U.S. Coral Reef Task Force

Handbook on Coral Reef Impacts:

Avoidance, Minimization, Compensatory Mitigation, 

and Restoration

Prepared by:

U.S. Coral Reef Task Force

Coral Injury and Mitigation Working Group

December 2016
i

Handbook on Coral Reef Impacts:

Avoidance, Minimization, Compensatory Mitigation, and Restoration

EXECUTIVE SUMMARY

In response to the National Ocean Council’s Implementation Plan (National Ocean Policy 

Implementation Plan, 2013) and U.S. Coral Reef Task Force’s (USCRTF) Resolution 16.7, the 

USCRTF developed the Handbook on Coral Reef Impacts: Avoidance, Minimization, 

Compensatory Mitigation, and Restoration. The Handbook is a review of the federal authorities, 

existing policies, and federal agency, state, and territory roles and responsibilities; a 

compendium of current best practices, science-based methodologies for quantifying ecosystem 

functions or services; and a general overview of basic protocols available for use when 

assessing impacts to coral reef ecosystems, and mitigating or restoring for unavoidable impacts

to coral reef ecosystems, including the use of appropriate compensatory action to replace the 

lost functions and services. The Handbook is a compilation of current coral reef mitigation and 

restoration best management practices. 

The target audience for this Handbook includes project applicants, proponents, permittees or 

consultants for projects that may affect coral reefs, or for responsible parties (RP) and their 

consultants in the event of unplanned impact events. This Handbook is also intended to be a 

reference for resource managers who are charged with project permitting, damage response, 

impact mitigation, and habitat restoration. 

This document is not official agency guidance, nor does it represent a comprehensive 

policy statement, and nothing herein replaces requirements contained within statute, 

codified in regulation, or agency policy, or guidance documents, and it is not intended to, 

and does not, create any right or benefit, substantive or procedural, enforceable at law or 

equity by a party against the United States, its departments, agencies, instrumentalities 

or entities, its officers or employees, or any other person.

Coral reefs are subject to numerous local, regional, and global stressors. Managers and 

regulators working to address impacts to coral reefs are further constrained by the difficulty in 

restoring and replacing these complex systems. Natural reefs are biologically, chemically, 

physically, and morphologically complex, take many years to develop, and are difficult to 

restore. Many coral species are particularly slow-growing (one-tenth of an inch per year) and 

long-lived (decades to centuries) resulting in a long response and replacement time.

While existing guidance and tools have been developed for mitigation and restoration of stream 

and wetland impacts, new guidance and tools are needed to guide mitigation and restoration for 

coral reef impacts due to their differences in ecological structure, function, and dynamics, and 

the difficulty in replacing lost functions. Mitigation and restoration technology for freshwater and 

terrestrial systems has a longer track record, and has been refined through substantial trial and 

error experience. When working in the marine environment, other factors such as site 

ownership, site protection, the remote and hazardous nature of working underwater, and longterm maintenance present challenging hurdles, and are presently managed on a case-by-case 

basis. To date, many mitigation options have only been implemented a few times and across a 

wide geographic area. Wide dissemination of the information learned from these mitigation 

options is needed to provide lessons learned to project proponents.

With the current worldwide decline of coral reef ecosystems, it is imperative that the United 

States consistently and effectively acts to avoid impacts to coral reef habitats. When impacts 
ii

cannot be avoided, measures should be taken to minimize adverse impacts. Unavoidable 

impacts may warrant compensatory mitigation through appropriate actions to replace losses of 

functions and services. Consistent and targeted efforts should be made to address as many 

coral reef stressors that can be controlled by management and regulatory actions. 

This Handbook provides a general summary of current avoidance, minimization, compensatory 

mitigation, and restoration strategies that may help address physical damage resulting from 

direct adverse impacts to coral reefs (e.g., dredging, placement of fill, vessel groundings, or 

accidental discharges like oil spills) and indirect adverse impacts to coral reefs (e.g., beach 

nourishment, sedimentation from poor land use practices, sedimentation from dredging or 

vessel movement, or storm water contaminants). In addition, the Handbook also reviews 

applicable policies and provides descriptions of various agency roles and responsibilities. The 

Handbook includes an evaluation framework for both planned impacts to coral reefs, and 

responding to unplanned impacts to coral reefs, recommendations for data collection for coral 

reef conditional assessment surveys, a summary of existing mitigation options for unavoidable 

impacts and key considerations for each option, and considerations for performance standards 

and monitoring of coral reef mitigation and restoration activities. Readers of this Handbook are 

advised to use this document for reference only. Although the Handbook is intended to 

summarize laws, regulations, policies, and best management practices it does not include a 

detailed overview of every agency’s authorities, policies, and guidance. Readers are advised to 

always seek the guidance of the local, state, and federal agencies that may have regulatory 

authority over a project or trust resources that have been or will be impacted. 

The USCRTF believes that due to the complex nature of the coral reef ecosystem, and the 

even more complex nature of identifying and providing appropriate compensatory 

mitigation for lost ecosystem services, the emphasis on maximizing avoidance and 

minimization of impacts cannot be overstated.
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TABLE OF CONTENTS

EXECUTIVE SUMMARY .............................................................................................................i

ACRONYMS..............................................................................................................................vi

DISCLAIMER............................................................................................................................ vii

1.0 BACKGROUND .................................................................................................................. 1

1.1 Introduction ......................................................................................................................1

1.2 Definitions ........................................................................................................................5

1.3 Legal and Policy Summary.............................................................................................10

1.4 Roles and Responsibilities .............................................................................................11

1.5 Coral Reef Ecosystems..................................................................................................17

1.6 Challenges to, and Opportunities for, Effective Coral Reef Impact Avoidance,

Minimization, Compensatory Mitigation, and Restoration...............................................20

2.0 EVALUATION FRAMEWORK FOR PLANNED IMPACTS TO CORAL REEF 

ECOSYSTEMS.........................................................................................................................23

2.1 Project Proponent Planning............................................................................................25

2.1.1 Pre-Application Agency Consultation and Coordination...........................................25

2.1.2. Mapping and Qualitative Characterization of Coral Reef Resources........................27

2.1.3 Quantitative Coral Reef Resource Surveys..............................................................30

2.1.4 Functional Assessment vs. Condition Assessment..................................................33

2.2 Alternatives Analysis ......................................................................................................35

2.2.1 Quantifying Direct and Indirect Impacts ...................................................................36

2.2.2 Analyzing Project Sites and Designs .......................................................................37

2.2.3 Avoid and Minimize Impacts ....................................................................................39

2.3 Compensatory Mitigation Planning .................................................................................47

2.3.1 Determining the Amount of Compensatory Mitigation Needed to Offset Impacts .....47

2.3.2 Develop a Mitigation Plan........................................................................................51

2.4 Post-Project Actions .......................................................................................................52

2.4.1 Conducting Post-construction Surveys ....................................................................52

2.4.2 Long-Term Management of Compensatory Mitigation .............................................52

2.4.3 Unauthorized Impacts to Coral Reefs During Construction......................................53

2.5 Emerging Tools and Strategies ......................................................................................53

2.5.1 Mitigation Banks and In-Lieu Fee Programs ............................................................53

3.0 FRAMEWORK FOR RESPONDING TO UNPLANNED CORAL REEF IMPACTS .............55

3.1 Natural Resource Damage Assessment and Restoration...............................................55

3.2 Response and Resource Protection ...............................................................................57

3.2.1 Vessel and/or Debris Removal ................................................................................57

3.2.2 Response-based Protection Tactics ........................................................................59
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3.3 Emergency Stabilization and Triage ................................................................................59

3.3.1 Substrate Stabilization..............................................................................................59

3.3.2 Biological Triage.......................................................................................................59

3.4 Assessing Impacts ..........................................................................................................59

3.4.1 Mapping the Impact Site...........................................................................................60

3.4.2 Coral Community Composition .................................................................................60

3.4.3 Topographic Complexity...........................................................................................61

3.5 Scaling Compensation ....................................................................................................62

3.5.1 Habitat/Resource Equivalency Analysis....................................................................62

3.5.2 Example Coral REA Scaling Approach.....................................................................63

3.6 Coral Reef Restoration....................................................................................................64

3.6.1 Development of Restoration Alternatives..................................................................64

3.6.2 Evaluation of Restoration Alternatives ......................................................................65

3.6.3 Development of Performance Criteria and Success Monitoring ................................66

3.6.4 Post-Restoration Actions ..........................................................................................67

4.0 CORAL REEF COMPENSATORY MITIGATION AND RESTORATION OPTIONS............68

4.1 The Approval Process .....................................................................................................69

4.1.1 Compensatory Mitigation Projects ............................................................................69

4.1.2 Restoration Projects .................................................................................................69

4.2 Evaluating the Options ...................................................................................................69

4.3. Portfolio of Compensatory Mitigation and Restoration Options......................................72

5.0 PERFORMANCE STANDARDS AND MONITORING ........................................................87

5.1 Administrative Measures ................................................................................................87

5.2 Ecological Performance Standards ................................................................................88

5.3 Adaptive Management Measures ...................................................................................89

5.4 Monitoring and Reporting of Project Performance ..........................................................89

6.0 RECOMMENDATIONS AND NEXT STEPS.......................................................................91

7.0 REFERENCES ..................................................................................................................92

APPENDICES...........................................................................................................................98

Appendix I – Legal and Policy Summary .............................................................................99

Appendix II – Agency Contact Information..........................................................................120

Appendix III – Coral Reef Mitigation and Restoration Planning: Endangered Species 

Considerations for Listed Corals..................................................................122

Appendix IV – Example of a Coral Transplantation Protocol ...............................................125
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LIST OF FIGURES

Figure 1: Map of tropical coral reef ecosystems within the U.S........................................20

Figure 2: A generalized process for addressing planned impacts to coral reefs...............24

Figure 3: Habitat map of Nawiliwili Harbor, Kauai, HI. ....................................................30

Figure 4: Example of Incremental Analysis comparison of compensatory mitigation 

alternatives. ....................................................................................................70

LIST OF TABLES

Table 1: Summary of trustee agency roles and responsibilities in the event of coral reef 

impacts. .............................................................................................................11

Table 2: A summary of definitions for the terms "coral reef" and "coral reef ecosystem" 

across regulatory and management agency mandates. .....................................18

Table 3: Ecosystem functions and corresponding goods and services for coral reefs ......34

Table 4: Example of a post-construction monitoring strategy 75

Table 5: Collection of federal laws and regulations that govern activities which may impact 

coral reefs. .......................................................................................................99

Table 6: Summary of state and territorial laws and regulations that govern activities which 

may impact coral reefs. ..................................................................................106

Table 7: Federal Agency Contact Information for coral reef impacts...............................120

Table 8: State and Territorial Agency contact information for coral reef impacts.............121

Table 9: ESA-listed corals confirmed in US waters, by geographic area.........................122
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ACRONYMS

ACI After Control Impact

BACI Before-After Control-Impact 

BMP Best Management Practice 

CCY Coral Colony Year

CEQ Council on Environmental

Quality

CERCLA Comprehensive Environmental 

Response, Compensation, and 

Liability Act of 1980 as amended

CFR Code of Federal Regulation

cm Centimeter

CNMI Commonwealth of the Northern 

Mariana Islands

CRCA Coral Reef Conservation Act 

CRCP Coral Reef Conservation 

Program

CTP Coral Transplantation Plan 

CZMA Coastal Zone Management Act 

CWA Clean Water Act

DA Department of the Army

DARRP Damage Assessment, Remediation, 

and Restoration Program

DGPS Differential Global Positioning 

System 

DLNR Hawaii’s Department of Land 

and Natural Resources

DOC Department of Commerce

DOD Department of Defense

DOI Department of the Interior

EFH Essential Fish Habitat

EIS Environmental Impact Statement

EO Executive Order

EPA Environmental Protection Agency

ER Engineering Regulation 

ERP Environmental Resources 

Permit

ESA Endangered Species Act 

FAC Florida Administrative Code

FDEP Florida Department of 

Environmental Protection

FKNMS Florida Keys National Marine

Sanctuary

FMP Fishery Management Plan

FS Florida Statute

FWCA Fish and Wildlife Coordination Act

FWS U.S. Fish and Wildlife Service 

HI State of Hawaii

JCP Joint Coastal Permit

LEDPA Least Environmentally Damaging 

Practicable Alternative

LiDAR Light Detection and Ranging

MMPA Marine Mammal Protection Act 

MPA Marine Protected Area 

MPRSA Marine Protection Research and

Sanctuaries Act 

MSA Magnuson-Stevens Fishery 

Conservation and Management 

Act 

NASA National Aeronautics and Space

 Administration 

NCP National Contingency Plan

NEPA National Environmental 

Policy Act 

NMFS NOAA’s National Marine Fisheries 

Service 

NMSA National Marine Sanctuaries Act 

NOAA National Oceanic and Atmospheric 

Administration 

NPDES National Pollutant Discharge 

Elimination System 

NPS National Park Service 

NRDAR Natural Resource Damage 

Assessment and Restoration 

NSF National Science Foundation

NWP(s) Nationwide Permit(s)

ODMDS Ocean Dredged Material Disposal 

Sites 

OPA Oil Pollution Act of 1990 

RHA Rivers and Harbors Act of 1899 

REA Resource Equivalency Analysis 

RI Rugosity Index 

RP(s) Responsible Party(ies) 

SUPSALV U.S. Navy Supervisor of 

Salvage

SURPA Systems Unit Resource Protection 

Act 

USACE U.S. Army Corps of Engineers 

U.S.C. U.S. Code 

USCG U.S. Coast Guard 

USCRTF U.S. Coral Reef Task 

Force 

USVI U.S. Virgin Islands 

WRDA Water Resources Development Act 
vii

DISCLAIMER

This document is not official agency guidance, nor does it represent 

a comprehensive policy statement, and nothing herein replaces 

requirements contained within statute, codified in regulation, or 

agency policy, or guidance documents, and it is not intended to, and 

does not, create any right or benefit, substantive or procedural, 

enforceable at law or equity by a party against the United States, its 

departments, agencies, instrumentalities or entities, its officers or 

employees, or any other person.
viii

The “Handbook on Coral Reef Impacts: Avoidance, Minimization, Compensatory

Mitigation, and Restoration” was formally adopted by the U.S. Coral Reef Task 

Force (USCRTF) on December 22, 2016. 

The USCRTF was established in 1998 by Presidential Executive Order to lead U.S. 

efforts to preserve and protect coral reef ecosystems. The USCRTF membership is 

represented by 12 federal agencies; seven states, territories, and commonwealths; and 

three Freely Associated States. 

The USCRTF helps build partnerships, strategies, and support for on-the-ground action 

to conserve coral reefs.

Members

Co-Chairs

U.S. Department of Commerce, National Oceanic and Atmospheric Administration 

(NOAA)

U.S. Department of the Interior (DOI) 

Federal Agency Members

U.S. Agency for International Development (USAID)

U.S. Department of Agriculture (USDA)

Department of Defense (DOD)

(Department of the Navy (Navy) and the U.S. Army Corps of Engineers 

(USACE)) 

U.S. Coast Guard (USCG)

U.S. Department of Justice (DOJ)

U.S. Department of State (DOS)

U.S. Department of Transportation (DOT)

U.S. Environmental Protection Agency (EPA)

National Aeronautics and Space Administration (NASA)

National Science Foundation (NSF)

State and Territory Members

Territory of American Samoa (AS)

Commonwealth of the Northern Mariana Islands (CNMI)

State of Florida (FL)

State of Hawaii (HI)

Territory of Guam (Guam)

Commonwealth of Puerto Rico (PR)

Territory of the U.S. Virgin Islands (USVI)

Freely Associated State Members

Federated States of Micronesia (FSM – non-voting affiliated)

Republic of the Marshall Islands (RMI – non-voting affiliated)

Republic of Palau (Palau – non-voting affiliated)
INTRODUCTION

USCRTF Handbook on Coral Reef Impacts – December 2016

1

1.0 BACKGROUND

1.1 Introduction

The purpose of this Handbook is to provide a summary of the current coral reef mitigation and 

restoration best management practices in the United States. This effort was adopted by the 

U.S. Coral Reef Task Force (USCRTF) that consists of 12 federal agencies and seven state or 

territorial governments that collectively strive to effectively manage the Nation’s coral reefs.

With the current worldwide decline of coral reef ecosystems, it is imperative that the United 

States consistently and effectively acts to avoid impacts to coral reef habitats. When damage 

cannot be avoided, measures should be taken to minimize adverse impacts. Unavoidable 

impacts may warrant compensatory mitigation through appropriate actions to replace losses of 

functions and services. Consistent and targeted efforts should be made to address as many 

coral reef stressors that can be controlled by management and regulatory actions. This 

Handbook provides a summary of current avoidance, minimization, and compensatory 

mitigation and restoration strategies that may help address physical damage resulting from 

direct adverse impacts to coral reefs (e.g., dredging, placement of fill, vessel groundings, or 

accidental discharges like oil spills) and indirect adverse impacts to coral reefs (e.g., beach 

renourishment, sedimentation from poor land use practices, sedimentation from dredging or 

vessel movement, or storm water contaminants). Effectively addressing adverse physical 

impacts to coral reefs will increase their resilience to other stressors, including climate change 

and ocean acidification, and the likelihood that coral reefs will continue to provide the valuable 

services our communities depend upon now, and into the future. As addressed in Section 1.6 of 

this document, the success of individual mitigation activities may depend in part on the effects 

that other stressors are having on a coral reef. Working closely with the appropriate permitting 

and management agencies is critical to ensure there is a clear understanding of the 

expectations and requirements for successful mitigation considering these factors. 

Federal agencies share responsibilities to avoid and minimize adverse impacts to, and to 

restore, aquatic ecosystems including coral reefs under the Clean Water Act (CWA), Executive 

Order (EO) 13089, the Magnuson-Stevens Fishery Conservation and Management Act 

(MSA),Oil Pollution Act (OPA), Rivers and Harbors Act of 1899 (RHA). Acknowledging these 

shared responsibilities, the USCRTF passed Resolution 8.4 in 2002 that established an 

interagency USCRTF working group to evaluate the effectiveness of coral reef mitigation efforts 

and to generate recommendations for the future. The resulting reports characterized federally

funded and authorized compensatory mitigation projects in both the Atlantic/Caribbean and 

Pacific oceans, and documented the poor or unassessed rates of success for such projects to 

date (Bentivoglio, 2003 and Yoshioka et al., 2004). The reports recommended formalization of 

a mechanism (e.g., technical advisory or regional interagency teams) for information exchange 

between federal, state, and territorial resource trustees and regulatory agencies to provide 

consistency, and to improve successful implementation of approaches for coral reef 

compensatory mitigation. 

Individual USCRTF working groups were convened to address issues surrounding planned and 

unplanned coral injuries and mitigation, respectively; these working groups eventually merged. 

State and territorial points of contact to the USCRTF identified a need to not only formalize 

communication between levels of government concerning the process of addressing impacts to 

coral reefs, but to document and share current best practices on topics such as coral reef 

BACKGROUND
INTRODUCTION

USCRTF Handbook on Coral Reef Impacts – December 2016

2

impact characterization, compensatory mitigation, and restoration strategies. The long-term 

goal of the working group is to reduce administrative burden and achieve better outcomes by 

creating a path toward consistency for projects in each of the seven U.S. coral reef jurisdictions

(American Samoa (AS), Commonwealth of the Northern Mariana Islands (CNMI), 

Commonwealth of Puerto Rico (PR), Guam, State of Florida (FL), State of Hawaii (HI), and the 

U.S. Virgin Islands (USVI)).

More recently, as part of the National Ocean Council’s National Ocean Policy Implementation 

Plan (NOC, 2013) and USCRTF Resolution 16.7, the USCRTF has committed to completing 

and disseminating a reference handbook to include a review of the federal authorities; existing 

policies; federal, state, and territorial agency roles and responsibilities; a compendium of best 

practices and science-based methodologies for quantifying ecosystem functions or services;

and a general overview of basic protocols for use when assessing impacts to coral reef 

ecosystems and mitigating or restoring for unavoidable impacts to coral reef ecosystems where 

warranted, including the use of appropriate compensatory action to replace the lost functions 

and services. The Handbook is a compilation of current coral reef mitigation and restoration 

best management practices. The Handbook is further supported by the Presidential 

Memorandum: Mitigating Impacts on Natural Resources from Development and Encouraging 

Related Private Investment, issued November 3, 2015.

This Handbook is the first attempt to deliver such a product summarizing the current U.S. 

government practices for responding to both planned and unplanned coral reef impacts. In this 

document, the various legal authorities and respective entities are presented as well as the 

related considerations to effectively govern impacts to coral reef. While focused on the federal 

legal and regulatory authorities, this Handbook also identifies several relevant state and 

territorial coral reef related authorities. These include strategies for assessing impacts to coral 

reef resources associated with federal, state, or territorial regulatory and permitting activities, as 

well as response actions. Where coral reef impacts are expected from government actions, the 

potential requirements of rehabilitation and mitigation activities in coral reefs and/or nearby 

lands or waters to protect or improve coral reef ecosystems and/or associated habitats, and the 

ecological functions and services, are discussed. 

The target audience for this Handbook includes project applicants, proponents, permittees, or 

consultants for projects that may adversely affect coral reefs, or for responsible parties (RP) and 

their consultants in the event of unplanned impact events. This Handbook is also intended to be 

a reference for resource managers who are charged with project permitting, damage response, 

impact mitigation, and habitat restoration. 

This document is not official agency guidance, nor does it represent a comprehensive 

policy statement, and nothing herein replaces requirements contained within statute, 

codified in regulation, or agency policy, or guidance documents, and it is not intended to, 

and does not, create any right or benefit, substantive or procedural, enforceable at law or 

equity by a party against the United States, its departments, agencies, instrumentalities 

or entities, its officers or employees, or any other person.

For planned events, such as dredging or in-water construction, federal, state, and territorial 

authorities have varying definitions of mitigation, as well as different requirements for 

determining appropriate compensatory mitigation under those authorities. The most 

comprehensive regulations are the U.S. Army Corps of Engineers (USACE) and the U.S. 

Environmental Protection Agency (EPA) regulations for compensating for unavoidable losses of 

BACKGROUND
INTRODUCTION

USCRTF Handbook on Coral Reef Impacts – December 2016 

3

aquatic resources (33 Code of Federal Regulation (CFR) part 332 and 40 CFR part 230, 

subpart J) (i.e., the 2008 Mitigation Rule). As such, the “2008 Mitigation Rule” serves as the 

primary guide for designing coral reef compensatory mitigation. For the purposes of this 

document, “mitigation” for planned events refers to the process of first avoiding, then 

minimizing, and lastly—in cases where unavoidable loss of natural resource will occur—

implementing compensatory mitigation. Compensatory mitigation is defined under the 2008 

Mitigation Rule, and informed by the Essential Fish Habitat (EFH) consultation requirements 

under MSA §305(b), and the U.S. Fish and Wildlife Service (FWS) mitigation policy, dated 

November 21, 2016 (Federal Register, Volume 81, Number 224, pages 83440-83492), through 

the authority of the Fish and Wildlife Coordination Act (FWCA) (16 U.S.C. 470 et seq.), among 

others. In many cases, if projects are able to avoid and minimize impacts to coral reefs in the 

planning process, a federal action, such as a federal permit, may not require compensatory 

mitigation. 

Additionally, this document summarizes the general process for unplanned events such as ship 

groundings. The process for unplanned events focuses on the replacement of public trust 

resources and is governed by specific authorities such as the OPA, National Marine Sanctuaries 

Act (NMSA), the Systems Unit Resource Protection Act (SURPA) (54 U.S.C. 100721), some 

state laws, and occasionally Admiralty Law.

1

 

For both planned and unplanned events impacting coral reefs, individual federal, state, and/or 

territorial authorities have defined the actions necessary to mitigate for and restore unavoidable 

adverse impacts to coral reefs. This Handbook provides generalized descriptions of the actions 

typically conducted. Often the process is iterative. It is best to work closely with the appropriate 

federal, state, and/or territorial authorities as they will take into account any resource 

considerations specific to the project and help identify potential solutions when necessary. 

With impacts of climate change and ocean acidification—such as sea level rise, warming sea 

surface temperatures, and decreasing pH—already threatening coral reefs and coastal 

communities, the USCRTF affirms that all coral reef conservation efforts should be considered 

within the context of these ongoing global changes (Resolutions 28.2 and 34.1). This view is 

consistent with EO 13653 "Preparing the United States for the Impacts of Climate Change," 

dated November 1, 2013, which directs federal agencies to "promote (1) engaged and strong 

partnerships and information sharing at all levels of government; (2) risk-informed decisionmaking and the tools to facilitate it; (3) adaptive learning, in which experiences serve as 

opportunities to inform and adjust future actions; and (4) preparedness planning" in order to 

improve the Nation's preparedness and resilience to these impacts. EO 13653 also directs 

each federal agency to “develop, implement, and update comprehensive plans that integrate 

consideration of climate change into agency operations and overall mission objectives.” In 

various sections, this Handbook highlights considerations of climate change in mitigation 

planning. As with the variations in requirements for coral reef mitigation specific to each federal 

agency authority, each federal agency has variations in how to best incorporate climate change 

into coral reef impact assessments. Project proponents should work closely with the 

appropriate permitting authorities to determine how to address climate change considerations in 

their projects and mitigation actions. 

In compiling this Handbook, it has become clear that there are both overlapping and potentially 

conflicting federal authorities and interpretations thereof, and therefore there may be a lack of 

 

1 The Foreign Claims Act (FCA) applies to damage claims outside of U.S. waters for damage caused by 

the federal government.

BACKGROUND
INTRODUCTION

USCRTF Handbook on Coral Reef Impacts – December 2016

4

consensus and consistency on how to best manage those authorities. However, there is 

agreement that due to the complex nature of the coral reef ecosystem, and the even more 

complex nature of identifying and providing appropriate compensatory mitigation for lost 

ecosystem services, the emphasis on maximizing avoidance and minimization of impacts 

is imperative. These considerations apply to both planned and unplanned coral reef impact 

events. Despite the different legal authorities, the following factors are common to both planned 

and unplanned coral reef mitigation/response efforts:

1. Defining planned actions or determining the actions that lead to the unplanned 

impacts must be fully understood. Defining the actions that will lead to or have led to 

coral reef impacts will drive the decisions on appropriate next steps. 

2. Avoiding impacts completely by not taking a certain action, or parts of an action, or redesigning the action to avoid adverse impacts to reefs. Avoiding impacts includes a 

cursory understanding of the affected environment. A more detailed characterization is 

needed when all avoidance and minimization actions have occurred (discussed in factor 

#4, below). In planned events, avoidance will occur in the planning stage to reduce 

impacts from an activity. Whereas, in the case of unplanned events, measures could be 

taken during response actions to prevent or reduce additional impacts to coral reefs. 

3. Minimizing adverse impacts by limiting the magnitude of the action and its 

implementation (including effects of operations and maintenance activities). In planned 

events, minimizing may include selecting a less damaging alternative (not applicable to 

an unplanned impact). Minimizing impacts may be challenging during unplanned events 

but, similar to avoiding impacts, actions can be taken during the incident response phase

to minimize additional injuries, such as defining an exit path for a grounded ship being 

removed from the coral reef.

4. Assessing the impacts by accurately characterizing the affected environment. In 

planned events where coral reef impacts have been avoided, a detailed characterization

is often not required. In some cases, this more detailed assessment will lead to the 

identification of additional ways to avoid and minimize impacts to sensitive resources. 

For unplanned events, a full injury assessment is important in determining the nature 

and extent of the impacts to the coral reef and its ecosystem.

5. Compensating for unavoidable coral reef impacts in planned events can be 

accomplished by replacing the lost ecosystem functions or services. In the case of 

unplanned events, the target would be replacement of public trust resources, including 

lost ecosystem functions or services.

The Coral Reef Injury and Mitigation Working Group of the USCRTF developed this Handbook

to summarize current practices, processes, and roles and responsibilities with a goal to increase 

consistency and success in the collective efforts to protect coral reef ecosystems. New tools 

and strategies for assessing coral impacts and mitigating for those impacts are being developed 

by agencies, project proponents, or responsible parties. As these tools and strategies mature in 

the future, the USCRTF will determine the most effective manner to provide updated 

information. 
DEFINITIONS

USCRTF Handbook on Coral Reef Impacts – December 2016

5

1.2 Definitions

Following are key terms and definitions used in this Handbook. Where possible, the terms and 

definitions were taken directly, or adapted from, existing regulations and policy documents. The 

definitions are provided to help readers work through this Handbook, not to redefine what is 

already written into statute and regulations. Readers should always confirm definitions with the 

appropriate permitting and management agencies for a specific project or event.

Activity: Options or actions that are proposed to occur in an area where coral reef habitat 

occurs or in an area with ecological or oceanographic connectivity that may convey adverse 

effects on coral reef habitat. 

Adverse Effect (impact): Any impact that reduces quality and/or quantity of species or habitat

(includes benthic community, water column, biological, chemical, and physical attributes) and 

may include direct (e.g., contamination or physical disruption), indirect (e.g., loss of prey, 

reduction in species’ fecundity), site-specific, or habitat-wide impacts, including individual, 

cumulative, or synergistic consequences of actions (adapted from 50 CFR 600.810). When an 

adverse effect to coral reef species or habitat is likely to occur, project proponents/permittees 

should seek to avoid and minimize the effect and may be required to implement compensatory 

mitigation for the unavoidable effects.

Aquatic: Of or relating to freshwater, estuarine, and marine habitats.

Baseline: The condition of the natural resources and services that would have existed had the 

incident not occurred. Baseline data may be estimated using historical data, reference data, 

control data, modeling, or data on incremental changes (e.g., number of dead animals), alone or 

in combination, as appropriate (15 CFR 990.30).

Climate Change: Climate change refers to a change in the state of the climate that can be 

identified (e.g., by using statistical tests) by changes in the mean and/or the variability of its 

properties, and that persists for an extended period, typically decades or longer. Climate change 

may be due to natural internal processes or external forcings such as modulations of the solar 

cycles, volcanic eruptions, and persistent anthropogenic changes in the composition of the 

atmosphere or in land use (IPCC, 2014, Annex II: Glossary).

Compensatory Mitigation (includes compensate(d), compensation): Those activities taken 

for the purposes of offsetting impacts to coral reef ecosystems that remain after all appropriate 

and practicable avoidance and minimization has been achieved. Compensatory mitigation may 

be required to satisfy applicable federal, state, or territorial regulations. Compensatory 

mitigation activities may include, but are not limited to, the re-establishment, rehabilitation, 

establishment (creation), enhancement, and/or preservation of coral reef ecosystems and/or 

associated habitats (adapted from 33 CFR 332.2, 40 CFR 230, and MSA; 16 U.S.C. 1855 (b) 

§305(b)).

Compensatory Mitigation Plan: The plan developed by the project proponent or resource 

agency and determined to be sufficient by the permitting authority or resource trustee agencies 

that identifies the objectives, site selection, site protection instrument, baseline information, 

determination of credits and debits, mitigation work plan, maintenance plan, performance 

standards, monitoring requirements, long-term management plan, adaptive management plan, 

financial assurances, and other pertinent information to address requirements of the permitting 

authority (adapted from 33 CFR 332.4 and 40 CFR 230).

BACKGROUND
DEFINITIONS

USCRTF Handbook on Coral Reef Impacts – December 2016

6

Condition: The relative state of an aquatic resource to support and maintain a community of 

organisms characterized by its species composition, diversity, and functional organization 

comparable to reference aquatic resources in the region (33 CFR 332.2 and 40 CFR 230). For 

the purpose of this document, as discussed in Section 2.1.4, condition assessments are used 

as an alternative to assess coral reef function.

Coral: Species of the phylum Cnidaria, including all species of the orders Antipatharia (black 

corals), Scleractinia (stony corals), Gorgonacea (horny corals), Stolonifera (organpipe corals 

and others), Alcyonacea (soft corals), and Helioporacea (blue coral) of the class Anthozoa; and 

all species of the families Milleporidea (fire corals) and Stylastreridae (stylasterid hydrocorals) of 

the class Hydrozoa.

Coral Reef: Limestone structures composed in whole, or in part, of living coral, skeletal 

remains, and including other corals, sessile marine animals, and plants. Reefs greatly vary in 

size from a few meters to several kilometers. Several individual reefs can form large reef 

complexes like the Great Barrier Reef of Australia, Papahānaumokuākea National Marine 

Monument, Great Bahama Bank, and the Florida Reef Tract.

Coral Reef Ecosystem: The system of coral reefs and geographically and ecologicallyassociated species, habitats, and environment, and the processes that control its dynamics. 

Often, other nearshore habitats such as seagrass, algae, and mangroves are part of the coral 

reef ecosystem. 

Coral Relocation: Moving a coral from a site not associated with an impact (e.g., a nursery 

location) to another site (e.g., a proposed compensatory mitigation site) (see Section 4.3, Option 

3).

Coral Transplantation (Translocation): Moving a coral from one site proposed for impact to 

another site, typically associated as an action to minimize impacts from a planned activity (see 

Section 2.2.3.2).

Credit: A unit of measure (e.g., a functional or areal measure or other suitable metric) 

representing the accrual or attainment of aquatic functions at a compensatory mitigation site. 

The measure of aquatic functions is based on the resources restored, established, enhanced, or 

preserved (33 CFR 332.2).

Debit: Debit means a unit of measure (e.g., a functional or areal measure or other suitable 

metric) representing the loss of aquatic functions at an impact or project site. The measure of 

aquatic functions is based on the resources impacted by the authorized activity (33 CFR 332.2).

Enhancement: The manipulation of the physical, chemical, or biological characteristics of an 

aquatic resource to heighten, intensify, or improve a specific aquatic resource function(s). 

Enhancement results in the gain of selected aquatic resource function(s), but may also lead to a 

decline in other aquatic resource function(s). Enhancement does not result in a gain in aquatic 

resource area.

Establishment: The manipulation of the physical, chemical, or biological characteristics 

present to develop an aquatic resource that did not previously exist.
DEFINITIONS

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Ecosystem Functions (Function(s)): The physical, chemical, and biological processes that 

occur in coral reef ecosystems or associated ecosystems (33 CFR 332.2 and 40 CFR 230). For 

the purpose of this document, as discussed in Section 2.1.4, there is currently limited ability to 

assess coral reef function, and therefore condition assessment is used generally.

Ecosystem Services: The benefits that human populations receive from functions that occur in 

ecosystems (adapted from 33 CFR 332.2 and 40 CFR 230). Alternatively, the functions 

performed by a natural resource for the benefit of another natural resource or the public (15 

CFR 990.30).

Federal Action: Any actions, authorization (permits, grants licenses, etc.), funding use or 

distribution, or efforts undertaken by a federal agency.

Impact: Refers to planned or unplanned loss of ecological functions or services.

Direct Impacts: Impacts that are caused by the planned or unplanned activity and occur at 

the same time and place (adapted from 40 CFR 1508.8(a)).

Cumulative Impacts: Impacts that result from the incremental impact of the action (i.e., the 

direct and indirect impacts caused by the action) when added to the impacts of other past, 

present, and reasonably foreseeable future actions regardless of what agency (federal or 

non-federal) or person undertakes those other actions (40 CFR 1508.7). Cumulative 

impacts can result from individually minor but collectively significant actions taking place

over a period of time. Assessment of cumulative impacts requires identifying a baseline 

condition, describing how that condition has changed over time as a result of past actions,

and how that condition is expected to change as a result of present actions and reasonably 

foreseeable future actions (adapted from “Considering Cumulative Effects under the 

National Environmental Policy Act,” Council for Environmental Quality, 1997).

Indirect Impacts: Impacts that are caused by, or associated with, the planned or unplanned 

activity. Impacts can be later in time, or farther removed in distance, but are still reasonably 

foreseeable (adapted from 40 CFR 1508.8(b)).

Permanent Impacts: Impacts that result in a complete loss of the resource with no ability for 

reasonable natural recovery in the foreseeable future (e.g., removing coral reefs from a 

navigation channel).

Planned Impacts: Those regulated activities that have the potential to impact coral reef 

ecosystems, which may require consultation between the permitting authority and resource 

trustees and approval from a permitting authority prior to implementation.

Temporary Impacts: Impacts that are short-term, where the resource is expected to 

recover to a certain level of function through natural processes (e.g., sediment accumulation 

on coral reef areas adjacent to channel dredging that would likely be removed by natural 

wave flushing).

Unplanned Impacts: Those activities that are not planned, anticipated, scheduled, or 

otherwise expected, and have impacts on coral reef ecosystems (e.g., vessel groundings, 

anchor and cable drags, or impacts unassociated with a planned project).

BACKGROUND
DEFINITIONS

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In-kind: A resource of a similar structural or functional type to the impacted resource (33 CFR 

332.2 and 40 CFR 230).

Injury: An observable or measurable adverse change in a natural resource, or impairment of a 

natural resource service. Injury may occur directly or indirectly to a natural resource and/or 

service. Natural resource trustees are authorized by OPA to assess damages for “injury to, 

destruction of, loss of, or loss of use of” natural resources. The definition of injury incorporates 

these terms. The definition also includes the injuries resulting from the actual discharge of oil, a 

substantial threat of a discharge of oil, and/or related response actions. Injury can include 

adverse changes in the chemical or physical quality, or viability of a natural resource (i.e., direct, 

indirect, delayed, or sub-lethal effects). Potential categories of injuries include adverse changes 

in: survival, growth, and reproduction; health, physiology, and biological condition; behavior; 

community composition; ecological processes and functions; physical and chemical habitat 

quality or structure; and services to the public. Although injury is often thought of in terms of 

adverse changes in biota, the definition of injury under the OPA regulations is broader. Injuries 

to non-living natural resources (e.g., oiled sand on a recreational beach), as well as injuries to

natural resource services (e.g., lost use associated with a fishery closure to prevent harvest of 

tainted fish, even though the fish themselves may not be injured) may be considered. (15 CFR 

990.30)

Mitigation (Sequential Mitigation): For the purposes of this Handbook this definition includes 

the sequential process involving first maximum avoidance, second minimization of 

unavoidable impacts, and then only after completion of minimization proceeding to

compensatory mitigation for any unavoidable impacts as the third step. Determination of the 

requirement for compensatory mitigation is at the discretion of the permitting authority in 

accordance with applicable regulatory requirements. Compensatory mitigation may not be 

required if the remaining unavoidable impacts are not significant enough to warrant 

compensatory mitigation under the applicable permitting authority’s regulations and policies.

Objectives: The description of the resource type(s) and amount(s) that will be restored as part 

of a mitigation plan or restoration project. Objectives identify whether an activity will reestablish, re-habilitate, establish (create), and/or preserve habitat. The objectives may also 

identify specific functions or services to be provided by the restoration of coral reef ecosystems 

and/or associated habitats (adapted from 33 CFR 332.4 and 40 CFR 230).

Ocean Acidification: Ocean acidification refers to a reduction in the pH of the ocean over an 

extended period, typically decades or longer, which is caused primarily by uptake of carbon 

dioxide from the atmosphere, but can also be caused by other chemical additions or 

subtractions from the ocean (IPCC, 2014, Annex II Glossary).

Off-site: A location that is not within the area of project activities, neither located on the same 

parcel of land or reef habitat area as the impact site, nor a parcel of land or reef habitat area 

contiguous to the parcel containing the impact site (adapted from 33 CFR 332.2 and 40 CFR 

230).

On-site: A location that is within the area of project activities.

Options: A variety of actions or methods that may be considered by a project proponent to 

restore coral reef ecosystems and/or associated habitats.
DEFINITIONS

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Out-of-kind: A resource of a different structural and/or functional type from that of the impacted

resource (33 CFR 332.2 and 40 CFR 230).

Outplanting: Taking a coral grown in a coral nursery, placing, and often attaching it onto the 

coral reef or an artificial structure.

Performance Standards: Observable or measurable physical (including hydrological), 

chemical, and/or biological attributes that are used to determine if a restoration or compensatory 

mitigation project meets its objectives (33 CFR 332.2, 40 CFR 230 or Engineering Regulation 

(ER) 1105-2- 100, 3-5.b(8)). This is synonymous with “performance criteria.” 

Permitting Authority: The federal, state, or territorial agency issuing the permit or license that 

authorizes an activity. There may be multiple permitting authorities with varying requirements 

for a single activity.

Preservation: The removal of a threat to, or preventing further decline of, aquatic resources by 

an action in or near those aquatic resources; includes activities commonly associated with the 

protection and maintenance of aquatic resources through the implementation of appropriate 

legal and physical mechanisms; does not result in a gain of aquatic resource area or functions 

(adapted from 33 CFR 332.2 and 40 CFR 230).

Project Proponent: The entity proposing the impact or restoration activity, including but not 

limited to: applicant, permittee, or responsible party.

Applicant: An individual or entity who proposes actions that could result in a planned 

adverse impact to coral reef resources who applies for authorization to conduct such 

activities from a permitting authority.

Permittee: An individual or entity whose actions, once authorized by a permitting authority, 

result in a planned adverse impact to coral reef resources.

Responsible Party: The individual, entity, or instrumentality whose actions result in an 

unplanned adverse impact to coral reef resources. The entity could be a federal, state, 

territorial, or tribal government or agency. When a vessel causes a coral injury, the responsible 

party may be broadly defined as the owner, operator, or manager of a vessel that caused an 

unplanned adverse impact or in some cases the instrumentality or vessel itself will be a 

responsible party. In some laws and regulations, responsible party is also used to define 

entities responsible for aspects of planned activities. For the purpose of this handbook, 

responsible party is only used to refer to unplanned activities. 

Recovery Plan: A document drafted by the FWS or National Marine Fisheries Service (NMFS) 

for threatened or endangered species that identifies: (1) objective, measurable criteria which, 

when met, would result in a determination that the species is no longer threatened or 

endangered; (2) site-specific management actions necessary to achieve recovery of the 

species; and (3) estimates of the time and costs required to achieve the plan's goal (adapted 

from the Endangered Species Act (ESA) §4(f)).

Re-establishment: The manipulation of the physical, chemical, or biological characteristics of 

a site with the goal of returning natural/historic functions to a former aquatic resource; results in 

rebuilding a former aquatic resource, and a gain in aquatic resource area and function (adapted 

from 33 CFR 332.2 and 40 CFR 230).

BACKGROUND
LEGAL AND POLICY SUMMARY

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Rehabilitation: The manipulation of the physical, chemical, or biological characteristics of a 

site with the goal of repairing natural/historic functions to a degraded aquatic resource; results in 

a gain in aquatic resource functions, but not a gain in aquatic resource area (adapted from 33 

CFR 332.2 and 40 CFR 230).

Resource: Functional groups, including physical, chemical, and biological structure, a habitat 

type, or ecosystem of concern. The resource may refer to coral reef ecosystems, other habitats,

or ecosystems that are being restored to improve the functions of coral reef ecosystems.

Restoration: Manipulation of the physical, chemical, or biological characteristics of a site with 

the goal of returning self-sustaining natural or historic structure and functions (Needelman, et al. 

2012).

Primary Restoration (Active): Physical relief restoration that, when combined with 

biological restoration, returns injured natural resources and services toward baseline sooner 

than natural recovery. The determination that primary restoration has been completed is 

dependent upon meeting specific procedural requirements and performance standards as 

defined by the appropriate regulatory authorities. 

Compensatory Restoration: Any action taken to compensate for losses of natural 

resources and services that occur from the date of the unplanned incident until recovery 

(adapted from 15 CFR 990.30).

Site Stabilization: Any action that will minimize potential for further injuries in an impacted 

area due to destabilized substrate (e.g. rubble/debris removal, fracture stabilization).

Transect: A standardized unit used to sample an impact area. A transect can be at a 

permanent or randomly selected location once the boundaries of a survey area have been 

defined. A transect always consists of a standard length with a defined width. These 

measurements may change depending on the circumstances and the resource being surveyed. 

These transects are commonly designated by using a surveyors tape to lay a straight line on the 

bottom, then a surveyor can record data points within the area of the transect. Different 

sampling methods can then be applied depending on the resources being surveyed. Transects 

may be used for multiple purposes, such as defining ecological distributions; distribution of 

sediments over hardbottom habitat; the ratio of rocky substrate versus loose (unconsolidated) 

sediment substrate; mitigation rock or modules versus loose sediments where rock or modules 

are deployed; evaluating distribution of coral reef injuries; and distribution of natural and artificial 

subjects on bottom and land.

1.3 Legal and Policy Summary

There are numerous laws and regulations that govern activities in and around coral reef 

ecosystems. In many instances multiple federal and state or territorial laws or regulations may 

apply to different aspects of the same activity. Project proponents may be most familiar with the 

RHA §10, CWA, ESA, EFH consultation under MSA §305(b), and FWCA, which include 

requirements for planned activities, and with the Natural Resource Damages Assessment and 

Restoration (NRDAR) requirements for unplanned impacts to coral reefs. Appendix I provides a 

more comprehensive list of laws and regulations that apply to activities and impacts within coral 

reef ecosystems. However, this list should not be considered an exhaustive list of every 

relevant federal, state, or territorial authority.
LEGAL AND POLICY SUMMARY

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1.4 Roles and Responsibilities

Across federal, state, and territorial agencies there are numerous legal authorities governing the 

planning, response, and damage assessment relative to coral reef impacts. Table 1 

summarizes the main roles and responsibilities for various federal, state, and territorial agencies 

relative to coral reef impacts including avoidance, minimization, response to unplanned events, 

damage assessments, restoration, and compensation for loss of coral reef functions and 

services. A more detailed list is provided in Appendix I. This list should not be considered an 

exhaustive list of all federal, state, or territorial legal authorities, roles, and responsibilities. 

There may be additional local (e.g., city or county) requirements that apply to a particular 

project; those are not discussed here and would need to be explored with the appropriate local

agency. Information on specific agency mandates, whether they play a lead or a participatory or 

consulting role, is included where available.

Project proponents and Responsible Parties (RPs) for planned and unplanned activities that 

may impact the marine environment, respectively, must comply with the applicable laws and 

regulations that apply to their project. Examples of planned and unplanned activities include, 

but are not limited to, anchor blocks, shoreline hardening, mooring or marker buoys, dumping, 

abandoned vessels, pier construction, dredging, land-based activities resulting in sediment or 

contaminant loads to coastal habitats, coastal road construction, wastewater treatment plant 

development and discharge, vessel groundings, or cable drags. The planned project or 

unplanned event scope, location, funding source(s), sponsor, agency with management and 

trust resources, and extent of impacts will dictate which authorities apply and which agencies 

must be consulted. As a general practice, project proponents and RPs should begin contacting 

the primary permitting authority or agency that has ownership or management authority over the 

coral reef resources that will be, or have been, impacted. Once initial contact has been made, 

early consultation and coordination with the other appropriate permitting, resource, and trustee 

agencies is strongly encouraged to determine the requirements for a particular project. 

Depending on the requirements within the authorities, some agencies may not be required to 

comment or respond to the inquiry. 

Project proponents and RPs are reminded that a permit or approval from one agency does not 

negate other permit requirements. An activity may require permits from federal agencies as well 

as state and territorial agencies. 

Table 1: Summary of trustee agency roles and responsibilities in the event of coral reef 

impacts.

Agency Planned Unplanned

Federal

EPA Legal Authorities:

• CWA §404: Review and 

comment on dredge and fill 

material placement permits 

issued by USACE. Potential 

denial or restriction of use of 

defined areas for disposal.

• CWA §301, §303 and §402: 

Addresses water quality 

standards and uses, 

Activities:

• Reporting of oil and hazardous 

substance spills under OPA.

. Emergency response planning 

as member of Oceanic 

Regional Response Team 

(inland federal coordinator).

BACKGROUND
LEGAL AND POLICY SUMMARY

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Agency Planned Unplanned

EPA (cont.) measures to address impaired 

water quality, and permitting 

of discharge of pollutants.

• CWA §309: Enforcement of 

the prohibition against 

unpermitted discharge, and 

permit violations under §402 

and §404.

• Marine Protection Research 

and Sanctuaries Act of 1972 

(MPRSA): Designation of 

Ocean Dredged Material 

Disposal Sites, review of 

alternative site selections, and 

concurrence on permits 

issued by USACE.

Participatory Authorities:

. National Environmental Policy 

Act (NEPA) and Clean Air Act 

§309: Conducts NEPA 

analyses when applicable. 

Reviews other federal 

agencies’ Environmental 

Impact Statements.

FWS Legal Authorities:

. Antiquities Act.

. ESA §7, §4(d), and §10. (Sea 

turtles on land)2.

. FWCA.

. Marine Mammal Protection Act 

(MMPA).

. Migratory Bird Treaty Act 

(MBTA).

. Sikes Act.

. Lacey Act.

. Conservation in Trade of 

Endangered Species (CITES).

. National Invasive Species Act 

(NISA). 

Participatory Authorities:

. NEPA.

• CWA §404.

• Federal Consistency for the 

Coastal Zone Management Act 

Legal Authorities:

• Antiquities Act.

• NRDAR (OPA).

• ESA §7 (Interagency 

Consultation).

• MMPA.

• MBTA.

• Sikes Act.

• CITES. 

• NISA. 

• Comprehensive Environmental 

Response, Compensation, and 

Liability Act (CERCLA).

Activities:

• Oil spill scientific and 

emergency response.

. Vessel grounding response, 

assessment and restoration.

 

2ESA consultations related to sea turtle activity and habitat on land often involve analysis of impacts to the 

coastal habitats that may also have direct or indirect impacts on the adjacent coral reefs.
LEGAL AND POLICY SUMMARY

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Agency Planned Unplanned

FWS (cont.) (CZMA).

. Compact of Free Association 

Agreement between the United 

States of America and the 

Republic of the Marshal Islands 

(RMI), Compact of Free 

Association Agreement 

between the United States of 

America and Federated States 

of Micronesia (FSM), and 

Compact of Free Association 

Agreement between the United 

States of America and Republic 

of Palau (Palau). (Commonly 

referred to as the Compact of 

Free Association for RMI, FSM, 

and Palau).

. Compact of Free Association 

for RMI, FSM, and Palau.

Department 

of Navy

(Navy)

Activities:

. Land manager for coastal and 

waterways associated with 

naval facilities.

Activities:

. U.S. Navy Supervisor of 

Salvage (SUPSALV), Fleet 

Task Forces, or Military Sealift 

Command act as On-Scene 

Commander for incident 

response. 

. SUPSALV integrates 

environmental planning and 

coral subject matter experts 

into incident response teams 

as soon as possible after the 

incident to ensure response 

plans consider environmental 

and natural resource concerns 

in parallel with the contingency 

response to adaptively 

manage and mitigate damage 

in real time.

National 

Oceanic and 

Atmospheric 

Administration 

(NOAA)

Legal Authorities:

. Antiquities Act.

. EFH (MSA §305(b)). This is 

separate and apart from the 

CWA.

. ESA §7 Consultation and ESA 

§4(d), §6 (potential funding 

source to states and territories 

for coral recovery), and §10.

. FWCA.

. MMPA.

. CZMA.

. NMSA.

Legal Authorities:

. Antiquities Act.

. NRDAR Procedures (OPA). 

. CERCLA.

. EFH Protection (MSA 

§305(b)).

. ESA §7 (Interagency 

Consultation).

. Natural Resource Trustee 

Representation (National 

Contingency Plan and OPA).

. MMPA.

. NMSA.

BACKGROUND
LEGAL AND POLICY SUMMARY

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Agency Planned Unplanned

NOAA (cont.) Participatory mandates:

. NEPA.

. CWA §404. 

. Sikes Act. 

. Compact of Free Association 

for RMI, FSM, and Palau. 

Activities: 

. NMFS provides technical 

assistance to states that issue 

National Pollutant Discharge 

Elimination System (NPDES) 

permits for large power plants 

and manufacturing facilities that 

withdraw at least 2 million 

gallons of cooling water.

. Compact of Free Association 

for RMI, FSM and Palau. 

Activities:

. Oil spill scientific support and 

emergency response. 

. Vessel grounding response, 

assessment and restoration.

National Park 

Service (NPS)

Legal Authorities: 

. Antiquities Act. 

. 54 U.S. Code (U.S.C.) Chapters 

1001-1007(Formerly Known as 

the NPS Organic Act) cover 

general provisions, 

establishment of the NPS, 

areas of the system, and 

resource management. 

. National Park Unit enabling 

legislation. 

. NEPA within NPS units. 

. Permitting agency for any 

activity within an NPS unit. 

. 36 Code of Federal 

Regulations (CFR). 

. Superintendent Compendiums. 

Activities: 

. Land manager of coral reef 

ecosystems, coastal and 

nearshore resources.

Legal Authorities:

. SURPA (54 U.S.C. 100721). 

. OPA. 

. CERCLA. 

. Enforcement Authority within 

NPS Units. 

. Antiquities Act. 

. CWA. 

. ESA. 

. Lacey Act. 

. 36 CFR (including damage 

to natural features). 

. Superintendents 

Compendiums. 

Activities:

. Oil spill emergency response. 

. Vessel grounding emergency 

response, damage 

assessment, and restoration. 

. Unplanned event emergency 

response, damage 

assessment, and restoration. 

. Permitting agency for any 

activity within an NPS unit. 

USACE Legal Authorities:

. CWA, §404.

. RHA, §9 and §10. 

Enforcement authority for 

unauthorized activities.

. MPRSA, §103.

. In general, various Water 

Legal Authorities (triggered by 

some unplanned events):

. CWA, §404. 

. RHA, §10. 

. MPRSA, §103. 

. RHA, §14 and codified in 33 

U.S.C. 408 (§408). 
LEGAL AND POLICY SUMMARY

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Agency Planned Unplanned

Resource Development Acts 

(WRDA) authorize USACE to 

implement certain water 

resource management 

projects in partnership with 

non-federal cost-sharing 

sponsors, such as harbor 

improvements and aquatic 

ecosystem restoration. 

• RHA, §14 (33 U.S.C. 408) 

(Taking possession of, use of, 

or injury to harbor or river 

improvements).

. NEPA – documentation for 

decisions on permit 

applications and federal water 

resources projects. 

Activities:

. USACE engagement varies 

based on the type, size, and 

impact of an unplanned event. 

Many unplanned events may 

be addressed within the 

Nationwide Permits, requiring 

limited USACE notification.

However, planned but 

unauthorized activities (e.g., 

construction of unauthorized 

boat ramps, dredging beyond 

the Department of the Army 

(DA) permit authorized limits, 

installation of unauthorized 

piers or mooring buoys, etc.) 

would be addressed via 

enforcement and compliance 

requirements in applicable 

legal mandates.

. USACE can issue after-thefact permits to authorize such 

activities, or take other steps to 

resolve unauthorized activities.

US Coast Guard

(USCG)

Legal Authorities:

. OPA: administration of OPA 

planning and responses, 

investigations of collisions or 

allusions, and maintenance of 

aids to navigation may be 

suitable content. 

. ESA: Enforcement Authority.

. MSA: Enforcement Authority.

Legal Authorities:

. OPA: Administration of OPA

planning and responses, 

investigations of collisions or 

allusions, and maintenance of

aids to navigation may be 

suitable content. 

. ESA: Enforcement Authority.

. MSA. Enforcement Authority.

States and Territorial Governments

Commonwealth 

of the Northern 

Mariana Islands 

(CNMI) 

Legal Authorities:

. Coastal Resource Management 

Rules and Regulations.

. Non-Commercial Fish and Wildlife 

Regulations.

. Submerged Lands Act.

. Commonwealth Environmental 

Protection Act.

. Fish, Game and Endangered 

Species Act.

. Moratorium on Seaweed, Sea 

Grasses, and Sea Cucumber.

. Fair Fishing Act.

Legal Authorities:

. Coastal Resource Management 

Rules and Regulations.

. Non-Commercial Fish and Wildlife 

Regulations.

. Commonwealth Environmental 

Protection Act.

Activities:

. Under Coastal Resource 

Management regulations, issues 

and enforces permits in the CNMI 

coastal zone. Assesses damage 

to reefs and issues penalties for 

BACKGROUND
LEGAL AND POLICY SUMMARY

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Agency Planned Unplanned

. Protecting of Rays and Sharks.

. Shark Finning Prohibition.

unplanned coral impact.

. Under non-Commercial Fish and 

Wildlife regulations, assess 

damage to fish and wildlife.

. Under the Commonwealth 

Environmental Protection Act, 

assess damage to water quality 

and reef.

State of Florida (FL) Legal Authorities: 

Florida Department of Environmental 

Protection (FDEP)

. Florida State Constitutional 

authority over all natural resources 

in FL, including submerged lands -

Chapters 253 and 258, Florida 

Statue (F.S.).

. Florida Coastal Management 

Program - Chapter 380, F.S., Part II, 

Coastal Planning and Management.

. Environmental Resource Permit 

(ERP) Program - Chapter 373, Part 

IV, F.S.

. Joint Coastal Permit (JCP) 

Program - Sections 161.021, 

161.041 and 161.055, F.S., Rule 

62B-41, Florida Administrative 

Code (F.A.C.).

Legal Authorities: 

Florida Fish 

and Wildlife 

Conservation 

Commission

. Constitutional authority over 

marine life, wild animal life and 

freshwater aquatic life (Article 

IV, §9).

. Assigned the powers, duties, 

responsibilities, and functions to 

develop restoration and 

management techniques for 

habitat and enhancement of 

plant and animal populations; 

and respond to and provide 

critical technical support for 

catastrophes including oil spills, 

ship groundings, major species 

die-offs, hazardous spills, and 

natural disasters (20.331, F.S.).

Guam Legal Authorities:

. EO 78-37. Coastal Zone Resource 

Policies.

. EO 2013-05: Coral Reef Resource 

Policies.

. Fish and Wildlife Regulations.

. Guam Endangered Species Act 

(territorial law).

. Submerged Lands Act; and Guam 

Exclusive Economic Zone.

. Organic Act of Guam.

. Guam Environmental Policy Act.

. Guam Water Pollution Control Act.

. Guam Territorial Seashore 

Protection Act.

State of Hawaii (HI) Legal Authorities:

. Constitutional authority over all 

natural resources in HI, including 

submerged lands.

. State of Hawaii Endangered 

Species Act (state law).

. Hawaii Environmental Impact 

Statements (Hawaii Revised 

Statutes (HRS) T19, Ch.343).

Department of Health (DOH) 

Legal Authorities:

. Constitutional authority over all 

natural resources in HI, 

including submerged lands.

. State of Hawaii Endangered 

Species Act (state law).

. Environmental Response Law 

(HRS, T10, Ch. 128D)

Activities:
LEGAL AND POLICY SUMMARY

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Agency Planned Unplanned

. CWA §401 Water Quality 

Certification.

Activities:

Department of Land and Natural 

Resources (DLNR) 

. DLNR Umbrella Aquatic Mitigation 

Bank.

DOH:

. Potential enforcement related to

pollution discharges.

Commonwealth of 

Puerto Rico (Puerto 

Rico)

Legal Authorities:

. Organic Law of the Planning 

Board of Puerto Rico.

. Public Environmental Policy Law 

of the Environmental Quality 

Board.

. Organic Law of the Administration 

of Regulations and Permits.

. Puerto Rico Permits Process 

Reform Act

U.S. Virgin Islands 

(USVI)

Legal Authorities:

. Establishment of Wildlife and 

Marine Sanctuaries.

. Protection of Indigenous, 

Endangered and Threatened Fish, 

Wildlife and Plants.

. Water Pollution Control.

. Commercial Fishing.

. Environmental Protection.

. Virgin Islands Coastal Zone 

Management Act.

1.5 Coral Reef Ecosystems

Across regulatory and management agencies and associated mandates, there is no consistent 

definition of coral reefs (Table 2). These inconsistencies can lead, and have led, to challenges 

and reduced effectiveness when implementing strategies aimed at reducing and mitigating 

impacts to coral reefs. The definitions are provided to assist the reader work through this 

Handbook, not to redefine what is already written into statute and regulations. Readers should 

always confirm definitions with the appropriate permitting and management agencies.

As noted in Section 1.2, for the purposes of this Handbook, the following definitions are used. 

These definitions were chosen as they were inclusive of various regulatory definitions. 

Coral: Species of the phylum Cnidaria, including all species of the orders Antipatharia (black 

corals), Scleractinia (stony corals), Gorgonacea (horny corals), Stolonifera (organpipe corals 

and others), Alcyonacea (soft corals), and Helioporacea (blue coral) of the class Anthozoa; and 

all species of the families Milleporidea (fire corals) and Stylastreridae (stylasterid hydrocorals) of 

the class Hydrozoa.

Coral Reef: Limestone structures composed in whole, or in part, of living coral, skeletal 

remains, and including other corals, sessile marine animals, and plants.

BACKGROUND
CORAL REEF ECOSYSTEMS

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Coral Reef Ecosystems: The system of coral reefs and geographically and ecologicallyassociated species, habitats, and environment, and the processes that control its dynamics. 

Table 2: A summary of definitions for the terms "coral reef" and "coral reef ecosystem" across 

regulatory and management agency mandates.

Law, Statute, 

Regulation, or Agency Definition of Coral Reef Definition of Coral Ecosystem

Coral Reef Conservation 

Act (CRCA) of 2000

16 U.S.C. §§6401-6409

Any reefs or shoals composed 

primarily of corals.

Coral and other species of reef 

organisms (including reef plants) 

associated with coral reefs, and 

the nonliving environment factors 

that directly affect coral reefs, that 

together function as an ecological 

unit in nature.

EO 13089

63 Federal Register (FR) 

32701 (June 11, 1998).

U.S. coral reef ecosystems means 

those species, habitats, and other 

natural resources associated with 

coral reefs in all maritime areas 

and zones subject to the 

jurisdiction or control of the U.S. 

(e.g., federal, state, territorial, or 

commonwealth waters); including 

reef systems in the south Atlantic, 

Caribbean, Gulf of Mexico, and 

Pacific Ocean.

CWA §404(b)(1) 

Guidelines

40 CFR 230

Coral reefs consist of the 

skeletal deposit, usually of 

calcareous or siliceous 

materials, produced by the 

vital activities of anthozoan 

polyps or other invertebrate 

organisms present in growing 

portions of the reef.

South Atlantic Fishery 

Management Council’s 

Fishery Management 

Plan (FMP) for Coral, 

Coral Reefs and 

Live/Hardbottom Habitat 

of the South Atlantic 

Region (Coral FMP).

Hardbottoms, nearshore 

hardbottoms, deepwater 

hardbottoms (including 

deepwater banks), patch reefs, 

and outer bank reefs.

Caribbean Fishery 

Management Council’s 

FMP for Corals and 

Reef-associated Plants 

and Invertebrates

Biologically constructed reef 

framework with or without 

active coral growth.

The interdependence of species in 

a community with one another and 

with their non-living environment.
CORAL REEF ECOSYSTEMS

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Law, Statute, 

Regulation, or Agency Definition of Coral Reef Definition of Coral Ecosystem

Florida Coral Reef 

Protection Act 

F.S. 403.93345

1) Limestone structures 

composed wholly or partially of 

living corals, their skeletal 

remains or both, and hosting 

other coral, associated benthic 

invertebrates, and plants, or

2) Hardbottom communities, 

also known as live bottom 

habitat or colonized pavement, 

characterized by the presence 

of coral and associated reef 

organisms or worm reefs 

created by the 

Phragmatopoma species.

Coral reefs are among the most biologically diverse ecosystems on Earth, despite the fact that 

they comprise less than one percent of the planet’s area. Healthy coral reefs are important not 

only for their biodiversity, but for the essential ecosystem services they provide such as coastal 

protection, supporting fisheries, jobs, recreation, tourism, educational, social and cultural 

opportunities, and medicinal products. These ecosystem services are important socioeconomically to the financial welfare in the states and territories where coral reefs occur, and 

support the national economy, as well. For example, the northern 100 miles of the Florida Reef

Tract provides for more than 60,000 jobs and more than six billion dollars to the state economy 

each year (Johns, et al., 2001). However, coral reefs are declining in the United States, and 

around the world, due to an increasing array of both natural and anthropogenic impacts. 

Threats from global issues such as climate change and ocean acidification, natural events such 

as hurricanes and diseases, and localized human-induced effects such as unsustainable fishing 

practices, recreational impacts, sedimentation, and pollution individually and cumulatively affect 

coral reef health and functions. 

Coral reef ecosystems under the jurisdiction of U.S. federal, state, and territorial government 

agencies occur in both the Atlantic/Caribbean and Pacific Ocean basins (Figure 1). Within the 

Atlantic/Caribbean/Gulf of Mexico region there are natural coral reefs located in and around the 

USVI, Puerto Rico, Navassa Island, southeast Florida (including the Florida Keys), and the 

northwestern Gulf of Mexico. Coral reefs in the Pacific region occur in American Samoa, the 

Hawaii archipelago, the Pacific Remote Islands (Palmyra Atoll, Baker Island, Jarvis Island, 

Johnston Atoll, Kingman Reef, Wake Atoll, and Howland Island), Midway Island, and the 

Mariana Islands archipelago (CNMI, Guam, and the Pacific Freely Associated States (RMI, 

FSM, and Palau)).

Approximately 70 species of scleractinian corals inhabit the reefs in the Atlantic/Caribbean/Gulf 

of Mexico region (Spalding, et al., 2001). The coral reefs in the region include fringing, patch, 

spur and groove, and wall formations and can be found near shore, mid-shelf, and at shelf 

edges. Atlantic/Caribbean/Gulf of Mexico reefs contain fewer species of scleractinian coral 

compared to their Pacific counterparts. In recent years, the region’s reefs have significantly 

declined due to coral bleaching events, disease outbreaks, loss of herbivore populations, loss of 

framework building species, and introduction of invasive species. Compounding these losses, 

due to their proximity to heavily populated coasts, many of the region’s reefs are directly 

threatened by human activities such as coastal and upland development, vessel impacts, and 

unsustainable fishing. In NOAA’s 2008 State of the Reefs Report, the majority of key reef 

BACKGROUND
CHALLENGES AND OPPORTUNITIES

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resources in the Atlantic/Caribbean/Gulf of Mexico region were reported to be in poor or fair 

condition, with the exception of Flower Garden Banks, located over 100 miles offshore of Texas,

which was reported to have key resources in good or excellent condition (Waddell, 2008).

Figure 1: Map of tropical coral reef ecosystems within the United States. This map provides the 

general geographic distribution of U.S. coral reef habitat. For project-specific information, more 

detailed habitat maps should be consulted and in-water assessments may be required. Image 

courtesy of NOAA.

Pacific coral reefs have similar formations and can form variable geomorphic types, including 

fringing and barrier reefs, atolls, and numerous smaller forms like pinnacles, knolls, patch reefs, 

as well as coral reef shoals or banks. While many reefs can be found close to heavily populated 

islands, others are remote and far removed from many human and land-based impacts. Pacific 

reefs are very diverse, with some regions containing more than 60% of known tropical coral 

species (Veron, 2000). Pacific reefs are affected by many of the same stressors impacting 

Atlantic/Caribbean reefs. However, U.S. Pacific reefs are in much better condition overall than 

their Atlantic/Caribbean/Gulf of Mexico counterparts. U.S. Pacific reefs are rated good or 

excellent in NOAA’s 2008 report, with the exception of harvested reef fish species and 

macroinvertebrates, which are reported to be in poor condition in the main Hawaiian Islands and 

fair condition throughout the rest of the Pacific.

1.6 Challenges to, and Opportunities for, Effective Coral Reef Impact 

Avoidance, Minimization, Compensatory Mitigation, and Restoration

Coral reefs are subject to numerous local, regional, and global stressors. Managers and 

regulators working to address impacts to coral reefs are further constrained by the difficulty in 

restoring and replacing these complex systems. Natural reefs are biologically, chemically, 

physically, and morphologically complex; take many years to develop; and are difficult to 

restore. Many coral species are particularly slow-growing (one-tenth of an inch per year) and 

long-lived (decades to centuries), resulting in a long response and replacement time.

While existing guidance and tools have been developed for stream and wetland mitigation and 

restoration, it is necessary to develop guidance and tools specific to coral reef systems. The 

development, structure, and function of coral reefs are quite different from the development, 

structure, and functions of streams and wetlands. Therefore, the guidance and tools needed
CHALLENGES AND OPPORTUNITIES

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for coral reef mitigation will be substantially different. Some basic principles for stream and 

wetland mitigation might be useful for coral reef mitigation, but ecologically successfully coral 

reef mitigation requires that those basic principles be translated for coral reefs. Mitigation 

and restoration technology for freshwater and terrestrial systems has a longer track record 

and has been refined through substantial trial and error experience. When working in the 

marine environment, other factors such as determining boundaries of site ownership, site 

protection, the remote and hazardous nature of working underwater, and long-term 

maintenance of sites present challenging hurdles and are presently managed on a case-bycase basis. It is important to note that the initial focus should always be on avoidance and 

minimization. It is possible that through such measures compensatory mitigation may not be

needed. If unavoidable loss of coral reef resources is going to occur, compensatory 

mitigation is likely needed. In marine systems, environmental and anthropogenic variables 

are more difficult to control compared to terrestrial systems. These factors tend to increase 

the cost and uncertainty of activities intended as compensatory mitigation or restoration of 

lost coral reef area and associated services and functions relative to similar efforts in 

terrestrial ecosystems, reinforcing the need to avoid impacts as much as practicable.

Historically, compensatory mitigation for coral reef losses has been poorly designed and

documented, and inadequately monitored so that demonstration of success is significantly 

lacking (Bentivoglio, 2003 and Yoshioka, et al., 2004). While a variety of mitigation options 

have been implemented, many have only been implemented a few times. Therefore, there is 

not a complete understanding of what types of coral reef compensatory mitigation and 

restoration can be successful and what thresholds are necessary for coral reef recovery. 

Work continues to be done to address these gaps.

In the Pacific, a few of the compensatory mitigation efforts have included education, 

establishment of marine protected areas (MPAs), watershed recovery actions to improve a 

degraded coral reef, coral transplantation, coral relocation, and installation of mooring buoys. 

Based on recent scientific findings associated with coral recovery, some of these strategies 

for compensatory mitigation may not be as effective as originally assumed (Bentivoglio, 2003 

and Yoshioka, et al., 2004). Chapter 4 identifies some of the challenges and considerations 

for various mitigation options. In the Atlantic and to a lesser degree in the Caribbean, 

boulder-based artificial reef construction was historically a common mitigation activity. 

However, boulder-based artificial reef construction is becoming less common given the 

challenges of artificial reefs fully replacing all the functions and services (i.e., equitable 

compensation) of a natural coral reef (Gilliam, 2012 and Thanner et al., 2006). Most of the 

efforts taken to date to compensate for coral reef impacts have focused on indirect impacts, 

and seek to improve the long-term health of coral reef resources. For example, placement 

and maintenance of aids to navigation can directly and indirectly improve the quality of coral 

reef habitats and prevent future loss of habitat by preventing ship groundings, but will not 

address the replacement of functions and services lost in a coral reef area. 

More recently activities in an adjacent watershed of a nearby land mass or island (e.g., 

reforestation, storm water controls, wetland enhancement) have been considered as

attractive components of compensatory mitigation. While these efforts usually target 

replacement of lost resources, it still represents a net loss in coral reef area. Greater effort is 

also needed in developing and defining ecological assessment tools and sensitive indicators 

to ensure measurable performance standards that can evaluate the outcome or success of a 

particular mitigation or restoration action.

BACKGROUND
CHALLENGES AND OPPORTUNITIES

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Further complicating the implementation of successful compensatory mitigation are the ongoing 

effects that climate change and ocean acidification have on coastal and coral reef ecosystems 

and, by extension, on the ability to successfully manage implemented compensatory mitigation 

activities. While direct global changes such as increased temperature and acidification cannot 

be controlled by the project proponent or coral reef manager implementing the compensatory 

mitigation action, there is growing scientific understanding of the mechanisms by which these 

drivers interact with and exacerbate other stressors that project proponents or coral reef 

managers may be able to control. As a result, there is a rapidly expanding body of theory and 

tools to help with designing coral reef mitigation or restoration activities to be as effective as 

possible within the context of these changes. Stein et al., 2014 provides a comprehensive 

review of this information for all natural resources, and a tailored version of the approach for 

coral reef management is under development (West et al., 2016). Therefore, while the 

Handbook aims to focus on the current status of mitigation planning and response, more 

information is likely to be available in the future to help project proponents and coral reef 

managers make adjustments to maximize management success in light of the shifting 

environmental context of climate change and ocean acidification.

The sections that follow lay out general structured frameworks for addressing planned and 

unplanned impacts to coral reef ecosystems. These frameworks are not inclusive of all 

agencies, regulations, policies, and guidance so project proponents and RPs should always 

consult with the appropriate agencies and only use this information as a reference. There are 

certain elements of each process that can be consistent regardless of the type of impact that 

might occur. However, due to the unique circumstances of each project or activity, and the 

large variations among affected habitats, there will need to be individual consideration on a 

project-by-project basis. While it is possible to develop comprehensive coral reef restoration 

strategies, these strategies require substantial specialized planning, conservative assignment of 

benefits, long recovery horizons that account for climate change, robust adaptive management, 

well-defined financial assurances, and well-established partnerships. Implementing such 

strategies is usually very costly, and again emphasizes the strong need to focus on avoidance 

as the recommended course of action wherever possible.

It is also critical to highlight that discussion and approaches tend to center around coral. 

However, the effort is clearly focused on coral reef ecosystems. In coral-dominated systems, it 

is assumed that if corals can be recovered, or successfully show a trajectory toward recovery, 

over the long term the coral reef ecosystem will recover and subsequently all the functions and 

services provided by the coral reef ecosystem will successfully be restored. Additionally, there 

are numerous examples of other resources that when dominant will drive the mitigation process,

such as mangrove systems, seagrass beds, algae beds, or unique assemblages of fish or

crustaceans. Although not addressed in this Handbook, a note should be made that planned or 

unplanned events that may impact coral reefs may also impact other non-natural resources 

including infrastructure (e.g., piers, aids to navigation, and signage) or historic resources such 

as shipwrecks. These types of resource impacts should be handled on a case-by-case basis 

with the appropriate agencies.
PLANNED IMPACT EVALUATION FRAMEWORK

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2.0 EVALUATION FRAMEWORK FOR PLANNED IMPACTS TO CORAL 

REEF ECOSYSTEMS

Planned activities in tropical marine waters such as harbor improvements (e.g., deepening, pier 

and breakwater construction or repairs), shoreline hardening, outfall construction, construction 

of offshore energy and aquaculture facilities, or delineation of anchorage areas often impact 

corals. This chapter is intended to provide a general framework to guide project proponents and 

agency staff through the steps for planning, permitting, and implementing planned activities.

For planned activities that are likely to impact coral reefs (e.g., dredge and/or fill, shoreline 

development, in-water construction, and capital improvement maintenance projects), multiple 

federal, state, and territorial permits may be required. There are certain elements of the 

process for assessing the impacts to coral reefs associated with a planned activity that are 

consistent, regardless of the type of impact that might occur. However, due to the unique 

circumstances of each project or activity, the large variations among affected habitats, and the 

variations in requirements for different permitting authorities, permitting authorities will consider 

each project individually to determine the appropriate process and requirements. Depending on 

the impacts associated with a planned activity, the generalized process described in Figure 2 

may apply, as is, or may include additional steps or multiple iterations. The size and type of the 

impact will likely affect the complexity of the response process. 

It is always recommended that the relevant permitting authorities and land management 

agencies be consulted as early as possible in the planning process to avoid unnecessary 

costs and time delays. At a minimum, a project proponent should consult with the USACE 

about permit requirements. Pre-application meetings with USACE and appropriate agencies—

such as EPA, NMFS, FWS, and state and territorial marine resource regulatory and 

management agencies, discussed further in Section 2.1.1—provide a useful venue to consult 

early with the applicable federal, state, and local agencies.

The following generalized planning steps may be needed for work with the potential to impact 

coral reefs, depending on the scope of the project.

. Map and characterize coral reef resources within the impact area.

. Quantify direct and indirect impacts of the project as proposed (including permanent 

and temporary effects).

. Analyze alternative project sites and designs as early as possible in the process.

. Define post-project actions such as monitoring and adaptive management.

If there will be unavoidable loss of coral reef resources, then the next steps may be needed.

. When required, develop a mitigation plan including identification of mitigation sites and 

determination of the amount of compensatory mitigation required (e.g., functional or 

conditional assessment).

. Assess resources at compensatory mitigation site(s) and estimate recovery potential.

. Develop a comprehensive biological and water quality (e.g., turbidity) monitoring plan 

where data collection occurs before, during and after project 

construction/implementation. The purpose of this monitoring is to assess the actual 

extent of impacts and to detect and correct problems as they develop.

. Implement the compensatory mitigation plan including any associated construction 

PLANNED IMPACTS PLANNED IMPACTS
PLANNED IMPACT EVALUATION FRAMEWORK

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management, site protection, financial assurances, performance standards, monitoring 

and long-term management activities required by the permitting authority.

. Review plans for post project actions, such as monitoring to assess progress toward 

performance standards.

. Implement potential adaptive management measures or additional mitigation if the 

performance standards are not met. 

This generalized process is depicted in Figure 2. These steps for planned impacts will be 

considered and described sequentially in more detail throughout Chapter 2. 

Figure 2: A generalized process for addressing planned impacts to coral reefs.
PROJECT PROPONENT PLANNING – PRE-APPLICATION

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The generalized process may be modified based on the requirements of various permitting 

authorities, or on a project-by-project basis depending on the degree to which coral reef 

resources may be impacted by a planned activity. For planned activities, the alternatives 

analysis involves early consideration of how to avoid and minimize adverse impacts to coral 

reefs, and what might be required for compensatory mitigation if there are unavoidable losses 

to coral reefs. The project proponent should consult with the permitting authorities and other 

key agencies regarding alternative technologies for project construction, such as alternative 

dredging technologies to maximize impact avoidance. In addition, the project proponent will 

also have to consider cumulative impacts of the planned activity in relation to other past, 

present, or reasonable foreseeable activities in the vicinity. 

2.1 Project Proponent Planning 

All in-water coastal construction will likely need a suite of federal, state, and local permits (such 

as a DA permit or a State CWA §401 Water Quality). Federal actions, including federal permit 

decisions, must comply with NEPA and other applicable federal laws (e.g., EFH consultation 

under MSA §305(b), ESA, and FWCA). States and territories often have equivalent state or 

local procedures for many of their permitting decisions. Project proponents should identify 

those required permits and meet with the permitting authorities early in the planning process. 

Each of these permits and authorizations have specific information needs that are best identified 

and coordinated with relevant agencies early. For example, if there are coral species that are 

listed under ESA, or designated critical habitat, compensatory mitigation plans for various 

permitting authorities, such as a DA permit, are typically incorporated as part of the overall 

proposed action. This unique consideration reinforces the importance of working closely with 

NMFS on how to appropriately address compensatory mitigation when consulting under ESA. 

2.1.1 Pre-Application Agency Consultation and Coordination

Pre-application meetings with the appropriate permitting authorities at the federal, state, 

territorial, or local level are strongly recommended to discuss clearance protocols, survey 

methods, required permits and consultations, project-specific issues or challenges with 

potential compensatory mitigation activities if unavoidable impacts are likely, and other 

information that would likely be required for a particular project. In these application meetings, 

requesting attendance of other agencies with permitting or reviewing authorities for the project 

is encouraged. This may include, but is not limited to, USACE, EPA, NMFS, FWS, and the 

state and territorial marine resource, water quality, and coastal zone regulatory and 

management agencies. If there will likely be unavoidable loss of coral reef resources that may 

require compensatory mitigation, project proponents are highly encouraged to consider 

reserving a contingency of funds early in the planning process to address potential information 

and planning needs in developing and implementing a mitigation plan (see Section 2.3.2). 

Early discussions with the appropriate regulatory agencies will help determine potential 

contingency amounts. 

Project proponents and RPs are reminded that a permit or approval from one agency does not 

negate other permit requirements. An activity may require permits from federal agencies as well 

as state and territorial agencies. 

PLANNED IMPACTS
PROJECT PROPONENT PLANNING – PRE-APPLICATION

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EXAMPLE PROCESS FROM FWCA

The FWS has an evaluation framework for water resources development under the FWCA that many 

may find useful in evaluating the alternatives, potential impacts, and compensatory mitigation needs for 

projects. This framework shows an alternative format for structuring the permitting process. As is 

highlighted in this example, each project proponent agency or permitting authority has similar but 

different methods for evaluating impacts. Please be sure to talk with the appropriate permitting 

authority to see what may be necessary for their processes. The key information the FWS looks for in 

their evaluation are:

1. Specify the resources likely to be evaluated. 

a) Identify the types, kinds, or categories of resources of concern (habitat, species, and life stages). 

b) List types of impacts to be evaluated. 

2. Adopt an evaluation method.

a) Determine how project impacts on coral reef resources will be measured.

b) Select a method that will measure change in quantity and quality of each resource category.

3. Define the baseline conditions and significant resources likely to be impacted. 

4. Determine the most probable future resource condition without a project. Describe the difference 

between the future without and the future with the project. 

5. Define Coral Reef Resource Planning Objectives. 

a) Identify opportunities to conserve resources.

b) Identify obstacles that may hinder meeting objectives. 

6. Define the project alternatives, including project design, implementation, and operational-related 

activities that may impacts fish and wildlife resources. 

7. Determine the most probable future resource condition with identified Project Alternatives: assess 

the future with the project. 

8. Define impacts: Identify and describe the effects of project alternative plans on coral reef 

resources.

a) Compare conditions with and without the project.

b) Describe all impacts (direct, indirect, and cumulative (consider location of impact, duration of 

impact, and magnitude of impact on coral reef resources)).

9. Evaluate and compare project alternatives: 

a) What is the significance of coral reef resources? 

b) Will impacts to coral reef resources be avoided or minimized? 

c) Has sufficient compensatory mitigation been planned to offset unavoidable impacts?

10. Formulate conservation measures: avoid, minimize, rectify (repair, rehabilitate, or restore), reduce 

or eliminate impact over time (maintenance operations), compensation (replace resources). 

11. Develop recommendations: 

a) Identify projects for compensatory mitigation.

b) Scientifically monitor mitigation.

c) Define performance standards for mitigation.

d) Effectiveness of implemented mitigation.

e) Best management practices (avoid/minimize).

f ) Adaptive management.

(Adapted from Smalley and Mueller, 2004.)
PROJECT PLANNING – QUALITATIVE RESOURCE CHARACTERIZATION

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2.1.2. Mapping and Qualitative Characterization of Coral Reef Resources 

Part of the project planning and permitting process includes data collection. Data about the 

resources in the proposed project area are required to support and inform the planning and 

permitting process. Diver-conducted surveys of the sea floor and benthos are generally 

required to characterize the coral reef and other biological resources that are likely to be 

impacted by in-water construction work. A variety of acceptable methods can be employed to 

collect the information necessary to adequately characterize the biological resources to guide 

avoidance and minimization activities and assess compensatory mitigation requirements for 

unavoidable adverse impacts. Two tiers of data collection categories are generally 

recommended. 

Tier 1: Qualitative Assessment The first step in this process is a qualitative characterization 

of the types of habitat and communities found in the project footprint and adjacent areas. 

Depending on the size and extent of impact, the qualitative characterization can range from a 

diver geo-locating major features, habitat boundaries, or sensitive resources, to a more detailed 

and georeferenced habitat map. Based on the qualitative assessment, a permitting authority 

may determine that no significant adverse impacts are likely to result and no further surveys, 

impact assessments, or mitigation would be needed. A permitting authority may alternatively 

determine that additional quantitative information (Tier 2) is needed. 

Tier 2: Quantitative Assessment Based on the Tier 1 qualitative assessment/habitat map, the 

need for additional quantitative survey of corals and other habitats can be determined. This 

determination is predicated on the complexity of the coral reef resources, the size of the impact 

area, and extent of expected impacts. If impacts cannot be avoided or mitigated with common 

best management practices (BMPs), then quantitative assessments may be necessary. 

The two tiers of biological assessment (qualitative and quantitative assessments) are described 

in more detail below, and in Section 2.1.3. While this section focuses on planned activities, the 

mapping methodologies discussed herein are often useful for unplanned activities. Project 

proponents and RPs need to work closely with the permitting authorities or resource trustees to 

determine assessment requirements and appropriate methodologies. 

2.1.2.1 Qualitative Coral Reef Assessment and Habitat Mapping 

A qualitative benthic assessment and characterization is a critical first step in determining the 

distribution and location of habitats and other resources within and adjacent to a planned project 

site. The characterization should cover areas of expected direct and indirect impacts from the 

proposed action(s). The distribution of habitats and the occurrence of any resources of concern 

(e.g., endangered species or unusually large coral colonies) within a project site may guide the 

development of a scientifically defensible quantitative survey design for the habitats and strata 

of concern, including coral reefs. 

Due to the highly variable nature (e.g., size, footprint, location, scope, and scale) of coastal 

development projects there is no “one size fits all” approach for coral reef qualitative surveys. 

For small projects or homogeneous sites, a rudimentary map or general characterization of the 

area that includes resources of concern may be sufficient. However, most projects can benefit 

from development of a qualitative benthic habitat map as a first step. Various federal, state, or 

territorial agencies may have existing characterization maps that may contain some of the 

PLANNED IMPACTS
PROJECT PLANNING – QUALITATIVE RESOURCE CHARACTERIZATION 

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information needed. Once again, it is important for project proponents to discuss with the 

appropriate permitting authorities what may be needed for a specific project and what readily 

available information may be referenced. 

Qualitative surveys and benthic habitat maps have important applications. Habitat maps can 

provide an overall spatial perspective to the project area and its resources, provide information 

used to inform the alternatives analysis (see Section 2.2), guide the avoidance and minimization 

measures, and provide information for planning appropriate compensatory mitigation for 

unavoidable adverse impacts (see Section 2.3). Additionally, habitat maps can be used to 

inform, plan, scale, and determine the quantitative sampling approaches, strata, and the 

samples needed per strata to provide an acceptable level of confidence in the site 

characterization (see Section 2.1.3). The qualitative habitat characterization may also be used 

for development of performance standards for the mitigation site and comparisons of the 

mitigation site(s) with the impact site. 

Numerous habitat mapping methods exist that can adequately characterize a project area. 

Methods utilized can be based on remote sensing technologies and/or in-situ data collection. 

The method selected depends on multiple factors, including the size, location, and scale of the 

project site, desired minimum mapping unit, advantages and disadvantages of methods 

available, available data, resources, capacity, and logistical limitations 

The use of unique or alternative habitat mapping efforts should be discussed prior to application 

with the permitting authorities to ensure appropriate compliance. Habitat maps derived from 

remote sensing products may have significant limitations in data interpretation and may require 

in-situ validation of classifications. However, diver-based in-situ methods have significant scale 

limitations for large projects; hence, larger projects may require a combination of remote 

sensing and in-situ (both instrument and diver) methodologies to produce a reliable habitat map. 

Habitat maps should have a well-defined methodology description so the user can understand 

how the maps were generated and the information the maps contain. As much as is practical, 

the methods should be standardized or congruent with existing methods. Terminology and the 

classification scheme used should be clearly defined and consistent with the Coastal and 

Marine Ecological Classification Standard (June 2012) as adopted by the U.S. Federal 

Geographic Data Committee. 

It is recommended that habitat maps contain a common set of information that provides specific 

information key to the overall project planning, natural resource characterization, and permitting 

review process for the proponent and regulatory agencies. Based on a review of the benthic 

habitat mapping conducted to date for planned activities, the recommended common 

information includes: 

. Survey dates. 

. Location (geo-referenced latitude and longitude when possible). 

. Name of person(s) or party conducting survey. 

. Project area defined, which includes area of the direct impact and potential areas 

subject to secondary impacts. 

. Methodology description: 

 A detailed description of the method used to collect data and generate the maps. 

 A clear description of how habitats are defined that include biotic (e.g., benthic 

organisms) and abiotic features (habitat geomorphology) of the area. 
PROJECT PLANNING – QUALITATIVE RESOURCE CHARACTERIZATION

USCRTF Handbook on Coral Reef Impacts – December 2016

29

 Minimum mapping unit or the amount of area surveyed within the project area.

 The classification system used for habitats and the resources assessed (e.g., 

NOAA National Centers for Coastal Ocean Science, 2007).

. Identification of mapping methods for other biological resources (e.g., fish, 

invertebrates, algae, seagrass, ESA-listed species, and other species of concern). 

. Review of existing data (light detection and ranging (LiDAR), multiband imagery such 

as World-View 2/3, Quickbird, IKONOS satellite imagery, backscatter and multi-beam 

data, or other digital elevation model data) and habitat maps (NOAA Habitat Benthic

Maps or other area-specific maps) within and adjacent to the project area. 

Additionally, some components and information to consider when generating habitat maps 

include:

. Estimate total area mapped (in acres (ac) or square meters (m2)).

. Estimate total area of proposed project footprint (ac or m2), including potential area of 

direct and indirect impacts.

. Estimate total area of each habitat within the mapped area, impacted by direct project 

footprint, and if possible, the area of secondary impacts (ac or m2).

. Identify, locate, and highlight boundaries of habitat geomorphology (e.g., reef 

geomorphology zone and reef geomorphology structure).

. Identify, locate, and characterize coral abundance, colony morphologies, and sizes 

(e.g., particularly large, unique, or rare colonies) to the extent feasible within the project 

area.

. Identify, locate, and characterize algal abundance and key functional groups within the 

project area.

. Identify, locate, and characterize invertebrate groups or species considered important in 

the project area.

. Identify, locate, and characterize known threatened or endangered species listed under 

ESA.3

. Identify and locate nearby habitats that may provide important ecological links (e.g., 

seagrass beds and mangroves).

. Identify areas of special interest or regulatory oversight such as special aquatic sites 

(CWA 404(b)(1) guidelines), EFH, ESA designated critical habitat, MPAs, or other 

spatial designations.

. Highlight areas identified as special high-value or high-function features (e.g., protected 

species, breeding areas, very large coral heads, high density coral).

For small projects with minimal impacts, a qualitative survey and map may be all that is 

required. The EFH provisions of the MSA §305(b) (50 CFR Part 600) state that the level of 

detail needed for an EFH assessment should be commensurate with the complexity and 

magnitude of the potential adverse effect of the action. Thus, for larger projects or projects that 

impact especially high quality biological resources, additional quantitative biological

assessments are likely to be needed; these are discussed in Section 2.1.3.

Figure 3 is an example of a qualitative benthic habitat map for relative coral abundance at 

Nawiliwili Harbor, Hawaii. The Nawiliwili Harbor habitat map was based on the standard 

mapping protocol used by the FWS Pacific Islands Fish and Wildlife Office. The habitat map 

showed that most of the coral habitat is outside of the federal navigation channel and can be 

 

3 Coral reef species identification should be as consistent as possible given established references, but 

field identification may be inconclusive.

PLANNED IMPACTS
PROJECT PLANNING – QUANTITATIVE RESOURCE CHARACTERIZATION

USCRTF Handbook on Coral Reef Impacts – December 2016

30

avoided during dredging. The map also showed that there are some coral areas that may be 

subject to indirect impacts from sedimentation. This habitat map helped provide useful 

information to the project proponent, USACE, in determining potential adverse impacts, and 

avoidance and minimization measures for those impacts, early in the planning process.

Figure 3: Habitat map of Nawiliwili Harbor, Kauai, Hawaii. The map shows the areas to be 

dredged within the federal channel as hatched. Coral abundance is shown in shades of blue. 

The proposed dredging avoids direct impacts to corals, but has potential indirect impacts to 

corals from sedimentation (habitat map courtesy of Mr. Tony Montgomery, FWS Honolulu).

2.1.3 Quantitative Coral Reef Resource Surveys

Once adequate habitat mapping, as determined by the appropriate permitting authorities 

based on the project scope and potential impact, has been conducted for a planned coral reef 

impact site, the coral reef and other biological resources located within the area may need to 

be assessed quantitatively. Permitting authorities and resource trustee agencies should be 

consulted to reach agreement on any additional, and more detailed data that may be 

necessary. Additional information gathered is also intended to be integrated into the habitat 

map. If additional assessment is required, recommended sampling considerations and 

reporting expectations are described in this section. 

Assessment of the temporal and spatial extent of direct, indirect, and cumulative impacts should 

be considered as part of a complete biological resource survey. Even within a single state or 
PROJECT PLANNING – QUANTITATIVE RESOURCE CHARACTERIZATION

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31

territory, depending on the location of the project, there may be various permitting authorities 

that have their own survey protocols and minimum reporting requirements (e.g., Florida Keys 

National Marine Sanctuary (FKNMS) Benthic Survey Protocols) that should be consulted and 

taken into consideration when developing project-specific biological resource survey 

methodologies.

The following is a general list of recommended steps and data to fully describe the impacted 

area and design the compensatory mitigation, if required. This information is based on a review 

of biological resource surveys conducted to date for planned activities. The suite of parameters 

measured for a quantitative assessment will likely be project-specific. Some items on this list 

will be unnecessary, whereas other types of data not on this list may be included. In addition to 

the project footprint, adjacent coral reef areas may need to be surveyed to address potential 

indirect impacts. In some cases, it is also useful to quantitatively assess control or reference 

site(s) outside of the area of project impacts. This data can inform potential compensatory 

mitigation actions if unavoidable adverse impacts are likely, or the assessment of impacts from

regional stressors not related to the project.

. Divide area into strata and determine the amount of quantitative sampling needed to 

reliably characterize the abundance of key benthos, including corals.

. Select methods for biological resource surveys (e.g., number of surveys, 

sampling stratification; locations, type of transects (belt, quadrat, etc.), or 

number of transects per site).

. Assess abundance and distribution of protected species (including ESA listed 

species): species, species distribution and density, location, noted behavior, and 

expected use of area.

. Determine biological, physical, and chemical data needed to characterize the 

site. 

. Assess coral species, species richness, size class abundance, density, partial 

coral mortality, and morphology (branching, encrusting, table, massives, etc.). 

. Asses algal species and percent cover.

. Assess sponge genera, size class distribution, and density.

. Assess fish species abundance by size class.

. Determine benthic percent cover, including coral, algae, and general substrate (mud, 

rock, sand, etc.).

. Determine topographic complexity (rugosity or complexity) for each habitat type.

. Collect fine-scale bathymetry to document reef geomorphology may be needed in some 

cases. This information is often necessary for hydrodynamic modeling and calculations 

of frictional drag and wave propagation across reefs to understand the potential services 

the reef is providing in terms of shoreline protection.

. Collect planar/various other photographic images

. For the Atlantic/Caribbean, collect Octocoral density, Octocoral genera richness and 

Octocoral size class distribution.

. Document any significant variation of the coloration, bleaching, paling, disease, and 

partial colony mortality of the corals, to understand the current stress the reefs may be 

under, and their potential resiliency to indirect impacts. 

As noted above, this is a general list of steps and data to be collected for a quantitative 

assessment and other measures may be required for some projects. 

The following information is also desirable for some projects that require compensatory 

PLANNED IMPACTS
PROJECT PLANNING – QUANTITATIVE RESOURCE CHARACTERIZATION 

USCRTF Handbook on Coral Reef Impacts – December 2016 

32

mitigation to model replacement and recovery for a compensatory mitigation site. This 

information can be useful for both the impact area as well as any affiliated compensatory 

mitigation site in which unavoidable adverse impacts are likely. 

. Baseline size frequency structure – Measures of the spatial distribution or frequency 

of coral sizes by morphology within the survey area at the impact site. 

. Recruitment rates (best fit, calculated, or observed) – Estimates of the recruitment 

rate for new coral colonies in the survey area at the impact site. 

. Proportional survival – Estimates of coral survival over time in relation or in proportion 

to the overall survey area. Determined from change across size frequency distributions 

gathered at the planned impact site prior to construction. 

. Growth – Estimates of the growth rate of the coral within the survey area. Best fit: 

measured at impact site, mitigation site, and/or inferred from literature. 

Additional useful information for quantitative surveys regarding the sampling design and effort, 

transect location, surveys of additional organisms, and conventions for organism counting is 

summarized below. 

Sampling design: In some cases it may be desirable to stratify project areas into separate 

habitat categories (e.g., shallow vs. deep, horizontal vs. slope, rugged micro-relief vs. flat, 

middle vs. outer reef, fore vs. back reef, high vs. low coral density). Targeted fixed sites may 

provide more useful information to determine temporal changes and are recommended for 

indirect impact sites and mitigation sites. 

Sampling effort: The appropriate number of sampling locations per habitat and number of 

transects per sampling site depend on project size and site characteristics. If previous data 

exist, such as the type of information listed earlier in this section, conducting a power analysis 

or other methods are recommended to assist in determining the appropriate number of 

transects per habitat. Other methods to determine the appropriate number of sampling sites per 

habitat and transects per sampling site may include species-area curves, performance curves, 

bootstrap estimates, and Pearson’s product moment correlations. If no such data exist, it is 

recommended that state, federal, and academic coral reef experts be consulted to determine 

appropriate sample size. 

Transect location: Biological resource surveys, for the purposes of assessing planned 

impacts, should be conducted at each sampling site identified on the habitat map of the impact 

site. Benthic transects should be oriented in the way that would best characterize the coral reef 

community. Typically transects are oriented perpendicular to the reef slope or parallel to depth 

contour lines. However, other methods depending on the reef characteristics, may include 

transect plots along the gradient of reef slope, or a plotless intercept method in a “fish bone” 

design (i.e., a long transect following the slope gradient and short transects perpendicular to the 

long transect following depth contours as in Loya, 1978). If there is minimal or no reef slope 

(i.e., similar depth contour), a random heading (0 ̊ to 360 ̊), rounded to the nearest 10 ̊, can be 

generated and used to determine the direction of transects. In the case of spur-and-groove 

habitat, it may be appropriate to orient transects along the coral habitat “spurs” in order to 

characterize the coral reef community impacted and avoid confounding the results with sand 

habitat (i.e., “grooves”). Heading restrictions are appropriate to ensure transects do not overlap 

and are kept within the specific habitat being surveyed. 
PROJECT PLANNING – FUNCTIONAL VS. CONDITION ASSESMENT

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Additional organism surveys: Additional surveys for keystone organisms should be identified 

with the appropriate regulatory agencies in pre-assessment coordination. These additional 

organism surveys may target important invertebrate species such as specific urchin groups, 

unique mollusk or crustacean assemblages, crown of thorns starfish, soft coral, sponges, 

observed large fish, sea turtles, and protected coral species. 

Organism counting for scleractinian coral, octocoral, and sponge surveys: A variety of 

conventions exist to determine which coral, sponge, octocoral, and other colonies are counted 

in sampling (e.g., entire colony within belt/quadrat, any part within the belt/quadrat, greater than 

or equal to (≥) 50% within the transect). Zvuloni, et al. (2008) provide a review of sizefrequency distribution biases that result from different counting methods with line-intercept, 

quadrat, and belt transect methods. Zvuloni, et al. (2008) provide equations to correct for 

biases identified in these common sampling methods, and also offer suggestions for nonbiased 

methodologies. The effects of sampling bias are minimized by using the same methodology 

within a Before-After Control-Impact (BACI) design framework. Once a method is selected, it 

must be used in all surveys (i.e., pre- and post-project, inside/outside impact area, mitigation 

sites, and future monitoring) so as to produce comparable results. Methods that are known to 

generate size-frequency distribution biases should implement the proper mathematical 

corrections to accurately characterize a site (see Zvuloni, et al., 2008 for details).

Absent adequate assessment, the precautionary principle would be applied and reasonable 

assumption would be used to err on the side of the resource, presuming that resources are 

present and impacts will need to be avoided and minimized. If the regulatory agency believes 

compensatory mitigation may be necessary, an adequate assessment should be done to 

determine the activity-specific compensatory mitigation requirements needed to offset the 

impacts. 

2.1.4 Functional Assessment vs. Condition Assessment

The 2008 Mitigation Rule recommends that condition or functional assessments be used to 

assess the extent of impacts, where these tools are developed and available. Both functional 

and condition assessments examine functions, but use different approaches. Functional 

assessments generally evaluate individual functions. Whereas condition assessments 

aggregate functions to determine the ecological integrity of an aquatic resource, and thus infer 

the level of functions being performed (Stevenson and Hauer, 2002; Fennessy et al., 2007; 

Stein et al., 2009). In other words, the condition of an aquatic resource is an integration of its 

functions, and if its functions are performing at a high level, its condition will also be rated at a 

high level (Fennessy et al., 2007). Condition assessments use an index or scoring to provide a 

measure of the ecological condition of a reef. Functional assessments, however, use indicators 

to estimate or infer the level of each function being performed (e.g., energy absorption, nitrogen 

fixation, nursery habitat, and food production) performed by a coral reef. At this time, the coral 

reef assessment methods in use are best described as condition assessments. 

The purpose of compensatory mitigation is to compensate for the loss of coral reef and 

affiliated ecosystem functions and services. Table 3 below, presents some of these 

ecosystem functions and the corresponding services for coral reefs. Based on the 

experience of coral reef permitting authorities in the Atlantic, Caribbean, and Pacific, the 

ability to conduct effective functional assessments is currently limited by technology, state of 

the science, cost, and the timeframe necessary to make decisions. 

PLANNED IMPACTS
PROJECT PLANNING – FUNCTIONAL VS. CONDITION ASSESMENT

USCRTF Handbook on Coral Reef Impacts – December 2016

34

Table 3: Ecosystem functions and corresponding goods and services for coral reefs (adapted 

from Costanza, et al., 1997, and Moberg and Fouke, 1999).

Ecosystem Functions Corresponding Goods 

and Services Examples within Coral Reefs

Maintenance of the integrity of 

ecosystem response to 

environmental fluctuations through 

capacitance and damping.

Regulation of 

disturbances.

Coastal protection and 

sediment retention.

Recovery of mobile nutrients and 

removal or breakdown of excess or 

xenic nutrients and compounds.

Waste treatment. Nitrogen fixation, CO2

assimilation, and Ca budget 

control.

Regulation of trophic dynamics 

within populations.

Biological control. Feeding places within an 

ecosystem and between 

ecosystems.

Provision of habitat for resident and 

transient populations.

Refugia. Habitat and nursery space.

Provision of extractable food as a 

portion of gross primary production.

Food production. Fish, invertebrates, algae, 

plants and other edible 

products.

Provision of extractable raw 

materials as a portion of gross 

primary production.

Raw materials. Sand, coral block, algae and 

plants, and materials for 

medicine, curio, and jewelry.

Provision of recreational 

opportunities.

Recreation. Tourism, recreational fishing, 

sport.

Provision of non-commercial use 

opportunities.

Cultural. Aesthetic, cultural, religious, 

spiritual and intrinsic values.

The 2008 Mitigation Rule recommends the use of functional or condition assessments, or other 

suitable metrics. Some individual federal, state, and territorial agencies, non-governmental 

organizations, and academia have developed recommended guidelines and protocols for 

condition assessments. Regional recommendations for condition assessments within the 

Pacific Islands are being developed, but no target date for completion has been set. Similar 

work is needed in the Atlantic/Caribbean.
ALTERNATIVES ANALYSIS – QUANTIFYING IMPACTS

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2.2 Alternatives Analysis

An alternatives analysis performed 

properly and early in project 

formulation can reduce project costs, 

streamline permitting, and result in 

avoidance and protection of valuable 

marine resources (Yocom et al., 

1989). An alternatives analysis is a 

process by which a project proponent 

or decision-maker looks at potential 

alternative actions or activities that 

could meet the intended purpose of 

the planned activity and address the 

need for that activity. The laws, 

regulations, and procedures that may 

apply to activities in coral reef 

ecosystems all require some level of 

alternatives analysis to ensure that 

project proponents and decisionmakers are fully considering the 

environmental impacts of an action 

(e.g., NEPA, ESA, MSA, and CWA). 

The CWA §404(b)(1) Guidelines (40 

CFR 230), referred to as the 

Guidelines, provide a framework for 

alternatives analysis and 

implementing avoidance and 

minimization actions before 

considering compensatory mitigation. 

The approach from the Guidelines 

can be applied to planned impacts to 

coral reefs, even if those impacts do 

not require a DA permit from USACE. 

The fundamental precept of the 

Guidelines is that discharge of 

dredged or fill material to a regulated 

aquatic habitat, such as coral reefs, 

should not occur unless it can be 

demonstrated that such discharges, 

either individually or cumulatively, will 

not result in unacceptable adverse 

effects on the aquatic ecosystem.

For activities that require DA permits in accordance with CWA §404, USACE is responsible for 

determining compliance with the Guidelines, and the permit applicant may be required to 

provide information to USACE to assist in that compliance determination. For proposed CWA 

§404 decisions, EPA may provide comments to USACE identifying its views regarding 

compliance with the Guidelines. The Guidelines require documentation of avoidance and 

minimization of impacts to aquatic resources prior to consideration of compensatory mitigation

When a planned project includes actions that are

regulated under CWA §404 (e.g., placement of 

dredged or fill material), specific requirements are 

placed on the alternatives analysis. Under CWA 

§404(b)(1) Guidelines, the fundamental precept is 

“no discharge of dredged or fill material shall be

permitted if there is a practicable alternative to the

proposed discharge which would have less adverse

impact on the aquatic ecosystem, so long as the

alternative does not have other significant adverse

environmental consequences” (40 CFR 230.10(a)).

This is referred to as the “least environmentally

damaging practicable alternative” or LEDPA. The 

preferred alternative must be the LEDPA. A

“practicable alternative” is considered any alternative 

that is “available and capable of being done after 

taking into consideration cost, existing technology, 

and logistics in light of the overall purpose” (40 CFR 

230.10(a)(2)).

CWA §404(b)(1) Guidelines also state that impacting 

“special aquatic sites” is “among the most severe

environmental impacts” covered by the Guidelines (40 

CFR 230.1(d)). Coral reefs, seagrass, and vegetated 

shallows are considered “special aquatic sites” (40 CFR 

230.44). Therefore, when a planned project also 

includes proposed impacts to a “special aquatic site” 

and the activity “does not require access or proximity 

siting within the special aquatic site” (40 CFR 

230.10(a)(3)), there is also a rebuttable assumption that 

practicable alternatives are available that would not

involve discharges into special aquatic sites and

those practicable alternatives have less impact on the 

aquatic ecosystem. If the project proponent is able to 

demonstrate there are no other practicable alternatives, 

then the focus is on ensuring that the impacts are 

avoided and minimized to the extent practicable and 

that unavoidable impacts are compensated when 

appropriate. Please review the full text of the 

Guidelines (40 CFR 230) for more detailed information 

on burdens of proof and required analysis. Local 

USACE Regulatory Offices are also available to explain 

the requirements on project-specific basis.

ALTERNATIVES ANALYSIS AND THE CWA §404

PLANNED IMPACTS
ALTERNATIVES ANALYSIS – QUANTIFYING IMPACTS

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for unavoidable adverse impacts. For activities that require DA permits in accordance with RHA 

§10, mitigation requirements are described in 33 CFR 320.4(r), as well as the 2008 Mitigation 

Rule. 

2.2.1 Quantifying Direct and Indirect Impacts

To fully consider the environmental impacts of various alternatives, the direct, indirect or 

secondary, and cumulative impacts of the project on coral reef, other biological resources, and

habitat types need to be identified. Although defined differently in various laws, regulations, and 

policies, the definition in NEPA for direct and indirect impacts is commonly used (40 CFR 

1508.8). Direct impacts are caused by the action or activity and occur at the same time and 

place. Indirect impacts (also known as secondary impacts or effects) are caused by the action 

or activity and are later in time or farther removed in distance, but are still reasonably 

foreseeable. Whether an impact is direct or indirect is not based on the severity of the impact,

but rather whether the impact resulted from an action elsewhere or directly from an action on 

site.

It is useful for a project description to include a table of projected direct and indirect impacts for 

each habitat type, and whether the impacts are permanent (e.g., fill) or temporary (e.g.,

sedimentation). Indirect impacts can be difficult to quantify, so at times might be described 

qualitatively. 

While agencies may define direct versus indirect impacts differently, generally in the marine 

environment, common actions having direct impacts include, but are not limited to:

. Dredging to widen or deepen harbors and channels, or to maintain channel depth.

. Depositing fill in marine waters to build piers, breakwaters, and protect eroding 

shorelines.

Common actions having indirect impacts in the marine environment include, but are not limited 

to:

. Sedimentation impacts from turbidity plumes. Sediments may bury, abrade, or shade 

corals, resulting in physiological stress or mortality. 

. Degradation of marine resources caused by induced excess human use. For example, if 

a project provides expanded docking or mooring for recreational and commercial 

vessels, overuse of nearby fishing or diving sites may degrade the condition of aquatic 

resources outside of the project footprint.

. Shading impacts on marine resources. Constructing overwater structures such as piers 

may change light levels and indirectly degrade the habitat underneath.

. Discharge of land-based pollutants. Land-based activities that have no direct impact to 

coral reef or nearshore habitat may result in significant indirect impacts from nutrients or 

pollutants if not adequately controlled and treated before discharge to the ocean.

In some instances, the damages associated with indirect or secondary impacts may exceed 

those caused by the direct impacts of a project. Therefore, comprehensive quantification of 

indirect impacts is important for defining the full scale of project impacts and for the purpose of 

determining compensatory mitigation. 
ALTERNATIVES ANALYSIS – SITES AND DESIGNS

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If indirect impacts are a substantial concern for a planned activity, project proponents may need 

to include monitoring of turbidity, sedimentation, and coral condition before, during, and after the 

construction activity or action to appropriately account for the indirect impacts. Careful 

monitoring can detect problems that need to be corrected in real time, allow for adaptive 

management to meet any requirements and standards, and determine if compensatory 

mitigation requirements for unavoidable adverse impacts need modification. Post-dredging 

surveys can determine if the dredging was restricted to the permitted area, or if the dredge 

caused direct impacts outside of the permitted area. Project proponents need to work closely 

with the appropriate permitting authorities to determine when this type of monitoring may be 

most effective.

Some of the more common indirect impacts encountered by resource managers and regulators 

are those associated with sedimentation caused by dredging activities. A variety of dredge 

plume models are designed to estimate indirect impacts from sedimentation. For example, the 

USACE has developed models for assessing such indirect impacts to provide site-specific data 

on the potential extent of impacts (Johnson et al., 2000). Such models have been used to 

assess impacts from hopper overflow and dredging activities. A good example of where models 

have been used to assess the site and project-specific extent of impacts is “Numerical 

assessment of the dispersion of over spilled sediment from a dredge barge and its sensitivity to 

various parameters” (Mestres et al., 2014). These models could also be used to determine 

which BMPs will result in the least amount of indirect impacts on the nearby sensitive 

hardbottom habitats. The Permanent International Association for Navigation Congresses 

(PIANC) guidance also recommends that predictive modeling be performed as it is a “critical 

tool for accurate assessment of dredging and port construction impacts on corals” (PIANC, 

2010). One concern regarding the accuracy of these models in coral reef areas, is that dredge

plume models often fail to include thresholds for turbidity and sedimentation rates that are 

protective of corals and other sensitive aquatic life.

2.2.2 Analyzing Project Sites and Designs

Once the direct and indirect impacts of project alternatives have been identified and 

summarized by habitat type, then the project proponent should consider what additional

modifications might be made to avoid and minimize impacts to the coral reef ecosystems by 

analyzing project sites and designs. Avoidance and minimization are not only integral steps in 

the mitigation process, they have also been shown to be more cost effective than the

compensatory mitigation analysis and implementation process. 

Planned activities that are likely to cause minor impacts may require less rigorous analysis of 

alternatives and may be able to readily avoid and minimize impacts to meet applicable federal, 

state, or territorial requirements. Planned activities with larger impacts to the aquatic 

environment, either individually or cumulatively, will likely require greater assessment specificity, 

as well as analysis, to meet appropriate avoidance, minimization, and compensatory mitigation 

requirements. 

If a DA individual permit is required, the NEPA decision document (environmental assessment 

(EA) or environmental impact statement (EIS)) requires an alternatives analysis. For RHA §10, 

the USACE regulations at 33 CFR 320.4(r) also require consideration of avoidance and 

minimization, as well as compensatory mitigation. For CWA §404, USACE will need to 

determine the LEDPA, based on documentation from the applicant and input from the regulatory 

agencies. Whether for a DA permit or other federal, state, or territorial permits, the applicant 

PLANNED IMPACTS
ALTERNATIVES ANALYSIS – SITES AND DESIGNS 

USCRTF Handbook on Coral Reef Impacts – December 2016 

38

needs to strive to provide the 

most accurate information for 

describing the proposed 

project, the project purpose, 

and a defined set of criteria 

used for screening each of the 

alternatives (e.g., project site, 

operational logistics, area of 

impact, presence of marine 

resources, social and cultural 

impacts, and itemized costs). If 

the applicant has sound 

reasoning as to why an 

alternative is desirable or 

should not be considered, 

these views should be 

presented with detailed 

justifications. 

For those alternatives that are 

determined to be practicable, 

further analysis of avoidance 

and minimization should be 

conducted to identify the 

alternative that will result in the 

least adverse impacts. To 

clearly represent the variations 

in alternatives and impacts, a 

good practice is to include a 

project map and description of 

the direct and indirect project 

footprints of the different project 

alternatives. The project map 

should include locations and 

configurations of any fill 

material, physical structures, 

dredging, or other work that 

contribute to impacts. In some 

cases, habitat maps exist for 

proposed project areas, or they 

are developed during the 

environmental review process 

or during the ESA, EFH, or 

FWCA consultations. 

Overlaying the footprints of the 

alternatives onto a benthic 

habitat map facilitates 

comparison of the alternatives 

and documentation of the 

The Mā‘alaea Harbor navigation improvement project on 

the island of Maui, Hawaii, proposed expanding the existing 

breakwater to improve access to a small boat harbor during 

certain wave conditions. Between 1982 and 1998, public 

comments on the environmental impact statement (EIS)

raised concerns regarding potential impacts to coral reef 

habitats and other issues. Due to funding constraints 

encountered when addressing the complex issues around 

coral reef mitigation, it took until 2012 for the project 

proponents—State of Hawaii and USACE—to make a final 

decision on the project.

As a result of public comment, the project proponents 

modified the alternatives analysis approach, to be a more

collaborative process with resource agencies and 

community groups. When updating models to better scale

the breakwater, USACE engaged with federal resource 

agencies to improve understanding of the resource, and 

communicate navigational and engineering constraints and 

technical issues for the project. In re-evaluating potential 

alternatives, USACE engaged FWS and NMFS in a phased 

approach to impact assessment, first mapping the extent of 

the coral reef habitat and rating areas of higher quality that 

would benefit from protection (i.e., avoidance). Based on 

the initial mapping, the potential alternatives were overlaid 

and re-evaluated to see where the best opportunity to 

maximize avoidance and minimization was. Through 

collaboration with community groups and users in 2010, 

USACE and the State of Hawaii developed a better 

understanding of the navigational constraints for the harbor,

and how users were adapting to the conditions.

Based on the input of the users, resource agencies, and 

the expertise of the coastal engineers, it was determined

that the best solution for the State of Hawaii was to 

terminate the proposed breakwater expansion and instead 

focus on facility improvements to better protect the vessels 

while moored. This avoidance and minimization measure 

was decided in large part by comparing the potential costs 

of coral reef compensatory mitigation along with

construction costs versus the potential benefits derived by 

the users of Mā‘alaea Harbor.

EXAMPLE: COLLABORATIVE ALTERNATIVES 

ANALYSIS PROCESS
ALTERNATIVES ANALYSIS – IMPACT AVOIDANCE AND MINIMIZATION

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process. Visualizing the different project footprints on a habitat map aids identification of any 

areas of special significance (e.g., special aquatic sites, EFH, ESA critical habitat, or sites 

where protected species are located) within the direct and indirect impact areas. Use of 

alternative footprint habitat overlays allows project proponents to see where designs can be

modified to avoid and minimize impacts to sensitive areas to the maximum extent practicable. 

Evaluating alternatives and modifying project designs to achieve avoidance and minimization of 

impacts through the use of habitat map overlays, is an effective way to document compliance 

with environmental requirements such as NEPA or state or territorial equivalent laws and 

regulations.

An analysis of alternatives should include examination of opportunities for use of upland areas 

and other aquatic sites that would result in less adverse impact on the aquatic ecosystem and 

environment, especially for habitats with specific regulatory designations, such as coral reefs 

and seagrass beds (designated as special aquatic sites under CWA, EFH under MSA, and in 

some areas critical habitat under ESA). 

The range of alternatives to consider may include:

• Upland alternatives that do not involve in-water work.

• Alternative sites with little to no coral reef resource (i.e., avoidance).

• Non-structural alternatives that meet the project purpose. For example, 

improved navigation technology or aids to navigation may meet the purpose of 

improving safety without the need for construction.

• Modifications to project size and footprint to avoid or minimize impacts to coral 

reefs and other sensitive ecosystems.

• Modifications to project design, which may include using pilings instead of fill, 

moving the facility shoreward to reduce in-water work, and reducing the length 

or width of a pier or breakwater.

• Alternative methods that avoid or minimize impacts such as horizontal 

directional drilling instead of trenching.

The result of the analysis of a full range of alternatives is identification of the practicable 

alternative with the smallest impact to the marine environment or to coral reefs and other 

sensitive sites. For projects permitted by USACE under the CWA, the alternatives analysis 

must demonstrate that the preferred alternative is the LEDPA.

Per the Presidential Memorandum: Incorporating Ecosystem Services into Federal Decision 

Making issued in October 2015, federal agencies are also directed to take into consideration the 

full range of benefits and trade-offs among ecosystem services associated with potential federal 

actions, including benefits and costs that may not be recognized in private markets because of 

the public-good nature of some ecosystem services.

2.2.3 Avoid and Minimize Impacts

Avoidance and minimization of impacts starts early in the alternatives analysis, with quantifying 

the direct and indirect impacts and analyzing the project sites and designs. Once a preferred 

alternative is identified by the project proponent through these measures and in consultation 

with the permitting authorities, additional avoidance and minimization can occur through such 

actions as evaluating construction technologies, and implementing biological or construction 

BMPs. The alternatives analysis and avoidance and minimization process is often iterative. For

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example, identification of a new construction technology may allow for a previous project site 

with less coral reef habitat that was determined to be technically infeasible to be reconsidered. 

Investigation into BMPs that were previously thought to be effective at reducing an impact may 

not be practicable at the project site, requiring reconsideration of other BMPs or other 

projectsites. This section provides information on best practices for in-water construction and 

dredging, and coral transplantation, which are often-used avoidance and minimization 

approaches used during planned impact activities.

2.2.3.1. Best Management Practices for In-water Construction and Dredging

A suite of BMPs should be employed during all in-water construction and dredging activities to 

minimize impacts. It is recommended that these construction projects develop a BMP plan in 

advance of starting work. The BMP plan should be specific to the site, equipment used, local 

conditions, and aquatic resources at risk. This section provides a menu of recommended BMPs 

for construction and dredging in marine waters. In addition, climate change adaptation BMPs 

are recommended where practicable, such as those defined in A Reef’s Manager’s Guide to 

Coral Bleaching (Marshall and Schuttenberg, 2006).

The range of BMPs discussed here is intended to present examples, and is not definitive. 

Federal, state, and local government entities may have BMP guidance, and these 

recommendations should be identified and incorporated during the permitting process. The 

FDEP’s BMP guidance for dredge and fill projects in tropical systems is an excellent resource 

for consideration (FDEP CRCP, 2008).

Biological BMPs:

. Clean vessels and construction equipment that may have any contact with the water to 

prevent introduction of alien and invasive species.

. Cease work during coral spawning periods.

. Avoid work during coral bleaching events.

. Transplant or relocate living corals and sensitive macro-fauna outside the impact 

footprint (see Section 2.2.3.2).

Construction BMPs:

. Reduce operational impact by using equipment or methods that minimize sediment 

resuspension (e.g., suction dredge, environmental bucket).

. Ensure that water column, current, and wave characteristics (circulation, temperature, 

biological attributes) are maintained as much as practicable during construction, and are 

restored post construction.

. Maintain ocean and coastal hydrodynamics (sedimentation, volume, flow) as much as 

practicable during construction, and restore post construction. 

. Prevent, if possible, all discharge to the ocean of storm water, return flows, and 

contaminants from construction and dewatering in nearby uplands, or apply 

appropriately strict sediment and contaminant limits to any unavoidable discharges. 

. Avoid upland and shoreline earth-moving activities during rainy season. 

. Establish protocols for confining the work area and ceasing operation due to inclement 

weather.

. Establish a contingency plan for removing equipment and securing the work site during 

storms.
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. Use silt curtains or other similar methods to confine suspended sediments for in-water 

activities when practicable. 

. Reduce potential contact with the substrate by equipment and tools.

. Minimize the duration of in-water work. 

. Prevent unnatural heating or cooling of water resources. 

. Prevent chemical spills, discharge, and site contamination.

. Properly size dredged material containment or dewatering operations to prevent or 

control overflow or return flow. 

. Dewater dredged material by evaporation and infiltration whenever possible, and 

manage any return flows to remove particulates and chemical contaminants before 

discharge.

. Avoid construction and earth moving activities during rainy periods and contain storm

water to prevent discharge of sediment-laden water to the ocean.

Dredging BMPs:

The 2010 PIANC guidance, “Dredging and Port Construction around Coral Reefs,” includes 

BMPs specific to dredging operations. These include:

. Choice of equipment.

. Prevention of leakage from equipment.

. Controlling the production rate.

. Overflow at keel-level and use of the environmental valve.

. Minimize propeller wash by limiting vessel movements to high tide.

. Restricted overflow.

. Environmental windows (periods of coral stress, tidal direction).

. Silt curtains, where appropriate.

. Define and manage work during appropriate wave and weather conditions.

The USACE paper “Dredging-Induced Near-Field Re-suspended Sediment Concentrations and 

Source Strengths” provides guidance on methods to evaluate and reduce the amount of 

sediment suspension through operational means (Collins, USACE, 1995). This document can 

be used to develop BMPs for cutterhead dredges such as: 

. Require ladder swing direction opposite to tangential velocity of the cutter head blades.

. Require full burial of the cutterhead. 

Additional BMPs for dredging operations:

. Enclosed clamshell dredge buckets reduce maximum suspended sediment 

concentrations by more than 50% (from 200mg/l to less than 80mg/l) (Welp et al., 

USACE, 2001). Enclosed clamshells (so called “environmental buckets”) must also be 

operated to minimize sediment suspension and fall-back. Vent flaps must close, and 

velocity of bucket drop and retrieval must be controlled to be slower than typical 

(unrestricted) bucket cycle times. 

. Water quality and benthic impacts can result from the turbidity and suspended 

sediments from overflow from hopper dredges or through-hull decanting of scows that 

are mechanically loaded; these impacts can be reduced or eliminated by eliminating 

overflow or through-hull decanting. Concentrations of suspended sediment within 200 

meters of the dredge are documented to be one to two orders of magnitude higher when 

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overflow is allowed (Palermo et al., USACE, 1990, and Collins, USACE, 1995). In order 

to minimize impacts to coral and hardbottom communities, overflow should be prohibited 

or restricted. It is recommended that overflow/through-hull flow restrictions be applied at 

the time of permitting and in contract specifications. 

. To minimize potential impacts to adjacent benthos and reef habitats associated with 

transport of material to the Ocean Dredged Material Disposal Sites (ODMDS), vessels 

transiting to and from the ODMDS should be restricted to navigation channels. It is 

recommended that the MPRSA 103 permit and the dredging project contract 

specifications include this restriction as a condition of the permit and contract. 

. To minimize potential impacts, vessels transporting dredged material should not be 

permitted to leak, spill, or overflow while transiting to and from the ODMDS, including 

within the navigation channels. It is recommended that the MPRSA 103 permit and the 

dredging project contract specifications include these restrictions as conditions of the 

permit and contract. 

. Financial assurances and compensatory mitigation requirements (see Section 2.3.2) 

should be established in the permit and contract language to ensure that any 

violations of the specifications are addressed.

For potentially useful indicators of coral reef condition in relation to sediment and water quality 

stressors, please refer to the USCRTF Watershed Partnership Initiative Priority Ecosystem 

Indicators, dated February 2016. 

2.2.3.2 Best Practice Considerations for Coral Transplantation 

Corals are broadly distributed on various substrates, with a general preference for hardbottom. 

Many coastal dredge and fill projects will have corals within the project footprint. After the 

footprint of the dredge and fill activity has been minimized to the extent practicable, and an 

effective BMP plan is in place for construction and dredging, transplantation of corals out of the 

project footprint can be an important component of minimization. In addition, where corals may 

be indirectly impacted outside of the project footprint from sedimentation associated with the 

dredge and fill activity, transplantation of at-risk corals may also be part of the minimization 

action. 

Transplantation of corals is not considered avoidance because the corals being transplanted as 

a result of a proposed activity would otherwise retain maximum functionality if left alone. 

Transplantation reduces the loss of corals, and by extension, reduces or minimizes a project’s

impact. For this reason, the act of transplantation is most appropriate in the minimization 

category.

The logic behind coral transplantation as minimization, is that the functions associated with the 

coral will also be transferred through the transplantation process. However, successful transfer 

of functions with transplantation does not always occur, such as when the receiving site has 

less-than-ideal physical conditions (e.g., solar irradiance, depth, water motion) that may limit the 

natural growth, reproduction, and survival of the transplanted corals, or when some of the 

species and size classes at the impact site may not be transplantable. In addition, some 

mortality is likely to occur during the transplantation process. The potential for coral losses 

during and after transplantation should be accounted for in mitigation planning and when 

determining the amount of compensatory mitigation needed to offset losses. On a coral reef, 

when coral transplantation is used for minimization there are additional considerations to those

functions associated with the coral. There are also ecosystem services associated with the 
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other resources at the site that need to be accounted for in the overall mitigation effort. These

include, but are not limited to, services associated with other invertebrates, algae, fish, 

substrata, refugia, connectivity.

After all practicable alternatives and measures to avoid impacts have been exhausted, coral 

transplantation could be recommended for most projects, large and small, to minimize losses of 

this important resource. Depending on the species and the size of the corals present, and the 

number of corals needing transplantation out of the project footprint, it may be possible to 

transplant most of the corals away from the impact site with relatively good survival, thereby

avoiding or significantly lessening the requirement for compensatory mitigation. For projects 

with large impacts to corals, the unavoidable impacts after accounting for transplantation, may 

also be large. In this case, compensatory mitigation may be required to offset permanent coral 

losses (e.g., corals not transplanted), permanent loss of waters (fill), and/or permanent 

alteration of habitat (e.g., depth, light penetration, current regime, and substrata) from dredging.

Project proponents should work with the appropriate permitting authorities to determine the 

appropriate transplanting criteria based on the project, the species present, and the species size 

and health. Multiple agencies, including the State of Hawaii DLNR Division of Aquatic 

Resources, NMFS, and the FKNMS are developing protocols for removal of corals, handling 

during transport, holding in aquaria, and attaching corals at the receiving site. This process is 

not perfect, but success and survival are improving as experience is gained. Certain corals 

(e.g., encrusting forms and small fragile corals) are difficult to remove from the native substrate 

and transplant success may not be achievable. Some mortality is to be expected during 

removal, transport, and holding. In some cases, trying to relocate small colonies may result in 

detrimental damage to the adjacent resource or a high mortality rate of the coral species being 

transplanted.

Selection of suitable receiving sites for transplanted corals is of critical importance. Factors to 

consider include:

• Potential for future destructive impacts at the receiving site (e.g., future dredging or 

harbor expansion).

• Potential for the receiving site to be impacted by construction activities (e.g., sediment 

plumes, dredge anchors and lines).

• Potential for spread of invasive species, disease, or predators to the receiving site.

• Substrate stability of the receiving site and potential impacts of sand transport,

scouring, and burial.

• Ability of transplanted corals to adapt to physical conditions at the receiving site.

• Capacity of the site to accommodate numbers of transplants.

• Potential site vulnerability/resilience to effects of climate change and other stressors.

To optimize success of coral transplantation, it is recommended that a Coral Transplantation 

Plan (CTP) be submitted to the appropriate permitting authority with the permit application, such 

as the DA permit application for in-water work in or near coral reefs. CTPs should include 

methods, criteria for selection of colonies to transplant (and not transplant), performance and 

survival standards, suitable locations to transplant the corals, protection and management 

plans, identification of monitoring duration to determine performance standards are met, and 

reporting elements that reflect progress toward performance standards. The CTP should 

include a performance standard for survival of the transplanted colonies. In general, 

transplanted colonies should be tagged and geo-located so that colony growth and mortality can 

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be tracked. An example CTP is included in Appendix IV. 

A recommended performance standard for transplantation is no less than 75% survival after two

years. In the Atlantic and Caribbean, it is common for coral transplantation projects to reach the 

performance requirement of 80% of corals exhibiting successful re-attachment and positive 

linear growth after two years of monitoring. If survival falls short of performance standards, 

additional compensatory mitigation may be required to compensate for these unexpected 

losses. Project proponents should be aware that some permitting authorities require that coral 

transplantation be monitored for a minimum of five years. 

Monitoring of corals after transplantation should be aimed at determining progress toward 

performance standards, and at a minimum should assess percent survival. Reference or 

control sites are useful to include in the monitoring of transplanted and relocated corals, to

compare the success and survival of transplanted corals with undisturbed corals, and in this 

way account for natural stresses unrelated to the relocation/transplantation. For example, if a 

large percentage of coral in the reference area were to be killed by bleaching, then high survival 

numbers at the transplantation site would not be expected. 

In some cases, corals transplanted from an impact site may be a component of compensatory 

mitigation (see Chapter 4 Option 3). For example, if a compensatory mitigation project’s 

objective is restoration of a site where coral has been degraded by sedimentation, an array of 

management actions may be components of the restoration plan. In this example, these may 

include transplantation of corals, targeted erosion control measures on land to control the 

sediment source, physical removal of sediments at the site, and restrictions on harvesting of 

herbivores. All four management actions are deemed necessary for successful site recovery, 

and coral transplantation would likely shorten recovery time, and therefore temporal losses.

Consideration of coral transplantation as a component of compensatory mitigation should be 

discussed with the permitting authority on a case-by-case basis. It should be understood that 

transplantation of corals is either a minimization measure that reduces the size of the impact, or 

a component of compensatory mitigation, but cannot be counted as both. As discussed in 

Chapter 4, coral relocation moves corals from a non-impact site, such as a nursery, to a new 

location. Coral relocation is different than transplantation where corals are being moved from 

an impact site to a new location. However, information on transplantation protocols may be 

applicable to coral relocation activities. 

In Florida, some compensatory mitigation credit has been given for outplanting corals from a 

coral nursery to a pre-approved wild site. An example from Florida, of the evolution of coral 

mitigation science, particularly coral propagation and relocation, and artificial reef performance, 

as well as important lessons-learned and considerations for applying these strategies in planned 

(and unplanned) impact scenarios, are presented in the following case study.
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The northern third of the Florida Reef Tract is sited off of a highly-urbanized shoreline that supports 

one-third of the State’s population (6 million people). Physical impacts to these coral reefs are caused 

by a variety of activities including human use, port expansion, beach renourishment, major vessel

groundings, and placement of fiber optic cables. Approaches to best mitigate these impacts have 

evolved over time, in part, as a result of improvements in stony coral relocation success, advances in 

coral propagation and outplanting throughout Florida and the U.S. Caribbean, and field studies that 

evaluate the equivalency of artificial reefs constructed to provide compensatory mitigation for impacts 

to natural reefs.

Until the early 2000s the placement of limestone boulder reefs or pre-fabricated reef modules was 

viewed as a popular approach to offset impacts to natural hardbottom and coral reef habitats. Artificial 

reefs have been deployed for fishery management and habitat enhancement for many years (Seaman, 

2000). For decades, this approach demonstrated success in serving as fish aggregating devices, 

replacing some functions that reef structure provides, and as a way to reduce fishing pressure from 

natural coral reef areas. During this time, experimental approaches were being tested to relocate 

corals outside of impact areas; however, until recently, data were limited to support inclusion of coral 

relocation as a best practice for minimizing coral impacts.

Between 2000 and 2010 results from key studies and monitoring reports from coral relocation efforts 

became accessible to the southeast Florida natural resource management community. Studies have 

shown small corals have been successfully transplanted, exhibiting greater than 80% survivorship after 

13 months (Brownlee, 2010). Monty et al. (2006) successfully transplanted 250 corals (14 species) 

ranging from 5 to 40 centimeters in diameter with a high rate of survivorship after 13 months, with eight 

coral species having 100% survivorship. Thornton et al. (2000) transplanted 271 corals from an outfall 

pipe in Broward and after 27 months, with 98% survival of the corals, as compared to 83% survival for 

corals on the nearby natural substrate. Stephens (2007) documented 92 - 100% of the transplants 

salvaged from a Broward County coastal construction impact site survived after 18 to 24 months. In 

addition, after 18 months of monitoring corals relocated from a beach renourishment project impact 

area, 100% of corals monitored remained securely attached, none showed evidence of disease, and 

over 97% of the colonies were showing active tissue growth over the cement (NOVA Southeastern 

University Oceanographic Center, 2006). Results from these studies supported the adoption of stony 

coral relocation as a routine BMP to minimize impacts to corals in southeast Florida. 

While issues such as minimum size class criteria for stony coral relocation and relocation of other reef 

organisms such as giant barrel sponges (i.e., Xestopongia muta), octocorals and gorgonians with 

strong central spines are still under evaluation. The general consensus among resource trustees and 

within the regulatory community is that stony corals greater than 10 centimeters in diameter can be 

successfully relocated. The size of relocatable corals, however, can vary across sites and can be 

considerably smaller for selected species. The basic target for success as an impact minimization 

measure is 85% survival of transplanted coral and no net loss of live tissue of transplanted coral after 

two years of monitoring.

During the same time period, coral propagation and outplanting techniques were improving. Coral 

colonies from propagation nurseries, and salvaged from impact areas have been successfully 

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outplanted to natural and artificial substrates (Brownlee, 2010; Epstein et al., 2001; HoroszowskiFridman et al., 2011; Monty et al., 2006; Rinkevich, 2005; Stephens, 2007; and Thornton et al., 2000). 

NOAA’s Restoration Center successfully uses this approach to mitigate damages to Caribbean reefs 

from vessel groundings. This mitigation approach is rated most favorably in southeast Florida based on 

coordination with 25 coral resource trustees and scientists working in Florida and the U.S. Caribbean 

(Ladd, 2012). Coral propagation and outplanting, predominantly using Acropora species (spp.), has 

been successfully used over the past decade in Florida and in the Caribbean for reef rehabilitation. 

Efforts to date have primarily focused on Acropora spp. because these species exhibit faster growth 

rates than other Caribbean coral species, reproduce predominantly via asexual fragmentation, and can

be propagated efficiently using both in-water and shore-based nurseries. Propagation and outplanting 

techniques are now being developed for additional Caribbean coral species. Scientifically-vetted best 

practices for nursery propagation, outplanting, and monitoring have been developed, and are used by 

nursery managers in the Florida Keys, Broward County, Puerto Rico, USVI, and other Caribbean islands 

to reproduce Acropora spp. asexually (Johnson et al., 2011). The FDEP has noted that recent microfragmenting techniques have offered hope for propagating slow-growing reef-building corals like 

Orbicella spp.

Also during the same time period, efforts were underway to examine the equivalency between 

natural and artificial reefs. Miller et al. (2009) examined four artificial reefs constructed of boulders 

in the Florida Keys 12 years after installation, and found the benthic communities on reference and 

boulder reefs were dissimilar. Cyanobacteria were abundant on boulder reefs (~8 to 33% cover), 

but virtually absent on natural reference reefs (0 to 6 percent cover). Cyanobacteria are not often 

quantified as a separate functional group in monitoring studies, but can inhibit coral recruitment, kill 

live coral tissue, limit coral recovery, and reduce overall coral cover (Kuffner et al., 2006). The most 

recent and inclusive study of boulder-based artificial reefs was conducted by Gilliam (2012). This 

review examines 10 artificial reefs offshore of Miami- Dade, Broward, and Palm Beach counties. 

The oldest of these reefs was examined 17 years after installation.

While the species richness of stony corals observed was similar between artificial and natural reefs, 

Gilliam (2012) concluded the overall composition of the benthic communities inhabiting the boulder 

reefs was dissimilar from those at reference sites. Smaller, “weedier” species were more common 

on boulder reefs. Larger, reef-structure-forming species were more common on the natural reefs. 

The giant barrel sponge, which is an important functional group for habitat structure and nutrient 

cycling, was completely absent from all boulder reefs examined. The density and species richness 

of gorgonians were also lower on boulder reefs compared to natural reefs. As the information 

above has become socialized within the natural resource management and regulatory community, 

combination approaches are commonly seen as more scientifically sound and effective ways of 

minimizing and compensating for coral reef impacts. Coral relocation as a minimization measure 

has become a routine BMP. In some cases, the corals are moved to artificial substrates to “jump 

start” the mitigation services. In addition, combination approaches using coral relocation, artificial 

reefs, and coral propagation and outplanting are being evaluated as a way to integrate BMPs from 

the coral reef damage assessment community with that of coastal coral reef managers and 

regulators in Florida.

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2.3 Compensatory Mitigation Planning 

2.3.1 Determining the Amount of Compensatory Mitigation Needed to 

Offset Impacts 

The final determination on the amount of compensatory mitigation needed to offset unavoidable 

adverse impacts is made by the appropriate permitting authority in accordance with applicable 

regulatory requirements. For example, for projects that require USACE authorization, final 

determination as to whether compensatory mitigation is required, or not, for a specific project 

lies with the USACE. EPA, NMFS, and FWS often provide comments and recommendations 

regarding the need for compensatory mitigation during their review of project proposals and 

biotic surveys. In the case of small projects where impacts to corals are not significant, and 

where a range of avoidance and minimization measures are applied, there may be no 

compensatory mitigation required. For larger projects where there are permanent impacts and 

unavoidable losses, compensatory mitigation is likely to be required to replace those losses. 

The goal of compensatory mitigation is to replace lost functions and services caused by 

unavoidable impacts. The determination of compensatory mitigation requirements for any 

project will vary based on the applicable authorities governing the activity, as well as the size 

and condition of the coral reef and affiliated ecosystems being impacted. Project proponents 

should work closely with the appropriate regulatory agencies and resource trustees in 

determining the compensatory mitigation requirements and processes as they pertain to their 

proposed project. Federal, state, and territorial permitting authorities have varying definitions of 

mitigation, as well as different requirements for determining appropriate compensatory 

mitigation under their applicable laws, regulations, and policies. If there is a conflict between 

the project proponent and multiple permitting authorities, the agencies with legal authority define 

how to resolve such conflicts. 

As stated in Section 1.1, the 2008 Mitigation Rule is the most comprehensive regulation for 

evaluating coral reef impacts and determining the required compensation for losses of aquatic 

resources. The 2008 Mitigation Rule establishes requirements and standards for the 

replacement of unavoidable, permitted losses of aquatic resources, and the functions and 

services they provide. Compensatory mitigation requirements must be commensurate with the 

amount and type of impact. A major focus of this approach is replacement of lost ecosystem 

functions and services. 

The EFH provisions of MSA §305(b) also provide authority for evaluating planned events that 

will impact essential fish habitat on coral reefs similarly using avoidance, minimization, and 

offset considerations. 

2.3.1.1 Challenges in Determining Compensatory Mitigation Requirements 

Studies to evaluate compensatory mitigation success for coral reefs prior to the 2008 Mitigation 

Rule, found that mitigation often consisted of financial compensation for natural resources or 

out-of-kind compensation (Bentivoglio, 2003 and Yoshioka et al., 2004). Most of the coral 

preservation or restoration efforts were either never implemented or never monitored so their 

ecological performance was difficult to evaluate. The complexity of coral reef ecosystems, the 

uncertainty of recovery and restoration, the incorporation of climate impacts, and the lack of 

baseline data for coral reefs pose great challenges in effectively implementing effective 

compensatory mitigation. Challenges associated with current mitigation strategies include the 

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lack of monitoring on past mitigation efforts in order to document success (or lack thereof), and 

that many coral restoration efforts that have been implemented are insufficient in duration to 

provide conclusive evidence of recovery in what are often slow-growing coral reef ecosystems. 

Additionally, the state of coral reef restoration science has only recently become available, and 

has not yet been incorporated into models and tools like those readily available for scaling 

compensatory mitigation in wetlands. 

The recommended strategy for coral reef mitigation emphasizes avoidance and 

minimization of impacts because compensatory mitigation for coral reefs is very 

challenging and expensive, and has substantial risk and uncertainty. There is limited 

experience in implementing successful coral reef restoration activities (Bentivoglio, 2003 and 

Yoshioka et al., 2004). 

In light of these challenges, if coral reef restoration is chosen and approved as acceptable 

compensatory mitigation, both the impact and mitigation sites need to be characterized. Models 

are often used to determine how much restoration is needed at the mitigation site to replace the 

losses at the impact site. These models were not specifically developed for coral reefs and 

therefore require modification. These models compare resource types (kind, size, abundance) 

to determine debts and credits for similar resources. While this is a fairly straightforward 

mathematical process, when there are significant differences between impact and mitigation 

sites in kind, size, or abundance of corals, the models need to be adjusted to account for these 

differences. Additionally, a mechanism for defining trade-offs of corals of the same kind but 

different sizes, and between different species between sites is recommended. The following list 

frames some of the key considerations that must be addressed in completing this process. 

. What are the specific “operational measures” to predict future conditions (e.g., coral growth 

rates, water quality requirements, anticipated water temperature changes/climate changes, 

recruitment sources)? This information tends to be site-specific, rather than derived from a 

larger scale (e.g., regional or island-wide). To a large extent, there is presently a high level 

of uncertainty in modeling future conditions 

. What is the extent of temporal loss for aquatic resources, between the time of impact and 

the projected date of full recovery at the compensatory mitigation site, to achieve 

replacement of lost resources? 

. What is the likelihood of success? Success for mitigation and restoration activities is 

typically defined as meeting a sufficient level of ecological performance. Often there is a lot 

of uncertainty regarding project success and it is difficult to define the degree of 

uncertainty. Additional compensatory mitigation may be required by the permitting 

authority if the proposed compensatory mitigation fails, or is only partially successful. In 

some models for calculating compensatory mitigation needs for coral reefs, the likelihood of 

success is called the “risk factor” (e.g., the State of Florida’s Uniform Mitigation 

Assessment Method). 

. What are the uncertainties associated with the success of the compensatory mitigation? 

Mitigation plans should address uncertainty, including adaptive management plans and 

financial assurances, to be implemented if outcomes are different than intended. 

. What is the methodology being used to scale the compensatory mitigation activity? There 

is no preferred methodology for defining confidence interval (e.g., precautionary principle, 

“most likely,” least cost). 

. How far removed (in geographic location) is the compensatory mitigation project? The 

proposed compensatory mitigation should be acceptable to the regulatory agencies in 

terms of offsetting the permitted impacts at the impact site. There should be consideration 
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of on-site and off-site alternatives to determine which is most appropriate and practicable to 

offset the permitted impacts. For example, an off-site compensatory mitigation option that 

reduces or reverses a stressor that adversely affects corals might be a more effective 

compensatory mitigation alternative than an on-site compensatory mitigation project that 

doesn’t address the stressor(s) that impair the coral reef. 

. Is the compensatory mitigation project in-kind (aquatic resource of similar structural and 

functional type to the impacted resource) or out-of-kind? Out-of-kind compensatory 

mitigation may require more compensatory mitigation than in-kind. 

. How will the compensatory mitigation activity be provided long-term protection? 

. If required by the permitting authority, what financial assurances will be provided to ensure 

that funding is available to complete, monitor, and manage the compensatory mitigation 

activity? 

. What activities are needed for long-term operation and management of the compensatory 

mitigation activities and how will those be funded (if required by the permitting authority)? 

For example, while mitigation activities are intended to be self-sustaining there may be a 

need for ongoing invasive species monitoring and control or debris removal. 

Through efforts to define and implement appropriate compensatory mitigation in coral reef 

ecosystems, several additional challenges and limitations have been identified, including the 

following. 

. Difficulty in defining a “mitigation credit” for mitigation banks and in-lieu fee programs. 

. Difficulty in dealing with dissimilar resources at impact and compensatory mitigation sites. 

. A limited number of projects have required compensatory mitigation for coral reefs to 

date, therefore experience is limited. 

. Limited record of demonstrated ecological performance. Past compensatory mitigation 

projects were not implemented, not adequately monitored, and/or lacked performance 

standards. 

. Potentially costly and time-intensive data collection. The same level of information for 

assessments is needed at both the impact and the compensatory mitigation sites, which 

may be costly and time-intensive depending on the project. 

. Difficulty in defining recovery potential for temporary impacts and at the mitigation sites. 

. Lack of knowledge about stressor thresholds for coral reefs (e.g., water quality 

conditions required for recovery). 

. Inability or infeasibility to alleviate some stressors successfully (e.g., climate change: 

ocean warming, sea level rise, ocean acidification). 

. Limited knowledge of the ecosystem functions and services of coral reefs provided on 

natural versus man-made coral habitat. Currently, man-made coral habitat is addressed 

on a case-by-case basis. 

. Coral reef-related compensatory mitigation projects start out with a high degree of 

uncertainty due to the complex local and global stressors that cumulatively act to degrade 

the ecosystem over time, resulting in potential shifting baselines,4 which may ultimately 

increase the risk of failure for the project. 

 

4 Shifting baseline refers to the condition where regional or global stressors cause an entire ecosystem 

(e.g., all coral reefs) to change from a previous point in time. Even the high-quality coral reefs today may 

not have the same species assemblages and conditions as those coral reefs in the past. The coral reefs 

of the future may not have the same species assemblage or conditions as the coral reefs of today due to 

global stressors such as sea level rise or changing sea temperatures.

PLANNED IMPACTS
COMPENSATORY MITIGATION PLANNING – DETERMINATION OF AMOUNT 

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While there are challenges to determining the compensatory mitigation required for coral reef

impacts, there are opportunities for improvement. There currently are no feasible local actions 

that can be taken to alter shifts in temperature and biochemistry associated with climate change 

and ocean acidification. However, there is a growing body of evidence that shows such impacts 

can be reduced by implementing efforts at a local level to increase reef resilience. There are a 

number of tools and approaches that acknowledge, and account for these stressors, in planning 

for projects. Ecological performance can also be improved by applying lessons learned from 

past coral reef ecosystem compensatory mitigation efforts (e.g., same teams working on similar 

actions, learning from past experiences, and making improvements to future efforts). There are 

efforts underway in the Pacific by an interagency team to address some of the issues and 

challenges in coral reef assessments, analysis of coral reef impacts, and identification of 

potential compensatory mitigation requirements. Similar work is needed in the 

Atlantic/Caribbean. 

2.3.1.2 Analytical Tools for Determining Compensatory Mitigation Requirements 

Once the impact and compensatory mitigation sites have been assessed, appropriate analytical 

tools to inform the compensation of lost functions are needed. As a starting point, in looking for 

possible modeling options, it has been logical to borrow from prior wetland modeling efforts. 

Those efforts fell largely into two categories, indexing and equivalency. Some assert that 

because of the complexity of fauna and habitats in coral reefs, indices may oversimplify reef 

condition and inadequately describe replacement of lost function. For this reason, many 

consider the coral reef habitat equivalency analysis (HEA) modeling concept more effective. 

HEA modeling has been used with success in injury cases (see Section 3.5.1). 

Present efforts assume that characterizing the condition of coral reefs is an appropriate proxy 

for function as a best science approach. In all cases, the limiting factor in identifying appropriate 

coral reef compensatory mitigation options, is finding a tool that can be applied with relative 

ease, and provide a repeatable, reasonable, and acceptable description of compensation 

needed to replace lost functions and services. 

In coral dominated systems, the modeling of replacement of loss is tied to the corals, because 

of the length of time it takes them to recover, and that they serve as structure for other fauna. 

Where other organisms dominate a coral reef ecosystem, those alternate fauna (e.g., seagrass, 

mangroves, soft corals, or macroalgae) could be used as surrogates for coral reef recovery, with 

the assumption that recovery of these alternate species that establish more quickly, indicate that 

the coral reef ecosystem as a whole is on a trajectory for successful recovery. The same 

information must be collected for any potential compensatory mitigation site with additional 

consideration given to recovery potential—the baseline of present condition at the recovery site 

compared with historical conditions and what could be recovered through proposed restoration 

activities as compensatory mitigation. 

Assessment tools to determine compensatory mitigation from other aquatic habitats, such as 

wetlands and streams, have required significant adjustments to be used in coral reef systems 

for the following reasons: 

. Experience in the study of coral reef habitats and coral reef restoration is more limited. 

. The number of successful coral reef restoration or coral reef compensatory mitigation 

projects implemented to date is limited. 

. The dominant organisms within coral reefs are more diverse and slower growing than 
COMPENSATORY MITIGATION PLANNING – PLAN DEVELOPMENT

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. those in wetland communities, requiring longer monitoring periods to confirm successful 

implementation.

To date there is no universally accepted model to determine the amount of coral reef 

compensatory mitigation. HEA is a tool that uses a defined unit, such as acre or coral colony 

years, to compare the impact area with a proposed restoration site. The determination of the 

appropriate unit of measure for HEA would need to be made in consultation with the applicable 

permitting authorities. The model could compare acres of coverage by the same forms of coral 

or compare the size and species of corals. This is done by characterizing the resources to be 

lost and tallying them against those to be recovered at the compensatory mitigation sites. A 

requirement of the model is that the same characterization data must be gathered at both the 

impact site and the proposed compensatory mitigation site. HEA has many assumptions, and 

has challenges in determining equivalence for dissimilar resources, as well as defining recovery 

potential at proposed recovery areas. A complicating factor of this method is the requirement to 

use similar units for both the impact area and the compensatory mitigation site. In wetlands, 

traditionally, the units have been an area-based unit combined with a measure of condition. 

However, in coral reef ecosystems, it is very difficult to define coral reef area units that are 

similar between reef sites. As a result, other units, like coral colony years, are often selected, 

and trade-off models for dissimilar units have been developed. Additionally, accounting for 

temporal losses and likelihood of success is challenging due to limited science and examples of 

success to frame these parameters. Present efforts are conducted on a case-by-case basis.

2.3.2 Develop a Mitigation Plan

A draft mitigation plan should accompany any permit applications and should include plans to 

provide long-term protection and management of the mitigation project. The 2008 Mitigation 

Rule includes a description of 12 elements that should be included in a mitigation plan. Even if 

the proposed project is not subject to the 2008 Mitigation Rule, these components are useful to 

consider when planning for protection and restoration of aquatic resources. The level of detail 

in the mitigation plan should be commensurate with the scope and scale of the impacts. The 

elements of a mitigation plan include:

. Objectives and method of compensation.

. Site selection.

. Site protection instrument describing legal arrangements.

. Baseline information on the mitigation site.

. Determination of credits.

. Mitigation work plan.

. Maintenance plan.

. Performance standards.

. Monitoring requirements.

. Long-term site management plan.

. Adaptive management plan.

. Financial assurances.

PLANNED IMPACTS
POST PROJECT ACTIONS

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2.4 Post-Project Actions

2.4.1 Conducting Post-construction Surveys 

Ideally, any required compensatory mitigation should be implemented before the start of 

construction. If not implemented before construction, then the compensatory mitigation action 

would be implemented no later than when the construction activity impacts the resource of 

concern. Sometimes, the permitting authority may allow the compensatory mitigation action to 

be implemented after the construction. In these cases, the compensatory mitigation action 

should be completed as soon as possible, in order to minimize temporal losses. Temporal

losses for coral reefs may be substantial because of the slow rate of coral growth and 

recruitment.

Surveys, such as those discussed in Section 2.2.1, may be needed post-construction to 

determine the actual losses to aquatic resources. Due to the difficulty in predicting indirect 

impacts, such as sediment and turbidity impacts during construction, the indirect impacts may 

be over- or under-estimated in the planning stage. The post-construction survey provides a 

method to adjust the amount of compensatory mitigation necessary to address the actual 

amount of loss occurred. The permitting authorities will determine what level of detail is needed 

for the post-construction survey in consultation with other agencies as appropriate.

2.4.2 Long-Term Management of Compensatory Mitigation

Implementing the compensatory mitigation action is only the beginning of the process of 

ensuring unavoidable losses to coral reef resources are adequately replaced per applicable 

laws and regulations. Once the compensatory mitigation action is constructed, appropriate 

measures need to be incorporated to ensure the long-term durability and sustainability of the 

compensatory mitigation action. 

Directly after the compensatory mitigation action is executed, the project proponent begins to 

implement a monitoring program as approved by the permitting authorities to ensure the 

compensatory mitigation action is meeting its identified performance standards. Duration of

monitoring will be determined by the permitting authority. Compensatory mitigation actions are 

typically monitored for 10 years, but the duration may be shorter or longer depending on how 

quickly the compensatory mitigation action is expected to meet its performance standards. In 

the event that the compensatory mitigation action is not performing as anticipated, 

implementation of adaptive management measures may be necessary. Chapter 5 provides 

more information on performance standards, monitoring, and adaptive management.

Once the permitting authority has concurred that the compensatory mitigation action is meeting 

the targeted performance standards, regular management of the compensatory mitigation action 

will likely still be necessary. Depending on the compensatory mitigation action, regular 

management may be minimal. In some cases, such as if control of invasive species is required, 

regular management may be a substantial commitment. Project proponents should identify the 

long-term management activities of the compensatory mitigation during the planning process,

and discuss long-term management commitments and expectations with the permitting 

authority.
EMERGING TOOLS AND STRATEGIES

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2.4.3 Unauthorized Impacts to Coral Reefs During Construction

Accidents happen and may be noted during construction or during the post-construction survey. 

When unauthorized impacts happen during a planned activity (e.g., cable drag, anchoring, 

turbidity plumes associated with a permitted dredging project, and dredging occurring outside of 

permitted area), it is important to work closely with the regulatory and management agencies to 

quickly quantify and address the unauthorized impacts. Depending on the type of unauthorized 

impact, injury characterization and response steps may follow the protocols outlined in Chapter 

3. Responses may include agency enforcement action or an increase in compensatory 

mitigation requirements in accordance with applicable laws and regulations. 

2.5 Emerging Tools and Strategies 

As mentioned throughout this document, mitigating and restoring coral reef ecosystems is a 

relatively new science compared to mitigation and restoration of many other aquatic and 

terrestrial habitats. The science of, and management strategies for, coral reef mitigation and 

restoration continue to evolve. This section highlights a few emerging strategies for addressing 

the challenges of coral reef compensatory mitigation and restoration.

There are efforts underway in the Pacific by an interagency team to address some of the issues 

and challenges related to compensatory mitigation for coral reefs. The team aims to develop a 

series of “tools,” including a coral reef assessment methodology suitable for assessing condition 

at impact and mitigation sites, a model for determining replacement of lost resources, tools for 

incorporating temporal loss and uncertainty into mitigation requirements, and recommendations 

on mitigation performance standards and mitigation monitoring. Similar work is needed in the 

Atlantic/Caribbean.

2.5.1 Mitigation Banks and In-Lieu Fee Programs

Tools such as in-lieu fee programs and mitigation banks, which have been developed to 

improve compensatory mitigation efforts for other habitats, are being considered for use in coral 

reef ecosystems. Use of in-lieu fee programs and mitigation banks have the potential to provide 

more effective compensatory mitigation outcomes because they usually conduct those activities 

within a larger contiguous area rather than multiple small and disconnected projects spread out 

over many different sites. These programs are generally overseen by government agencies or 

conservation organizations with experience and a track record in restoration, and thus have a 

high likelihood of success. In the 2008 Mitigation Rule, USACE and EPA established a 

preference for using federally approved in-lieu fee programs and mitigation banks for 

compensatory mitigation over permittee-responsible mitigation sites. These tools and 

associated terms are defined below, and a short discussion of activities currently underway to 

develop these tools for use in coral reef systems follows. 

A significant challenge for these programs in marine systems is ownership, because 

government entities often own the submerged land, thus coral reefs are not usually privately 

owned. Legal agreements or permit approvals may be required for private entities to 

establish banks on government-owned submerged land. 

A mitigation bank is a site, or suite of sites, where resources (e.g., coral reef ecosystems, 

wetlands, streams, riparian areas) are restored, established, enhanced, and/or preserved for the 

purpose of providing compensatory mitigation for impacts authorized by federal, state, or 

PLANNED IMPACTS
EMERGING TOOLS AND STRATEGIES

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territorial permitting authorities. In general, a mitigation bank sells compensatory mitigation 

credits to a project proponent/permittee whose obligation to provide compensatory mitigation is 

then transferred to the mitigation bank sponsor. Credits are the unit of measure (e.g., a 

functional or area measure or other suitable metric) representing an attainment of ecological 

functions or condition at a compensatory mitigation site. The measure of function is based on 

the resources restored, established, enhanced, or preserved. Credits are defined specifically 

for each mitigation bank or in-lieu fee program, depending on the appropriate metrics or tools 

available for the resource type or the geographic area. Credits may be defined as acres, 

through the results of ecological assessment methods, such as functional or condition 

assessments, or other types of metrics. The operation and use of a mitigation bank are 

governed by a mitigation banking instrument approved by the applicable permitting authority (33 

CFR 332.2 and 40 CFR 230).

Hawaii is developing a proposal representing the first mitigation bank for coral reefs. The 

Hawaii DLNR mitigation bank site currently focuses on protection and restoration of corals in 

Kaneohe Bay. For more information on this effort, contact the USACE Honolulu District Office 

or Hawaii DLNR.

An in-lieu fee program is one involving the restoration, establishment, enhancement, and/or 

preservation of aquatic (includes both freshwater and marine) resources through funds paid to a 

governmental or non-profit natural resource management entity to satisfy compensatory 

mitigation for impacts authorized by federal, state, or territorial permitting authorities.

Similar to mitigation banks, an in-lieu fee program sells compensatory mitigation credits to 

project proponents/permittees whose obligation to provide compensatory mitigation is then 

transferred to the in-lieu fee program sponsor. However, subject to the approval of the 

permitting authority the in-lieu fee program may be allowed to sell “advance” credits prior to full 

implementation of the activity. The rules governing the operation and use of in-lieu fee 

programs are somewhat different from the rules governing operation and use of mitigation 

banks. The operation and use of an in-lieu fee program is governed by an in-lieu fee program 

instrument approved by the applicable permitting authority (33 CFR 332.2 and 40 CFR 230).

The USACE Honolulu District has received a proposal by the Micronesia Conservation Trust for 

an in-lieu fee program on Guam that would consist of terrestrial and marine compensatory 

mitigation projects to establish, restore, enhance, and/or preserve coral reefs. That project is 

currently on hold. For more information, contact USACE Honolulu District Office.
UNPLANNED IMPACT RESPONSE FRAMEWORK

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3.0 FRAMEWORK FOR RESPONDING TO UNPLANNED CORAL REEF 

IMPACTS

Unplanned impacts to coral reefs are caused by actions such as ship groundings, anchor drags, 

or exposure to oil and hazardous substances that cause injury to the reefs. There are certain 

elements of the processes for evaluating planned and unplanned coral reef impacts that are 

similar, such as minimizing response actions to reduce further injury, quantifying the impact, 

determining replacement value, evaluating restoration options, and quantifying the amount of 

restoration needed to restore the injury. However, there are many legal authorities that govern 

the response to, assessment of, and the determination of damages for unplanned coral reef 

events. Depending on the nature and location of the incident, there are multiple legal pathways 

that could be triggered at the federal, state, or territorial level.

As lead agencies can differ based on location of the injury (even within states and territories), it 

is recommended that the RP always consult with the land management agency first. Additional 

regulatory and management authorities will need to be consulted prior to taking any response

action. For events that occur within the boundaries of a National Park or National Marine 

Sanctuary, specific laws and regulations apply (e.g., for National Parks, the SURPA and for 

Marine Sanctuaries, the NMSA). For impacts due to oil or hazardous substance exposure, the 

NRDAR provisions found in OPA or CERCLA may apply. In cases where coral species listed as 

threatened or endangered under the ESA or their designated critical habitat are potentially 

impacted, consultation with NMFS may be required prior to any response action. State, 

territorial, or local laws may also apply and a detailed list of regulations that cover response and 

restoration activities to coral reef injury is found in Appendix I. Based on these laws and 

regulations, permits may also need to be obtained to authorize the recovery action.

In the aftermath of an unplanned impact the first priority, after human health and safety, is 

eliminating the source of the injury, such as a removing a grounded vessel or cleaning up an oil 

spill. Once the emergency actions have been completed, the process typically moves into 

conducting an injury assessment and determining restoration needs. The assessment and 

restoration methods listed in the following sections can be similar regardless of the source of 

injury, although there may be case-by-case variation. Again, the specific federal, state, 

territorial, or local agencies must be engaged early in the response to determine the specific 

laws, regulations, policies, and guidance that cover any response and restoration activities.

3.1 Natural Resource Damage Assessment and Restoration

Under OPA or CERCLA, NRDAR is the legal process that federal agencies, together with the 

states and tribes, use to evaluate the impacts of oil spills, hazardous waste sites, and ship 

groundings on natural resources, both along the nation's coast and throughout its interior. The 

agencies, referred to collectively as natural resource trustees, work together to identify the 

extent of natural resource injuries, the best methods for restoring them, and the type and 

amount of restoration required. In smaller vessel groundings, large groundings with no threat of 

oil or hazardous materials releases, and other unplanned events, other processes are used. 

Although similar to NRDAR there can be many variations depending upon the land 

management agency that has had trust resources impacted, and the legal authority under which 

those agencies work. For example, the NPS has specific guidance for unplanned events, which 

UNPLANNED IMPACTS
NATURAL RESOURCE DAMAGE ASSESSMENT AND RESTORATION

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can be found in the 2003 NPS Damage Assessment and Restoration Handbook.

The intent of the NRDAR process is to document, then restore, rehabilitate, replace, or acquire 

the equivalent of injured natural resources and services. It is not designed to impose punitive 

measures upon the RP, nor obtain money for other purposes, although some agencies have 

additional authorities to seek criminal and civil penalties associated with unplanned events. An 

injury is defined as any observable or measurable adverse change in a natural resource, or 

resource service. Extent of injury and restoration actions are usually determined relative to a 

baseline, which is defined as the condition that would have existed had the injury not occurred. 

Baseline is not necessarily constant, nor is it the same as the condition that occurred 

immediately prior to the injury, or the same as a long-term average condition. Following injury, 

primary restoration actions are intended to return the injured resource to baseline, while 

compensatory restoration provides compensation for the interim services or resources lost until 

the injury recovers. In addition to natural resource losses, impacts to coral reefs can also create 

losses to human use. Lost human use is not addressed in this Handbook.

The legal authorities that provide for damage assessment and restoration authorities vary (OPA, 

CERCLA, NMSA, SURPA, and individual state statutes) and, depending on the nature and 

location of the incident, there are multiple legal pathways that could be triggered at the federal, 

state, or territorial level. However, all generally follow the framework outlined below:

. A preliminary assessment is conducted to determine whether any impacts have 

occurred. Scientists may collect data, review scientific literature, and use mathematical 

models to help predict the effects of the incident on trust resources.

. A formal injury assessment and restoration determination or planning phase, 

during which the trustees quantify the injuries through scientific and economic studies 

and then identify potential restoration projects to offset the loss (e.g., beach and 

shoreline enhancements, creation of oyster reefs or other shellfish habitats, and 

programs to monitor the recovery of species and habitats). Under OPA, the restoration 

plan is released for public feedback. However, this is not a requirement of all legal 

authorities.

. Restoration selection and implementation aims to return the injured resources to 

their original condition and compensate the public for interim losses, e.g., the time it 

takes the resources to recover, as well as lost human use of the resources. Throughout 

the damage assessment process, the co-trustees may decide to work with the RP (the 

entity whose property or actions caused the injury). The RP may be requested to pay 

for the assessment and restoration, and may be invited to participate in restoration 

activities.

The process of determining restoration projects is driven by law, science, economics, and under 

OPA public input, and is led by designated federal, state, territorial, and tribal trustee agencies. 

The outcome of the damage assessment process is generally a settlement with an RP for 

“damages,” which can include agency response costs, the trustees’ cost of the damage 

assessment, and the cost of restoration (to be implemented by the trustees or RP), monitoring, 

and trustee oversight. Under OPA, in the event that the RP refuses to pay damages, NOAA 

and its co-trustees may file a lawsuit or submit a claim to the Oil Spill Liability Trust Fund.

Restoration under the damage assessment process generally falls into one of three categories 

outlined below:
RESPONSE AND RESOURCE PROTECTION

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. Emergency Restoration actions are those taken by trustees to prevent or reduce 

continuing resource injuries and avoid potentially irreversible loss of natural resources. 

In the case of unplanned coral reef impacts, these can include righting and stabilizing 

dislodged corals, removal or stabilization of rubble, and removal of other immediate 

threats such as anti-fouling paint.

. Primary Restoration includes actions conducted by trustees to return injured natural 

resources to the condition that would have existed if the incident had not occurred (this 

condition is usually referred to as the baseline). Some natural resources (such as coral 

reefs) might recover very slowly, or not even recover at all, from injuries. Trustees are 

authorized to conduct primary restoration to speed the recovery of the injured resources, 

such as reconstructing physical habitat that was destroyed, or taking measures to 

protect or increase the population of a threatened or endangered species. In the case of 

coral reef injuries this can include rebuilding structural complexity of the impact site, 

augmenting biological recovery with coral transplants, removing opportunistic species 

that could result in a phase shift at the site, or other actions that would facilitate recovery 

the injury site to baseline. Primary restoration will also include monitoring to ensure that

recovery of the resource impacts is proceeding.

. Compensatory Restoration includes actions conducted by the trustees to address the 

lost natural resource services that accrue from the date of injury until recovery to prespill conditions is completed. These projects typically occur offsite of the injuries but in 

rare occasions can also be onsite. While the resource is impaired, it is unable to provide 

services on which other parts of the ecosystem and the public rely. Trustees are 

authorized to ensure that compensatory restoration projects are implemented to 

compensate the public for these interim losses.

3.2 Response and Resource Protection

Following notification of the appropriate federal, state, and territorial agencies that an unplanned 

impact has occurred, emergency response activities may be initiated by a response agency 

and/or other resource agencies. The section below outlines two response actions that are 

specific to coral environments:

3.2.1 Vessel and/or Debris Removal 

Activities may be undertaken to remove the source of the impact (e.g., refloat and/or remove the 

vessel in the event of a grounding) and to prevent additional impacts such as fuel or oil release,

or injury caused by debris associated with the initial impact. In consultation with the appropriate 

agencies, the response agency may be required to prevent additional impacts resulting from the 

response prior to initiating emergency response actions. There are numerous examples of 

unplanned impacts to coral reefs resulting from vessel groundings in which the emergency 

response activities resulted in significant additional damage to the resource (e.g., the T/V 

Margara Puerto Rico grounding in 2006 and the M/V Jireh grounding in Puerto Rico in 2012). 

BMPs to avoid and minimize natural resource injuries to coral reef habitat benefit everyone 

involved, in that avoiding and minimizing these injuries reduces overall settlement costs to 

industry, as well as, helps resource agencies fulfill their mandates for public trust resources. 

Below is a list of BMPs that may help minimize the potential for additional impacts during a

vessel removal. This list is not all-inclusive and the trustee and regulatory agencies will make 

UNPLANNED IMPACTS
RESPONSE AND RESOURCE PROTECTION

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the final decisions as to when these activities are appropriate.

. Determine a vessel extraction path that will have the least impact to the surrounding 

coral habitat (may or may not be the same as the ingress path). This process can be 

facilitated through the use of bathymetric charts, aerial/satellite photography, and rapid 

area surveys by qualified divers (this practice is codified within the Wildlife sections of 

some USCG Area Contingency Plans and should only be undertaken in conjunction 

with emergency response actions to ensure the safety of participants collecting data).

. Temporary buoys should be used to mark the extraction path and differential global 

positioning system (DGPS) plots of the extraction path should be input into the 

grounded vessel and all towing vessels’ navigational systems to assist the salvers in

staying on course to avoid coral areas to the maximum extent possible.

. Portable DGPS units should be maintained at the bow and stern of the grounded vessel 

at all times to record any shift in the vessel’s position, as well as to record an accurate 

track of the extraction path prior to sinking.

. Grounded vessels often choose to take on ballast water to stabilize vessel and prevent 

rolling while salvage efforts are mobilized. Caution is needed in taking this action due 

to increased risk of impacts to resources, and the potential for releasing invasive 

species when the ballast water is released. As a general practice, petroleum products

often are removed immediately to prevent a spill. 

. If anchoring or mooring the grounded vessel or salvage vessels, minimize the number 

of anchors or spuds, control drag, and seek appropriate anchoring locations devoid of 

sensitive benthic habitats like coral reefs and sea grasses.

. Take actions to avoid prop scars and prop wash injuries to marine resources with all 

vessels, barges, and tugboats involved in salvage operations. In shallow water, avoid 

using the propulsion systems and, if possible, moor the tugs and use a ground tackle 

system to provide maneuvering and pull.

. Salvage activities should be conducted at sufficient tide and water depths to minimize 

any risk to reef resources and other sensitive habitats.

. Create and use designated anchorage areas that have been surveyed by divers and 

are absent of coral. It is further recommended that all anchors be placed with the 

assistance of divers to avoid all coral resources. Anchoring should not occur outside of 

the designated anchor grid boxes.

. Use floating lines for anchoring and salvage operations or secure lines to prevent line 

sweeping of coral and sea bed. If non-floating lines are used, line sweeping should be 

accounted for within the designated anchorage area.

. Install, monitor, and remove underwater equipment or booms to prevent coral damage 

or fish and wildlife entrapment.
EMERGENCY STABILIZATION AND TRIAGE

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3.2.2 Response-based Protection Tactics

Response-based protection tactics may be undertaken to “minimize or mitigate” impacts to 

natural resources or services. When there is a threat of oil or hazardous materials releases, 

decisions regarding response actions are made by response agencies, with technical input from 

resource agencies. When there is no threat of a release the decisions for response actions may 

fall to the land management agency. Response actions can be implemented either by a 

response agency (e.g., USCG), or an RP under the authority of the response agency or land 

management agency. These actions could include proactively removing and relocating 

sensitive resources such as corals, in order to minimize damage, allow the removal of a 

grounded vessel, to enable responder access, or refloat the vessel.

3.3 Emergency Stabilization and Triage

Often, it is possible to act to protect or save damaged corals and other organisms from 

additional impacts and mortality through site stabilization and biological triage.

3.3.1 Substrate Stabilization

Fractured substrate and loose rubble is of concern in large reef injuries associated with vessel 

groundings and commercial anchor drags. Unless fractured substrate is repaired, it may 

continue to erode the reef framework. Un-stabilized rubble may roll around and cause 

additional damage to the site and/or previously un-impacted areas if it is not removed. Rubble 

may need to be stabilized and/or incorporated into reef framework repair. However, rubble not 

used in those processes may need to be disposed of appropriately. Depending on the size and 

severity of the injury, substrate stabilization may be incorporated into the larger primary 

restoration plan.

3.3.2 Biological Triage 

Biological triage activities should occur as soon as possible following an injury. Fractured, 

dislodged, and overturned corals have a short window of opportunity in which they can be 

salvaged and stabilized. The goal of biological triage is to save those organisms that are at risk 

of mortality and/or loss from fragmentation or dislodgment from the reef. Biological triage may 

occur simultaneously with the initial site assessment, and should consist of saving as many atrisk corals as possible. Any biological triage activities that are conducted should be coordinated 

so as not to interfere with any response activities and evidence or data collection.

3.4 Assessing Impacts

During this phase, quantitative surveys are conducted to identify and quantify the negative 

impacts of the incident, including those resulting from cleanup or other actions taken as part of a 

response. Ecological studies are conducted to evaluate how, and to what degree, natural 

resources may have been injured. Morphological and geological studies may be conducted to 

evaluate the impacts to the substrate. Economic studies are used to determine how 

recreational activities, such as fishing and swimming, have been affected. If other resources 

such as infrastructure or cultural/historical resources have been impacted, the assessment will 

UNPLANNED IMPACTS
ASSESSMENT OF IMPACTS

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also include the nature and extent of those injuries including losses to the services those 

resources provide.

There are multiple assessment methods that can be used to characterize the extent of a coral 

reef impact. The degree of data collection necessary will be informed by multiple considerations 

such as those discussed above. A useful injury assessment should provide an estimate of the 

size of the impact, types and amounts of substrate damage, and reef habitat complexity, and 

describe the coral community composition including coral densities, size distribution, and 

species diversity. When possible, the injury assessment is used to compare the impact site to 

an un-impacted reference site that may have also been assessed, to provide baseline 

information for targeting restoration actions (Quataert et al., 2015). This information is used to 

quantify the injury to coral reef resources, inform the development of a restoration plan, and 

scale compensatory restoration options.

The following discussion of assessment techniques is based on the current detailed site 

assessment protocol that is used by the NOAA Damage Assessment and Restoration Program 

in responding to vessel groundings. The use of these techniques may vary by agency and other 

federal, state, and territorial agencies may use additional techniques not listed here. 

3.4.1 Mapping the Impact Site

The size of the impact can be estimated using multiple methods depending on the resources 

available. The use of traditional methods (measuring tapes, lines and buoys, and surface 

DGPS) can be difficult and time consuming, and can introduce measurement errors. While 

there is a possibility for error, these methods are sufficient for preliminary assessments to 

estimate the scale of the impact, and in cases where funding for more advanced assessment 

techniques is limited. These methods may also be sufficient to calculate damages when 

assessing small injuries.

In cases where there is a large impact, an underwater sonar mapping system like Aquamap is a 

good alternative, as it can precisely map the dimensions of the impact. Both side scan and 

multi-beam bathymetric survey methods are excellent remote mapping methodologies. A 

photomosaic of the impacted and surrounding reef area is an excellent tool for collecting highdefinition, large format images. Photography of the impacted and non-impacted reef sites 

should be performed as soon after the grounding as possible in order to visualize the contrast of 

white impacted reef, compared with the surrounding un-impacted reef. These actions provide 

photographic evidence of the entire site that can be used to help inform activities in the field, 

both pre- and post-reef restoration. If the technology is available, high-definition video of the 

site should be collected by divers in addition to photographs of the site.

3.4.2 Coral Community Composition

In order to describe the reef community present at various grounding sites, transects are 

typically performed outside the impact area by trained marine scientists. For injuries impacting 

large areas, 10 m2(10 m x 1 m) belt transects are typically performed. For injuries impacting 

smaller areas, normally four transects are sufficient. Within each transect the following data are 

recorded:

. The number of each coral type to lowest taxon (hard or soft corals where applicable).

. The size class of each colony (maximum height or width).
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. Condition of each coral (live, partial mortality, bleached, healthy, etc.). 

The data collected help determine the density of corals, their size distribution, species 

composition, and condition of the colonies found on the reefs outside the impact area. 

Depending on the reef community, other groups are sometimes included in the sampling 

protocol (e.g., sponges, giant clams). This information provides a better understanding of the 

resources lost within each of the grounding sites. The number and location of transects to be 

performed are determined once the extent of the impact has been delineated. A minimum of 10 

transects should be distributed around the perimeter of the impact, as long as the reference 

area that is being surveyed is believed to be similar to the impacted habitat. Sometimes 

transects cannot be done immediately adjacent to the impact because there is the potential for 

partial impacts from the grounding, or different habitat types are present. In that situation, areas 

that are as similar as possible to the impact are surveyed. 

Sampling sites can be stratified into different habitat types immediately adjacent to the injury to 

represent resources lost in those specific zones. Since coral demographics are highly 

influenced by depth, care should be taken to make site comparisons within similar depth zones. 

Depending on the reef type, belt transects are normally positioned perpendicular to the reef 

slope and include both spurs and grooves along the reef shelf at the same depth as the impact. 

Some transects may be placed inshore of the impact if the depth remains constant. If there is a 

change in depth, it could affect the composition of the reef community in the assessment area. 

Once transects are laid out, the location of each transect is mapped or recorded using buoys 

and a handheld DGPS. The direction and depth of each transect are also recorded. 

3.4.3 Topographic Complexity 

In order to estimate the topographic complexity of an impacted reef, measurements are taken to 

calculate the Rugosity Index (RI). RI is the ratio between the total length of a chain and the 

length of the same chain when molded to a reef surface. A perfectly flat surface has an RI of 

one. Higher numbers indicate a greater degree of architectural complexity. Rugosity transects 

are typically performed using a 10 to 20 m chain in similar areas as the belt transects. 

Measurements focus on the structural complexity of the reef substrate itself, and do not include 

octocorals. Side scan and multi-beam bathymetric surveys are an excellent method to conduct 

site rugosity calculations. The survey can cover 100% of the area, rather than the 

measurements a diver can collect by chain, which would then be averaged across the whole 

site. Bathymetric survey methods are safer (no divers in the water), faster (one boat, one day), 

and replicable, and the results can be pulled into graphic outputs that all users can understand. 

Transects can be cut through the survey data to calculate the RI for any of the locations on the 

impact site. Topographic complexity may also be calculated on multiple scales using LiDAR

data (Brock et al., 2006). 

Large sandy areas are normally left out of the rugosity measurements since they are usually 

identifiable in the mapping process, and are not included in the lost habitat estimates. Sand 

channels may or may not be included depending on the habitat type, size of sand channels, 

whether or not sand channels were able to be mapped, and how the rugosity measurements will 

be used. In addition to being a strong indicator of habitat refuge, rugosity is also a key measure 

of coastal protection in dissipating wave and water energy. 

There are two accepted equations to calculate rugosity: R = (l/d) and C = (1 – (d/l)), where “R” 

is a measure of rugosity, “C” measures complexity, “l” is the length of the fully extended chain, 

UNPLANNED IMPACTS
SCALING COMPENSATORY RESTORATION

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and “d” is the distance covered by the conformed chain. Returning rugosity to within 10% of the 

reference area is recommended as a restoration performance criteria target after groundings. 

To clarify this restoration target, the calculation method used must be specified. If the rugosity 

calculation (R) is used, then the rugosity should be returned to within five percent of the 

reference area. If the complexity equation (C) is used, 10% may be acceptable.

3.5 Scaling Compensation

The general framework used for determining how much a compensatory restoration action will 

offset a resource injury over time is referred to as the scaling approach. Where planned 

restoration actions are going to provide the same or comparable resources or services, the 

objective of scaling is to ensure that the quantity of the resources or services provided through 

restoration will be equivalent to interim losses (with discounting). Resource-to-resource or 

service-to-service techniques are usually rooted in the HEA or a Resource Equivalency Analysis 

(REA) method (Julius et al., 1995; Milon and Dodge, 2001).

3.5.1 Habitat/Resource Equivalency Analysis

The HEA method is generally used where the resource injury and/or the restoration action can 

(i) be generalized into categories (e.g., reef flat, reef crest, or outer reef) that represent their 

overall habitat services and functions and (ii) where the overall services per unit of injury 

(percent of service loss) or restoration (percent of service gain) and rate of recovery (shape and 

time) can be applied uniformly over a discrete area of injury or area of restoration. As 

mentioned in Section 2.3.1.2, HEA may also be used for crediting associated with DA permits 

for CWA §404 authorizations, mitigation banks, or in-lieu fee programs. Injury assessment data 

(e.g., degree and duration of oiling) are often used to attribute a degree of service loss for areas 

similarly affected, as well as, to predict an overall recovery timeframe for that area. Even in this 

relatively simple model, site-specific differences in coral abundance, coral and invertebrate 

species assemblages, location of other marine habitats such as seagrass, and other factors 

may need to be taken into account.

In order to effectively use HEA/REA, the spatial and temporal extent of the injury must first be 

quantified. This can be accomplished with a variety of field assessment approaches. An 

incremental approach can be used in which lost area or lost organisms are measured. A 

before-after-control-impact (BACI) monitoring design can be used to compare changes in 

abundance before and after an impact between control and impact sites (this is less commonly 

done for unplanned impacts, but can be appropriate for intentional injuries, such as 

development). After Control Impact (ACI) can be used to compare relative abundances

between control and impact sites; while less powerful than BACI (because poorly executed ACI 

can confound natural differences in trajectory among sites), ACI is often the best tool available 

for injury assessment following coral reef groundings. There are also a variety of ways to 

quantify biota, including:

. Counts per m2, extrapolated to a total population estimate.

. Percent cover, extrapolated to total m2 of biota.

. Biomass per unit area, extrapolated to total biomass.

. Volume per unit area, extrapolated to total volume of a species. 
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It is the process of determining how to quantify the lost biota at a site that, by default, ultimately 

selects a “metric” for the HEA/REA calculation. 

Generally speaking, indices (such as scores or ranks), qualitative data (rare, common, etc.) and 

quadrat counts (using arbitrary rules for counting what is in or out) are problematic metrics,

because they are difficult to defend for objectivity, or extrapolate to determine total loss. For 

coral reef injuries, the most common metrics are percent coral cover, total amount (hectares, 

etc.) of a given type of habitat, or counts (direct or extrapolated) of coral colonies by species 

and size categories. While typically more time-intensive to gather, count data is often more 

informative. Count data can provide an itemized inventory of colonies—which can be used to 

help calculate recovery (by providing detailed species demographic information), and can be 

modeled to account for differences in services provided among species or colony sizes. Some 

injuries may cause a relatively small loss in total coral cover, but result in a huge loss in the total 

number of coral colonies; count data is particularly useful in such instances. If needed, count 

data can also be used to back-calculate to alternative metrics such as percent cover, tissue, etc. 

while the reverse is more problematic.

Once the metric is selected, an HEA or REA is used to balance injury loss against restoration 

gain. Custom-developed spreadsheets, such as those used by NOAA, or publicly available 

HEA freeware (Kohler and Dodge, 2006) can be used to perform HEA. Though some federal 

agencies have utilized HEA/REA to work across habitat or ecosystem types, HEA/REA works 

best when the injured and restored habitats are directly comparable. The mathematical 

framework is relatively straightforward, but fundamentally an HEA is only as good or reliable as 

the input data for the calculation. 

A summary of the current REA scaling approach being used for coral reef injuries is described 

in the section below:

3.5.2 Example Coral REA Scaling Approach

A coral reef is a significantly more complex ecological system than the habitats for which REA 

and HEA were originally conceived. From site to site, reefs may be highly variable in terms of 

structure, rugosity, core species, species assemblages, and species diversity. Each reef 

“habitat” may also have many different core species of various sizes/ages. Further, each coral 

species present, is itself both a specific living resource and a feature that helps define a reef’s 

particular characteristics and services as habitat to other dependent natural resources. One 

square meter of reef can easily contain more than 20 individual stony or octocorals plus 

numerous other species (algae, sponges, invertebrates, crustaceans, small fish, etc.) that help 

comprise and/or rely upon the reef ecosystem. 

Depending on the type and degree of impacts and environmental setting, some individual 

resources may have the potential to recover relatively quickly (in years) while others (e.g., large 

and/or rare corals) may have very long recovery horizons (decades to centuries) or may never 

recover at all. 

In the U.S. Caribbean, generalizing losses and restoration relationships across all injured corals 

would likely result in under- or overestimation of interim coral losses and compensatory 

restoration needs. Therefore, a model comprised of a matrix of independent REAs that 

considered the injuries to, and recovery characteristics of, each core reef component (by 

species class) would better represent the complexities associated with the coral reef losses. 

UNPLANNED IMPACTS
DEVELOPMENT OF RESTORATION ALTERNATIVES

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Such a model would also provide a better estimate of both the interim coral losses, and the 

scale of restoration needed to restore the same or comparable resources or services to

compensate for those losses. As described in Kolinski et al. (2007) and Viehman et al. (2009),

this modified type of REA uses a resource-to-resource method that references the number 

organisms lost and the number gained through restoration. This approach examines the size 

distribution of species or functional groups of different corals and allows for comparisons 

between ecological services. This method allows for the quantification and aggregation of

losses across species, taking into account the different species injured, the sizes/ages lost, 

anticipated recovery rates, and, similarly, to identify the scale of the proposed restoration 

required to restore or replace coral species comparable to those lost over time.

Using this approach, the metric for scaling is a coral colony year (CCY). A CCY is not equal to 

the coral age. CCY is a proxy for services provided and/or, in the case of any injury, lost during 

a one-year period of time for a particular size and type of coral. While the initial CCY value is 

only directly comparable to others within the same size/species group, equivalency between 

sizes and groups can be gained by utilizing a combination of a linear size and service weighting. 

The key inputs into this analysis are the size/species distribution and the recovery time. The 

analysis also considers discounting and other inputs used in REA, such as relative function, 

time to maturity, and project lifespan. 

3.6 Coral Reef Restoration 

3.6.1 Development of Restoration Alternatives 

The goal of restoration planning is to identify and implement restoration actions that are 

appropriate to restore the natural resources or services equivalent to those injured or lost. As 

noted previously, restoration planning may involve two components: primary restoration and 

compensatory restoration. 

Restoration planning may be approached with the view that the injured areas are part of an 

integrated coral reef ecosystem and that restoration should be sited in a relevant geographical 

area. In addition, restoration actions should be consistent with local community objectives, and 

will also need to be consistent with the land management agencies’ policies. 

Potential project ideas vary but could generally be grouped into the following restoration 

alternatives (other options may be available that are not listed here): 

. Enhancement of Corals and Coral Reef Ecosystems 

This alternative is comprised of projects or activities that would directly enhance corals 

or other elements of the reef ecosystem. Potential projects could include coral 

transplantation, propagation of corals for relocation, translocation, and propagation of 

other keystone species such as Diadema antillarum (long spiny sea urchin). 

. Restoration of Existing and Future Impacts to Coral Reefs 

This alternative would include projects or activities that would restore coral reefs that 

have been impacted but where restoration would otherwise not occur. Potential 

projects could include the restoration at historic, orphan grounding sites to improve 

recovery, emergency restoration of corals harmed by future orphan groundings, and/or 

storm events. 
EVALUATION OF RESTORATION ALTERNATIVES

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. Prevention of Future Physical Impacts to Coral Reefs 

This alternative encompasses projects or activities that would be likely to prevent future 

physical harm to coral reefs, such as from vessel groundings, anchoring on reefs, 

smothering by invasive algae, and marine debris. Potential projects could include 

improved aids to navigation, improved nautical charts, improvements to pilotage 

systems for commercial vessels, and removal of marine debris that is harmful to, or 

threatens to harm coral resources. 

. Elimination and Reduction of External Reef Stressors

This alternative would include projects or activities that would decrease other external 

reef threats and stressors, such as from pollution, climate change, and overfishing. 

Potential projects could include implementation of BMPs to reduce land-based sources 

of pollution, improving MPA effectiveness, and implementation of projects to promote 

reef resilience.

. Restoration of Associated Habitats

This alternative would include projects or activities that would restore habitats 

commonly associated with coral reefs (but not the reefs themselves) and/or habitats 

that support the same fish species as coral reefs. Potential projects could include 

mangrove restoration, seagrass restoration, and coastal wetlands restoration.

3.6.2 Evaluation of Restoration Alternatives

The following criteria are generally used to evaluate restoration project alternatives and identify 

the restoration actions proposed for implementation (based on OPA but can be applicable to 

other unplanned events):

. The extent to which each alternative is expected to meet the restoration goals and 

objectives: This criterion addresses whether or not the restoration project can fully 

restore lost resources. In essence, to what degree can the project make the environment 

and public “whole” again after an injury.

. The likelihood of success of each restoration alternative: The technical factors that 

represent risk to successful project implementation, project function, long-term viability,

and sustainability of a restoration action need to be considered prior to implementation.

Alternatives susceptible to future degradation or loss, such as due to subsidence or 

erosion, are considered less viable. In addition, also consider whether difficulties in 

project implementation are likely and whether long-term maintenance of project features 

is likely to be necessary and feasible. 

. The extent to which each alternative will avoid collateral injury to natural 

resources as a result of implementing the alternative: Restoration actions should 

not result in significant additional losses of natural resources and should minimize the 

potential to affect surrounding resources during implementation. Restoration actions with 

less potential to adversely impact surrounding resources are generally viewed more 

favorably. Compatibility of a restoration action with surrounding land use, and potential 

conflicts with endangered species are also considered. 

. The extent to which each alternative benefits more than one natural resource or 

service: This criterion addresses the interrelationships among natural resources, and 

UNPLANNED IMPACTS
PERFORMANCE CRITERIA AND SUCCESS MONITORING

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between natural resources and the services they provide. Projects that provide benefits 

to more than one resource and/or yield more beneficial services overall are viewed more 

favorably.

. The effect of each alternative on public health and safety: Restoration actions that 

would negatively affect public health or safety are not appropriate. 

. The cost to carry out the alternative: When all other evaluation criteria above are 

considered equal between alternatives, then the costs of implementation factor into the 

evaluation of restoration alternatives. Factors that can affect and potentially increase the 

costs of implementing a restoration alternative can include project timing, access to the 

restoration site (e.g., with heavy equipment or for public use), acquisition of state or 

federal permits, acquisition of the land needed to complete a project, measures needed 

to provide for long-term protection of the restoration site, and the potential liability from 

project construction. The cost of monitoring sufficient to document restoration 

performance is a necessary component. 

However, the first criterion listed above has generally been a primary consideration, because it 

is critical to ensure that restoration will make the public whole for resource injuries and losses 

attributed to an incident. The evaluation of restoration alternatives using these criteria involves 

a balancing of interests in order to determine the best way to meet the restoration objective. 

3.6.3 Development of Performance Criteria and Success Monitoring

Performance criteria define short-term milestones that, if met, will provide reasonable assurance 

of project success in the long term. Monitoring provides the information necessary to determine 

whether the project is trending toward these milestones, or whether corrective action may be 

appropriate. Monitoring protocols may vary depending on the type of restoration required at 

different sites.

Following are examples of performance criteria developed by NOAA’s Restoration Center for 

primary restoration of a Caribbean vessel grounding site:

. Topographic complexity created by the non-live-coral substratum is returned to within 

10% of agreed reference areas using the calculation for topographic complexity that is C

= (1-d/l).

. Coral reef structures are expected to remain stable and intact. Corrective actions will be 

necessary if substantial loss of reattached material occurs (approximately 10% or more) 

or if dislodged or failing coral reef structures are likely to cause ancillary damage to the 

restored area or to adjacent reef.

An example from NOAA’s Restoration Center of success monitoring for restoration of that same 

Caribbean vessel grounding site is as follows:

. Restoration monitoring will be conducted at scheduled intervals following construction. 

Annual monitoring events will assess the structural stability of the restoration features, 

survival and stability of the reattached corals, and recruitment/colonization trends to 

determine that recovery is underway. The post-restoration monitoring plan would be 

initiated 90 days after construction is completed. After this, data would be collected 
POST-RESTORATION ACTIONS

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annually for five years, and then again at years seven and 10. A temperature logger 

would be deployed at the site during the initial monitoring and changed out during each 

of the subsequent monitoring events to account for potential climate change stressors 

that may impact the rate of recovery. Other visits may be required periodically to inspect 

the restoration site for potential damage due to effects of storms or other events. The 

schedule and objectives of a sample post-construction monitoring event are shown in 

Table 4.

Table 4: Example of a Post-Construction Monitoring Strategy.

Monitoring Objective Characteristics to Evaluate Methods

Structural Stability.

Scouring at the base of coral 

reef structures.

Tagging individual structures, 

photo- documentation, data 

collection, observations 

throughout the site.

Stability of coral reef 

structures (e.g., stable, loose, 

detached or missing).

Tagging individual structures, 

photo- documentation, data 

collection, observations 

throughout the site.

Coral Recruitment and 

Colonization.

Settlement and survival of 

coral recruits.

Permanent 50 cm X 50 cm 

quadrats.

Community composition of 

biota colonizing the restoration 

structures.

Permanent 50 cm X 50 cm 

quadrats, belt transects.

Coral Reattachment 

success.

Survival and stability of 

coral transplants.

Tagging individual colonies, 

photo-documentation, and 

data collection.

3.6.4 Post-Restoration Actions

The evaluation of service loss resulting from an impact, and gains from a restoration activity, are 

usually based on the assumption that both coral reef structure and biota provide overall coral 

reef services. Outside of the NPS, provided that coral reef structure is stable and the impacted 

area is returned by the restoration effort to rugosity levels similar to reference reef areas, the 

injury to the habitat component of service may be considered fully restored.

The biotic component of service is typically estimated by using reference transect data from 

adjacent areas to estimate the abundance and size distribution of biota that were impacted. 

After taking into account the survival of reattached biota in the injury area, the total surviving 

reattached corals would be subtracted from the estimates of total impacted corals to quantify the 

remaining loss of biological resources.

Corrective actions or compensatory mitigation may be necessary if the selected coral reef 

restoration actions are not meeting the performance criteria set forth in the restoration plan. 

These corrective actions may be minor or major.

UNPLANNED IMPACTS
PORTFOLIO OF MITIGATION AND RESTORATION OPTIONS

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4.0 CORAL REEF COMPENSATORY MITIGATION AND 

RESTORATION OPTIONS

The purpose of this section is to identify potential options that could be implemented as part 

of a coral reef restoration or compensatory mitigation activity, to meet federal, state, or 

territorial regulatory requirements, and to increase the chances of success of compensatory 

mitigation or restoration actions. Options suitable to be considered as compensatory 

mitigation activities are a subset of the broadly defined restoration activities, and must meet 

more stringent requirements by the permitting authority. Often similar goals, objectives, and 

methodologies are needed to identify, plan, and implement a restoration activity as a 

compensatory mitigation activity. For DA permits issued by USACE, compensatory mitigation 

plans must address the 12 mitigation plan elements listed in section 2.3.2, and described

more fully, at 33 CFR 332.4(c) and 40 CFR 230.

This section also provides information that can be used to evaluate whether options may be 

suitable for compensatory mitigation and/or restoration. The approval and permitting 

requirements and process for restoration projects vary between regulating authorities and 

funding organizations.

The options identified herein are not exhaustive but are based on review of proposed and/or 

implemented restoration activities. Depending upon the goals or objectives of a particular 

restoration or compensatory mitigation activity, the project proponent may combine several 

options together to meet those goals or objectives. In many cases the options listed in this 

chapter have been implemented as part of ecological restoration grants or activities, and not 

as compensation for a planned or unplanned injury. When activities are not implemented as 

compensation for a planned or unplanned coral reef injury, the degree of monitoring and 

performance evaluation may not be as thorough as would be required under a permitted

compensatory mitigation activity.

Restoration or compensatory mitigation activities should be planned and designed to meet 

the goals, objectives, and other requirements of those projects. Based on lessons learned, 

this section identifies potential opportunities or challenges that a project proponent may need 

to consider if incorporating these options into a coral restoration or compensatory mitigation 

plan. For each option, jurisdictions are identified where the options or specific activities have 

been implemented, either as general restoration activities, or compensatory mitigation.

This document represents the best available and most current information to date. This does 

not supersede or substitute for agency regulations or mandates. Please contact the 

appropriate agency(ies) for more specific information. See Appendix II for contact 

information for federal, state, and territorial agencies.

For compensatory mitigation, permanent loss should be permanently replaced. How this is 

accomplished varies across agencies, regions, and projects. Presently, it is essential that 

project completion be defined within the compliance processes. 
PROJECT APPROVAL PROCESS

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4.1 The Approval Process

4.1.1 Compensatory Mitigation Projects

Coral restoration activities may be conducted as compensatory mitigation for permits issued 

by federal, state, or territorial permitting authorities, or to fulfill enforcement requirements for 

unplanned coral resource impacts. The project proponent or RP should coordinate with the 

appropriate permitting or enforcement authorities to determine if there are any applicable 

regulations, guidance, or policy documents relevant to the coral restoration activity. For 

activities requiring USACE permits, the 2008 Mitigation Rule and its requirements apply.

5 The 

approval of the final compensatory mitigation plan lies with the applicable permitting 

authority. Project proponents and RPs need to work directly with the appropriate permitting 

or enforcement authorities (e.g., USACE, EPA, FWS, NMFS, and/or state or territorial 

agencies) to identify specific requirements and processes for developing their compensatory 

mitigation plans. The development of compensatory mitigation proposals is usually the 

responsibility of the permit applicant.

4.1.2 Restoration Projects

The approval requirements and process for restoration projects vary between the applicable 

regulations. A project proponent or RP should coordinate directly with the appropriate 

agencies to identify approval and associated permitting requirements. Restoration projects, 

regardless of the funding source, must comply with all regulatory requirements, as applicable, 

including any required federal, state, territorial, or local permits—such as DA permits issued 

by USACE. Project proponents should contact the appropriate federal, state, territorial, or 

local permitting authorities to determine if permits are required for the restoration projects.

Consideration of the most appropriate restoration approach by regulatory and management 

agencies and the project proponent or RP can inform the selection of options for coral reef 

restoration. There are various restoration approaches and the selection of a particular 

approach will be dependent on the ecological target(s), agency missions, and stakeholder 

interests and values.

4.2 Evaluating the Options

Many coral reef compensatory mitigation or restoration options are complementary and can 

be combined to increase the likelihood of project success and effective replacement of lost 

coral reef habitat, functions, and services. The strategic use of multiple options may be 

especially crucial to counteract the amplified stresses associated with climate change and 

ocean acidification (Stein et al., 2014).

Compensatory mitigation, or offset for coral reef ecosystems, is a relatively new science. 

Like restoration science for other aquatic habitats, such as wetlands or streams, it will take 

time and testing of methods to develop a solid compensatory mitigation standard for coral 

 

5 For USACE Civil Works projects the components of a mitigation plan as outlined in the 2008 Mitigation 

Rule apply. However, USACE Civil Works mitigation analysis follows the requirements in ER 1105-2-100.

OPTIONS
COMBINING OPTIONS

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With large activities that may have unavoidable impacts to complex coral reef ecosystems, it is often 

difficult to identify one type of compensatory mitigation action that would be adequate to address all of 

the lost functions and services resulting from the unavoidable impacts. Often “combination strategies” 

may be required. An example of how to determine the best “combination strategy” can be found in the 

USACE Cost Effectiveness/Incremental Cost Analysis requirements for ecosystem restoration and 

compensatory mitigation in the Civil Works Planning program. Under the USACE Civil Works planning 

process, after all avoidance and minimization measures are incorporated to the extent practicable, 

USACE determines—with consultation with resource agencies—the targeted compensatory mitigation 

requirements for the unavoidable impacts in terms of functional improvement to the habitat. Through an 

incremental analysis focusing on how different compensatory mitigation strategies or combinations of 

strategies at the same site or multiple sites improve the habitat, USACE first determines which individual 

strategies are acceptable to address different functional losses. Then USACE looks at what combination 

of the acceptable strategies provide the best return on investment in terms of habitat created. 

For example, a project that results in both biological and structural losses will likely require a combination 

of biological and structural mitigation. If multiple sites are proposed, USACE also evaluates and consults 

with other federal and state agencies to determine if the site locations are acceptable to address the 

functional losses from a perspective of a large coral reef system. In such an example, available 

alternatives may include increasing herbivore populations, improving water quality through removal of 

introduced sediments and nutrients, and removal of a nuisance algal species at Site A, and enhancement 

of coral structure to increase fish refugia and shore protection at Site B. These four activities would be 

compared individually, and in combination, to see which would provide the best option to address the 

individual functions that are needed to meet the compensatory mitigation requirement or target. 

Figure 4: Example of Incremental Analysis comparison of compensatory mitigation 

alternatives.

While structural enhancement may rank high for its abilities to compensate for structural losses, it is not 

always appropriate to compensate for biological losses. However, in this example herbivory 

enhancement, water quality improvements, or algae removal may be available alternatives that do 

address biological losses. Therefore, to meet the compensatory mitigation requirement or target, it will 

take a combination of structural enhancement at Site B, and herbivory enhancement and water quality 

improvements at Site A, and/or algae removal at Site A. An analysis of the available compensatory 

mitigation sites/options, likelihood of success, and cost are then used to determine which combination of 

the structural and biological alternatives provides the best return on investment. Figure 4 depicts an 

example where the combination of herbivory enhancement and water quality improvements at Site A and 

structural enhancements at Site B together may meet the compensatory mitigation requirement for 

habitat improvement. However, when algae removal is added at Site A there is minimal added 

improvement to the habitat, or minimal return on investment for the additional effort.

EXAMPLE: DETERMINING THE BEST OPTION FOR “COMBINATION STRATEGIES”
EVALUATING THE OPTIONS

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reef ecosystems. In the arena of unplanned coral reef impacts, there have been valuable 

advances in defining replacement, and these lessons should be shared across agencies and 

regions to maximize the transfer of knowledge and development of standards. Cost of a 

particular option can be difficult to quantify, because cost is location-specific and highly 

variable across options. Additionally, regulations are not consistent on how cost should be 

considered. For example, under NRDAR cost is only a deciding factor when all others are 

equal. Therefore, cost has not been included in the description of the various options that 

follow. For the NRDAR process, public comment may also weigh in as a factor in 

determining appropriate mitigation options. More detailed information on potential 

compensatory mitigation and restoration options is included in the following section. 

Information provided is categorized as follows:

Option Description: A general description of the option. The description also identifies 

other options that may be complementary and result in increased success. 

Case Study Examples: This section includes examples of projects that have included 

activities associated with that option. In most cases, the options have been implemented as 

restoration activities, or for purposes other than coral reef compensatory mitigation or 

compensatory restoration. There is limited experience in implementing these options as 

compensatory mitigation or compensatory restoration. This information can guide a project 

proponent to potential sources of information. 

Possible Activities: A list of various activities or methods related to the option. 

Considerations: This section considers key questions to determine which options may 

be best suited to meet compensatory mitigation or restoration requirements. The 

questions include: 

. What is the target resource/habitat being restored or mitigated? 

. What is the primary objective of the option going to address? 

. What are specific functions or services that the option is likely to provide? 

Opportunities: The opportunities listed are general considerations to help the project 

proponent identify which of these options may be best suited to their situation. The 

opportunities may not apply to all projects and locations and additional opportunities may exist 

that have not been identified. 

Challenges: This section identifies challenges particular to that option that may help the project 

proponent in determining the level of effort or coordination that may be necessary to propose or 

implement the option. The challenges may not apply to all projects and locations, and additional 

challenges may exist that have not been identified. 

It is necessary to consider that the type of impact is critical in the determination of mitigation 

appropriateness. For example, if impacts are direct removal of coral reef habitats, then creation 

(e.g., boulder reefs) may be the most appropriate type of compensatory mitigation. If impacts 

are a temporary degradation of the function of a coral reef ecosystem, then alternative 

mitigation methods, such as outplanting of corals, may be appropriate. Nursery grown corals 

and outplanting activities are worthwhile. However, these activities do not replace all of the 

functions provided by natural coral reefs. It is also important to consider that nursery grown 

species may not reflect the natural community composition of reefs. For example, slow-growing 

species or species that are not listed under ESA may be underrepresented in nursery stocks. 

Therefore, a portfolio of compensatory mitigation and restoration options is presented in Section

OPTIONS
WATER QUALITY IMPROVEMENTS

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4.3 that can be used as a tool for developing combination strategy proposals as described. 

The ability to establish appropriate performance criteria that can be quantitatively evaluated is 

still needed for most agencies to permit innovative mitigation options with limited or no history of 

successful implementation. Therefore, it is imperative to work with the regulatory and 

management agencies to select appropriate suites of options before investing significant time or 

effort on their development.

4.3. Portfolio of Compensatory Mitigation and Restoration Options

OPTION 1: Water Quality Improvements

Implement water quality improvement activities within the watershed to reduce erosion, runoff, 

sediment, and pollutant loads that are impacting the near shore waters.

Case Study Examples: Kaneohe Bay sewage diversion (Evans et al., 1986 and Hunter and 

Evans, 1995), Hawaii; removal of tuna effluent from Pago Pago Harbor, American Samoa; 

erosion control in Kahoolawe, Hawaii (Jokiel et al., 1995).

Possible Activities: 

. Terrestrial revegetation.

. Wetlands/stream restoration, enhancement.

. Storm water BMPs.

. Erosion control practices.

. Wastewater system improvements.

. Land acquisition, conservation easements, or protection of stabilized buffer areas.

Considerations:

. Targeted resource/habitat being restored/mitigated: Improving water quality improves 

the coral habitat.

. Primary objective: Reduce sediment and nutrient loading. Credit can only be received for 

new work that only resulted from mitigation, for example, not as response to a violation.

. Specific functions or services provided: Improved water quality would indirectly improve 

coral habitat condition, support recruitment and increased growth/fecundity, and improve 

recreational human use services provided by the habitat.

Opportunities:

. Potential to address a primary stressor to many coral reef ecosystems at the source.

. Science supports coral reef restoration with water quality improvements (Clark & Edwards, 

1999; Futch et al., 2011; Jokiel et al., 1995).

. Existing technology/ BMPs available for many storm water and wastewater improvements.

. In line with USCRTF watershed partnership initiative (Resolution 28.1).

Challenges:

. Difficult to link specific water quality improvements to amount of coral functional lift.

. Best when watershed plans or pollution budgets exist for the site, otherwise may require 

studies and planning prior to implementation to identify priority locations for action. 

. May take a long time to see coral reef response.

. Some sites may require large-scale implementation to significantly reduce sediment loads 

and runoff volumes.

. Challenges associated with land ownership, maintenance, and long-term management of 

water quality management measures.

. Climate change impacts may require altering the design of water quality improvement 

activities (e.g., due to a change in runoff because of extreme events or sea level rise) for 

them to be effective.
WATER QUALITY IMPROVEMENTS

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Pollution control activities in watersheds adjacent to coral reefs have been approved as compensatory 

mitigation for unavoidable coral impacts associated with some in-water projects. Such strategies may 

include: terrestrial revegetation, stream or conveyance stabilization, stream and wetland restoration, 

stream and coastal buffers, storm water retention and treatment, and wastewater treatment 

improvements. The theory behind use of these types of strategies is that by improving terrestrial 

areas upland, or adjacent to coral reef habitats, transport of land-based sources of pollution (e.g., 

sediment, nutrients, chemicals, pathogens) can be reduced, thereby improving water quality in 

receiving waters. Land-based sources of pollution are a primary threat to coral reefs; they can reduce 

coral growth and reproduction, increase incidence of harmful algal species, and cause diseases of reef 

organisms. The intended benefit to corals from pollution control activities is restoration of water quality 

conditions that are conducive to reef health, coral spawning, and recruitment.

A significant challenge in implementing water quality strategies as compensatory mitigation has been 

quantifying the ecological targets: What reduction in terrestrial pollutants must occur to achieve a 

particular gain in coral and thus achieve project success? This uncertainty is a barrier to determining 

the amount of mitigation required to achieve the desired result. However, water quality improvements 

have been demonstrated to result in coral improvement. Ongoing work to quantify the relationship 

between sediment loads and suspension and coral condition will help address this uncertainty.

There are two projects in Guam that illustrate particular challenges with this approach, and should be 

considered when evaluating compensatory mitigation options intended to improve water quality: Kilo 

Wharf and Alpha Bravo. It is important to recognize that both of these projects were permitted prior 

to 2008, thus the mitigation plans were not subject to the current standards of the 2008 Mitigation 

Rule.

The Kilo Wharf project consisted of dredge and fill to enlarge an existing wharf within Apra Harbor, 

Guam. The project was estimated to result in direct dredge and fill impacts to 4.75 ac of marine 

habitat, including approximately 0.4 ac of coral reef. To offset the losses associated with direct 

impacts of wharf expansion, reforestation of approximately 500 ac of grassland in Cetti Bay 

watershed was planned. Cetti Bay has been significantly impacted by erosion and sediment inputs 

from the adjacent watershed, affecting water quality and degrading its coral reefs. In this case, the 

size of the reforestation effort was determined by negotiation, as no data or models were available to 

estimate the amount of reforestation and reduction in sediment loads required to restore the Cetti Bay 

reefs. This project encountered challenges to the implementation of the reforestation effort. Local 

hunters use burning as a strategy to make game more visible, resulting in uncontrolled fires that 

destroy existing and replanted vegetation and expose soil. In this case, if legal protections for the 

land being reforested in perpetuity, such as a conservation easement, were implemented as part of 

the mitigation plan, the likelihood of success would have improved. No monitoring of sediment loads 

or coral recovery was required, therefore data to evaluate the success of this mitigation project are 

lacking.

The Alpha Bravo project involved fill for pier construction and dredging of 103 ac in Apra Harbor, 

Guam. Dredging impacted approximately 7.1 ac of coral. Off-site revegetation of a wetland area and 

reforestation of slopes above a stream and reservoir in the Piti watershed were approved as 

compensatory mitigation for impacts to corals. Similar to the Kilo Wharf mitigation, the amount of

revegetation undertaken was not based on knowledge of the effectiveness of the action in terms of 

coral restoration. While reforestation progress has been made, this project was not required to 

monitor sedimentation or to accomplish coral reef recovery. The requirement to monitor the coral reef 

system to track changes and complete the reforestation strategy would have improved the 

understanding of the effectiveness of this approach.

For more information on the Kilo Wharf or Alpha Bravo projects contact the USACE Honolulu District 

Regulatory Office.

EXAMPLE: IMPROVING WATER QUALITY TO MITIGATE FOR CORAL IMPACTS

OPTIONS
ENHANCE/INCREASE HERBIVORE POPULATIONS

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OPTION 2: Enhance/increase herbivore (e.g., fish, urchins) populations

Conduct activities that will enhance or increase populations of herbivorous fish and 

invertebrates on coral reefs. This is particularly appropriate where algal overgrowth is a 

direct threat to corals.

Case Study Examples: Kahekili Fishery Management Area, HI; Tripneustes gratila 

culture and outplanting in Kaneohe Bay, Oahu, HI; Diadema antillarum aquaculture and 

outplanting, FL.

Possible Activities:

. Herbivore aquaculture and release onto reefs.

. Herbivore fishery management.

Considerations:

. Targeted resource/habitat being restored/mitigated: Improving the herbivore population 

reduces algae and enhances coral recruitment and survival.

. Primary objective: Reduce invasive species and/or detrimental algae abundance.

. Specific functions or services provided: improved reef habitat supports 

recruitment, biodiversity, and invasive species control and improves recreational 

human use value.

Opportunities:

. Science supports importance of herbivores in maintaining healthy reefs.

. Benthic herbivores (urchins) can target specific areas (will not swim away like fish can).

. Demonstrated to increase coral growth and decrease macro-algal cover on reefs (in small 

scale).

. Culture is potentially feasible for some fish and invertebrate species.

. May shorten recovery time or enhance functional gains of natural coral reefs when

combined with other mitigation options (e.g., coral reef restoration).

. Could result in long-term benefits if populations are maintained.

Challenges:

. Some target species are difficult to culture.

. Public support for fishery restrictions can be challenging.

. May be difficult to define functional benefits (because it has not been done yet).

. May require perpetual re-stocking.

. Need to identify areas that could benefit from herbivore enhancement.

. Harvesting control would be needed to maintain released herbivore populations in wild.
CORAL RELOCATION

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OPTION 3: Coral relocation and corals of opportunity.

Collection and movement of at risk or damaged corals out of project footprint or damage area 

and stabilizing them either on-site, in a nursery for holding, or an alternate location.

Case Study Examples: Broward Segment III Shore Protection Project (FL), Key West (FL), HI 

(in progress).

Possible Activities:

. Collection of damaged coral colonies or fragments resulting from natural or anthropogenic 

direct impacts (e.g., corals of opportunity).

. Movement of at-risk corals from a project site.

. Relocating impacted or at-risk corals to suitable areas such as nurseries, adjacent reef 

areas, or restoration sites.

Considerations:

. Targeted resource/habitat being restored/mitigated: Rescue, stabilization, and storing 

or outplanting of at-risk corals enhances coral reef habitat quality by restoring biological 

and structural components of the habitat.

. Primary objective: Preserve coral colonies and live coral cover.

. Specific functions or services provided: Preservation of impacted or at-risk corals 

supports biodiversity, coral reef structure, and recreational and coastal protection human 

use services.

Opportunities:

. Successful relocations have been implemented.

. Rescues organisms that would otherwise be lost.

. May shorten recovery time of mitigation sites if used in conjunction with other mitigation 

projects (e.g., coral reef restoration).

. May increase coral reproduction and larval supply.

. Provides live topographic complexity that could further develop.

. May be advantageous for ESA listed corals.

. Opportunity to expand the scope to include octocorals and sponges.

Challenges: 

. May require unconventional approaches to define functional benefits.

. Potential to spread disease or other invasive species with transplanted corals.

. Not all species and sizes may be able to be transplanted.

. Additional work is needed on relocation/transplantation techniques for non-coral 

organisms (e.g., large habitat forming sponges).

. Consider assessment of relative reef resilience to assist in the selection of nursery and 

relocation/transplantation sites.

OPTIONS
OFFSITE PLACEMENT OF PHYSICAL STRUCTURE

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OPTION 4: Offsite placement of physical structure

This option could include multiple types of offsite structures (including artificial reefs) placed in an 

effort to compensate for coral reef that was impacted.

Case Study Examples: Port of Miami Phase I; Bal Harbor beach re-nourishment; Broward 

County Beach Shore Protection Project Segment III (all FL).

Possible Activities:

. Placement of material in a way that mimics natural coral reef structure.

. Deposition of boulders or other artificial material.

. Deposition of coarse dredge spoil.

. Placement of artificial reef modules.

. Outplanting of corals of opportunity or corals relocated as impact minimization onto 

structure.

Considerations:

. Targeted resource/habitat being restored/mitigated: Providing artificial structure has 

the potential to enhance fish and invertebrate habitat and coral establishment.

. Primary objective: To provide replacement substrate for the portions of the resource 

that were lost due to impacts or injuries.

. Specific functions or services provided: Providing replacement structure has the 

potential to enhance recruitment substrate for biological reef components and 

enhance recreational and coastal protection human use services.

Opportunities:

. Artificial structures have been implemented in most jurisdictions as a fisheries 

enhancement tool.

. Ample monitoring reports and literature available to help define functional benefits.

. Methodology for deployment/implementation relatively straightforward.

. Permission to place artificial structure within federal/state/territorial government owned 

submerged lands for compensatory mitigation generally is provided along with the impact 

authorization.

. If properly designed, can provide durable and stable substrate for recruitment of some 

coral species.

. Beneficial use potential to make reef structures from dredged coral.

. Potential to divert stressors from natural reefs to artificial reefs (e.g., diving).

. Much has been learned that can inform defining performance standards and monitoring.

. When used in conjunction with coral transplantation/relocation, could reduce time for 

coral function replacement.

Challenges:

. There is debate about whether constructed reefs can provide equivalent coral reef 

structure function and services to natural reef systems.

. Constructed reefs can have different, simpler structure and function than natural reef 

systems (Gilliam, 2012; Miller et al., 2009).

. May require additional regulatory reviews/approvals to place structure within waters 

regulated by federal, state, or territorial governments.

. Could result in significant additional negative impacts in some situations (e.g., aggregation 

of fish at detriment to other areas, easier fishing, change in water movement, physical 

damage in storms, unnatural blooms, and loss of existing habitat) (Kuffner et al., 2006).

. Site selection criteria must be established to minimize adverse effects to natural coral 

reefs.

. Difficult to design in a manner that mimics natural areas.

. Impacts to un-vegetated soft bottom habitats not well-understood.
MARINE DEBRIS AND DERELICT VESSEL REMOVAL

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OPTION 5: Removal of Marine Debris and Derelict Vessels

This option includes activities that would remove marine debris and/or derelict vessels, thereby 

reducing threats to coral reef habitat from future or sustained impacts from the debris.

Case Study Examples: Mitigation in Florida Keys National Marine Sanctuary for corals and 

seagrass (FL); removal of vessels at Palmyra atoll.

Possible Activities:

. Removal and disposal of derelict vessels.

. Removal of derelict fishing gear and other debris.

. Removal of tires.

Considerations:

. Targeted resource/habitat being restored/mitigated: Removal of marine debris reduces 

threats to coral reef habitat.

. Primary objective: Reduce physical damage to corals by removing marine debris. In 

some cases, remove pollution sources that can negatively affect reef habitat (e.g., algal 

blooms caused by metals from ship hulls).

. Specific functions or services provided: Removal of marine debris would protect 

sessile biological components of coral reef habitat and enhance recreational human use 

services.

Opportunities:

. May provide opportunities for community involvement and outreach.

. Easy to scale benefits.

. Many past programs as models.

. May help reduce stress on existing coral.

. Recent tsunamis provide good opportunities.

. May facilitate recovery of degraded sites.

. May prevent additional damage to coral reefs by moving debris that could migrate with 

storm and wave action into un-impacted areas.

. Considered a visual enhancement.

Challenges:

. Depending on the source of the marine debris, this may only provide short-term benefits (if 

one-time removal) or require a long-term commitment.

. Marine debris can be a chronic issue that may require long-term/permanent commitment or 

site protection requirements.

. May be difficult to define measurable performance standards.

. Need to remove fuel.

. Disposal options can be complicated and/or expensive.

. RPs can generally be identified for large affected sites, leaving only very small sites for use 

as compensatory mitigation.

. If there are regulations in place requiring the RP for the orphaned vessel or grounding to 

address removal and injuries, may not be able to be used as compensatory mitigation.

OPTIONS
 ENHANCE COMPLIANCE CAPACITY

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OPTION 6: Enhance Compliance Capacity

This option includes activities to meet compliance capacity gaps to manage MPAs or pro-active 

coral reef restoration areas (i.e., not associated as compensatory activities for planned or 

unplanned activities) or increasing education and awareness of existing federal, state, and 

territorial coral reef protection laws and requirements. It may also include increasing awareness 

and compliance with recommended actions to address unregulated issues impacting coral reefs 

(e.g., no authority to modify certain land use, recreational, or fishing practices that may be 

adversely impacting coral reefs). 

It is not acceptable to supplement funding for existing enforcement operations under 

designated federal, state, or local regulatory authorities.

Case Study Examples: There are currently no examples of this option being used as an 

element of compensatory mitigation or restoration, but this option is well-suited as a component 

of an overall mitigation package, as such enhancements to management actions can positively 

impact coral reef habitat condition.

Possible Activities:

. Fund staff to provide compliance oversight (overtime, night pay, special surveillance activity).

. Purchase of equipment to aid compliance activities (vessel, drop cameras, DGPS units).

. Support for or development of new volunteer surveillance with ability to call in enforcement 

officers.

. Conduct a threat assessment—inventorying threats to resources, identifying those threats that 

can be thwarted or influenced, and then prioritizing/assigning responsibility and actions to 

reduce threats. 

Considerations:

. Targeted resource/habitat being restored/mitigated: Enhanced compliance capacity can 

protect coral reefs, their structure, and their associated communities from negative impacts.

. Primary objective: Supplement enhanced compliance with targeted performance standards 

for an existing restoration project that was not implemented in association with a legal 

requirement (e.g., not associated with a planned or unplanned activity). This enhancement 

could improve the success of these other restoration options.

. Specific functions or services provided: Enhancing compliance with measures to reduce 

unregulated threats to coral reefs or providing outreach and awareness of existing federal,

state, or territorial coral protection regulations would improve coral reef habitat quality and

associated biological communities.

Opportunities:

. Provides good awareness and outreach, which could improve area-wide or jurisdiction-wide 

compliance.

. Enhanced compliance of performance standards at proactive restoration sites could help 

reduce stress on existing coral communities (e.g., stress from overfishing).

. When used in conjunction with other options, may help to ensure overall project success.

. Enhanced compliance at an MPA site or other area may increase awareness and reduce local 

stressors on a habitat or species.

Challenges:

. Need to ensure that compliance activity where capacity needs to be increased is not already an 

enforcement responsibility of a federal, state, territorial, or local agency.

. Need to ensure that funds for the compliance activity are not illegally or inappropriately 

supplementing a federal, state, territorial, or local program.

. Providing funds for long-term compliance support of appropriate activities may be difficult to 

maintain.

. Difficult to define performance standards and measures of success for increasing compliance 

capacity in terms of relating it directly to recovery of coral reef resources.
 CHALLENGES WITH MARINE PROTECTED AREAS

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MPAs are defined as “any area of the marine environment that has been reserved by federal, state, 

tribal, or territorial laws or regulations to provide lasting protection for part or all of the natural and 

cultural resources therein” (EO 13158). Large MPAs can include a zoning framework —a variety of 

smaller zones—to address various management objectives, such as no-take reserves where all 

extraction is prohibited, or areas that may be zoned to accommodate multiple uses. MPAs have 

been used effectively to regulate activities that can result in negative impacts to corals, including 

physical damage from improper vessel use, recreational overuse, and unsustainable or undesirable 

fishing practices.

MPAs appear to be an attractive option for consideration, in that they could provide an 

appropriate mechanism for long-term protection of compensatory mitigation activities if long-term 

management funds are allocated for the management and enforcement of the MPA. MPAs also 

provide a mechanism to prevent destruction or adverse modification of the coral reef habitat by 

managing human activities, such as fishing and recreation, to limit impacts from overuse. There 

is the potential for the establishment of an MPA to be considered as generating compensatory 

mitigation credit through preserving coral reefs that are at risk of future degradation. 

However, MPAs as a compensatory mitigation tool can be problematic. The first challenges arise in 

scaling of compensatory credit and addressing management costs over the long term. The social 

and cultural considerations may be more involved due to the perception of stakeholders and 

resource users having to bear the cost of compensatory mitigation or restoration for an impact 

through regulation of their activities. There are also legal, financial, and human resource 

commitments that are necessary for an MPA to be effective at meeting stated goals, objectives, and 

performance standards.

If an MPA approach were to be pursued, the use of relative reef resilience assessment and 

resilient MPA design tools should be part of the establishment process for new MPAs, expanding 

existing MPAs, and/or to consider additional restrictions (McClanahan et al., 2012; Gombos et al., 

2013; Green et al., 2014; Maynard et al., 2015). Reef resilience assessments include, among 

other things, incorporation of climate change considerations into those actions. This would be 

especially important in the case of existing MPAs as this assessment and analysis could provide 

spatial recommendations for new management activities or restrictions.

Activities aimed at increasing the effective management capacity of existing MPAs might be 

suitable as mitigation tools. However, in each case, careful estimates of benefits attributed to 

increasing the effective management capacity of existing MPAs, or creating new MPAs, should

be performed and compared to losses in natural reef or hardbottom ecosystems as a result of a 

project impact.

CHALLENGES WITH MARINE PROTECTED AREAS

OPTIONS
NUISANCE SPECIES REMOVAL

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OPTION 7: Nuisance species removal

Removal of nuisance and harmful species such as invasive algae, crown of thorns, and lionfish 

would reduce threats to coral reef habitats.

Case Study Examples: Lionfish (FL and USVI); Supersucker (Kaneohe Bay, Oahu, HI).

Possible Activities:

. Removal derbies or tournaments.

. Supersucker removal of invasive algae.

. Bounties to collect and remove nuisance species (e.g., lionfish).

. Volunteer efforts to remove nuisance species.

. Removal of corallivores (snails, crown of thorns).

Considerations:

. Targeted resource/habitat being restored/mitigated: Removal of nuisance or invasive 

species would improve coral reef habitat and condition of biological components.

. Primary objective: Removal of nuisance or invasive species that compete with, or prey 

upon, corals.

. Specific functions or services provided: Removal of nuisance or invasive species from 

reef habitat would restore coral reef habitat and function, natural species composition and 

diversity, and enhance recreational human use services.

Opportunities:

. Has been successful in Hawaii for some invasive algae.

. Potential for immediate restoration of some habitat functions in the short term.

. Provides for increased outreach opportunities and public awareness.

. Potential to use volunteers to assist in removal.

. Advances have been made in the science and techniques of invasive species removal in 

many jurisdictions.

. May prevent accelerated habitat decline caused by outbreaks/overgrowth of nuisance 

species.

Challenges:

. Based on available techniques, some invasive species are nearly impossible to control 

once they become established.

. Some locations may require long-term and ongoing removal strategies to meet 

performance standards.

. Long-term solutions to nuisance algae must also involve nutrient reduction and/or 

herbivory enhancement.

. Corallivore removal can expedite recovery.
RECREATIONAL MOORING BUOYS

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OPTION 8: Recreational Mooring Buoys

The purchase and installation of recreational mooring buoys could help to prevent future impacts

to coral reefs and allow recovery of sites impacted by overuse.

Case Study Examples: FKNMS, FL; Hilo Harbor, HI.

Possible Activities:

. Purchase of mooring supplies and equipment.

. Installation of new permanent moorings.

. Maintenance of broken moorings.

. Use surveys.

Considerations:

. Targeted resource/habitat being restored/mitigated: Coral reef habitat, sessile 

biological components, reef structure. 

. Primary objective: Prevent anchor and human use damage to corals and allow recovery 

of sites degraded from overuse.

. Specific functions or services provided: Coral reef structure and habitat, biological

components of habitat, and recreational and coastal protection human use services.

. Requires USACE authorization under the RHA.

Opportunities:

. Recreational mooring buoys have been implemented in many jurisdictions as a method to 

manage and reduce impacts to coral reef ecosystems.

. May prevent some damage from boat anchors.

. For compensatory mitigation, mooring buoys could be categorized as taking actions to 

reduce stressors on a habitat or species.

. Implementation is relatively straightforward.

. Potential for positive social and/or recreational impacts.

Challenges:

. Potential for habitat improvement is unknown and not demonstrated.

. May require additional enforcement capacity.

. May be limited to only those federal, state, and territorial agencies that have authority to 

implement and enforce recreational mooring activities.

. Requires long-term maintenance.

. May require additional regulatory reviews or approvals to place structure within waters 

regulated by federal, state, or territorial governments.

. Potential for damage to reefs from overuse at mooring sites.

. Depending on location and proposed restrictions, potential for increased tension between 

user groups and agency regulating and enforcing use. OPTIONS
AIDS TO NAVIGATION

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OPTION 9: Aids to Navigation

The purchase and installation of navigational aids could help to prevent future impacts to coral 

reefs and provide for increased enforcement of protected areas.

Case Study Examples: There are currently no examples of this option being used as an 

element of compensatory mitigation or restoration.

Possible Activities:

. Purchase of supplies and equipment.

. Installation of aids to navigation.

. Maintenance of navigation aids.

Considerations:

. Targeted resource/habitat being restored/mitigated: Coral reef habitat, biological 

components, reef structure.

. Primary objective: Preservation of existing reef areas through prevention of groundings.

. Specific functions or services provided: Coral reef habitat, recreational, coastal 

protection, and human use services.

. Requires USACE authorization under the RHA. 

. Requires state and USCG approval.

Opportunities:

. Relatively low-cost opportunity to prevent damage in areas where navigation problems 

exist or where MPA boundaries are unclear.

. May prevent unplanned vessel grounding impacts.

. May reduce the need for widening and deepening harbor entrance channels and 

turning basins.

Challenges:

. Established baseline documentation of vessel impacts is needed prior to implementation in 

order to accurately credit any benefit or impact reduction resulting from the project.

. Difficult to predict functional lift.

. Project is more preventative than direct restoration.
CONTROL AND REMOVAL OF TERRIGENOUS SEDIMENT

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OPTION 10: Control and removal of terrigenous sediment deposits.

The physical removal of sediment from coral reef habitat could enable biological recovery after 

smothering, and reduce future threats from sediment re-suspension and movement.

Case Study Examples: There are currently no examples of this option being used as an element 

of compensatory mitigation or restoration. In Lake Worth Lagoon (FL) this has been done for

seagrass restoration, see: http://www.co.palm-beach.fl.us/erm/lakes/estuarine/ibis/.

Possible Activities:

. Suction dredging.

. Sand capping.

. Mitigation actions, including soil stabilization and erosion control practices that reduce 

sediment inputs into the water column that can adversely affect coral reef habitat.

. Improvement in freshwater sheet flow and ground water discharge to reduced 

suspended solid and chemical contaminants as well as ocean water circulation to 

minimize sedimentation.

Considerations:

. Targeted resource/habitat being restored/mitigated: Coral reef habitat, biological 

components.

. Primary objective: Restore reef substrate conditions to promote re- establishment of 

coral reef ecosystem.

. Specific functions or services provided: Restoration of reef substrate would improve 

coral reef ecosystem condition, function, and recreational human use services.

Opportunities:

. Enables or potentially accelerates habitat recovery.

. Circulation improvements in habitat.

. Best practices from the treasure salvage industry could be adopted or refined.

Challenges:

. When proposing this activity near an active harbor basin, consideration needs to be given 

to the potential for ongoing introduction of terrigenous sediments and/or resuspension of 

terrigenous sediments and the potential impact on the mitigation location.

. Need to combine with water quality improvement/erosion control options to reduce future 

inputs of sediments.

. Often difficult to determine how much sediment needs to be removed to have a 

measurable recovery of coral reef resources.

. Removal process requires appropriate equipment and methodology to reduce potential 

impacts to entrainment of sensitive species.

. If there is potential for sediments to be contaminated, may require additional regulatory 

reviews/approvals, including sediment testing, to address disposal requirements.

. As compensatory mitigation, may require federal/state mechanism to meet site 

protection requirements (e.g., Fisheries Management Area designation). OPTIONS
CORAL POPULATION ENHANCEMENT

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OPTION 11: Active coral population enhancement (propagation and outplanting) 

Propagation of corals in a nursery setting using best husbandry practices. Corals can be used for 

mitigation or restoration activities.

Case Study Examples: Coral nurseries in FL, Puerto Rico, USVI; HI (in progress).

Possible Activities:

. In-water coral propagation (nurseries).

. Land-based propagation (aquaria).

. Corals of opportunity/caching.

. Outplanting of coral colonies into restoration locations.

. Remove corallivores (snails).

Considerations:

. Targeted resource/habitat being restored/mitigated: Coral reef habitat and structure.

. Primary objective: Improve coral reef ecosystem condition by increasing rugosity, 

habitat complexity, and live coral cover.

. Specific functions or services provided: Coral reef habitat, structure, function, species 

diversity, and recreational and coastal protection human use services.

. Using local corals that have been identified as, or cultured to be more resistant and/or 

resilient to climate change, ocean acidification, and/or disease, can maximize success.

Opportunities:

. Successful examples in Atlantic/Caribbean.

. Recent advances in scaling the mitigation requirement could inform planning.

. Growing list of successes and protocols developed (e.g., for staghorn coral Acropora 

cervicornis).

. Result in net gain of coral colonies.

. Genetic bank to safeguard against extreme events.

. Corals from coastal construction project impact areas could be used for propagation.

. Potential to enhance coral reproduction.

. For land-based propagation, ability to control conditions and relatively easy to monitor 

growth.

. Could enhance recovery strategies for ESA listed corals.

. Predator removal can expedite settlement and survivorship.

Challenges:

. Need to have multiple in-water sites to minimize risk of impact from mortality events and 

weather events.

. May have to increase capacity of existing nurseries or build new nurseries for large-scale 

projects.

. Outplanting site selection criteria are needed (with consideration of relative resilience 

assessment in this process). 

. Requires maintenance (e.g., predator removal).

. As compensatory mitigation, may require federal/state mechanism to meet site protection 

requirements (e.g., Fisheries Management Area designation).

. May require additional regulatory reviews/approvals to place structures or outplantings 

within waters regulated by federal, state, or territorial governments.

. Predator removal can be labor-intensive.
SAND AND RUBBLE STABILIZATION OR REMOVAL

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OPTION 12: Sand and rubble stabilization or removal

Stabilization or removal of sand and rubble generated by an impact to minimize physical damage 

to existing coral reef habitat and improve the chance for natural recovery (Gilliam, 2012) to occur.

Case Study Examples: Cape Flattery, HI

Possible Activities:

. Removal of rubble or sand to offshore or land-based dumping areas.

. Stabilization of rubble or sand using cement or artificial structures.

. Dredging sand and rubble.

Considerations:

. Targeted resource/habitat being restored/mitigated: Coral reef habitat, sessile 

biological organisms.

. Primary objective: Reduce physical damage to coral reef habitat caused by loose 

rubble and sand generated by an impact.

. Specific functions or services provided: Coral reef species diversity.

Opportunities:

. May facilitate recovery at sites that currently cannot recover naturally.

. May increase connectivity between natural reef communities.

. May help to prevent future direct impacts from loose material.

. Easier to implement at a small scale.

Challenges:

. If there is potential for sediment to be contaminated, may require additional regulatory 

reviews/approvals, including sediment testing, to address disposal requirements.

. BMPs for removal need to be developed. Large-scale activities may be complex to 

implement.

. May lose functions provided by sand and rubble communities.

. As compensatory mitigation, may require federal/state/territorial government approval or 

permit to place artificial structure in submerged lands.

OPTIONS
STABILIZATION AND ENHANCEMENT OF IMPACTED REEF STRUCTURE

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OPTION 13: Stabilization and enhancement of impacted coral reef structure

On-site action to stabilize and enhance impacted coral reef structure after an impact; structure 

should be comparable in order to mimic size, complexity, and height of the original community,

and provide appropriate surface for recruitment and natural recovery. This option could help to 

prevent future direct impacts from loose material.

Case Study Examples: FKNMS Wellwood grounding site.

Possible Activities:

. Engineering services.

. Construction services.

. Removal of debris.

. Re-cementing severed corals.

. Coral propagation and outplanting.

Considerations:

. Targeted resource/habitat being restored/mitigated: Coral reef habitat, structure, 

biological components.

. Primary objective: Improve the quality of damaged reef habitat.

. Specific functions or services provided: Coral reef habitat, structure, function, species 

diversity, and recreational and coastal protection human use services.

Opportunities:

. Successful examples in FL for grounding scars.

. Allows natural recruitment and could be seeded with transplants from impact area or 

nursery-reared corals.

. Restores function and habitat structure.

. Easier to implement at a small scale.

. Able to define functional benefits.

Challenges:

. Must ensure coral reef stability in wave events.

. As compensatory mitigation, may require federal/state/territorial government approval or 

permit to remove unconsolidated substrata from submerged lands.
PERFORMANCE STANDARDS AND MONITORING

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5.0 PERFORMANCE STANDARDS AND MONITORING

Effective compensatory mitigation or restoration is the replacement or improvement of ecosystem 

functions and services by achieving the objectives of compensatory mitigation or restoration projects. 

Objective and verifiable performance standards are critical for assessing the success of a compensatory 

mitigation or restoration project in meeting those objectives. Since each compensatory mitigation 

activity has its own unique conditions and requirements, performance standards define what success 

looks like for that specific project—clarifying for the project proponent and the permit authorities when 

the compensatory mitigation activity will be considered completed. Performance standards are

benchmarks for evaluating the attainment of project objectives, and allow project evaluators to 

determine if the site is developing into the desired resource type and providing the expected functions.

Performance standards are normally established prior to implementing a compensatory mitigation or 

restoration project, and the standards should be based on attributes that are observable or measurable. 

Performance standards will usually be tailored to the objectives that are specific to the individual project,

because each site and its restoration potential will likely be different. Since there have only been a 

limited number of coral reef compensatory mitigation activities implemented, and site conditions for each 

are unique, hypothetical performance standards are provided in this section to provide examples for a 

project proponent to consider when developing performance standards.

It is generally recommended that each project have performance standards in three categories. 

All three are observable, measurable, trackable, and necessary for the sustainability of the site. 

Performance measures are needed to better ensure successful and sustainable compensatory 

mitigation and restoration activities given the uncertainty inherent in coral reef restoration 

projects. The categories are:

. Administrative Measures.

. Ecological Performance Standards.

. Adaptive Management Measures. 

5.1 Administrative Measures

Administrative measures ensure work is accomplished, monitored, maintained, and managed, 

and that corrective actions are taken as needed. These are the easiest performance 

measures to define and track. Administrative measures may include: the entity responsible 

for implementing the project; the financial arrangements including provisions for short-term 

(guarantees for any construction and monitoring) and long-term funding (including financing);

the size of the project site; the work to be done to reduce stressors or transplant corals; the 

parameters to be measured; requirements for marking and protecting the compensation area;

and frequency of monitoring.

Hypothetical example Administrative Standards:

. Coral Lovers Forever shall outplant 10,000 staghorn coral (Acropora cervicornis) nubs 

> 3 cm to Polypy Bay at depths of 3 - 10 m between January 1 and March 30, 2015 

using methods “x”, “y”, and “z”.

. Percent survival and percent partial colony survival of outplanted staghorn coral in 

Polypy Bay shall be monitored at six months, one year, and annually for five years. 

PERFORMANCE STANDARDS

& MONITORING
ECOLOGICAL PERFORMANCE STANDARDS

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. Reports summarizing current and past survival shall be submitted to Department of 

Coral Protection within two months after completion of monitoring. Reports shall 

include an executive summary, monitoring methods, a graph showing percent 

survival over time, and recommended corrective actions.

. Department of Coral Protection shall remove invasive macroalgae by the 

Supersucker from 20 ac of patch reef in Polypy Bay by January 1, 2015.

. The number of fishing violations based on inspections for four hours per week at 

random times shall decline by 75% from baseline.

5.2 Ecological Performance Standards

Ecological performance standards ensure that the compensatory mitigation project or 

restoration site achieves the ecological condition expected as a result of the restoration. 

Ecological performance standards should assess the ecological response to a compensatory 

mitigation action or restoration action, to help determine whether the activity is going to result 

in the desired ecological structure, function, or condition. Ecological performance standards 

are also used to assess the ecological response to compensatory mitigation or restoration 

actions, to help determine whether the compensatory mitigation project or restoration project 

will be providing the desired ecological functions and services. Ecological performance 

standards can measure reduction in stressors, such as fishing pressure, algal cover, sediment 

inputs, or water quality conditions. Performance standards intended to measure stressor 

reduction based on water quality monitoring and pollutant inputs should be used with caution. 

These parameters are extremely variable, and expensive to measure reliably. It is very 

challenging to distinguish real changes resulting from implementation of pollution controls from 

natural variation in pollutant concentrations and loads. Existing information collected by other 

entities may be available to define baseline conditions and monitor changes. For example, 

where available, U.S. Geological Survey stream gauges may be collecting useful information 

related to water quality parameters. 

In addition, or alternatively, ecological measures can involve structural or condition 

measurements of the coral reef ecosystem. Structural and condition measurements may be 

based on measurements or metrics used in the condition or functional assessment method, 

and/or comparisons to reference sites where human disturbance is minimal. For example, 

ecological measures may involve percent coral cover, number of colonies by size and/or 

morphology, number of coral species, and abundance or biomass of herbivorous fish. 

Ecological performance standards should also take into account the expected stages of 

restoration or recovery. This allows performance standards to reflect measurements of 

ecosystem attributes that are expected to be exhibited during the required monitoring period,

which might occur when the project is still in the restoration or recovery stage (i.e., these 

measurements may be different from those of fully restored/recovered ecosystems). Tailoring 

ecological performance standards to different stages of recovery will also help Identify 

potential problems early, signaling the need to potentially initiate adaptive management 

strategies.

Hypothetical examples of Ecological Performance Standards:

. Based on monthly water quality samples at three sites, the mean nitrate 

concentration shall decline at least 20% from baseline values measured monthly for 

one year prior to restoration actions.
ADAPTIVE MANAGEMENT MEASURES

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. Average percent macroalgal cover shall be <10% each quarter.

. Average density of coral colonies shall be >3 per m2. At least 15% of colonies 

must be >40 cm.

. Survival of transplanted coral colonies must be >80% over five years. Partial colony 

survival must average >50%.

Useful information on ecological performance standards and potential thresholds, especially as 

it relates to measuring performance of land-based pollution reduction measures, can be found in 

the USCRTF’s Watershed Partnership Initiative Priority Ecosystem Indicators (2016).

5.3 Adaptive Management Measures

Adaptive management measures are typically considered as an aspect of administrative 

measures. However, adaptive management measures may also apply to ecological 

performance standards. If an existing ecological performance standard were not adequate to 

evaluate the performance, it may need to be modified to better evaluate the success of the 

compensatory mitigation activity. For example, the performance standard may have defined an 

acceptable level of sediment or turbidity in the water that is too large of a range to distinguish a 

difference in coral recovery; that performance standard may need to be modified to better 

distinguish the changes in sediment and turbidity to evaluate if the compensatory mitigation 

activity is on the desired trajectory. For compensatory mitigation activities that may have a high 

risk or uncertainty of success in part of the performance, it is a good practice to develop an 

adaptive management plan to identify when and what type of corrective actions may be needed 

if the activity is not meeting the performance standards. USACE developed “The application of 

adaptive management to ecosystem restoration projects” (Fischenich et al., 2012). This report 

is a good resource for understanding how to develop adaptive management plans for 

restoration and compensatory mitigation actions. Following are hypothetical examples of 

adaptive management standards.

Hypothetical examples of Adaptive Management Standards:

. In the event that >50% of outplanted staghorn coral die or are lost within the first five 

years, an equal number of nubs >5 cm will be outplanted to Polypy Bay within three

months of the mortality.

. In the case that an unforeseen event severely damages the Polypy Bay restoration 

project and impedes recovery, Coral Lovers Forever shall convene a meeting within 

one month of the event with Department of Coral Protection to determine how to 

proceed with this or an alternative restoration project. Coral Lovers Forever shall be 

prepared to present options for consideration.

5.4 Monitoring and Reporting of Project Performance

Monitoring provides the information necessary to determine whether a project is progressing 

toward the stated performance standards. If the project is not meeting performance 

standards or targets as anticipated, adaptive management or other corrective actions may be 

necessary to get the mitigation area on a track to success. Monitoring programs should be 

created along with the development of the compensatory mitigation plan, to ensure that the 

PERFORMANCE STANDARDS

& MONITORING
MONITORING AND REPORTING PROJECT PERFORMANCE

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monitoring strategy is consistent with the performance standards and provides an effective 

incremental assessment of the mitigation action's progress toward successfully meeting those 

standards. When monitoring programs are developed after the mitigation plan and/or 

developed separately by third parties, a wide variety of information may be collected on the 

area but that information may not be relevant to measuring the mitigation areas progress 

toward successfully meeting the performance standards. Assessing progress of the 

restoration project is critical because decisions about adaptive management will be based on 

progress toward achieving performance standards. The monitoring program must include the 

specific parameters to be measured or assessed by the applicable performance standards. 

The monitoring report should include data to demonstrate whether a particular performance 

standard is met. The monitoring program may also identify adaptive management or 

corrective actions that can be taken to attempt to achieve the performance standards that are 

not being met.

Performance monitoring need not be as comprehensive as the initial characterization of the 

impact site. In fact, performance monitoring might focus entirely on measuring stressor 

reduction, rather than on condition of the coral reef ecosystem. In most cases, ecological 

performance monitoring should use coral ecosystem assessment methods that are 

compatible with the original impact characterization so that recovery can be assessed against 

the original loss. A common problem with monitoring programs is that many criteria may be 

monitored, but unless the monitoring program was appropriately designed to answer the 

correct question (i.e., the success criteria), the data may fail to directly address progress 

toward the performance standards.

Compensatory mitigation or restoration projects should specify monitoring and reporting 

requirements. These requirements should include the frequency of monitoring, which 

performance standards should be assessed at a particular time during the monitoring period, 

the content of monitoring reports, and when monitoring reports need to be submitted to 

regulatory agencies, resources agencies, or other parties (e.g., annual monitoring reports). 

Monitoring reports should be made available to interested parties to share information on 

project outcomes and lessons learned to advance the science and practice of coral reef 

compensatory mitigation and restoration.
RECOMMENDATIONS AND NEXT STEPS

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6.0 RECOMMENDATIONS AND NEXT STEPS

This Handbook is the first attempt to document and summarize the current state of practice 

with respect to addressing coral reef impacts from planned and unplanned activities. As 

stated earlier, agreement and consistency is growing across the regulatory and management 

agencies about BMPs for mitigation and restoration of impacts. However, there may still be 

challenges working with multiple agencies that have varying mandates and policies. 

With the ongoing and increasing threats from climate change and ocean acidification, project 

proponents should work closely with the appropriate permitting authorities to determine how to 

address climate change considerations in their projects and mitigation actions. Incorporating 

climate change considerations in mitigation planning helps to incorporate risk-informed 

decision-making, adaptive learning, and preparedness planning, as promoted in EO 13653. 

Climate change adaptation is a burgeoning area—including growing availability of information,

resources, and tools. As these tools become more readily available, the USCRTF will seek

the best methods to share this information with USCRTF members, stakeholders, and the 

public.

The USCRTF is particularly well-suited to facilitate the sharing of information on the continued 

evolution of coral impact response. All the relevant federal, state, and territorial agencies that 

deal with either planned or unplanned impacts to corals are members of the USCRTF. Many 

of these agencies have participated in the Coral Injury Working Group, and in the development 

of this Handbook. As noted within the Handbook, addressing coral reef impacts is complex, 

and there is a great deal of uncertainty surrounding many of the currently available options 

and tools. 

It is the recommendation of USCRTF, that due to the complex nature of the coral reef 

ecosystem, and the even more complex nature of identifying and providing appropriate

compensatory mitigation for lost ecosystem services, the emphasis on maximizing

avoidance and minimization of impacts cannot be overstated.

There are many emerging tools and strategies for addressing coral impacts from planned or 

unplanned events. As more options are implemented, BMPs will be better defined for the 

avoidance, minimization, compensation for, and restoration of impacts to coral reefs. In its role 

in facilitating the sharing of information that promotes the protection and restoration of coral 

reefs, the USCRTF will determine the most effective manner to provide updated information as 

tools, strategies, and BMPs mature in the future.

RECOMMENDATIONS & 

NEXT STEPS
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Fischenich, C. (2012). The application of Adaptive Management to ecosystem restoration 

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Quataert, E., Storlazzi, C., van Rooijen, A., Cheriton, O, and van Dongeren, A (2015). The 

influence of coral reefs and climate change on wave-driven flooding of tropical 

coastlines. Geophysical Research Letters, 42(15): 6407-6415.

Rinkevich, B. (2005). Conservation of coral reefs through active restoration measures: recent 

approaches and last decade progress. Environmental Science Technology, 29: 4333-

4342.

Seaman, W. (2000). Artificial Reef Evaluation: With application to natural marine habitats. 

Boca Raton, FL: CRC Press.

Smalley, D.H. and Mueller, A.J. (2004). Water Resources Development under the Fish and 

Wildlife Coordination Act. Prepared under contract for the Division of Habitat and 

Resource Conservation, U.S. Fish and Wildlife Service.

Spalding, M. D., Ravilious, C., and Green, E. P. (2001). World Atlas of Coral Reefs. Berkeley: 

University of California Press.

Stephens, N. R. (2007). Stony coral transplantation associated with coastal and marine 

construction activities. Master’s Thesis. NOVA Southeastern University 

Oceanographic Center.

Stevenson, R.J. and Hauer, F.R. (2002). Incorporating hydrogeomorphic and index of 

biological integrity approaches for environmental assessment of wetlands. Journal of 

North American Benthological Society, 21: 502-513.

Stein, B.A., P. Glick, N. Edelson, and A. Staudt (eds.) (2014). Climate-Smart Conservation: 

Putting Adaptation Principles into Practice. National Wildlife Federation, Washington, 

D.C. http://www.nwf.org/pdf/Climate-Smart-Conservation/NWF-Climate-SmartConservation_5-08-14.pdf. 

Stein, E.D., Brinson, M., Rains, M.C., Kleindl, W., and Hauer, F.R. (2009). Wetland 

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Thanner, S. E., McIntosh, T. L., McIntosh, Blair, S.M. (2006). Development of benthic and 

fish assemblages on artificial reef materials compared to adjacent natural reef 

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growth of corals transplanted to concrete armor mat tiles in southeast Florida: 

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REFERENCES

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Unsworth, R., and Bishop, R. (1994). Assessing natural resource damages using 

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http://www.coris.noaa.gov/activities/uscrtf_watershed_tools/Priority_Ecosystem_Indic

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Viehman, S., Thur S.M., and Piniak, G.A. 2009. Coral reef metrics and habitat equivalency 

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Yoshioka, B., Adams, T., Rieck, B., and Cynthia, B. (2004). Final Report - Investigations of 

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APPENDICES

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APPENDICES
APPENDIX I – LEGAL AND POLICY SUMMARY

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99

Appendix I – Legal and Policy Summary 

There are numerous laws and regulations that govern activities in and around coral reef ecosystems. 

In some instances, activities in coral reefs may trigger multiple authorities across various federal, 

and state, or territorial agencies. Project proponents may be most familiar with the permitting 

requirements under CWA §404, and EFH consultation requirements under MSA §305(b) for planned 

activities, and with the NRDAR requirements for unplanned impacts. This appendix provides a more 

comprehensive list of laws and regulations that apply to activities and impacts within coral reef 

ecosystems. However, this is not an exhaustive list of every relevant federal, state, territorial, or 

Tribal authority. 

The following two tables present the federal (Table 5), and state or territorial (Table 6) laws, 

regulations, and statutes that govern activities that may impact coral reefs. Specific sections of 

various regulations have been listed separately, because they are particularly applicable to activities 

that may impact coral reefs; however, it should be noted, that they are not the only sections of the 

relevant policies listed here that may apply in each situation. Links to the full language for each 

have been provided where possible. 

Table 5: Collection of federal laws and regulations that govern activities that may impact coral reefs. 

Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

Abandoned

Shipwreck Act

43 U.S.C. §§2101-

2106

NPS Requires states to protect and preserve abandoned 

shipwrecks in their waters for recreational and 

historical purposes, encouraging the creation of 

underwater parks to provide additional protection.

Antiquities 

Act/National 

Monuments

54 U.S.C. §320301 

U.S. President Authorizes the President to designate landmarks, 

structures, and “other objects of historic or scientific 

interest” as national monuments. 

Clean Water Act

33 U.S.C. §§1251-

1387 and it’s 

implementing 

regulations. 

EPA, USACE, and

States/Territories

 (S/T)

The CWA prohibits the unauthorized discharge of 

pollutants into U.S. waters in an effort to restore and 

maintain physical, chemical and biological integrity of 

waters. Particular sections of note include: 

. CWA §301, the prohibition against unauthorized 

discharge, technology-based pollutant reduction 

requirements for industrial and municipal 

permittees. 

. CWA §303 water quality standards (WQS) 

program. States, tribes, and territories establish 

designated uses, water quality criteria, and an 

anti-degradation policy for waters within their 

jurisdictions, which are then submitted to EPA for 

review and approval or disapproval. Water quality 

standards are not “effective” for Clean Water Act 

purposes until approved or established by EPA. 

. CWA §309, EPA authority to initiate administrative 

and judicial enforcement of the prohibition against 

unpermitted discharge, and violations of discharge 

permits and dredged material permits. 
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

. CWA §316(b), implemented through discharge 

permits, requires that the location, design, 

construction, operation, and capacity of cooling 

water intake structures reflect the best technology 

available for minimizing adverse environmental 

impacts. 

. CWA §319, nonpoint source management control 

program, federal grant program administered by 

states, tribes, and territories.

. CWA §401, water quality certifications, 

administered primarily by states and territories 

discharges associated with any federally licensed 

or permitted activity comply with approved water 

quality standards. 

. CWA §402, National Pollutant Discharge 

Elimination System, discharge permitting 

programs administered primarily by states and 

territories subject to EPA minimum program 

requirements and permit oversight, but also by 

EPA in some jurisdictions. Point discharges are 

permitted under NPDES. 

. CWA §404, permitting program for discharge of 

dredged or fill material in waters of the United 

States, administered by USACE with oversight by 

EPA. EPA approves and oversees the delegation 

of CWA §404 authority to states and ensures state 

programs meet minimum program requirements 

and oversight.

. Compensatory Mitigation for Losses of Aquatic 

Resources, regulatory program applicable to CWA 

§404 permitting, commonly known as the 2008

Mitigation Rule, 33 CFR Part 332, implemented by

the USACE and EPA.

Comprehensive 

Environmental 

Response, 

Compensation and 

Liability Act 

(CERCLA)

42 U.S.C. Ch.103

EPA CERCLA, commonly known as Superfund, provides 

broad federal authority to respond directly to releases 

or threatened releases of hazardous substances that 

may endanger public health or the environment and 

created a tax on the chemical and petroleum 

industries. In addition, CERCLA provides for the 

assessment and restoration of Natural Resource 

Damages.

Coastal Barriers 

Resources Act

(CBRA)

16 U.S.C. §§3501-

3510

NOAA and S/T CBRA encourages the conservation of hurricane 

prone, biologically rich coastal barriers by restricting 

federal expenditures that encourage development, 

such as federal flood insurance. Areas within the 

CBRS can be developed provided that private 

developers or other non-federal parties bear the full 

cost.

Coastal Zone 

Management Act 

(CZMA)

NOAA and Dept. 

of Interior (DOI)

CZMA provides federal funding to assist states in 

developing and administering coastal zone 

management plans (CMPs) to carry out its purpose to 
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

16 U.S.C. §§1451-

1466

“preserve, protect, develop, and where possible, to 

restore or enhance the resources of the Nation’s 

coastal zone for this and succeeding generations.” 

CZMA §307, commonly called the Federal 

Consistency Provision, requires that federal actions, 

within and outside the coastal zone, that have 

reasonably foreseeable effects on any coastal use 

(land or water) or natural resource of the coastal zone 

be consistent with the enforceable policies of a state’s 

federally approved coastal management program.

Coral Reef 

Conservation Act

(CRCA)

16 U.S.C. §§6401-

6409

NOAA and DOI CRCA aims to preserve and protect coral reef 

ecosystems, to effectively manage those ecosystems 

with the aid of scientific research, and to fund 

programs consistent with those goals. It requires, in 

conjunction with existing environmental laws, coral 

reefs to be monitored, mapped, and researched in 

order to better understand how to manage their 

ecosystems.

Endangered 

Species Act of 1973 

(ESA)

16 U.S.C. §1531 et 

seq.

NOAA, FWS, 

and USCG

ESA provides for the conservation of endangered 

and threatened species and for the conservation of 

“the ecosystems upon which endangered species 

and threatened species depend.”

USCG has enforcement authority.

Executive Order 

13089 – Coral Reef 

Protection

63 FR 32701 (June

11, 1998)

USCRTF The EO creates task force charged with overseeing 

the mapping and monitoring of all U.S. coral reefs, 

researching coral degradation, conserving and 

restoring coral reefs, and promoting coral reef 

conservation internationally.

Executive Order 

13158 - Marine 

Protected Areas 

65 FR 34909 (May

31, 2000)

NOAA and DOI The EO is intended to (a) strengthen the 

management, protection, and conservation of existing 

MPAs and establish new or expanded MPAs; (b) 

develop a scientifically based, comprehensive 

national system of MPAs representing diverse U.S. 

marine ecosystems, and the Nation’s natural and 

cultural resources; and (c) avoid causing harm to 

MPAs through federally conducted, approved, or 

funded activities.

Fish and Wildlife 

Coordination Act

(FWCA)

16 U.S.C. §§661-

667e

FWS, NMFS,

and S/T

FWCA states that “whenever the waters of any 

stream or other body of water are proposed or 

authorized to be impounded, diverted, the channel 

deepened, ...or modified for any purpose whatever, 

...by any department or agency of the U.S., or by any 

public or private agency under Federal permit or 

license, such department or agency first shall consult 

with the FWS, and with the head of the agency 

exercising administration over the wildlife resources 

of the particular State wherein the impoundment, 

diversion, or other control facility is to be constructed, 

with a view to the conservation of wildlife resources 

by preventing loss of and damage to such resources 

as well as providing for the development and 
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

improvement thereof in connection with such waterresource development.”

Lacey Act

16 U.S.C. §§3371-

3378

NOAA and

FWS

The Lacey Act prohibits the importation, exportation, 

sale, receipt, acquisition, or purchase of any fish, 

wildlife, or plant taken in violation of U.S., foreign, or 

Indian tribal law or in interstate or foreign commerce 

in violation of any state or foreign law.

Magnuson Stevens 

Fishery 

Conservation and 

Management Act

(MSA) 

16 U.S.C. §§1801-

1891

NMFS and

USCG

In the regulatory context, one of the most important 

provisions of the MSA for conserving fish habitat is 

that which requires federal agencies to consult with 

NMFS when any activity proposed to be permitted, 

funded, or undertaken by a federal agency may have 

adverse effects on designated EFH. The consultation 

requirements in the MSA direct federal agencies to 

consult with NFMS when any of their activities may 

have an adverse effect on EFH. Furthermore, with 

goals to reduce bycatch and overfishing, fishery 

management plans may prohibit or limit fishing 

practices that are harmful to coral reefs. MSA directly 

protects deep-sea corals through the Deep-Sea Coral 

Research and Technology Program, as well as the 

MSA’s authorization to designate zones to protect 

deep-sea corals. Coral reefs designated as essential 

fish habitat in FMPs will receive additional protection. 

USCG has enforcement authority.

Marine Mammal 

Protection Act 

(MMPA) 16 U.S.C. 

§§1361-1423

NOAA and FWS MMPA prohibits the “take” of marine mammals in 

U.S. waters and by U.S. citizens on the high seas, 

and the importation of marine mammals and marine 

products in the United States. The MMPA states that 

the essential habitats, which may include coral reef 

ecosystems, used by marine mammals should be 

protected, and marine mammals should be protected 

from the harmful actions of man. NMFS can 

authorize take under certain activities and conditions.

The Marine 

Protection, 

Research, and 

Sanctuaries Act 

(MPRSA) of 1972

33 U.S.C. §§1401-

1445

USACE and EPA MPRSA, specifically Title I, sometimes referred to as 

the Ocean Dumping Act, generally prohibits (1) the 

transportation of material from the United States for 

the purpose of ocean dumping; (2) transportation of 

material from anywhere for the purpose of ocean 

dumping by U.S. agencies or U.S.-flagged vessels; 

(3) dumping of material transported from outside the

United States into the U.S. territorial sea. A permit is

required to deviate from these prohibitions. The

standard for permit issuance is whether the dumping

will "unreasonably degrade or endanger" human

health, welfare, or the marine environment. USACE

issues permits for the ocean disposal of dredged

material; EPA issues permits for other materials.

Disposal sites are designated by EPA. USACE

authorizes clean dredged material disposal in

consultation with EPA.
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

MARPOL –

International 

Convention for the 

Prevention of 

Pollution by Ships

The objective of MARPOL is to limit ship-borne 

pollution by restricting operational pollution and 

reducing the possibility of accidental pollution. 

MARPOL specifies standards for stowing, handling, 

shipping, and transferring pollutant cargoes, as well 

as standards for discharge of ship-generated 

operational wastes. The United States is party to 

Annexes I-III, V, and VI and they have been 

incorporated into U.S. law. Although Annex IV has 

not been ratified, the United States has equivalent 

regulations under the CWA for the treatment and 

discharge of sewage from vessels.

National 

Environmental 

Policy Act (NEPA)

42 U.S.C. §§4321-

4370

CEQ, applies to 

all federal 

agencies

NEPA requires all federal agencies to analyze the 

potential environmental impacts of their proposed 

actions “significantly affecting the quality of the 

human environment,” which could include actions’

effects on coral reef ecosystems.

National Marine 

Sanctuaries Act

(NMSA)

16 U.S.C. §§1431-

1445

NOAA and S/T NMSA designates “areas of the marine environment 

which are of special national significance” as national 

marine sanctuaries, providing for their protection, 

management, and conservation.

Natural Resource 

Damage 

Assessment and 

Restoration 

(NRDAR)

Procedures 

43 CFR 11

42 U.S.C. 9651(c)

DOI and Dept. of 

Commerce

NRDAR is the legal process that federal agencies like 

NOAA, together with the states and Indian tribes, use 

to evaluate the impacts of oil spills, hazardous waste 

sites, and ship groundings on natural resources both 

along the Nation's coast and throughout its interior.

54 U.S.C. Chapters 

1001-1007 cover 

general provisions, 

establishment of the 

NPS, areas of the 

system, and 

resource (formerly 

known as the NPS 

Organic Act)

NPS 54 U.S.C. §§1001-1007 establishes the NPS and 

authorizes it to regulate the National Park System.

Presidential 

Memorandum: 

Mitigating Impacts on 

Natural Resources from 

Development and 

Encouraging Related 

Private Investment.

(November 3, 2015)

DOI, USDA, EPA,

and NOAA

The memorandum directs agencies to adopt a clear and 

consistent approach for avoidance and minimization of, 

and compensatory mitigation for, the impacts of their 

activities and the projects they approve.
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

Presidential 

Memorandum: 

Incorporating Natural 

Infrastructure and 

Ecosystem Services in 

Federal DecisionMaking. (October 7, 

2015)

Federal Agencies The memorandum directs federal agencies to factor the 

value of ecosystem services into federal planning and 

decision-making. 

Oil Pollution Act

(OPA)

33 U.S.C. §§2701-

2762

USCG, EPA, and 

NOAA

OPA created a comprehensive prevention, response, 

liability, and compensation regime to deal with 

vessel- and facility-caused oil pollution to U.S. 

navigable waters. OPA greatly increased federal 

oversight of maritime oil transportation, while 

providing greater environmental safeguards by:

. Setting new requirements for vessel construction 

and crew licensing and manning.

. Mandating contingency planning.

. Enhancing federal response capability.

. Broadening enforcement authority.

. Increasing penalties.

. Creating new research and development 

programs.

. Increasing potential liabilities.

. Significantly broadening financial responsibility 

requirements. 

Full description can be found at 

http://www.uscg.mil/npfc/About_NPFC/opa.asp under 

the OPA Overview Section.

Resource 

Conservation and 

Recovery Act 

(RCRA)

40 CFR Parts 239 –

282.

42 U.S.C. §6901 et 

seq.

EPA RCRA regulates the management of solid waste 

(e.g., garbage), hazardous waste, and underground 

storage tanks holding petroleum products or certain 

chemicals to protect human health and the 

environment from the potential hazards of waste 

disposal, to conserve energy and natural resources, 

to reduce the amount of waste generated, and to 

ensure that wastes are managed in an 

environmentally sound manner.

Rivers and Harbors 

Act of 1899 (RHA)

33 U.S.C. §§401-

426

USACE RHA regulates construction and prohibits the 

discharge of “any refuse matter of any kind” into 

navigable waters in the United States. Of particular 

note, RHA §10 applies to physical structures or work 

in navigable waters.

Sikes Act

16 U.S.C. §§670a670o

Dept. of Defense, 

NOAA, and FWS

Sikes Act requires development of integrated natural 

resource management plans for military installations

in consultation with FWS and NOAA.

System Unit 

Resource Protection 

Act 54 U.S.C. 

100721 (SURPA)

NPS Gives NPS authority to seek damages from 

responsible parties for injuries to system unit 

resources within park system units. System unit 

resources include natural, cultural, and facility living 

or non- living resources. Also give NPS the authority 

to retain damages to be used to restore resource 

injuries.
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

Water Resources 

Development Act 

Citations include, but 

are not limited to: 

WRDA 1986, Pub.L. 

99–662 

WRDA 2000, Pub.L. 

106– 

541

WRDA 2007, Pub.L. 

110–114; 

WRDA 2014, Pub. 

L 113-121

USACE The WRDAs provide the authority for the federal 

government to assist states and territories in the 

development of water resource management 

activities including navigation, flood risk 

management, and aquatic ecosystem restoration. 

Eligible projects are shown to have a federal interest 

to national economic development and/or national 

ecosystem restoration goals and objectives.
APPENDIX I – LEGAL AND POLICY SUMMARY

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Table 6: Summary of state and territorial laws and regulations that govern activities that may impact 

coral reefs.6

Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

Commonwealth of the Northern Mariana Islands (CNMI)

Coastal Resource 

Management Rules 

and Regulations

(NMIAC 15-10)

Division of 

Coastal 

Resources 

Management

Chapter 15-10 primarily outlines permitting criteria 

and enforcement of permitting for projects in the 

coastal zone. The law states that “significant adverse 

impacts to reefs and corals shall be prevented” and 

there shall be no “destruction of reefs and corals not 

associated with permitted projects.” 

(a) Lagoon and Reef Area of Particular Concern

(APC); Management Standards.

(b) Lagoon and Reef APC; Use Priorities.

(1) General Lagoon and Reef APCs.

(2) Lagoon and Reef APC; Managaha.

(3) Lagoon and Reef APC; Anjota Island.

(4) Lagoon and Reef APC; Coral Reefs.

(f) Mitigation of Adverse Impact. Wherever

practicable, adverse impact of the proposed

project on the environment shall be mitigated.

http://www.cnmilaw.org/admincode/Title15/

T15.html

Coastal Resources 

Management Act of 

1983

(2 CMC §§1501 et 

seq).

Division of 

Coastal 

Resources 

Management

This law established DCRM and outlines its purpose, 

including: manage ecologically significant resource 

areas for their contribution to marine productivity and 

value as wildlife habitats, and preserve the functions 

and integrity of reefs, marine meadows, salt ponds, 

mangroves, and other significant natural areas.

http://www.cnmilaw.org/pdf/public_laws/03/pl03-

47.pdf

Non-Commercial Fish 

and Wildlife 

Regulations 

(NMIAC 85-30.1)

Division of Fish 

and Wildlife

(DFW)

Collection of Hard Corals Prohibitions: The collection 

and/or removal from the waters of the CNMI of any 

and all species of hard Hermatypic reef building 

corals, soft corals, or stony hydrozoans, is prohibited, 

except as specifically allowed by this section. 

Marine Reserves: The Director may acquire and 

designate aquatic habitats or easements as marine 

reserves in accordance with 2 CMC §5104(a)(5). 

Marine reserves are created to protect important fish 

and aquatic species populations and their 

habitats.http://www.cnmilaw.org/admincode/Title85/

T85.html

Submerged Lands Act

2 CMC §§ 1201 et seq.

Department of 

Lands and 

Natural 

Resources

The purpose of this chapter is to provide for water 

and non-water-dependent uses of CNMI-owned 

submerged lands and to provide for the exploration, 

development of, and extraction of petroleum deposits 

6 Depending on the federal action, some of the state and territorial laws may not apply. Work closely with the 

state or territorial regulatory office to determine which laws apply to the proposed activity.
APPENDIX I – LEGAL AND POLICY SUMMARY

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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

or mineral deposits in submerged lands of the 

Northern Mariana Islands.

http://www.cnmilaw.org/pdf/cmc_section/T2/1211.

pdf

The department shall consider the natural values of 

CNMI-owned submerged lands as wildlife habitat, 

natural area preserve, representative ecosystem, or 

spawning area prior to issuing any initial lease or 

authorizing any change in use. The department may 

withhold from leasing lands which it finds to have 

significant natural values, or may provide within any 

lease for the protection of such values. 

http://www.cnmilaw.org/pdf/cmc_section/T2/1221.

pdf

Commonwealth 

Environmental 

Protection Act

2 CMC §§ 3101 et seq.

Division of 

Environmental 

Quality (DEQ)

The legislature declares that it is the policy of the 

CNMI: 

. To affirmatively protect the right of each person to 

a clean and healthful public environment.

. To establish and enforce environmental 

standards to protect and preserve the marine 

resources of CNMI.

This law charges DEQ with administering water 

quality programs and regulating earth-moving, 

including disturbances to the sea floor, lagoon

bottom, or coral reef. 

http://www.cnmilaw.org/pdf/cmc_section/T2/3111.

pdf

Water Quality 

Standards

Bureau of 

Environmental 

and Coastal 

Quality

9.6 (b)(3) Dredging and Discharge of Dredged of Fill 

Material. Dredging and the discharge of dredged or 

fill material can adversely affect colonies of reef 

building organisms by burying them, by releasing 

contaminants such as hydrocarbons into the water 

column, by reducing light penetration through the 

water, and by increasing the level of suspended 

particulates. Coral organisms are extremely sensitive 

to even slight reductions in light penetration or 

increases in suspended particulates (i.e., turbidity). 

These adverse effects will cause a loss of productive 

colonies which in turn provide habitat for many 

species of highly specialized aquatic organisms.

For activities which have the potential to adversely 

affect coral reproduction, a stoppage period of 21 

days, starting five days after the late May or early 

June full moon (to be determined by DEQ), is 

required. The stoppage period, if determined to be 

applicable, shall be no less than twenty one (21) 

calendar days. In determining whether an activity 

has the potential to affect coral spawning, DEQ shall 

consider all of the following: 
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Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

1) the magnitude of the sediment plume generated by

the proposed activity;

2) the most likely extent and direction(s) of drift of the

sediment plume;

3) the type of sediment and its composition; and

4) the proximity of broadcast spawning coral species

to the proposed activity and expected sediment

plume.

Fish, Game and 

Endangered Species 

Act

2 CMC §§5101 et seq.

DFW The protection of fish, game, and endangered and 

threatened species is vested exclusively in the 

department.

This law gives DFW jurisdiction over fish and wildlife 

including determining the status of, and any 

requirement for the survival of, resident species of 

fish, wildlife, or plants. 

http://www.cnmilaw.org/pdf/cmc_section/T2/5104.

pdf

Moratorium on 

Seaweed, Sea 

Grasses, and Sea 

Cucumber

2 CMC §5601

Coastal 

Resources 

Management 

Office

There is hereby established for a period of at least 

ten years a moratorium on the harvest of all noncommercially grown seaweed, sea grass, or sea 

cucumbers or other edible echinoderms.

Any hotel directly fronting or adjacent to the Saipan 

lagoon shall be exempted from subsection (a). The 

Coastal Resources Management Office in 

consultation with the DFW shall promulgate rules 

governing the area of allowance for the removal of 

seaweed and sea grass. 

http://www.cnmilaw.org/pdf/cmc_section/T2/5601.

pdf

Fair Fishing Act

2 CMC 

§5631

Department of 

Lands and 

Natural 

Resources

Except as provided in subsections (b) and (c), it shall 

be unlawful for any commercial and non-commercial 

fishermen to use explosives, poisons, electric 

shocking devices, scuba tank or hookah when fishing 

for reef fish and harvesting other marine life within 

waters of CNMI.

www.cnmilaw.org/pdf/cmc_section/T2/5631.pdf

Protecting of Rays 

and Sharks

2 CMC §5641, §5642

DFW It shall be unlawful for any person, within the CNMI or 

any place subject to the jurisdiction thereof, to 

knowingly, or with wanton disregard for the 

consequences of his act, feed, take, possess, sell, 

purchase, barter, offer to sell, purchase or barter, 

transport, export or import, at any time or in any 

manner any ray, alive or dead, or any part thereof, 

without being permitted to do so as provided in this 

section, or to violate any permit or regulation issued 

pursuant to this section. 

http://www.cnmilaw.org/pdf/cmc_section/T2/5641.

pdf
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It is unlawful for any person, within the nearshore 

waters of the CNMI to knowingly, or with wanton 

disregard for the consequences of this act feed in any 

manner any shark, without first obtaining a permit 

from the Director of the DFW, or violates any permit 

or regulation issued pursuant to this section. 

http://www.cnmilaw.org/pdf/cmc_section/T2/5642.

pdf

Shark Finning 

Prohibition

2 CMC §5651

Department of 

Lands and

Natural 

Resources 

It shall be unlawful for any person to possess, sell, 

offer for sale, trade, or distribute shark fins in the 

CNMI.

http://www.cnmilaw.org/pdf/cmc_section/T2/56

51.pdf

State of Florida

Environmental 

Resource Permitting 

Florida Statute (F.S.) 

§373.129., .413 & .414

Florida 

Department of 

Environmental 

Protection 

(FDEP)

Within FDEP the Submerged Lands and 

Environmental Resources Program (SLERP) 

administers Environmental Resources Permits 

(ERPs). ERPs regulate activities involving the 

management and alteration of surface water flows. 

This includes upland construction activities that 

generate storm water runoff, which contributes to 

such aspects as: 

. Runoff quantity (i.e., storm water attenuation 

and flooding of other properties) in both 

wetlands and uplands; 

. Water quality (i.e., storm water treatment) in 

both wetlands and uplands; and, 

. Dredging and filling in most surface waters and 

wetlands (whether isolated or connected to 

other waters). In addition, this includes the 

alteration of mangroves. 

The ERP also handles the submerged lands 

authorization for any construction on or use of 

submerged lands owned by the state of Florida. 

The ERP program is authorized pursuant to Chapter 

373, Part IV, F.S., Management and Storage of 

Surface Waters and implemented by a variety of 

Florida Administrative rules. A list of the rules are 

available at the following webpage: 

http://www.dep.state.fl.us/water/wetlands/erp/rul

es/index.htm. 

A Joint Coastal Permit (JCP) program involves 

concurrent processing of applications for a coastal 

construction authorization, an ERP, and a sovereign 

submerged land authorization. A JCP is required for 

construction activities on Florida’s natural sandy 

beaches, adjacent state sovereignty lands and 

associated inlets, or activities that are likely to have 

a material physical effect on existing coastal 
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conditions, natural shore processes, or inlet 

processes. The JCP is authorized pursuant to 

Sections 161.021, 161.041 and 161.055, F.S., Rule 

62B-41, F.A.C., Rules and Procedures 22 Florida 

Coastal Management Program Guide for Application 

for Coastal Construction Permits, and Rule 62B-49, 

F.A.C., Joint Coastal Permits and Concurrent 

Processing of Proprietary Authorizations.

Surface Water Quality 

Standards Florida 

Administrative Code

(F.A.C) 62 – 302.500 

&

530

FDEP 62-302.500, F.A.C. – Minimum & General Criteria.

Turbidity cannot exceed 29 Nephelometric Turbidity

Units (NTUs) above natural background conditions

in Class I – V Waters. Turbidity cannot exceed

ambient background conditions in Aquatic

Preserves due to their status as Outstanding Florida

Waters (OFW).

62–302.530, F.A.C. – Surface WQ Standards. This 

rule defines the general state water quality 

standards for all activities. If an activity will 

potentially violate these standards, then it will likely 

require a FDEP permit (ERP or Joint Coastal 

Permit) unless eligible for exemption.

Permit Guidelines, 

Mixing Zones F.A.C. 

62 – 4.242 &.244

FDEP 62-4.242&.244, F.A.C. – Mixing Zones. Mixing

zones can be granted for selected projects that

otherwise can’t meet water quality standards within

close proximity to the construction activity. More

information is available at:

https://www.flrules.org/gateway/RuleNo.asp?id

=62-4.244

Protection of 

Sovereign Submerged 

Lands

F.S. §253.04

FDEP Chapter 253 FS addresses the state’s administration 

of public lands and property of this state. The 

statute provides direction regarding the acquisition, 

disposal, and management of all state lands.

The Board of Trustees of the Internal Improvement 

Trust Fund (Board) of the state is vested and 

charged with the acquisition, administration, 

management, control, supervision, conservation, 

protection, and disposition of all lands owned by the 

state, except for lands acquired for certain purposes. 

18-14, F.A.C., implements the fine schedule for

violations.

Pollution Control

F.S. § 403.121 & .201 

(&

others)

FDEP §403.121, F.S.: The Environmental Litigation

Reform Act (ELRA): Allows swifter, more efficient

use of administrative process for imposing damages

and penalties (up to $10,000 per offense). Outlines

administrative penalties for specified violations rules

and statutes.

§403.141 and §403.161, F.S. Allow imposition of

damages and civil liability for causing pollution that
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harms aquatic life. Remedies are all judicial rather 

than administrative.

For adjusted penalties >$10,000, FDEP instead 

considers program specific guidelines for 

characterizing violations and assessing penalties. If 

a settlement cannot be reached consistent with 

FDEP’s Settlement Guidelines for Civil and 

Administrative Penalties (FDEP Directive 923), 

FDEP will file an enforcement action in state court.

Florida Coastal 

Management Program 

Chapter 380, F.S., 

Part II, Coastal 

Planning and 

Management

FDEP FDEP’s Florida Coastal Office, is charged with 

overseeing the state’s coastal management program 

and handles the following Florida Coastal 

Management Program (FCMP) activities: 

. Compiles and submits the federal applications 

for receiving funds pursuant to the CZMA. 

. Adopts rule procedures and criteria for the 

evaluation of Coastal Partnership Initiative (CPI) 

and state agency sub-grant applications for 

funds allocated to the state under the CZMA.

. Administers the Coastal and Estuarine Land 

Conservation Program (CELCP), a federallyfunded land acquisition program. 

. Conducts the CZMA § 309 assessment and 

strategies for coastal resource issues. 

. Administers the Beach Access Sign Program, 

the Beach Warning Flag Program, and the Rip 

Current Awareness Program. 

. Prepares routine program updates to 

incorporate annual statutory changes. 

. Guides the coordination of the Federal 

Consistency review process. 

“Federal Consistency” is the requirement that 

federal actions that affect any land, water, or natural 

resource of a state’s coastal zone must be 

consistent with the enforceable policies of the state. 

The FCMP federal consistency process consists of a 

network of 24 Florida Statutes (i.e., enforceable 

policies) administered by FDEP and a group of 

partner agencies responsible for implementing the 

statutes.

Joint Coastal Permit 

F.S. §161.054 & .055

FDEP The Joint Coastal Permit (JCP) Program allows 

FDEP to concurrently process applications for 

coastal construction permits, environmental 

resource permits, and sovereign submerged lands 

authorizations.

The consolidation of these programs and the 

assignment of responsibility to a single bureau has 

eliminated the potential for conflict between 

permitting agencies and helped ensure that reviews 
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are conducted in a timely manner. JCP permit 

applications are forwarded to the USACE from 

FDEP or SFWMD for separate processing and 

review.

Marine Life Rule 

68B-42.009, F.A.C.

Florida Fish and 

Wildlife 

Conservation 

Commission 

(FWC)

Harvest of any hard or stony coral (Order 

Scleractinia), black coral (Order Antipitharia), fire 

coral (Genus Millepora), or sea fans (Gorgonia 

flabellum or G. ventalina) is prohibited.

Special Activity License

68B-8, F.A.C.

Florida FWC Authorization required for the collection or take of 

corals for education, research, enhancement, 

restoration, or mitigation activities.

Coral Protection in 

State Parks 

F.S.§258.008(3)(a)

FDEP Any person who engages in any of the following 

activities within the boundaries of a state park without 

first obtaining the express permission of the Division 

of Recreation and Parks commits a misdemeanor of 

the second degree, punishable as provided in s. 

775.082 or s. 775.083, and shall be ejected from all 

property managed by the division:

(a) Cutting, carving, injuring, mutilating, moving,

displacing, or breaking off any water-bottom

formation or coral.

(b) Capturing, trapping, or injuring a wild animal.

(c) Collecting plant or animal specimens.

(d) Leaving the designated public roads in a vehicle.

(e) Hunting.

Rules Relating to 

Endangered or 

Threatened Species

68A-27, F.A.C.

Florida FWC Staghorn coral (Acropora cervicornis)

Elkhorn coral (Acropora palmata) 

Pillar coral (Dendrogyra cylindrus) 

Lobed star coral (Orbicella annularis)

Mountainous star coral (Orbicella faveolata) Boulder 

star coral (Orbicella franksi)

Rough cactus coral (Mycetophyllia ferox)

Guam

E.O. 78-37 Bureau of 

Statistics and 

Plans, Guam 

Coastal

Management 

Program

Coastal Zone Resource Policies: Sets forth criteria 

and enforceable policies determining permitting for 

projects in the coastal zone. This law establishes 

management policies for Guam’s ecologically 

significant resource areas for their contribution to 

marine productivity and value as wildlife habitats, and 

preserves the functions and integrity of reefs, 

beaches, marine preserves, mangroves, hydrological 

systems, and other significant natural coastal areas.

E.O. 2013-05 Bureau of 

Statistics and 

Plans, Guam 

Coastal 

Management 

Program

Coral Reef Resource Policies: Establishes the 

Guam Coral Reef Initiative Coordinating Committee 

to develop, update, and monitor Guam’s Local Action 

Strategies, funding, and determine management 

policies to preserve the function and integrity of 

Guam’s coral reef ecosystems.

Fish and Wildlife 

Regulations

Guam 

Department of 

Statutory and regulatory rules governing fish and 

wildlife resources for the territory of Guam, including 
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Agencies Description

(5 Guam Code 

Annotated, Chapter 63, 

Article 1, §§63101 et 

seq.)

Agriculture, 

Division of 

Aquatic and 

Wildlife 

Resources

coral protection, hunting and fishing regulation, and 5 

existing limited take Marine Preserves.

Guam Endangered 

Species Act 

5 Guam Code 

Annotated, Chapter 

63, Article 2, §§63201 

et seq.

Guam 

Department of 

Agriculture, 

Division of 

Aquatic and 

Wildlife 

Resources

Protection of Fish, Game, and Wildlife: Protects 

fish, game, and wildlife, including determining the 

status of, and any requirement for the survival of, 

resident species of fish, wildlife, or plants; particularly 

any species of plant or wildlife which appears likely, 

within the foreseeable future, to become endangered 

and which has been so designated by the Guam 

Department of Agriculture, or that has been 

determined to be listed as an endangered or 

threatened species pursuant to the U.S. ESA.

Submerged Lands Act; 

and Guam Exclusive 

Economic Zone 

(Ocean Resources) 

Public Law 93-435

Department of 

Land 

Management 

Submerged Lands of Guam: Provides for water 

and non-water-dependent uses of Guam-owned 

submerged lands; for concurrent local and federal 

jurisdiction for civil and criminal offenses; and for 

Guam’s ownership of the rights to management, 

exploration, development of, and extraction of 

petroleum or mineral deposits in submerged lands of 

Guam; and the natural values of Guam-owned 

submerged lands as wildlife habitat, natural area 

preserve, representative ecosystem, or spawning 

area with respect to leasing or authorizing any use of 

these submerged lands.

Organic Act of Guam

Article 1§1704 et seq.; 

& 1 Guam Code 

Annotated § 402

Department of 

Land 

Management

Concurrent Resource natural resource jurisdiction on 

submerged lands adjacent to federal property and 

oversight of submerged lands from the high tide mark 

out to three miles in territorial waters.

Guam Environmental 

Protection Agency Act

10 Guam Code 

Annotated, Chapter 

45, §§45101 et seq.

Guam 

Environmental 

Protection 

Agency

Water Quality Standards: Provides that the policy 

of Guam is to affirmatively protect the right of each 

person to a clean and healthful public environment; 

and to establish and enforce environmental 

standards to protect and preserve the environmental 

health of Guam, including its marine resources.

This law charges Guam EPA with administering 

water quality programs and regulating earth-moving, 

including disturbances to the sea floor, lagoon 

bottom, or coral reef.

Guam Water Pollution 

Control Act 

10 Guam Code 

Annotated, Chapter 

47, §§47101 et seq.

Guam 

Environmental 

Protection 

Agency

Water Pollution Control: Prohibits the discharge of 

pollutants into or upon all of the waters of Guam, 

including inland waters and coastal waters, beaches, 

or lands adjoining the coasts of Guam. Pollution is 

defined as the presence in the outdoor atmosphere 

or waters of Guam any one or more substances or 

pollutants in quantities which are or may be 

potentially harmful or injurious to life, including 

wildlife, fish and aquatic life; and which may 
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progressively obstruct agricultural, industrial, 

recreational, and other beneficial uses of water.

Guam Territorial 

Seashore Protection 

Act 

21 Guam Code 

Annotated, Chapter 

63, §§63101 et seq.

Guam 

Department of 

Land 

Management, 

and Guam 

Land Use 

Commission

Seashore Reserve: Creates a Seashore Reserve 

area in Guam, consisting of the land and water 

area of Guam extending seaward to the ten-fathom 

contour, and recognizes that the Seashore Reserve 

is a distinct and valuable natural resource 

belonging to all the people of Guam and existing as 

a delicately balanced ecosystem; provides for the 

protection of the natural, scenic, historical 

resources, wildlife, marine life, and other ocean 

resources, and the natural environment of the 

seashore reserve by limiting and prescribing 

development within the Seashore Reserve area.

State of Hawaii

Hawaii Constitution, 

Article XI

Art. XI, §1 (Conservation and Development of 

Resources) “For the benefit of present and future 

generations, the State and its political subdivisions 

shall conserve and protect Hawaii's natural beauty 

and all natural resources, including land, water, air, 

minerals and energy sources, and shall promote the 

development and utilization of these resources in a 

manner consistent with their conservation and in 

furtherance of the self- sufficiency of the State. All 

public natural resources are held in trust by the State 

for the benefit of the people.” This section embodies 

Hawaii’s public trust doctrine.

Art. XI, §2 (Management and Disposition of 

Natural Resources)

Art. XI, §6 (Marine Resources) “The State shall 

have the power to manage and control the marine, 

seabed and other resources located within the 

boundaries of the State, including the archipelagic 

waters of the State, and reserves to itself all such 

rights outside state boundaries not specifically limited 

by federal or international law.”

Art. XI, § 11 (Exclusive Economic Zone)

Hawaii Revised Statute

(HRS) Chapter 343

Depends Chapter 343 is Hawaii’s Environmental Policy Act 

(HEPA). Chapter 343 requires that an agency or 

applicant prepare an environmental assessment or 

an environmental impact statement if a proposed 

action meets any of nine “triggers” listed in the 

statute.

HRS Chapter 171 Department of

Land and 

Natural 

Resources 

(DLNR)

Chapter 171 addresses Hawaii’s management of its 

public lands (including submerged lands) through the 

DLNR. DLNR is tasked with managing and

administering the “aquatic life, aquatic life 

sanctuaries, public fishing areas, boating, ocean 
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recreation, coastal programs . . . and other functions 

assigned by law.” DLNR is authorized to recover 

natural resource damages for violations of the 

chapter. Violations include engaging in prohibited 

activities or prohibited uses.

HRS Chapter 183C DLNR Chapter 183C provides a framework for Hawaii to 

manage lands in the conservation district, including 

the ocean and submerged lands, in a manner that 

protects and preserve the natural ecosystems within 

them. DLNR is responsible for managing lands in the 

Conservation District. These responsibilities include 

the following: maintaining an inventory of lands 

classed conservation lands; identifying and zoning 

lands in the district; establishing conditions on use 

and categories of use and activities; adopting rules; 

and setting and enforcing land use regulations. HRS 

§ 183C-7 describes the penalties for violating the

chapter: “Any person violating this chapter or any rule

adopted in accordance with this chapter shall be

fined not more than $15,000 per violation in addition

to administrative costs, costs associated with land or

habitat restoration, and damages to public land or

natural resources, or any combination thereof.”

Willful violations may result in an additional fine of “up

to $15,000 per day per violation for each day in which

the violation persists.” In addition, the Board of Land

and Natural Resources “may set, charge, and collect

the fine based on the value of the natural resource

that is damaged, the market value of the natural

resource damaged, and any other factor it deems

appropriate, such as the loss of the natural resource

to its natural habitat and environment and the cost of

restoration or replacement. The remedies provided

for in this subsection are cumulative and in addition

to any other remedies allowed by law.”

HRS Chapter 187A DLNR Chapter 187A authorizes DLNR to manage and 

administer Hawaii’s aquatic life and aquatic resource 

including: 

1) establish, manage, and regulate public fishing

areas, artificial reefs, fish aggregating devices,

marine life conservation districts, shoreline

fishery management areas, refuges, and other

areas pursuant to title 12;

2) enforce all laws relating to the protecting, taking,

killing, propagating, or increasing of aquatic life

within the State and the waters subject to its

jurisdiction;

3) issue permits for take of aquatic life and recover

penalties for violations of the chapter; and

4) formulate and from time to time recommend to

the governor and legislature such additional

legislation necessary or desirable to implement
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the objectives of title 12.

HRS Chapter 190 DLNR Chapter 190 provides that all of Hawaii’s marine 

waters are constituted marine life conservation 

areas to be managed by DLNR. Under HRS § 190-

3, DLNR is responsible for adopting rules regulating 

the take and conservation of marine species, 

including rules that prohibit the disruption, alteration, 

and degradation of marine environment. HRS § 

190-4.5 requires DLNR to adopt rules for the

regulation of boating, anchoring, and mooring in the

conservation area.

HRS Chapter 195D DLNR Chapter 195D is Hawaii’s version of the U.S. ESA: 

“Any species of aquatic life, wildlife, or land plant 

that has been determined to be an endangered 

species pursuant to the ESA shall be deemed to be 

an endangered species under this chapter and any 

indigenous species of aquatic life, wildlife, or land 

plant that has been determined to be a threatened 

species pursuant to the ESA shall be deemed to be 

a threatened species under this chapter. The 

department may determine, in accordance with this 

section, however, that any such threatened species 

is an endangered species throughout all or any 

portion of the range of such species within this 

State.”

DLNR is authorized to issue licenses for the take of 

certain species for limited durations of time. Chapter 

195D also contains provisions for conservation 

programs and habitat conservation plans.

HRS Chapter 200 DLNR Chapter 200 governs ocean recreation and coastal 

areas programs, including limitations of private use 

of ocean waters, permits for boat harbors, and 

boating laws.

Hawaii Administrative 

Rule (HAR)

Chapter 13-95

DLNR “Live rock” defined as any natural hard substrate to 

which marine life is visibly attached or affixed.

“Stony coral” defined as any invertebrate species 

belonging to the Order Scleractinia, characterized by 

having a hard, calcareous skeleton that are native to 

the Hawaiian Islands.

It is unlawful for any person to:

1) take, break, or damage any stony coral or live

rock;

2) damage any stony coral or live rock by any

intentional or negligent activity causing the

introduction of sediment, biological contaminants,

or pollution into state waters; or,

3) to sell any live rock or stony coral, except that

stony coral rubble pieces or fragments imported

for the manufacture and sale of coral jewelry, or

dead stony coral obtained through legal dredging
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operations in Hawaii for agricultural or other 

industrial uses, may be sold.

HAR Chapters 13-(28, 

29, 30, 31, 32, 33, 34, 

35, 37, 37, 38)

DLNR These chapters govern Marine Life Conservation 

Districts.

HAR Chapter 124 DLNR Chapter 124 expands on Hawaii’s Endangered 

Species Act (HRS Chapter 195D), including 

prohibited activities; scientific, propagation, and 

educational permits; and lists of indigenous, 

threatened, and endangered wildlife.

2010 Hawaii Coral 

Reef Strategy

DLNR The 2010 Hawaii Coral Reef Strategy (HCRS) is the 

guiding coral reef management document used by 

the DLNR Division of Aquatic Resources with 

support from the NOAA Coral Reef Conservation 

Program.

2013 Hawaii Ocean 

Resources 

Management Plan

Office of 

Planning, 

various

The Hawaii Ocean Resources Management Plan 

(ORMP) is a comprehensive state plan that provides 

a framework for ocean and coastal resource 

management in Hawaii. The ORMP lists marine 

resources and coral reefs as management priorities 

4 and 5, respectively.

HAR Chapter 11-54 Department of 

Health (DOH)

Establishes beneficial uses and water quality 

standards for all waters, enables biological criteria, 

and includes bottom criteria for coral reefs.

HAR Chapter 11-55 DOH Hawaii’s NPDES rules regulating point discharges 

including construction general permit for sites > 1 ac

and municipal storm water.

Puerto Rico

Organic Law of the 

Planning Board of 

Puerto Rico 

(Law 75) 5-24-1975

Puerto Rico 

Planning Board 

(PRPB)

The PRPB is responsible for setting standards for 

the development of a society based on a sustainable 

economy, while conserving and protecting the 

environment for the benefit of future generations. 

The PRPB is composed of several programs and 

subprograms responsible for permitting, project 

design, and land use including the Coastal Zone 

Unit which implements the Federal Consistency 

evaluation process according to CZMA regulations.

Public Environmental 

Policy Law of the 

Environmental Quality 

Board (Law 416) 9-22-

2004

Environmental 

Quality Board 

(EQB)

The EQB has the principal function of protecting and 

conserving the environment using the resources 

necessary to impede or eliminate environmental 

damage and maintain a balance between economic 

development and the environment. The EQB Water 

Quality Area division is required to monitor, protect, 

improve, and maintain water quality in water bodies 

in order to achieve the propagation and preservation 

of desirable species and human consumption of 

water, among other uses. This area determines 

whether waters can be used for domestic, 

recreational, agricultural, and industrial purposes, as 

well as establishing regulations for the disposal of 

wastewater from these activities.
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Organic Law of the 

Administration of 

Regulations and 

Permits 

(Law 76) 5-24-1975

Administration of 

Regulation and 

Permits (ARPE)

The primary function of ARPE is to apply existing 

laws, ordinances, or regulations to the use and 

development of lands, construction, use or alteration 

of buildings or structures, and the installation of 

signs and announcements island-wide. Any building 

development requires ARPE permit and in most 

cases an endorsement from DNER.

Puerto Rico Permits 

Process Reform Act

(Law 161)

Office of Permits

Management 

(OGPE)

Act 161 created the OGPE to improve the quality 

and efficiency in the management of the process 

regarding the evaluation of applications for the

approval or denial of final determinations and 

permits for the development of construction projects 

in Puerto Rico. The Environmental Compliance 

Division of the OGPE is responsible for conducting 

the environmental impact review under the Law 416 

and issuing its recommendations. This division also 

evaluates “Green Permits” as categorical exclusions 

if the proposed project complies with green design 

guidelines.

U.S. Virgin Islands

Establishment of 

Wildlife and Marine 

Sanctuaries 

Virgin Islands Code 

(VIC) Ch 1 Subch VII 

§96 - 99

USVI

Department of 

Planning and 

Natural 

Resources 

(DPNR)

Gives authority to Commissioner of DPNR to 

establish wildlife and marine sanctuaries inside 

which, without a permit, no one can take or possess 

any bird, fish, or other wildlife from the designated 

sanctuary or throw, place, or deposit any waste 

within a designated sanctuary.

Establishes the St. Croix East End Marine Park 

(STXEEMP) and authorizes the territorial system of 

marine parks.

This authority has since been used to create the St. 

Thomas East End Reserve.

Protection of 

indigenous, 

endangered and 

threatened fish, wildlife 

and plants

12 VIC Ch 2 §101-107

DPNR Establishes the Endangered Species Preservation 

Commission, which has the responsibility to take 

action to identify and preserve threatened and 

endangered species in the territory and implement 

the U.S. ESA.

Covers all animal life including all coral reef 

vertebrate and invertebrate species, mangroves,

and seagrasses.

Permits for exceptions may be issued by the 

Commissioner on a case-by-case basis. Examples: 

scientific research, aquarium collectors, propagation 

activities, etc.

Water Pollution 

Control 

12 VIC Ch 7 §181 -

198

DPNR Declares public policy of the USVI to conserve the 

waters of the USVI and to protect, maintain, and 

improve the quality thereof for public water supplies, 

the propagation of wildlife, fish, and aquatic life, and 

for domestic, recreational, and other legitimate 

beneficial uses; to provide that no waste be 

discharged into any waters of the USVI without 
APPENDIX I – LEGAL AND POLICY SUMMARY

USCRTF Handbook on Coral Reef Impacts – December 2016

119

Statutes, 

Regulations, and 

Policies

Implementing 

Agencies Description

treatment. Authorizes the USVI to implement the 

provisions of the CWA.

Commercial Fishing

12 VIC Ch 9A §301 -

326

DPNR –

Division of Fish 

and Wildlife

To preserve, manage, and protect the fishery 

resources, to regulate fishing and to secure its 

increase and development in all marine, estuarine 

and freshwaters within the jurisdiction of the USVI.

This document is broad when referring to limits on 

seasons and size; it is simply setting up the authority 

of the commissioner to determine the limitations. 

Species-specific size regulations and closed seasons 

are found in the Virgin Islands Rules and 

Regulations.

Environmental 

Protection 

12 VIC Ch 13 §531-

539

DPNR –

Environmental 

Protection 

Program

States that the lands and waters comprising the 

watersheds of the USVI are great natural assets and 

resources. Improper development of land results in 

changed watershed conditions, which can negatively 

impact fish and marine life. In order to protect these 

resources, it is necessary to establish by law an 

environmental protection program for land 

development to prevent soil erosion.

Virgin Islands Coastal 

Zone Management act 

of 1978

12 VIC Ch 21 §901 -

914

DPNR –

Coastal Zone 

Management 

Program 

(CZMP)

Establishes the Coastal Zone Management Program 

and defines its many goals concerning the 

protection and sustainable development of the 

coastal zone and the limiting of any negative impact 

on natural resources.

Approves the coastal land and water use plan.

Gives CZMP power to recommend designation of 

areas of particular concern (APCs).
APPENDIX II – AGENCY CONTACT INFORMATION

USCRTF Handbook on Coral Reef Impacts – December 2016

120

Appendix II – Agency Contact Information

Table 7: Federal Agency Contact Information for coral reef impacts.

Federal Agencies

Agency Atlantic/Caribbean Office Pacific Office

FWS Florida

South Florida Ecological Services 

Field Office

Vero Beach, FL

(722) 562-3909

Puerto Rico & USVI

Caribbean Ecological Services Field 

Office

Boqueron, PR

(787) 851-7297

https://www.fws.gov/southeast/

Pacific Islands Fish and Wildlife Office

300 Ala Moana Boulevard

Room 3-122, Box 50088

Honolulu, HI 96850 

(808) 792-9400

(808) 792-9580 fax

http://www.fws.gov/pacificislands/

EPA Florida:

EPA Region 4

Sam Nunn Atlanta Federal Center 61 

Forsyth Street, SW

Atlanta, GA 30303-8960

(404) 562-9900

http://www2.epa.gov/aboutepa/abo

ut- epa-region-4-southeast

Puerto Rico & USVI:

EPA Region 2

290 Broadway

New York, NY 10007-1866

(212) 637-3000

http://www2.epa.gov/aboutepa/eparegion-2

EPA Region 9 – Pacific Islands Contact 

Office

PJKK Federal Building

300 Ala Moana Blvd., 

Room 5-152

Honolulu, HI 96850

(808) 541-2710

http://www.epa.gov/region9/islands/

NPS National Park Service

National Damage Assessment Office

Environmental Quality Division

Resource Protection Branch

1201 Oakridge Dr.

Fort Collins, CO 80525

National Park Service

National Damage Assessment Office

Environmental Quality Division

Resource Protection Branch

1201 Oakridge Dr.

Fort Collins, CO 80525

NOAA - NMFS NOAA Fisheries Service

Southeast Regional Office

263 13th Avenue South

St. Petersburg, FL 33701

(727) 824-5301

http://sero.nmfs.noaa.gov/

NOAA Fisheries Service

Pacific Islands Regional Office

NOAA Inouye Regional Center (IRC)

1845 Wasp Blvd., Bldg. 176

Honolulu, HI 96818

(808) 725-5000

http://www.fpir.noaa.gov/

USCG USCG Seventh District 

Brickell Plaza Federal Building

909 SE 1st Avenue

Miami, FL 33131-3050

https://www.uscg.mil/d7/

USCG Fourteenth District

300 Ala Moana Blvd, 

Room 9-204

Honolulu, HI 96850-4982

https://www.uscg.mil/d14/
APPENDIX II – AGENCY CONTACT INFORMATION

USCRTF Handbook on Coral Reef Impacts – December 2016

121

USACE U.S. Army Corps of Engineers

Jacksonville District Office

P.O. Box 4970

Jacksonville, FL 32232-0019

(904) 232-2568

http://www.saj.usace.army.mil/

U.S. Army Corps of Engineers Honolulu 

District Office Building 230, Room 302

Ft. Shafter, HI 96858 

(808) 835-4004

http://www.poh.usace.army.mil/

Table 8: State and Territorial Agency contact information for coral reef impacts.

State and Territorial Agencies

Jurisdiction Agency Contact

American Samoa American Samoa Department of Marine 

and Wildlife Resources

DMWR Building – Fagatogo

Pago Pago, AS 96799

Ph: (684) 633-4456

http://www.americansamoa.gov/depar

tment-of-marine-wildlife

CNMI CNMI Bureau of Environmental and 

Coastal Quality

Gualo Rai Center, Suite 201F

P.O. Box 501304 

Saipan, CNMI

Ph: (670) 664-8525

www.crm.gov.mp

Florida Florida Department of Environmental 

Protection

Florida Coastal Office 3900 

Commonwealth Blvd.

Tallahassee, FL 32399-3000

Ph: (850) 245-2095

http://www.dep.state.fl.us/coastal/

Florida Fish and Wildlife Commission, 

Division of Marine Fisheries

Farris Bryant Building

620 S. Meridian Street

Tallahassee, FL 32399-1600

(850) 487-0554

http://myfwc.com/

Guam Guam Bureau of Statistics and Plans, 

Coral Reef Conservation Program.

Bureau of Statistics and Plans, 

Coral Reef Conservation Program

513 Ricardo J. Bordallo Governor’s 

Complex

W. Marine Corps Drive

Adelup, Guam 96910

Hawaii Department of Land and Natural 

Resources

Kalanimoku Building 

1151 Punchbowl St.

Honolulu, HI 96813

Ph: (808) 587-0400

http://dlnr.hawaii.gov/

Puerto Rico Oficina de Gerencia de Permisos (OGPe) P.O. Box 41179

San Juan, PR 00940-1179

(787) 721-8282

USVI Department of Planning and Natural 

Resources

Cyril E. King Airport Terminal 

Building, 2nd Fl. St. Thomas, 

VI 00802

Ph: (340) 774-3320

http://dpnr.vi.gov/
APPENDIX III – ESA CONSIDERATIONS FOR LISTED CORALS 

USCRTF Handbook on Coral Reef Impacts – December 2016 

122

Appendix III – Coral Reef Mitigation and Restoration Planning: Endangered 

Species Considerations for Listed Corals

Endangered Species Act

A total of 25 reef-building coral species are listed under the ESA, including seven Caribbean species 

and 18 Indo-Pacific species. The seven listed Caribbean species are all found in U.S. waters. Of 

the 18 listed Indo-Pacific species, seven species are confirmed in U.S. waters, five species may 

occur in U.S. waters but have not been confirmed, and the remaining six species are known to occur 

only in foreign waters. The following sections provide background information, and a summary of the 

ESA’s regulatory processes for listed corals within U.S. waters.

Background

In 2006, Caribbean elkhorn (Acropora palmata) and staghorn corals (A. cervicornis) were listed as 

threatened under the ESA (71 FR 26852). These species occur within the U.S. waters of Florida, 

Puerto Rico, and the U.S. Virgin Islands, as well as throughout the wider Caribbean. In 2008, a final 

“ESA §4(d) rule” prohibiting the take of these listed species was published (73 FR 64264), and 

critical habitat was designated within U.S. waters (73 FR 72210). In 2014, an additional 20 coral 

species were listed as threatened, which included five Caribbean species and 15 Indo-Pacific 

species (79 FR 53852). In 2015, three foreign coral species were listed as endangered under the 

ESA (80 FR 60560). The number of listed corals confirmed found in each U.S. geographic area 

varies, as shown in Table 9 below. For more general information on listed corals, including 

distributions and species reports, please see the NMFS Pacific Islands Regional Office and 

Southeast Regional Office ESA Corals webpages:

http://www.fpir.noaa.gov/PRD/prd_coral.html

http://sero.nmfs.noaa.gov/protected_resources/coral/

Table 9: ESA-listed corals confirmed in U.S. waters, by geographic area.

Threatened Corals

*Listed as Threatened

in 2006

Confirmed in These Geographic Areas

Caribbean Waters FloridaAtlantic Puerto Rico USVI Gulf of Mexico

Acropora cervicornis* X X X

Acropora palmata* X X X X

Mycetophyllia ferox X X X

Dendrogyra cylindrus X X X

Orbicella annularis X X X X

Orbicella faveolata X X X X

Orbicella franksi X X X X
APPENDIX III – ESA CONSIDERATIONS FOR LISTED CORALS 

USCRTF Handbook on Coral Reef Impacts – December 2016 

123

Threatened Corals

*Listed as Threatened

in 2006

Confirmed in These Geographic Areas

Pacific Waters Guam CNMI PRIA American 

Samoa

Acropora globiceps X X X X

Acropora jacquelineae X

Acropora lokani 

Acropora pharaonis 

Acropora retusa X X X

Acropora rudis 

Acropora speciosa X X

Acropora tenella 

Anacropora spinosa 

Euphyllia paradivisa X

Isopora crateriformis X

Montipora 

australiensis 

Pavona diffluens 

Porites napopora 

Seriatopora aculeata X X

Regulatory Processes

As of November 2015, the ESA’s regulatory processes for listed corals within U.S. waters differs 

substantially between the two Caribbean species listed in 2006, versus the 20 Caribbean and Pacific 

species listed in 2014, even though all are listed as threatened. For the species listed in 2006, take 

was prohibited with two exceptions by the 4(d) rule, and critical habitat was designated, both in 2008 

(see above citations). The regulatory implications of the ESA §4(d) rule are that it is illegal to directly 

or incidentally “take,

7

listed Caribbean Acropora corals without authorization from NMFS, with two 

exceptions for specific research and restoration activities. Such authorization is provided either by 

ESA §7 consultation (for federal actions) or ESA §10 conservation planning (for non-federal actions). 

The regulatory implication of the critical habitat rule is that federal actions cannot destroy or 

adversely modify designated critical habitat. For the species listed in 2014, take has not been 

prohibited and critical habitat has not been designated, nor have either been proposed, although 

both could be in the future. For all listed coral species, whether listed in 2006 or 2014, federal 

actions cannot jeopardize their continued existence. Thus, federal actions that may affect listed 

corals are subject to ESA §7 consultation to ensure that jeopardy is avoided, as described in more 

detail below. 

ESA §7 consultation is the ESA’s primary regulatory process that affords protection to listed corals 

and their designated critical habitats occurring within U.S. waters. ESA §7 requires federal agencies 

to ensure that actions they authorize, fund, or carry out do not jeopardize the existence of any 

species listed under the ESA, or destroy or adversely modify their designated critical habitats. Thus, 

ESA §7 requires consultation by the federal “action agency” (the agency authorizing, funding, or 

carrying out the action) with NMFS on any action that may affect listed corals or their designated 

7

 The term "take" means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to 

attempt to engage in any such conduct (16 U.S.C. 1532(19)). 
APPENDIX III – ESA CONSIDERATIONS FOR LISTED CORALS 

USCRTF Handbook on Coral Reef Impacts – December 2016 

124

critical habitats. For such actions, ESA §7 consultation provides opportunities to reduce the impact 

of the proposed action on listed corals through both informal and formal process. Informal 

consultation is limited to proposed federal actions that are not likely to adversely affect listed corals, 

and may result in implementation of measures to minimize impacts of the action on listed corals. For 

proposed federal actions that cannot avoid adversely affecting listed corals, formal consultation is 

carried out to ensure that the action does not jeopardize the listed species. Formal consultation 

typically requires implementation of measures to minimize impacts of the proposed federal action to 

listed corals. In both informal and formal consultation, collaboration between the action agency and 

NMFS staff can provide significant conservation benefits for listed corals and coral reef ecosystems. 

In the case of proposed federal actions that also affect designated critical habitat for the two 

Caribbean corals listed in 2006, ESA §7 consultation includes analysis of the impact of the action on 

critical habitat, and may result in measures to minimize the actions’ impacts on it.

For more information on ESA §7 and listed corals, please see the NMFS Pacific Islands Regional 

Office and Southeast Regional Office ESA § 7 webpages:

http://www.fpir.noaa.gov/PRD/prd_esa_section_7.html

http://sero.nmfs.noaa.gov/protected_resources/section_7/index.html
 APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL 

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125

Appendix IV – Example of a Coral Transplantation Protocol

Florida Fish and Wildlife Conservation Commission (FWC) Coral and 

Octocoral Mitigation Relocation Recommendations – August 2016

FWC Coral and Octocoral Visual Health Assessment Protocols for 

Mitigation Relocation Activities – July 2016
 APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL 

 USCRTF Handbook on Coral Reef Impacts – December 2016 

126

Florida Fish and Wildlife Conservation Commission (FWC)

Coral and Octocoral Mitigation Relocation Recommendations

FWC Authorization Required

A Stock Collection and Release, Special Activity License (SAL) is required for all marine 

species relocation activities statewide, including but not limited to mitigation relocation 

activities. Information on the SAL Program and applications are available here: 

http://myfwc.com/license/saltwater/special-activities/

Definitions

For purposes of these Recommendations:

1) “Coral” is a fragment or colony of any species of the Order Scleractinia, Order

Antipitharia, and Genus Millepora.

2) “Interior waterways” are aquatic areas that have experienced physical restructuring of the

shoreline (e.g., inner port harbors, marinas), or naturally occurring areas of low flushing

(e.g., shallow bays, seawalls.)

3) “Listed or Proposed” are species that are state-listed pursuant to 68A-27, F.A.C.,

federally-listed pursuant to the Endangered Species Act, or proposed to be federallylisted pursuant to the Endangered Species Act.

4) “Octocoral” is a colony of any species of the Subclass Octocorallia, excluding encrusting

octocorals (e.g., Erythropodium caribaeorum, Briareum asbestinum).

5) “Relocation” includes all activities that move coral or octocoral fragments or colonies from

one place to another (e.g., transplanting, outplanting), including but not limited to moving

them into and out of temporary holding locations (e.g., cache, staging, acclimation

locations) or nurseries.

Coral and Octocoral Removal and Relocation

Removal and relocation of corals and octocorals to suitable sites in regionally appropriate 

densities (current or historical) should occur on all coastal projects where complete avoidance 

is not possible. These coral and octocoral removal and relocation activities should be 

considered as minimization of project impacts and not as compensatory mitigation. Coral and 

octocoral removal and relocation activities conducted to minimize project impacts can be 

accommodated in both Florida Uniform Mitigation Assessment Method (UMAM) and Habitat 

Equivalency Analysis (HEA) mitigation assessment methodologies, and would result in lower 

amounts of compensatory mitigation required for the project relative to the amount of mitigation 

that would be required if coral and octocoral removal and relocation was not performed. 

Compensatory mitigation should be required for all corals and octocorals that will not be 

removed and relocated.

On a case-by-case basis, the FWC will evaluate any request for removal and relocation of 

corals that are not listed or proposed and are considered by the FWC to be sub-adult sized, to 

be used as a compensatory mitigation measure to offset the loss of indirect effects (i.e., 

secondary impacts)8that are temporary (e.g., temporary reduction in larval output, temporary 

reduction in settlement). Evaluation of such requests will be based on available and 

8

Indirect effects (impacts) as defined by 40 CFR §1508.8.
 APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL 

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127

appropriate documentation of sub-adult relocation activities (e.g., literature, monitoring 

reports), and amount of credit that is proposed to be provided for such activities.

Coral and octocoral removal and relocation activities should not occur during times of severe 

stress (e.g., disease outbreak, coral bleaching, cold stress, significant algal blooms), or from 

locations being impacted by significant stress events (e.g., areas being impacted by dredging 

activities or storm water run-off events), unless there are extreme circumstances that warrant 

an exception. FWC will support coral and octocoral removal and relocation activities during 

times of severe stress or from locations being impacted by significant stress events on a caseby-case basis when resource or project impacts are imminent and cumulatively harmful, and 

when benefits outweigh potential risks. Please see the “Health Assessment” section of these 

Recommendations for exceptions that are applicable to coral and octocoral removal and 

relocations during times of severe stress or from locations being impacted by significant stress 

events.

Coral Removal and Relocation Activities

For purposes of these Recommendations, the FWC has determined corals that are ≥ 5 cm 

(measured as live tissue diameter - continuous live tissue patch with a diameter of 5 cm or 

greater) to be adult, although corals < 5 cm have been observed to be reproductive (Soong 

1993, Lazar et al. 2011, Coastal Eco-Group Inc., 2015.) The FWC determination of adult coral 

size was not solely based on reproductive capabilities and additionally considered:

1) At the 5 cm size, corals have a sufficient number of polyps and colony structure to obtain

a positive identification using standard surveying methodologies. Corals below this size

would require different surveying methodologies.

2) Corals ≥ 5 cm are generally considered to be adults (Bak and Engel 1979, Miller et al.

2000), based on average growth rates (Vaughn 1915) and estimated age of sexual

maturity (Connell 1973.)

The FWC recommends removal and relocation of all listed or proposed species of corals 

regardless of size, unless a coral displays signs of disease pursuant to the attached “FWC 

Coral and Octocoral Visual Health Assessment Protocols.” The species that are currently listed 

or proposed are as follows:

 Acropora cervicornis (ESA and state listed as Threatened)

 Acropora palmata (ESA and state listed as Threatened)

 Dendrogyra cylindrus (ESA and state listed as Threatened)

 Mycetophyllia ferox (ESA and state listed as Threatened)

 Orbicella annularis (ESA and state listed as Threatened, formerly Montastraea)

 Orbicella faveolata (ESA and state listed as Threatened, formerly Montastraea)

 Orbicella franksi (ESA and state listed as Threatened, formerly Montastraea)

For coral species that are not listed or proposed, the FWC recommends removal and 

relocation of all adult corals (corals ≥ 5 cm in diameter), unless a coral displays signs of 

disease pursuant to the attached “FWC Coral and Octocoral Visual Health Assessment 

Protocols.” Corals ≥ 5 cm in diameter can be successfully relocated. Brownlee (2010) 

successfully transplanted small corals (Siderastrea siderea, Dichocoenia stokesii, and Porites 

porites) with greater than 80 percent survivorship after 13 months. Monty et al. (2006)
 APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL 

 USCRTF Handbook on Coral Reef Impacts – December 2016 

128

successfully transplanted 250 corals (14 species) ranging from 5 to 40 cm in diameter with a 

high rate of survivorship. These corals were monitored for 13 months. Eight species had 100 

percent survivorship, including 78 Siderastrea siderea. Thornton et al. (2000) transplanted 

271 corals from an outfall pipe in Broward County to an articulated concrete mat. Siderastrea 

siderea comprised 90 percent of the corals <1 to 100 square centimeters in size. After 27 

months, 266 of the corals had survived (87 percent), as compared to 83 percent survival for 

corals on the nearby natural substrate. In addition, Stephens (2007) analyzed monitoring 

data from a transplantation effort that salvaged multiple species of coral from a coastal 

construction impact site in Broward County; survival of the species ranged between 92 and 

100 percent during monitoring periods varying between 18 and 24 months.

The potential exists for corals to break upon removal. For smaller-scale relocation activities 

and for all listed or proposed species (regardless of relocation activity size), it is feasible for all 

fragments of the same broken coral to be kept together and reattached as close together as 

possible (like puzzle pieces – reattached within 0 - 5 cm apart from one another), to promote 

successful fusing. The re-constructed corals should be considered as one single coral for 

monitoring purposes. Research has shown that fragments of the same genet are known to 

readily and successfully fuse (Raymundo and Maypa 2004). For larger-scale restoration 

activities, only fragments of broken corals that are ≥ 5 cm in live tissue diameter should be 

relocated and reattached, and considered as separate corals for monitoring purposes.

The FWC has further prioritized coral species for removal and relocation (in addition to 

species identified above) in the event that all corals ≥ 5 cm in diameter will not be removed 

and relocated. These coral species have been prioritized and binned based on a high 

conservation value (i.e., rare, slow-growing, low genetic diversity, slow to recover, sensitive to 

stress, poor-recruiter, high post-settlement mortality), and the list is as follows:

HIGH PRIORITY SPECIES

 Order Antipatharia

 Agaricia fragilis

 Agaricia lamarcki

 Colpophyllia natans

 Dichocoenia stokesii

 Diploria labyrinthiformis

 Favia fragum

 Isophyllia spp.

 Leptoseris cucullata

 Madracis spp.

 Manicina areolata

 Meandrina meandrites

 Montastraea cavernosa

 Mussa angulosa

 Mycetophyllia spp.

 Oculina diffusa

 Oculina robusta

 Solenastrea hyades

MEDIUM PRIORITY SPECIES

 Eusmilia fastigiata

 Porites divaricata, P. furcata, P.

porites

 Pseudodiploria spp. (formerly Diploria)

 Siderastrea siderea ≥10 cm

 Solenastrea bournoni

 Stephanocoenia intersepta ≥10 cm

 Undaria spp. (formerly Agaricia)
 APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL 

 USCRTF Handbook on Coral Reef Impacts – December 2016 

129

LOW PRIORITY

A lower amount of effort should be attributed to removing and relocating the following species, 

and compensatory mitigation should be designed to offset the loss of any corals not 

relocated. Alternatively, if the impact area is dominated by these species, effort would be 

justified to remove and relocate the following species:

 Porites astreoides

 Siderastrea radians

 Siderastrea siderea <10 cm

 Stephanocoenia intersepta <10 cm

 Cladocora arbuscula

 Phyllangia spp.

 Scolymia spp.

FWC supports efforts to relocate corals that are less than 5 cm (sub-adult sized), however we 

are aware that this may increase project costs due to additional survey design measures

needed to accurately identify corals of this small size. For corals that will not be relocated (of

any size), FWC recommends coordination with permitted/approved coral nursery/research

facilities within the region to determine if they have interest and financial resources to remove

corals or accept donated corals.

Octocoral Removal and Relocation Activities

The FWC recommends removal and relocation of all Gorgonia species and other octocoral 

species ≥ 10 cm in height, based on the prioritized list below. Similar to corals, these octocoral 

species are also prioritized based on a high conservation value (i.e., state prohibited species, 

conservation need, local abundance/density, growth rates, relocation success, and ability to 

recover naturally). In general, more robust rod species are slow growing and have low 

recruitment, but transplant well and seem to recover quickly from being transplanted (e.g., 

growing a new holdfast over attachment material) (Brinkhuis 2009). Plumes are low on the list 

because they recruit very quickly after a disturbance and have high growth rates so their 

potential for natural recovery is greater. Additionally, more delicate plume species have less 

tissue (e.g., thinner tissue = less potential/resources for healing after clipping) and are inferior 

transplantation candidates. However, plumes can be transplanted successfully (Brinkhuis 

2009). The prioritized list is as follows:

 Antillogorgia (formerly

Pseudopterogorgia)

 Eunicea

 Gorgonia (state prohibited species)

 Leptogorgia

 Muricea

 Muriceopsis

 Plexaura

 Plexaurella

 Pseudoplexaura

 Pterogorgia
 APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL 

 USCRTF Handbook on Coral Reef Impacts – December 2016 

130

In addition to the species previously listed, the following are priority genera if deeper 

relocation sites are targeted (>60 ft. or >18 m):

 Diodogorgia

 Ellisella

 Iciligorgia

 Swiftia

 Telesto
APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL

USCRTF Handbook on Coral Reef Impacts – December 2016

131

Florida Fish and Wildlife Conservation Commission (FWC)

Coral and Octocoral Visual Health Assessment Protocols for Mitigation Relocation

Temporary Holding of Corals and Octocorals Prior to Reattachment

If corals and octocorals will be placed in a temporary holding location after removal and prior to 

reattachment at the relocation site (for caching, staging, acclimation, etc.), the FWC 

recommends the following criteria be adhered to:

1) The temporary holding location for corals and octocorals must be located in a stable area

(e.g., low energy, low sedimentation, minimal temperature flux, minimal freshwater input),

and err conservatively on the side of being slightly farther from expected projectassociated direct and indirect impact areas.

2) Corals must be maintained in a temporary holding location where sediment does not collect,

be affixed to an elevated structure, or placed in a suspended container in a manner wherein

they are above the sea floor and do not touch each other. If corals are to remain in the

temporary holding location for longer than two weeks, they must be cemented or epoxied

to an elevated structure or to the sea floor.

3) Octocorals must be maintained in a temporary holding location where sediment does not

collect, be affixed to an elevated structure, or placed in a suspended bag in a manner

wherein they are above the sea floor and have adequate water flow (i.e., bags should not

be crowded). If octocorals are to remain in the temporary holding location for longer than

two weeks, they must be attached with zip ties by their holdfast or base to an elevated

array or line system previously installed on the sea floor. Orientation is less important, but

octocorals must not touch each other.

4) The installation of any structure to facilitate the temporary holding of corals and octocorals

prior to reattachment must also be authorized pursuant to permits that authorize the

placement of structures on submerged lands (e.g., Environmental Resource Permit

(ERP), Joint Coastal Permit (JCP), USACE Dredge and Fill Permit, Florida Keys National

Marine Sanctuary Permit).

Relocation Site Selection

The FWC recommends that the selection of an appropriate relocation site(s) for both corals 

and octocorals meet the following general criteria:

1) Relocation site must be suitable reef habitat, be within the known range of the species or

genera, and have historic presence of the species to be relocated (in recent decades).

2) Optimally, the relocation site should be located in similar water depths and have similar

physical conditions (e.g., light availability, water quality, water circulation) to those at the

removal site.

3) Optimally, the relocation site should have similar substrate orientation to removal site; i.e.,

if corals or octocorals are being removed from a vertical or sloped elevated surface, then

the relocation site should have similar vertical or sloped areas for relocation.

4) The relocation site must be as close in proximity to the removal area as possible to preserve

the functional ecosystem value of the surrounding areas provided by the resources to be

relocated, but err conservatively on the side of being slightly farther from expected projectassociated direct and indirect impact areas.

5) Relocation site must not contain large amounts of loose rubble and should not be a high

energy environment (Edwards and Clark 1998).
APPENDIX IV – EXAMPLE CORAL TRANSPLANTATION PROTOCOL

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6) Relocation site must not be located within a direct or indirect impact area for any

permitted, authorized or reasonably foreseeable marine coastal construction activity (e.g.,

dredging, beach nourishment, pipeline or communication cable installations), or within

exclusion or buffer areas (e.g., military, aquaculture).

7) Relocation site must have adequate and appropriate space to allow for: a) colony growth,

tissue re- colonization and plating based on colony size, species growth rates, and

maximum size capacity; and b) attachment density commensurate with regionally

appropriate densities.

Health Assessment

To minimize the risk that diseases are not being spread from the removal area to a temporary 

holding or relocation site, the FWC recommends a visual health assessment of each coral or 

octocoral slated for temporary holding or direct relocation be conducted immediately prior to 

removal pursuant to the attached “FWC Coral and Octocoral Visual Health Assessment 

Protocols” (Health Protocols). Corals and octocorals exhibiting visual signs of disease should 

not be removed, held temporarily, or relocated. Exceptions:

1) As identified in the “Coral and Octocoral Removal and Relocation” section of these

Recommendations, there may be extreme circumstances in which the FWC will support

coral and octocoral removal and relocation during times of severe stress or significant

stress events. For corals and octocorals that will be removed and relocated during times

of severe stress or from locations being impacted by significant stress events, FWC can

provide an exception on a case-by-case basis from the “bleaching and partial bleaching”

and “stress indicators” criterion identified in the Health Protocols (“Coral Visual Health

Assessment” section, numbers 1)a. and 1)e. respectively, and “Octocoral Visual Health

Assessment” section, numbers 2)a. and 2)e. respectively.) If an exception is provided by

the FWC, these corals and octocorals may be removed and relocated provided that all

other criterion in the Health Protocols are met.

2) Corals and octocorals surviving in interior waterways have demonstrated resilience in

spite of the poor environmental conditions they are growing in and as such, have strong

survival capabilities (potentially genetic) that are highly valued. Corals and octocorals

that will be removed and relocated from interior waterways are provided with an automatic

exception from the “bleaching and partial bleaching” and “stress indicators” criterion in the

Health Protocols (“Coral Visual Health Assessment” section, numbers 1)a. and 1)e.

respectively, and “Octocoral Visual Health Assessment” section, numbers 2)a. and 2)e.

respectively), and may be removed and relocated provided that all other criterion

identified in the Health Protocols are met.

Corals and octocorals held in a temporary holding location should again be visually assessed 

for health pursuant to the Health Protocols immediately prior to removal from the temporary 

holding location and reattachment at the relocation site. Exception - The visual health 

assessment does not need to be conducted for corals and octocorals that have been 

maintained in a temporary holding location for 48 hours or less. Any corals or octocorals 

displaying signs of disease in the temporary holding location should either be: a) removed, 

disposed of and not reattached, or b) donated for ex-situ research.

If the visual health assessment is required as a condition of a permit, the FWC also requests 

documentation of the following information as identified in the Health Protocols be included as 
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a requirement for any post-relocation reporting requirements:

1) Numbers of corals by species and size that were viable candidates for relocation but were

not removed and relocated because they failed the visual health assessment, must be

noted in any post-relocation reporting documentation.

2) Corals that are located in a temporary holding location when the visual health assessment

is conducted and are exhibiting visual signs of disease must be removeand disposed of or

donated for ex-situ research, and disposition must be noted in any post-relocation

reporting documentation.

3) Numbers of corals that are relocated containing boring sponges of the Genus Cliona must

be noted in any post-relocation reporting documentation.

4) Numbers of relocated corals that are experiencing active predation and the type of

predation (prior to removal of predators) must be noted in any post-relocation reporting

documentation.

Removal, Relocation and Reattachment Methodologies

The FWC is available to provide technical expertise to assist with the review or development 

of appropriate methodologies for the removal, relocation, and reattachment of corals and 

octocorals for mitigation purposes. The FWC would appreciate the ability to provide additional 

comments on relocation methodologies and relocation methodology revisions if such 

information becomes available in the future.

Staff of the Florida Department of Environmental Protection – Coral Reef Conservation 

Program, NOAA Florida Keys National Marine Sanctuary (Monroe County) and NOAA 

National Marine Fisheries Service are also available to provide technical expertise on coral 

removal, relocation and reattachment based on lessons learned on the Florida Reef Tract. 

Contacts for each of these agencies respective programs can be provided on request.

Mitigation Plans

The FWC is available to provide technical expertise to assist with the development of 

appropriate mitigation plans to avoid, minimize, and offset project impacts. The FWC would 

appreciate the ability to provide additional comments on mitigation plans and mitigation plan 

revisions if such information becomes available in the future.

Monitoring Plans

The FWC recommends corals and octocorals that are removed and relocated specifically for 

mitigation purposes are monitored for overall survival and attachment success at one week 

(may be conducted at any time during the seven days beginning the day immediately after the 

day relocation is conducted), one month, three months, six months, one year and two years 

post-relocation. The FWC emphasizes the need for all of these recommended monitoring 

events to be performed and the recommended activities/data collection identified below 

performed during the monitoring events, in order to appropriately determine achievement of 

performance standards and mitigation success.

At time of relocation

1) If the total quantity of corals or octocorals (considered separately for monitoring purposes)

to be relocated comprises less than 4,000 colonies: select a representative subset of

relocated corals/octocorals to be used for monitoring events, comprising 25% (or 1,000
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corals/octocorals maximum) of the total number of corals/octocorals relocated. This 

subset must be representative of the species composition and size classes of the total 

relocated corals/octocorals, with no less than 10 corals/octocorals of each species 

monitored. If less than 10 corals/octocorals are relocated from a species, all relocated 

corals/octocorals of that species must be included in the subset. It is possible that for 

smaller-scale relocation projects, one or both of these requirements will result in all of the 

relocated corals/octocorals needing to be monitored.

2) Tag or map this subset (including assignment of an identification number for each

coral/octocoral) so that they can be tracked individually over time for monitoring events.

3) This same subset of corals/octocorals must be used for all of the monitoring events.

4) If the total quantity of coral/octocorals to be relocated exceeds 4,000 colonies, the FWC

will reach a consensus with the applicant and the permitting agency on the number of

representative subset corals/octocorals that will be monitored (the minimum will be 1,000

corals/octocorals),

During each monitoring event

1) All loose or detached relocated corals/octocorals (not just the ones from the monitoring

subset) must be re-affixed to their structure or substrate.

2) Data to be collected for each monitoring event for the monitoring subset are as follows

(recommended data sheet is attached):

 Identification (species, ID#)

 Attachment success (firm, loose, detached, missing)

 Coral size – maximum diameter and maximum height. Coral max diameter is measured

as the outward-facing surface of the colony (perpendicular to the axis of growth). The

maximum diameter measurement includes both living tissue and dead areas of the

colony. Coral max height is measured parallel to the axis of growth, perpendicular to

growth bands, as viewed from the side of the colony.

 Coral Skeletal Area – this is not data that needs to be collected; this is calculated based

on coral max diameter and height metrics that are collected ((D+H)/2)^2

 Coral Tissue Condition – the visual estimate of percent live/dead tissue cover per colony

– percent live tissue (including bleached tissue) + percent dead tissue = 100%

 Coral Tissue Area Index - this is not data that needs to be collected; this is calculated

based on coral max diameter, max height, and % live tissue metrics that are collected

((D+H)/2)^2*%L

 Octocoral size – maximum height measured from the base of the holdfast attachment to

the top of the colony (following the axis of growth) as seen from the side

 Presence of conditions (bleaching, predation, disease, Cliona)

 Within Comments/Observations section, note any anomalous conditions of interest,

including “reconstructed colony” as described above in the Coral Removal and Relocation

Activities section.

The data requested for collection are specific to determining overall survival and attachment 

success, thus determining achievement of performance standards for mitigation actions (i.e., 

mitigation success), and assist with determining potential factors that may have contributed to 

the inability for mitigation actions to achieve performance standards (i.e., mitigation failure) 

such as regional disease or bleaching events, severe storm events, relocation contractor 

performance, etc.
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Reporting Schedule

The data collected during each monitoring event must be submitted according to the following 

schedule:

 One week event – information must be submitted within 14 days post-event

 One month through 2 year monitoring events - information must be submitted within 30

days post-event

The FWC is available to provide technical expertise to assist with the development of 

monitoring plans to help gauge mitigation success and identify project impacts, and would 

appreciate the ability to provide additional comments on monitoring plans and monitoring plan 

revisions if such information becomes available in the future.

Performance Standards

Corals

In order to assess mitigation success, FWC recommends evaluating overall survival of 

relocated corals via Tissue Area Index. A Tissue Area Index is calculated by averaging the 

coral maximum diameter and coral maximum height, then squaring the average dimension to 

determine Skeletal Area, then multiplying by the percent live tissue; formula as follows: 

((D+H)/2)^2*%L (Williams and Miller 2012). All of the metrics needed to determine Tissue Area 

Index are requested for collection in the Monitoring section above, and reflected in the data 

sheet provided. Overall survival of corals shall be defined as no net loss in pooled (by 

species) Tissue Area Index or an increase in pooled (by species) Tissue Area Index.

The performance standard to determine mitigation success for coral relocation activities should 

be at least 85 percent overall survival (as defined directly above) of all relocated species, with 

secure substrate attachment, two years after relocation.

Octocorals

In order to assess mitigation success, FWC recommends evaluating overall survival of 

relocated octocorals via maximum height, and this metric is requested for collection in the 

Monitoring section above and reflected in the data sheet provided. Overall survival shall be 

defined as no change in maximum height or an increase in maximum height.

The performance standard to determine mitigation success for octocoral relocation activities 

should be proposed by the applicant, and supported by available and appropriate 

documentation of octocoral relocation activities (e.g., literature, monitoring reports.) FWC will 

review these proposals as they are submitted to determine if the documentation submitted 

supports the performance standard as proposed.

The FWC is available to provide technical expertise to assist with the development of coral and 

octocoral performance standards, and would appreciate the ability to provide additional 

comments on performance standards and performance standard revisions if such information 

becomes available in the future.

Summary

In summary the FWC recommends:

 Coral and octocoral removal and relocation activities should be considered as
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 minimization of project impacts and not as compensatory mitigation. However, the FWC

will evaluate any request for removal and relocation of corals that are not listed or

proposed and are considered by the FWC to be sub-adult sized, to be used as a

compensatory mitigation measure to offset the loss of indirect (secondary) impacts.

 Removal and relocation of all listed or proposed corals of any size, unless they display

signs of disease pursuant to the attached “FWC Coral and Octocoral Visual Health

Assessment Protocols” (Health Protocols.)

 Removal and relocation of all non-listed or proposed adult corals (corals ≥ 5 cm in live

tissue diameter) and octocoral species ≥ 10 cm in height, unless they display signs of

disease pursuant to the attached Health Protocols.

 Both temporary holding sites (for caching, staging, acclimation, etc.) and relocation sites

should be selected pursuant to the criteria provided in these Recommendations.

 A visual health assessment should be required for each coral or octocoral immediately

prior to removal and relocation (for temporary holding or direct relocation) pursuant to the

attached Health Protocols. Corals and octocorals exhibiting visual signs of disease should

not be removed, held temporarily, or relocated (unless identified exceptions are

applicable or provided by the FWC.) Documentation of specific items identified in the

“Health Assessment” section above is requested for inclusion as part of any required

post-relocation reporting requirements.

 Relocated corals should be monitored at one week (may be conducted at any time during

the seven days beginning the day immediately after the day relocation is conducted), one

month, three months, six months, one year and two years post-relocation. A data sheet is

provided to facilitate capturing the data requested for monitoring purposes. Again, the

FWC emphasizes the need for all of these recommended monitoring events to be

performed in order to appropriately determine mitigation success.

 The performance standard to determine mitigation success for coral relocation activities

should be at least 85 percent overall survival (defined as no net loss in pooled (by

species) Tissue Area Index or an increase in pooled (by species) Tissue Area Index) of all

relocated species, with secure substrate attachment, two years after relocation.

 The performance standard to determine mitigation success for octocoral relocation

activities should be proposed by the applicant, and supported by available and

appropriate documentation of octocoral relocation activities (e.g., literature, monitoring

reports.) FWC will review these proposals as they are submitted to determine if the

documentation submitted supports the performance standard as proposed.
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Literature Cited

Bak R, Engel M (1979) Distribution, abundance and survival of juvenile hermatypic corals 

(Scleractinia) and the importance of life history strategies in the parent coral community. 

Marine Biology 54: 341-352.

Brinkhuis VIP (2009) Assessment of gorgonian transplantation techniques offshore Southeast 

Florida. M.S. Thesis. Nova Southeastern University. pp. 96.

Brownlee A (2010) Transplantation and parrotfish predation: A study on small Siderastrea 

siderea offshore Broward County, FL USA. M.S. Thesis.: Nova Southeastern University.

Coastal Eco-Group, Inc. (2015). Town of Palm Beach Coral Nursery Mitigation and Port of 

Palm Beach Slip 3 Coral Relocation Project – Year 1 Post-Transplant Monitoring Report. 27 

pp.

Connell J (1973) Population Ecology of Reef-Building Corals. In: OA Jones RE, editor. Biology 

and Geology of Coral Reefs. New York: Academic Press. pp. 205-245.

Edwards, AJ, S Clark (1998) Coral transplantation: a useful management tool or misguided 

meddling? Marine Pollution Bulletin 37: 474-487.

Lazar, K.E., Frazer, T.K, Jacoby, C.A., St Mary, C.M. 2011. Reproductive strategy of 

Siderastrea radians in the St. Martins Keys, Florida. Bulletin of Marine Science, 87(1):91-111.

Miller M, Weil E, and A Szmant (2000) Coral recruitment and juvenile mortality as structuring 

factors for reef benthic communities in Biscayne National Park, USA. Coral Reefs 19: 115-123.

Monty J, Gilliam, DS, Banks, KW, Stout, DK, and RE Dodge (2006) Coral of opportunity 

survivorship and the use of coral nurseries in coral reef restoration. Proc 10th ICRS: 1665-

1673.

Raymundo, LJ and Maypa, AP. 2004. Getting bigger faster: Mediation of size-specific 

mortality via fusion in juvenile coral transplants. Ecological Applications 14(1): 281-295.

Soong K. 1993. Colony size as a species character in massive reef corals. Coral Reefs 12(2): 

77-83.

Stephens NR (2007) Stony coral transplantation associated with coastal and marine 

construction activities. M.S. Thesis. Nova Southeastern University.

Thornton S, Dodge, RE, Gilliam, DS, DeVictor, R, and P Cook (2000) Success and growth of 

corals transplanted to concrete armor mat tiles in southeast Florida: Implications for reef 

restoration. Proc 9th ICRS 2: 23-27.

Vaughn T (1915) The geological significance of the growth-rate of the Floridian and Bahamian 

shoal-water corals. Journal of Washington Academy of Sciences 5: 591-600.
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Williams DE, Miller MW (2012). Atttributing mortality among drivers of population decline in 

Acropora palmata in the Florida Keys. Coral Reefs 31:369-382.

CORALS

Definitions

For purposes of these Protocols:

1) “Coral” is a fragment or colony of any species of the Order Scleractinia, Order

Antipitharia, and Genus Millepora.

2) “Bleaching” for purposes of coral relocation is defined as 100% of coral tissue is

discolored due to the loss or reduction in number of endosymbiotic algae (zooxanthellae

(Genus Symbiodinium)). During bleaching, tissue is present but is pale to white in color.

3) “Interior waterways” are aquatic areas that have experienced physical restructuring of the

shoreline (e.g., inner port harbors, marinas), or naturally occurring areas of low flushing

(e.g., shallow bays.)

4) “Partial bleaching” is where only a portion of the coral has lost its zooxanthellae, and the

remaining areas of tissue appear normal in color.

5) “Old mortality” is the non-living portion of exposed coral skeleton that has been overgrown

by algae and other biofouling organisms and where the corallite structure has eroded over

time and is no longer identifiable. *Not to be confused with “recent mortality.”

6) “Recent mortality” is the non-living portion of recently exposed coral skeleton (i.e.,

skeleton is white and corallite structures are intact and identifiable), including the

development of fine “fuzz” or turf algae on exposed skeleton (i.e., skeleton is yellowish in

appearance and corallite structure may be slightly eroded but still identifiable), indicating

that the mortality occurred within a couple of weeks prior to observation. *Not to be

confused with “old mortality.”

7) “Relocation” includes all activities that move coral fragments or colonies from one place to

another (e.g., transplanting, outplanting), including but not limited to moving them into and

out of temporary holding locations (e.g., cache, staging, acclimation locations) or

nurseries.

Coral Visual Health Assessment

Each coral fragment or colony selected for relocation must be visually assessed pursuant to 

these Protocols to ensure that they appear to be in good health and are free from suspected 

disease. This visual health assessment must be conducted immediately prior to removal from 

each and any location, and may need to be conducted more than once before the relocation 

activity is completed (e.g., immediately prior to removal from an original collection location, a 

culture location (nursery), or a temporary holding location established for purposes of caching, 

staging, acclimation, etc.). Exception - The visual health assessment does not need to be 

conducted for coral fragments or colonies that have been maintained in a temporary 

holding location for 48 hours or less.

Coral fragments or colonies that are located in an original collection or culture location when 

the visual health assessment is conducted and are exhibiting visual signs of disease may not 

be removed and relocated to other in-water locations. Coral fragments or colonies that are 

located in a temporary holding location when the visual health assessment is conducted and 

are exhibiting visual signs of disease must be removed and disposed of, and this disposition 
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must be noted in any post-relocation reporting documents. Field personnel conducting coral 

visual health assessments should be proficient with species identification, and trained 

in coral disease, predation identification and removal, and survey techniques to assure 

accuracy of the assessment. Each coral fragment or colony must meet the following criteria 

prior to relocation:

1) Show no visible signs of disease based on the presence of:

a. Bleaching or partial bleaching. Exceptions:

1. Partial bleaching is acceptable for relocation of specific coral species for

which it is recognized as a part of these coral species’ normal, healthy state.

These coral species are as follows: Oculina spp., Agaricia fragilis, Helioseris

cucullata, Orbicella franksi, Siderastrea radians, and Undaria humilis. Partial

bleaching <2 cm on healthy, growing branch tips is also considered

acceptable and normal for branching coral species including Acropora

cervicornis, Acropora palmata, Acropora prolifera, Millepora alcicornis and

Millepora complanata.

2. As identified in the Mitigation Relocation Recommendations, “Coral and

Octocoral Removal and Relocation” section, there may be extreme

circumstances in which the FWC will support coral removal and relocation

during times of severe stress or significant stress events. On a case-bycase basis, FWC can provide exception to this criterion for corals that will be

removed and relocated during times of severe stress or from locations being

impacted by significant stress events.

3. Exception to this criterion is automatically provided for corals that are being

removed and relocated from interior waterways as identified in the Mitigation

Relocation Recommendations, “Health Assessment” section.

b. Recent mortality greater than 1% tissue loss exposing underlying skeleton.

Exception - Old mortality is acceptable for corals that are to be relocated.

c. Active disease (e.g., white/black/yellow/red band diseases, white pox or plague

diseases, white Beggiatoa mats, dark (purple) spot/blotch diseases, growth

anomalies).

d. Suspect disease indicators (e.g., bands, spots, microbial mats, cyanobacteria

colonization).

e. Stress indicators (e.g., tissue sloughing, swelling, or thinning; excessive

sedimentation; excessive mucous production). Exceptions:

1. As identified in the Mitigation Relocation Recommendations, “Coral and

Octocoral Removal and Relocation” section, there may be extreme

circumstances in which the FWC will support coral removal and relocation

during times of severe stress or significant stress events. On a case-bycase basis, FWC can provide exception to this criterion for corals that will be

removed and relocated during times of severe stress or from locations being

impacted by significant stress events.

2. Exception to this criterion is automatically provided for corals that are being

removed and relocated from interior waterways as identified in the Mitigation

Relocation Recommendations, “Health Assessment” section.

f. Predators or evidence of predation from organisms that cannot be removed (e.g.,

peeled off) prior to relocation such as: fireworms (Hermodice caruncunculata),

snails (e.g., Coralliophila abbreviata, Thais deltoidea), or damselfish (e.g.,
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Stegastes planifrons, Microspathodon chrysurus); invasive, encrusting and/or 

overgrowing tunicates (e.g., Genus Symplegma, Genus Botryllus), sponges, 

octocorals (e.g., Erythropodium caribaeorum, Briareum asbestinum), or zoanthids 

(e.g., Genus Palythoa). Exception - Corals containing boring sponges of the 

Genus Cliona are acceptable for relocation. Numbers of corals that are relocated 

containing boring sponges of the Genus Cliona must be noted in any postrelocation reporting documents.

2) Corals that are experiencing active predation (e.g., presence in feeding position along

tissue loss margin of Coralliophila abbreviata and/or Hermodice carunculata), may be

relocated once all predators are removed. Numbers of relocated corals that are

experiencing active predation and the type of predation (prior to removal of predators)

must be noted in any post-relocation reporting documents.

OCTOCORALS

Definitions

For purposes of these Protocols:

1) An “octocoral” is a colony of any species of the Subclass Octocorallia, excluding

encrusting octocorals (e.g.,

Erythropodium caribaeorum, Briareum asbestinum).

2) A “rod” is characterized as having thick branches, and usually secondary branches

with thick tissues.

3) A “seafan” is characteristically fan shaped with interconnected net-like branching with

thin tissues.

4) A “plume” is characterized as having thin pinnate (feather-like) branches and

branchlets with thin tissues.

5) A “holdfast” is the base of an octocoral that attaches the colony to the substrate.

6) The “axis” of an octocoral is the central supporting skeletal structure made out of

proteinaceous gorgonin that is dark brown to black in color.

7) “Bleaching” for the purposes of octocoral relocation is defined as 100% of octocoral

tissue is discolored due to the loss or reduction in number of endosymbiotic algae

(zooxanthellae). During bleaching, tissue is present but is pale to white in color.

8) “Partial bleaching” is where only a portion of the octocoral tissue has lost its

zooxanthellae, and the remaining areas of tissue appear normal in color. *Note that

octocorals rarely bleach and generally tend to exhibit partial bleaching at their branch

tips closest to the water’s surface.

9) “Recent mortality” is the non-living portion of recently exposed octocoral axis skeleton

(i.e., axis is dark brown to black), including the development of fine “fuzz” or turf algae

on exposed axis, indicating that the mortality occurred within a few days prior to

observation. *“Old mortality” is not determinable in octocorals.

10) “Relocation” includes all activities that move octocoral colonies from one place to

another (e.g., transplanting, outplanting), including but not limited to moving them into

and out of temporary holding locations (e.g., cache, staging, acclimation locations) or

nurseries.

Octocoral Visual Health Assessment

Each octocoral colony selected for relocation must be visually assessed pursuant to these 

Protocols to ensure that they appear to be in good health and are free from suspected disease. 

This visual health assessment must be conducted immediately prior to removal from each and 
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any location, and may need to be conducted more than once before the relocation activity is 

completed (e.g., immediately prior to removal from an original collection location, a culture 

location (nursery), or a temporary holding location established for purposes of caching, 

staging, acclimation, etc.). Exception - The visual health assessment does not need to be 

conducted for octocoral colonies that have been maintained in a temporary holding location for 

48 hours or less.

Octocoral colonies that are located in an original collection or culture location when the visual 

health assessment is conducted and are exhibiting visual signs of disease may not be 

removed and relocated to other in-water locations. Octocoral colonies that are located in a 

temporary holding location when the visual health assessment is conducted and are exhibiting 

visual signs of disease must be removed and disposed of, and this disposition must be noted 

in any reporting or monitoring documents. Field personnel conducting octocoral visual 

health assessments should be proficient with species identification, and trained in 

octocoral disease, predation identification and removal, and survey techniques to 

assure accuracy of the assessment. Each octocoral colony must meet the following criteria 

prior to relocation:

1) Rod, plume, and seafan colonies must have at least 10 cm (approx. 4”) of linear

growth (height).

2) Show no visible signs of disease or mechanical injury based on the presence of:

a. Bleaching or partial bleaching. Exceptions:

1. As identified in the Mitigation Relocation Recommendations, “Coral and

Octocoral Removal and Relocation” section, there may be extreme

circumstances in which the FWC will support octocoral removal and

relocation during times of severe stress or significant stress events. On a

case-by-case basis, FWC can provide exception to this criterion for

octocorals that will be removed and relocated during times of severe

stress or from locations being impacted by significant stress events.

2. Exception to this criterion is automatically provided for octocorals that are

being removed and relocated from interior waterways as identified in the

Mitigation Relocation Recommendations, “Health Assessment” section.

b. Recent mortality greater than 5% of tissue loss exposing axis.

c. Active disease (e.g., purple spot, aspergillosis, red band disease, black wasting

disease, and growth anomalies (severely altered morphology of tissues and

skeleton)).

d. Suspect disease indicators (e.g., bands, spots or rings (identified by severe dark

purpling (25% or greater) or blackening of tissues); microbial mats;

cyanobacteria colonization).

e. Stress indicators (e.g., tissue sloughing or swelling; excessive sedimentation;

excessive mucous production). Exceptions:

1. As identified in the Mitigation Relocation Recommendations, “Coral and

Octocoral Removal and Relocation” section, there may be extreme

circumstances in which the FWC will support octocoral removal and

relocation during times of severe stress or significant stress events. On a

case-by-case basis, FWC can provide exception to this criterion for

octocorals that will be removed and relocated during times of severe

stress or from locations being impacted by significant stress events.
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2. Exception to this criterion is automatically provided for octocorals that are

being removed and relocated from interior waterways as identified in the

Mitigation Relocation Recommendations, “Health Assessment” section.

3) Octocorals that are experiencing active predation (e.g., presence of predators,

including Cyphoma gibbosum and/or Hermodice carunculata, in feeding position

along tissue loss margin), may be relocated once all predators are removed.

Exception – Colonies of Gorgonia ventalina with active predation of the nudibranch

Tritonia hamnerorum, cannot be relocated.