v>EPA
United States
Environmental Protection
Agency
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
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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 . , 0 i-
... .. ._ . „. . . Leska S. Fore
Atlantic Ecology Division Statistical Desian
MUPPRi npn oiaiisucai uesign
QQP fn S H 136NW40thSt.
33 East Quay Road 0 ... ,.,.^0^0^
Key West, FL 33040 Seattle, WA 98107
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.
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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, Rl. 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
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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.
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 CWA 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
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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
Policy Makers
Environmental Managers
Natural Resource Managers
Local Government Managers
Role
Develop laws and regulations
Implement and enforce federal/
state/territorial environmental
laws and regulations
Manage parks, sanctuaries,
refuges, etc.
Enforce land-use rules, permits
and zoning
Scale
Federal/Regional/State
Regional/State
Federal/Regional/State
Local
IV
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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.
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
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Why You 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
of many on-the-reef approaches to management. This
document will show you how to use the Clean Water Act
(CWA) and coral reef biological criteria (biocriteria) as part
of a comprehensive framework to organize your protection
efforts and make them more meaningful through enforceable
coastal and watershed regulations.
If you are a stakeholder, this document will show you how
the CWA and other management tools can be combined into
a comprehensive watershed-based management approach
for coral reefs and other coastal ecosystems.
The responsibility for implementing coral reef biocriteria lies
with the state and federal coral reef managers. However, to
be successful, their actions must be guided and informed by
the knowledge, energy and resources of scientists and other
stakeholders.
description of the desired
natural aquatic community
based on the numbers
and kinds of organisms
expected to be present in
a water body and serve as
the standard against which
assessment results are
compared. Biocriteria can
also be used to determine
aquatic life use attainment
and can be formally adopted
into a State's water quality
standards (EPA 2002).
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
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• 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).
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 concepts are emphasized in these boxes.
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
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
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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.
#
1
2
3
4
5
6
7
8
9
10
Steps to Coral Reef Biocriteria
Planning
Establish aquatic life protection goals
for state waterbodies and identify
designated uses
Develop an antidegradation policy
and implementation procedures
Develop a conceptual coral reef
Biological Condition Gradient (BCG)
to target potential decision points
Assessment
Develop indicators that are relevant,
efficient and responsive to human
disturbance
Characterize reference conditions
(minimal human disturbance) and
select decision thresholds (criteria)
that support designated uses
Initiate a long-term monitoring
program to determine aquatic life use
attainment
Management Response
Report reef conditions and status of
attainment for designated uses and
aquatic life use goals
Determine cause(s) of any impaired
waterbodies
Implement management activities
that restore the biological condition of
impaired waterbodies
Review aquatic life protection goals
and the relationship to designated
uses
Responsible Parties
State water quality agency, coral reef
managers and stakeholders through a
public process
State water quality agency with public
notification and participation
State water quality agency, reef
scientists and managers
State water quality agency and reef
scientists
State water quality agency and reef
scientists
State water quality agency and reef
scientists
State water quality agency
State water quality agency and reef
scientists
State water quality agency, reef
scientists, reef and watershed
managers with notification of
stakeholders
State water quality agency, reef and
watershed managers with stakeholder
through a public process
Chapters
1,2,3
1
6
4
6,7
5
1,8
9
9
1,2,3
Additional material is provided in the Appendices, including a list of Acronyms (A), a Glossary (B),
a Bibliography (C), and Common Questions and Their Answers (D).
VIM
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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
Chapters. 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
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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
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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
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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
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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
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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 C02 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
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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
(EPAORD/NHEERL/AED), Wendy Wiltse (EPA Region 9), Jim Maragos (U.S. Fish and Wildlife
Service), and Wayne Davis (EPAOEI).
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 Hawaii, Hawaii 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
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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
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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. JJ
- 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 Clean Water Act (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
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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.
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.
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
be made of the water; set criteria
necessary to protect the uses;
and protect water quality through
antidegradation provisions.
While the CWA gives 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 v^^V^-H" ' ^i;"^.< "'\J:;";' ''-.•.(>\v;;?' ''•.':;'• :'•'• •":. ,/•-"•''' ''•';:'•]
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.
Key Points regarding the Clean Water Act and Coral Reefs
1. The objective of the CWA is to restore and maintain
physical, chemical, and biological integrity
2. Coral reef organisms can be protected by the CWA at levels
necessary to sustain biological integrity
3. Biological integrity includes integrity of all aquatic
organisms residing in or migrating through a waterbody
4. Authority of CWA water quality standards extends to coral
reefs in territorial seas, a belt of water extending seaward
from the coast for three miles or more.
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Chapter 1 — The Clean Water Act: A Critical Asset
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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
(Phylum Porifera)
-100
-25
Corals, anemones, jellies
(Phylum Cnidaria)
>200
-80
Segmented worms,
polychaetes
(Phylum Annelida)
100's
-40
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-3
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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
(Phylum Mollusca)
100's
100's
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
^S=i\
*A
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Chapter 1 — The Clean Water Act: A Critical Asset
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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.
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 offish, 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
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Criteria
(narrative or
numeric)
Designated
Uses
Anti-
degradation
Policy
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.
Figure 1-1. Components of Water Quality Standards
1.2.1 Designated Uses
The first step for developing water quality standards is to
designate the purposes, or uses, to be protected for each
waterbody. It is in designating uses that states establish
the environmental goals for their water resources and are
allowed to evaluate the attainability of those goals.
Designated Uses: Uses
specified in Water Quality
Standards for each water
body or segment whether
or not they are being
attained (40 CFR131.3f).
Designated uses are a
state's concise statements of
its management objectives
and expectations for each of
the individual surface waters
under its jurisdiction.
Designated uses are those uses specified in the water
quality standards for each water body or segment,
whether or not they are being attained (See 40 CFR 131.3
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 Clean Water Act 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.
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Chapter 1 — The Clean Water Act: A Critical Asset
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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.
California Example
In their water quality standards, the State of California
provides over 20 use classifications, including Municipal and
Domestic Water Supply, Water Contact Recreation, Ocean
and Commercial Sportfishing, Warm Freshwater Habitat, Cold
Freshwater Habitat, Fish Spawning, Shellfish Harvesting,
Marine Habitat, and Preservation of Areas of Special
Biological Significance.
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.
A beneficial use
designation in which the waterbody provides
suitable habitat for survival and reproduction
of desirable fish, shellfish, and other aquatic
organisms (EPA2009a).
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.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 1-7
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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
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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
of native aquatic life." States can define narrative
biological criteria early in program development
without conducting biological assessments.
To support the narrative criteria, a state needs
protocols that describe standardized procedures for
data collection, analysis and interpretation. Once
vetted through a rigorous scientific process, these
protocols provide the legal and programmatic basis
for numeric criteria (EPA 1990; Karr 1991).
Numeric criteria identify specific values for
measurements that are expected to support the
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
use (EPA 2002).
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.
Descriptions of
conditions necessary for the water
body to attain its designated use.
Specific numeric
values expressed as maximum
acceptable chemical concentrations,
an acceptable range of physical
factors or acceptable condition of
biological resources.
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 EPAs 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 EPAs 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
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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.
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.
The antidegradation policy is particularly important for
waterbodies of exceptional or ecological significance (EPA
2009a). Coral reefs often inhabit waterbodies of exceptional
or ecological significance.
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 water.
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
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Chapter 1 — The Clean Water Act: A Critical Asset
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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 Submitted 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 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
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While water quality standards have been used to protect inland waters and estuaries, 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; EPA2009a).
1.4 Emergence of Biological Criteria
The CWAs 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).
Biological
Integrity
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).
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Chapter 1 — The Clean Water Act: A Critical Asset
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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 (EPA2009a).
# of sites
r
Phosphorus
criterion
, 1
50
Total P (ug/L)
Haulover Reef,VINP St. John, USVI
40
20
2003
2004
2005
2006
2007
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
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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 overtime. 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.
Q: Is this waterbody meeting its designated use?
• A state reports that their marine waters containing
coral reefs are meeting designated uses because
chemical and physical criteria such as dissolved
oxygen, phosphorus, and turbidity have met the
established criteria.
• However, monitoring data for various coral reef
communities (stony and soft corals, fishes, seagrasses)
show a marked decline in biotic condition.
A: If only chemical and physical criteria have been adopted
by the state, then the waterbody is meeting its
designated uses. The waterbody could only be
considered impaired if biological criteria were in place
and the biological condition, measured using acceptable
bioassessments, did not meet the established thresholds.
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Chapter 1 — The Clean Water Act: A Critical Asset
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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.
The chemical, physical and biological
condition expected to be found in unimpaired waterbodies of
a similar type. This can be determined by sampling at unim-
paired 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 human-
generated 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 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
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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
(Figure 1-4). 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).
Oregon DEQ - April 2002
Chemical versus Biological Indicators of Aquatic Life Use
Impairment - Macroinvertebrates & Vertebrates (N=150)
Agreement - Not Impaired
Agreement - Impaired
Biology detects impairment
while chemistry doesn't
Chemistry detects impairment
while biology doesn't
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.
Atypical 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.
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Chapter 1 — The Clean Water Act: A Critical Asset
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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, fungi, 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.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 2-1
-------
Figure 2-3. Coral reefs provide important graphic and design elements.
2-2
Chapter 2 — Why Do We Care About Coral Reefs?
-------
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, C02,
water, temperature, humidity, pH, and availability of nitrogen.
• The conditions of existence such as temperature, light, etc.
Coral reef ecosystem function includes the following processes:
• 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.
The physical and
spatial aspects of
an ecosystem that
are contributed by
the biotic and abiotic
composition.
Physical, chemical,
and biological
processes that occur in
ecosystems.
Benefits that human
populations receive
from functions that
occur in ecosystems.
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 (MEA2005), 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).
t/) •£»
= •8
* §
£ §,
a>
to
3
+j
o
0)
a)
to
Renewable
Fisheries and
Pharmaceuticals
Physical
Shoreline protection,
land accretion, lagoon
formation, beach sand
Information
Research, education,
pollution record, climate
record
Non-renewable
Construction materials (coral blocks and
sand) and decorative items (curios and
jewelry)
Biological
Ecosystem Integrity
(biodiversity, genetic
repository, ecosystem
regulation, ecosystem
resilience)
Biogeochemical
Nitrogen fixation,
C02 regulation,
primary production
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 DPS IR 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
Our appreciation of coral reefs is remarkable. A nation-wide
poll by The Ocean Foundation (2007) found:
• 80% of American adults believe that healthy coral reefs
are important to the overall health of the ocean
• 69% believe that coral reefs are important to human
well-being
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).
FLORIDA -
RHF3E
ect Our Reefs m * T
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 yr1) 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.
Quantifying Ecosystem Services
The concept of ecosystem services is not new and services have
been quantified by several authors (e.g.,Spurgeon 1992, Pendleton
2009). Many studies place a monetary value on reef
services—monetary valuation is widely applied, broadly accepted
and can be highly influential in decisions and policies. But coral reefs
provide more than direct (e.g., fishing, tourism) and indirect uses
(e.g., habitat, shoreline protection), so a strictly monetary approach
can overlook important benefits (see Bateman 1993). An approach
used in environmental economics, called "total economic value"
includes monetary values but also provides a context for
non-monetary social, cultural and historical values.Total economic
value includes direct and indirect uses,option values and non-use
values. Option values reflect the willingness to preserve an option
for potential future use and non-use value (existence or bequest
value) is placed on a resource that will never be used. Many
ecosystem valuation studies provide a total economic value (e.g.,
Gren et al. 1994), but incorporating non-monetary values into
decision scenarios presents a significant challenge.
A few studies have extrapolated coral reef monetary values (direct
and indirect uses) to a worldwide scale. Because of different
approaches, the values range from $377 billion yr1 (Constanza et al.
1997) to $30 billion yr1 (Cesar et al. 2003), with a more recent
estimate at $172 billion yr1 (TEEB 2009).GIobal estimates are coarse
and generally not useful for local decisions, however, they provide
an important context.Valuation at the local scale is more relevant to
most decisions. In 2000, NOAA's National Ocean Service initiated this
Nation's first attempt to link socioeconomic monitoring and
ecological monitoring in the Florida Keys National Marine Sanctuary
(see NOAA 2009a).The baseline socioeconomic study showed that
in 2000-2001, all uses of the artificial and natural reefs of the
Sanctuary generated over $504 million in Sales/Output, including
multiplier impacts.This generated $140 million in income in
Montroe County, which supported almost 10,000 full and part-time
jobs.
Many authors incorporate "ecological integrity" resilience, or
biodiversity as an ecosystem service (Turner et al. 2005). Without
these characteristics, the ecosystem would ultimately fail and other
services would decline.The Millennium Ecosystem Assessment (MEA
2005) identified these as supporting services.This ecosystem "glue"
which all other services depend upon, is often viewed as a biological
service, directly benefiting components of the ecosystem and
indirectly benefiting human society.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 2-5
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3. What Should Be Protected?
11 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. J J
BabaDioum, 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 offish, 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
Coral reef
communities
Coral reef
communities
Coral reef,
seagrass, and
mangrove
communities
Fish spawning,
aggregation and
nursery areas
Ecosystem
Function
Nutrient cycling;
herbivory
Calcification and
skeletal growth;
photosynthesis
and water clarity
Competition and
predation
Complex trophic
structure and food
web dynamics
Biological
Components
Rare and colorful fish and
invertebrates; abundant herbivores
such as urchins and parrotfish
Large, abundance scleractinian
(stony) corals and crustose
coralline algae to bind them
Taxonomic diversity
Habitat and food provided by
corals, seagrasses, and mangroves
Ecosystem
Services
Tourism and
Recreation
Shoreline
Protection
Pharmaceuticals
Fisheries
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 3-1
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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
Aquatic Habitat
Biodiversity
Fisheries
Industrial
Research
Shoreline protection
Tourism and Recreation
Transportation
Designated Use
Coastal Habitat Protection and
Restoration
Preservation of natural
phenomena requiring special
conditions (National Parks)
Propagation of shellfish and
other marine life
Conservation of coral reefs
and wilderness areas
Commercial, recreational and
subsistence fishing
Support and propagation of
shellfish
Industrial water supply
Scientific investigations and
oceanic research
Coastal erosion and sediment
control
Primary contact recreation
(swimming, snorkeling, scuba
diving, etc.)
Aesthetic enjoyment
Boat launch and harbor
Commercial and recreational
boating
Used By
U.S. Virgin Islands (USVI)
USVI
Commonwealth of the
Northern Mariana Islands
(CNMI), Hawaii
CNMI, Hawaii
American Samoa
American Samoa, Florida,
Hawaii, USVI
American Samoa
CNMI, American Samoa
USVI
American Samoa, CNMI,
Hawaii, USVI
American Samoa, CNMI,
Hawaii
American Samoa
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
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USVI Case Study
In 2007, USVI Department of Planning and Natural Resources (DPNR) began revision of designated uses for three
classes of waterbodies.
By 2009, the public comment period was completed and new designated uses are expected to come into effect in
2010. One major change is the inclusion of a definition of biocriteria, which lays the foundation for the various
designated uses:
Biocriteria: The Territory shall preserve, protect, and restore water resources to their most natural condition. The
condition of these waterbodies shall be determined from measures of physical, chemical, and biological
characteristics of each waterbody class, according to its designated use. As a component of these measures, the
Territory may consider the biological integrity of the benthic communities living within waters. These
communities shall be assessed by comparison to reference conditions(s) with similar abiotic and biotic
environmental settings that represent the optimal or least disturbed condition for that system. Such reference
conditions shall be those observed to support the greatest community diversity, and abundance of aquatic life
as is expected to be or has been historically found in natural settings essentially undisturbed or minimally
disturbed by human impacts, development, or discharges. This condition shall be determined by consistent
sampling and reliable measures of selected indicator communities of flora and/or fauna and may be used in
conjunction with other measures of water quality. Waters shall be of a sufficient quality to support a resident
biological community as defined by metrics based upon reference conditions. These narrative biological criteria
shall apply to fresh water, wetlands, estuarine, mangrove, seagrass, coral reef and other marine ecosystems
based upon their respective reference conditions and metrics.
A second major change is the proposed change to designated uses that highlights coral reefs and reef functions:
Proposed Water Quality Standards Excerpted from USVI § 186-2. Class A Waters.
(a) Best usage of waters: Preservation of natural phenomena requiring special conditions, such as the Natural
Barrier Reef at Buck Island, St. Croix and the Under Water Trail at Trunk Bay, St. John. These are outstanding
natural resource waters that cannot be altered except towards natural conditions. No new or increased
dischargers shall be permitted.
(b) Quality criteria: Existing natural conditions shall not be changed. The biological condition shall be similar or
equivalent to reference condition for biological integrity.
Proposed Water Quality Standards Excerpted from USVI § 186-3. Class B Waters
(a) Best usage of waters: For maintenance and propagation of desirable species of aquatic life (including
threatened, endangered species listed pursuant to section 4 of the federal Endangered Species Act and
threatened, endangered and indigenous species listed pursuant Title 12, Chapter 2 of the Virgin Islands
Code) and for primary contact recreation (swimming, water skiing, etc.). This Class allows minimal changes in
structure of the biotic community and minimal changes in ecosystem function. Virtually all native taxa are
maintained with some changes in biomass and/or abundance; ecosystem functions are fully maintained
within the range of natural variability.
(b) Quality criteria: The biological condition shall reflect no more than a minimal departure from reference
condition for biological integrity.
Proposed Water Quality Standards Excerpted from USVI § 186-4. Class C Waters
(a) Best usage of waters: For maintenance and propagation of desirable species of aquatic life (including
threatened and endangered species listed pursuant to section 4 of the federal Endangered Species Act and
threatened, endangered and indigenous species listed pursuant Title 12, Chapter 2 of the Virgin Islands
Code) and for primary contact recreation (swimming, water skiing, etc.). This Class allows for evident changes
in structure of the biotic community and minimal changes in ecosystem function. Evident changes in
structure due to loss of some rare native taxa; shifts in relative abundance of taxa (community structure) are
allowed but sensitive-ubiquitous taxa remain common and abundant; ecosystem functions are fully
maintained through redundant attributes of the system.
(b) Quality criteria: The biological condition shall reflect no more than a minimal departure from reference
condition as observed at the least disturbed reference site(s) within Class C waters.
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 Information based on measured
message in a simplified, useful manner. data used to represent a particular attribute,
An indicator can be a measure, an index of characteristic, or property of a system.
measures, or a model that characterizes some
critical component of the system.
4.1 Selecting Indicators
There has been a long-standing
interest in indicators both to
Indicator Guidelines
Relevance to purpose
Relevance to ecological structure and function
characterize ecological condition ' Responsiveness to human influence
(e.g., McKenzie et al. 1992; ' ^er to detect differences
Cairns et al. 1993) and to inform ' ^easiblllty of implementation
regulatory applications and ' Interpretation and utility for management
public decisions (e.g., Hunsacker
and Carpenter 1990; Reams
etal. 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
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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 (EPA2006a). 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.
The purpose for biocriteria is to help determine
whether a waterbody meets its designated use(s).
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
identify causes of impairment and guide
for indicator selection.
Industrial area
Stations • • •
Replicates ° °
Different habitat
o \ o
, Area of disturbance -100 m
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.
specific biological indicators, this link can potentially
restoration plans; however a causal link is not necessary
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.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-3
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Long-term monitoring is an essential component of
effective biocriteria programs.
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 offish 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 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.
Carefully reviewing, testing and analyzing candidate
measurements constitute a sound investment for a
biocriteria program.
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.
Measurement
St.
St.
Abundance and Composition
Coral density
Species richness
Species frequency
Unique species
Tolerant richness
Intolerant richness
Number of corals per m2
Number of species
Number occurrences
Number of taxa that are rare,
unique or protected
Number of taxa
Number of taxa
Decrease
Depends
on species
Physical Stature
Reef surface area
Reef structure
Community
topographic complexity
Total 3D surface area (m2) of corals
Total volume (m3) of corals per m2
Coefficient of variation for coral
colony surface area
Decrease
Decrease
Decrease
Decrease
Decrease
Decrease
Biological Condition
Reef percent live coral
Reef live surface area
Reef live to dead
surface area
Average percent live coral for all
colonies
Sum of live colony surface areas
for all colonies
Ratio of live to dead coral surface
area for all colonies
Decrease
Decrease
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-5
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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 causes(s) if 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.
Multimetric index to assess coral condition
1) Select indicators that correlate with human disturbance
Candidate Metric
# coral taxa
# coral colonies
Colony size
CV (colony size)
Coral cover
% living tissue
Live coral cover
% live coral
Metric
— 0.20
s.
5 016
I0'12
J 0.08
1 004
IKIIJ
•20 2 4 6 8 10 12 14 16
Distance to docks (km)
# coral taxa
Colony size
CV (colony size)
Coral cover
Live coral cover
2) Adjust expectations
for metric values based
on habitat differences
3) Score metrics
and calculate multimetric index
10
8
flj 6
o
o
en 4
2
0
^••''
/
/
/
Coral cover
West
Metric scores for a reef site
# coral taxa
Colony size
CV (colony size)
Coral cover
Live coral cover
Multimetric index
(Average x 1 0)
5
4
8
4
5
52
South
North
4) Assess and report condition of coral reefs
"24% of coral reefs
are impaired (below
biocriteria threshold)"
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 4-7
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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?
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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 for freshwater systems, standardized methods appeared only after
about 30 years of monitoring (EPA2006a).
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 are 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; NOAA2009a), 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
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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; Olsenetal. 1999).
Different types of monitoring answer different questions
Successful regional monitoring programs typically include three
types of sampling designs.
Status monitoring assesses the current condition of the resource
and is designed to answer questions such as:
• What percentage of coral colonies are composed of living
tissue in the near shore environment?
Trend monitoring detects change over time:
• Across the region, has coral surface area decreased?
Targeted sampling evaluates conditions and processes at specific
locations:
• How does sediment affect corals?
^ " VU
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 (EPA2008a). EPAs probabilistic survey design is more efficient because sites are
5-2
Chapter 5 — How Do We Assess Reef Condition?
-------
A type of random sampling that yields a spatially
balanced subset of sites, and avoids the clumping associated with simple
random sampling.
Sampling every member of the population, i.e., every site on
every coral reef.
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.
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, EPAs probabilistic survey in USVI collected data from all coral reef areas in St.
Croix because EPAs mandate is to assess the condition of the entire water resource (Figure
5-1). Although regionally more comprehensive for USVI's nearshore areas, EPAs 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
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St. Croix
St. Croix. USVI 2007
Coral Sampling Design
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 additional sampling around 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.
5-4
Chapter 5 — How Do We Assess Reef Condition?
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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.
Random site selection ensures that the condition of the sites surveyed can be used to infer the
condition of the entire resource, including areas not visited. In contrast, data from a non-random
site selection apply only to the sites sampled and their immediate surrounding area.
Non-Random Sampling
Random Sampling
Three reef types are shown with sampling points
indicated by black circles.
Results apply only to the small area surrounding
the sampling sites (indicated by shaded area).
Results apply to the entire reef area from which
locations were selected (shaded area). Note that
linear reef was not included in the sampling and
results do not apply to that area.
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
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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 (EPA2008a). 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" typically refers to a single group within a species, in
statistics population refers to the complete set of whatever you are
sampling. For example, the target population for coral reefs might
be defined as "all hardbottom substrate within 1.5 km of shore to a
depth of 12 m." Sonar mapping technology cannot reliably distinguish
between hardbottom with or without coral, nor can it discern whether
the coral are living; therefore, the target habitat is typically referred
to collectively as hardbottom substrate. Different shapes and types
of hardbottom can be distinguished such as linear reef, spur and
groove, or pavement. As a consequence, survey designs can
selectively emphasize different types of reef.
The
entire aggregation
of items from which
samples can be
drawn. Populations
may be discrete
(made up of separate
individuals) or
continuous (without
break or interruption).
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.
The population to be assessed must be explicitly defined.
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.
We should be able to quantify the probability that a location
may be included in a sample. All locations do not need to
have an equal probability of inclusion.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 5-7
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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?
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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 (EPA2008a).
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 EPAs 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
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6 \ low Art; r^
Coral Coral Biocriteria
Monitoring Programs Monitoring Programs
Are coral reefs improving or Are coral reefs improving or
declining? , 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
-------
Maximum
t
CO
0)
CO
u
o
m
Minimum
Low
Disturbance
High
Disturbance
Gradient of Disturbance
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 (EPA2006a; EPA2006b). 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 and 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
undisturbed or minimally disturbed by
human activity
Minimally disturbed condition:
Areas with a minimal amount of human
disturbance
Least disturbed condition: Areas with
the least amount of disturbance in altered
landscapes
Biological condition gradient (BCG): A
scientific model that describes biological
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, EPA2005a),
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
aquatic life use is no longer supported.
Major changes in structure &
moderate changes in function
Severe changes in structure & fun
ural structure & function of biotic community maintained
Minimal changes in structure & function
Evident changes in structure &
ninimal changes in function
•ate changes in structure &
inimal changes in function
Low
Level of Stressors
High
Figure 6-2. Biological Condition Gradient (BCG).
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 6-3
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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
,1
6-4
Chapter 6 — How Are Reefs Doing?
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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 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 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 (EPA2009b).
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 WQS 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?
-------
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.
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.
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
more 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
East St.
Croix
West St.
Croix
St.
Thomas
St.
John
Numbers and Types of Stations per Year
Years
1,5,9...
1 0 trend
40 status
Years
2,6,10...
1 0 trend
40 status
Years
3,7,11...
1 0 trend
40 status
Years
4,8,12...
1 0 trend
40 status
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 6-7
-------
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.
ft
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 small-
scale 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;
Rodgersetal. 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
to 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).
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Historical
Data
• Uses available data
• Provides a
permanent
benchmark
• Only generate once
• Compelling vision
for stakeholders
• Rare or extirpated
species can be
included
• Data may be
limited
• Studies likely
were designed for
different purposes
• Human impacts in
historic times were
sometimes severe
Present-Day
Biology
• Realistic
description of
current best
condition
• Based on current
sampling methods
~ ^
• Any assemblages
or communities
can be used
• Even best
available sites
have experienced
human influence
• Potential for
shifting baselines
Predictive
Methods
• Uses existing
data, avoids
expensive
sampling
• Results can be
extended to areas
without data
• Inference beyond
existing data is
risky
• Can be subjective
when data are
unavailable
Best Professional
Judgment
• Perspective and
experience of
professionals
with specific
ecological
knowledge of
the specific
region is
valuable
• Could apply
expert
consensus rules
for reference
conditions
• 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 CWAfrom
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. J J
-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.
While probabilistic design works well to estimate condition,
targeted monitoring is needed to identify the causes and
sources of impairment.
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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
-------
Fishing;
loss of grazers
by-catch
Groundings
anchor damage
dive tourism
Loss and decline
of coral, fish
habitat, fish food
Loss of fish
Coral disease
Reduced light
Physical damage
Conversion
from reef to
simple hard
bottom
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 (EPA2007a) 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
Global climate change
Ocean acidification
Coral disease
Fishing
Land-based pollutants
Boating and shipping
Invasive species
Tourism & recreation
Biological response
• Coral bleaching, loss of Acropora spp.
• Decrease in calcification rates; decreased coral growth
• Lesions, banding, or bleaching
• Reduced herbivores and large predators
• Increased growth of macro-algae
• Loss of appropriate substrate for coral recruitment
• 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
• Broken colonies, marine debris, dredged channels
• Loss of fish taxa richness due to predation by lion fish
• Broken colonies, anchor damage
The 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. J J
— 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
-------
Marine Protected
Areas (MPAs)
Wet Water Discharge
(CSOs, Stormwater)
Listing of
Impaired Waters
(CWA303d)
Marine Point
Source Discharge
Permitting
(CWA403C)
Point-source
Discharge
Permitting
(CWA402)
Coral Reef
Biocriteria
Coastal Zone
Management (CZM)
Comprehensive
Watershed
Assessments
Evaluation and
Permitting of Habitat
Modifications
(CWA404)
Point Source
Discharge Permitting
(CWA402)
Nonpoint Source
Assessment
(CWA319)
Sewage
Treatment Plant
Discharges in
Marine Waters
(CWA301h)
Figure 9-1. Examples of coral reef management programs that may be supported by biocriteria.
9.1 CWAand 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 Areas (MPA). Among the most used
management tools for coral reefs is the Marine Protected Area.
Creation of MPAs is one of nine actions recommended by Dodge
et al. (2008) to reverse the decline of coral reefs. There are
many types of MPAs, including national marine sanctuaries,
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 131582000).
9-2
Chapter 9 — What Can We Do to Protect Reefs?
-------
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 (Fore et al. 2009).
Actions of Dodge et al. (2008)
(i) Cut C02 emissions
(ii) Eliminate open-access fisheries in coral
reef ecosystems and establish and enforce
sustainable fisheries regulations.
(iii) Ban the harvest of coral reef herbivores,
including parrotfish.
(iv) Establish and enforce Marine Protected
Areas that include No-Take Areas.
(v) Effectively manage the waters in between
Marine Protected Areas.
(vi) Maintain connectivity between coral reefs
and associated habitats such as mangroves,
sea grass beds, and lagoons.
(vii) Report regularly and publicly on the health
of local coral reefs.
(viii) Recognize the links between what we do
on land and how it affects the ocean.
(ix) Bring together industry, civil society, local
government, and the scientific community to
develop a vision of healthy reefs.
Addressed by CWA?
Yes; possible precedent with acid rain in
northeastern states
CWA protects water quality suitable for
protection and propagation of fish, shellfish and
wildlife; other laws manage fisheries
CWA protects water quality suitable for
protection and propagation of fish, shellfish and
wildlife; other laws manage fisheries
No
Yes; all waters of the territorial seas are
required to have designated uses and
standards to protect uses
Yes; authority to set water quality standards in
all types of habitats within the territorial seas
Yes; mandate for states and territories to report
biological condition of water resources (305b)
Yes; authority to regulate terrestrial pollutants
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
(NOAA2009c). 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
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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).
Figure 9-2. Managing tourism. Jurisdictions
implement a variety of approaches to manage
tourists, including mooring buoys and use
permits.
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.
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Chapter 9 — What Can We Do to Protect Reefs?
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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 (NOAA2009d; 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.
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.
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 (EPA2008b). Biocriteria can be developed
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure 9-5
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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?
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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.
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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 2008; Houk and Musberger 2007). 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?
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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.
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 (EPA2009c). Watershed-
based 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 (e.g., a three mile territorial sea, a 12-mile contiguous zone, and beyond in the
ocean). 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.
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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 (C02) 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 C02 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 C02 emissions. Yet, past experience
has shown that the CWA can complement the Clean Air Act (CAA), which regulates all forms of
air pollution, including C02 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?
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10. Do Our 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 much harder to measure but just as important to understand how much worse coral reefs
would be in the absence of past and current 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.
Local jurisdictions were found to be in compliance with the new requirements, so there was
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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
is a good start. Along with understanding the regulatory options, there must be a will to use
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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 (MEA2003).
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
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Appendix A: Acronyms and Abbreviations
BCG
BMP
CAA
CCMP
CFR
CNMI
CO,
CROP
CREMP
CSOs
CWA
CWSRF
DEP
DNR
DO
DOH
DOI
DPNR
DPSIR
EO
EPA
ESRP
FDEP
FKNMS
FL
FRRP
FWS
IBI
ICI
ICRS
LDI
MBI
MPA
MS4s
Biological Condition Gradient
Best Management Practices
Clean Air Act
Comprehensive Conservation & Management Plans
Code of Federal Regulations
Commonwealth of the Northern Mariana Islands
Carbon Dioxide
Coral Reef Conservation Program (NOAA)
Coral Reef Ecosystem Monitoring Program (EPA& FKNMS)
Combined Sewer Outfalls
Clean Water Act
Clean Water State Revolving Fund
Department of Environmental Protection (Florida)
Department of Natural Resources
Dissolved Oxygen
Department of Health (Hawaii)
Department of the Interior
Department of Planning and Natural Resources (USVI)
Driving Forces, Pressures, State, Impacts, and Response
Executive Order
U.S. Environmental Protection Agency
Ecosystem Services Research Program
Florida Department of Environmental Protection
Florida Keys National Marine Sanctuary (NOAA)
Florida
Florida Reef Resilience Program (TNC)
Fish & Wildlife Service
Index of Biotic Integrity
Invertebrate Community Index
International Coral Reef Symposium
Landscape Development Intensity Index
Macroinvertebrate Biotic Index
Marine Protected Area
Municipal Separate Storm Sewer Systems
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure A-1
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NCA
NEP
NEPA
NGO
NMS
NMSA
NMSP
NOAA
NPDES
NPS
NPS
ONRW
POTWs
QHEI
SCI
SCUBA
SEFCRI
SEP
TMDL
TNC
UAA
USCRTF
USVI
WQ
WQC
WQS
WWTP
National Coastal Assessment
National Estuary Program
National Environmental Policy Act
Non-Governmental Organization
National Marine Sanctuary
National Marine Sanctuaries Act
National Marine Sanctuary Program, NOAA National Oceanic and Atmospheric
Administration, (U.S. Department of Commerce)
National Oceanic and Atmospheric Administration
National Pollutant Discharge Elimination System
National Park Service (U.S. Department of the Interior)
Non-Point Source
Outstanding National Resource Waters
Publicly Owned Treatment Works
Qualitative Habitat Evaluation Index
Stream Condition Index
Self-Contained Underwater Breathing Apparatus
Southeast Florida Coral Reef Initiative
Supplemental Environmental Protection
Total Maximum Daily Load
The Nature Conservancy
Use Attainability Analysis
U.S. Coral Reef Task Force
U.S. Virgin Islands
Water Quality
Water Quality Criteria
Water Quality Standards
Waste Water Treatment Plant
A-2
Appendix A: Acronyms and Abbreviations
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Appendix B: Glossary
106. The section of the Clean Water Act that authorizes the USEPAto 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
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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
ACOE1999).
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 Staghom 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
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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 palmate (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 inhibitors 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
(EPA2009a).
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
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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 saltwater, 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 (EPA2009a).
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 (MEA2009).
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
(EPA2009a).
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 (EPA2009a).
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 (MEA2009).
B-4 Appendix B: Glossary
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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 (EPA2009a).
biomass. The mass of living tissues in either an individual or cumulatively across organisms in a
population or ecosystem (MEA2009).
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] (EPA2009a).
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
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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 (EPA2009a).
Compact of Free Association. The status of free association recognizes an island government
as a sovereign, self-governing state with the capacity to conduct foreign affairs consistent with
the terms of the Compact. The Compact places full responsibility for military defense with the
United States. The basic relationship of free association continues indefinitely; the economic
provisions of the Compact are subject to renegotiation at the end of 15 years (DOI 2009).
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.
B-6 Appendix B: Glossary
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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.
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 (EPA2009a).
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 (EPA2009a).
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 oxygen-
demanding substances that, when decomposing, consume dissolved oxygen.
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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 (MEA2009).
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
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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 (MEA2009).
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
C02.
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).
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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 (EPA2009a).
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 (EPA2009a).
impervious cover. Surfaces where the infiltration of water is impossible, including roads,
sidewalks, driveways, parking lots, swimming pools, and buildings.
incorporated territory. A United States insular area, of which only one territory exists currently,
Palmyra Atoll, in which the United States Congress has applied the full corpus of the United
States Constitution as it applies in the several States. Incorporation is interpreted as a
perpetual state. Once incorporated, the Territory can no longer be de-incorporated (DOI 2009).
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 (MEA2009).
B-10 Appendix B: Glossary
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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.
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 (MEA2009).
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 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 (MEA2009).
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) (EPA2009a).
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).
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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
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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
(EPA2009a).
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-13
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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 (EPA2009a).
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 (C02) 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 (C02_3) ions, and lowers the saturation state of the
major shell-forming 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 best-
known 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 act. The body of laws that the United States Congress has enacted for the government
of a United States insular area; it usually includes a bill of rights and the establishment and
conditions of the insular area's tripartite government (DOI 2009).
organic matter. Natural or synthetic substances based on carbon.
B-14 Appendix B: Glossary
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organized territory. A United States insular area for which the United States Congress has
enacted an organic act (DOI 2009).
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.
pathogens. An agent of disease. A disease producer. The term pathogen most commonly is
used to refer to infectious organisms. These include bacteria (such as staph), 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). ApH 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
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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. Also, the degree of
accuracy (MEA 2009).
predation. The consumption of animals by other animals (MEA 2009).
prediction (orforecast). 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
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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 reefs 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 (MEA2009). 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
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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 %o.
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 he 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
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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 marine-
based 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,
elkhorn, and 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
(EPA2009a).
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
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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 non-
random 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) (MEA2009).
taxonomic. Referring to the science of hierarchically classifying animals by categories (phylum
(pi. phyla), class, order, family, genus (pi. 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. A point or level at which new properties emerge in an ecological, economic, or other
systems, invalidating predictions based on mathematical relationships that apply at lower
levels. For example, species diversity of a landscape may decline steadily with increasing
habitat degradation to a certain point, then fall sharply after a critical threshold of degradation
is reached. Human behavior, especially at group levels, sometimes exhibits threshold effects.
Thresholds at which irreversible changes occur are especially of concern to decision-makers
(MEA2009).
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.
B-20 Appendix B: Glossary
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Total Maximum Daily Load (TMDL). A water quality improvement plan. ATMDL 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).
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.
unincorporated territory. A United States insular area in which the United States Congress
has determined that only selected parts of the United States Constitution apply. There are
currently thirteen, three in the Caribbean (Navassa Island, Puerto Rico and the United States
Virgin Islands) and ten in the Pacific (American Samoa, Baker Island, Guam, Howland Island,
Jarvis Island, Johnston Atoll, Kingman Reef, Midway Atoll, the Northern Mariana Islands and
Wake Atoll) (DOI 2009).
unorganized territory. An unincorporated United States insular area for which the United
States Congress has not enacted an organic act (DOI 2009).
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 (sociology, ecology,
and so on) (MEA2009).
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure B-21
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value. Defined by Webster to be 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.
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 beneficial 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
(40CFR131.3).
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).
B-22 Appendix B: Glossary
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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.
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).
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C-18 Appendix C: Bibliography
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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-of-
pipe 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 naTve 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 defined
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
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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 effluent-
free 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 chemical-
specific 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 chemical-
specific criteria provide the basis for regulation.
D-2
Appendix D: Common Questions and Their Answers
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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, specific methods for
data collection the least 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. 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.
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.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure D-3
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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
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DPSIR
Driving Forces
Socioeconomic sectors and
cultural factors that drive
human activities (causes)
Pressure
Human activities that
place stress on the
environment (pollutants)
Response
Response of society to
environmental situation
(policies, decisions)
State
Condition of the
environment (composition,
distribution, quality)
Impact
Socioeconomic sectors and
cultural factors that drive
human activities (causes)
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
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Appendix F: Ocean Acidification
Since the Industrial Age began, burning of fossil fuels has added significant amounts of carbon
dioxide (C02) 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 C02, 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 C02 will still influence ocean chemistry a decade
from now (Veron et al. 2009). Once dissolved, C02 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 C02 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 C02 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 C02? 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 (EPA2009d).
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, about how to proceed with
regard to the interplay between ocean acidification and the 303(d) program based on information
received from this FR notice as well as information from other ongoing Federal efforts that are
taking place on issues related to ocean acidification.
Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure F-1
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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
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Management Area
Description
Application of Biocriteria
Damage Assessment and
Restoration
Restoring coral reefs orseagrass
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)of1969
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: CWAand Existing Coral Reef Management Programs
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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 R10 explicitly
mentioned the application
of biological monitoring and
biocriteria that lead to improved
TMDLs in their Request for
Initial Proposals.
2050) and
604(b)
Water Quality
Management
Planning
Authorizes grants to states1 and funding
forsubstate 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 no-
discharge zone status.
To establish thresholds to
gauge the effectiveness of no-
discharge 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
BMPsforNPS.
320
National Estuary
Program (NEP)
Authorizes grants to statesl 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
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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 fora 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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