference site through a 

progressive loss of structure and function 

as a result of human disturbance. At some 

point along this gradient, the designated 

Figure 6-2. Biological Condition Gradient (BCG). aquatic life use is no longer supported. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 6-3
 
 

Across the range of biological condition, the BCG recognizes ten biological attributes (see 

text box) of aquatic systems which respond predictably to increasing human disturbance (e.g., 

pollution, sediment, loss of habitat and overfishing). The attributes of biological systems included 

in the BCG were developed initially for freshwater systems and though generally applicable 

to marine systems, may change somewhat when the BCG is applied to coral reefs. The BCG 

attributes relate to taxa richness of sensitive, rare, tolerant, and non-native taxa, the physical 

condition of individual organisms, and other measures of ecosystem processes and function. 

While these ten attributes are measurable, some are not routinely quantified in monitoring 

programs, but may be inferred via the community composition data. For example, productivity 

might be inferred from the abundance of taxa that prosper with nutrient enrichment. 

The BCG provides a very useful general framework for summarizing and communicating the 

ecological condition of any aquatic community for any type of waterbody. The BCG for freshwater 

streams was developed, evaluated and implemented by aquatic biologists during a series of 

national workshops sponsored by EPA (Davies and Jackson 2006; Stoddard et al. 2006). The 

framework for the BCG is generally applicable to any biological water resources, but has yet to be 

applied to coral reefs. 

Assigning waterbodies with coral reefs into BCG tiers will help to provide a more refined 

assessment tool for evaluating and protecting coral reefs. Consideration of biological, physical, 

chemical, and hydrological data in the context of the BCG allows scientists and managers to 

strategically address the following questions: 

•		 What is the current condition of this waterbody? 

•		 What is its highest achievable goal condition? 

•		 What are the actions needed to protect/restore it to maintain/attain its goal condition? 

•		 Did the actions taken achieve the desired results, in terms of optimal biological 

outcome? 

Several state freshwater 

monitoring programs are now 

based upon sound applications 

of BCG-based biocriteria. 

These programs are producing 

more effective and innovative 

water resource management 

approaches to prevent and to 

solve biological problems (e.g., 

Best Management Practices 

to reduce effects of impervious 

cover; evolution of progressive 

10 Attributes of Biotic Condition

 1. 	 Historically documented, sensitive, long-lived or regionally endemic taxa

 2. 	 Sensitive and rare taxa

 3. 	 Sensitive but ubiquitous taxa

 4. 	 Taxa of intermediate tolerance

 5. 	 Tolerant taxa

 6. 	 Non-native taxa

 7. 	 Organism condition

 8. 	 Ecosystem functions

 9. 	 Spatial and temporal extent of detrimental effects 

10. Ecosystem connectivity 

6-4 Chapter 6 — How Are Reefs Doing? 
 

land-use and shoreline protection rules; and tiered aquatic life use (TALU) standards that trigger 

antidegradation provisions under the CWA). The clarity and simplicity of the BCG facilitates 

understanding of highly technical biological assessment and stressor information by upper 

management and the public. The BCG is an invaluable communication and learning resource that 

adds value to all aspects of the biological management of water quality. 

6.2 Application of Thresholds 

For coral reef communities, thresholds have yet to be defined as biological criteria. For 

Mesoamerican reefs in the western Caribbean, threshold values were defined for indicators of 

coral cover, herbivores and algal cover using a reference site approach (HRI 2008). Results were 

summarized in the style of a regional report card illustrating where reef condition ranges from 

good to poor condition. 

Preliminary results in the U.S. Virgin Islands have identified indicators related to coral and sponge 

condition that were correlated with independent measures of human disturbance (Figure 6-3). 

Using the BCG, generalized reef conditions and potentially even thresholds could be derived from 

these data but would need to be confirmed with data from other regions and vetted by regional 

coral experts. 

Figure 6-3. Human Disturbance Gradient. Human disturbance around St. 

Thomas Harbor was summarized according to a qualitative description of human 

disturbance (low, medium and high) related to industrial development, residential 

development, cruise ship traffic, small boat traffic and roads. Measures of reef 

cover, stony corals, octocorals, and fish were compared across the gradient. As 

human disturbance increased, rugosity, stony coral and octocoral cover, stony 

coral colony size, surface area, live surface area and variability of colony size all 

declined; the number of sponges increased. In addition the number of colonies 

of four reef building stony coral species also declined. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 6-5
 
Before biocriteria are adopted, they undergo public comment on their scientific merit. 

Once agreement is reached, then the thresholds can be incorporated into legally-binding water 

quality standards regulations. 

There is potential for confusion around the term biological criteria. As a first step toward numeric 

criteria, states often define narrative criteria to protect aquatic life; but, states still need quantitative 

thresholds to determine whether designated uses are supported. Typically these are defined 

in standard operating protocols that may not be part of the of water quality standards. These 

quantitative thresholds are also referred to as biocriteria even though they are not explicitly 

documented in water quality standards. Thus, biocriteria may refer to 1) the procedures used to 

establish benchmarks and determine whether aquatic life designated uses are being met and 

2) the numeric criteria in water quality standards. In other words, biological criteria can be used 

to assess attainment of aquatic life designated uses without being formally adopted into a state 

water quality standard. 

The impairment threshold is particularly important, but the BCG can highlight the need for 

other thresholds relevant to the third component of state water quality standards, that is, the 

antidegradation policy. The antidegradation policy is intended to ensure: 

1.	 The water quality necessary to support existing uses is maintained. 

2.	 Water quality is maintained and protected wherever water quality exceeds 

the minimum level necessary to support protection and propagation of 

fish, shellfish, and wildlife, and recreation in and on the water (“fishable/ 

swimmable”), unless, through a public process, some lowering of water 

quality is deemed necessary to allow important economic or social 

development to occur. 

3.	 Water quality is maintained and protected for waterbodies of exceptional 

recreational or ecological significance (EPA 2009b). 

One application of the BCG is to help define high quality and outstanding waters and ensure 

that they are protected. The BCG can also be used to distinguish between the aquatic life uses 

that were supported historically but that cannot be attained today. Thus, the BCG provides a 

framework to evaluate biological assemblages according to six categories of condition ranging 

from natural condition to severely altered condition and provides a conceptual model to identify 

different tiers of aquatic life use to set appropriate expectations for protection (Davies and Jackson 

2008; EPA 2005). 

A state following this independent applicability approach would identify a waterbody as attaining 

a particular water quality standard only when all of these applicable numeric and narrative criteria 

(including biocriteria) are in attainment, that is, supporting the designated uses (EPA 2005). 

6-6 Chapter 6 — How Are Reefs Doing? 
 

 

 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 6-7

6.3 Threshold Trends 

The goal of trend monitoring (Section 5.3) is to detect actual change in reef condition throughout 

the region of interest. Existing monitoring programs sometimes track condition at trend sites that 

were selected in the past based on best professional judgment or other non-random criteria. 

Biocriteria thresholds for water quality standards may be used when reporting the results of trend 

monitoring. From a probabilistic survey design, the percentage of sites supporting their designated 

uses can be calculated along with a confidence interval for the percentage. The percentage 

of sites supporting their designated uses can be compared across years and if the differences 

exceed the confidence intervals around the percentages, a statistically significant change would 

be reported. 

Monitoring for temporal change 

requires a long-term commitment 

to repeat sampling and a specific 

survey design. At the outset, an 

estimate is made of the number of 

sites that can be sampled each year. 

These sites should be allocated to 

status, trend and targeted sampling 

according to agency needs. A 

rotating panel design is an efficient 

way to structure monitoring and 

sampling effort over time (Table 6-1). 

The area of the target population 

is first divided into subregions – 

the “panels.” Each year a different 

panel of sites (subregion) is visited 

and sampled – the “rotation.” 

Sampling within each subregion 

saves money by reducing travel 

time to sampling sites. After a certain number of years, typically three to five, the original panel is 

visited and sampled again. Sampling the same trend sites every year is inefficient when change 

occurs slowly. In this design, trend sites are sampled every year, but from different panels. Thus, 

comparisons occur every fifth year if sites are grouped into four panels. 

The key point to a rotating panel survey design is that the same sites on each panel must be 

sampled during their designated year. If a trend site is lost for any reason, another site cannot 

simply be substituted. In addition, a panel of sites must be sampled according to the same 

schedule; sites must not wander from one panel or sampling period to another. The success of 

any long-term monitoring depends entirely on an adequate data management plan in order to 

keep the data alive through time. Comparisons may be made 5, 10 or 15 years later; therefore, 

the data archive must be resilient enough to survive personnel changes and computer upgrades. 

Subregion 

Numbers and Types of Stations per Year 

Years 

1, 5, 9... 

Years 

2, 6, 10... 

Years 

3, 7, 11... 

Years 

4, 8, 12... 

East St. 

Croix 

10 trend 

40 status 

West St. 

Croix 

10 trend 

40 status 

St. 

Thomas 

10 trend 

40 status 

St. 

John 

10 trend 

40 status 

Table 6-1. Example of a rotating panel design for the U.S. Virgin 

Islands. The panels represent three subregions of the U.S. Virgin 

Islands (the larger St. Croix divided in two parts). During the first 

year, 50 sites would be randomly selected: 10 for trend and 40 for 

status reporting. During the next 3 years, similar sites would be 

selected in the remaining subregions. During the 5th year, the first 

subregion is visited again and the same 10 trend sites are sampled 

along with 40 new random locations for status monitoring. 

 

 

7. How Do We Account for Reef Variability?
	

Those familiar with coral reefs know there can be dramatic differences from one reef to the next. 

Coral communities occur in different locations and are composed of many different organisms 

living in a variety of physical and chemical environments. Without these differences, reefs would 

lose much of their value. But variability among reefs can complicate the use of standardized 

measurements and thresholds. Similarly, changes in reef condition over time create challenges for 

establishing reference conditions. But spatial and temporal variability are not unique to coral reef 

ecosystems, and strategies have been developed to account for this variability. 

7.1 Spatial Variability 

Coral reefs vary across locations, even locations that 

are close to one another. Should we, in spite of this 

variability, use the same measurements and thresholds for 

all locations? Or should we develop unique approaches 

for any locations that differ in substrate, habitat, biota, 

hydrology or other environmental factors? During the 

development of biocriteria for freshwater systems, 

researchers grappled with this issue—how to best minimize 

the effects of spatial variability on measurements and 

thresholds. Fortunately, the strategies that were developed 

can be directly applied to coral reefs. Two strategies relate 

to the concepts of ecoregions and microhabitats (Figure 

7-1). 

Ecoregion: A relatively 

homogeneous ecological 

area defined by similarity 

of climate, landform, 

soil, potential natural 

vegetation, hydrology, or 

other ecologically relevant 

variables (also known as 

bioregions). 

Microhabitat: Small-scale 

changes in habitat that alter 

ecosystem structure and 

function. 

Figure 7-1. Scales and coral reef communities. The left graphic shows the microhabitat scale, the right 

graphic shows the geographic or ecoregion scale (NOAA 2009b). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 7-1
 
Fish communities found in streams flowing through forested foothills differ radically from fish 

communities in streams of plains and deltas. To address this variability, an ecoregion approach 

has been used to identify unique geographic areas based on geology, soils, geomorphology, 

dominant land uses, and natural vegetation (Hughes and Larsen 1988). Typically, indicators are 

tested and selected within an ecoregion. Indicator values from undisturbed sites are compared 

across ecoregions (and sub-ecoregions if necessary) to determine whether expectations 

(thresholds) should be raised or lowered. If no differences are found in indicator values, the 

classification is unnecessary and ecoregions can be combined. 

Although ecoregions have not been developed for coral reefs, we know that reefs in the Caribbean 

and western Atlantic Ocean are substantially different from reefs in the Pacific. These two large 

geographic areas could be defined as separate ecoregions with different reference conditions, 

indicators and thresholds. But there could also be finer ecoregion classifications. For example, 

reefs of the Florida Keys (dominated by large scleractinian corals) differ markedly from reefs of 

southeast Florida (dominated by gorgonian octocorals). The State of Florida could potentially 

develop biocriteria that rely on different taxa and region-specific thresholds. Comparisons across 

regions could be used to determine if this is appropriate or even necessary. 

A single standardized protocol for biocriteria is more efficient and makes comparisons and 

reporting easier, particularly at the national level. EPA recently completed a nationwide survey 

using standardized data collection and analysis protocols for assessing stream condition (EPA 

2006a). Nonetheless, many states still use protocols for bioassessment that are calibrated more 

specifically to their regional conditions. 

Variability also occurs at a smaller scale related to microhabitat differences. 

“Micro” does not refer to the importance of the differences—the differences can be quite 

dramatic—but to the spatial scale. For coral reefs, microhabitat differences might be associated 

with depth or wave energy (Glynn 1976; Grigg 1983). The challenge for biocriteria development is 

to select measurements and thresholds that are relevant at a regional scale despite microhabitat 

variability. The best solution is to identify indicators that are immune to microhabitat differences, 

but this is not always possible. A variety of strategies have been used to address microhabitat 

differences. 

For example, in the Chesapeake Bay benthic invertebrates are collected to assess the biological 

condition of the estuary. The indicators used to summarize biological condition vary according 

to salinity of the water and the amount of silt in the sediment. To compensate for these smallscale differences, expectations for benthic invertebrates are defined for seven habitat types: tidal 

freshwater, oligohaline, low mesohaline, high mesohaline sand, high mesohaline mud, polyhaline 

sand, and polyhaline mud habitats. The benthic index is scaled for each of these habitat types so 

that the final index values are comparable for all estuarine sites across the region. 

Similar strategies could be used to identify the most important natural features that influence coral 

reefs. The driver could be habitat type (e.g., fore reef, back reef, patch reef) or underlying physical 

processes (currents, depth, wave energy). Fisher et al. (2008) identified indicators of stony coral 

that showed a consistent response to human disturbance despite differences in reef habitat type. 

However, if greater detection power were needed, data collection might be limited within a region 

7-2 Chapter 7 — How Do We Account for Reef Variability? 
 

to a single habitat type. Alternatively different expectations of condition could be established for 

different physical environments. Despite potential strategies and promising indicators, the natural 

spatial variability of coral reefs is an area where research is still needed (Jameson et al. 2003; 

Rodgers et al. 2010). 

7.2 Temporal Variability 

The intent of the CWA is to restore and maintain the biological integrity of aquatic resources to a 

level matching conditions unaffected by human disturbance. Yet finding reference locations with 

no human impact is unlikely. So, we must decide whether to establish reference conditions from 

minimally-impacted locations with present-day measurements, or to rely on historical data—and if 

so, how far back in history should we reach? 

Historic conditions, especially those that preceded human activity, would be rated high on the 

BCG. Setting expectations at historic levels of biological integrity would certainly be protective; 

however, defining historic conditions requires historic reef assessments that are both scientifically 

defensible and provide a reasonable characterization of biological condition for the region. Rarely 

are such data available. 

Historic data for coral reef ecosystems is scarce because they could not be widely studied until 

the late 20th century when diving equipment became available. Relevant data on conditions prior 

to human influences are rare, although a few studies provide valuable insights to previous, if not 

historic, condition (Dustan 1977; Dustan and Halas 1987; Porter and Meier 1992). 

Consequently, coral reef biocriteria may have to rely on reference conditions derived from present 

day reef assessments, which are unlikely to represent the biological integrity typical of historic 

condition. Loss of integrity over time can result in a shifting baseline, that is, a lowering of our 

expectations for what good conditions should look like (Pauly 1995; Sheppard 1995; Knowlton and 

Jackson 2008; Sandin et al. 2008). 

Use of the BCG addresses the complexity of temporal variability and changing reference 

conditions by placing contemporary measurements within a context of regional potential. Historic 

data, empirical models and expert consensus have been used to develop BCGs for highly 

disturbed resource types, e.g., streams in the agricultural plains. For this type of situation, the 

BCG provides a framework to compare current biological conditions to natural (historic) conditions 

and develop reasonable expectations for restoration and protection (Herlihy et al. 2008). 

Table 7-1 shows various ways to establish reference condition, and the strengths and weaknesses 

of each approach. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 7-3
 
Table 7-1. Comparison of approaches for defining reference condition (Stoddard et al. 2006).
	

Historical 

Data 

Present-Day 

Biology 

Predictive 

Methods 

Best Professional 

Judgment 

Strengths 

• Uses available data 

• Provides a 

permanent 

benchmark 

• Only generate once 

• Compelling vision 

for stakeholders 

• Rare or extirpated 

species can be 

• Realistic 

description of 

current best 

condition 

• Based on current 

sampling methods 

• Any assemblages 

or communities 

can be used 

• Uses existing 

data, avoids 

expensive 

sampling 

• Results can be 

extended to areas 

without data 

• Perspective and 

experience of 

professionals 

with specific 

ecological 

knowledge of 

the specific 

region is 

valuable 

• Could apply 

included expert 

consensus rules 

for reference 

conditions 

Weaknesses 

• Data may be 

limited 

• Studies likely 

were designed for 

different purposes 

• Human impacts in 

historic times were 

sometimes severe 

• Even best 

available sites 

have experienced 

human influence 

• Potential for 

shifting baselines 

• Inference beyond 

existing data is 

risky 

• Can be subjective 

when data are 

unavailable 

• May be 

qualitative 

description 

of “ideal” 

communities 

• Experts might 

be biased 

7-4 Chapter 7 — How Do We Account for Reef Variability? 
7.3 Climate Change Variability 

Global climate change introduces a high degree of variability into coral reef ecosystems and has 

generated new challenges for biocriteria development. Reefs are protected by the CWA from 

anthropogenic degradation, not natural changes. Historically, most anthropogenic degradation 

was believed to have a local origin. Regional and global factors, such as climate, currents, ocean 

temperatures, storm events and wind patterns, were generally perceived to be natural and outside 

the authority of the CWA. Yet many of these global factors, particularly elevated sea temperatures 

and ocean acidification (See Appendix F), are now recognized as the result of human activities. 

The issue for biocriteria arises from the need to define expectations. Should a state set its goals to 

attain conditions that existed prior to climate change effects, even though it has no management 

control over climate change? Or should it tie expectations to the control of local activities only, 

essentially ignoring global change effects? 

There are at least two unwanted consequences of setting expectations that ignore climate change 

effects. The first is that coral reefs will not be adequately protected from human disturbance. The 

second is that the public may be misled. One of the most influential parts of the CWA is reporting 

under Section 303(d), which alerts the public and Congress as to whether state waterbodies 

support designated uses. If climate change effects are not considered, stakeholders might infer 

that coral reefs are in acceptable condition. This incorrect message will stymie efforts to control 

the root causes of climate change. 

But if waterbodies are impaired by global pollution that cannot be controlled by a state, what good 

does it do to list them? Biocriteria are, first and foremost, a reporting mechanism. The greatest 

purpose for biocriteria is to identify and report impairment, even if causes are unknown. A similar 

situation existed with acid rain. Coal-fired power plants in the Midwest U.S. caused acidic rainfall 

in the northeast which affected the biota of lakes and streams. Despite the fact that impacted 

states had no control over the emissions, documentation of stream and lake impairment alerted 

officials and the public and supported regulatory actions taken under the Clean Air Act (Menz and 

Seip 2004). Similar legal documentation of declining coral reef condition may also serve to alert 

officials at regional, national and even international levels to the growing global crisis for coral 

reefs. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 7-5
 

8. What Is Causing Reefs to Change?
	

It is a curious situation that the sea, from which life first arose, should now “ be threatened by the activities of one form of that life. ” ~Rachel Carson, 1960 

When the biological condition of reef sites falls below the criteria for support of designated uses, 

the reasons for impairment must be determined before the sites can be protected or restored. In 

order to reverse declining trends in coral reef condition, we need to know which human actions 

are most damaging to coral reefs. Reducing known sources of impairment before damage occurs 

may provide the best protection. 

The probabilistic survey design that detected a loss or change in the biological condition of a reef 

area is unlikely to provide the type of information that will identify the cause. Identification of the 

sources and causes of biological degradation at specific locations may require different types of 

data collected at specific targeted sites. 

A particular challenge is to distinguish local stresses from global and regional stresses. Biological 

impairment resulting from global and regional stressors should be reported, but local management 

actions can do little to reduce these threats. Nonetheless, resource managers need to identify 

sources and causes of degradation that can be eliminated through local management practices. 

Even a single human activity can have multiple effects on a coral reef, and that activity may be 

anywhere in the watershed. Human activities can affect coral reefs through changes in water 

quality (increased sediment), habitat structure (construction of docks), flow regime (freshwater 

releases from upstream dams), food sources (loss of prey from shoreline armoring) and biotic 

interactions (fishing). The relative risk to coral reef ecosystems associated with different stressors 

(e.g., toxic chemicals vs. sediment) is not known, but synergistic effects of multiple stressors from 

across the watershed is likely. 

Stressor identification is an emerging field; it is made difficult by the fact that the variety of human 

actions that degrade coral reefs rarely occur independently (Figure 8-1). If each watershed 

had only one human activity, direct connections could be made between specific stressors and 

changes in coral reefs, but most watersheds contain a mix of activities and stressors. All these 

influences are then further mixed by ocean currents. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 8-1
 
Figure 8-1. Conceptual model of stressors impacting a coral reef. 

Causal analysis and stressor identification cannot be accomplished with a simple statistical test or 

a single process model. Although discussion of potential approaches is beyond the scope of this 

manual, EPA guidance (EPA 2007a) recommends a qualitative and logical approach to diagnosis. 

Causal analysis should start with a candidate list of causes and the ecological theory supporting 

those candidates, in other words, scientific studies that support the proposed causal relationship. 

Next, available data from the impaired sites are considered along with maps and other supporting 

material. Perhaps there has been recent suburban growth into forested areas; or, a new chemical 

plant has gone on-line in the near-coastal watershed. Data from other studies or similar sites 

should also be considered. The final step, deciding the cause of the impairment, relies on a careful 

examination of the evidence and well-reasoned discussion regarding the probable cause of the 

impairment in biological condition. 

Although unique biological indicators have not been identified for all the stressors that affect coral 

reefs, some relationships are emerging (Table 8-1 for examples). Coral bleaching has increased 

dramatically in recent years in response to elevated sea temperatures, particularly for Acropora 

and Pocillopora species; however, bleaching is also a sign of excessive sediment as well as other 

stressors. Nonetheless, the pattern and timing of bleaching, as well as the species that bleach, 

could be used to characterize the influence of different stressors. 

8-2 Chapter 8 — What Is Causing Reefs to Change? 
Table 8-1. Examples of commonly observed biological responses characteristic for particular coral 

reef stressors. 

Stressor Biological response 

Global climate change • Coral bleaching, loss of Acropora spp. 

Ocean acidification • Decrease in calcification rates; decreased coral growth 

Coral disease • Lesions, banding, or bleaching 

Fishing • Reduced herbivores and large predators 

• Increased growth of macro-algae 

• Loss of appropriate substrate for coral recruitment 

Land-based pollutants • Loss of coral cover and increased macroalgae cover due 

to nutrients 

• Loss of appropriate substrate for coral recruitment and 

reduction of growth in large colonies due to sediments 

• Increased coral mucus associated with sewage outfalls 

and sediment 

• Inhibition of photosynthesis and metamorphosis of coral 

larvae due to herbicides 

• Altered genetic expression due to heavy metals 

• Elevated RNA/DNA ratio related to turbidity 

Boating and shipping • Broken colonies, marine debris, dredged channels 

Invasive species • Loss of fish taxa richness due to predation by lion fish 

Tourism & recreation • Broken colonies, anchor damage 

A key point is that managers should not wait to report the extent of coral reef loss until the causes 

of the problem has been identified. The purpose of CWA Section 305(b) reporting and 303(d) 

listing of reef sites is to document that problems exist. After listing, other processes are used to 

evaluate the causes and sources of impairment within the context of stressor identification. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 8-3
 

9. What Can We Do to Protect Reefs?
	

The problem is not to manage the reefs but to manage 

“

human population and their activities. ” — Bernard Salvat, 1995 

Coral reef ecosystems not only fall under the states’ jurisdictions, but also under the jurisdiction 

of the National Oceanic and Atmospheric Administration (NOAA), National Park Service (NPS), 

and Fish and Wildlife Service (FWS). Each agency has its own mandates and legislative purview. 

Consequently there are diverse legislative actions and initiatives to protect reefs. Recent 

declines in reef health have been met with legislation to promote interagency cooperation and 

collaboration. An Executive Order issued by President Clinton in 1998 (EO 13089 1998, Coral 

Reef Protection) established the interagency U.S. Coral Reef Task Force to enhance reef 

conservation and stewardship. In the Coral Reef Conservation Act of 2000 (16 USC § 6401 2000), 

Congress authorized the Secretary of Commerce to establish a national monitoring program to 

promote the understanding, conservation, and sustainable use of coral reef ecosystems. 

Less auspicious but highly significant was submission of the President’s Ocean Action Plan (The 

White House 2004) to Congress in 2004. Under this plan, the U.S. EPA was directed to develop 

biocriteria and assessment methods for states and territories to evaluate the condition of coral 

reefs and surrounding marine water quality. Biocriteria can be used to establish acceptable 

thresholds of biological condition, effectively integrate the cumulative effects of human influence 

(Karr and Yoder 2004), and are easy for the public to understand and support because they focus 

on benefits to society. 

Perhaps less obvious is that the process of developing biocriteria, summarized in this manual, is 

a legally defensible means to translate scientific understanding into legal and regulatory authority. 

Because of these characteristics, biocriteria and the process to develop biocriteria support and 

complement a variety of existing management and regulatory programs (Figure 9-1), some of 

which fall within the aegis of other federal agencies. 

In particular, the process for developing biocriteria compels states to engage stakeholders to 

determine what should be protected (what has societal value) and at what level (thresholds). 

Biocriteria also require defensible assessment methods. Bioassessments for coral reef condition 

are required for many different management and regulatory actions. Thresholds, codified as 

biocriteria, can be applied to determine high-quality waters for greater protection and to gauge the 

effectiveness of management actions. Biocriteria should not be considered a stand-alone CWA 

regulatory tool, but rather a legally defensible method to support biological integrity goals for many 

different authorities and legislations. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 9-1
 
 

Figure 9-1. Examples of coral reef management programs that may be supported by biocriteria. 

9.1 CWA and Existing Coral Reef Management Programs 

Dodge et al. (2008) outlines a series of actions needed to reverse the decline of coral reefs (Table 

9-1). Their list highlights the inability of existing watershed and coastal management practices 

to protect coral reefs from land-based activities or other threats that originate outside their 

boundaries. 

Several commonly-used management approaches for coral reef resources can be advanced 

by application of CWA methods for development of biocriteria, including designated uses, 

bioassessment procedures, biological condition gradient 

(BCG), and thresholds (criteria) to protect designated uses. 

The process of developing biocriteria includes community 

decisions to be made on what to protect and at what level, and 

provides an easy mechanism to identify high-quality waters and 

gauge management success. Some of the programs that can 

benefit from biocriteria are characterized below. They are also 

summarized in Appendix G. 

Marine Protected Area 

(MPA): Any area of the 

marine environment 

that has been reserved 

by federal, state, tribal, 

territorial, or local laws 

or regulations to provide 

Marine Protected Areas (MPA). Among the most used lasting protection for part 

management tools for coral reefs is the Marine Protected Area. or all of the natural and 

Creation of MPAs is one of nine actions recommended by Dodge cultural resources therein 

et al. (2008) to reverse the decline of coral reefs. There are (EO 2000). 

many types of MPAs, including national marine sanctuaries, 

9-2 Chapter 9 — What Can We Do to Protect Reefs? 
 

Table 9-1. Biocriteria can be used to identify waterbody impairments for coral reefs (Fore et al. 2009) and the U.S. 

Clean Water Act can be used to address many of them. 

Actions of Dodge et al. (2008) Addressed by CWA? 

(i) Cut CO2

 emissions Yes; possible precedent with acid rain in 

northeastern states 

(ii) Eliminate open-access fisheries in coral 

reef ecosystems and establish and enforce 

sustainable fisheries regulations. 

CWA protects water quality suitable for 

protection and propagation of fish, shellfish and 

wildlife; other laws manage fisheries 

(iii) Ban the harvest of coral reef herbivores, 

including parrotfish. 

CWA protects water quality suitable for 

protection and propagation of fish, shellfish and 

wildlife; other laws manage fisheries 

(iv) Establish and enforce Marine Protected 

Areas that include No-Take Areas. No 

(v) Effectively manage the waters in between 

Marine Protected Areas. 

Yes; all waters of the territorial seas are 

required to have designated uses and 

standards to protect uses 

(vi) Maintain connectivity between coral reefs 

and associated habitats such as mangroves, 

sea grass beds, and lagoons. 

Yes; authority to set water quality standards in 

all types of habitats within the territorial seas 

(vii) Report regularly and publicly on the health 

of local coral reefs. 

Yes; mandate for states and territories to report 

biological condition of water resources (305b) 

(viii) Recognize the links between what we do 

on land and how it affects the ocean. Yes; authority to regulate terrestrial pollutants 

(ix) Bring together industry, civil society, local 

government, and the scientific community to 

develop a vision of healthy reefs. 

Yes; long history of examples 

national parks and wildlife refuges, state parks and conservation areas, and a variety of fishery 

management closures. MPAs vary in what is protected, the size of the area protected and the 

form of enforcement. The United States has developed a national system of MPAs to advance 

the conservation and sustainable use of the nation’s vital natural and cultural marine resources 

(NOAA 2009c). Specifically for coral reefs, the U.S. Coral Reef Task Force (USCRTF) has 

developed a strategy for building a national network of marine protected areas, and has published 

“Coral Reef Protected Areas: A Guide for Management” to assist those involved in planning 

and managing programs for coral reef protected areas (16 USC § 6401 2000). Biocriteria can 

be used to identify waters with outstanding biological condition, establish desired thresholds for 

reef condition and to gauge effectiveness of the MPA. Also, biocriteria can be used to manage 

waters between MPAs, either by protecting connectivity and resilience or by protecting organisms 

inhabiting interstitial areas. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 9-3
 
Managing Fisheries. Fishing regulations are designed and implemented to enforce sustainable 

fisheries. These actions can also protect coral reef ecosystems. Basic fisheries management 

practices include restricting the numbers of people or number of boats fishing, the time allowed 

for fishing, the fishing area, type of gear or technology, and the species and sizes that can be 

harvested (ISRS 2004). Fisheries management could incorporate biocriteria to establish size class 

and abundance minima for harvested species to protect the fishery (“fishable” waters). Declines 

below these thresholds would trigger changes in fishery practices and regulations. In a related 

example, the Supreme Court blocked construction of the Dosewallips River Dam (Washington) to 

protect the state’s CWA designated use for migration, rearing and spawning of salmonids (Ransel 

1995). 

Managing Tourism. The unique and diverse biota 

of coral reefs provide many attractions for tourists. 

However, tourism development projects and the 

behavior of tourists themselves can contribute to 

significant reef losses and coral reef degradation 

(GEF 1996). Some jurisdictions have implemented 

management practices that regulate tourism and 

tourist activities. Practices include placement of 

mooring buoys to limit anchor damage, permits 

for diving, fishing, and boating, user fees, and 

navigational aids such as buoys to mark reef 

locations and documenting reef locations on 

international nautical charts. Biocriteria can be used 

to identify waters of outstanding biological condition 

and evaluate the success of tourism management 

practices. Development of a BCG, driven by expert 

analysis, can be useful for determining acceptable 

levels of tourism (Figure 9-2). 

Managing Endangered Species. The Endangered Species Act (ESA) (16 USC §1531 et seq. 

1973) provides a program for conserving threatened and endangered plants and animals and 

their habitats. A species is considered endangered if it is in danger of extinction throughout all 

or a significant portion of its range. A species is considered threatened if it is likely to become an 

endangered species within the foreseeable future. The listing of a species as endangered makes 

it illegal to “take” (harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect) that 

species. In May 2006, FWS listed Acropora palmata (elkhorn coral) and Acropora cervicornis 

(staghorn coral) as vulnerable under the ESA because of widespread decline throughout their 

Caribbean range. More recently, the Center for Biological Diversity filed a formal petition seeking 

to protect an additional 83 imperiled coral species under the ESA. The corals occur in both 

Atlantic/Caribbean and Pacific waters and face a growing threat of extinction from rising ocean 

temperatures and ocean acidification. Biocriteria can be applied to specifically protect ESA 

species; this normally would require that a state cites protection of that species or any endangered 

species as a designated waterbody use. Biocriteria in combination with a BCG can be used to 

gauge the effectiveness of the protective measures and can also be used to determine the point at 

which a coral species has recovered and no longer requires protection of the ESA. 

Figure 9-2. Managing tourism. Jurisdictions 

implement a variety of approaches to manage 

tourists, including mooring buoys and use 

permits. 

9-4 Chapter 9 — What Can We Do to Protect Reefs? 
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 9-5

Coastal Zone Management (CZM). A partnership between the federal government and U.S. 

coastal states was authorized by the Coastal Zone Management Act of 1972 (CZMA) (16 USC 

§1451 1972). The CZMA encourages states to preserve, protect, develop, and where possible, 

restore or enhance valuable natural coastal resources (Figure 9-3) such as wetlands, floodplains, 

estuaries, beaches, dunes, barrier islands, and coral reefs, as well as the fish and wildlife using 

those habitats. To encourage states to participate, the act makes federal financial assistance 

available to any coastal state that is willing to develop and implement a comprehensive coastal 

management plan (CCMP). NOAA administers the program at the federal level and works with 

coastal states to develop and implement their coastal zone management plans. In the Coastal 

Zone Act Reauthorization Amendments of 1990 (CZARA), Congress added Section 6217, which 

calls upon states with federally approved coastal zone management programs to develop and 

implement coastal nonpoint pollution control programs. The section 6217 program is administered 

at the federal level jointly by EPA and NOAA (NOAA 2009d; EPA 1993). Biocriteria have an 

opportune role to reinforce the integrated and comprehensive nature of CZMA and CZARA. The 

CZMA provides umbrella coverage across all aquatic resources, not just coral reefs, so biocriteria 

and physical/chemical water quality standards can be used to protect the entire ecological system 

that comprises coral and its associated habitats. A CCMP can employ biocriteria to establish 

valued attributes (designated uses) and derive acceptable thresholds for different organisms, 

habitats and ecosystems. Attaining biocriteria goals is a quantitative reflection on the success of 

the management plan. 

Watershed Management. A watershed is the area of land from which rainfall drains into a single 

point. Watersheds are also sometimes referred to as drainage basins or drainage areas. Ridges 

of higher ground generally form the boundaries between watersheds. At these boundaries, rain 

falling on one side flows toward the low point of one watershed, while rain falling on the other side 

of the boundary flows toward the low point of a different watershed. 

A watershed management plan usually considers the entire watershed with a goal to protect and 

restore an environmentally and economically healthy watershed that benefits all stakeholders. 

This generally means to sustain and enhance watershed functions that affect the plant, animal, 

and human communities within a watershed boundary. Agencies manage activities in the 

watershed such as water supply, water quality, drainage, stormwater runoff, water rights, and 

the overall planning and utilization of watersheds (EPA 2008b). Biocriteria can be developed 

SATURATED WATER 

UNSATURATED 

WATER 

groundwater flow 

percolation 

& uplflow 

infiltration 

evaporation 

transpiration 

precipitation 

runoff 

surfacesaturated 

exchanges 

SURFACE 

WATER 

Figure 9-3. The coastal watershed. 

Water enters the watershed through 

precipitation, and then travels 

throughout the watershed in myriad 

ways including runoff to creeks, 

streams, and rivers, making its way 

to lower elevations, and eventually 

to the coastal waters and coral reefs. 
 

and implemented for any lake, river, stream and estuary in a U.S. watershed. This serves to 

protect downstream resources as well, such as coral reefs. Likewise, biocriteria for protection of 

coral reefs can benefit upstream resources. An integrated plan to employ biocriteria for valued 

populations and ecosystems throughout the watershed can work interactively to protect resources 

and identify sources of pollution that are causing impairment. 

Damage Assessment and Restoration. Seagrasses, mangroves and coral reefs that are 

physically damaged by human actions are addressed through a process that allows resource 

managers to identify injured resources, recover damages from responsible parties, restore 

habitats and resources to pre-injury/pre-exposure conditions, and compensate the public for the 

loss of ecological and visitor use services. Some restoration activities now underway include 

active propagation and selection of stress-resistant colonies (e.g., staghorn coral restoration by 

The Nature Conservancy, www.nature.org). Development of a BCG can assist in the identification 

of pre-injury/pre-exposure conditions. Biocriteria can be used to establish thresholds to measure 

the effectiveness of restoration efforts. 

National Environmental Policy Act (NEPA). Federal agencies are required under the National 

Environmental Policy Act (NEPA) to integrate environmental values into decision-making by 

considering the environmental impacts of proposed actions and possible alternatives. The 

Act requires preparation of Environmental Impact Statements (EIS), which are full disclosure 

documents detailing the developmental process for federal projects. The EIS describes existing 

resources and environmental condition, including the social, economic and ecological settings 

surrounding the project and any environmentally sensitive features that may be impacted. An EIS 

also describes the environmental impacts of project alternatives and potential measures that could 

be taken to mitigate these impacts. Biocriteria can be used to describe and compare the condition 

of resources to be impacted under the alternatives. Biocriteria and a BCG can also be used to 

determine whether the project has complied with the approved EIS and associated project permits 

and is protecting the natural resources that were identified. 

9.2 Biocriteria and Other CWA Programs 

One strength of the CWA is that it provides multiple ways to protect biological integrity of the 

Nation’s waters. Chapter 4 provided an overview of water quality standards (designated uses, 

water quality standards [including biocriteria], and antidegradation) described in Sections 303, 

304 and 305 of the CWA. Other sections establish a variety of other programs to achieve CWA 

goals. Biocriteria and bioassessment methods, in ways similar to those described above, can work 

interactively with other CWA programs to protect coral reefs. 

CWA Section 104(b)(3): Wetlands Program Development Grants. EPA is authorized to provide 

federal assistance to states (including territories, the District of Columbia), Indian Tribes, and local 

governments to conduct projects that promote the coordination and acceleration of research, 

investigations, experiments, training, demonstrations, surveys, and studies relating to the causes, 

9-6 Chapter 9 — What Can We Do to Protect Reefs? 
effects, extent, prevention, reduction, and elimination of water pollution. Coral reefs, mangroves, 

and seagrasses are considered special aquatic sites and wetlands under CWA 404, and Section 

104(b)(3) grants can directly fund monitoring and assessment of coral reefs and development of 

biocriteria for coral reefs. EPA Region 9 has awarded Wetlands Program Development Grants to 

support coral reef biocriteria development for Hawaii and CNMI. 

CWA Section 106: Grants for Pollution Control Programs. EPA is authorized to provide federal 

assistance to states (including territories, the District of Columbia) and Indian Tribes and interstate 

agencies to establish and implement ongoing water pollution control programs. These grants 

may be used to fund a wide range of water quality activities including: water quality planning 

and assessments; development of water quality standards; ambient monitoring; development 

of total maximum daily loads (TMDLs); issuing permits; ground water and wetland protection; 

compliance and enforcement activities; non-point source control activities (including non-point 

source assessment and management plans); and Unified Watershed Assessments (UWA) under 

the Clean Water Action Plan (CWAP). EPA Region 10, in a 2009 Request for Initial Proposals for 

TMDL Grants, explicitly mentioned the application of biological monitoring protocols and biocriteria 

(including narrative biocriteria) that lead to improved TMDLs. 

CWA Sections 205(j) and 604(b): Water Quality Management Planning Grants. EPA is 

authorized to provide grants to assist state water quality management agencies and others in 

carrying out water quality management planning. State agencies are encouraged to give priority 

to watershed restoration planning. Comprehensive water quality management programs include 

development and implementation of biocriteria, the development of which can be supported under 

these grants. 

CWA Section 301(h): Effluent Limitations. The CWA provides an opportunity for a variance from 

technology-based secondary treatment standards for publicly owned treatment works discharging 

into marine waters, provided that the applicant demonstrates that, among other things, the 

discharge subject to the variance would not adversely affect biological communities. To obtain 

this variance, extensive biological monitoring is required to detect any potential effects on the 

biological communities. Biocriteria and a BCG can be used to demonstrate a no-effect threshold. 

In one example, EPA determined in 2009 that the discharges from two Honolulu wastewater 

treatment plants did not meet all applicable water quality standards. Discharges from both plants 

failed to protect recreational use or marine life in the vicinity of the ocean outfalls. 

CWA Section 312: Marine Sanitation Devices. The CWA mandates the use of marine sanitation 

devices (MSDs), on-board equipment for treating and discharging or storing sewage, on all 

commercial and recreational vessels that are equipped with installed toilets. It also mandates the 

development of MSD standards and regulations to implement the requirements of the statute. 

Under CWA Section 312, EPA or states may establish “no-discharge zones” for sewage from 

vessels. State water quality standards, including biocriteria, can be applied to identify appropriate 

locations for no-discharge zones, and biocriteria can be used to identify locations with outstanding 

biological condition that would benefit from a no-discharge zone status. Biocriteria can also be 

used to establish thresholds to gauge the effectiveness of no-discharge zones. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 9-7
 
CWA Section 319: Nonpoint Source Program (NPS). A voluntary non-point source control 

program allows states to control the impacts of watershed runoff. Since 1990, Congress has 

annually appropriated grant funds to states for a wide variety of activities including technical 

assistance, financial assistance, education, training, technology transfer, demonstration projects, 

and monitoring to assess the success of specific nonpoint source implementation projects. 

Biocriteria can be used to assess the impacts of nonpoint source pollution and to determine the 

effectiveness of nonpoint source controls. An example of successful use of biocriteria in managing 

nonpoint source pollution is the American Samoa Piggery Compliance Program. Six coral reef 

habitats were assessed on Tutuila to characterize the relationship between NPS pollution and 

coral reef habitat (Houk and Musberger 2007; Houk and Musberger 2008). Five of the six habitats 

were found to only partially support aquatic life uses and one was not supporting. Because it 

was a baseline study, the results did not draw any direct links to NPS pollution. Nonetheless, the 

degraded condition of coral reefs was used to more strongly enforce compliance for pig facilities 

(i.e., remove illegal piggery discharges). The American Samoa EPA Piggery Compliance Team 

has recently reduced nutrient loads to nearby waters by more than 5000 kg of nitrogen and 1800 

kg of phosphorus. 

CWA Section 320: National Estuary Program (NEP). A CWA program to identify, restore and 

protect nationally significant estuaries was established in 1987 by amendments to the CWA. 

EPA administers the National Estuary Program (NEP), but program decisions and activities are 

conducted by committees of local government officials, private citizens, and representatives 

from other federal agencies, academic institutions, industry, and estuary user-groups. When an 

estuary is admitted into the program, a management conference is convened to characterize the 

environmental issues, including relationships between pollutant loading and impacts on living 

resources, and to develop a comprehensive plan to resolve priority problems. EPA is authorized 

to award grants for development of the management plan and implementation projects. The intent 

of NEP management plans is to restore and protect water quality (as defined by the CWA); this 

translates to restoring and protecting the chemical, physical and biological integrity of the estuary. 

Biocriteria establish thresholds for biological integrity and can be developed as an integral part 

of the management plan. There is currently only one NEP with corals – the San Juan Estuary in 

Puerto Rico. 

CWA Section 401: State Water Quality Certification. Any activity that requires a federal license 

or permit that may result in a discharge to waters of the U.S. must first obtain a CWA Section 

401 water quality certification from the relevant state or territorial water quality agency to ensure 

the project will comply with applicable water quality standards. Federal Energy Regulatory 

Commission hydro licenses and U.S. Army Corps of Engineers (Corps) dredge and fill permits, for 

example, trigger the requirement for CWA Section 401 certification. For example, when offshore 

projects are under construction in Florida, the Florida Department of Environmental Protection 

requires that procedures are employed to protect water quality and potential sedimentation on 

the reefs. Biological monitoring is necessary to document the effects of construction projects 

on natural resources. Biocriteria can be used to provide a threshold to estimate dredge and 

fill impacts on biological communities. Biocriteria can also be helpful in evaluating a range of 

alternatives for dredge and fill activities and for identifying the least damaging alternative, as 

required by CWA Section 404. 

9-8 Chapter 9 — What Can We Do to Protect Reefs? 
CWA Section 402: National Pollutant Discharge Elimination System (NPDES). It is illegal 

under the CWA to discharge any pollutant to waters of the United States from a point source 

unless authorized by a National Pollutant Discharge Elimination System (NPDES) permit. Typical 

point sources regulated under the NPDES program include: municipal wastewater systems, 

municipal and industrial storm water systems, industries and commercial facilities, Concentrated 

Animal Feeding Operations (CAFOs), and large aquaculture facilities. 

Point source is defined by the CWA as “any discernible, confined 

and discrete conveyance, including but not limited to any pipe, ditch, 

channel, tunnel, conduit, well, discrete fissure, container, rolling stock, 

concentrated animal feeding operation, or vessel or floating craft, 

from which pollutants are or may be discharged.” This includes certain 

municipal, industrial, and construction site discharges of storm water. 

An NPDES permit limitation is required in any case where a discharge is expected to have 

the reasonable potential to cause, or contribute to non-attainment of a water quality standard, 

including biological impairments. NPDES permits establish pollutant discharge limits based on 

treatment technology performance, the quality of the water into which pollutants are discharged, 

and the potential adverse impact of the discharge on water quality standards. EPA oversees the 

NPDES program and also approves submissions by states to administer state NPDES permitting 

programs in lieu of EPA administration. EPA is promoting a watershed-based NPDES permitting 

that emphasizes consideration of all stressors within a hydrologically-defined drainage basin 

rather than individual pollutants on a discharge-by-discharge basis (EPA 2009c). Watershedbased permitting can encompass a variety of activities ranging from synchronizing permits within 

a basin to developing water quality-based effluent limits using a multiple discharger modeling 

analysis. Biocriteria have several applications in NPDES programs. Biocriteria can be used in 

determining the condition of a waterbody prior to issuance of a permit and during discharge to 

ensure that state water quality standards are being met. They can also be used to evaluate the 

effectiveness of any controls implemented by the discharger. Florida uses freshwater biocriteria to 

identify “hot spots” and evaluate the effectiveness of NPDES stormwater management programs 

on stream biota. 

CWA Section 403(c): Ocean Discharge Program. There are special requirements applicable to 

NPDES permits for discharges into the ocean, including three different ocean regions defined in 

the CWA (i.e., a three mile territorial sea, a 12-mile contiguous zone, and waters beyond the 12­

mile zone). The permitting process requires that the permitting agency determine for any permitted 

ocean dischargers that the discharge will not cause an unacceptable degradation of the marine 

environment, including the biological community in the area surrounding the discharge. Biocriteria 

provide defensible measures of biological communities and thresholds to estimate the impact of 

ocean discharge on biological communities. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 9-9
 
 

CWA Section 404: Permits for Dredged and Fill Material. Establishes a permit program to 

regulate the discharge of dredged and fill material into waters of the United States, including a 

three mile territorial sea. Dredge and fill discharge permits are jointly administered by the U.S. 

Army Corps of Engineers and EPA, but permits are issued by the Army Corps. The FWS and 

National Marine Fisheries Service (NOAA) play special advisory roles because of their expertise 

in wildlife habitat and endangered species. EPA issues certain rules and guidelines to guide Corps 

permit decisions. EPA can veto a permit issued by the Corps. Biocriteria can provide methods 

and thresholds to identify high value areas for protection to determine dredged and fill discharge 

impacts on biological communities. When marine projects are under construction in Florida, 

the Department of Environmental Protection ensures that methods are implemented to protect 

water quality and potential sedimentation on the reefs. Biocriteria and a BCG can also be used to 

identify acceptable sites for disposal of dredged and fill material. 

CWA Section 603: Clean Water State Revolving Fund (CWSRF). Capitalization grants are 

made available to each state for the purpose of establishing a Clean Water State Revolving Fund 

(CWSRF) to provide independent and permanent sources of low-cost financing for (1) construction 

of publicly owned wastewater treatment works, (2) implementing nonpoint source management 

activities included in State Plans developed pursuant to Section 319, and (3) developing and 

implementing an estuary conservation and management plan under Section 320. Today, all 

50 states and Puerto Rico are operating successful CWSRF programs. Funds to establish or 

capitalize the CWSRF programs are provided through federal government grants and state 

matching funds. In recent years EPA has provided more than $5 billion annually to fund a variety 

of water quality projects. Total funds available to the program since its inception exceed $70 

billion. Biocriteria can provide a threshold to measure the degree to which water quality projects 

reduce human impacts on biological communities. 

A table summarizing these CWA sections can be found in Appendix H. 

9.3 Biocriteria Can Link CWA and CAA to Address Ocean Acidification 

Ocean acidification is a major threat to coral reefs. The cause of ocean acidification, high levels 

of carbon dioxide (CO2) in the atmosphere, is an air quality issue over which states have little 

influence. Even though each state has contributed to ocean acidification, emissions of CO2

 are 

worldwide. At first glance it doesn’t appear that the CWA has any role in resolving this issue, even 

though coral reefs are among those highly threatened by CO2

 emissions. Yet, past experience 

has shown that the CWA can complement the Clean Air Act (CAA), which regulates all forms of 

air pollution, including CO2

 emissions. The CWA can be used to assess waterbody impairment 

caused by ocean acidification, which can trigger action under the CAA. A similar approach was 

applied in the 1980s with creation of the Acid Rain Program. Streams in the northeastern U.S. 

were becoming increasingly acidic and stream biota were adversely impacted. Listing streams on 

the 303(d) impaired waters list triggered regulatory action under the CAA at the national level. 

9-10 Chapter 9 — What Can We Do to Protect Reefs? 
10. DoOur Efforts Protect Reefs?
	

For all the effort that goes into protecting coral reefs, we must always ask whether or not we are 

making a difference. How do we know that our policies and management strategies are protecting 

reefs? The most reliable answer to this question would come from trend monitoring stations. If, 

over time, repeat sampling indicates an upward trend in coral reef condition, we would have a 

positive answer that, yes, our efforts are working. This is called effectiveness monitoring. Given 

the scale of protection and restoration efforts compared to the magnitude of environmental change 

associated with modern human life, a measurable improvement at the regional scale may be an 

unlikely outcome. Unfortunately, rather than a measurable improvement, it may be in some cases 

that our efforts can only slow the decline of coral reefs. 

It’s more difficult to quantify but very important to understand how much damage to coral reefs 

has been avoided by past and existing management efforts. Reefs were in some measure 

spared when a toxic effluent was not released, when soil was not eroded, and young fish were 

not harvested. We don’t typically measure or report damage that was avoided, even though it is 

an important outcome of conservation practices. This is sometimes called silent evidence (Taleb 

2007). Our inability to measure how much worse the environmental condition would have been 

if we had done nothing is a difficult concept to quantify and can be a source of frustration for 

resource managers. 

The best opportunity to see measurable improvement in resource condition is at a relatively small 

spatial scale. For example, some marine protected areas have shown an increase in fish species 

or other measures of biological condition within the boundaries of marine protected areas (Halpern 

2003). Nonetheless, the initial hope that protected areas would adequately support biota in the 

unprotected areas has faded somewhat (Kareiva 2006). 

In the Florida Keys National Marine Sanctuary (FKNMS), over 300 mooring buoys have been 

placed throughout the park to reduce anchor damage from recreational boats. Sanctuary scientists 

and managers also defined zones for shipping to prevent groundings by large vessels. A dramatic 

drop in the number of groundings resulted. We can assume that if the changes were not made, 

the rate of coral loss would have continued and the “savings” in coral reef can be calculated. 

Other FKNMS programs are not as easily evaluated. Sanctuary managers have worked to 

eliminate the discharge of untreated sewage to meet a 2010 deadline set by EPA. They have 

implemented wastewater treatment, injection wells to replace ocean outfalls, eliminated septic 

systems, repaired leaky wastewater systems, and established no-discharge zones for cruise 

ships and other vessels. How can we tell if these nutrient reduction projects have improved reef 

condition? 

There are multiple approaches to evaluate the success of these efforts. First, was untreated 

sewage eliminated? At a local scale, the success of this program has been measured in terms 

of fewer exceedances for fecal coliform and enterococcus bacteria and reduced beach closures. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 10-1
 
Local jurisdictions were found to be in compliance with the new requirements, so there was 

successful implementation. These types of summary statistics represent compliance monitoring, 

that is, tracking whether the mandated changes were accomplished. For reduction of sewage 

discharge in FKNMS, the answer seems to be yes. 

Connecting changes in nutrient concentration at a larger spatial scale is more challenging. 

Beginning in 1995, a regional water quality monitoring program was implemented to collect water 

samples from 154 locations located offshore of south Florida, in Florida Bay, and around the 

Florida Keys (Boyer and Briceno 2006). Natural variability and other larger sources of nutrients, 

such as those originating from Florida Bay, have made it difficult to detect changes in nutrient 

levels related to human sources and natural processes (Lirman and Fong 2007). The answer to 

whether the projects have reduced nutrient concentrations is therefore largely unanswered. 

The most challenging question is, do these changes protect coral reefs? Elimination of sewage 

reduces nutrients and pathogens that threaten corals and other biota. Nonetheless, during this 

same period of increased efforts to improve water quality, coral cover has been in a steep decline. 

For Florida reefs, from 1996 to 2006 coral cover has declined from 12% to 6%, a 50% loss 

(Callahan et al. 2007). Similarly the number of coral taxa typically found in a standard transect has 

declined by a total of 4 taxa from an expected number of about 17. The continued decline of coral 

reefs doesn’t mean that the sewage treatment efforts were not successful, because we don’t know 

how many fish or corals were actually protected. What we know is that in spite of our efforts, coral 

reefs are still declining. That means that we are not controlling other important stressors unrelated 

to nutrient and contaminant pollution. 

How can we be more effective? Resource managers responsible for coral condition probably need 

more help because the problem is bigger than we initially realized. One way to get more attention 

on the problem and more help is through reporting. The Clean Water Act provides a formal 

reporting mechanism to report to Congress, stakeholders, and local jurisdictions the condition 

of coral reefs, e.g., “30% of coral reef area fails to support aquatic life use.” The key to effective 

protection and restoration is to measure and report on the water resources we truly care about. In 

this case, nutrient reduction was identified as a threat to corals, but it wasn’t the only threat. Work 

and research remains to determine the risks associated with different human activities and to 

prioritize our efforts to reduce those threats. 

Effectiveness monitoring takes people and dollars, resources that may be subtracted from more 

or better conservation and restoration programs. A good argument can be made for both needs. 

Evidence of a significant difference resulting from a management practice may take very intensive 

sampling, but it is hard to keep implementing programs if you don’t know they are working. One 

approach is to perform effectiveness monitoring at a small spatial scale and then decide whether 

any changes are enough to mandate a program at a larger regional scale. Modeling represents a 

way to evaluate the potential regional effect if the management program were implemented across 

a larger area (Zitello et al. 2008). 

The outlook for coral reefs is potentially grim, but protection and restoration can arise from 

multiple sources. A broader recognition of regulatory and legal actions, such as the Clean Water 

Act (and many other state and federal laws), that are available to protect water and reef resources 

10-2 Chapter 10 — Do Our Efforts Protect Reefs? 
is a good start. Along with understanding the regulatory options, there must be a will to use 

these instruments to their full capability. Another approach involves fostering a more widespread 

understanding that economic prosperity is founded on natural capital, such as the natural 

resources associated with coral reefs (MEA 2003). 

A different perspective is gained when we think about the problem of resource degradation as a 

society. In the early years of the Clean Water Act, the focus was on “polluters” and efforts were 

directed toward eliminating industrial sources. In recent years, the balance has shifted and we 

know that much of the damage to water resources derives from the cumulative effects of average 

citizens living their everyday lives (NRC 2008). This is a profound shift. Individual citizens and 

independent groups around the world recognize that the responsibility for the natural world is not 

just the government’s job, but a responsibility shared by all (Hawken 2007). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 10-3
 

Appendix A: Acronyms and Abbreviations 
	

BCG Biological Condition Gradient 

BMP Best Management Practices 

CAA Clean Air Act 

CCMP Comprehensive Conservation & Management Plans 

CFR Code of Federal Regulations 

CNMI Commonwealth of the Northern Mariana Islands 

CO2 Carbon Dioxide 

CREMP Coral Reef Ecosystem Monitoring Program (EPA & FKNMS) 

CWA Clean Water Act 

CWSRF Clean Water State Revolving Fund 

DEP Department of Environmental Protection (Florida) 

DO Dissolved Oxygen 

DOH Department of Health (Hawaii) 

DOI Department of the Interior 

DPNR Department of Planning and Natural Resources (USVI) 

DPSIR Driving Forces, Pressures, State, Impacts, and Response 

EO Executive Order 

EPA U.S. Environmental Protection Agency 

ESRP Ecosystem Services Research Program 

FKNMS Florida Keys National Marine Sanctuary (NOAA) 

FL Florida 

FRRP Florida Reef Resilience Program (TNC) 

FWS Fish & Wildlife Service 

LDI Landscape Development Intensity Index 

MPA Marine Protected Area 

NEP National Estuary Program 

NEPA National Environmental Policy Act 

NMSA National Marine Sanctuaries Act 

NOAA National Oceanic and Atmospheric Administration 

NPDES National Pollutant Discharge Elimination System 

NPS National Park Service (U.S. Department of the Interior) 

NPS Non-Point Source 

ONRW Outstanding National Resource Waters 

POTWs Publicly Owned Treatment Works 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure A-1
 
 

SCUBA Self-Contained Underwater Breathing Apparatus 

TMDL Total Maximum Daily Load 

TNC The Nature Conservancy 

UAA Use Attainability Analysis 

USCRTF U.S. Coral Reef Task Force 

USVI U.S. Virgin Islands 

WQ Water Quality 

WQC Water Quality Criteria 

WQS Water Quality Standards 

A-2 Appendix A: Acronyms and Abbreviations 
Appendix B: Glossary 
 

106. The section of the Clean Water Act that authorizes the USEPA to provide federal 

assistance to states (including territories, the District of Columbia, and Indian tribes) and 

interstate agencies to establish and implement ongoing water pollution control programs. 

Prevention and control measures supported by state water quality management programs 

include permitting, pollution control activities, surveillance, monitoring, and enforcement; advice 

and assistance to local agencies; and the provision of training and public information. 

301. The section of the Clean Water Act that establishes the national policy regarding discharge 

of pollutants from a point source to waters of USA, shorelines and waters of contiguous zones. 

303(d). The section of the Clean Water Act that requires a listing by states, territories, and 

authorized tribes of impaired waters, which do not meet the water quality standards that states, 

territories, and authorized tribes have set for them, even after point sources of pollution have 

installed the minimum required levels of pollution control technology. 

304. The section of the Clean Water Act that authorizes EPA to develop criteria for water quality 

that accurately reflects the latest scientific knowledge. These criteria are based solely on data 

and scientific judgments on pollutant concentrations and environmental or human health effects. 

Section 304(a) also provides guidance to states and tribes in adopting water quality standards. 

Criteria are developed for the protection of aquatic life as well as for human health. 

305(b). The section of the Clean Water Act that requires EPA to assemble and submit a report 

to Congress on the condition of all waterbodies across the country as determined by a biennial 

collection of data and other information by states and tribes. 

312. The section of the Clean Water Act that regulates vessel sewage discharge through the 

mandatory use of marine sanitation devices (on-board equipment for treating and discharging 

or storing sewage) on all commercial and recreational vessels that are equipped with installed 

toilets. Under Section 312 states may request a No-Discharge Zone (NDZ) designation that 

prohibits the discharge of sewage from all vessels into defined waters. 

319. The section of the Clean Water Act that authorizes EPA to provide federal funding to states, 

territories, and Indian tribes to help focus state and local nonpoint source efforts. Funding can 

be received for a wide variety of activities including technical assistance, financial assistance, 

education, training, technology transfer, demonstration projects, and monitoring to assess the 

success of specific nonpoint source implementation projects. 

320. The section of the Clean Water Act that directs EPA to develop plans for attaining or 

maintaining water quality in estuaries that are part of the National Estuary Program. This 

includes protection of public water supplies and the protection and propagation of a balanced, 

indigenous population of shellfish, fish, and wildlife, and allows recreational activities, in and 

on water, and requires the control of point and non-point sources of pollution to supplement 

existing controls of pollution. Each National Estuary Program establishes a Comprehensive 

Conservation and Management Plan to meet the goals of Section 320. Section 320 also allows 

a state to use the Clean Water State Revolving Fund (CWSRF) to fund publicly and privately 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-1
 
 

 

owned projects as long as the project is part of the state’s Comprehensive Conservation and 

Management Plan (CCMP) and is sanctioned in the plan. 

401. The section of the Clean Water Act that requires an applicant for a federal license or 

permit to obtain a certification that any discharges from the facility will comply with state laws, 

including water quality standards. 

402. The section of the Clean Water Act that specifically required EPA to develop and 

implement the NPDES program. The CWA allowed EPA to authorize the NPDES Permit 

Program to state governments, enabling states to perform many of the permitting, 

administrative, and enforcement aspects of the NPDES Program. In states that have been 

authorized to implement CWA programs, EPA still retains oversight responsibilities. NPDES is 

not delegated to Guam, Commonwealth of the Northern Mariana Islands, American Samoa or 

Puerto Rico. Florida, Hawaii, and the USVI have delegated authority from EPA. 

403. The section of the Clean Water Act that specifically required EPA to promulgate ocean 

discharge guidelines for determining the degradation of the waters of the territorial seas, the 

contiguous zone, and the oceans. The ocean discharge criteria must become a part of any 

National Pollutant Discharge Elimination System (NPDES) permit that EPA or a state issues for 

discharges of pollutants into ocean and coastal waters. Section 403 requirements are intended 

to ensure that no unreasonable degradation of the marine environment will occur as a result of 

the discharge and to ensure that sensitive ecological communities are protected. 

404. The section of the Clean Water Act that authorizes EPA to restrict or prohibit the use of 

an area as a disposal site for dredged or fill material if the discharge will have unacceptable 

adverse effects on municipal water supplies, shellfish beds and fishery areas, wildlife or 

recreational areas. Along with wetlands, coral reefs are designated as “special aquatic 

sites” and afforded special protection under CWA 404. In 1999, EPA and the Army Corps 

jointly issued guidance to emphasize the protection afforded the Nation’s valuable coral reef 

ecosystems under the Clean Water Act (CWA) Section 404 regulatory program (EPA and 

ACOE 1999). 

603. The section of the Clean Water Act that allows the use of state revolving funds to assist 

municipalities to construct publicly owned treatment works and to implement a nonpoint source 

pollution management plan as provided for in Section 319 of the Clean Water Act. 

abiotic. Non-living components of the environment, including chemicals in the air, water and 

soil, and the level and variability of solar radiation and other aspects of the climate. 

acid rain. A complex chemical and atmospheric phenomenon that occurs when emissions of 

sulfur and nitrogen compounds and other substances are transformed by chemical processes 

in the atmosphere, often far from the original sources, and then deposited on earth in wet form. 

Acropora cervicornis (aka Staghorn coral). This species of coral has cylindrical branches 

ranging from a few centimeters to over two meters in length and height. It occurs in back reef 

and fore reef environments from 0 to 30 m depth. Staghorn coral is found throughout the 

Florida Keys, the Bahamas, and the Caribbean islands. The northern limit is on the east coast 

B-2 Appendix B: Glossary 
 

 

of Florida, near Boca Raton. Since 1980, populations have collapsed throughout their range 

from disease outbreaks, with losses compounded locally by hurricanes, increased predation, 

bleaching, and other factors. This species is also particularly susceptible to damage from 

sedimentation and sensitive to temperature and salinity variation. Populations have declined 

by up to 98% throughout the range, and localized extirpations have occurred. On May 4, 2006, 

Staghorn coral was recognized as a threatened species and placed on the Endangered Species 

List (71 Federal Register 89 2006). 

Acropora palmata (aka Elkhorn coral). This species of coral is structurally complex with many 

large branches. These branches create habitats for many other reef species such as lobsters, 

parrot-fish, snappers, and other reef fish. Elkhorn coral was once one of the most abundant 

species of coral in the Caribbean and the Florida Keys. Since 1980 it has been estimated 

that 90-95% of Elkhorn coral has been lost. Threats to Elkhorn coral include disease, coral 

bleaching, predation, climate change, storm damage, and human activity. All of these factors 

have created a synergistic affect that greatly diminishes the survival and reproductive success of 

Elkhorn coral. Natural recovery of coral is a slow process and may never occur with this species 

because there are so many threats to its survival. On May 4, 2006 Elkhorn coral was recognized 

as a threatened species and placed on the Endangered Species List (71 Federal Register 89 

2006). 

algae. Any of various primitive, chiefly aquatic, one- or multi-celled, nonflowering plants that 

lack true stems, roots, and leaves, but usually contain chlorophyll. Algae convert carbon 

dioxide and inorganic nutrients, such as nitrogen and phosphorus, into organic matter 

through photosynthesis and form the basis of the marine food chain. Common algae include 

dinoflagellates, diatoms, seaweeds, and kelp. 

algorithm. A precise rule (or set of rules) specifying how to solve some problem. 

ambient. Enveloping or surrounding. 

anemone. A solitary soft-bodied marine animal belonging to Phylum Cnidaria. 

anthropogenic. Originating from man, not naturally occurring. 

antidegradation. An integral part of state water quality standards designed to help protect 

existing and designated uses, to maintain that quality which is better than the applicable criteria, 

and to protect Outstanding National Resource Waters. 

aquatic community. Association of interacting assemblages in a given waterbody, the biotic 

component of an ecosystem (see also aquatic assemblage). 

Aquatic Life Use (ALU). A beneficial use designation in which the waterbody provides suitable 

habitat for survival and reproduction of desirable fish, shellfish, and other aquatic organisms 

(EPA 2009a). 

aquatic. Living in the water. 

assemblage. An association of interacting populations of organisms in a given waterbody. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-3
 
 

 

 

 

 

 

attribute. A measurable component of a biological system (Karr and Chu 1999). 

back reef. The landward side of a reef between the reef crest and the land. 

ballast water. Fresh or salt water, sometimes containing sediments, held in tanks and cargo 

holds of ships to increase stability and maneuverability during transit. This water can be 

pumped on or off a ship. 

benthic macroinvertebrates. Animals without backbones, living in or on the sediments, a 

size large enough to be seen by the unaided eye, and which can be retained by a U.S. 

Standard No. 30 sieve (28 openings/inch, 0.595-mm openings). Also referred to as benthic 

macroinvertebrates, infauna, or macrobenthos (EPA 2009a). 

benthic. Living in or on the bottom of a body of water. 

best management practices (BMPs). Management practices (such as nutrient management) or 

structural practices (such as terraces) designed to reduce the quantities of pollutants — such 

as sediment, nitrogen, phosphorus, and animal wastes — that are washed by rain from farms 

into nearby receiving waters, such as lakes, creeks, streams, rivers, estuaries, and ground 

water. 

bias. Systematic error in a data set due to approaches and methods and their application in 

sampling, investigation, measurement, classification, or analysis (MEA 2009). 

binomial. Having two possible values, in general x and y. A coin toss may come down only 

heads (H) or tails (T), and is thus binomial. 

bioerosion. The erosion of undersea rock or coral reefs by mollusks and other organisms. 

biogeography. The study of living systems and their distribution to understand where and why 

animals and plants live in certain places. 

biological assessments (bioassessments). Evaluation of the biological condition of a waterbody 

using biological surveys and other direct measurements of resident biota in surface waters 

(EPA 2009a). 

biological condition gradient (BCG). A scientific model that describes biological response to 

increasing levels of stressors. 

biological criteria (biocriteria). Narrative expressions or numeric values that describe the 

biological condition (structure and function) of aquatic communities inhabiting waters of a 

designated aquatic life use. Biocriteria are based on the numbers and kinds of organisms 

present and are regulatory-based biological measurements (EPA 2009a). 

biological diversity (biodiversity). The variability among living organisms from all sources 

including terrestrial, marine, and other aquatic ecosystems and the ecological complexes of 

which they are part; this includes diversity within and among species and diversity within and 

among ecosystems (MEA 2009). 

B-4 Appendix B: Glossary 
 

 

 

 

biological integrity. The ability of an aquatic ecosystem to support and maintain a balanced, 

adaptive community of organisms having a species composition, diversity, and functional 

organization comparable to that of natural habitats within a region (Karr and Dudley 1981). 

biological monitoring. Use of a biological entity as a detector and its response as a measure to 

determine environmental conditions. Toxicity tests and ambient biological surveys are common 

biological monitoring methods (EPA 2009a). 

biomass. The mass of living tissues in either an individual or cumulatively across organisms in a 

population or ecosystem (MEA 2009). 

biota. The animal and plant life of a given region. 

biotic. A term applied to the living components of an area. 

bivalves. Marine or freshwater mollusks having a soft body with plate like gills enclosed within 

two shells hinged together (e.g., mussels, clams, oysters). 

bleaching. The loss of symbiotic zooanthellae from corals. Bleaching is usually caused by 

elevated sea surface temperatures, but it can also be caused by sedimentation, salinity 

variation, or bacterial infection. 

bryozoans. Aquatic animals forming mossy colonies of small polyps each having a curved or 

circular ridge bearing tentacles; attach to stones or seaweed and reproduce by budding. 

calcification. The deposition of calcium carbonate skeletons by aquatic plants or animals. In 

reef-building corals, calcium is deposited in its aragonitic mineral form. 

carbon dioxide (CO2

). A heavy odorless colorless gas formed during respiration and by the 

decomposition of organic substances; absorbed from the air by plants in photosynthesis. It is 

also a by-product of burning fossil fuels and biomass, as well as land-use changes and other 

industrial processes. It is the principal anthropogenic greenhouse gas that affects the Earth’s 

radiative balance. 

carbon footprint. The total amount of greenhouse gas emissions produced by a person, 

organization or state in a given time. For simplicity of reporting, it is often expressed in terms of 

the amount of carbon dioxide emitted. 

census. Sampling every member of the population, i.e., every site on every coral reef. 

Clean Water Act (CWA). An act passed by the U.S. Congress to control water pollution (also 

known as the Federal Water Pollution Control Act (33 U.S.C. 1251 et seq.) [As Amended 

Through P.L. 107–303, November 27, 2002] (EPA 2009a). 

climate change (also referred to as “global climate change”). The term “climate change” is 

sometimes used to refer to all forms of climatic inconsistency, but because the Earth’s climate 

is never static, the term is more properly used to imply a significant change from one climatic 

condition to another. In some cases, “climate change” has been used synonymously with the 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-5
 
 

 

 

term, “global warming”; scientists however, tend to use the term in the wider sense to also 

include natural changes in climate (EPA 2010). 

commonwealth. An organized United States insular area, which has established with the 

Federal Government, a more highly developed relationship, usually embodied in a written 

mutual agreement. Currently, two United States insular areas are commonwealths, the 

Northern Mariana Islands and Puerto Rico. A United States insular area from April 11, 1899, the 

Philippine Islands achieved commonwealth status on March 24, 1934 (Public Law 73-127), and 

remained as such until the United States recognized the Philippine Islands’ independence and 

sovereignty as of July 4, 1946 (DOI 2009). 

community. All the groups of organisms living together in the same area, usually interacting or 

depending on each other for existence (EPA 2009a). 

composition. The species found in a particular area. 

concentration. The relative amount of a substance in a given medium. 

condition. The relative ability of an aquatic resource to support and maintain a community of 

organisms having a species composition, diversity, and functional organization comparable to 

reference aquatic resources in the region. 

connectivity. A topological property relating to how geographical features are attached to one 

another functionally, spatially, or logically. 

contaminant. A substance that is not naturally present in the environment or is present in 

amounts that can, in sufficient concentration, adversely affect the environment. 

continuous. Without break or interruption. 

coral. The term “coral” means species of the phylum Cnidaria, including-- (A) all species of 

the orders Antipatharia (black corals), Scleractinia (stony corals), Gorgonacea (horny corals), 

Stolonifera (organpipe corals and others), Alcyanacea (soft corals), and Coenothecalia (blue 

coral), of the class Anthozoa; and (B) all species of the order Hydrocorallina (fire corals and 

hydrocorals) of the class Hydrozoa (16 U.S.C. 6401 et seq 2000). 

coral cover. The covering of the sea floor by coral. It can be measured in square miles/ 

kilometers or as a percent of area with cover. 

coral reef. The term “coral reef” means any reefs or shoals composed primarily of corals. 

coral reef ecosystem. Coral and other species of reef organisms (including reef plants) 

associated with coral reefs, and the nonliving environmental factors that directly affect coral 

reefs, that together function as an ecological unit in nature. 

B-6 Appendix B: Glossary 
 

 

 

 

coral reef managers. Coral reef managers work for many different organizations both within 

government (at the federal, state, and local levels) and for non-profit organizations. While 

they all have a general responsibility to protect coral reefs, their authorities and roles can be 

quite varied, including: pollution prevention, including various permitting authorities; coral reef 

protection; coral reef restoration; fisheries management; and park/sanctuary management. 

coral reef restoration. The process of replacing damaged and disturbed reefs with fully 

functional, restored ecosystems. Ideally restoration is accomplished by restoring conditions 

such as water and substrate quality that allow natural recruitment and growth. Most coral reef 

restoration programs have been focused on repairing reef frameworks damaged by vessel 

groundings to avoid continued loss of habitat associated with erosion. They also may involve 

the reattachment or transplantation of corals and other organisms to restore community 

composition and accelerate recovery of the habitat. New coral reef restoration approaches 

include efforts to restore trophic structure through reintroductions of key missing links or 

removal of pest species. 

criteria. Statements of the conditions presumed to support or protect the designated use or uses 

of a waterbody. Criteria may be narrative or numeric (EPA 2009a). 

designated use. Classification specified in water quality standards for each waterbody or 

segment describing the level of protection from perturbation afforded by the regulatory 

programs. The designated aquatic life uses established by the state or authorized tribes set 

forth the goals for restoration and/or baseline conditions for maintenance and prevention from 

future degradation of the aquatic life in specific waterbodies (EPA 2009a). 

diatoms. Microscopic algae with cell walls made of silicon and have two separating halves. 

direct use values. Economic values derived from direct use or interaction with a biological 

resource or resource system. 

discrete. Made up of separate individuals. 

disease. An abnormal condition of an organism that impairs physiological function. Disease 

may be caused by external factors, such as infectious disease or exposure to toxicants, or by 

internal dysfunctions that may come from nutritional or genetic abnormalities. Coral bleaching, 

though not usually caused by an infectious agent, can be considered a disease. 

dissolved oxygen. Oxygen that is dissolved in water and therefore available for use by plants 

(phytoplankton), shellfish, fish, and other animals. If the amount of oxygen is too low, aquatic 

plants and animals may die. In addition, aquatic populations exposed to low dissolved oxygen 

concentration may be more susceptible to adverse effects of other stressors (e.g., disease, 

toxic substances). Wastewater and naturally occurring organic matter contain oxygendemanding substances that, when decomposing, consume dissolved oxygen. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-7
 
 

 

 

 

DPSIR. A decision support framework for capturing the physical and human processes in 

a decision process; it includes the identification of the Drivers (socioeconomic sectors that 

drive human activities), Pressures (human activities that stress the environment), resulting 

environmental and ecological States (reflect condition of the natural and living phenomena), 

Impacts on services and values (effects of environmental degradation of ecological attributes 

and ecosystem services), and Responses to those impacts (policies and responses). 

driving force. A “driving force” is a need. Examples of primary driving forces for an individual 

are the need for shelter, food and water, while examples of secondary driving forces are the 

need for mobility, entertainment and culture. For an industrial sector, a driving force could be 

the need to be profitable and to produce at low costs, while for a nation a driving force could 

be the need to keep unemployment levels low. 

ecological indicator. A characteristic of an ecosystem that can provide quantitative information 

on ecological structure and function. An indicator can contribute to a measure of integrity and 

sustainability. 

ecological integrity. The condition of an unimpaired ecosystem as measured by combined 

chemical, physical (including physical habitat), and biological attributes (Karr and Dudley 

1999). 

ecology. The scientific study of relationships between organisms and their environment. 

ecoregion. A relatively homogeneous ecological area defined by similarity of climate, landform, 

soil, potential natural vegetation, hydrology, or other ecologically relevant variables (also 

known as bioregions). 

ecosystem. A dynamic complex of plant, animal, and microorganism communities and their 

nonliving environment interacting as a functional unit (MEA 2009). 

ecosystem functions. Physical, chemical, and biological processes that occur in ecosystems. 

ecosystem services. Benefits that human populations receive from ecosystems. 

ecosystem structure. The individuals and communities of plants and animals of which 

an ecosystem is composed, their age and spatial distribution, and the non-living natural 

resources present. The elements of ecosystem structure interact to create ecosystem 

functions. 

effluent. The discharge to a body of water from a defined or point source, generally consisting 

of a mixture of waste and water from industrial or municipal facilities. 

empirical. Derived from experiment and observation rather than theory. 

endangered species. Animals, birds, fish, plants, or other living organisms threatened with 

imminent extinction and officially declared as “endangered” under the Endangered Species 

Act. 

B-8 Appendix B: Glossary 
 

 

 

environment. The complete range of external conditions, physical and biological, that affect a 

particular organism or community. 

Environmental Impact Statement (EIS). A document required of federal agencies by the National 

Environmental Policy Act for major projects or legislative proposals significantly affecting the 

environment. A tool for decision making, it describes the positive and negative effects of the 

undertaking and cites alternative actions (EPA 2010). 

erosion. Wearing away of rock or soil by the gradual detachment of soil or rock fragments by 

water, wind, ice, and other mechanical, chemical, or biological forces. 

estuary. A coastal water resource where fresh water from rivers mixes with salt water from the 

ocean. 

extent. The length or area over which observations were made or for which an assessment was 

made or over which a process is expressed (MEA 2009). 

fauna. Animal life, especially the animals characteristic of a region, period, or special 

environment. 

fecundity. Reproduction potential. Fecundity is usually measured by the number of eggs a 

female produces. 

fixed stations. A type of monitoring approach where the same sites are repeatedly sampled at 

regular time intervals over a long period of time. Fixed station designs are used to estimate 

temporal variance and monitor trends. 

flora. Plant life, especially the plants characteristic of a region, period or special environment. 

foraminiferans. Shelled amoeboid protozoans, very small one-celled animals. Primarily marine 

although a few live in freshwater or in brackish conditions. 

fore reef. The seaward edge of a reef that is fairly steep and slopes down to deeper water. 

functions. The physical, chemical, and biological processes that occur in ecosystems. 

global climate change. Refers to a suite of changes in the Earth’s climate, including phenomena 

such as global warming, severe storm frequency and intensity, and glacial melting. Increasingly, 

scientists believe that global climate change is being accelerated by anthropogenic inputs of 

CO2

. 

gorgonians. Corals having a horny or calcareous branching skeleton (e.g., Sea Fans). 

habitat. A place where the physical and biological elements of ecosystems provide a suitable 

environment including the food, cover, and space resources needed for plant and animal 

livelihood (EPA 2009a). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-9
 
 

 

 

 

hardbottom. Shallow and deep-water habitats with solid floor that can provide an attachment 

surface for sessile organisms such as corals. 

health. Health is the general condition of a person in all aspects, including physical and mental. 

The term health is also sometimes used to represent condition of other organisms and even 

ecosystems, ecosystem health being synonymous with ecosystem integrity. Organism and 

ecosystem health usually implies a functioning system absent of disease. 

heavy metals. Metallic elements with high atomic weights (e.g., mercury, chromium, cadmium, 

arsenic, and lead); can damage living things at low concentrations and tend to accumulate in 

the food chain (EPA 2010). 

herbicides. Chemicals used to destroy or inhibit the growth of undesirable vegetation. 

herbivores. An animal that feeds on plants (EPA 2010). 

historical data. Data sets from previous studies, which can range from handwritten field notes to 

published journal articles (EPA 2009a). 

Human Disturbance Gradient (HDG). A model that documents the level of human induced 

impacts on the biological, chemical, and physical processes of surrounding lands or waters 

along a gradient from high to low. Methods can range from a single measurement (e.g., percent 

of impervious surface) to the Landscape Development Intensity Index (LDI) that uses land use 

data and a development-intensity measure derived from energy use per unit area. 

impact. An adverse effect. 

impaired waters. Surface and ground waters that are negatively impacted by pollution resulting 

in water quality that prevents attainment of the designated use. 

impairment. Detrimental effect on the biological integrity of a waterbody caused by an impact 

that prevents attainment of the designated use (EPA 2009a). 

impervious cover. Surfaces where the infiltration of water is impossible, including roads, 

sidewalks, driveways, parking lots, swimming pools, and buildings. 

index. A usually dimensionless numeric combination of scores derived from biological measures 

called metrics (EPA 2000). 

indicator. Information based on measured data used to represent a particular attribute, 

characteristic, or property of a system (MEA 2009). 

indirect use values. The regulating services that control water or air quality that can be 

estimated from how we behave as consumers. For example, although we might not pay for the 

maintenance of a healthy coral reef, we may be willing to pay a higher price for a house near 

such a coral reef or to drive longer to dive or snorkel this coral reef. 

B-10 Appendix B: Glossary 
 

 

institutions. The rules that guide how people within societies live, work, and interact with each 

other. Formal institutions are written or codified rules. Examples of formal institutions would 

be the constitution, the judiciary laws, the organized market, and property rights. Informal 

institutions are rules governed by social and behavioral norms of the society, family, or 

community (MEA 2009). 

insular area. A jurisdiction that is neither a part of one of the several states nor a federal 

district. This is the current generic term to refer to any commonwealth, freely associated state, 

possession or territory and from July 18, 1947, until October 1, 1994, the Trust Territory of the 

Pacific Islands. Unmodified, it may refer not only to a jurisdiction which is under United States 

sovereignty but also to one which is not, i.e., a freely associated state or, 1947-94, the Trust 

Territory of the Pacific Islands or one of the districts of the Trust Territory of the Pacific Islands 

(DOI 2009). 

integrity. The extent to which all parts or elements of a system (e.g., an aquatic ecosystem) are 

present and functioning. 

landscape. An area of land that contains a mosaic of ecosystems, including human-dominated 

ecosystems. The term cultural landscape is often used when referring to landscapes containing 

significant human populations (MEA 2009). 

land-use. The way land is developed and used in terms of the kinds of anthropogenic activities 

that occur (e.g., agriculture, residential areas, industrial areas). 

league. An obsolete unit of distance of variable length (usually 3 miles). 

least disturbed condition. Areas with the least amount of disturbance in altered landscapes. 

macroalgae. Non-rooted aquatic plants commonly referred to as seaweed. 

macroinvertebrates. Animals without backbones of a size large enough to be seen by the 

unaided eye and which can be retained by a U.S. Standard No. 30 sieve (28 meshes per inch, 

0.595 mm openings) (EPA 2009a). 

macrophytes. Large aquatic plants that may be rooted, non-rooted, vascular or algiform (such 

as kelp); including submerged aquatic vegetation, emergent aquatic vegetation, and floating 

aquatic vegetation (EPA 2000). 

mangroves. Salt-tolerant woody plants that grow in muddy swamps inundated by tides. 

Mangrove plants form communities that help stabilize banks and coastlines (Conservation 

International 2009). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-11
 
 

 

 

 

 

 

marine ecosystems. The complex of living organisms in the ocean environment. They include 

oceans, salt marshes, estuaries, lagoons, mangroves, and coral reefs. 

Marine Protected Area (MPA). Any area of the marine environment that has been reserved by 

federal, state, tribal, territorial, or local laws or regulations to provide lasting protection for part 

or all of the natural and cultural resources therein (EO 13158 2000). 

marine sanitation devices (MSDs). Any equipment or process installed on board a vessel to 

receive, retain, treat, or discharge sewage. 

measurement error. The extent to which there are discrepancies between survey results and the 

true value of what the survey researcher is attempting to measure. 

Mesoamerica. Mexico and Central America. 

mesohaline. Waters having salinity between 5 and 18 ppt (EPA 2000). 

metamorphosis. A biological process by which an animal physically develops after birth or 

hatching, involving a conspicuous and relatively abrupt change in the animal’s body structure 

through cell growth and differentiation. Some insects, amphibians, mollusks, crustaceans, 

Cnidarians, echinoderms and tunicates undergo metamorphosis, which is usually (but not 

always) accompanied by a change of habitat or behavior. 

metric. A calculated term or enumeration representing some aspect of biological assemblage, 

function, or other measurable aspect and is a characteristic of the biota that changes in some 

predictable way with increased human influence. A multimetric approach involves combinations 

of metrics to provide an integrative assessment of the status of aquatic resources (Karr and 

Chu 1999). 

microhabitat. A small area with physical and ecological characteristics that distinguish it from its 

immediate surrounding area. 

minimally disturbed condition. Areas with a minimal amount of human disturbance. 

minimally impaired. Sites or conditions with slight anthropogenic perturbation relative to the 

overall region of the study (EPA 2009a). 

model. A physical, mathematical, or logical representation of a system of entities, phenomena, 

or processes; i.e., a simplified abstract view of the complex reality. For example, meteorologists 

use models to predict the weather. 

monitoring. A periodic or continuous measurement of the properties or conditions of something, 

such as a waterbody. 

multimetric. Analysis techniques using several measurable characteristics of a biological 

assemblage (Karr and Chu 1999). 

multimetric index. A combination of several measurable characteristics of the biological 

assemblage to provide an assessment of the status of water resources (EPA 2000). 

B-12 Appendix B: Glossary 
 

 

 

 

 

 

multiplier. How many times money spent on an activity circulates through an economy. For 

example, money spent on recreational diving helps create jobs directly in the dive company, 

but it also creates jobs indirectly elsewhere in the economy. The dive company, for example, 

has to buy gasoline from the marina, which may spend some of this money on food or boating 

supplies. 

narrative biological criteria. General statements of conditions of biological integrity and water 

quality for a given designated aquatic life use (EPA 2009a). 

narrative criteria. Part of water quality standards that addresses pollutants, such as color 

and odor, that can’t be measured with numeric criteria. Narrative criteria are statements that 

describe a desired water quality goal, such as waters being “free from” pollutants such as oil 

and scum, color and odor, and other substances that can harm people, fish, and other coral reef 

biota. 

National Pollutant Discharge Elimination System (NPDES). A national program established by 

the Clean Water Act for permitting point sources of pollution. Discharge of pollution from point 

sources is not allowed without a permit. EPA has delegated NPDES authority to some states 

and territories. 

no-discharge zone. An area where the discharge of polluting materials is not permitted. 

non-indigenous. Species that have become able to survive and reproduce outside the habitats 

where they evolved or spread naturally. Other names for these species include alien, exotic, 

injurious, introduced, invasive, and non-native. 

nonpoint source (NPS) pollution. Any source of water pollution that does not meet the 

legal definition of “point source” in section 502(14) of the Clean Water Act. NPS pollution is 

widespread because it can occur any time activities disturb the land or water. Agriculture, 

forestry, grazing, septic systems, recreational boating, urban runoff, construction, physical 

changes to stream channels, and habitat degradation are potential sources of NPS pollution. 

NPS pollution includes adverse changes to the vegetation, shape, and flow of streams and 

other aquatic systems. 

NPS pollution also results from land runoff, precipitation, atmospheric deposition, drainage, 

seepage or hydrologic modification that can pick up pollutants, and deposit them into rivers, 

lakes and coastal waters or introduces them into ground water. NPS sources are automobile 

emissions, road dirt and grit, and runoff from parking lots; runoff and leachate from agricultural 

fields, barnyards, feedlots, lawns, home gardens and failing on-site wastewater treatment 

systems; and runoff and leachate from construction, mining and logging operations. Most NPS 

pollutants fall into six major categories: sediment, nutrients, acid and salts, heavy metals, toxic 

chemicals and pathogens. The cumulative impact of nonpoint source pollution is significant. 

nonpoint source controls. General phrase used to refer to all methods employed to control or 

reduce nonpoint source pollution. NPDES. National Pollutant Discharge Elimination System 

(EPA 2009a). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-13
 
 

 

 

 

non-random sampling design. A sample that is not random. Some examples of non-random 

samples are convenience samples and best professional judgment samples. 

numeric biocriteria. Numerical indices that describe expected attainable community attributes 

for different designated aquatic life uses (EPA 2009a). 

nudibranch. A mollusk that has no protective covering as an adult. Gills or other projections on 

the dorsal surface carry on respiration. 

numeric criteria. Values in water quality standards that should rarely be exceeded if beneficial 

uses are to be supported. Individual criteria are based on specific data and scientific 

assessment of adverse effects. Numeric guidelines assign numbers that represent limits and/or 

ranges of chemical concentrations, like oxygen, or physical conditions, like water temperature. 

nutrients. Chemicals that are needed by plants and animals for growth (e.g., nitrogen, 

phosphorus). In water resources, if other physical and chemical conditions are optimal, 

excessive amounts of nutrients can lead to degradation of water quality by promoting excessive 

growth, accumulation, and subsequent decay of plants, especially algae. Some nutrients can be 

toxic to animals at high concentrations. 

ocean acidification. The decrease in the pH of the Earth’s oceans caused by the uptake of 

carbon dioxide (CO2

) from the atmosphere. When atmospheric carbon dioxide dissolves in 

seawater it produces carbonic acid, which subsequently lowers pH of surrounding seawater, 

decreases the availability of carbonate ions, and lowers the saturation state of the major shellforming carbonate minerals. Current research indicates the impact of ocean acidification on 

marine organisms will largely be negative, and the impacts may differ from one life stage to 

another. 

octocorals. Water-based organisms formed of colonial polyps with 8-fold symmetry. 

oligohaline. Waters having salinity less than 5 ppt (EPA 2000). 

open source software. Software available free of charge as an alternative to conventional 

commercial models. Open source software can be used and disseminated at will, and the 

source code is open and can be changed as required. The only condition is that the user 

make such changes known and pass this information on to others. Open source software is 

the shared intellectual property of all developers and users and, thanks to the collaboration, 

achieves a higher level of quality than software produced using conventional means. The bestknown example of open source software is the Linux operating system. 

option values. The value placed upon goods and services for their potential to be available in 

the future. 

organic matter. Natural or synthetic substances based on carbon. 

B-14 Appendix B: Glossary 
 

 

 

 

 

ostracods. Tiny marine and freshwater crustaceans with a shrimp-like body enclosed in a 

bivalve shell. 

Outstanding Natural Resource Waters (ONRW). Outstanding National Resource Waters (ONRW) 

designations offer special protection (i.e., no degradation) for designated waters. These are 

areas of exceptional water quality or recreational/ecological significance. 

over-fishing. Occurs when fishing activities reduce fish stocks below a level that is biologically 

or economically sustainable. 

patch reef. Small circular or irregular reefs that arise from the floor of lagoons, behind barrier 

reefs, or within an atoll. 

pathogen. An agent of disease. A disease producer. The term pathogen most commonly is used 

to refer to infectious organisms. These include bacteria (such as staphylococcus), viruses 

(such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious 

agent of disease such as a chemical (MedicineNet.com 2010). 

pesticide. Any substance that is intended to prevent, destroy, repel, or mitigate any pest. 

pH. The negative log of the hydrogen ion concentration. It is a measure of the acidity or basicity 

of a solution. Water ranges from very acid (pH=1) to very alkaline (pH=14). A pH of 7 is neutral. 

EPA recommends the range of pH 6.5 to 8.5 for coral reefs. 

pharmaceuticals. Man-made and natural drugs used to treat diseases, disorders, and illnesses. 

phosphorus. An element essential to the growth and development of plants, but which, in 

excess, can cause unhealthy conditions that threaten aquatic animals in surface waters. 

photosynthesis. The manufacture by plants of carbohydrates and oxygen from carbon dioxide 

mediated by chlorophyll in the presence of sunlight (EPA 2010). 

phylum. A taxonomic rank below Kingdom and above Class. 

phytoplankton. Minute plant life usually containing chlorophyll, that passively drifts or weakly 

swims in a water body. 

plot (sampling plot). Plot sampling is most often used to intensively study a small portion of the 

system in question in order to obtain a representative sample. 

point source. Any confined and discrete conveyance from which pollutants are or may be 

discharged. These include pipes, ditches, channels, tunnels, conduits, wells, containers, and 

concentrated animal feeding operations. 

point source pollution. Water pollution that is discharged from a discrete location such as a 

pipe, tank, pit, or ditch. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-15
 
 

 

 

 

pollutant. Dredged spoil, solid waste, incinerator residue, sewage, garbage, sewage sludge, 

munitions, chemical wastes, biological materials, radioactive materials, heat, wrecked or 

discarded equipment, rock, sand, cellar dirt, and industrial, municipal, and agricultural waste 

discharged into water (CWA §502 (6)). The term includes nutrients, sediment, pathogens, 

toxic metals, carcinogens, oxygen-demanding materials, and all other harmful substances. 

Pollutants adversely alter the physical, chemical, or biological properties of the environment 

pollution. The man-made or man-induced alteration of the chemical, physical, biological, and 

radiological integrity of water (CWA §502 (19)). 

polychaetes. A class of annelid worms, generally marine. Each body segment has a pair of 

fleshy protrusions that bear many bristles made of chitin. Polychaetes are sometimes referred 

to as bristle worms. 

polyhaline. Waters having salinity greater than 18 ppt. 

population. The entire aggregation of items from which samples can be drawn. Populations 

may be discrete (made up of separate individuals) or continuous (without interruption). 

precision. The ability of a measurement to be consistently reproduced. 

predation. The consumption of animals by other animals (MEA 2009). 

prediction (or forecast). The result of an attempt to produce a most likely description or 

estimate of the actual evolution of a variable or system in the future. See also projection and 

scenario (MEA 2009). 

pressures on the environment. Human activities exert “pressures” on the environment, as a 

result of production or consumption processes, which can be divided into three main types: 

(i) excessive use of environmental resources, (ii) changes in land use, and (iii) emissions (of 

chemicals, waste, radiation, noise) to air, water and soil. 

primary contact recreation. A beneficial use as defined in water quality standards. Applies to 

waters where people engage in activities that involve immersion in, and likely ingestion of, 

water, such as swimming and water skiing. 

primary production. The production of organic compounds from atmospheric or aquatic 

carbon dioxide, principally through the process of photosynthesis. 

probabilistic sampling. A type of random sampling that yields a spatially balanced subset of 

sites, and avoids the clumping associated with simple random sampling. 

propagation. The act of multiplication by a plant or animal by any process of natural 

reproduction from the parent stock. 

qualitative. Descriptive of kind, type, or direction. 

B-16 Appendix B: Glossary 
 

 

 

 

quantitative. Descriptive of size, magnitude, or degree. 

random sampling. Selects a subset of all coral reef sites to ensure that the sample is 

“representative” of all coral reefs and the estimate condition is unbiased. 

reef mooring buoys. Mooring buoys are used to keep one end of a mooring cable or chain on 

the water’s surface so that ships or boats can tie on to it. Mooring buoys have proven to be an 

effective tool around the world in reducing the damage to coral reefs caused by anchors. They 

eliminate the need to drop anchor on coral reefs by providing boaters with a convenient means 

of securing their boats. 

reference condition. The chemical, physical and biological condition expected to be found in 

unimpaired waterbodies of a similar type. This can be determined by sampling at unimpaired 

or minimally impaired reference sites, from historical data and information, or through modeling 

and estimations. 

reference site. Specific locality on a waterbody which is unimpaired or minimally impaired and 

is representative of the expected biological integrity of other localities on the same waterbody 

or nearby waterbodies (EPA 2009a). 

refugia. An area or refuge where biota can live and breed without the worry of predation from 

other organisms. 

replicate. Taking more than one sample or performing more than one analysis (EPA 2000). 

representative sample. A portion of material or water that is as similar in content and 

consistency as possible to that in the larger body of material or water being sampled. 

resilience. The ability of a system to absorb or recover from disturbance and change, while 

maintaining its functions and services (Carpenter et al. 2001). For example a coral reef’s ability 

to recover from a bleaching event. 

responses. The term “response” is used in two contexts in this report: 1) Human actions, 

including policies, strategies, and interventions, to address specific issues, needs, 

opportunities, or problems. In the context of ecosystem management, responses may be 

of legal, technical, institutional, economic, and behavioral nature and may operate at local 

or micro, regional, national, or international level and at various time scales (MEA 2009). 2) 

Ecosystem processes occurring due to the effect of some stressor or combination of stressors. 

rugosity. A measure of small-scale variations or amplitude in the height of a surface. In coral 

biology, high rugosity is often an indication of the presence of coral, which creates a complex 

surface as it grows. A rugose seafloor’s tendency to generate turbulence is understood to 

promote the growth of coral and coralline algae by delivering nutrient-rich water after the 

organisms have depleted the nutrients from the envelope of water immediately surrounding 

their tissues (Wikipedia 2009). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-17
 
 

salinity. A measurement of the amount of salt in water. Generally reported as “parts per 

thousand” (i.e., grams of salt per 1,000 grams of water) and abbreviated as “ppt” or ‰. 

scale. The physical dimensions, in either space or time, of phenomena or observations 

(source: MEA). There is no single natural scale at which ecological phenomena should be 

studied; systems generally show characteristic variability on a range of spatial, temporal, and 

organizational scales (Levin 1992). 

scenarios. A coherent, internally consistent, plausible description of a possible future state of 

the world. Scenarios are used in assessments to provide alternative views of future conditions 

considered likely to influence a given system or activity. 

scleractinians. Corals that have a hard limestone skeleton and belong to the order Scleractinia. 

scuba. An apparatus carried by a diver, which includes a tank holding a mixture of oxygen and 

other gases, used for breathing underwater. 

seagrasses. Flowering plants from one of four plant families (Posidoniaceae, Zosteraceae, 

Hydrocharitaceae, or Cyomodoceaceae), all in the order Alismatales (in the class of 

monocotyledons), which grow in marine, fully-saline environments (Wikipedia 2009). 

secondary production. The generation of biomass through the transfer of organic material 

between trophic levels. 

sediment. Particles and/or clumps of particles of sand, clay, silt, and plant or animal matter that 

are suspended in, transported by, and eventually deposited by water or air. 

sedimentation. The removal, transport, and deposition of detached soil particles by flowing 

water or wind. 

services. The benefits that human populations receive from functions that occur in ecosystems. 

shapefile. A data storage format for storing the location, shape, and attributes of geographic 

features. 

shifting baseline. A term used to describe the way significant changes to a system are 

measured against previous baselines, which themselves may represent significant changes 

from the original state of the system (Wikipedia 2009). 

ship grounding. A type of marine accident that involves the impact of a ship on the seabed. Can 

cause damage to both the ship and the sea bottom including the resident biota (seagrasses 

and coral reefs). 

soft corals. A term often used to describe a group of coral species (octocorals, Alconyonaria) 

that actually include soft coral, blue coral, sea pens and gorgonians (sea fans and sea whips). 

Octocorals are generally thick and fleshy and resemble stony corals in polyp size. Because 

they lack a calcium carbonate skeleton, octocorals move with ocean currents. 

B-18 Appendix B: Glossary 
 

 

 

sovereign. An independent or non-independent jurisdiction which itself possesses or whose 

people possess in their own right the jurisdiction’s supreme authority, regardless of the 

jurisdiction’s or people’s current ability to exercise that authority (DOI 2009). 

species. A category of taxonomic classification, ranking below a genus or subgenus and 

consisting of related organisms capable of interbreeding. Also refers to an organism belonging 

to such a category. 

sponge. A primitive multi-cellular marine animal whose porous body is supported by a fibrous 

skeletal framework; usually occurs in sessile colonies. 

spur and groove reef. A reef formation where the barrier reef parallel to shore puts off 

intermittent ridges which grow away from shore. These ridges, or spurs, alternate with grooves, 

where the sandy bottom lies in view 30 to 60 feet (10-20 meters) below. 

stakeholder. Someone having a stake or interest in a physical resource, ecosystem service, 

institution, or social system, or someone who is or may be affected by a public policy (MEA 

2009). All citizens of the nation are stakeholders, including residents of local communities 

adjacent to coral reefs, tourists and the tourism industry, fishermen and other marinebased industries, land-based industries, conservation and environmental groups, research 

organizations, and educational institutions. 

stony corals. A group of coral species known as hard coral that form the hard, calcium 

carbonate skeleton. Such types include the brain corals, fungus or mushroom corals, Staghorn 

and Elkhorn corals, table corals, flower pot corals, bubble corals and lettuce corals. 

stormwater. Water from rain that flows over the ground surface and is subsequently collected 

by natural channels or artificial conveyance systems, and also includes water that has infiltrated 

into the ground but nonetheless reaches a stream channel relatively rapidly and that contributes 

to the increased stream discharge that commonly accompanies almost any rainfall event in a 

human-disturbed watershed. 

stressors. Physical, chemical and biological factors that adversely affect aquatic organisms 

(EPA 2009a). 

subsistence fishing. Fishing for food (consumed by the local group of people who do the 

fishing), not for commercial sale. 

sustainability. A characteristic or state whereby the needs of the present and local population 

can be met without compromising the ability of future generations or populations in other 

locations to meet their needs (MEA 2009). 

substrate. A surface on which a plant or animal grows or is attached. 

surface water. Water found over the land surface in rivers, streams, creeks, lakes, ponds, 

marshes, or oceans. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-19
 
 

 

 

 

 

 

targeted sampling. Targeted sampling may also be referred to as judgment sampling and 

selects sites according to a particular condition or to test a scientific hypothesis. Most nonrandom sampling plans would probably be included in this category. Targeted sampling is the 

best approach when a specific question is being evaluated, e.g., the effect of restoration or best 

management practices on stream condition. 

taxa. Nested groups of species that reflect similarity. Familiar taxa are birds (which belong to the 

class Aves) and fig trees (which belong to the genus Ficus) (MEA 2009). 

taxonomic. Referring to the science of hierarchically classifying animals by categories (phylum 

(pl. phyla), class, order, family, genus (pl. genera), species and subspecies) that share common 

features and are thought to have a common evolutionary descent. 

technology based standards. Industry-specific effluent limitations applicable to direct and 

indirect sources that are developed on a category-by-category basis using statutory factors, not 

including water-quality effects (EPA 2010). 

territorial seas. Defined in section 502(8) of the Clean Water Act to be the belt of the seas 

measured from the line of ordinary low water along that portion of the coast which is in direct 

contact with the open sea and the line marking the seaward limit of inland waters, and extending 

seaward a distance of 3 nautical miles. 

territory. Under Article IV of the U.S. Constitution, territory is subject to and belongs to the 

United States (but not necessarily within the national boundaries or any individual state). This 

includes tracts of land or water not included within the limits of any state and not admitted as a 

state into the Union. U.S. territories with coral reefs include American Samoa, Commonwealth 

of the Northern Mariana Islands (CNMI), Guam, Puerto Rico, and the U.S. Virgin Islands (USVI). 

threatened species. Species, determined by the U.S. Fish and Wildlife Service, that are likely to 

become endangered within the foreseeable future throughout all or a significant portion of their 

range. 

threshold. Numeric standards and guidelines to determine whether a waterbody supports its 

designated use. 

tidal freshwater. Freshwater (0-0.5 ppt) that is tidally influenced. 

Tiered Aquatic Life Use (TALU). A conceptual model predicting the response of aquatic 

communities to increasing human disturbance. It is a draft framework for using biological 

assessment information to refine designated aquatic life uses. 

topography. The physical features of a surface area including relative elevations and the 

position of natural and man-made (anthropogenic) features. 

Total Maximum Daily Load (TMDL). A water quality improvement plan. A TMDL is the calculation 

of the maximum amount of a pollutant that a waterbody can receive and still meet water quality 

standards and an allocation of that amount to the pollutant’s source (EPA 2009a). 

B-20 Appendix B: Glossary 
 

 

 

 

toxic pollutants. Pollutants that are poisonous, carcinogenic, or otherwise directly harmful to 

plants and animals. 

toxics. Any chemical listed in EPA rules as “Toxic Chemicals Subject to Section 313 of the 

Emergency Planning and Community Right-to-Know Act of 1986” (EPA 2010). 

transect. A path along which one records and counts occurrences of the phenomena of study 

(e.g., corals, noting each instance). 

trophic. Describing the relationships between the feeding habits of organisms in a food chain. 

turbidity. The amount of solid particles that are suspended in water and that cause light rays 

shining through the water to scatter. Thus, turbidity makes the water cloudy or even opaque in 

extreme cases. High levels of turbidity are harmful to aquatic life. 

Unified Watershed Assessment (UWA). A cooperative approach promoted by EPA to restoring 

and protecting water quality in which state, federal, tribal, and local governments work with 

stakeholders and interested citizens to (1) identify watersheds not meeting clean water and 

other natural resource goals and (2) work cooperatively to focus resources and implement 

effective strategies to solve these problems. 

Use Attainability Analysis (UAA). A structured scientific assessment of the factors affecting 

the attainment of uses specified in Section 101(a)(2) of the Clean Water Act (the so-called 

“fishable/swimmable” uses). The factors to be considered in such an analysis include the 

physical, chemical, biological, and economic use removal criteria described in EPA’ s water 

quality standards regulation (40 CFR 131.10(g)(1)-(6)). 

U.S. jurisdictions. In the context of this document, we mean the states, territories and 

commonwealths with coral reef ecosystems. 

valuation. The process of expressing a value for a particular good or service in a certain 

context (e.g., of decision-making) usually in terms of something that can be counted, often 

money, but also through methods and measures from other disciplines (e.g., sociology and 

ecology) (MEA 2009). 

value. The quality of a thing according to which it is thought of as being more or less desirable, 

useful, estimable or important. Using this definition the value of an ecosystem might be 

defined in terms of its beauty, its uniqueness, its irreplaceability, its contribution to life support 

functions or commercial or recreational opportunities, or its role in supporting wildlife or 

reducing environmental or human health risks, or providing many other services that benefit 

humans (Ecosystem Valuation 2009). 

wastewater treatment plant. A facility containing a series of tanks, screens, filters and other 

processes by which pollutants are removed from water. 

wastewater treatment system. A system for disposing of wastewater. There are generally 

two types of systems: centralized and decentralized. Centralized systems are “public sewer 

systems” and usually serve established towns and transport wastewater to a central location 

for treatment. Decentralized systems are systems that do not connect to a public sewer 

system. They may treat wastewater on-site or may discharge to a private treatment plant. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-21
 
 

 

 

 

 

 

wastewater. Spent or used water, such as from households and businesses that contains 

enough harmful material to damage the water’s quality. Every building with running water 

generates some sort of wastewater. 

waterbody. A stream, river, lake, estuary, coastline, or other water feature, or portion thereof. 

Water Pollution Control State Revolving Loan Fund. A fund to provide below-market-rate 

interest loans to help build new or repair existing wastewater treatment facilities. Eligible 

facilities include treatment plants, interceptor sewers, and collector sewers. 

water pollution. The man-made or man-induced alteration of the chemical, physical, biological, 

and radiological integrity of water. 

water quality. A term for the combined biological, chemical, and physical characteristics of 

water with respect to its suitability for a designated use. 

water quality assessment. An evaluation of the condition of a waterbody using biological 

surveys, chemical-specific analyses of pollutants in waterbodies, and toxicity tests. 

water quality criteria. Elements of state water quality standards, expressed as constituent 

concentrations, levels, or narrative statements, representing a quality of water that supports 

a particular use. When criteria are met, water quality will generally protect the designated use 

(40 CFR 131.3). 

water quality standards. Provisions of state or federal law which consist of a designated use 

or uses for the waters of the United States, water quality criteria for such waters based upon 

such uses. Water quality standards are to protect public health or welfare, enhance the quality 

of the water and serve the purposes of the Act (40 CFR 131.3). 

watershed. The area of land from which rainfall drains into a single point. Watersheds are 

also sometimes referred to as drainage basins or drainage areas. Ridges of higher ground 

generally form the boundaries between watersheds. At these boundaries, rain falling on one 

side flows toward the low point of one watershed, while rain falling on the other side of the 

boundary flows toward the low point of a different watershed. 

B-22 Appendix B: Glossary 
wetlands. A type of ecosystem, generally occurring between upland and deepwater areas, 

that provides many important functions including fish and wildlife habitat, flood protection, 

erosion control, water quality maintenance, and recreational opportunities. A wetland is an 

area that is covered by water or has water-saturated soil during a portion of the growing 

season. In general, it is often considered the transitional area between permanently wet 

and dry environments. The Ramsar Convention on Wetlands identifies the following Marine/ 

Coastal wetlands: permanent shallow marine waters; marine sub-tidal aquatic beds (kelp 

beds, sea-grass beds, tropical marine meadows); coral reefs; rocky marine shores (including 

rocky offshore islands and sea cliffs); sand, shingle or pebble shores; estuarine waters; 

intertidal mud, sand or salt flats; intertidal marshes (includes salt marshes, salt meadows, 

saltings, raised salt marshes); intertidal forested wetlands (includes mangrove swamps, nipah 

swamps, and freshwater tidal brackish and freshwater marshes); coastal brackish/saline 

lagoons; coastal freshwater lagoons; and marine and coastal karst and other subterranean 

hydrological systems (UN 2001). 

zooplankton. Free-floating or drifting animals with movements determined by the motion of 

the water (EPA 2000). 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-23
 

 

 

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U.S. Environmental Protection Agency (EPA). 2009. Biocriteria Website. URL: http://www.epa. 

gov/bioindicators/coral/index.html. 

Veron JEN. 2008. A Reef in Time: The Great Barrier Reef from Beginning to End. Harvard 

University Press, Cambridge, Massachusetts. 

Wells JW. 1957. Scleractinia. (In RC Morre (Ed.), Treatise on invertebrate paleontology. Part F. 

Coelentrata. Pp. 328-444. Geological Society of America, Boulder, Colorado). 

Westra LP, Miller P, Karr JR, Rees WE and Ulanowicz RE. 2000. Ecological integrity and the 

aims of the global integrity project. Pages 19-41 in D Pimentel, L Westra, and RF Noss 

(Eds). Ecological Integrity: Integrating Environment, Conservation, and Health. Island 

Press, Washington, DC. 

White AT and Courtney CA. 2000. Policy Instruments for Coral Reef Management and their 

Effectiveness. Worldfish Center. P 128-148. (In M Admed, CK. Chong and H Cesar (Eds.), 

Economic Valuation and Policy Priorities for Sustainable Management of Coral Reefs, 

2004. Worldfish Center Conference Proceedings 70, 222 Pp.). 

Wilkinson CR. 1996. Global change and coral reefs: impacts on reefs, economies and human 

cultures. Global Change Biology 2:547-558. 

Wilkinson C (Ed.). 2004. Status of coral reefs of the world: 2004. Vol.1. Townsville, 

Queensland, Australia: Australian Institute of Marine Science. 

Woodwell GM. 1977. Biological Integrity. (In RK Ballentine and LJ Guarraia (Eds.). The 

Integrity of Water. Proceedings of a Symposium, March 10-12, 1975, Pp. 141-147. U.S. 

Environmental Protection Agency, Washington, D.C.). 

Wooldridge SA. 2009. Water quality and coral bleaching thresholds: formalizing the linkage for 

the inshore reefs of the Great Barrier Reef, Australia. Marine Pollution Bulletin 58:745–751. 

Yoder CO and Rankin ET. 1998. The role of biological indicators in a state water quality 

management process. Environmental Monitoring and Assessment 51:61-88. 

C-18 Appendix C: Bibliography 
 

 

 

 

 

 

 

 

 

Appendix D: Common Questions and Their Answers
	

Q. Isn’t the Clean Water Act only about clean water? 

A. In the early days of implementing the act, what 

was most obvious was the pollution from point 

sources. The thought was that once the end-ofpipe effluent was cleaned up, the waters would 

be restored. Today we have a more complete 

understanding of the diversity of point source and 

non-point source pollution that degrades water 

resources. Although the goal of the act is to protect 

“physical, chemical and biological integrity,” early 

emphasis on chemical measurements may have 

reflected the naïve hope that clean up of industrial 

users was all that was needed. Since that time our 

appreciation of the primary importance of living, 

biological systems has supplemented the narrow 

focus on chemical water quality. If our goal is to 

protect and restore the biota, clean water is not 

enough. We must also address human-induced 

changes related to hydrology, habitat, food and 

energy sources, and biological interactions. 

Q. How will implementing biological criteria benefit 

state water quality programs? 

A. State water quality programs could benefit from 

biological criteria because they: 

a) directly assess impairments in ambient biota 

from adverse impacts on the environment; 

b) are defensible and quantifiable; 

c) document improvements in water quality 

resulting from agency action;
 

d) reduce the likelihood of false positives (i.e., a 

conclusion that attainment is achieved when it 

is not); 

e) provide information on the integrity of 

biological systems that is compelling to the 

public. 

Q. Should biocriteria be able to identify or 

characterize the sources of impairment? 

A. No, while advantageous, this is not necessary 

for biocriteria. Biocriteria have the sole purpose of 

determining whether a waterbody has achieved its 

biological condition as defined by designated uses. 

Q. Can biocriteria trigger actions unrelated to the 

regulatory authority of the Clean Water Act? 

A. Yes. Once biocriteria have been used to 

determine impairment, jurisdictions can use any 

of the authorities available to them to respond to 

the impairment. Chapter 9 includes a discussion of 

how biocriteria can be used in support of various 

programs and legislative authorities. 

Q. How will biological criteria be used in a permit 

program? 

A. When permits are renewed, records from 

chemical analyses and biological assessments 

are used to determine if the permit has effectively 

prevented degradation and led to improvement. The 

purpose for this evaluation is to determine whether 

applicable water quality standards were achieved 

under the expiring permit and to decide if changes 

are needed. Biological surveys and criteria are 

particularly effective for determining the quality of 

waters subject to permitted discharges. Because 

biosurveys provide both integrative evaluations 

of current biological condition and the information 

needed to determine if that condition diverges from 

the biological integrity goal, permit writers can make 

informed decisions on whether to maintain or modify 

permits. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure D-1
 
 

 

 

 

 

 

 

Q. What expertise and staff will be needed to 

implement a biological criteria program? 

A. Staff with sound knowledge of state aquatic 

biology and scientific protocol are needed to 

coordinate a biological criteria program. Actual field 

monitoring could be accomplished by summer-hire 

biologists led by permanent staff aquatic biologists. 

Most states employ aquatic biologists for monitoring 

trends or issuing site-specific permits. 

Q. Which management personnel should be 

involved in a biologically-based approach? 

A. Management personnel from each area within 

the standards and monitoring programs should 

be involved in this approach, including permit 

engineers, resource managers, and field personnel. 

Q. How much will this approach cost? 

A. The cost of developing biological criteria is a 

State-specific question depending upon many 

variables. However, states that have implemented a 

biological criteria program have found it to be cost 

effective. Biological criteria provide an integrative 

assessment over time. Biota reflect multiple 

impacts. Testing for impairment of resident aquatic 

communities can actually require less monitoring 

than would be required to detect many impacts 

using more traditional methods (e.g., chemical 

testing for episodic events). 

Q. What are some concerns of dischargers? 

A. Dischargers are concerned that biological criteria 

will identify impairments that may be erroneously 

attributed to a discharger who is not responsible. 

This is a legitimate concern that the discharger 

and state must address with careful evaluations 

and diagnosis of cause of impairment. However, 

it is particularly important to ensure that waters 

used for the reference condition are not already 

impaired. Although a discharger may be contributing 

to surface water degradation, it may be hard to 

detect using biosurvey methods if the waterbody 

is also impaired from other sources. This can be 

evaluated by testing the possible toxicity of effluentfree reference waters on sensitive organisms. 

Dischargers are also concerned that current permit 

limits may become more stringent if it is determined 

that meeting chemical and whole-effluent permit 

limits are not sufficient to protect aquatic life from 

discharger activities. Alternative forms of regulation 

may be needed; these are not necessarily financially 

burdensome but could involve additional expense. 

Burdensome monitoring requirements are additional 

concerns. With new rapid bioassessment protocols 

available for stony corals, and under development 

for other coral reef biota (e.g., fish, soft corals and 

sponges), monitoring resident biota is becoming 

more straightforward. Since resident biota provide 

an integrative measure of environmental impacts 

over time, the need for continual biomonitoring is 

actually lower than chemical analyses and generally 

less expensive. Guidance is being developed to 

establish acceptable research protocols, quality 

assurance/quality control programs and training 

opportunities to ensure that adequate guidance is 

available. 

Q. What are the concerns of environmentalists? 

A. Environmentalists are concerned that biological 

criteria could be used to alter restrictions on 

dischargers if biosurvey data indicate attainment 

of a designated use even though chemical criteria 

and/or whole-effluent toxicity evaluations predict 

impairment. Evidence suggests that this occurs 

infrequently (e.g., in Ohio, 6 percent of 431 sites 

evaluated using chemical-specific criteria and 

biosurveys resulted in this disagreement). In those 

cases where evidence suggests more than one 

conclusion, independent application applies. If 

biological criteria suggest impairment but chemicalspecific and/or whole-effluent toxicity implies 

attainment of the use, the cause for impairment of 

the biota is to be evaluated and, where appropriate, 

regulated. If whole effluent and/or chemical-specific 

criteria imply impairment but no impairment is found 

in resident biota, the whole-effluent and/or chemicalspecific criteria provide the basis for regulation. 

D-2 Appendix D: Common Questions and Their Answers 
 

 

 

 

Q. Do biological criteria have to be codified in state 

regulations? 

A. State water quality standards require three 

components: (1) designated uses, (2) protective 

criteria, and (3) an antidegradation policy and 

implementation procedures. Criteria may be codified 

in regulations. Codification could involve general 

narrative statements of biological criteria, numeric 

criteria, and/or criteria accompanied by specific 

testing procedures. Codifying general narratives 

provides the most flexibility for incorporating new 

data and improving data gathering methods as the 

biological criteria program develops. States should 

carefully consider how and when to codify these 

criteria. 

Q. How will biocriteria fit into the agency’s method of 

implementing standards? 

A. Resident biota integrate multiple impacts over 

time and can detect impairment from known 

and unknown causes. Biocriteria can be used to 

verify improvement in water quality in response to 

regulatory efforts and detect continuing degradation 

of waters. They provide a framework for developing 

improved best management practices for nonpoint 

source impacts. Numeric criteria can provide 

effective monitoring criteria for inclusion in permits. 

Q. Who determines the values for biological criteria 

and decides whether a waterbody meets the criteria? 

A. The process of developing biological criteria, 

including refined use classes, narrative criteria, 

and numeric criteria, must include agency 

managers, staff biologists, and the public through 

public hearings and comment. Once criteria are 

established, determining attainment/nonattainment 

of a use requires biological and statistical evaluation 

based on established protocols. Changes in the 

criteria would require the same steps as the initial 

criteria: technical modifications by biologists, 

goal clarification by agency managers, and 

public hearings. The key to criteria development 

and revision is a clear statement of measurable 

objectives. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure D-3
 

Appendix E: DPSIR Framework 
	

DPSIR is a general framework for organizing information about state of the environment. This 

framework was adopted by the European Environmental Agency (RIVM 1995; UNEP/RIVM 

1994) and has been used by the United Nations to organize information about the state of the 

environment in relation to human activities (UNEP 2007). It is a human-centric framework, focused 

on human activities that affect the environment and the consequences of those activities. 

EPA’s Coral Reefs Ecosystem Services Research Program (ESRP) has adopted the DPSIR 

framework to show the broad array of human interactions with coral reefs, and for examining 

consequences (e.g., changes in benefits, costs and sustainable delivery of ecosystem services) 

across ecological and multiple socioeconomic sectors. The utility of a DPSIR framework lies in its 

transparency (readily obvious to coral reef managers and stakeholders) and its capacity to isolate 

particular linkages and interactions while retaining conceptual relevance to the larger system. The 

framework does not capture every situation perfectly, but is a reasonable means to organize the 

many social, economic and ecological interactions. 

The framework assumes cause-effect relationships between interacting components of social, 

economic, and environmental systems (Pierce 1998; Smeets and Weterings 1999), which are: 

• Driving forces: Socio-economic sectors that describe basic needs of human society such as 

food, water, fuel and shelter, and secondary needs such as recreation, cultural heritage and 

sense of place 

• Pressures: Driver-generated human activities that affect the environment 

• State: status of the environment and ecological resources, including attributes that provide 

services; state is altered by changes in pressure 

• Impacts: changes in coral reef persistence and delivery of services as a consequence of 

changes in ecological state 

• Response: societal reactions to changes in ecosystem services, values and sustainability 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure E-1
 
Figure E-1. Conceptual relationships among DPSIR sectors 

Generation of a comprehensive framework to link ecological and socioeconomic factors, even 

an introductory version, is significant because it has never been attempted for coral reefs. 

For decades scientists have conducted research to assess and understand the ecological 

phenomena of coral reefs around the world. While the body of information is extensive, it is 

unevenly distributed across disciplines, times and places. Consequently, the information has not 

been effectively used to identify gaps and prioritize research; nor has it been easily synthesized 

into concepts and tools for conservation that resonate with stakeholders and influence 

management. This situation is not unique to coral reefs. Curran (2009) suggests that there are no 

programs capable of delivering overall support (including social and economic perspectives) to 

environmental decision-making. Curran also emphasizes the need for further research on viable 

decision-support frameworks. 

Application of the DPSIR framework will better ensure that we do not overlook critical relationships 

and that we recognize the full consequence of a decision to related parts of the larger system 

(O’Connor and McDermott 1997). It is anticipated that the DPSIR framework will be ultimately 

expanded into a human-inclusive ecosystem model. 

E-2 Appendix E: DPSIR Framework 
Appendix F: Ocean Acidification 
	

Since the Industrial Age began, burning of fossil fuels has added significant amounts of carbon 

dioxide (CO2

) into the atmosphere. Concentrations have risen from 280 ppm in the atmosphere to 

today’s level of 387 ppm (Feely et al. 2004). About a third of atmospheric CO2, approximately 22 

million tons per day, is absorbed into oceans. The estimated time lag for absorption is at least 10 

years, meaning that today’s level of atmospheric CO2

 will still influence ocean chemistry a decade 

from now (Veron et al. 2009). Once dissolved, CO2 reacts with the seawater to form carbonic acid, 

which dissociates into hydrogen and bicarbonate and decreases ocean pH. During the last 250 

years, oceans have become more acidic by 0.1 pH units (Feely et al. 2004). This may at first seem 

small but the pH scale is logarithmic so this represents a 30% increase in acidity. Models forecast 

continued acidification—another 0.3 to 0.4 pH units—by the end of this century. 

Oceanic absorption of atmospheric CO2

 mitigates some climate change impacts, but may 

generate others. Increased absorption has led to a decline in ocean saturation state for aragonite 

and calcite, forms of calcium carbonate incorporated into shells and skeletons of many marine 

organisms (Kleypas et al. 1999). Reduced saturation states reduce the ability to form shells and 

tests, and consequently reduce the growth of organisms such as corals, mussels, oysters, snails, 

sea urchins, and a wide variety of microscopic plants and animals. Many other physiological 

effects on marine life may result from changes in ocean chemistry from CO2

 absorption. Overall, 

little is known about the effects on particular species or on population and community interactions. 

The Center for Biological Diversity has petitioned EPA to tighten water quality standards to 

no observable change in pH for marine coastal waters (see Craig 2009). This raises several 

questions: Is there evidence that slight changes in pH are affecting designated uses? Are states 

responsible for global atmospheric CO2? Can pH be effectively monitored across spatial and 

temporal scales? Since few of the answers to these questions are known, EPA issued a Notice 

of Data Availability (NODA) to solicit additional pertinent data or scientific information that may be 

useful in addressing ocean acidification (EPA 2009d). 

Specifically, EPA solicited information on measurement of ocean acidification in marine coastal 

waters, on effects of ocean acidification on marine biota, and scientific views of current knowledge 

and literature. EPA also asked for information and views on EPA’s current CWA Section 304(a) 

recommended pH criterion for marine waters, on implementation of the current recommended pH 

criterion, and on potential implementation of a new criterion based on information related to ocean 

acidification. Finally, EPA solicited information that could help develop strategies for coordinated 

state and federal data collection and information that could be used to develop guidance for 

information pursuant to Clean Water Act Section 304(a)(2) for states and the public on ocean 

acidification. EPA expects to make a decision by November 15, 2010, on how to proceed with 

regard to the interplay between ocean acidification and the 303(d) program based on information 

from the NODA as well as other ongoing federal efforts. 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure F-1
 

Appendix G: CWA and Existing Coral Reef 

Management Programs
	

Management Area Description Application of Biocriteria 

Marine Protected Areas (MPAs) Selecting MPA Sites • To identify waterbodies that have 

outstanding biological condition 

and require protection 

Managing MPAs • To establish thresholds against 

which to measure effectiveness 

of MPAs 

Effectively manage the waters 

between MPAs 

• With establishment of designated 

uses, to protect those uses (i.e., 

connectivity) 

Managing Fisheries Eliminate open-access fisheries in 

coral reef ecosystems and establish 

sustainable fisheries regulations 

• To establish levels (e.g., taxa 

richness, abundance) expected 

to sustain reef fisheries 

• Degradation can trigger 

changes in fishery practices and 

regulations 

Restricting the species being 

selected (e.g., coral reef herbivores, 

including parrotfish) 

• To establish expected or desired 

levels of individual species (e.g., 

abundance, biomass) 

• Degradation can trigger 

changes in fishery practices and 

regulations 

Managing Tourism Mooring Buoys • To identify locations with 

outstanding biological condition 

that would benefit from the 

protection of mooring buoys 

Permits – diving, fishing, boating • With establishment of designated 

uses, to protect those uses 

Watershed Management Regulating activities in the watershed • To establish thresholds against 

which to measure effectiveness 

of permits 

Coastal Zone Management Regulating Coastal Development • To support setting goals for 

watershed and regional planning 

• To prioritize watershed goals and 

actions 

• To develop management plans 

Maintain connectivity between coral 

reefs and associated habitats such 

as mangroves, sea grass beds, and 

lagoons 

• All nearshore environments are 

protected by the CWA 

• Coral reefs, mangroves, sea 

grass beds, and lagoons can be 

specifically protected when they 

are identified in water quality 

standards 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure G-1
 
Management Area Description Application of Biocriteria 

Damage Assessment and 

Restoration 

Restoring coral reefs or seagrass 

meadows damaged by boats and 

anchors 

• To establish thresholds against 

which to measure effectiveness 

of restoration efforts. 

Managing Endangered Species 

(Endangered Species Act) 

Protecting rare, threatened and 

endangered species 

• To establish expected or desired 

levels of individual species (e.g., 

abundance, biomass). 

• To establish thresholds against 

which to measure effectiveness 

of legal protection. 

National Environmental Policy Act 

(NEPA) of 1969 

Environmental Impact Statements • To identify where site-specific 

criteria modifications may be 

needed to effectively protect a 

waterbody. 

• To assess the overall ecological 

effects of regulatory actions. 

G-2 Appendix G: CWA and Existing Coral Reef Management Programs 
Appendix H: Biocriteria and Other CWA Programs 
	

Program Title Description Biocriteria Use(s) 

104(b)(3) Wetlands 

Program 

Development 

Grants 

Authorizes grants to states1

, and local 

governments to conduct projects that 

promote the coordination and acceleration 

of research, investigations, experiments, 

training, demonstrations, surveys, and 

studies relating to the causes, effects, 

extent, prevention, reduction, and 

elimination of water pollution. Coral reefs, 

mangroves, and seagrasses are considered 

special aquatic sites and wetlands under 

CWA 404, and Section 104(b)(3) grants can 

directly fund monitoring and assessment of 

coral reefs and development of biocriteria 

for coral reefs. 

• Providing a threshold 

against which to measure 

detrimental effects on biological 

communities. 

• EPA Region 9 has awarded 

Wetlands Program 

Development Grants to 

support coral reef biocriteria 

development for Hawaii and 

CNMI. 

106 Grants for 

Pollution Control 

Programs 

Authorizes federal grants to states1

 to 

support the development and operation of 

state programs implementing the CWA. 

• In 2009, EPA Region 10 

explicitly mentioned the 

application of biological 

monitoring and biocriteria 

that lead to improved TMDLs 

in their Request for Initial 

Proposals. 

205(j) and 

604(b) 

Water Quality 

Management 

Planning 

Authorizes grants to states1

 and funding 

for substate agencies for water quality 

planning. 

• To develop water quality 

criteria, including biocriteria. 

301(h) Effluent 

Limitations 

Waiver to defer secondary treatment 

if discharge does not adversely affect 

biological communities. 

• Providing a threshold 

against which to measure 

detrimental effects on biological 

communities. 

312 Marine Sanitation 

Devices 

No discharge zones. • To identify appropriate locations 

for no-discharge zones. 

• To identify locations with 

outstanding biological integrity 

that would benefit from a nodischarge zone status. 

• To establish thresholds to 

gauge the effectiveness of nodischarge zones. 

319 Nonpoint Source 

Program (NPS) 

Every 5 years, states report to EPA on 

their NPS pollution problems, including 

categories of NPS pollution and measures 

used to reduce that pollution. 

• Assessing impacts of NPS 

pollution. 

• Determining effectiveness of 

NPS controls. 

• Site-specific assessment of 

BMPs for NPS. 

320 National Estuary 

Program (NEP) 

Authorizes grants to states1

 for 

development of NEP management plans 

and implementation projects. 

• To establish thresholds for 

biological integrity as part of the 

management plan. 

1 When the term “states” is used, it implies “states, territories and tribes” 

Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure H-1 
Program Title Description Biocriteria Use(s) 

401 State Water 

Quality 

Certification 

Requires that before issuing a license or 

permit that may result in any discharge 

to waters of the United States, a federal 

agency must obtain from the state in 

which the proposed project is located, a 

certification that the discharge is consistent 

with the CWA, including attainment of 

applicable state ambient water quality 

standards. 

• Providing a threshold against 

which to measure dredge/ 

fill impacts on biological 

communities. 

• Identify acceptable sites for 

disposal of dredge and fill 

material. 

402 National Pollutant 

Discharge 

Elimination 

System (NPDES) 

The CWA makes it illegal to discharge 

pollutants from a point source to the waters 

of the United States. Point sources must 

obtain a discharge permit from the proper 

authority (usually a state, sometimes EPA, 

a tribe, or a territory). The permits set the 

limit on the amounts of various pollutants 

that a given source can discharge in a 

given time. 

• Determining condition of a 

waterbody prior to issuance of 

a permit. 

• Providing a threshold against 

which to measure discharger 

impacts on biological 

communities. 

• Evaluating effectiveness of 

implemented controls. 

• Helping to verify that NPDES 

permit limits are resulting in 

achievement of state water 

quality standard. 

403 Ocean Discharge 

Program 

Establishes special requirements for point 

source permits for discharges into all three 

ocean regions defined in the CWA (e.g., the 

territorial sea, the contiguous zone and the 

ocean) 

• Providing a threshold against 

which to measure discharger 

impacts on biological 

communities. 

404 Permits for 

Dredged or Fill 

Material 

Establishes a permit program to regulate 

the discharge of dredged and fill material 

into waters of the U.S. Jointly managed by 

EPA and U.S. Army Corps of Engineers. 

The Corps handles the actual issuance 

of permits (both individual and general); it 

also determines whether a particular plot 

of land is a wetland or water of the United 

States. The U.S. Fish and Wildlife Service 

and National Marine Fisheries Service 

play special advisory roles because of 

their expertise regarding wildlife habitat. 

EPA issues certain guidelines and policies, 

including methods for determining whether 

a particular tract is a wetland. EPA can 

actually veto a Corps-issued permit (a step 

rarely taken). EPA is also responsible for 

determining whether portions of the 404 

program should be turned over to a state. 

• Providing g a threshold against 

which to measure dredge/ 

fill impacts on biological 

communities. 

• Identify acceptable sites for 

disposal of dredge and fill 

material. 

• Determine the effects of the 

disposal. 

603 Clean Water 

State Revolving 

Fund (CWSRF) 

Authorizes annual capitalization grants to 

States1

 who in turn provide low interest 

loans for a wide variety of water quality 

projects. 

• To provide a threshold to 

measure the degree to which 

water quality projects reduce 

human impacts on biological 

communities. 

H-2 Appendix H: Biocriteria and Other CWA Programs 

 

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