September 2011

CONDITION

REPORT 2011 Florida Keys

National Marine Sanctuary

Office of National Marine Sanctuaries

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

Rebecca M. Blank, Ph.D., Acting Secretary

National Oceanic and Atmospheric Administration

Jane Lubchenco, Ph.D., 

Administrator Under Secretary of 

Commerce for Oceans and Atmosphere 

National Ocean Service

David M. Kennedy, Assistant Administrator

Office of National Marine Sanctuaries

Daniel J. Basta, Director

National Oceanic and Atmospheric Administration

Office of National Marine Sanctuaries 

SSMC4, N/ORM62

1305 East-West Highway

Silver Spring, MD 20910

301-713-3125

http://sanctuaries.noaa.gov

Southeast Atlantic, Gulf of Mexico and Caribbean Region

NOAA Office of National Marine Sanctuaries

33 East Quay Road

Key West, Florida 33040

305-809-4670

Florida Keys National Marine Sanctuary

33 East Quay Rd.

Key West, FL 33040

305-809-4700

http://floridakeys.noaa.gov

Report Preparers:

Florida Keys National Marine Sanctuary:

Scott Donahue, Joanne Delaney, Brenda Altmeier

Southeast Atlantic, Gulf of Mexico, and Caribbean 

Region:

Billy Causey, Sarah Fangman, Brian D. Keller

Office of National Marine Sanctuaries:

Kathy Broughton, Michelle A. Johnston, Steve Gittings, 

Vernon R. Leeworthy

Copy Editors: Matt Dozier, Sharon Sirkis 

Layout: Matt McIntosh, Jason Lentz

A Tribute to a Friend and Colleague

This report is dedicated to Dr. 

Brian Keller, a longtime member 

of the sanctuary science team. 

Brian was a sage scientist, patient 

mentor and committed conservationist, a caring friend and beloved 

husband who touched countless 

lives with his science and his 

humanity over the course of an outstanding 40-year career in the 

Florida Keys and Caribbean. In the 10 years that Brian worked for 

NOAA, he was a true leader in the study, management and conservation of the marine ecosystems of the Florida Keys, Gulf of Mexico and 

Caribbean. In his role as science coordinator with the National Marine 

Sanctuary System, Brian dedicated himself to finding innovative ways 

to understand marine ecology and to creating new tools for conserving the ocean world he loved.

Brian came to NOAA in 2000, joining the staff of Florida Keys National Marine Sanctuary as science coordinator after more than two 

decades of distinguished work in Florida and the Caribbean. During 

his time with the sanctuary system, he helped lay the foundation for 

management zones in the Florida Keys and led efforts to measure 

their effectiveness. He was the architect of the sanctuary’s research 

and monitoring plans, and a report he authored that highlights a 

decade of success for sanctuary management of the Keys. 

Not only was Brian an accomplished scientist and fervent ocean advocate, he was a close friend to many throughout the international science 

community. He was a man who was knowledgeable and passionate 

about his work, as well as deeply warm in his personal relationships.

Brian will be greatly missed, and his memory will live on in the 

hearts and scientific work of his friends and colleagues in the 

national marine sanctuaries and beyond.

Cover credits:

Map: 

Bathymetric Grids provided by Department of Commerce, National 

Oceanic and Atmospheric Administration, National Ocean Service, 

Special Projects Office. 1998. Estuarine Bathymetric Digital Elevation Models (30 meter resolution) Derived From Source Hydrographic Survey Soundings Collected by NOAA. Silver Spring, MD. 

NOAA’s Ocean Service, Special Projects (SP)

Photos (from top left, clockwise): 

Photo credits (clockwise from top left): Elkhorn coral (Cory Walter, Mote 

Marine Laboratory), permit fish spawning (Jiangang Luo, Rosenstiel 

School), kayakers in mangrove forest (NOAA/FKNMS), FKNMS Atlas 

map (see above credit), diver over Mike’s wreck (NOAA/FKNMS), 

vessel grounding (FWC), Azure Vase Sponge (Geoff Cook), grouper 

(NOAA/FKNMS), Caribbean spiny lobsters mating (NOAA/FKNMS)

Suggested Citation:

Office of National Marine Sanctuaries. 2011. Florida Keys National 

Marine Sanctuary Condition Report 2011. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of 

National Marine Sanctuaries, Silver Spring, MD. 105 pp.
1

About This Report ........................................................................................................2

Summary and Findings................................................................................................3

National Marine Sanctuary System and System-Wide Monitoring..............................

3

Condition Summary Table............................................................................................

4

Site History and Resources.........................................................................................10

Geology ........................................................................................................................10

Water Circulation ..........................................................................................................11

Early Exploration and Settlement .................................................................................12

Development of the Florida Keys..................................................................................12

Commerce ....................................................................................................................13

Designation of the Sanctuary........................................................................................14

Habitats.........................................................................................................................16

Living Resources ..........................................................................................................18

Maritime Archaeological Resources .............................................................................19

Pressures on the Sanctuary........................................................................................20

Pressures on Water Quality..........................................................................................20

Commercial and Recreational Fishing..........................................................................23

Bleaching Events and Climate Change ........................................................................24

Weather Disturbances ..................................................................................................26

Diseases of Marine Organisms.....................................................................................26

Vessel Use....................................................................................................................28

Coastal Development ...................................................................................................29

Non-Indigenous Species...............................................................................................30

Wildlife Disturbance......................................................................................................30

Artificial Reefs...............................................................................................................31

Marine Debris ...............................................................................................................31

Military Use...................................................................................................................32

Pressures to Maritime Archaeological Resources ........................................................33

State of Sanctuary Resources.....................................................................................34

Water ............................................................................................................................35

Habitat ..........................................................................................................................40

Living Resources ..........................................................................................................46

Maritime Archaeological Resources .............................................................................60

Response to Pressures...............................................................................................61

Marine Zoning...............................................................................................................61

Research and Monitoring..............................................................................................63

Management Responses to Water Quality Pressures..................................................64

Commercial and Recreational Fishing..........................................................................66

Climate Change, Bleaching Events, and Weather Disturbances..................................67

Diseases of Marine Organisms.....................................................................................68

Vessel Use....................................................................................................................69

Coastal Development ...................................................................................................69

Non-Indigenous Species...............................................................................................70

Wildlife Disturbance......................................................................................................71

Artificial Reefs...............................................................................................................72

Marine Debris ...............................................................................................................72

Military Use...................................................................................................................73

Management Responses to Pressures Impacting Maritime Archaeological Resources......73

Concluding Remarks..................................................................................................75

Acknowledgements....................................................................................................76

Cited Resources..........................................................................................................77

Additional Online Resources .....................................................................................92

Appendix A: Rating Scheme for System-Wide Monitoring Questions........................93

Appendix B: Consultation with Experts and Document Review...............................103

Table of Contents
Florida Keys National Marine Sanctuary

2 Florida Keys CONDITION REPORT 2011

About this Report 

This “condition report” provides a summary of resources in the National Oceanic and Atmospheric Administration’s Florida Keys National 

Marine Sanctuary (sanctuary), pressures on those resources, current 

conditions and trends, and management responses to the pressures 

that threaten the integrity of the marine environment. Specifically, the 

document includes information on the status and trends of water quality, habitat, living resources and maritime archaeological resources, 

and the human activities that affect them. It presents responses to a 

set of questions posed to all sanctuaries (Appendix A). Resource status of Florida Keys is rated on a scale from good to poor, and the timelines used for comparison vary from topic to topic. Trends in the status 

of resources are also reported, and are generally based on observed 

changes in status over the past five years, unless otherwise specified. 

Sanctuary staff consulted with a group of outside experts familiar 

with the resources and with knowledge of previous and current scientific investigations in the sanctuary. Evaluations of status and trends 

are based on interpretation of quantitative and, when necessary, nonquantitative assessments, and the observations of scientists, managers and users. The ratings reflect the collective interpretation of 

the status of local issues of concern among sanctuary program staff 

and outside experts based on their knowledge and perception of local 

problems. The final ratings were determined by sanctuary staff. This 

report has been peer reviewed and complies with the White House 

Office of Management and Budget’s peer review standards as outFlorida Keys National Marine Sanctuary

■	 Congressionally designated on Nov. 16, 1990, as a national marine sanctuary

■	 2,896 square nautical miles (9,933 square kilometers)

■	 Surrounds the Florida Keys community of more than 72,000 year-round residents and 3–3.3 million annual

visitors. The “functional population” (number of people in the Keys on an average day) ranges from 115,000 to

117,000 during the winter season and 101,000 to 104,000 during the summer season

■	 Utilizes over 900 mooring buoys and boundary buoys to protect corals and seagrass from anchors and guide

public use

■	 Approximately 60% of the sanctuary is state of Florida waters, and 40% is federal waters

■	 Shares boundaries with three national parks (Everglades, Biscayne, and Dry Tortugas National Parks)

■	 Overlaps four national wildlife refuges, six state parks, three state aquatic preserves, and two previously designated national marine sanctuaries (Key Largo, designated in 1975, and Looe Key, designated in 1981)

■	 Shares trusteeship of marine resources with the state of Florida, the South Atlantic Fishery Management Council, the Gulf of Mexico Fishery Management Council, and NOAA Fisheries Service

■	 Includes mangrove, seagrass, hardbottom, and coral reef habitats in coastal and oceanic waters

■	 Home to more than 6,000 species of marine life

■	 Approximately 1,700 islands with a combined shoreline length of 1,815 miles (2,920 kilometers)

■	 Marine zones for multiple uses, including 24 highly protected “no-take” areas (6% of the sanctuary)

■	 An “Area to be Avoided” codified into sanctuary regulations prohibits ships larger than 50 meters in length,

except in corridors into Key West Harbor

■	 Extensive education and outreach, research, monitoring, and law enforcement programs

■	 Contains an estimated 400 underwater historical sites, 14 of which are listed in the Department of the Interior’s

National Register of Historic Places

Despite a large diversity in habitat types and communities within the Florida Keys sanctuary, a single, sanctuary-wide status and trend rating is given for each

question. Although the ratings are generalized for the

entire sanctuary, text found in the report section titled

“State of Sanctuary Resources” provides a detailed

description of the basis for judgment for each question, and may include recognition and description of

any conditions that are not consistent with the rating.
Florida Keys National Marine Sanctuary

CONDITION REPORT 2011 Florida Keys 3

lined in the Final Information Quality Bulletin for Peer Review.

This is the first attempt to describe comprehensively the status, 

pressures and trends of resources at Florida Keys National Marine Sanctuary. Additionally, the report helps identify gaps in current monitoring efforts, as well as causal factors that may require 

monitoring and potential remediation in the years to come. The data 

discussed will enable resource managers and stakeholders to not 

only acknowledge prior changes in resource status, but will provide 

guidance for future management challenges.

Summary and Findings

Florida Keys National Marine Sanctuary is one of the largest marine 

protected areas in the United States, encompassing 2,896 square nautical miles (9,933 square kilometers). It was designated by Congress 

and exists under federal law, and became effective in state waters with 

the consent of the state of Florida. Marine zones for multiple uses, 

including 24 highly protected “no-take” areas (6% of the sanctuary), 

have been in place since 1997. The sanctuary helps protect more than 

6,000 species of marine life, including the nation’s only bank-barrier 

coral reef that lies adjacent to the continent, and one of the largest seagrass communities in this hemisphere. An estimated 400 underwater 

historical sites also lie within sanctuary waters, 14 of which are listed 

on the Department of the Interior’s National Register of Historic Places.

The Florida Keys and their environs have a long history (>100 

years) of exploitation, thus many pressures on sanctuary resources 

are chronic, and to some degree cumulative. A historical perspective of sanctuary biodiversity suggests that the populations of many 

higher-trophic-level species, such as marine mammals and predatory 

fishes, were dramatically reduced by hunting and fishing prior to the 

sanctuary’s designation. Today, pressures on the resources include 

commercial and recreational fishing, disturbances to wildlife, coastal 

development, harmful algal blooms, marine debris, vessel groundings, 

the introduction of non-indigenous species, and vessel traffic. Humandriven factors such as climate change, sea level rise and ocean acidification are large-scale issues that may also affect sanctuary resources.

Generally, the status and trends of the resources protected by Florida Keys National Marine Sanctuary reflect the inherited condition of a 

system that has been heavily exploited during the past century, more 

so than the relatively short time frame that these resources have been 

managed at the current geographic scale. For example, many of the 

historically abundant species (e.g., green turtles) and biogenic habitats 

had already been severely altered or reduced when the sanctuary was 

designated. Thus, resource managers are working to conserve pieces 

of the former system so that it can be restored to an improved state. 

However, understanding the degree of change in biodiversity that has 

occurred over time and how the coral reef ecosystem functioned in a 

“pre-exploitive” state can help managers and stakeholders identify realistic ecological and socioeconomic targets for maintaining or improving 

ecosystem services. For example, there are positive signs that some 

ecosystem services are responding to recent management actions, 

most notably in the form of recovering fish spawning aggregations, and 

increasing sizes and abundances of economically important fisheries 

species inside the larger ecological reserves. 

The current management plan for Florida Keys National Marine 

Sanctuary was released in December 2007, and it contains a number 

of management actions that address current issues and concerns. The 

plan stresses an ecosystem-based approach to management, which 

requires consideration of ecological interrelationships not only within 

the sanctuary, but within the larger context of the Gulf of Mexico and 

South Atlantic ecosystems. The management plan includes 14 action 

plans that will guide sanctuary management for the next few years.

National Marine Sanctuary System 

and System-Wide Monitoring

The National Marine Sanctuary System manages marine areas in both 

nearshore and open ocean waters that range in size from less than one 

to almost 140,000 square miles (362,598 square kilometers). Each area 

has its own concerns and requirements for environmental monitoring, but 

ecosystem structure and function in all these areas have similarities and 

are influenced by common factors that interact in comparable ways. Furthermore, the human influences that affect the structure and function of 

these sites are similar in a number of ways. For these reasons, in 2001 

the program began to implement System-Wide Monitoring (SWiM). The 

monitoring framework (NMSP 2004) facilitates the development of effective, ecosystem-based monitoring programs that address management 

information needs using a design process that can be applied in a consistent way at multiple spatial scales and to multiple resource types. It 

identifies four primary components common among marine ecosystems: 

water, habitats, living resources and maritime archaeological resources.

By assuming that a common marine ecosystem framework can be 

applied to all places, the National Marine Sanctuary System developed 

a series of questions that are posed to every sanctuary and used as 

evaluation criteria to assess resource condition and trends. The questions, which are shown on the following page and explained in Appendix 

A, are derived from both a generalized ecosystem framework and from 

the National Marine Sanctuary System’s mission. They are widely applicable across the system of areas managed by the sanctuary program 

and provide a tool with which the program can measure its progress toward maintaining and improving resource quality throughout the system.

Similar reports summarizing resource status and trends will be 

prepared for each marine sanctuary approximately every five years 

and updated as new information allows. The information in this report 

is intended to help set the stage for the management plan review 

process. The report also helps sanctuary staff identify monitoring, 

characterization and research priorities to address gaps, day-to-day 

information needs and new threats. 
Florida Keys National Marine Sanctuary

4 Florida Keys CONDITION REPORT 2011

The following table summarizes the “State of Sanctuary Resources” section of this report. The first two columns list 17 questions 

used to rate the condition and trends for qualities of water, habitat, 

living resources, and maritime archaeological resources. The Rating column consists of a color, indicating resource condition, and 

a symbol, indicating trend (see key for definitions). The Basis for 

Judgment column provides a short statement or list of criteria used 

to justify the rating. The Description of Findings column presents the 

statement that best characterizes resource status, and corresponds 

to the assigned color rating. The Description of Findings statements 

are customized for all possible ratings for each question. Please see 

# Questions/Resources Rating Basis for Judgment Description of Findings Sanctuary Response

WATER

1

Are specific or multiple stressors, 

including changing oceanographic and atmospheric conditions, 

affecting water quality and how 

are they changing?

▼

Large-scale changes in flushing 

dynamics over many decades 

have altered many aspects of 

water quality; nearshore problems 

related to runoff and other 

watershed stressors; localized 

problems related to infrastructure.

Selected conditions may inhibit the 

development of assemblages and may 

cause measurable but not severe declines in living resources and habitats.

In conjunction with the Environmental Protection Agency and 

Florida Department of Environmental 

Protection, the sanctuary will continue 

implementation of its Water Quality 

Protection Program and conduct longterm water quality monitoring and 

research to understand the effects of 

water transported from near-field and 

far-field sources, including Florida 

Bay on water quality in the sanctuary. 

New regulations prohibit discharge 

or deposit of sewage from marine 

sanitation devices (MSD) within the 

boundaries of the sanctuary and 

require MSDs be locked to prevent 

sewage discharge or deposit while 

inside sanctuary boundaries. The 

marine area surrounding the Florida 

Keys has been designated as a 

Particularly Sensitive Sea Area by the 

International Maritime Organization. 

Florida Department of Health Florida 

Healthy Beaches Program tests for 

the presence of fecal coliform and 

enterococci bacteria in beach water 

on a weekly basis, at 17 locations 

throughout the Keys. The MEERA 

Project, which is designed to provide 

early detection and assessment of 

biological events occurring in the 

Florida Keys and surrounding waters, 

continues to be supported by the 

sanctuary. A well-established law 

enforcement program is in place, 

including NOAA Fisheries Service, 

Florida Fish and Wildlife Conservation 

Commission, and U.S. Coast Guard.

2

What is the eutrophic condition 

of sanctuary waters and how is it 

changing?

–

Long-term increase in inputs from 

land; large, persistent phytoplankton bloom events, many of which 

originate outside the sanctuary 

but enter and injure sanctuary 

resources.

Selected conditions have caused or 

are likely to cause severe declines in 

some but not all living resources and 

habitats.

3

Do sanctuary waters pose risks 

to human health and how are 

they changing? –

Rating is a general assessment 

of “all waters” of the sanctuary, 

knowing that in very specific locations, the rating could be as low 

as “poor.” Increased frequency 

of HABs and periodic swim 

advisories.

Selected conditions have resulted in 

isolated human impacts, but evidence 

does not justify widespread or persistent concern.

4

What are the levels of human 

activities that may influence 

water quality and how are they 

changing?

▲

Historically, destructive activities 

have been widespread throughout 

the Florida Keys, but many recent 

management actions are intended 

to reduce threats to water quality.

Selected activities have caused or are 

likely to cause severe impacts, and 

cases to date suggest a pervasive 

problem.

Appendix A for further clarification of the questions and the Description of Findings statements. The Response column describes current or proposed management responses to pressures impacting 

sanctuary resources.

Status: Good Good/Fair Fair Fair/Poor Poor Undet.

 Trends: Conditions appear to be improving................................ p

Conditions do not appear to be changing...................... –

Conditions appear to be declining ................................. q

Undetermined trend....................................................... ?

 Question not applicable................................................. N/A

Table is continued on the following page.

Florida Keys National Marine Sanctuary Condition Summary Table
Florida Keys National Marine Sanctuary

CONDITION REPORT 2011 Florida Keys 5

Table is continued on the following page.

Florida Keys National Marine Sanctuary Condition Summary Table (Continued)

# Questions/Resources Rating Basis for Judgment Description of Findings Sanctuary Response

Habitat

5

What are the abundance and 

distribution of major habitat types 

and how are they changing? –

In general, mangrove and benthic 

habitats are still present and their 

distribution is unchanged, with the 

exception of the mangrove community, which is about half of what 

it was historically. The addition 

of causeways has changed the 

distribution of nearshore benthic 

habitats in their vicinity.

Selected habitat loss or alteration has 

taken place, precluding full development of living resource assemblages, 

but it is unlikely to cause substantial 

or persistent degradation in living 

resources or water quality.

Marine zoning is used in the sanctuary to protect sensitive habitats like 

shallow coral reefs. Mooring buoys 

have been installed as a threatreduction measure. Sanctuary staff 

and volunteers educate and inform 

boaters about the unique nature of 

the coral reef habitat, and organize 

shoreline clean-up and marine 

debris removal efforts. Sanctuary 

staff assess and restore vessel 

grounding injuries to seagrass and 

coral habitats, as well as perform 

coral rescue activities associated with 

coastal construction. Large vessel 

avoidance and Racon beacons in 

lighthouses have resulted in declines 

in large vessel groundings. An Area 

To Be Avoided was established to 

prevent ships larger than 50 meters in 

overall length from transiting through 

sensitive areas in the sanctuary. A 

well established permitting program is 

in place to issue a variety of permits 

for activities that are otherwise 

prohibited by sanctuary regulations. 

There is also a well-established law 

enforcement program in place, including NOAA Fisheries Service, the 

Florida Fish and Wildlife Conservation Commission, and the U.S. Coast 

Guard. State of Florida’s Magrove 

Trimming and Preservation Act of 

1996 (§403.9321-403.9333) regulates 

how mangroves can be trimmed and 

altered, and by whom.

6

What is the condition of biologically structured habitats and how 

is it changing?

q

Loss of shallow (<10 meters) 

Acropora and Montastraea corals 

has dramatically changed shallow 

habitats; regional declines in coral 

cover since the 1970s have led to 

changes in coral-algal abundance 

patterns in most habitats; destruction of seagrass by propeller scarring; vessel grounding impacts on 

benthic environment; alteration 

of hard-bottom habitat by illegal 

casitas.

Selected habitat loss or alteration has 

caused or is likely to cause severe 

declines in some but not all living 

resources or water quality.

7

What are the contaminant concentrations in sanctuary habitats 

and how are they changing?

? Few studies, but no synthesis of 

information. N/A

8

What are the levels of human 

activities that may influence 

habitat quality and how are they 

changing?

q

Coastal development, highway 

construction, vessel groundings, 

over-fishing, shoreline hardening, 

marine debris (including derelict 

fishing gear), treasure salvaging, 

increasing number of private 

boats, and consequences of 

long-term changes in land cover 

on nearshore habitats.

Selected activities have caused or are 

likely to cause severe impacts, and 

causes to date suggest a pervasive 

problem.
Florida Keys National Marine Sanctuary

6 Florida Keys CONDITION REPORT 2011

Florida Keys National Marine Sanctuary Condition Summary Table (Continued)

# Questions/Resources Rating Basis for Judgment Description of Findings Sanctuary Response

Living Resources

9 What is the status of biodiversity 

and how is it changing? ▼

Relative abundance across a spectrum of 

species has been substantially altered, with 

the most significant being large reef-building 

corals, large-bodied fish, sea turtles, and 

many invertebrates, including, the longspined sea urchin. Recovery is questionable.

Selected biodiversity loss has 

caused or is likely to cause 

severe declines in some but 

not all ecosystem components 

and reduce ecosystem integrity.

Marine zoning assists in the 

protection of the biological diversity 

of the marine environment in the 

Keys. Mooring buoys have been 

installed in these zones to reduce 

anchor damage to coral reef biota. 

The sanctuary’s education and 

outreach team established the 

“Blue Star” program to help reduce 

the impact of divers and snorkelers 

on the coral reef ecosystem. NOAA 

has also established the Dolphin 

SMART program encouraging responsible viewing of wild dolphins. 

Sanctuary staff assesses and 

restores vessel grounding injuries 

to seagrass and coral habitats, 

as well as performs coral rescue 

activities associated with coastal 

construction. NOAA Fisheries 

Service (American Recovery and 

Reinvestment Act) awarded $3.3 

million to support Acropora coral 

recovery and restoration in Florida 

(including the Keys) and the U.S. 

Virgin Islands. Other coral nursery 

efforts are also underway that contribute to coral restoration. Private 

efforts examining potential of longspined sea urchin recovery via 

nursery propagation and rearing 

are also underway. A well-established permitting program is in 

place to issue a variety of permits 

for activities that are otherwise prohibited by sanctuary regulations, 

including removal of the invasive 

lionfish from the small no-take 

zones. The Florida Keys “Bleach 

Watch” Program utilizes volunteers 

to provide reports from the reef 

on the actual condition of corals 

throughout the bleaching season. 

The sanctuary also participates in 

oil spill drills sponsored by the U.S. 

Coast Guard and is a partner in the 

Florida Reef Resilience Program. 

There is a well-established law 

enforcement program in place.

10

What is the status of environmentally sustainable fishing and 

how is it changing?

?

Historical effects of recreational and 

commercial fishing and collection of both 

targeted and non-targeted species; it is too 

early to determine ecosystem effects of 

new fishery regulations and new ecosystem 

approaches to fishery management. 

Extraction has caused or is 

likely to cause severe declines 

in some but not all ecosystem 

components and reduce 

ecosystem integrity.

11

What is the status of nonindigenous species and how is 

it changing

▼

Several species are known to exist; lionfish 

have already invaded and will likely cause 

ecosystem level impacts; impacts of other 

non-indigenous species have not been 

studied.

Non-indigenous species 

may inhibit full community 

development and function, 

and may cause measurable 

but not severe degradation of 

ecosystem integrity.

12 What is the status of key species 

and how is it changing? —

Reduced abundance of selected key species 

including corals (many species), queen 

conch, long-spined sea urchin, groupers and 

sea turtles.

The reduced abundance of 

selected keystone species has 

caused or is likely to cause 

severe declines in ecosystem 

integrity; or selected key species are at severely reduced 

levels, and recovery is unlikely.

13

What is the condition or health 

of key species and how is it 

changing?

▼

Hard coral and gorgonian diseases and 

bleaching frequency and severity have 

caused substantial declines over the last two 

decades; long-term changes in seagrass 

condition; disease in sea turtles; sponge 

die-offs; low reproduction in queen conch; 

cyanobacterial blooms; lost fishing gear and 

other marine debris impacts on marine life.

The comparatively poor condition of selected key resources 

makes prospects for recovery 

uncertain.

14

What are the levels of human 

activities that may influence 

living resource quality and how 

are they changing?

—

Despite the human population decrease 

and overall reduction in fishing in the Florida 

Keys since the 1990s, heavy recreational 

and commercial fishing pressure continues 

to suppress biodiversity. Vessel groundings 

occur regularly within the sanctuary. Annual 

mean number of reported petroleum and 

chemical spills were around 150 during that 

time period, with diesel fuel, motor oil, and 

gasoline representing 49% of these incidents 

collectively. Over the long term, localized 

direct impacts may be overwhelmed by the 

adverse and wide-ranging indirect effects of 

anthropogenic climate change resulting in 

sea level rise, abnormal air and water temperatures, and changing ocean chemistry.

Selected activities have caused 

or are likely to cause severe 

impacts, and cases to date 

suggest a pervasive problem.

Table is continued on the following page.
Florida Keys National Marine Sanctuary

CONDITION REPORT 2011 Florida Keys 7

# Questions/Resources Rating Basis for Judgment Description of Findings Sanctuary Response

Maritime Archaeological Resources 

15

What is the integrity of known 

maritime archaeological resources and how is it changing?

▼

Resources are non-renewable 

and are subject to deterioration 

or loss resulting from looting, 

chemical processes, shifting sediments, marine life, fishing gear 

entanglement and vessel groundings (the last two are increasing in 

frequency).

The diminished condition of selected 

archaeological resources has substantially reduced their historical, scientific, 

or educational value and it likely to 

affect their eligibility for listing in the 

National Register of Historic Places.

Proactive management of submerged 

archaeological resources in sanctuary 

waters is occuring in conjunction with 

the state of Florida and the Advisory 

Council on Historic Preservation. 

This partnership is responsible for 

managing cultural resources in the 

sanctuary consistent with the Federal 

Archaeology Program, the Abandoned Shipwreck Act of 1987 and the 

National Historic Preservation Act. 

The sanctuary’s education team has 

also developed a historic Shipwreck 

Trail, which highlights nine historic 

vessels that sank in sanctuary waters 

and represents three broad periods 

of keys maritime history. Sanctuary 

regulations prohibit alteration of the 

seafloor, thus commercial salvage 

in the sanctuary must go through a 

review process before a permit for 

salvage is issued. A well-established 

law enforcement program is in place, 

including NOAA Fisheries Service, 

the Florida Fish and Wildlife Conservation Commission, and the U.S. 

Coast Guard.

16

Do known maritime archaeological resources pose an 

environmental hazard and is this 

threat changing?

—

Movement of sunken vessels 

during storm threatens nearby 

resources.

Selected maritime archaeological 

resources may pose isolated or limited 

environmental threats, but substantial 

or persistent impacts are not expected. 

17

What are the levels of human 

activities that may influence 

maritime archaeological resource quality and how are they 

changing?

▼

Reports of looting and vessel 

grounding cases involving potential resources are increasing.

Selected activities have caused or are 

likely to cause severe impacts, and 

cases to date suggest a pervasive 

problem.

Florida Keys National Marine Sanctuary Condition Summary Table (Continued)
Figure 1. The 2,896 square-nautical-mile (9,844 square kilometer) Florida Keys National Marine Sanctuary surrounds the majority of the Florida Keys archipelago and includes productive waters 

8 Florida Keys CONDITION REPORT 2011
 of Florida Bay, the Gulf of Mexico and the Atlantic Ocean.

Map: NOAA/FKNMS

CONDITION REPORT 2011 Florida Keys

9
Site History and Resources

10 Florida Keys CONDITION REPORT 2011

Florida Keys National Marine Sanctuary covers 2,896 square nautical miles (9,933 square kilometers) and is one of the largest marine protected areas in the United States. It spans a shallow-water interface between the Gulf of Mexico and the Atlantic Ocean, and is adjacent 

to most of the relatively shallow estuarine waters of south Florida, including those of Florida Bay and Biscayne Bay. The sanctuary surrounds more than 1,700 islands, which constitute most of the limestone island archipelago of the Florida Keys. This archipelago extends from the 

Florida peninsula south and westward over 220 miles (354 kilometers), terminating at the islands of Dry Tortugas National Park. Hawk Channel 

is located “ocean side”, between the island chain and the extensive bank reef tract (about 5 miles offshore). The oceanic boundary of the sanctuary is the 300-foot isobath (~100 meter depth), beyond which the Florida Straits separate the Florida Keys from both Cuba and the Bahamas. 

Site History and Resources

The western tip of the Florida Keys sanctuary lies in an area of high 

diversity due to the presence of both tropical and subtropical species, 

with an intermingling of a tropical biota characteristic of the greater Caribbean and the warm-temperate biota of the Gulf of Mexico (Figure 1; 

Pages 8 and 9). Though the sanctuary surrounds much of the Florida 

Reef Tract, this subtropical region also sustains many other interdependent habitats including fringing mangroves, seagrass meadows, 

hard-bottom regions, and patch reefs. Together, this diverse set of habitats supports significant commercial and recreational activities including scuba diving, fishing, and other water-based tourism. This marine 

ecosystem supports more than 6,000 species of plants, fishes, and 

invertebrates, and also has the largest documented contiguous seagrass community in the northern hemisphere. The coral reefs and associated soft-sediment communities comprise one of the most unique 

and diverse assemblages of plants and animals in North America.

The sanctuary is also home to maritime heritage resources that 

encompass a broad historical period from the European Colonial 

Period to the Modern Era. Because of the Keys’ strategic location 

in early European shipping routes, the area’s shipwrecks reflect the 

history of the entire period of discovery and colonization. The Florida 

Keys sanctuary has an extensive education and volunteer program 

focused on the protection of maritime heritage resources. Volunteers 

on the Submerged Cultural Resources Inventory Team have documented more than 400 underwater historical sites in the sanctuary. 

Approximately 1,680 square nautical miles (5,762 square kilometers), or 60%, of sanctuary waters are under Florida state jurisdiction, and numerous state and federal parks and reserves are located 

within the sanctuary’s boundaries (NOAA 1996). The sanctuary is 

administered by the Department of Commerce’s National Oceanic 

and Atmospheric Administration (NOAA) and is managed by both 

NOAA and the state of Florida’s Board of Trustees of the Internal 

Improvement Trust Fund through the Florida Department of Environmental Protection (FDEP).

 Geology

The Florida Keys are a chain of limestone islands that extends 

from the southern tip of the Florida mainland southwest to the Dry 

Tortugas, a distance of approximately 220 miles (354 kilometers). 

The islands are the fossilized (lithified) remnants of ancient coral 

reefs and sand bars that flourished during a period of higher sea 

levels approximately 125,000 to 100,000 years ago during the last 

interglacial period of the Pleistocene epoch (Hoffmeister and Multer 

1968, Shinn 1988, Lidz and Shinn 1991). Today those remnants are 

known as Key Largo Limestone and Miami Oolite, respectively. During this period of lower sea level, the Florida land mass was much 

larger than today, and the area now referred to as Florida Bay was 

forested. As glaciers and polar ice caps started melting 15,000 years 

ago, sea level rise and flooding of land combined with tidal influence 

to create the geography of the Keys and their surrounding areas. 

Florida Bay formed about 4,000 years ago, during a time when 

coral communities thrived along the entire seaward edge of the Keys. 

As sea level continued rising, tidal passes started forming, which facilitated the export of terrestrial material, sediments, and organic matter from both Florida and Biscayne Bays toward the Atlantic Ocean. 

In the Middle Keys in particular, tidal passes that formed allowed for 

inimical waters to flow offshore, resulting in conditions less favorable 

for coral reef development (Ginsburg and Shinn 1964, Shinn et al. 

1989, Lidz and Shinn 1991, Shinn et al. 1994, Ogden et al. 1994). 

This is reflected, for example, in the sparse present-day distribution 

of patch reefs and offshore bank reefs between Alligator Light and 

Moser Channel (Seven Mile Bridge) (Marszalek et al. 1977). In the 

upper and lower Keys, ocean-side habitats were less influenced by 

these waters due to the size and orientation of the islands, so relatively vigorous coral reef growth continued (Lidz and Shinn 1991, Shinn 

et al. 1989). Thus, prior to human impacts in south Florida, water 

exchange between inshore and offshore environments significantly 

impeded coral reef (and seagrass) development in the same areas.
Site History and Resources

CONDITION REPORT 2011 Florida Keys 11

Today, the Florida Keys outer reefs are a semi-continuous series of offshore bank reefs located at the northern zoogeographic 

boundary of tropical waters. They began forming between 6,000 to 

10,000 years ago during the Holocene sea-level rise and all presentday bank reefs are located on pre-existing topographic highs in the 

Pleistocene bedrock (Shinn et al. 1977, 1989). Due to its location 

at the northern limit of coral reef development, Florida Keys reefs 

regularly experiences natural stresses such as winter temperatures 

below those normally associated with vigorous coral reef development (Roberts et al. 1982). Also, the reef system experiences higher 

summer temperature extremes than many other reefs in the Caribbean basin (Vaughn 1918, Kruczynski and McManus 2002). 

The Florida Keys sanctuary also includes the Florida Plateau, 

which extends 223 miles (360 kilometers) from Miami to the Dry 

Tortugas. This shelf forms part of the Florida-Bahamas carbonate 

province and is the only area in the continental U.S. where active 

carbonate deposition is occurring on a large scale (Enos 1977, Shinn 

et al. 1989). The Florida Plateau is bounded by the Florida Straits to 

the east and south and by the Gulf of Mexico to the west.

Water Circulation

South Florida is located at the convergence of the subtropical and 

temperate climate zones. Physical oceanographic processes in the 

Florida Keys region consist of oceanic currents, tides and wind-driven 

currents, along with upwelling along the outer reef tract (Enos 1977, 

Schomer and Drew 1982, Brooks 1990, Leichter et al. 1998, 2003). The 

physical environment of the Florida Straits is dominated by the Florida 

Current, a strong surface current originating in the South Atlantic and Caribbean Sea (Figure 2) (Lee et al. 1992, Lee and Smith 2002). The Florida Current is the convergence of the Yucatan Current and Gulf of Mexico 

Loop Current off peninsular Florida. The Florida Current is renamed the 

Gulf Stream System off the southeastern U.S. (Lee et al. 1992). The 

Florida Current transports warm water from the Caribbean and is the 

major reason for reef development and the occurrence of tropical marine biota in the Florida Keys (Jaap 1984). The Florida Current comes 

within 9 miles (15 kilometers) of the upper Florida Keys, but runs further 

offshore, around 50 miles (80 kilometers), off Key West. Differences in 

the proximity of the Florida Current to the Florida Keys seascape result in complex circulation patterns on the south Florida shelf (Lee et al. 

1994). For example, eddies of 31 to 62 miles (50 to 100 kilometers) in 

diameter frequently form when meanders break free from the main axis 

of the Loop Current. These eddies move into the Florida Straits and are 

trapped between the Florida Current to the south and the Dry Tortugas 

to the north. These “Tortugas gyres” can remain stationary for 50 to 140 

days until they are pushed out by the arrival of the next gyre moving 

along the Loop Current. Once displaced, they are transformed into the 

smaller “Pourtales Gyre” by their movement downstream and the narrowing of the distance between the Florida Current and the Keys (Lee 

et al. 1994, Lee and Williams 1999). These gyres potentially contribute 

to the nutrient and larval transport between the Loop Current and the 

Florida Keys system, and may also serve to retain coastal-derived larvae 

that would otherwise be carried away by the Florida Current (Cowen et 

al. 2006, Sale 2006). On a more localized scale, tides and wind-driven 

currents are the dominant processes affecting circulation in the Florida 

Keys and Florida Bay (Schomer and Drew 1982). The Florida Keys and 

Florida Bay are micro-tidal environments (<3.3 feet or one meter); tidal 

exchange between Florida Bay and Hawk Channel mostly occurs in the 

middle Florida Keys, and to a lesser extent in the lower Florida Keys. 

From November to February, atmospheric cold fronts from the north supplement tidal flow out of Florida Bay (Smith 1994, Smith and Lee 2003).

Nearshore waters of the Florida Keys, defined as from the shoreline to the seaward edge of Hawk Channel, generally experience 

high variability in temperature, salinity and other factors relative 

to the reef tract further offshore. Differences in circulation and the 

physical and chemical characteristics of water in the Florida Keys 

reflect exchange processes between Florida Bay and the Atlantic 

Ocean, the influence of the Florida Current, and wind-driven currents 

in Hawk Channel. Nearshore waters in the upper Florida Keys are 

generally well-flushed and dominated by seagrasses, large sandy 

shoals (e.g., White Banks), and large patch reef areas (e.g., Mosquito Bank). They are not as significantly influenced by Florida Bay 

because of the larger sizes of islands and the absence of larger 

tidal passes in the northern Keys. The nearshore environment of the 

Figure 2. Schematic of general surface circulation of southern and southwestern Florida coastal waters. Subregions include: (1) Keys coastal zone, 

with Upper, Middle, Lower, and Western Keys localities; (2) Florida Bay; 

and (3) the Southwest Florida Shelf. Major tidal passages are indicated 

by the arrows immediately west (Seven-Mile Bridge) and east (Long Key 

Channel) of Marathon; additional tidal passages lie east of Long Key Channel (Channels 5 and 2) and between some of the lower Keys. Major boundary currents are the Loop and Florida Currents. Depth contours in meters. 

Source: redrawn from Lee et al. 2002
Site History and Resources

12 Florida Keys CONDITION REPORT 2011

middle Florida Keys is characterized by significant exchange of water between Florida Bay and the Atlantic Ocean. The sea bottom in 

areas adjacent to tidal channels consists of seagrasses, bare sand, 

low-relief hard-bottom communities, and patch reefs. Nearshore waters in the lower Florida Keys are influenced by exchange of water 

between the eastern Gulf of Mexico and Atlantic Ocean. Bottom or 

benthic habitats consist mostly of seagrass and bare sand, low-relief 

hard bottom, and abundant nearshore and mid-channel patch reefs.

With the exception of nutrient variability from upwelling events, offshore waters of the Florida Keys are relatively stable in terms of some 

water quality parameters compared to nearshore areas, particularly 

temperature, salinity, and dissolved oxygen. Distinct gradients can occur in circulation patterns and water residence time from the upper 

to lower Florida Keys. The offshore environment of the upper Florida 

Keys is relatively well-circulated, and dominated by Florida Current 

circulation (Klein and Orlando 1994). The upper Florida Keys area 

has the most robust reef development, most likely due to the warmwater influence of the Florida Current coupled with the lack of water 

exchange with Florida Bay. The offshore waters of the middle Florida 

Keys exchange with Florida Bay via tidal channels, thus reef development is relatively poor. The offshore waters of the lower Florida Keys 

are influenced by wind-driven circulation in Hawk Channel and offshore gyres (or smaller circular currents) of the Florida Current. The 

offshore waters of the lower Florida Keys have a significantly longer 

residence time than other offshore areas. This has considerable implications for nekton, plankton, and larval transport in these areas. In 

the offshore environment of the lower Florida Keys, there is moderate 

bank reef development, with several well-developed bank reefs (e.g., 

Sand Key, Eastern Sambo) and patch reef areas (Jaap 1984). 

Early Exploration and Settlement

Indigenous peoples have long resided throughout the Florida 

peninsula and on the surrounding islands. The southernmost regions of Florida, including the Florida Keys, were dominated by the 

Tequesta and the Calusa tribes, who arrived in the region about 

7,000 years ago, probably from northeast Florida (Carr 1991). These 

Native Americans depended on the sea for almost everything they 

needed, subsisting on fish, turtle, crabs, clams, lobster, and mollusks 

(Tilmant 1989). The bountiful marine resources in the Florida Keys 

provided a cultural subsistence tradition that remained unchanged 

for at least 4,000 years, until European contact served to eliminate 

the Native American population, mostly through disease (Carr 1991).

The first confirmed European contact with the Keys was made in 

1513 by Ponce de Leon of Spain, while exploring the Florida Straits 

(Wells 1991). In 1519, the Spanish established Havana, Cuba, and 

by the mid-1500s and throughout the 1600s, they colonized Florida. In 

1763, the Spanish ceded Florida to the British in a trade for the port of 

Havana. The treaty was unclear as to the status of the Florida Keys. An 

agent of the king of Spain claimed that the islands, rich in fish, turtles and 

mahogany for shipbuilding, were part of Cuba, fearing that the English 

might build fortresses and dominate the shipping lanes. The British also 

realized the treaty was ambiguous, but declared that the Keys should 

be occupied and defended as part of Florida. Although the British claim 

was never officially contested, ironically, the British gave the islands back 

to Spain in 1783 in order to keep them from the newly formed United 

States. In 1821, however, all of Florida, including the Florida Keys, officially became American territory, followed by formal statehood in 1845.

Development of the Florida Keys

The 20th century brought major changes to the Florida Keys in 

terms of transportation and residential and commercial infrastructure. 

In the early 1900s, travel between many of these islands was only possible by boat. However, this changed in the 1890s when Henry Flagler, 

president of the Florida East Coast Railway, brought the Overseas Railroad down Florida’s east coast to Miami. The railroad was later extended to Key West in 1912 (Parks 1968). On Labor Day 1935, a hurricane 

struck the upper Florida Keys and permanently destroyed the railroad. 

The railroad’s right-of-way was then sold and rebuilt into the Overseas 

Highway, which opened in 1938. This replacement road, which includes 

more than 40 bridges connecting the islands, eliminated the ferry rides 

and narrow wooden bridges of the first highway, making the Florida 

Keys more accessible from the Florida mainland (Marzyck 1991).

Between 1938 and the early 1980s, vehicles traveled down the 

Keys on a narrow two-lane roadway that was built on top of the old 

railroad bridges. The narrow Overseas Highway restricted or deterred 

the movement of wide vehicles to some extent. Large recreational vehicles, camper trailers, and wide boats seldom ventured south of the 

upper Keys. Several events occurred in the early 1980s that permanently changed the infrastructure and subsequently the economy of the 

Keys. First was the construction of wider bridges from Key Largo to Key 

West. Additionally, the roadway was widened to allow passage of supply trucks and the safe transit of recreational vehicles, camper trailers, 

and wide boats. Along with the bridges came a larger water pipeline that 

supplied the Keys with fresh water from the well-fields in Florida City and 

a new electrical line to supply dependable power throughout the islands.

Another benchmark of change came when the Monroe County 

Tourist Development Council was created in 1982, which is currently 

funded through a “bed tax.” A portion of this bed tax was and remains 

dedicated to advertising to attract more visitors to the Keys. From 

2002 to 2009, the total revenue from the bed tax fluctuated between 

$14 million and $15.5 million. The peak was 2005 at $15.5 million but 

declined to $14.1 million in 2009.

Development of the islands outside of Key West began slowly in 

the 1940s and boomed from the 1950s to 1990s, thus allowing for a 
Site History and Resources

CONDITION REPORT 2011 Florida Keys 13

significant growth in population (Figure 3). The population of Monroe 

County rose from 17,114 in 1900 to 78,024 by 1990. The population 

increased more slowly between 1990 and 2000 and was 79,589 by 

2000. However, the population has been steadily declining in Monroe 

County since 2000 and as of July 1, 2009, the population is estimated 

at 73,165 (U.S. Census Bureau 2010).

Population growth in and development of Monroe County have been 

driven largely by the tourism industry, but also the Florida Keys as a place 

for retirement, commercial fisheries, the military, and the upper part of the 

Keys as a “bedroom community”1

 for South Florida. These are referred 

to by economists as “basic industries” as they bring new dollars into the 

community, which then have ripple effects on the rest of the economy. 

These industries are discussed further in the “Commerce” section below. 

From 2007 to 2008, there were about 73,300 year-round residents 

and about 3.3 million visitors to the Florida Keys. This translates into a 

“functional population”2

 of between 116,000 and 118,000 during the winter season and 102,000 –105,000 during the summer season. The peak 

functional population was estimated between 150,000 and 152,000 during the winter season (December–May) and 132,000 – 135,000 during 

the summer season (June–November). (Leeworthy et al. 2010) 

Commerce

Five primary factors influence population growth and land development in Monroe County: 1) the tourism industry; 2) Florida as a 

retirement destination; 3) the commercial fishing industry; 4) the military; and 5) the “bedroom community” nature, particularly in the upper Keys due to their proximity to Miami-Dade and Broward counties. 

These factors each bring dollars into the Florida Keys community, 

which then have multiplier impacts on the rest of the economy.

Florida’s coral reefs are located near the four most densely popu1 Bedroom community refers to the people who live in the Florida Keys/Monroe County but commute to work outside the Florida Keys/Monroe County area. 

2 An important concept for planning for growth management that is a result “basic industry” drivers is the “functional population.” The “functional population” is the number of people in the Florida Keys on an average or peak day. This is the relevant population for growth management planning since it is the 

number of people that require housing, water, sewage, electric, transportation and other infrastructure services. In the Florida Keys the “peak” functional 

population is also used for planning hurricane evacuation, which is a limiting factor in the growth of the Monroe County population.

Figure 3. (a) The population change in the four counties of southeast Florida 

from 1920 to 2009. (b) The population change in Monroe County, Florida from 

1920 to 2009; note the axis uses a different scale than figure 2(a).

Source: U.S. Census Bureau

Figure 4. Snorkelers visit the Florida Keys National Marine Sanctuary. 

Photo: NOAA/FKNMS

Since 1995, the Florida Keys have lost over 500 campsites because those lands were sold to developersto build

condominiums. In addition,several hotels have been converted to condominiums. We hypothesize that this change

in development pattern will change the goods and services and recreational activitiesin which people participate.

We further hypothesize that the changes will be towards

less natural resource-dependent and water-based activitiesthan those chosen by people who stayed in campsites.

lated counties of the state. The combined population of these counties is over 5.6 million, with 1.2 million in Palm Beach, 1.77 million in 

Broward, 2.5 million in Miami-Dade, and 73,200 in Monroe (Figure 3; 

U.S. Census Bureau 2010). 

Tourism is the number one industry of the Florida Keys economy. 

Resident and visitor use includes activities such as guided ecotours, diving and snorkeling trips (Figure 4), and recreational fishing. 

A. Change in Population of Southeast Florida

Population Estimate

B. Change in Population of Monroe County

Population Estimate
Site History and Resources

14 Florida Keys CONDITION REPORT 2011

Monroe County residents spend significantly more days snorkeling, 

scuba diving and fishing in comparison to visitors. In addition, reef 

diving and reef fishing are equally common, while snorkeling is more 

common than scuba diving (Johns et al. 2003). During 1995 to 1996, 

2.54 million visitors spent $1.63 billion (2008 $) in Monroe County, 

which in turn generated $1.82 billion dollars in sales, $693 million in 

income, and supported over 21,800 jobs. By 2008, 3 million visitors 

increased their spending impact by 22% to $1.99 billion in Monroe 

County, which generated $2.23 billion in sales, $970 million in income, and supported 32,000 jobs (Leeworthy 2010)3

. 

The next largest industry is the retirement and “bedroom community” nature of the Florida Keys. Over 50% of the income received 

by Monroe County residents is not related to work in Monroe County; 

retirement income in the form of social security and pensions make 

up most of this income.

The commercial fishery industry also has a significant impact on the 

Florida Keys economy. The economic impact of this industry is great, 

representing close to 5% of the Monroe County economy in terms of 

output and sales and close to 9% of employment. In 1994, the total 

economic contribution of the commercial fishery industry to the Monroe 

County economy was estimated (CEMR 1995, Leeworthy 1995), with 

revenue from fisheries landings in at approximately $56.5 million (1994 

$). This revenue can then be converted to total impacts generated 

through the wholesale, processing, retail, restaurant, and export markets to have a total economic impact in Monroe County of $92.2 million 

in sales, $58.2 million in income and supported 4,130 jobs (1994). 

The military is also a major industry in Monroe County, with the 

U.S. Navy located in Key West. Until September 2001, the Navy was 

down-sizing its operations in Key West and giving up properties for 

other development. For example, the sanctuary’s Key West office and 

Eco-Discovery Center are both located on a small portion of former 

Navy property (Truman Annex), which was transferred to NOAA during this down-sizing operation. In 1995, the military directly contributed $81.6 million in income to Monroe County and supported 2,028 

employees. In 2007, the direct income received by military personnel 

increased to $147.66 million, but the number of employees declined 

to 1,670. The military directly accounts for about 7% of Monroe County’s income by place of work and in 2007 accounted directly for 2.9% 

of employment (U.S. Bureau of Economic Analysis 2010). 

Designation of the Sanctuary

The lure of the Florida Keys has attracted explorers and visitors 

for centuries. The clear tropical waters and appealing natural environment are among the many qualities that attract visitors to the Keys. 

However, warning signs, including the loss of habitat and living resources, came early, indicating that the Keys’ environment and natural resources are fragile, and not infinite. As early as 1957, a group 

of conservationists and scientists held a conference at Everglades 

National Park to discuss the demise of the coral reef resources in the 

Keys. This conference resulted in the creation of John Pennekamp 

Coral Reef State Park in 1960, the world’s first underwater park. However, a little more than a decade following, public outcry sounded that 

pollution, overfishing, physical impacts, overuse, and user conflicts 

continued to occur in the Keys. Those concerns were echoed by environmentalists and scientists alike as monitoring of the Florida Keys 

reefs began in the late 1970s, throughout the 1980s and into the 21st 

century. As a result, additional management efforts were instituted to 

protect the Keys’ coral reefs. In the upper Keys, Key Largo National 

Marine Sanctuary was established in 1975 to protect 103 square nautical miles (353 square kilometers) of coral reef habitat from north of 

Carysfort Lighthouse to south of Molasses Reef. In the lower Keys, 

the 5.32 square-nautical-mile (18.25 square-kilometer) Looe Key National Marine Sanctuary was established in 1981. (NOAA 2007) 

In 1989, mounting threats to the health and ecological future of 

the coral reef ecosystem in the Florida Keys prompted Congress to 

take action to further protect this fragile natural resource. The threat 

of oil drilling off the Florida Keys in the mid-1980s, in combination 

with reports of deteriorating water quality throughout the region, the 

die-off of the long-spined sea urchin (Diadema antillarum), loss of 

living coral cover on reefs, a major seagrass die-off, declines in reef 

fish populations, and the spread of coral diseases, were topics of major scientific concern and the focus of several scientific workshops. 

While these scientific pursuits were underway, three large ships (M/V 

Elpis, M/V Alec Owen Maitland and Mavro Vetranic) ran aground on 

the coral reef tract within an 18-day timeframe in fall 1989. These 

cumulative events of environmental degradation that prompted Congress to designate the 2,800 square-nautical-mile (9,603 squarekilometer) Florida Keys National Marine Sanctuary on Nov. 16, 1990, 

in order to expand the scale of resource protection beyond the existing Key Largo and Looe Key national marine sanctuaries; these two 

smaller sanctuaries then became a type of marine zone (Existing 

Management Areas) within the larger sanctuary. This was the first 

national marine sanctuary to completely surround a community.

Beginning in 1998, a public process was initiated to create additional protection for the region surrounding the Dry Tortugas archipelago. This public process included a comprehensive characteriza3 As a share of the total Monroe County economy, recreating visitors in 2007 to 2008 accounted for about the same share of output/sales as 1995 to 

1996 (60.5% in 1995 to 1996 and 59.9% in 2007 to 2008), a slight increase in income received by place of work (45% in 1995 to 1996 and 46.9% in 

2007 to 2008), and a significant increase in employment (46.5% in 1995 to 1996 and 57% in 2007 to 2008). 
Site History and Resources

CONDITION REPORT 2011 Florida Keys 15 Source: NOAA/FKNMS

tion of the ecological and socioeconomic importance of the area. 

On July 1, 2001, the Tortugas Ecological Reserve (TER), a no-take 

zone, was designated in order to protect the diverse marine life and 

lush coral reefs of the Tortugas. The TER is divided into two separate sections: 

■ TER North - adjacent to Dry Tortugas National Park, comprises 

90 square nautical miles (309 square kilometers) of ocean habitat, and contains relatively extensive areas of spectacular deeper 

(>50 feet or 15 meters) coral reef formations in the Florida Keys. 

TER North incorporated 54 square nautical miles (186 square 

Figure 5. (a) Original boundary of the 

sanctuary in 1990, (b) and the modified 

boundary of 2001, which includes the 

Tortugas Ecological Reserve.

kilometers) of existing sanctuary area and added 36 square nautical miles (123 square kilometers) to the original boundary by 

“squaring off” the northwestern corner.

■ TER South - located to the southwest of Dry Tortugas National Park, 

comprises 60 square nautical miles (205 square kilometers) of ocean 

and includes the critical fish spawning grounds of Riley’s Hump. 

The TER expanded the boundary of the sanctuary from 2,800 

to 2,896 square nautical miles (9,603 to 9,933 square kilometers) 

in 2001(Figure 5). 
Site History and Resources

16 Florida Keys CONDITION REPORT 2011

Figure 7. Mangroves are integral components of the Florida Keys ecosystem. They provide food and serve as nursery grounds for many species, in 

addition to stabilizing shorelines.

Photo: NOAA/FKNMS

Figure 6. This image shows some of the major habitat types found in the 

Florida Keys: mangrove, seagrass, patch reef, hard bottom and bank reef.

Source: NOAA

Shoreline mangroves

Seagrass

Hard bottom

Bank reef

Patch reef

Habitats

The boundaries of the sanctuary encompass numerous habitats 

and structural zones (Figure 6). Benthic habitats include unconsolidated sediments (e.g., sand and mud), mangrove, submerged 

aquatic vegetation (e.g., seagrass and algae), coral reefs and colonized hard-bottom habitats (e.g., spur and groove reefs, individual 

and aggregated patch reefs, and gorgonian-colonized pavement), 

and uncolonized hard bottom (e.g., reef rubble). Some of the major habitat types of the Florida Keys are shown in Figure 6, starting 

with fringing mangrove or sandy shorelines, progressing through 

nearshore seagrass and hard-bottom habitat, to mid-channel and 

offshore seagrass beds and patch reefs, and finally to the offshore 

bank reef system. Typical coral reef structural zones include the back 

reef, reef flat, reef crest, and fore reef.

Mangroves

Florida’s estimated 496,000 acres (200,724 hectares) of mangrove forests contribute to the overall health of the state’s southern 

coastal zone (Figure 7). Red mangrove (Rhizophora mangle) trees 

fringe much of the 1,700 islands and 1,815 miles of shoreline within 

the sanctuary, and they are a vital component of the Florida Keys 

ecosystem. In the abiotic realm, mangroves act as important wave 

attenuation barriers for all points landward, buffering the action of 

waves and storm surges associated with both frontal and tropical 

storms. Thus, they provide important shoreline protection services 

in the Florida Keys, as in all coastal locations where they occur. 

They also assist in trapping and cycling various organic materials, 

chemical elements and important nutrients throughout the interconnected reef-seagrass-mangrove system. Mangrove forests play an 

important role in the carbon cycle by removing CO2

 from the atmosphere and storing it as carbon in plant materials and soils in a 

process called sequestration. Layers of soil and peat that make up 

the mangrove substrate have a high carbon content, and when they 

are disturbed or removed, carbon is released into the atmosphere. 

In addition, mangrove roots provide attachment surfaces for various 

marine organisms, especially on their partially submerged prop roots. 

Many of these attached organisms filter water and, in turn, trap and 

cycle nutrients.

The relationship between mangroves and their associated marine 

life cannot be overemphasized. Mangroves provide protected nursery 

areas for young fishes, crustaceans, shellfish and other invertebrates 

(Drew and Eggleston 2008). Many of these species are food for a 

multitude of fish species such as snapper, jack, snook (Centropomus 

undecimalis), tarpon (Megalops atlanticus), sheepshead (Archosargus probatocephalus), and red drum (Sciaenops ocellatus). 

Florida’s important recreational and commercial fisheries will decline 

without healthy mangrove forests to support them. Many animals find 

shelter either in the roots or canopies of mangroves. Mangrove tree canopies serve as rookeries, or nesting areas, for coastal birds such as brown 

pelicans (Pelecanus occidentalis) and roseate spoonbills (Platalea ajaja).
Site History and Resources

CONDITION REPORT 2011 Florida Keys 17

Seagrass Beds

The Florida Keys ecosystem includes one of the world’s largest 

seagrass beds, which are among the richest, most productive, and 

most important submerged coastal habitats. Seagrasses are flowering plants that live in the ocean (Figure 8). Like land plants, seagrasses utilize carbon dioxide and produce oxygen. Seagrass occurs 

throughout the soft-bottom, shallow-water areas of the sanctuary 

wherever water quality is sufficient to allow light penetration to the 

seafloor to enable photosynthesis. Like mangroves, seagrasses also 

serve important ecosystem functions, often acting as a kind of “link 

in the chain” between the reef and mangrove systems, both spatially 

and in terms of food webs (Valentine et al. 2008). Likewise, seagrass 

meadows also perform certain coastline services such as stabilizing the bottom with their roots and rhizomes in much the same way 

that land grasses retard soil erosion, and maintaining water clarity by 

trapping fine sediments and other particles in their leaves and root 

system. Like mangroves, seagrasses sequester carbon. They also 

offer habitat and protection for many fishes and invertebrates, crustaceans (such as lobster and shrimp), and shellfish; provide food for 

marine animals including green sea turtles (Chelonia mydas), West 

Indian manatee (Trichechus manatus), parrotfishes, and sea urchins; 

and serve as a nursery area for recreationally and commercially important marine life (Rudnick et al. 2005, Acosta et al. 2007).

The Florida Keys ecosystem includes five species of seagrasses, 

with turtle grass (Thalassia testudinum), manatee grass (Syringodium filiforme), and shoal grass (Halodule wrightii) making up most of 

the coverage of seagrass beds in the sanctuary (NOAA 1996, 2007). 

Data from the sanctuary’s Water Quality Protection Program indicates approximately 4,942 square miles (12,800 square kilometers) 

of seagrass beds lie within and adjacent to the sanctuary.

Macroalgae

Monitoring of benthic communities by the National Undersea 

Research Center (NURC) and the University of North Carolina at 

Wilmington has documented that species of simple plants classified 

as algae dominate many benthic habitats throughout the sanctuary 

(NOAA 2007). Due to their ability to grow in the marine environment, 

fleshy macroalgae are commonly referred to as “seaweeds.” Turf 

algae often form dense, lettuce-like patches on dead coral or other 

rocky bottoms. There are three basic types depending on the color 

of the photosynthetic pigments that predominate: green, red, and 

brown. Like land-based “weeds,” seaweeds grow faster when they 

are fertilized and tend to grow rapidly when they are not grazed by 

sea urchins or fish, just as land plants in a pasture might grow when 

they are not grazed by cattle or sheep. 

To a major extent, macroalgae compete with coral for living space 

on the seafloor, but it is important to note that macroalgae are a common and natural component of every coral reef system. Like other 

plants, it is a food source for a number of reef-dwelling animals, especially sea urchins and certain reef fishes such as surgeonfishes 

and parrotfishes. Typically, it is only when the ecological balance of 

a reef is upset (e.g., by widespread coral mortality from bleaching or 

disease) that it tends to become overgrown by the rapidly growing 

macroalgae (Maliao et al. 2008).

Coral Reefs and Hard-bottom Habitats

The Florida Reef Tract is the most extensive living coral reef ecosystem in North American waters and the third-largest barrier reef 

in the world. Coral reefs are created by calcareous marine algae, 

reef-building corals, and other marine invertebrates that produce 

skeletons or structures made of calcium carbonate (CaCO3

, or limestone). The skeletons of corals and other marine life combine to form 

a rigid, wave-resistant structure called a reef. 

An individual coral animal, called a polyp, resembles a miniature 

sea anemone just a few millimeters in size. Like anemones, a coral 

polyp is soft-bodied, tubular, and topped by a ring of tentacles. Unlike 

an anemone, a reef-building coral polyp builds a hard external skeleton that forms a protective cup, or calice, around its base, creating 

a corallite. Hundreds to thousands of coral polyps together make up 

a reef-building coral colony. Each polyp is connected to the next by a 

thin layer of tissue, creating a living mat over a shared skeleton. Colonies grow by progressively building more and more skeletal mass.

Figure 8. The Florida Keys ecosystem includes one of the world’s largest 

seagrass beds, which are among the richest, most productive, and most 

important submerged coastal habitats.

Photo: NOAA/FKNMS
Site History and Resources

18 Florida Keys CONDITION REPORT 2011

Invertebrates

Invertebrates in the sanctuary are highly diverse. Resident phyla include, but are not limited to, Cnidaria (corals, sea anemones, jellyfish), 

Platyhelminthes (flatworms), Porifera (sponges), Annelida (segmented 

worms), Arthropoda (crustaceans), Ectoprocta (bryozoans), Mollusca 

(bivalves and snails), Echinodermata (sea stars, sea urchins and sea cucumbers). With the exception of a few “fishery” crustaceans (e.g., shrimp, 

lobster, stone crab), the ecological roles of many of these invertebrates 

are not well understood and continue to be studied (Levy et al. 1996). 

Porifera (sponges) are important components of coral reef ecosystems, and some species grow quite large, often more than three feet 

(one meter) in height. Besides filtering large amounts of water, sponges 

in nearshore hard-bottom habitat are critical shelter habitat for a myriad 

of obligate and opportunistic invertebrates and fish such as crabs, 

shrimps and brittle stars (McMurray et al. 2008). In the Keys, there is 

even a certain genus of sponge (Cliona) that serves as an aggressive 

coral bioeroder, thus providing a key process in a reef’s carbonate budget. This genus has been on the increase in recent years, and several 

of its members are now among the dominant sponge species in the 

Florida Keys (Keller and Donahue 2006, Chiappone et al. 2007).

Caribbean spiny lobsters (Panulirus argus) are one of the Florida 

Keys’ most economically important commercial fisheries, and the 

Florida Keys stock is heavily exploited by both the commercial fishery and by recreational divers and snorkelers. Between the two fisheries, a large percentage of the available adult population is removed 

each year (Cox and Hunt 2005).

Sea urchins, more specifically the long-spined sea urchin (Diadema 

antillarum), were historically one of the most important invertebrate grazers on coral reefs in the Florida Keys, helping control the abundance 

of algae. Though in some parts of the Caribbean the long-spined sea 

urchin played a major role in controlling algal biomass (Levitan 1988), the 

roles of both piscine herbivores and sea urchins in controlling algal dominance on coral reefs are still being discovered (Furman and Heck 2008). 

Fish

Because of the Florida Keys’ connection to adjacent aquatic environments, a variety of different fish assemblages rely on sanctuary resources for all, or part of, their life history. Whether fishes are estuarine, 

demersal, or pelagic, their species richness is correlated with temporal 

and seasonal influences. Historic long-term studies, using both visual 

and consumptive sampling techniques, yielded between 389 and 440 

total fish species (Longley and Hildebrand 1941, Starck 1968). 

Birds

The Florida Keys host more than 285 species of birds, many of 

which are seabird or shorebird species. Birds most frequently encountered in and around the water include terns, gulls, plovers, cormorants, 

Figure 9. Coral reefs help to protect the shoreline from destructive storms 

and provide habitat for marine species. 

Photo: NOAA/FKNMS

Within the tissue of most reef-building corals live small microscopic algae called zooxanthellae. These algae produce energy and 

oxygen for the coral as byproducts of photosynthesis. Some coral 

species are predominantly reliant on this energy source, whereas 

other species are less reliant on the photosynthetic byproducts and 

acquire their most of their energy by suspension feeding. Zooxanthellae also aid in calcium carbonate production by the coral colony, 

promoting the growth of coral skeletons.

Coral reefs generally are restricted to the tropics, where waters are 

generally warm, clear, low in nutrients like nitrogen and phosphorus, 

and have stable temperature and salinity. The Florida Reef Tract is 

one example in which the warm waters of the Florida Current and 

Gulf Stream expand the range of corals north of the tropics (Figure 9). 

Coral reefs create important habitat for various organisms including both sessile and mobile invertebrates, as well as highly 

diverse reef fish. In turn, many of these animals provide food for 

predators that often visit reefs, such as sharks, sea turtles and 

dolphins. Similar to mangroves and seagrasses, corals also perform vital coastal shoreline services. For example, coral reefs can 

protect a coastline from wave action, storm surges, and even tsunamis (Cochard et al. 2008). 

Living Resources

The Florida peninsula and the Florida Keys archipelago serve as a 

biogeographic transition zone between the warm-temperate waters of 

the Gulf of Mexico and the adjacent tropical to subtropical waters of the 

Atlantic Ocean. This division has resulted in a distribution of marine fauna and flora characterized as having both a warm-temperate and tropical Caribbean component (NOAA 1996). The following section contains 

general descriptions of select taxa, but a complete list of the marine and 

terrestrial species found in Florida Keys National Marine Sanctuary can 

be found at http://floridakeys.noaa.gov/scipublications/speciesList.pdf 

(Levy et al. 1996).
Site History and Resources

CONDITION REPORT 2011 Florida Keys 19

pelicans, herons, egrets, osprey (Pandion haliaetus) and the Magnificent Frigatebird (Fregata magnificens). The Florida Keys are also an 

important stop-over point for other migratory birds and waterfowl.

Turtles

Five of the seven extant sea turtles frequent the waters of the 

sanctuary, and some species including the green, loggerhead (Caretta caretta) and leatherback (Dermochelys coriacia) sea turtles nest 

along the Florida coastline. All marine turtles are either threatened or 

endangered and thus protected by the Endangered Species Act in 

U.S. territorial waters (ESA; see following subsection). The highest 

densities of sea turtles in the Gulf of Mexico region are observed in 

waters surrounding the Florida Keys (McDaniel et al. 2000).

Marine Mammals

The Florida Keys and the sanctuary are within the seasonal geographic range of a variety of marine mammals. Thirteen species of 

whales, seven species of dolphins and the West Indian manatee either 

reside in or travel through the sanctuary at some point in their lifetimes.

Endangered and Threatened Species

A variety of plants, invertebrates, fishes, reptiles, birds, and mammals that use or contribute to sanctuary resources in the Florida Keys 

are protected at the federal or state level. Each of these species is a 

valuable natural resource that contributes to the ecological balance of 

the sanctuary. Animal species at risk are dependent on the sanctuary’s 

diverse habitats, including mangroves, beaches (below high water 

mark), seagrass beds, and coral reefs. State and federally threatened 

and endangered marine and aquatic fauna include, but are not limited 

to, elkhorn coral (Acropora palmata), staghorn coral (A. cervicornis), 

pillar coral (Dendrogyra cylindrus), all five species of sea turtles found 

in the western Atlantic — loggerhead, green, hawksbill (Eretmochelys 

imbricata), Kemp’s Ridley (Lepidochelys kempii), and leatherback — 

the American alligator (Alligator mississippiensis), American crocodile 

(Crocodylus acutus), smalltooth sawfish (Pristis pectinata), Roseate 

Tern (Sterna dougallii), Least Tern (Sterna antillarum), and the West 

Indian manatee. The sanctuary is also in the migratory range of three 

species of whales: humpback (Megaptera novaeangliae), fin (Balaenoptera physalus), and North Atlantic right (Eubalaena glacialis).

Maritime Archaeological Resources

Florida Keys National Marine Sanctuary is the trustee for maritime 

heritage resources located within its boundaries (Figure 10). Maritime 

heritage resources are defined as those possessing historical, cultural, 

archaeological, or paleontological significance. The sanctuary’s maritime archaeological resources are unique, non-renewable remnants of 

the area’s colorful maritime and submerged prehistoric past and include hundreds of documented shipwreck sites and artifacts, cultural 

remains of early peoples and historical activities, railroad remnants, 

and historical offshore structures. The sanctuary’s maritime archaeological resources encompass a broad historical range from the European Colonial Period to the Modern Era. Because of its unique geographical position on the European and American trade routes, shipwrecks 

in the Keys contain a record of the 500-year history of the Americas. 

An estimated 2,000 shipwrecks are thought to have occurred in the 

Florida Keys since European exploration of the Western Hemisphere. 

Approximately 669 historic artificial reefs have been documented to 

date (Halas 1988). Currently, 14 shipwrecks and two lighthouses within 

the sanctuary are listed in the National Register of Historic Places.

Key West has been the crossroads of the Caribbean since the colonial era, and the sea has remained the common thread through the 

region’s culture and history. The importance of the region’s maritime 

heritage resources is great, and the possibility exists for discovering 

some of the earliest archaeological sites in North America. A detailed 

description of the cultural and historical resources of the Florida Keys 

is contained in the “Description of the Affected Environment,” of the 

Environmental Impact Statement (NOAA 1996).

Figure 10. National Association of Black Scuba Divers (NABS) conducting an 

archeological survey of the shipwreck City of Washington in the Florida Keys.

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

20 Florida Keys CONDITION REPORT 2011

Numerous human activities and natural events and processes affect the condition of natural and maritime heritage (archaeological) 

resources in marine sanctuaries. This section describes the nature and extent of the most prominent pressures in Florida Keys 

National Marine Sanctuary, many of which originate outside its boundaries.

ally due to rainfall moving over and through the ground and carrying various chemicals. As the runoff moves, it picks up and carries 

away pollutants, finally depositing them into surface and subsurface 

(groundwater) waters. Pollutants and contaminants include excess fertilizers, herbicides, and insecticides from agricultural lands 

and residential areas; oil, grease, and toxic chemicals from urban 

runoff and energy production; sediment from improperly managed 

construction sites and dredging operations; bacteria and nutrients 

from birds and other wildlife: pet wastes; and faulty septic systems. 

Eutrophication (an outcome of excess nutrients in the water, such as 

fertilizers) of nearshore waters has been an ongoing, documented 

problem in the nearshore waters of the Florida Keys. The process 

of eutrophication has the potential to shift primary productivity from 

the slower-growing flora (e.g., seagrasses) to faster-growing species 

(e.g., macroalgae and microalgae). In time, eutrophication may result in a shift from one type of biological community to one that is 

adapted to the higher-nutrient conditions (Fourqurean et al. 2003, 

Wagner et al. 2008).

Because they are generally more soluble than toxicants such 

as oil and lipid-soluble contaminants, nutrient and organic inputs 

may affect the environment over a greater spatial area. In addition, 

while toxicants affect localized environments such as marinas, canals, and areas surrounding industry, nutrients are more susceptible 

to transport and represent a greater threat to seagrass and coral 

Pressures on the Sanctuary

Pressures on Water Quality

Water quality is a key element that unites all sanctuary resources 

and is essential to maintaining the richness and diversity of its varied 

environments. Water quality is both a spatial and temporal phenomenon and can be affected by both natural and anthropogenic influences. Under certain conditions, external sources adjacent to the 

sanctuary (e.g., Gulf of Mexico Loop Current and Florida Current, 

land based activities, and atmospheric inputs) can dominate water 

quality patterns. Pressures on water quality in the sanctuary are described below.

Point Sources of Pollution and Contamination

Point source pollution results when a pollutant is discharged directly 

into surface waters from a definite location, such as the pipes of industrial waste facilities or domestic sewage treatment plants. Pollutants 

can be natural substances, like nutrients, that are present in unusually 

high quantities due to human influence. Contaminants are typically 

chemicals not found normally in the environment such as industrial 

chemicals, pesticides, PCBs, and other toxicants. Point source pollution can also include discharge resulting from urban stormwater runoff 

if coming from a drainage pipe. The effects of point source effluents 

on receiving surface waters may include the introduction of additional 

flow, increased microbial abundance, suspended sediments, nutrients 

(e.g., nitrogen and phosphorus), metals, and organic compounds. In 

the Florida Keys, wastewater and stormwater treatment and solidwaste disposal facilities were highly inadequate, directly affecting 

nearshore water quality (Kruczynski and McManus 2002). 

When the sanctuary was designated in 1990, there were 19 facilities actively discharging effluent directly into nearshore waters, 

including water treatment plants, power plants, a desalination plant, 

and other industrial facilities (NOAA 1996). Today, Monroe County 

and local municipalities are undergoing extensive upgrades in 

wastewater infrastructure that provide advanced wastewater treatment, significantly reducing wastewater impacts and pressures in the 

area (Figure 11). 

Nonpoint Sources of Pollution

Unlike point source pollution, nonpoint source pollution comes 

from many diffuse sources. Nonpoint source water pollution is usuFigure 11. Sewer pipes are being placed in the ground throughout the 

Florida Keys to carry wastewater to advanced wastewater treatment plants 

being constructed throughout the keys.

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 21

reef communities (NOAA 1996). Residential canals in the Florida 

Keys were often dug too deep, and the length and complexity of the 

residential canal systems also limit flushing with nearshore waters 

of the sanctuary. They frequently experience microalgal blooms and 

have anaerobic sediments containing accumulated chemicals and 

organic matter. While some studies have been conducted, the exact 

extent to which residential canals affect sanctuary waters has not 

been fully studied at this time (Chesher 1974, Lapointe and Clark 

1990 and 1992). 

Domestic wastewater from illegal cesspits and outdated septic 

systems has been contributing to nonpoint source pollution in the 

Keys, but is expected to decline due to improvements being made 

in wastewater treatment, which involves decommissioning the septic 

systems and cesspits. Other sources of nonpoint source pollution 

include abandoned landfills, marinas and live-aboard vessels (collectively), and stormwater runoff (NOAA 1996).

Swimming Advisories

Runoff and spills have periodically resulted in high levels of fecal 

coliform and enterococci bacteria in the Florida Keys, resulting in 

swimming advisories for nearshore waters and beaches (Figure 12). 

Enterococci bacteria and fecal coliform bacteria are often used as 

indicator organisms in nearshore water quality monitoring, and while 

they may not cause diseases in humans, their presence can indicate that water may be contaminated with organisms that cause human health impacts such as fever, flu-like symptoms, ear infection, 

respiratory illness, rashes, gastroenteritis, cryptosporidiosis, and 

hepatitis. Sources of polluted and contaminated water include runoff 

from urban, suburban and rural areas, aging sewer infrastructure 

systems pressed to meet increasing demands, and contaminated 

flows from other upland sources. Contributing factors that generate these sources include illicit storm drain connections, improper 

disposal of materials or maintenance that clog pipes and cause 

overflows, cracked or damaged pipes, overflow of sewer systems 

during storm events, septic system leaching, and various domestic 

and wildlife sources. 

External Input

External sources of pollutants and contaminants also affect the 

sanctuary’s water quality. Examples of this input could include Florida Bay, Biscayne Bay and canal structures operated by the local 

water management district. Additionally, the sanctuary is considered 

downstream of currents in the region, like the Loop and Florida currents that transport much of the water from the western coast of Florida, Mississippi River outfall, contributions from Central America and 

northern South America (Orinoco Flow), and various islands of the 

Caribbean. Lastly, eddies that form along boundary currents paralleling the shore line can cause periodic upwelling of cold, nutrient-rich 

waters (e.g., Tortugas and Pourtales gyres) (NOAA 1996, Szmant 

and Forrester 1996, Leichter et al. 2003).

Harmful Algal Blooms

A harmful algal bloom (HAB) can occur when certain types of microscopic algae grow quickly in water, forming visible patches that 

may harm the health of the environment, plants, or animals. HABs 

are attributed to two primary factors: natural processes such as 

warm water and poor water circulation and flow, and anthropogenic 

causes such as nutrient loading leading to eutrophication. These 

processes can result in large amounts of certain types of macroalgae or phytoplankton (e.g., dinoflagellates) accumulating in the water. Aggregations of these organisms can discolor the water, giving 

rise to red, mahogany, brown, or green tides. Red tides occur every 

year off Florida and are known to deplete the available oxygen supply and block sunlight. In addition, some HAB-causing algae (e.g., 

Figure 12. The Florida Department of Health posts swimming advisories at 

beaches throughout the Florida Keys. This sign indicates if it is advisable 

or not to swim due to water quality issues such as fecal coliform levels.

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

22 Florida Keys CONDITION REPORT 2011

dinophytes) can release toxins into the water that adversely impact 

aquatic organisms and humans. Impacts include fish kills, coral 

stress and mortality, and skin and respiratory problems in humans. 

HABs have occurred in the waters of almost every U.S. coastal state. 

Over the last several decades, HABs have caused more than $1 

billion in economic losses in the U.S. due to closures of shellfish 

beds and coastal fisheries, detrimental impacts on tourism and service industry revenues, and public illnesses (Abbott et al. 2009a). 

Data suggests that HABs are increasing in frequency within the last 

couple of decades (Harvell et al. 1999). 

Of significance, the sanctuary had high concentrations of the microscopic alga that causes red tide (Karenia brevis) at the offshore 

reefs during the 2009 and 2010 annual red tide ‘seasons.’ Although 

the first red tide was officially recorded in Florida in 1844, these recent occurrences of K. brevis on the reef-line are the first on record. 

Karenia brevis kills fish by producing a powerful toxin (brevetoxin) 

that affects the central nervous system of fishes. In addition, brevetoxins can become concentrated in the tissues of shellfish that feed 

on K. brevis. People who eat these shellfish may suffer from neurotoxic shellfish poisoning, a food poisoning that can cause severe 

gastrointestinal and neurologic symptoms, such as tingling fingers 

or toes. It can also affect birds, mammals, and other marine animals 

higher up the food chain.

In early 2002, a patch of “black water” more than 60 miles (100 

kilometers) in diameter formed off southwestern Florida (Figure 13). 

Currents carried the black water to the ocean side of the Florida Keys, 

where it resulted in severe coral reef stress and death (Keller and 

Causey 2005). Microscopic organisms and toxins contained in the 

dark water stressed the coral reef system resulting in a 70% decrease 

in stony coral cover, a 40% reduction of coral species, and a nearelimination of clionid sponge colonies at two reef sites after the dark 

water passed (Hu et al. 2003). Though a similar black water event was 

blamed for declines in Acroporid species in the Dry Tortugas in 1878, 

its origin and composition were never discovered (Jaap et al. 1989). 

Marinas and Boats

Water pollution from activities associated with marinas and boating within the sanctuary is also a threat to sanctuary resources (Figure 14). Boater-generated impacts on water quality generally fall into 

four categories: toxic metals primarily from anti-fouling paints, hydrocarbons from motor operations and maintenance procedures, solid 

waste and marine debris from overboard disposal, and bacteria and 

nutrients from boat sewage. 

Cruise Ships

A few cruise ships started visiting the Port of Key West infrequently in the late 1980s, by 2010 between five and 13 cruise ships visit 

Key West weekly. Each ship can carry more than 3,000 people and 

arguably provide local businesses with positive economic benefits. 

For example, from 1995 to 1996 approximately 350,000 cruise ship 

passengers arrived at the Port of Key West, 90% of which departed 

the ships to participate in recreational activities in Key West (Leeworthy and Wiley 1996). By 2008, numbers nearly doubled and 740,000 

passengers visited Key West on the 346 cruise ships that ported 

Figure 13. 2002 satellite image of a “black water” event north of the lower 

Florida Keys.

Photo: NASA

Figure 14. Boating is a popular activity in the Florida Keys National Marine 

Sanctuary, however boating activities can have impacts to sanctuary resources.

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 23

that year (Leeworthy et al. 2010). In 2003, cruise ship passengers 

reached a peak of over 1 million passengers (City of Key West, Finance Department 2005). 

Concerns exist about environmental impacts of cruise ships, 

including discharges impairing water quality and sediment erosion. 

Cruise ships are floating cities that are capable of carrying as many 

as 3,000 passengers and crew members, and thus need to provide 

many of the same services as their land-based equivalent. The main 

pollutants generated by cruise ships include bilge water (water that 

collects in the lowest part of the ship’s hull that may contain oil, 

grease, and other contaminants), blackwater (sewage), graywater 

(waste from showers, sinks, laundries, and kitchens), ballast water 

(water taken onboard or discharged from a vessel to maintain its 

stability), and solid waste (food waste and garbage). Ocean currents 

have the potential to transport these pollutants into sanctuary waters. 

Although cruise ships are capable of generating volumes of waste 

comparable to a small city (though many incinerate large portions of 

their wastes), they are not subject to the same environmental regulations and monitoring requirements as a land-based equivalent. 

Cruise ships also have the potential to cause benthic disturbances 

with each porting. Wakes generated by vessels and propeller turbulence re-suspends sediment and transports it elsewhere. 

Petroleum (hydrocarbons) and Other Chemical Spills

Petroleum (oil, gasoline, other hydrocarbons) and chemical spills 

in the sanctuary can potentially range from small, localized spills 

to large events that span hundreds of miles of coastline. The most 

common and chronic form of spill is from small boat engine operations and usually involves small discharges of fuel, oil, or hydraulic 

fluid. Other small spills tend to be associated with oil and fuel discharges due to small vessel (<65 feet or 20 meters) groundings or 

sinkings and plane crashes. Effects of small spills have not been 

adequately documented. A larger oil or chemical spill may result 

from offshore shipping traffic, a cruise ship disaster, or offshore oil 

and gas drilling and production operations (e.g., upstream Gulf of 

Mexico sources and potential Cuban sources). A large spill could 

have a major impact on sanctuary biota including coral reefs, foraging birds, marine mammals, fishes, and fringing mangrove habitat. 

Tourism and the coastal economy would be also negatively affected 

by this type of spill.

Live-aboard Vessels

Disposal of wastewater from live-aboard vessels has historically 

been a significant localized problem because of the low level of treatment, the tendency for live-aboard vessels to congregate in certain 

marinas or anchorages, and the potential adverse health effects of 

discharging untreated wastewater. Many live-aboard vessels are 

permanently anchored and mobile pump-out facilities are required to 

service those vessels (Figure 15).

Mosquito Control

Application of insecticides to control mosquito-borne pathogens 

like West Nile virus, Dengue fever, and viral encephalitis affect nearshore waters of the sanctuary. Waters are vulnerable to insecticide 

runoff and overspraying, while toxic effects may affect non-target organisms, such as the queen conch (Strombus gigas) (McIntyre et al. 

2006, Glazer et al. 2008). 

Commercial and Recreational Fishing

Fishing is the most widespread exploitative activity in coastal 

ecosystems and poses significant threats to the biodiversity and 

condition of marine ecosystems (Ault et al. 2005a, Chiappone et 

al. 2005). Threats are in the form of direct take, by-catch, indirect 

effects, and habitat damage from the use and loss of fishing gear 

Figure 15. Numerous live-aboard vessels are anchored around the Florida Keys.

Photo: NOAA/FKNMS

Figure 16. Fly-fishing is a popular way to fish for bonefish in the Florida Keys. 

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

24 Florida Keys CONDITION REPORT 2011

(Figure 16). For example, the removal of targeted species and 

coincident mortality of non-target species (by-catch) may result in 

cascading ecological effects (Frank et al. 2005). Because fishing is 

also size-selective, concerns exist about ecosystem disruption by 

removal of ecologically important key species such as top predators 

(e.g., groupers, snappers, sharks, and jacks) and their prey (e.g., 

shrimps and baitfish).

Both commercial and recreational fishing are economically important to the Florida Keys. In terms of volume of seafood landed, 

the Florida Keys is the most important area in the state of Florida 

for landings, dockside value, and numbers of commercial fishing 

vessels, most of which target the highly valued invertebrate fisheries (Adams 1992). Although fishing pressure (i.e., number of trips, 

traps, angler days, etc.) from both the commercial and recreational 

fisheries declined from 1995 to 2008, it is uncertain if these trends 

will continue. For example, information from socioeconomic surveys in 1995-96 showed over 572,000 visitors and residents did 

over 2.8 million days of recreational fishing in the Florida Keys 

(Leeworthy and Wiley 1996, Leeworthy 1996, Leeworthy and 

Wiley 1997). Similar surveys in 2007 and 2008 showed almost 

416,000 visitors and residents did almost 2.1 million days of fishing in the Florida Keys and Key West (Leeworthy and et al. 2010 

and Leeworthy and Morris 2010). This represents a 25% decline 

in recreational fishing effort over the 12-year period. However, this 

decrease in pressure has an offsetting trend in that the growth in 

average fishing power (the proportion of stock removed per unit 

of fishing effort) may have quadrupled in recent decades. This 

increase results from technological advances in fishing tackle, 

hydroacoustics (depth finders and fish finders), navigation (charts 

and global positioning systems), communications, and vessel propulsion (Bohnsack and Ault 1996, Mace 1997). Because of this, 

there remains a significant but largely undocumented effect of 

tens of thousands of recreational fishers who target hundreds of 

species using mostly hook-and-line and spear guns (Figure 17; 

Bohnsack et al. 1994a). Reef damage may also occur from anglers anchoring on reefs (Davis 1977), as well as gear impacts 

from lost fishing gear. 

Marine debris in the form of derelict fishing gear can destroy benthic organisms, entangle both benthic and mobile fauna (Donohue 

et al. 2001), and reduce the structural complexity of habitats (Chiappone et al. 2002a). For example, commercial fisheries targeting 

lobsters and stone crabs utilize traps that are deployed in habitats 

adjacent to reefs. Currents associated with strong storms can move 

traps onto reefs, where corals and other benthic organisms are damaged or killed (e.g., Sheridan et al. 2005). In 2005, it was estimated 

that approximately 300,000 lobster traps were lost during a series of 

hurricanes and strong storms (Clark 2006). The ecological impacts 

caused by fishing gear that is lost when cut or broken after snagging on the bottom is a growing concern to managers and scientists 

(Chiappone et al. 2005). 

Bleaching Events and Climate Change 

Seasonal and yearly seawater temperature extremes, increasing 

UV penetration in the water column, and atmospheric changes all 

affect the Florida Keys ecosystem. These impacts are most evident 

in coral disease and bleaching events, which have increased in frequency, duration and range, coinciding with the 10 warmest years on 

record (1999 to 2009). However, additional human-induced stresses 

are likely affecting the ability of these organisms to adequately recover from climate fluctuations (Wagner et al. 2010).

During the 20th century, the global mean near-surface air temperature over land and mean sea surface temperature (SST) increased 

0.6 ± 0.2°C, with the 1990s constituting the warmest decade in the 

instrumental record and 1998 the warmest year since instrumental 

records began in 1861 (IPCC 2001). Additionally, so far in the 21st 

century, mean monthly global ocean temperature anomalies have 

been 0.45°C above the 20th century mean (NOAA NCDC data). 

These increasing temperatures have the potential to increase the 

frequency and intensity of both coral bleaching events and summertime tropical weather disturbances. Coral diseases and hurricane 

damage have been identified as the main source of mortality of two 

important reef-building corals in the Caribbean region: elkhorn coral 

and staghorn coral. These coral species have undergone such a 

drastic decline in abundance that the NOAA Fisheries Service listed 

these corals as ‘threatened’ species under the U.S. Endangered 

Species Act in 2005.

Elevated water temperatures cause corals and other reef organisms such as sponges and gorgonians to bleach, a process characterized by the loss of zooxanthellae (a symbiotic microalgae) 

Figure 17. Recreational vessel registrations in Monroe County increased 

more than 1,000% from 1964 to 2010. Commercial vessel registrations increased by about 100% from 1964 to 1998, but have since decreased by 37%. 

Source: Florida Statistical Abstracts and Florida Department of Highway Safety and Motor 

Vehicles; Ault et al. 2005b
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 25

from coral tissues (Figure 18). High ultraviolet irradiance, typically 

from unusually calm, clear waters, may exacerbate the impact of 

increased temperatures (Lesser and Lewis 1996). Although corals 

may recover from brief episodes of bleaching, if ocean temperatures 

warm too much or remain high for an extended period, bleached corals will often die. Several correlative field studies show a close association between warmer-than-normal conditions (at least 1°C higher 

than the annual maximum) and the incidence of bleaching (HoeghGuldberg 1999). In 1997 and 1998, an estimated 16% of the world’s 

coral reefs were seriously damaged in one of the most geographically extensive and severe bleaching events in recorded history 

(Wilkinson et al. 1999), which caused significant mortality worldwide 

(Baird and Marshall 2000). The stress for many of these coral reef 

systems was associated with high sea surface temperature over a 

12-week period that was apparently enhanced by an extreme El Niño 

Southern Oscillation event (Wilkinson et al. 1999). A U.S. Department of State report to the U.S. Coral Reef Task Force (Pomerance 

et al. 1999) concluded that the severity and extent of the 1998 event 

cannot be explained by El Niño alone, and that the “...geographic 

extent, increasing frequency, and regional severity of mass bleaching events are likely a consequence of a steadily rising baseline of 

marine temperatures...”. There is some debate whether or not coral 

bleaching is a disease, but we know it is a physiological response to 

stressors. While records show that coral bleaching events have been 

occurring for many years in the Florida Keys (Jaap 1979, 1984), indications are that the frequency, duration, and severity has steadily 

increased over the past 20 years (Waddell and Clark 2008). Largescale coral bleaching was first recorded in the lower Keys in 1979 

along the outer reef tract, where shallow fore-reef habitats were the 

most affected areas (Jaap 1979). Bleaching expanded and intensified with events in 1987 and 1990, and culminated with mass coral 

bleaching events in 1997 and 1998 that impacted nearshore and 

offshore reefs throughout the Florida Keys. Coral bleaching and the 

secondary impact of coral disease is likely responsible for some of 

the dramatic declines in stony coral cover observed sanctuary-wide 

in the last two decades (Causey 2008).

Sponges are also susceptible to bleaching events. The Caribbean 

barrel sponge (Xestospongia muta) is a large and common member 

of coral reef communities at depths greater than 10 meters, and has 

been called the “redwood of the reef” (McMurray et al. 2008). Like reef 

corals, this sponge is subject to bleaching in which it expels the symbiotic microorganisms living within its tissues, often resulting in death. 

Tissues of X. muta contain very primitive cyanobacterial symbionts 

belonging to the Synechococcus-Prochlorococcus clade (Gómez et 

al. 2004, Steindler et al. 2005) that impart the reddish-brown to browngray coloration of the sponge. The first report of a massive die-off of 

X. muta in the Florida Keys was in 1979 (Causey 2008). Hundreds of 

X. muta were observed dying in a one-month time frame on the reef 

tract, south of Bahia Honda Pass. Other reports of bleaching of X. 

muta, along with other symbiont-containing sponges, began to appear along with reports of coral bleaching events over a decade ago 

(Vincente 1990). In some cases, bleached sponges deteriorated and 

disintegrated. Moreover, bleached X. muta were more susceptible to 

predation by parrotfishes and generalist predators (Dunlap and Pawlik 1998). Bleaching and subsequent mortality of sponges has since 

been observed throughout the Caribbean (Nagelkerken et al. 2000). 

Coral communities are also susceptible to cold water. For example, in January 1977, an extreme cold “front” passed through southern 

Florida, causing water temperatures to drop to 14 – 16°C. Following 

this thermal stress event there was extensive mortality of branching 

scleractinia corals. Major mortality of Staghorn coral (Acropora cervicornis) was observed, with over a 90% loss from 1976 numbers. In addition, there was also a significant loss of Elkhorn coral (A. palmata), 

with over two-thirds being killed by the cold water. (Davis 1982)

Along with extreme temperature fluctuations from a changing climate, ocean acidification may also affect coral reefs in the Florida 

Keys as atmospheric carbon dioxide levels continue to increase. The 

ocean takes up around 25% of atmospheric CO2

 produced by humans through land use changes and the burning of fossil fuels, which 

then dissolves in seawater to form carbonic acid. Since humans have 

contributed to greater amounts of CO2

 into the atmosphere over the 

past century, the ocean has absorbed CO2

 at an increasingly rapid 

rate, changing the ocean’s chemistry and leading to ocean acidification. The acidity of seawater has increased by 30% since the beginning of the Industrial Revolution over 250 years ago, lowering the 

ocean’s natural basic (alkaline) status to an acidic imbalance (Ocean 

Acidification Reference User Group 2009). 

Figure 18. Bleached and moribund Elkhorn coral (Acropora palmata).

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

26 Florida Keys CONDITION REPORT 2011

Due to the increased acidity of seawater, many of the animals 

and plants in the ocean that have calcium carbonate skeletons or 

shells, such as corals, may experience reduced growth or ability to 

generate hard shells. For example, in Australia’s Great Barrier Reef, 

corals have already reduced their calcification rates, most likely in 

response to elevated water temperature and ocean acidification 

impacts (De’Ath et al. 2009). In a study by Hoegh-Guldberg et al. 

(2007), it is predicted that if atmospheric CO2

 levels continue to increase, the structure and function of coral reef ecosystems around 

the world will be compromised and some coral species will become 

extinct. Ocean acidification could prompt a chain reaction of impacts 

through the marine food web, beginning with larval fish, shellfish, and 

corals, cutting valuable ecosystem services provided by coral reefs 

such as food security, tourism, shoreline protection, and biodiversity 

(Ocean Acidification Reference User Group 2009). 

Weather Disturbances

Climatic events play an important role in the ecosystem dynamics of the sanctuary. South Florida experiences more tropical depressions and hurricanes than any other area in the United States 

(Schomer and Drew 1982). Tropical storms typically occur between 

June and November, peaking in late September and early October. Winter storms are also common (Roberts et al. 1982). Tropical 

storms, which include hurricanes, can cause major damage to the 

marine environment, affecting the abundance and condition of benthic organisms including corals. Large blocks of coral can be broken 

from reefs and moved great distances, and sediments can abrade 

organisms or bury them completely. Damage patterns to coral reefs 

are commonly influenced by the strength, path and duration of each 

storm event, storm frequency, and prior disturbance history (Witman 1992, Harmelin-Vivien 1994, Lirman and Fong 1997a, b, Lirman 2000). Recovery of coral colonies is often influenced by colony 

morphology of corals (Gardner et al. 2005), and may, in some cases, 

take several decades. The topography of the Florida Keys contributes to their vulnerability to such storms — 96% of the area’s land 

mass is less than 6.5 feet (2 meters) above sea level (Cross 1980).

The record breaking 2005 Atlantic Hurricane Season produced 

a total of 28 named tropical storms, 15 of which attained hurricane 

strength throughout the Atlantic, Caribbean Sea, and Gulf of Mexico. 

Five tropical cyclones (Arlene, Dennis, Katrina, Rita, and Wilma) directly impacted the Florida coastline and sanctuary resources. Hurricane Wilma (Figure 19) produced a six- to eight-foot storm surge 

throughout the middle and lower Keys. 

Diseases of Marine Organisms

Mass die-offs of marine life due to disease outbreaks have increased 

in frequency and intensity in the past two decades, affecting numerous 

taxa in the oceans (Harvell et al. 1999). For many marine organisms, 

including corals and marine mammals, reports of the frequency of epidemics and the number of new diseases is increasing. Recently, the 

Caribbean basin has emerged as a disease “hot spot” (Harvell et al. 

1999, Weil 2004). Mass mortalities of plants, invertebrates, and vertebrates can result in dramatic shifts in community structure. Additionally, 

diseases affecting benthic marine species such as corals and seagrasses can have disproportionate impacts on the ecosystem because 

of the changes in habitat and ecosystem function that can result. Despite these impacts the causative agents and the factors contributing 

disease outbreaks are poorly understood due to lack of information on 

normal disease levels in the ocean. However, it is believed that factors such as long-term warming trends and human activities, including 

habitat degradation and pollutant inputs, may play important roles in the 

transport and spread of diseases (Harvell et al. 1999). 

Figure 19. Hurricane Wilma was the 13th hurricane in 2005. It reached 882 

mbar pressure in a span of 24 hours, making it the fastest pressure drop of 

any storm in the Atlantic Basin. At its peak intensity, the eye of Wilma was 

about 3 miles (5 kilometers) in diameter, the smallest known eye of an Atlantic 

hurricane. The blue line shows the approximate trajectory of the hurricane.

Photo: NOAA
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 27

The first documented epizootic event in the Caribbean was the 

mass mortality of commercial sponges in the northern Caribbean. In 

December 1938, a blight resulting from a fungus-like filament struck 

sponge beds in the Bahamas, causing their skeletons to disintegrate 

(Witzell 1998, McClenachan 2008). The blight quickly reached epidemic proportions, leaving the ocean floor covered with thousands 

of bleached and rotten sponges, and by February 1939 all spongebearing banks were affected (McClenachan 2008). In March, signs 

of the disease appeared in Key West, and by May sponges showed 

considerable damage from blight. By the end of 1939, yellow and 

vase sponges had suffered nearly 100% mortality, while 70% of the 

commercially valuable sheepswool sponges had been eliminated 

from the Florida Keys altogether. The disease eventually spread 

northward and caused extensive mortality to sponges as deep as 70 

feet (20 meters). By the end of 1940, the sponge fishery was nonexistent in Florida due to the devastating effects of disease on sponge 

populations (Shubow 1969). 

Another well-studied marine epidemic was the virtual eradication 

of the long-spined sea urchin. This Caribbean-wide event in 1983 

– 1984 spread rapidly in about one year and was caused by an unidentified pathogen which appeared in the Florida Keys in July 1983 

(Lessios et al. 1984, Miller et al. 2009). The pathogen was circulated 

widely throughout the Caribbean by surface currents that connect 

the southwestern Caribbean with the Florida Keys. In many Caribbean locations, loss of this keystone herbivore contributed to phase 

shifts from coral- to macroalgae-dominated reefs, especially noticeable in areas where herbivory was nearly solely dependent upon sea 

urchin grazing because of overfishing (Hughes 1994). Due apparently to low larval supply, recovery of the long-spined sea urchin has 

generally been slow and incomplete in the Florida Keys since the 

1983 and 1991 mortality events (Miller et al. 2009).

Coral diseases have been identified as a significant contributor 

to coral mortality (Weil 2004, Voss 2006). Although little is known regarding the factors that drive coral disease distributions and dynamics, monitoring of coral diseases in the Florida Keys indicates that 

there has been an increase in the number of new diseases (Goreau 

et al. 1998). Coral diseases were first described in the Caribbean in 

the early-to-mid-1970s (Antonius 1973, Weil 2004). The white plague 

was the first epizootic event occurring in 1975 and resulted in significant coral mortality. In the 1980s, a white-band disease epizootic 

event significantly reduced populations of acroporid corals (A. palmata and A. cervicornis), leading to a reduction in habitat and refuge 

space and biodiversity (Santavy et al. 2001). The loss of coral cover 

was correlated with significant increases in algal cover and lack of 

herbivory, thus changing the community structure and dynamics of 

shallow coral reef habitats. The first widespread outbreak of blackband disease in the Florida Keys occurred in May 1986 from Looe 

Key Reef to Western Dry Rocks (Causey 2008). Prior to this outbreak, 

only scattered, isolated outbreaks had been reported (Antonius1973, 

1981, Dustan 1977). Following the 1986 massive outbreak, blackband disease became one of the more common coral diseases observed in the 1990s and 2000s. In the 1990s, several new coral diseases were reported, including red-band disease, white-band type II, 

white plague type II, yellow blotch, dark spots, and white-pox disease. 

As of 2010, causative agents have only been identified for black-band 

disease (Bruckner 2000), white-band (Ritchie and Smith 1998), white 

plague II (Denner et al. 2003), and white pox disease (Patterson et 

al. 2002). Tumors, as well as lesions associated with parasites, ciliates, bacteria, and fungi, have also been found on a number of coral 

species. Gorgonians such as sea fans have also been affected by 

increased disease incidence since 1981 (Nagelkerken et al.1997), 

primarily due to exposure to a terrestrial fungus (Aspergillus sydowii) 

(Geiser et al. 1998). Increasing anthropogenic impacts and increasing ocean temperatures may contribute to disease occurrence.

Fibropapillomatosis (FP) is a viral disease specific to sea turtles, 

although it most commonly affects juvenile green turtles in nearshore 

habitats around the world (Herbst 1994, Ene et al. 2005). In some 

localities, such as the Indian River Lagoon, Florida Bay, and the 

Florida Keys, 50 to 70% of the green turtles are affected (Ene et al. 

2005). FP is a debilitating neoplastic disease that can result in benign 

cauliflower-like tumors on the soft and hard tissues of turtles, both 

internally and externally. These tumors can disrupt locomotion, feeding, respiration, and vision. While external tumors can be surgically 

removed, internal tumors cannot and are nearly always fatal. Since 

the early 1980s, the percentage of green turtles stranded in Florida 

with FP has been escalating at a rate of 1.2% per year, and based on 

research from the Florida Sea Turtle Stranding and Salvage Network 

database, 22% of dead or debilitated green turtles (sample size = 

6,027) found in Florida between 1980 and 2005 had tumors (Foley 

et al. 2005). Although the cause of FP is still not fully understood, 

recent research has strongly indicated a viral origin. The virus may 

be spread through biological vectors and specific biotoxins may increase the prevalence of tumors (Foley et al. 2005). Turtles affected 

by FP are often found in shallow water with poor water circulation, 

leading to the speculation that environmental factors may play a role 

in the distribution or prevalence of the disease (Foley et al. 2005). 

Panulirus argus virus 1 (PaV1), a lethal herpes-like virus, infects 

juvenile Caribbean spiny lobster (Behringer et al. 2006). It is transmitted among lobsters via inoculation, prolonged contact with infected lobsters, ingestion of infected tissue, and over short distances 

in the water (Butler et al. 2008). Because Caribbean spiny lobsters 

are social and share communal dens, the virus can spread quickly 

with devastating consequences. PaV1 is the first naturally occurring, 

pathogenic virus known to infect the Caribbean spiny lobster (Beh-
Pressures on Sanctuary Resources

28 Florida Keys CONDITION REPORT 2011

ringer et al. 2008, Butler et al. 2008) affects as many as 16% of 

the juvenile Caribbean spiny lobster populations sampled from the 

mid- to lower Florida Keys (ICES 2003). The virus attacks haemocytes, blood cells that are part of the animal’s immune system, causing the blood to become milky white, and appears to affect juveniles 

only. The virus is highly lethal in experimental conditions. Given its 

virulence, PaV1 represents a serious threat to both commercial and 

recreational fisheries (Butler et al. 2008).

Cleaner fishes and shrimp in tropical marine habitats assist in 

keeping the levels of most pathogens and parasites quite low in wild 

fish populations (Peters 1997). However, injured or weakened reef 

fish species may become infected with marine bacteria, fungi, protozoans or parasites resulting in lesions, tumors or mortality. In 1980, 

1993 and 1994, mass mortality of tropical reef fishes occurred in 

coastal regions of southeastern Florida and the Florida Keys (Burns 

1981, Landsberg 1995, Causey 2001). The affected fish were adult 

herbivores and omnivores such as angelfishes, parrotfishes, surgeonfishes, and butterflyfishes. Some piscivores and cleanerfishes 

were also affected. Fishes were observed to have lesions and ulcerated body sores, fin and tail rot, and a heavy mucus coating on 

the body surface (Landsberg 1995). Causey (2001) noted the close 

association of these fish mortalities with elevated temperatures that 

also caused widespread coral bleaching. Landsberg (1995) detected 

parasites and bacterial infestations in preserved tissues of these 

fishes, but suggests that ingesting toxins from macroalgae or dinoflagellates may have compromised their health, and the infestations 

resulted from the fishes’ weakened state caused by these toxins.

Vessel Use

A significant threat to the protection and health of sanctuary resources is the impacts from vessels including oil pollution, vessel 

groundings, noise pollution, and dredged material resulting from 

maintenance of shipping channels. The Florida Straits have historically been the access route for all commercial vessels entering the 

Gulf of Mexico from the north and east and, consequently, these waters are some of the most heavily trafficked in the world. It is estimated 

that 40% of the world’s commerce passes within 1.5 days sailing time 

of Key West (U.S. Department of the Navy 1990). In addition, oil tankers transit the coast daily, including very large and ultra-large crude 

carriers. 

Large commercial vessels are of particular concern because of 

the potential for oil spills. These vessels often travel close to shore 

and can carry upwards of 1 million gallons of bunker fuel, a heavy, 

viscous fuel similar to crude oil that is used to power the ships. As described earlier in this report, a large spill could have a major impact 

on foraging birds, marine mammals and fishes, as well as important 

habitats like sandy beaches, mangroves and other intertidal habitats, 

seagrass beds, and coral reefs, and therefore could have serious 

consequences for tourism and the coastal economy. 

In addition to the threat of oil spills, more than 300 vessel groundings (vessels 50 feet or less; FKNMS unpub. data) are reported annually within the sanctuary, causing physical damage to sanctuary 

resources such as seagrass, hard-bottom, and coral reef habitats. 

There are also many grounding incidents that damage resources but 

are not reported (NOAA 2007). Although large vessel groundings often result in highly visible, immediate resource devastation with longterm impacts, the vast majority of grounding incidents are caused by 

smaller recreational vessels. Even so, the cumulative detrimental effect of smaller groundings can also have long-lasting impacts. Vessel 

groundings from large tankers play a role in the history of the sanctuary. Within a three-week period in 1989, the M/V Elpis and the M/V 

Alec Owen Maitland ran aground on two different shallow bank reefs, 

and a third vessel, the Mavro Vetranic, ran aground in Dry Tortugas 

National Park, killing and displacing corals, gorgonians, and other 

benthic organisms, in addition to destroying the physical structure of 

the underlying reef. These three large vessel groundings were important factors in the congressional designation of Florida Keys National 

Marine Sanctuary and led to the creation of an “Area to be Avoided,” 

which, through sanctuary regulations, prohibits ships greater than 50 

meters in length from entering certain areas of the Florida Keys.

Because coral reefs and seagrass beds are found predominantly 

in shallow water, they are susceptible to a variety of direct impacts 

from smaller commercial and recreational vessels that may not result in actual groundings. These impacts include damage from the 

propeller, hull, engine, and keel of these types of vessels. Physical 

impacts can also result from anchors, anchor chains and cables, unmanned barges, dredge lines, dredge cutter heads, and cables used 

to tow barges and dredges. Anchor damage, propeller scarring, and 

other vessel impacts occur frequently and may cause enough damage that impacted reefs and seagrass beds cannot recover. Vessel 

“strikes” also impact motile fauna such as sea turtles and marine 

mammals (e.g., dolphins and the West Indian manatee) (Figure 20). 

Figure 20. West Indian manatee with old boat propeller scars (as identified 

with arrows) that biologists use to identify this individual. 

Photo: USGS Sirenia Project
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 29

Large commercial shipping traffic and recreational and commercial vessels can also affect noise levels in the marine environment. 

Certain anthropogenic noise is thought to mask sounds used by 

marine mammals for mating, feeding, and avoiding predators. Responses vary depending on the acoustic frequency, decibel level, 

proximity to the source and other species-specific sensitivity factors. 

Long-term cumulative impacts are uncertain and range from minimal 

impacts in some situations, to possible physical damage to hearing 

structures, to stranding events. 

Most of these impacts from vessel use correlate with the ever-increasing number of vessels transiting within and around the sanctuary. 

Recreational vessel registrations in Monroe County increased more 

than 1,000% from 1964 to 2006, whereas commercial vessel registrations increased by about 100% from 1964 to 1998, but have since decreased by 37% (Figure 17; see page 24). There were 25,370 pleasure 

and 2,653 commercial vessels registered in Monroe County in 2007 

(Federal Register Vol. 74 No 219). These statistics are also reflected 

in the number of derelict and abandoned vessels located in the Florida 

Keys in any given year. Monroe County typically has the highest number of derelict or abandoned vessels in the state of Florida, and like 

marine debris these vessels pose threat to the marine environment, 

human health, and navigation. From a criminal viewpoint, derelict and 

abandoned vessels have the potential to be locations for illegal activity, 

illegal housing, and opportunities for theft and vandalism. 

Combined with transits around the sanctuary each year by large 

shipping vessels (greater than 300 gross tons), cruise ships, and military ships, vessel traffic affecting the sanctuary is continuing on an upward trend. For example, from 2000 to 2005, cruise ships based out 

of Miami ferried approximately 24.5 million passengers to various locations throughout the greater Caribbean region, including Key West. Additionally, the potential for extremely large vessels traveling the Florida 

Straits exists when the Panama Canal expansion project is completed 

over the next few years. Expansion of the Port of Miami is underway to 

accommodate larger ships en route from the Pacific Ocean.

Coastal Development

Changes to Hydrologic Patterns Associated with Important Nearby Estuaries

South Florida has experienced drastic changes to its freshwater 

wetlands of the Everglades, and such changes threaten its estuaries 

(especially Florida Bay), which ultimately could affect the entire sanctuary. During the past century, the pattern (timing, volume, and quality) 

and intensity of freshwater flows to these estuaries has been significantly altered and reduced due to intense municipal and agricultural 

activities plus the construction of the Central and Southern Florida 

Project for Flood Control and Other Purposes (commonly known as 

the Project). The Project is a surface-water management facility designed by the U.S. Army Corps of Engineers in the 1950s to drain land, 

provide flood protection, and regulate South Florida’s water supply. 

Through the Project, enormous volumes of fresh water originally destined for the Everglades and its estuaries have been drained, diverted, 

or stored in “water conservation areas.” The resulting alteration of the 

natural freshwater cycle has interrupted the distribution, flow, timing, 

and quality of freshwater delivery through South Florida’s wetlands. 

Altered flows and drainage canals have also reduced the natural 

recharge of fresh water to the Biscayne aquifer, the water-bearing 

limestone beneath southeast Florida and the Everglades. The aquifer is the source of drinking water for all of southern Florida and the 

Florida Keys via an aqueduct. This long-term reduction in groundwater recharge has gradually allowed salt water to intrude inland from 

the coast and has reduced freshwater wetlands. A recharged aquifer 

serves to prevent saltwater intrusion and helps sustain wetlands in 

times of drought. Reduced freshwater flows over a long period of time 

and pulses of large amounts of fresh water during heavy rains for flood 

control have had significant ecological impacts on the two main estuaries adjacent to the sanctuary: Florida Bay and southern Biscayne Bay. 

Card and Barnes Sounds, which are part of the southern Biscayne Bay 

system, lie within sanctuary boundaries and have also been affected 

by reduced freshwater input (USACE 1999). These once-productive 

estuarine systems have become more marine in species composition 

over time; negatively affecting their function as a nursery for certain 

key species like pink shrimp. The impact of this loss of estuary function is not fully known, but restoration projects on the mainland are 

expected to begin improving flow conditions to both bays in the future.

Nearshore Construction

In addition to altered water flows, shallow, nearshore habitats of the 

Florida Keys continue to be affected by coastal construction. Rate of 

growth ordinances for several incorporated Keys communities and Monroe County prevent rapid and uncontrolled development and associated 

impacts, but some new construction does continue to occur. The small 

land mass comprised by the individual islands of the Keys, along with the 

desire by most homeowners to have easy water access, have directed 

most development to the land-water interface. As such, existing structures such as residential docks, seawalls, and other shoreline protection 

features are abundant throughout the Florida Keys and are in constant 

need of repair. Commercial fish houses and similar businesses may be 

re-purposed for high-end private marinas, often necessitating expansion into nearby coastal habitats. Public infrastructure projects, including 

bridge and utility line repairs, may encroach into sanctuary waters.

New construction, repairs, or rehabilitation of existing structures 

in the coastal zone can result in impacts to mangroves, seagrass 

beds, submerged aquatic algae, nearshore hard-bottom habitat, and 
Pressures on Sanctuary Resources

30 Florida Keys CONDITION REPORT 2011

coral reefs. While regulations on mangrove destruction and limits on 

trimming have been in place for many years by the FDEP (Chapter 

403 Florida Statutes), protections to less visible, or what may be perceived as “less valuable,” species are not consistent among resource 

agencies. Specific jurisdictions of various agencies and the natural 

resources they protect may vary, and exemptions to permitting rules 

for small projects may inadvertently result in impacts to nearshore 

resources. For example, several ubiquitous stony coral species will 

recruit to artificial structures such as concrete seawalls and bridge 

pilings, and may be injured or destroyed during the course of permitted repairs. The manner by which these nearshore corals contribute 

to the health of the marine ecosystem is an under-studied topic. 

Interestingly, some research indicates that corals found in nearshore habitats have higher growth rates and lower partial mortality, 

despite living in an environment of seemingly poorer water quality 

(Lirman and Fong 2007). Continued observation of these “hardy” 

nearshore corals has prompted inquiries about connectivity to their 

offshore counterparts. While impacts to corals and other species during coastal construction projects may be found to be individually insignificant, this could represent a cumulative threat over space or time to 

species and habitats, many with unidentified ecosystem worth.

Dredging

As noted in the “Vessel Use section, an increasing number of boats 

are operating within the sanctuary every year. Dredging activities in the 

Keys are usually limited to small, private projects, many associated with 

dock or seawall construction discussed above. Dredging is also occasionally required for maintaining canals or expanding dockage of a local 

marina. In 2007, the U.S. Navy finished maintenance dredging on the 

main shipping channel into Key West in preparation for increased fleet 

presence. The sediment removed from this operation was disposed of 

at both an upland and offshore disposal site, the latter of which was outside sanctuary boundaries and permitted by the EPA, U.S. Army Corps 

of Engineers and FDEP. Dredging impacts seafloor communities both 

at the dredging site and at the disposal site. The physical disturbance 

of dredging damages or removes organisms living in or on the seafloor and can resuspend buried chemical contaminants. The disposal 

of dredge material can smother organisms and introduce chemical 

contaminants at the disposal location. Pipelines or barge routes necessary for upland disposal may impact natural habitats, as can discharges 

from dredge spoil containment areas. In addition, dredging to deepen 

channels in harbors can alter water flow dynamics and future sediment 

deposition rates in the harbor and adjacent habitats. 

Beach Nourishment

Sandy beaches are not a prevalent shoreline habitat type in the Florida Keys in comparison to many other counties in the state of Florida. 

Florida boasts 825 miles of sandy beach, but just 26 of those miles (42 

kilometers) are located within Monroe County. However, several active 

hurricane seasons, most notably in 2005 and 2006, exacerbated beach 

erosion and led to the need to supplement local beaches with imported 

sand. A 2010 report by the Florida DEP Bureau of Beaches and Coastal 

Systems categorized around 10 miles (16 kilometers) of beach in Monroe County as “critically eroded.” The economic benefits of lush sandy 

beaches in a tourism community are well recognized. However, replenishing beaches with sand may result in direct impacts such as burial 

of natural, functional nearshore habitats (seagrasses, algae, and hard 

bottom), especially if unsuitable sediment is used (Wanless and Maier 

2007). Indirect impacts may include localized turbidity and increased 

sedimentation at both the beach and borrow sites (Jordan et al. 2010), 

as well as a decrease in resident fish assemblages when habitat is lost 

(Lindeman and Snyder 1999). Sand placement may also change beach 

attributes, such as burying sea turtle nests, if it is conducted during the 

active nesting season due to nest burial or changes in beach attributes.

Non-Indigenous Species

Non-indigenous species are recognized worldwide as a major 

threat to ecosystem integrity when they become invasive. Non-indigenous species in the marine environment can alter community 

composition, reduce the abundance and diversity of native marine 

species (Olden et al. 2004), interfere with ecosystem function, alter habitats, disrupt commercial and recreational activities, and in 

some instances cause extinctions of indigenous plants and animals 

(Clavero and Garcia-Berthou 2005). They can cause local extinction 

of native species either by preying on them directly or by out-competing them for food or space. Once established, non-indigenous species can be difficult, if not impossible, to eradicate. 

Invasions by non-indigenous aquatic species (e.g., lionfish, orange cup coral, Red-tipped Sea Goddess) are increasingly common 

worldwide in coastal habitats due to shipping traffic, world travel, and 

intentional or accidental releases by individuals. Though the most 

significant global mechanism for the introduction of aquatic species 

is ship ballast water, it can occur via other mechanisms such as improper disposal of household aquarium pets, commercial aquaculture operations, and research activities. 

Wildlife Disturbance

The sanctuary provides many opportunities for wildlife observation, thus the 3 million annual visitors to the region results in a high 

level of visitation that can have significant direct and indirect effects 

on the ecosystem. Both motorized (e.g., party boats, jet skis and 

other personal watercraft) and non-motorized vessels (e.g., kayaks 

and canoes) are used throughout the sanctuary, often for viewing 

marine mammals and seabirds. With the multitude of opportunities 
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 31

for observation come the potential for wildlife disturbance including flushing birds from 

their nests or roosts and harassing marine 

mammals. Other tourism activities such as 

diving and snorkeling can also impact resources. The former Key Largo and Looe 

Key National Marine Sanctuaries included 

prohibitions on damaging coral in response 

to increasing threats by recreational visitors. 

In addition to physical impacts, some 

wildlife species are undergo behavioral 

changes after they are fed by well-intentioned humans. Sharks, manatees, and 

numerous bird species (most notably pelicans and herons) are routinely fed fish, fish 

carcasses, lettuce, fresh water, and other 

items for the purposes of attraction and 

viewing, or inadvertently though improper 

disposal. These species may develop unnatural behavioral patterns 

leading to unsafe interaction with humans or vessels (e.g., sharks 

and manatees). Wild birds often suffer from punctured gizzards or 

other internal organs from digesting fish carcasses at marinas and 

docks where fish are cleaned and carcasses are discarded.

Artificial Reefs 

A number of artificial reefs (primarily intentionally sunken ships) 

have been placed in the sanctuary. General agreement exists in the 

scientific community that artificial reefs can be effective fish attractants; however, most published research addresses the building of 

artificial reefs or descriptive studies detailing successional changes 

in fish species composition (Bohnsack and Sutherland 1985, Kruer 

and Causey 1992). The effects of artificial reefs on fish and invertebrate populations and habitats, and the longevity of these structures, 

are not fully known. Whether artificial reefs attract fish from nearby 

natural habitats or serve as a “production” point where new fish can 

settle remains a debate among the scientific community, but likely 

depends on multiple factors (Bohnsack et al. 1994b, Osenberg et al. 

2002, Powers et al. 2003). Research in nearby Miami-Dade County 

found that fish assemblages on an artificial reef are more variable 

than those on nearby natural reefs, leading to additional questions 

about whether artificial structures can replace lost reef function (Thanner et al. 2006). As such, thorough research is needed on these 

topics to determine whether the placement of artificial reefs is consistent with the goals and objectives of the sanctuary.

The sanctuary has experienced first-hand that stability of artificial 

reefs can be variable despite the best attempts to ensure proper deployment. In 1998, the passing of Hurricane Georges caused the Eagle, a Dutch freighter sunk in 1985 six miles 

(nine kilometers) off Lower Matecumbe Key, 

to break in half. The USS Spiegel Grove, 

scuttled in 2002 as an artificial reef off Key 

Largo, landed upside down upon sinking. 

An unplanned, unfunded salvage effort successfully moved the ship onto its starboard 

side, and the force of Hurricane Dennis in 

July 2005 righted the ship to its originally intended position. Federal and state permit requirements for artificial reefs typically include 

thorough stability analyses and the ability for 

the structure to withstand 100-year storm 

events. However, it is not until after deployment that these parameters can be tested in 

the environment and in the face of unforeseen natural events. Logically, the NOAA 

administration supports a precautionary approach when considering the deployment of artificial reefs, and notes 

that “NOAA will continue to emphasize the protection, restoration, 

and enhancement of natural habitats, as opposed to constructing 

artificial habitats” (J. Dunnigan, pers. comm. NOAA, Dec. 8, 2009). 

Some socioeconomic research on the human-use patterns of artificial reefs on nearby natural reefs has been completed for the USS Spiegel Grove off Key Largo. The results indicated that visitation declined 

by 13.7% on the surrounding natural reefs, lead to a 160.5% increase 

in artificial reef use, and a net increase in total artificial and natural reef 

use of 9.3% (Leeworthy et al. 2006). While the recreational use of the 

surrounding natural reefs decreased, the local dive charter business increased, and the local economy grew in terms of both income and employment (Leeworthy et al. 2006). This represents a positive increase 

to total business, while reducing pressure on the natural reefs. Similar 

research is underway for the USS Vandenberg, sunk off Key West.

Marine Debris

Marine debris is defined as any persistent, manufactured, or 

processed solid material that is directly or indirectly, intentionally or 

unintentionally, disposed of or abandoned into the marine environment (NOAA 2008). Marine debris includes a wide variety of objects 

(e.g., derelict fishing gear, lost vessel cargo, plastics, etc.) that pose 

a threat to the marine environment, human health, and/or navigation. 

Various types of debris, including fishing gear, plastic bags, foamed 

polystyrene, balloons, and other consumer goods, are known to have 

adverse effects on marine species, and increasing levels of debris in 

both the ocean and at the land-sea interface are of growing concern 

to sanctuary managers (Figure 21). Ingestion and entanglement are 

two of the many problems associated with marine debris, and may 

Figure 21. Sanctuary staff and volunteers conduct regular marine debris cleanup efforts in 

the sanctuary. 

Photo: NOAA/FKNMS
Pressures on Sanctuary Resources

32 Florida Keys CONDITION REPORT 2011

lead to death in sea turtles, marine mammals, and benthic organisms. Plastics in the marine environment may never fully degrade, 

and recent studies found that various types of plastic are consumed 

by organisms at all levels in marine food webs (Derraik 2002). 

While the effects of fishing on marine ecosystems are a continuing 

concern for resource management, the wide-ranging effects of lost 

or discarded (derelict) fishing gear on organisms and ecological processes is still largely unknown in many coastal areas. Marine debris, 

in the form of derelict fishing gear, can reduce the structural complexity of habitats and devastate benthic organisms. Derelict gear can 

also smother and entangle both benthic and mobile fauna, including 

endangered species (Donohue et al. 2001, Chiappone et al. 2002a). 

Derelict gear can also create long-term entrapment mechanisms 

that continuously kill mobile fauna (e.g., fish, lobsters, sea turtles) for 

several years. Because net materials are constructed to be strong 

and resilient, they can persist in the environment for decades and 

prevent the escape of entangled wildlife. Angling is the predominant 

form of recreational fishing in the Florida Keys and most of the environmental impact to the benthos from derelict gear results from 

lost monofilament line, fishing wire, leaders, lead sinkers, and hooks; 

however, a large percentage of impacts also stem from lost stone 

crab and lobster traps (DiDomenico 2001, Chiappone et al. 2002a). 

Lost cage traps catch prey on a continuing cycle as predators enter 

the traps to feed on previously entrapped organisms that are dead 

or dying. Nets and traps, when combined with high wave energy, 

can also physically scrape organisms such as sponges and corals 

or sweep immobile invertebrates from sandy areas (Chiappone et al. 

2002a, Miller et al. 2010). 

In a recent study by Miller et al. (2010) of 145 hard-bottom and 

coral reef sites from northern Key Largo to Key West, surveys of 480 

belt transects comprising 77,500 square feet (7,200 square meters) 

of hard bottom and coral reef habitat yielded a total of 218 marine 

debris items, comprising 28 different items or combinations of items. 

Of these 28 diverse debris types, 10 were hook-and-line angling gear 

and five were lost lobster and crab trap gear. Debris was encountered 

on the seabed at 85% of the surveyed reef and hard-bottom sites, indicating the pervasive pattern of debris entangled in benthic habitats.

Military Use

Military use of the sanctuary includes surface and underwater 

activities. Under normal circumstances, pressures to sanctuary resources are related to conflicts and disturbances with marine life or 

benthic habitat, and disturbance of seabird roosting areas by aircraft. 

In the worst case, military pressures to sanctuary resources can include the direct and indirect effects of military aircraft crashes, possible grounding of military ships, jet fuel pipeline ruptures caused 

by storms, maintenance dredging of shipping channels or harbors, 

and habitat loss due to facility improvements or expansion. Military 

presence in the Florida Keys is detailed in the following paragraphs.

The U.S. Department of Defense (DOD) has played an important 

role in Monroe County (Florida Keys) since the early 1800s, when 

the federal government established a small naval operation in Key 

West to control piracy in nearby waters. The DOD currently maintains several sites in the Keys, including the largest unencumbered 

airspace available for training on the East Coast. Although all of the 

military departments are represented in the region, the Navy’s presence is the most significant.

The Navy’s location in the Keys has international significance, as 

it maintains the closest military installation in the continental United 

States to Cuba, Central and South America, and the Caribbean. All 

of the Navy’s facilities are in the lower Keys, with the majority in Key 

West. The largest is the Naval Air Station Key West (NAS Key West) 

on Boca Chica Key (Monroe County Board of County Commissioners 1986). Key West harbor, including piers at Trumbo Point Annex 

and the Truman Annex, is also the site of the only active Navy facility 

within the sanctuary, where Navy vessels conducting operations in 

the area are berthed, and where naval acoustic research vessels 

conduct operations. Fuel deliveries and other logistical actions are 

also conducted to support training and operations. The Navy recently 

needed to restore to original capability as well as modernize and 

update its infrastructure and facilities to provide both improved and 

additional capabilities essential to support aircraft squadrons and 

ships visiting at NAS Key West. The modernization was completed 

by 2006 and required maintenance dredging of the main shipping 

channel into Key West and Truman Harbor, and refurbishing seawalls and mole piers. 

NAS Key West’s fuel supplies come by sea by way of Key West’s 

main shipping channel. One Military Sealift Command (MSC) tanker 

every eight to 12 weeks delivers aviation fuel. Diesel is delivered 

solely via tanker truck to U.S. Coast Guard Sector Key West two to 

three times per year. The Key West Pipeline Company owns three 

tender tanks for receipt and storage of aviation fuel and a pipeline 

that runs between Trumbo Point Annex and Boca Chica Field. The 

pipeline is four inches in diameter and approximately seven miles of 

it runs underwater in the sanctuary. 

The U.S. Army operates the U.S. Army Special Forces Combat 

Divers School in Key West. They parachute into the sanctuary at 

Shark and Sand Key Drop Zones, and occasionally into other areas 

of the Gulf. 

The Coast Guard (Department of Homeland Security) also maintains a significant presence in the region. It has five primary missions: search and rescue, law enforcement, marine safety, marine 

environmental protection, and the operation and maintenance of 

navigational aids (e.g., channel markers, navigational lights, and 
Pressures on Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 33

lighthouses). Because of these responsibilities and the vast expanse 

of waters along the Keys, the Coast Guard provides an important 

public function in the sanctuary. It is responsible for more than 560 

miles (900 kilometers) of coastline and 34,170 square miles (88,500 

square kilometers) of ocean area, and typically has several vessels 

and over 600 personnel located at three stations (Islamorada, Marathon, and Key West) in the area. The largest vessels operate out of 

Trumbo Annex in Key West. 

The U.S. Air Force operates a Tethered Aerostat Radar System 

(TARS) at Cudjoe Key for aerial surveillance radar. The system is 

designed to detect low-altitude aircraft, providing detection and monitoring capability in the Florida Straits and a portion of the Caribbean. 

The TARS surveillance data are used to support customs and border 

protection.

Pressures to Maritime Archaeological Resources

As modern underwater technology such as scuba gear, metal 

detectors and remote-sensing devices are developed, both professional and amateur treasure hunters are able to improve their search 

for lost and submerged maritime archaeological resources (Gerard 

1992). For the purposes of this report, three general types of treasure salvors were categorized, each assumed to exert different (but 

unquantified) levels of pressure on these resources: 1) souvenir collectors/hobbyists who combine the search for treasure with their recreational diving activities; 2) paraprofessionals who hunt for treasure 

on a regular part-time basis, but for whom treasure salvage is not 

their primary source of income or full-time job; and 3) professional 

treasure hunters whose search, recovery, sale and display of recovered items is a full-time endeavor and primary source of income. 

While not a common practice, the development of propeller-wash 

deflection devices (e.g., “mailboxes”) have enabled professional 

treasure hunters to excavate crater-like holes in the seafloor, allowing the discovery of shipwreck materials more than 20 feet (6 meters) 

below the surface on the seabed. Indiscriminate use of mailboxes 

can cause significant damage to natural resources as well as cultural 

resources, including reducing the quality and amount of contextual 

information. In addition, recreational wreck divers may illegally remove resources from a deepwater shipwreck to keep as a souvenir. 

Although the degree to which looting occurs is not quantified, the 

cumulative impacts of this activity can affect the condition of wrecks. 
State of Sanctuary Resources

34 Florida Keys CONDITION REPORT 2011

This section provides summaries of the conditions and trends within four resource areas: water, habitat, living resources, and maritime 

archaeological resources. For each, sanctuary staff and selected outside experts considered a series of questions about each resource 

area. The set of questions is derived from the Office of National Marine Sanctuaries’ mission, and a system-wide monitoring framework 

(NMSP 2004) developed to ensure the timely flow of data and information to those responsible for managing and protecting resources in 

the ocean and coastal zone, and to those that use, depend on, and study the ecosystems encompassed by the sanctuaries. The questions address information needs that are common to nearly all sanctuaries throughout the sanctuary system. Appendix A (Rating Scheme for System-Wide Monitoring 

Questions) clarifies the set of questions and presents statements that were used to judge the status and assign a corresponding color code on a scale 

from “good” to “poor.” These statements are customized for each question. In addition, the following options are available for all questions: “N/A” – the 

question does not apply; and “undetermined” – resource status is undetermined. In addition, symbols are used to indicate trends: “ ▲” – conditions 

appear to be improving; “▬” – conditions do not appear to be changing; “ ▼” – conditions appear to be declining; and “?” – the trend is undetermined. 

This section of the report provides answers to the set of questions. Despite a large diversity in habitat types and communities within the 

Florida Keys sanctuary, a single, sanctuary-wide status and trend rating is given for each question. Although the ratings are generalized for 

the entire sanctuary, text found in the following section provides a detailed description of the basis for judgment for each question, and may 

include recognition and description of any conditions that are not consistent with the rating. Answers are supported by specific examples of 

data, investigations, monitoring and observations, and the basis for judgment is provided in the text and summarized in the table for each 

resource area. Where published or additional information exists, the reader is provided with appropriate references and Web links.

Judging an ecosystem as having “integrity” implies the relative wholeness of ecosystem structure and function, along with the spatial and 

temporal variability inherent in these characteristics, as determined by the ecosystem’s natural evolutionary history. Ecosystem integrity is 

reflected in the system’s ability to produce and maintain adaptive biotic elements. Fluctuations of a system’s natural characteristics, including 

abiotic drivers, biotic composition, complex relationships, and functional processes and redundancies are unaltered and are either likely to 

persist or be regained following natural disturbance. 

State of Sanctuary Resources
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 35

Figure 23. Mean tide measurements from tide station KYWF1 - 8724580 at Key West harbor. The mean sea level 

trend is +2.24 millimeters/year with a 95% confidence interval of +/- 0.16 mm/yr based on monthly mean sea level 

data from 1913 to 2006 which is equivalent to a change of 0.73 feet in 100 years. 

Source: NOAA Coral Reef Watch

Figure 22. Annual Pathfinder satellite sea surface temperature from eleven 31 mile (50 kilometer) pixels in Florida Bay and around the Florida Keys from 1985 - 2006. Annual maximum SST has a slope = +0.29 °C/decade 

(p=0.014). Annual mean SST shows no trend. Mean minimum SST has a slope = -0.66 °C/decade (p<0.001).

Photo: NOAA

Water

The following information provides an assessment by sanctuary 

staff and experts in the field of the status and trends pertaining to the 

current state of water quality in Florida Keys National Marine Sanctuary:

1.	 Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water quality and how are they changing? 

An increasing number of stressors to water quality over the last 

several decades may cause measurable but not severe declines in living resources and habitats. For this reason, the rating 

for this question is “fair.” The trend 

is rated as “declining” because 

stressors affecting water quality 

in the sanctuary have been increasing since its establishment, 

and the predicted effects of global 

climate change are likely to exacerbate conditions via changes 

in storm frequency and intensity, 

upwelling frequency and duration, 

changing variability of seawater 

temperature (Figure 22), sea level 

rise (Figure 23), and other changes to oceanographic patterns and 

ocean chemistry.

Climate and weather affect 

water quality through winds and 

storms, precipitation, evaporation, 

surface water input, sea level and 

tides, and “boundary” currents 

(e.g., Loop and Florida Currents), 

all of which play an important 

role in the ecosystem dynamics 

of Florida Bay and the sanctuary. During the last half-century, 

regional water management practices have evolved to temper the 

way climate and weather affect 

human health and well-being. 

However, water management during this time has also had direct 

and indirect impacts on nearshore 

water quality within the sanctuary. In the latter third of the 20th 

century, it was recognized that 

flood control modifications to the 

drainage of fresh water in the south Florida region resulted in 

serious environmental effects due to altered water delivery into 

the surrounding estuarine system, specifically Florida Bay. Although some freshwater flow is currently being restored (via the 

Comprehensive Everglades Restoration Plan, as approved and 

amended in the Water Resources Development Act of 2000), it 

can never be restored to its native state due to the needs of the 

surrounding human population.

Depending on the geographic scale at which water quality within the sanctuary is considered, monitoring results show 
State of Sanctuary Resources

36 Florida Keys CONDITION REPORT 2011

Figure 24. Fifteen year cumulative dissolved inorganic nitrogen (DIN) concentrations in the Florida Keys. Box plots show data distribution and median (line).

Source: Boyer and Briceño 2009

there are distinct regional and smaller-scale patterns in water 

chemistry, some of which are addressed in Question 2. However, in response to this question, we describe and qualify the 

state of water quality stressors in the sanctuary as a whole, as 

opposed to separating the various geographic and hydrographic 

areas of the Florida Keys and their individual states. Detailed 

water quality information for specific areas of the sanctuary can 

be found in several references (MACTEC 2003, Hunt and Nuttle 

2007, Boyer and Briceño 2009). Generally, we know that the 

individual “state” of residential canal water tends to have low dissolved oxygen levels, high hydrogen sulfide content, and higher 

potential for nutrient loading in comparison to the adjacent nearshore waters that have better flushing and flow regimes. In turn, 

areas of nearshore waters may have eutrophic signals that attenuate further offshore where regional water flows have more 

substantial influences. The sanctuary is directly influenced by 

the Florida Current, the Gulf of Mexico Loop Current, inshore 

currents of the Southwest Florida Shelf (Shelf), discharge from 

the Everglades through the Shark River Slough, and by tidal 

exchange with both Florida Bay and Biscayne Bay (Lee et al. 

1994, Lee et al. 2002). Thus, not all influences on water quality 

originate from sources within the Florida Keys. Likewise, Boyer 

and Briceño (2009) point out that trends observed at smaller (local) scales may also occur across the whole region but at more 

damped amplitudes. This spatial autocorrelation in water quality 

is an inherent property of highly interconnected systems such as 

coastal and estuarine ecosystems driven by similar hydrological and climatological forcings. There have been large changes 

in the sanctuary’s water quality over time, and some sustained 

monotonic trends have been observed over the last 15 years. 

However, trend analysis is limited to the window of observation; 

trends may change, or even reverse, with additional data collection (Wagner et al. 2008, Boyer and Briceño 2009). 

Finally, during the last 100 years, the Florida Keys island 

chain has been physically altered to accommodate passenger 

trains and vehicles by filling in island passes to create highways 

and railroad beds. This alteration has permanently affected the 

flushing dynamics (e.g., oceanographic processes) between the 

four prominent water bodies adjacent to the sanctuary. With the 

exception of new bridge construction in upper Key Largo, where 

flow between water bodies is being enhanced, most altered flow 

in the Keys is unlikely to change in the immediate future. 

2. What is the eutrophic condition of sanctuary waters 

and how is it changing? Water quality in the sanctuary is 

influenced by waters emanating from freshwater and estuarine 

habitats near the Florida Everglades, shallow nearshore areas, 

and deeper (>100 m) offshore areas. Distinguishing internal from 

external sources of nutrients in the sanctuary is a difficult task, 

and the finer discrimination of internal sources from external natural and anthropogenic inputs is even more difficult. Regardless 

of the source(s), enough evidence exists to rate this question as 

“fair/poor” because selected conditions have caused or are likely 

to cause severe declines in some but not all living resources and 

habitats. The trend is rated as “not changing” because results of 

the sanctuary’s long-term water quality monitoring program do 

not suggest eutrophic conditions are changing at large spatial 

scales at this time (Boyer and Briceño 2009). 

A large-scale water quality monitoring program was established in the sanctuary in 1995 and provides quarterly sampling 

of a suite of 18 variables at 155 stations in the sanctuary, extending from the southern boundary of Biscayne National Park 

to the Dry Tortugas. Several important results have been obtained from this project. First, elevated nitrate has been documented in the inshore waters of the Florida Keys (Figure 24) 

since the first sampling event in 1995 and continues to be a 

characteristic of the ecosystem. Interestingly, this nitrate gradient was not observed in a comparison transect from the Dry 

Tortugas (where there is minimal human impact), thus the nitrate 

distribution implies a localized, land-based source, which is diluted by lower-nutrient waters of the Atlantic Ocean. Sampling 

studies also show that there is a similar gradient in total organic 

carbon as well as a decrease in the variability of salinity moving 

offshore, further supporting the theory that the source is localized and land-based. There have been no reported trends in either total phosphorous or chlorophyll-a with distance from land. 

Second, the highest chlorophyll-a concentrations, which are 

indicative of phytoplankton in the water column, are present on 
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 37

the southwest Florida Shelf and diminish gradually towards the 

Marquesas and Dry Tortugas (Figure 25). Water with higher total 

phosphorus concentrations from the shelf is carried south along 

the southwest coast of Florida, where it fuels the phytoplankton 

blooms in the region (Boyer and Briceño 2009). 

Generally, trends in most measured nutrient variables since 

1995 show relative consistency from year to year, with some exhibiting seasonal variations. Overall, Boyer and Briceño (2009) 

found that there were statistically significant decreases in dissolved inorganic carbon, total organic nitrogen (except for increases in the Tortugas), total phosphorus, total organic carbon, 

and dissolved oxygen throughout the region. This is contrary to 

some of the trend analyses reported in previous years. Most of 

the important local anthropogenic inputs are regulated and controlled by management activities; other studies have shown that 

nutrients from shallow sewage injection wells may be leaking 

into nearshore surface waters (Corbett et al. 2000). There have 

been large changes in sanctuary water quality over time, and 

some sustained monotonic trends have been observed; however, trend analysis is limited to the window of observation, and 

trends may change, or even reverse, with additional data collection. Thus, when looking at what are perceived to be local 

trends it also seems to occur across the whole region but at 

more damped amplitudes (Boyer and Briceño 2009). 

Large, persistent cyanobacterial blooms originating in 

Florida Bay have been associated with sponge die-offs (as well 

as seagrass die-offs) and the associated community dependent 

upon them (Butler et al. 1995, Fourqurean and Robblee 1999, 

Hunt and Nuttle 2007). These blooms are not necessarily triggered or sustained by a single change in nutrient load, but rather 

reflect a combination of multiple biotic and abiotic factors that 

contribute to their intensity and duration. Unfortunately, we do 

not have sufficient data at this time to predict cyanobacterial 

bloom initiation or longevity, thus there is a need to integrate 

existing biological, climatological, and oceanographic research 

efforts so that predictive models can be further developed and 

refined to support management decisions for control efforts.

It is clear that trends observed within the sanctuary are 

influenced by regional conditions outside the sanctuary boundaries (Boyer and Briceño 2009). Nutrients originating north of 

the sanctuary on the Gulf side of Florida may have increased 

the size and persistence of various harmful algal blooms (ranging from red tides to black-water events). As these phenomena 

have been correlated with fish kills and seagrass die-offs, their 

increasing geographic influence could put resources at risk that 

have not been so previously (including those on the ocean side 

of the Florida Keys). 

3. Do sanctuary waters pose risks to human health and 

how are they changing? Harmful algal blooms (e.g., red 

tides), fecal coliform and enterococci bacteria, and ciguatera 

fish poisoning have the potential to affect human health in the 

sanctuary, thus the rating for this question is “fair” because selected conditions have resulted in isolated human impacts, but 

evidence does not justify widespread or persistent concern in 

addition, the trend is rated as “not changing” because there is 

no evidence to suggest conditions are changing at this time.

Depending on the geographic scale considered, some small 

patterns in human health emerge. However, for the purposes of 

this question, we describe and qualify the state of sanctuary waters on human health as a “whole,” as opposed to separating the 

various geographic/hydrographic areas of the Florida Keys and 

their individual status. As outlined in Question 1, water quality in 

most residential canals is poor (small-scale, local) when comFigure 25. Fifteen-year medians of cholrophyll-a (A) and total phosphorus median concentrations (B) in the Florida Keys and the west Florida shelf.

Source: Boyer and Briceño 2009

A B
State of Sanctuary Resources

38 Florida Keys CONDITION REPORT 2011

4

A joint venture between the Mote Marine Laboratory and the Florida Keys National Marine Sanctuary, the Marine Ecosystem Event Response and Assessment Project (MEERA) is designed to provide early detection and assessment of biological events occurring in the Florida Keys and surrounding waters. 

The goal of the project is to help the scientific community better understand the nature and causes of marine events that adversely affect marine organisms, and assist ongoing research efforts to assess and monitor events as they develop. Understanding these events will help scientists and managers 

determine whether such events are natural or linked to human activities (www.mote.org/MEERA).

pared to nearshore and oceanic waters (large-scale, regional). 

Thus swimming in residential canal water may pose risks to 

human health (e.g., result in gastroenteritis). The same is true 

for swimming in areas of residential canal outflows. In addition, 

during the “Swim Around Key West” event in 1999, 30% of swimmers reported at least one symptom of a waterborne disease 

and 20% reported two or more symptoms (Nobles et al. 2000). 

However, nearshore and offshore waters are not considered to 

pose risks to human health.

As described in the “Pressures” section of this document, 

harmful algal blooms (HABs) have increased in frequency 

within the last few decades (Harvell et al. 1999). Though no 

cases of human illness have been documented in association 

with the consumption of fish during Florida red tide blooms (Abbott et al. 2009b), fishes exposed to red tides can concentrate 

brevetoxin in their viscera, but levels in the muscle tissue do 

not suggest a health risk to humans. Notably, sanctuary waters 

had high concentrations of the microscopic alga that causes 

red tide on offshore reefs during the 2009 and 2010 red tide 

“seasons” (MEERA4

), which is the first documented occurrence 

of this phenomenon.

Periodic swim advisories and warnings are issued 

by the Florida Department of Health due to the presence of pathogen indicators (enterococci and fecal 

coliform bacteria). High concentrations of these bacteria and viruses may indicate the presence of microorganisms that could cause gastrointestinal distress, 

disease, infections, or rashes in people swimming in 

nearshore waters (Nobles et al. 2000). Advisories and 

warnings are common at some locations in Monroe 

County, specifically at South and Higgs Beaches in Key 

West, which have the highest frequencies of warnings 

issued per beach since weekly testing began in 2003 

(Figure 26). Swim advisories and warnings pertain to 

very specific areas and the nearshore waters adjacent 

to them. Therefore, the advisories reflect water quality 

conditions in specific areas and do not reflect risks to 

human health throughout the entire sanctuary. 

Ciguatera fish poisoning (CFP) occurs throughout the tropical Pacific and the Caribbean. CFP is a 

reportable disease in Florida (Chapter 64D-3, Florida 

Administrative Code) (Abbott et al. 2009b). Reported 

CFP cases in Monroe County are rare, with the most recent case 

in 2006. However, it is well documented that certain fishes such 

as grouper, moray eel, jacks, kingfish, snapper, hogfish (Lachnolaimus maximus) and barracuda (Sphyraena barracuda) are 

more prone to be ciguatoxic due to their position in the food chain 

and large adult size (de Sylva 1994, Abbott et al. 2009a). While 

CFP is an issue regionally and has been reported locally in the 

Florida Keys, there is no evidence that the incidence of ciguatera 

is increasing in the sanctuary. 

4.	 What are the levels of human activitiesthat may influence water quality and how are they changing? Water 

quality within the boundary of the sanctuary is affected by a combination of regional oceanographic patterns, climatology, and regional and localized anthropogenic influences. As discussed in the 

“Site History” and “Pressures” sections of this document, during 

the last century destructive activities (e.g., dredge and fill, untreated storm water, discharge of poorly treated sewage) have been 

widespread throughout the region, thus the rating for this question 

is “fair/poor” because many human activities have caused or are 

likely to cause severe impacts, and cases to date suggest a pervaFigure 26. Swim advisories issued in southern Florida. Pie charts represent the mean 

annual proportion of time per condition per beach from 2003 to 2009. Red indicated swim 

advisory was issued and green indicated no swim advisory issued.

Source: Florida Department of Health; Map created by: NOAA/FKNMS
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 39

sive problem. However, the trend is rated as “improving” because 

management responses are addressing the widespread, pervasive problems, leaving issues that are more localized. 

As stated previously, the degree to which human activities 

influence water quality depends on the scale under consideration. At smaller, localized scales, water quality in the Keys has 

been affected by the dredging of dead-end residential canals. 

Most of these canals have poor flushing because of the way they 

were constructed. Depending on wind and currents, these residential canals accumulate seagrass “wrack” which depletes dissolved oxygen during decomposition and increases the level of 

nutrients and hydrogen sulfide gas in the water. Hydrogen sulfide 

gas is toxic and residences near heavily polluted canals may be 

at risk. Furthermore, residential canals receive additional nutrient 

and chemical loading via stormwater runoff. At larger, regional 

scales, island passes that were filled in to create highways and 

railroad beds have permanently altered the flushing dynamics 

(e.g., oceanographic processes) between the four prominent 

water bodies adjacent to the sanctuary. 

In addition to the human activities stated in Question 1 (e.g., 

flood control modifications, runoff, highway/railroad construction), another that affects water quality is mosquito control. The 

Florida Keys are subtropical in climate and subject to mosquitoborne pathogens like West Nile virus, Dengue fever and viral 

encephalitis. Successful application of insecticides from both airborne platforms and vehicles is subject to climatological conditions. In the past, the Florida Keys Mosquito Control District used 

thermal fogging to apply pesticides (specifically adulticides). The 

pesticide was diluted with diesel oil and either passed through 

the engine of the plane or through a blower applicator mounted 

in the back of a truck. This delivery process produced a thick 

cloud of smoke easily observed by residents. It also produced a 

certain level of pollution due to the fumes of the diesel oil. Now 

the district uses ultra-low volume applications, in which a very 

small amount of pesticide is used to achieve the same results 

while eliminating pollution caused by the diesel oil carrier. 

Nevertheless, though most insecticides are successfully 

delivered to their target, nearshore waters of the sanctuary 

are still susceptible to over-spraying, insecticide runoff, and 

sublethal and lethal effects on non-target organisms (i.e., other 

invertebrates that are harmed by the poisons used). The Florida 

Water Quality Status & Trends

# Issue Rating Basis for Judgment Description of Findings

1 Stressors ▼

Large-scale changes in 

flushing dynamics over 

many decades have 

altered many aspects of 

water quality; nearshore 

problems related to 

runoff and other watershed 

stressors; localized 

problems related to 

infrastructure.

Selected conditions 

may inhibit the 

development of assemblages and may 

cause measurable but 

not severe declines in 

living resources and 

habitats.

2 Eutrophic 

Condition —

Long-term increase in 

inputs from land; large, 

persistent phytoplankton 

bloom events, many of 

which originate outside the 

sanctuary but enter and 

injure sanctuary resources.

Selected conditions 

have caused or 

are likely to cause 

severe declines in 

some but not all 

living resources and 

habitats.

3 Human 

Health —

Rating is a general assessment of “all waters” 

of the sanctuary, knowing 

that in very specific 

locations, the rating could 

be as low as “poor.” 

Increased frequency of 

HABs and periodic swim 

advisories.

Selected conditions 

have resulted in isolated human impacts, 

but evidence does 

not justify widespread 

or persistent concern.

4 Human 

Activities ▲

Historically, destructive 

activities have been 

widespread throughout 

the Florida Keys, but 

many recent management 

actions are intended to 

reduce threats to water 

quality.

Selected activities 

have caused or are 

likely to cause severe 

impacts, and cases 

to date suggest a 

pervasive problem.

Status: Good Good/Fair Fair Fair/Poor Poor Undet.

Trends: Improving (p), Not Changing (–), Declining (q), 

Undetermined Trend (?), Question not applicable (N/A)

Keys Mosquito Control District has a research program focused 

on basic and applied aspects of mosquito biology and control; 

however the impacts of mosquito spraying on non-target marine organisms need further research. The Fish and Wildlife 

Research Institute has conducted research that demonstrates 

that mosquito control pesticides are detrimental to queen conch 

(McIntyre et al. 2006, Glazer et al. 2008). 
State of Sanctuary Resources

40 Florida Keys CONDITION REPORT 2011

Habitat

The following information provides an assessment by sanctuary staff 

and experts in the field of the status and trends pertaining to the current 

state of marine habitats in Florida Keys National Marine Sanctuary:

5. What are the abundance and distribution of major

habitat types and how are they changing? Generally, 

at larger spatial scales, nearshore habitats are still present in the 

geographic areas they occupied through the history of the sanctuary, which suggests the abundance and distribution of the coral, 

seagrass, and hard-bottom habitat types in the sanctuary have 

changed little over the last 20 years. With the exception of the 

water column realm, the major habitat types in the sanctuary are 

benthic and biogenic in nature and are defined by dominant fauna 

or flora: coral reefs, seagrass meadows, hard-bottom communities 

(a mix of hard corals, gorgonians and sponges), and mangrove 

habitats. In order to answer this question, the absolute “number” 

and the “geographic extent” of the major habitat types found in the 

sanctuary were examined. Questions 6, 9, 12, and 13 of this report 

will address the “health and condition” of these biogenic habitats. 

With this in mind, the response to this question is rated “good/

fair” because selected habitat loss or alteration has taken place 

(principally due to nearshore development), precluding full development of living resource assemblages, but it is unlikely to cause 

substantial or persistent degradation in living resources or water 

quality. The trend is rated as “not changing” because there is no 

evidence to suggest that the conditions that affect the abundance 

and distribution of all habitat types are changing significantly. 

During the 20th century, nearshore habitat alteration in the 

Florida Keys was extensive, with much of the physical alteration 

occurring from the 1950s through the 1970s to support the growing human population. During that period, many acres of tropical 

hardwood hammocks were cleared to provide land for housing 

and commercial development. The attractiveness of waterfront 

development prompted the creation of “fastland” through dredging and filling of mangrove forests and seagrass beds to construct networks of finger-fill residential canals. Approximately 

50% of the historic mangrove habitat has been eliminated. More 

than 200 canals and access channels were dredged during that 

period (FDER 1987, Kruczynski and McManus 2002). Turbidity from the dredging and filling operations smothered adjacent 

areas of hard-bottom and seagrass habitats (MACTEC 2003). 

The sanctuary encompasses over 2,800 square nautical 

miles and encompasses a majority of the archipelago of the 

Florida Keys. Recently, efforts have been made to accurately 

map the abundance and distribution of habitat types at a finer 

scale. In 1998, NOAA and the FWC’s Fish and Wildlife Research 

Institute released habitat maps for the Florida Keys (Figure 27), 

representing the first large-scale effort to accurately map coral 

ecosystem habitats in the Florida Reef Tract, from Biscayne Bay 

to the Dry Tortugas (http://flkeysbenthicmaps.noaa.gov). The 

1998 NOAA and FWC effort was a duplication of a 1970s effort 

to map the basic habitat of the Keys (Marszalek et al. 1977), but 

utilized more advanced technology. Habitats were delineated 

based on visual interpretation of 450 aerial photographs collected in 1991 to 1992 (FFWCC et al. 1998). The atlas was revised 

in 2000, but because it has large areas of unmapped seafloor, 

a new mapping effort is underway to address this shortcoming. 

The sanctuary has also benefited from highly detailed 

bathymetric maps of portions of the Florida Reef Tract produced 

by partnerships between USGS, NASA, and the NPS (using LiDAR technology; http://ngom.usgs.gov/dsp/pubs/ofr/index.html) 

and from multi-beam sonar surveys performed by the NOAA 

ship Nancy Foster. In spite of these combined efforts, more 

than 50% of the sanctuary remains to be adequately mapped. 

As of 2009, a higher proportion of nearshore areas (< 150 feet 

in depth) were mapped in comparison to deeper areas, thus 

limiting the ability to quantitatively estimate the abundance and 

distribution of sanctuary.

6. What is the condition of biologically structured habitats and how is it changing? Marine life depends on the 

integrity of its habitats, and that integrity is largely determined by 

the condition of particular living organisms. Coral reefs may be 

the best known examples of such biologically structured habitats. 

Not only is the substrate itself biogenic, but the diverse assemblages residing within and on the reefs depend on and interact 

with each other in tightly linked food webs. Based on results from 

multiple long-term monitoring programs within the sanctuary and 

separate, focused research projects, this question is rated as 

“fair/poor” because selected habitat loss or alteration has caused 

Figure 27. Nearshore habitat types in the sanctuary were mapped based 

on visual interpretation of aerial photography and hyperspectral imagery.

 Source: NOAA NCCOS and FWC
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 41

or is likely to cause severe declines in some but not all living 

resources or water quality. In addition, evidence suggests conditions appear to be “declining.” 

Coral habitats throughout the sanctuary have been in decline 

since the late 1970s, principally due to white-band disease and 

several bleaching events (Dustan and Halas 1987, Jaap 1988, 

Porter and Meier 1992). Prior to Caribbean-wide coral decline, 

many reef areas displayed a zonation pattern dominated by three 

scleractinian coral species: elkhorn coral, staghorn coral, and 

boulder corals of the genus Montastraea (Jackson 1992). Populations of elkhorn and staghorn coral underwent a region-wide 

decline during the 1980s and 1990s, with losses of 95% or more 

in some areas, principally due to white-band disease and locally 

due to storm damage (Figure 28; Gladfelter 1991, Bythell et al. 

1993, Aronson and Precht 2001, Gardner et al. 2003). Some scientists have suggested that the loss of these species may have 

led to increases in algae, reduced rates of reef accretion, and 

erosion of the reef framework (Aronson and Precht 2001). 

In 1995, the Florida Keys Coral Reef Evaluation and Monitoring Project (CREMP) was initiated to provide data on status 

and trends of hard-bottom and coral reef habitat in the Florida 

Keys. This long-term monitoring of nearshore coral habitats indicates both a decline in coral species richness and coral cover at 

the stations surveyed. Since the first monitoring event in 1996, 

mean species richness has declined sanctuary-wide, with an 

average loss of two species per survey station. This loss is attributed to a significant decline in the presence of 13 of the 46 

species reported for the sanctuary, perhaps most importantly 

boulder coral (Montastraea spp.). Similarly, the percent of stony 

coral cover declined from 12.7% to 6.6% sanctuary-wide (Figure 29), most precipitously from 1996 to 1999 (falling from 12.7 

% to 7.9%). Between 1996 and 2008, coral cover reached its 

lowest level in 2006 (6.4%) and has remained relatively similar 

since. For example coral cover was 6.6% in 2008 (Ruzicka et 

al. 2010). However, it is noted that these data have an inherent 

bias in that the study sites do not encompass all the diverse 

hard-bottom and coral reef habitats that vary in topographic 

complexity, depth, cross-shelf position, geological development 

and ecological history within the sanctuary.

For example, a complementary sanctuary-wide monitoring 

program conducted by University of North Carolina, Wilmington 

since 1998 corroborates some of the findings presented in the previous two paragraphs, with the following notable exceptions. Many 

areas, especially patch reefs and the deeper fore-reef environment, 

continue to exhibit relatively high cover (>25%) by reef-building corals. Low-relief, hard-bottom areas, which tend to be dominated by 

turf algae, sponges and gorgonians, have exhibited little change in 

over 10 years of surveys. Although declines in the number of corals 

are apparent for certain habitats, this is not a universal pattern (see 

Table 3 in Rutten et al. 2009), indicative of the high degree of spatial 

and temporal variability of hard-bottom and coral reef habitats in the 

Florida Keys (Miller et al. 2002, Rutten et al. 2009).

Figure 28. Mean annual percent cover for the four major benthic taxa recorded in CREMP image analysis. Mean percent cover is pooled from 97 

stations in the Florida Keys excluding the Dry Tortugas stations. A mixed 

model regression indicates a decreasing trend for stony corals and sponges (p<0.001), an increasing trend for octocorals (p<0.001), and no trend 

for macroalgae (p>0.05). 

Source: Ruzicka et al. 2010

Figure 29. Change in percent coral cover across the Caribbean basin 

during the past three decades. By the time the Water Quality Protection 

Program began in 1995, there was already extensive decline in coral 

cover throughout the region, principally due to coral and urchin diseases, 

bleaching events, and storms. Annual coral cover estimates (triangles) are 

weighted means with 95% bootstrap confidence intervals. Also shown are 

unweighted mean coral cover estimates for each year (solid circles), the 

unweighted mean coral cover with the Florida Keys Water Quality Protection Program’s Coral Monitoring Project (1996–2001) omitted (x), and the 

sample size (number of studies) for each year (o).

Source: adapted from Gardner et al. 2003

White Band Disease

Bleaching

Bleaching

Diadema Dieoff

FKNMS
State of Sanctuary Resources

42 Florida Keys CONDITION REPORT 2011

Figure 30. Map of permanent, long-term seagrass monitoring stations 

depicting where Thalassia testudinum is decreasing (red) in relative importance (showing signs of increasing nutrification), where it is becoming more 

dense (showing initial signs of increasing nutrification) shown in yellow, 

and where there has been no change (green).

Source: Fourqurean 2008

The seagrass beds that carpet most of the south Florida 

shelf, including the sanctuary, are part of the largest documented contiguous seagrass beds on Earth (Fourqurean et al. 2002). 

Seagrass habitats have been monitored as part of the Water 

Quality Protection Program since 1995. These extensive meadows are vital for the ecological health of the sanctuary and the 

marine ecosystems of all of south Florida. This seagrass monitoring program has yielded evidence showing more widespread, 

long-term changes in the seagrass communities at stations that 

are annually surveyed. These changes are consistent with model predictions of nutrient-induced changes of these systems. 

Although no significant overall loss of seagrass coverage in 

the sanctuary has occurred since monitoring began, there have 

been significant changes in the species composition of seagrass 

communities. For example, 13 of the 30 permanent monitoring 

stations exhibited shifts in the dominant species of seagrass, 

which points to increasing nutrient availability at those sites. In 

other words, slower-growing species (i.e., turtle grass, Thalassia testudinum) are being replaced by faster-growing species 

(i.e., shoal grass, Halodule wrightii) (Figure 30). Three of the 30 

permanent monitoring stations were buried by sand and have 

remained so since Hurricane Georges in 1998. The spatial pattern of changes and the agreement of the changes with models 

of the system suggest that there is regional-scale change in nutrient availability that is causing changes in seagrass beds over 

a wide portion of the sanctuary (Fourqurean 2009). 

From 1987 to 1991, a significant seagrass die-off occurred in 

Florida Bay (Robblee et al. 1991, Zieman et al. 1999). It is not completely understood what caused this event, however salinity, nutrient conditions, and light levels are thought to be potential causes. 

Following the seagrass die-off, an algae bloom occurred, followed 

by sponge die-off (Butler et al. 1995, Hunt and Nuttle 2007). 

Injuries to seagrass caused by small boats are also a chronic problem. Monroe County has approximately 30,000 acres of 

significantly scarred seagrass beds, more than any other county 

in Florida. Most propeller scarring is due to the actions of inexperienced or careless boaters. Propeller damage not only destroys 

the seagrasses, but also results in a change in the hydrology of 

the bed from the altered movement of water through the channel within the scar. Propeller scars may take anywhere from two 

to 26 years to recover (censu Hammerstrom et al. 2007). If the 

prop scar is deep enough, it will require filling to allow rhizomes 

to grow across the un-vegetated gap (Kenworthy et al. 2002).

Many acres of coastal mangrove habitat have been lost 

from the Florida Keys due to historic and continuing shoreline 

development. Many canal communities were created by dredging areas dominated by mangroves and filling areas adjacent to 

the canal cuts to create land for development. Loss of mangrove 

habitat has severely reduced the ecosystem’s ability to filter 

runoff, thus causing an increase in nutrient export to adjacent 

waters. A healthy mangrove community is critical to stabilizing 

shorelines, sustaining economically important fisheries by providing nursery habitat, providing nesting and roosting sites for 

birds, and maintaining the character and beauty of the Florida 

Keys. Mangrove resources are vast and the trusteeship for 

these important communities is shared between the sanctuary 

and the FDEP. NOAA Fisheries Service also plays an important 

role in protecting mangrove habitat, which serves as essential 

fish habitat for managed fish species. Because there have been 

no comprehensive time-series studies of mangrove abundance 

and distribution throughout the Florida Keys (but see Strong and 

Bancroft 1994), sanctuary staff have identified this need in the 

Florida Keys National Marine Sanctuary Comprehensive Science Plan (2002), specifically to assess historic shoreline conditions using aerial photography and evaluate these data and develop priority restoration plans for mangroves in the sanctuary.

Coastal habitats are often drastically altered or compromised 

by the effects of hurricanes and associated strong winds, storm 

surges, flooding, and high-energy waves. For example, increases 

in hydrodynamic activity can compromise the structural integrity 

of reef zones by fracturing or dislodging corals. Sediment is often 

shifted and subsequently can bury corals or seagrasses. Storm 

surge and winds can uproot mangroves and modify beaches. In-
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 43

creased runoff resulting from heavy rains and wind can result in 

increased pollution (e.g., raw sewage, bacteria, pesticides, fertilizers, oil and gas spills, toxic chemicals, etc.) entering the system, 

thus making it difficult for corals and other habitat-forming biota to 

regenerate. Hurricanes can also increase the rate of erosion or 

result in land subsidence. To date, such effects of hurricanes in 

the sanctuary are estimated and anecdotal because only a few 

biological studies have been completed (see Fong and Lirman 

1994, Fong and Lirman 1995, Lirman and Fong 1997a, b).

Fishing gear and associated marine debris can have a detrimental effect on the condition of biologically structured habitats. 

For example, in 2010 500,000 lobster traps and 315,000 (commercial) stone crab traps licensed by the Florida Fish and Wildlife Conservation Commission (FWC) in the Florida Keys. Although routine 

trap placement and retrieval causes few, small injuries to sessile 

flora and fauna, only 34% of those injuries recover (Matthews et 

al. 2004). Furthermore, the FWC estimates that upwards of 20% of 

trap gear is “lost” annually (up to 100,000 traps), with even higher 

losses (>75%, such as during 2005) during active storm years. Because of their high number, long-term placement, and potential to 

move during storms, lost traps may have a chronic effect on sessile 

flora and fauna (Matthews et al. 2004).

The placement of illegal casitas (lobster attraction structures) 

and the subsequent lobster capture is common in the backcountry 

area north of the lower Keys. Casitas are usually constructed from 

materials such as concrete cinder blocks, tin roofing material and 

modified trash dumpsters. There is concern among wildlife management agencies that there could be detrimental effects to natural habitat and lobster population dynamics as a result of this type 

of debris. Placement of these structures on the seafloor violates 

sanctuary regulations and alters sanctuary habitats, and when disrupted by storms have the potential to damage marine resources. 

Furthermore, in a typical year, approximately 100 boats are 

abandoned in the Florida Keys. In addition to this number, the 

2004 and 2005 hurricane seasons caused more boats to be 

moved into sensitive habitats like seagrass beds and mangrove 

islands. After the 2005 hurricane season, Monroe County initially 

surveyed 355 vessels aground, but cleanup operations ultimately removed nearly 500 vessels from the water. A concerted effort 

to document the spatial extent, amount and impacts of marine 

debris in 2008 indicated derelict angling and trap gear is ubiquitous in the sanctuary, even within no-take zones. The sheer 

amount of debris recovered annually is testament to an increasingly visited and exploited marine ecosystem (Miller et al. 2008).

Vessel groundings in the Florida Keys occur regularly, and 

each impacts the benthic environment. The significance of these 

groundings, and associated restoration alternatives, was detailed 

in the Florida chapter of the “State of the Coral Reef Ecosystems 

of the United States and Pacific Freely Associated States: 2005” 

(Andrews et al. 2005). In the Florida Keys, the number of reported vessel groundings decreased annually from 2002 to 2006 

(from 721 groundings in 2002 to 301 in 2006). However, it is not 

possible to determine if this trend is a result of fewer boaters in 

the sanctuary, higher fuel costs, increased boater awareness, 

or a decreased willingness to call for assistance if boaters run 

aground. Generally, there has been no proportional shift in impact to different habitat types, with approximately 14% of groundings in coral reef habitats, an estimated 85% in seagrass and 

about 1% on hard bottom (Donahue et al. 2008). 

7. What are the contaminant concentrations in sanctuary habitats and how are they changing? Contaminants of 

concern that are addressed in this question include pesticides, pharmaceutical products, hydrocarbons, and heavy metals. Toxins that 

are produced by harmful algal blooms and other water quality parameters are addressed in other sections of this document. To date, 

there have only been a few studies (e.g., Glynn et al. 1989, Singh et 

al. 2010) investigating the effects of contaminants on marine organisms in the Florida Keys; therefore, little synthesis of information is 

possible at this time to indicate a) the geographic extent and spatial 

variation in concentrations of various contaminants, b) the temporal 

variability of these concentrations, and c) contaminant pervasiveness and toxicity to organisms. As a result, this question is rated as 

“undetermined” and similarly the trend is rated as “undetermined.” 

Although a comprehensive report on contaminants in the 

sanctuary is not available, it is known or suspected that:

■ Some nearshore waters of the Florida Keys are contaminated to an unknown extent from pharmaceuticals in sewage. 

Potential local sources of contamination include: solid waste 

and sewage disposal practices, marinas and live-aboards, 

seepage from municipal landfills, mosquito control programs, 

and surface water runoff (Rumbold and Snedaker 1999).

■ The practice of soaking wooden lobster traps in used engine oil, or similar products, prior to their deployment was 

outlawed in 1993. At that time, approximately 670,000 traps 

were fished statewide, with more than 90% of traps deployed 

in Monroe County (FWC Fishery Statistics); a wooden trap 

was estimated to soak up about a quart of oil. 

■ It is still common practice in the sponge fishery to use vegetable 

oil as a way to increase “visibility” through the surface of the water while poling for sponges (S. Donahue, FKNMS, pers. obs.).
State of Sanctuary Resources

44 Florida Keys CONDITION REPORT 2011

■ Of the more than 300 small-vessel groundings that occur each 

year in the sanctuary, a few are associated with fuel and shipboard chemical spills (e.g., lubricants, solvents, and paints). 

Over time, these spills dissipate or break down, but their constituent chemicals may remain in the habitat for years. 

■ Because of the Florida Keys’ proximity to a heavily used shipping lane, potential oil and other chemical spills from container ship and transport vessels remains a threat.

8. What are the levels of human activities that may influence habitat quality and how are they changing?

The level of human activity impacting sanctuary habitat quality 

is rated as “fair/poor,” because selected activities have caused 

or are likely to cause severe impacts, and cases to date suggest 

a pervasive problem. The trend is rated as “declining” because 

of continued impacts from a diversity of activities and increasing 

levels of visitation to the Keys. 

The Florida Keys and its environs have a long history (>100 

years) of exploitation, thus many of this historically abundant 

megafauna (e.g., green turtles) and habitats have already been 

severely altered or reduced. As a result, resource managers are 

conserving pieces of the former system. For example, green sea 

turtles once served an important role in maintaining seagrass habitat quality; however, these turtles were extensively hunted for food 

in the Keys before the 19th century and suffered drastic population 

declines (Jackson et al. 2001). Jackson et al. (2001) suggested 

herds of turtles cropped the turtle grass very short when grazing, 

which helped keep organic matter from accumulating in the sediments. This accumulation now fuels microbial populations and promotes low-oxygen conditions in the sediments beneath the plants. 

Manatees, which were also more abundant in the past, played a 

similar role in keeping the seagrasses cropped. Because people 

have hunted and depleted these key species to endangered status, seagrasses often become so overgrown that they shade the 

bottom habitat and start to decompose in place, thus making the 

seagrass susceptible to wasting disease (Robblee et al. 1991).

As was previously described, habitat destruction resulting 

from human population increases over the past century has resulted in a decline of mangroves, corals and seagrass. These 

losses have cascading impacts on other ecosystem services. 

The construction of the Overseas Highway, uncontrolled upland 

development (including dredge and fill operations), and shoreline hardening (via seawall construction) are further examples of 

human activities that have damaged habitat quality through the 

1970s. Although many of these activities still occur within the 

sanctuary boundaries, they are now highly regulated. 

Despite the fact that the human population in the Keys has 

decreased over the short term, coastal development and land 

use will continue to impact habitat quality. Urban runoff from 

nonpoint pollution sources can diminish water quality and transport pollutants to the marine environment. Illegal discharges 

also have the potential to increase nutrients in surrounding 

waters. Illicit discharges occurring outside sanctuary boundaries (e.g., as evidenced by tar balls) can introduce toxins to the 

nearshore environment. Other anthropogenically driven factors 

such as climate change, sea level rise and ocean acidification 

are large-scale issues that may also affect habitat quality.

Since the 1990s, fishing pressure from the commercial sector 

has decreased, although recreational and commercial fishing pressure continues to affect habitat quality. For example, damage to the 

benthic habitat can result when mobile fishing gear, such as trawl 

nets or traps, are utilized. Derelict fishing gear and other marine 

debris can also scar or destroy benthic habitat, such as reefs or 

seagrasses, when entangled or dragged on the sea floor (Donohue et al. 2001, Chiappone et al. 2005). In recent surveys, marine 

debris in the Florida Keys including derelict fishing gear has been 

recorded in similar or greater amounts when compared to surveys 

from the past ten years (Chiappone et al. 2005, Miller et al. 2010).

Surveys of marine debris, including derelict fishing gear, 

entangled on the seabed in hard-bottom and coral reef habitats 

have been conducted intermittently by UNCW during 2000-2001, 

2008, and 2010 in the Florida Keys (Chiappone et al. 2002a, 

2004, 2005). Earlier (2000-2001) surveys indicated that hookand-line gear, especially monofilament line, and remnant lobster 

traps, especially buoy lines, were the predominant debris items. 

Debris types causing the greatest degree of abrasion damage to 

sessile invertebrates such as sponges and corals were hook-andline gear (68%), especially monofilament line (58%), followed by 

debris from lobster traps (26%), especially rope (21%). A concerted effort to document the spatial extent, amount, and impacts of 

marine debris in 2008 indicated derelict angling and trap gear is 

ubiquitous in the sanctuary, even within no-take zones. The sheer 

amount of debris recovered annually is testament to an increasingly visited and exploited marine ecosystem (Miller et al. 2008). 

During 2008, a total of 686 pieces representing 59 different 

debris items or categories were recovered from 34,800 square 

meters (374,600 square feet) of sampled benthic habitat at 

145 sites from Key Largo to Key West, with 443 kilograms (980 

pounds) (wet weight) of debris removed. Of the 686 total debris 

items counted and retrieved, 363 (53%) items were hook-and-line 

gear (monofilament, wire leaders, hooks, lead sinkers, etc.), followed by 241 trap debris items (35%), and other debris (82 items, 

12%). A total of 156,515 feet (477.6 meters) of angling gear was 
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 45

measured and retrieved from the bottom, mostly represented by 

monofilament line and wire leader. Over 3,000 feet (940 meters) 

of trap rope, either free (not attached to something), or attached 

to wooden slats or metal gratings, was measured and retrieved. 

Hook-and-line gear was the most frequent category of marine debris in terms of the number of sites and number of items encountered. Lost angling gear is ubiquitous throughout the Florida Keys, 

and was present at 59% of the sites sampled. Mid-channel patch 

reefs (1.35 ± 0.49 items per 60square meters) and high-relief 

spur and groove (0.66 ± 0.15) yielded the greatest angling gear 

densities. No-fishing zones and corresponding reference areas 

were roughly similar in terms of lost hook-and-line gear densities 

for most habitats, and in several instances, angling gear densities 

were greater within sanctuary no-take zones. 

Lobster and crab trap debris was the second most frequent 

category of marine debris encountered in 2008 in terms of the number of sites present and the number of items retrieved. Trap debris 

consisted of rope, wooden slats, cement slabs, plastic pot openings 

and metal mesh trap grating, not including intact but un-buoyed 

traps on the seabed. The distribution of trap debris indicates that, 

like trap gear, it is ubiquitous throughout the Florida Keys in all of 

the habitats sampled (58.6% of sites). Nearshore habitats yielded 

greater densities than offshore habitats, and, similar to lost hookand-line fishing debris, no-take zones and reference areas were 

roughly similar in terms of trap debris for several of the habitat types.

Groundings by small vessels less than 50 feet (15 meters) 

in length occur regularly and cause measurable impacts to habitat quality in the Florida Keys. Grounding damage from the propeller, hull, engine, or anchor usually results in significant injury 

to coral reefs and seagrass habitat (NOAA 2007). Although the 

number of reported vessel groundings has decreased annually 

since 2002, unreported groundings are known to occur by the 

damage they leave behind. Groundings often cause immediate 

habitat devastation with long-term impacts that require years to 

decades to recover (Donahue et al. 2008, Farrer 2010).

Diver impacts from recreational snorkeling or scuba diving 

can damage habitat in locations that receive heavy visitation. 

For example, inexperienced divers often damage coral as a 

result of excessive contact with corals due to poor buoyancy 

control (Talge 1989). 

Lastly, the severity of the impacts from treasure salvaging 

(i.e., activities by those entities with legitimate admiralty judgment and rights) on sanctuary resources is somewhat unknown, 

but is regulated. This activity is only allowed through a Research 

and Recovery Permit in areas devoid of coral, hard-bottom and 

seagrass communities. The use of so called “mailboxes” or blowers to remove sand from a target site on the seafloor can create 

Habitat Status & Trends

# Issue Rating Basis for Judgment Description of 

Findings

5 Abundance/

Distribution —

In general, mangrove 

and benthic habitats are 

still present and their 

distribution is unchanged, 

with the exception of the 

mangrove community, 

which is about half of 

what it was historically. 

The addition of causeways has changed the 

distribution of nearshore 

benthic habitats in their 

vicinity.

Selected habitat 

loss or alteration 

has taken place, 

precluding full 

development of 

living resource 

assemblages, but it 

is unlikely to cause 

substantial or persistent degradation 

in living resources 

or water quality.

6 Structure ▼

Loss of shallow (<10 

meters) Acropora and 

Montastraea corals has 

dramatically changed 

shallow habitats; regional 

declines in coral cover 

since the 1970s have led 

to changes in coral-algal 

abundance patterns in 

most habitats; destruction 

of seagrass by propeller 

scarring; vessel grounding impacts on benthic 

environment; alteration 

of hard-bottom habitat by 

illegal casitas.

Selected habitat 

loss or alteration 

has caused or 

is likely to cause 

severe declines in 

some but not all 

living resources or 

water quality.

7 Contaminants ? Few studies, but no synthesis of information. N/A

8 Human 

Activities ▼

Coastal development, 

highway construction, 

vessel groundings, 

over-fishing, shoreline 

hardening, marine debris 

(including derelict fishing 

gear), treasure salvaging, 

increasing number of 

private boats, and consequences of long-term 

changes in land cover on 

nearshore habitats.

Selected activities 

have caused or 

are likely to cause 

severe impacts, 

and causes to date 

suggest a pervasive 

problem.

Status: Good Good/Fair Fair Fair/Poor Poor Undet.

Trends: Improving (p), Not Changing (–), Declining (q), 

Undetermined Trend (?), Question not applicable (N/A)

three- to five-meter diameter holes; however, the depressions 

are likely to fill back in over time as influenced by daily current, 

wave action and storm events. Most legitimate treasure salvage 

activity is presently occurring in the Hawk Channel and Quicksands area around the Marquesas in the lower Keys, with a 

limited amount occurring over sandy bottoms in the upper Keys.
State of Sanctuary Resources

46 Florida Keys CONDITION REPORT 2011

5 Fisheries are not regulated by NOAA’s Office of National Marine Sanctuaries but are regulated by FWC and NOAA Fisheries Service.

Living Resources 

The following information provides an assessment by sanctuary 

staff and experts in the field of the status and trends pertaining to the 

current state of the sanctuary’s living resources:

9. What is the status of biodiversity and how is it changing? Selected biodiversity loss has caused or is likely to cause 

severe declines in some but not all ecosystem components and 

reduce ecosystem integrity; therefore, this question is rated as 

“fair/poor.” Recently the relative abundance and diversity across a 

spectrum of species has been substantially altered by both natural 

and anthropogenic pressures, particularly large reef-building corals, long-spined sea urchins, and large-bodied fish. Combine the 

changes in abundance with low recruitment rates of those same 

species and the likelihood that those species will rebound in abundance is questionable. Furthermore, numerous fisheries5

 (e.g., lobster, crab, shrimp, sponges, fin-fish, aquarium trade) continue to remove individuals from the system, affecting sanctuary biodiversity 

and function. For these reasons, the trend is rated as “declining.” 

It is important to note that the “declining” trend rating could 

be open to interpretation because of the difficulty in applying a 

single trend rating that is representative of all individual trends 

in species abundance. For example, it is thought that species 

richness, as defined by the number of species found in a particular area, has changed little over the last four decades. Similarly, no species in the sanctuary are known to have become 

locally extinct during the same time period, although there are 

species which are threatened or endangered with extinction. At 

least three exotic species (described in Question 11) have also 

recently become established. Shifts in the relative abundance 

of multiple species, especially those at higher trophic levels, 

are indicators of compromised native biodiversity and stability in the 

system that can impact community 

and ecosystem structure and function. Understanding the degree of 

change in biodiversity that has occurred over time and how the coral 

reef ecosystem functioned in a “preexploitive” state can help managers 

and stakeholders identify realistic 

ecological and socioeconomic targets for maintaining or improving 

ecosystem services. 

A historical perspective of sanctuary biodiversity suggests that 

many of the higher-trophic-level species, such as marine mammals 

and predatory fishes, were dramatically reduced by hunting and fishing prior to the sanctuary’s designation. Current research on the historical ecology in the Florida Keys documents only one species extinction in the last 200 years — the Caribbean monk seal (Monachus 

tropicalis). Monk seals were historically ubiquitous and abundant in 

the Caribbean and the Florida Keys, but were hunted to extinction 

by the early 20th century (McClenachan and Cooper 2008). As such, 

the Caribbean monk seal was listed in the Endangered Species Act 

(1967-2008; 73 FR 63901). Other marine mammals found in the 

area of the sanctuary include cetaceans and manatees, although 

there is no historical record of those taxa being hunted or fished in 

significant numbers. However, fisheries for reef fishes and mollusk 

and crustacean invertebrates (conch, shrimp, stone crab, lobster) 

have existed in the Florida Keys in some cases for almost 300 years.

Numerous fish species in the sanctuary have been heavily 

exploited since the 18th century and have experienced population 

declines during the 20th century to unprecedented low population 

levels. Native Americans fished for reef fishes on Florida reefs long 

before the arrival of European settlers (Oppel and Meisel 1871). Reef 

fishing accelerated in the 1920s. Following growing public conflicts 

and sharp declines in catches, monitoring programs at the species 

level began in the early 1980s (Bohnsack et al. 1994a, Bohnsack 

and Ault 1996, Harper et al. 2000, Ault et al. 2005a). Ault et al. (1998) 

assessed the status of reef fish stocks and determined that 13 of 

16 groupers, seven of 13 snappers, one wrasse (hogfish) and two 

of five grunts were overfished according to federal (NOAA Fisheries 

Service) standards (Figure 31). In addition, some stocks appeared to 

have been chronically overfished since the 1970s, with the largest, 

Figure 31. Spawning potential ratio (SPR) for 34 exploited species in the snapper-grouper complex 

from the Florida Keys from 2000-2002. Dark bars indicate overfished stocks and open bars indicate 

stocks that are above the 30% spawning potential ratio standard.

Source: redrawn from Ault et al. 2005a

Overfishing (30% SPR)
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 47

are still present. Researchers from NOAA Fisheries Service and 

Florida’s Fish and Wildlife Research Institute have been monitoring one recovering spawning aggregation for mutton snapper (Lutjanus analis) at Riley’s Hump in the Tortugas Ecological 

Reserve (South) since 2004. According to observers in 2009, 

“thousands” of mutton snapper (Lutjanus analis) aggregated for 

spawning purposes at this site (Figure 32; Burton et al. 2005).

Sea turtles have been hunted for centuries throughout the Caribbean and have lost essential nesting beaches throughout their 

range. McClenachan et al. (2006) showed that although some 

nesting sea turtle populations are beginning to recover, the longterm effect of reduced numbers of sea turtles and nesting beaches 

will delay the recovery of the green and hawksbill species in the 

Caribbean basin. American crocodiles also utilize components of 

the sanctuary for their survival. They were listed as endangered 

species in 1975 due to the loss of critical habitat from coastal 

development, but have been gradually recovering throughout its 

range. The species was recently upgraded on the federal listing to 

“threatened” but remains on the state of Florida’s endangered list.

The smalltooth sawfish once ranged from New York to 

Florida to the U.S. Gulf Coast. It was listed as an endangered 

species in 2003. Its decline was the result of habitat degradation 

and loss and mortality resulting from both targeted fishing and 

by-catch from other fisheries (Carlson et al. 2007). The smalltooth sawfish was the first cartilaginous fish to be included on 

the Endangered Species List. Today, the population center is 

located in Florida Bay and the Ten Thousand Islands area of 

the Everglades National Park , but individuals are occasionally 

encountered in the sanctuary as far west as the Marquesas. 

Biodiversity change is hard to measure for seabirds in the 

sanctuary. In recent times, no seabird species have been lost or 

Subject to Overfishing Overfished

Vermillion snapper (South Atlantic only) Red snapper

Red snapper Snowy grouper (South Atlantic only)

Snowy grouper (South Atlantic only) Black sea bass (South Atlantic only)

Red grouper (South Atlantic only) Red porgy (South Atlantic only)

Black sea bass (South Atlantic only) Pink shrimp (South Atlantic only)

Gag grouper Red grouper (South Atlantic only)

Speckled hind (South Atlantic only) Gag grouper (Gulf of Mexico only)

Warsaw grouper (South Atlantic only) Gray triggerfish (Gulf of Mexico only)

Tilefish (South Atlantic only) Greater amberjack (Gulf of Mexico only)

Greater amberjack (Gulf of Mexico only)

Gray triggerfish (Gulf of Mexico only)

Table 1. Southeast regional stocks that are subject to overfishing or are 

overfished as defined by NOAA Fisheries Service. Although the sanctuary 

does not manage fisheries, it straddles both the South Atlantic and Gulf of 

Mexico fisheries management council jurisdictions. The below list includes 

species in both the South Atlantic and Gulf of Mexico fishery management 

council jurisdictions as of 2009. (Source: NMFS 2010)

Figure 32. Mutton snapper (Lutjanus analis) spawning inside the Tortugas 

Ecological Reserve (South) at Riley’s Hump.

Photo: C. Parsons

most desirable species depleted first, followed by increasingly 

smaller and less desirable species with time (Ault et al. 1998). 

The average size of adult black grouper in the upper Keys was 

about 40% of its 1940 value, and the spawning stock for this 

species was less than 5% of its historical, unfished maximum 

potential (Ault et al. 2001). In subsequent analyses, Ault et al. 

(2005a and 2005b) determined that 25 of the 34 species within 

the snapper-grouper complex for which sufficient data were 

available were experiencing overfishing. Closures of the fisheries 

at the state and federal levels for goliath (Epinephelus itajara; 

1990) and Nassau (Epinephelus striatus; 1992) grouper remain 

in effect, although the goliath grouper stock continues to indicate 

signs of slow recovery (Porch et al. 2003, 2006) to the extent that 

considerable debate occurs regarding re-opening of that fishery. 

In its 2010 report to Congress, the NOAA Fisheries Service classified nine species that are landed in the Florida Keys as overfished (i.e., depleted below minimum standards), and 11 species 

as subject to overfishing (i.e., being fished at a rate that would 

lead to being overfished), with some overlap between the two 

categories (NMFS 2010) (Table 1).

The resulting reduction in numbers of large fishes and loss 

of spawning aggregations affects ecosystem integrity and biodiversity. Former spawning aggregation sites are not functioning 

the way they did historically and quantitative anecdotes from 

experienced fishers point towards reduced numbers of spawning aggregations and fewer, smaller individuals within those that 
State of Sanctuary Resources

48 Florida Keys CONDITION REPORT 2011

extirpated from sanctuary waters. Nesting species, roosting species, wintering species and species migrating through are still 

being recorded in roughly the same numbers. The sanctuary has 

more information for coastal species such as magnificent frigatebirds, least terns (Sternula antillarum), roseate terns (Sterna 

dougallii), bridled terns (Onychoprion anaethetus), sooty terns 

(Onychoprion fuscatus), brown noddies (Anous stolidus) and 

masked boobies (Sula dactylatra), but little to no information on 

most pelagic species (those which spend most of their life at sea 

and do not breed in Florida) such as shearwaters and petrels.

Invertebrate biodiversity has changed during the last century. Studies of invertebrate populations have shown that:

■ The long-spined sea urchin is considered an important herbivore on Caribbean coral reefs. Populations, especially in 

areas where overfishing has reduced populations of herbivorous fishes, suffered a mass mortality event in the Caribbean 

basin, including the Florida Keys, from 1983 to 1984 (Lessios 

et al. 1984, Lessios et al. 2001). This mortality event is recognized as “one of the most spatially expansive and prolonged 

disturbances to reef ecosystems in the region” (Carpenter 

1988, Lessios 1988, 2005, Miller et al. 2008). The Florida 

Keys population suffered a second die-off event in 1991 (Forcucci 1994). Although long-term monitoring shows increased 

long-spined sea urchin occurrence and average size since 

1999, there has been slow recovery of adult long-spined sea 

urchins in most habitats, with the exception of patch reefs 

(Miller et al. 2008, Chiappone et al. 2008). 

■ Sponge populations in hard-bottom areas have been periodically decimated since 1844 (Donahue 2008), most recently 

by two Synnechococcus sp. cyanobacterial blooms in 1995 

and 2007. The historical sponge fishery also greatly reduced 

the density and abundance of certain sponge species. 

Over the entirety of the intensive sponge fishery (ca. 1850 

to 1940), it is estimated that 1.5 billion pounds of sponges 

were removed from the northern Caribbean (McClenachan 

2008). The decline of the sponge population has impacted 

ecosystem services, such as water filtration and ontogenetically important shelter habitat for fishes and invertebrates. 

■ Queen conch were commercially and recreationally fished 

until a moratorium was instituted by the state of Florida in 

1985 due to concerns of overfishing. Results of a long-term 

monitoring program show adult queen conch density and 

abundance have increased at least three-fold from 1992 to 

2006, but greater increases were negated due to the active 

hurricane seasons of 2004 and 2005 (Hunt 1987, Glazer and 

Delgado 2003). The ecosystem effects of a reduced queen 

conch population are not definitively known. However, researchers (Stoner et al. 1995, Torres 2003) have shown that 

queen conch strongly affect community structure, through 

their roles as herbivores and detritivores, by influencing the 

vegetative structure that provides forage and shelter for other benthic invertebrates. The removal of such a previously 

abundant invertebrate may also have an impact on species 

(e.g., Caribbean spiny lobster, loggerhead turtles, other marine snails) that use queen conch as prey.

■ The commercial collection and sale of live reef species is a 

small but well-managed fishery in the Florida Keys (otherwise known as the marine aquarium or ornamental trade). 

State-wide landings in 2005 included 147,290 total finfish and 

8,611,912 individual invertebrates (e.g., polychaete worms, tunicates, crabs, sea stars and anemones). The fishery has been 

regulated by the state fisheries agency (currently the FWC) 

since 1991. Although Florida Keys fishermen have been exemplary in initiating regulations for their fishery, and noting fluctuations in the variety of species they fish, there are currently 

no independent stock assessments for the species they target. 

Approximately 147 endorsements (permits) were issued for the 

live collection of ornamental vertebrates and invertebrates for 

sale in the aquarium industry in Monroe County in 2007.

Lastly, it should be noted that the status and changes to the 

biodiversity of habitat-forming organisms (e.g., coral, seagrass) 

were described in the “Habitat” section of this report.

10. What is the status of environmentally sustainable 

fishing and how is it changing?The status and trend 

ratings for this question are based on the available scientific 

knowledge from published studies, unpublished data, and expert opinion for targeted and non-targeted living resources that 

are directly and indirectly affected by fishing. Because this is 

the sanctuary’s first condition report, the rating combines the 

historical view of the potential effects of fishing activity on biological community development, and ecosystem function and 

integrity, with the targeted research of species-specific fisheries 

over the last three to four decades. The rating reflects conditions 

in the sanctuary but does not serve as an assessment of the 

status of current fisheries management practices in the region. 

However, the determination of the trend rating for this question 

reflects recent changes in fisheries management practices that 

may have potential beneficial effects on living resources in the 
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 49

sanctuary. The response to this question is a rating of “fair/poor” 

because fisheries extraction has caused or is likely to cause 

severe declines in some but not all ecosystem components 

and reduce ecosystem integrity. The trend is rated as “undetermined” because predictions are difficult to make regarding 

potential ecological gains resulting from newer fishing regulations and sanctuary zones that prohibit extraction. Benefits of 

recent management changes could be offset by illegal fishing 

practices, changing patterns and amounts of recreational fishing 

effort, chronic marine debris in the form of trap fishery losses 

and illegal casitas placement, and invasive marine species (e.g., 

Indo-Pacific red lionfishes Pterois volitans and P. miles and orange cup coral Tubastrea coccinea). Less than 6% of the sanctuary’s waters are considered “no-take.”

Environmentally sustainable fishing or ecologically sustainable fishing may be defined as fishing at a level that the ecosystem can sustain without shifting to an alternative or undesirable 

state. To determine if environmental sustainable fishing is occurring, one has to simultaneously consider the impacts of all 

exploited species on an ecosystem, including its stability and 

resilience (Zabel et al. 2003). In addition, fishery yield and the 

integrity of ecosystem structure, productivity, function, and biodiversity (including habitat and associated biological communities) 

must also be considered. The past decade has seen a paradigm shift in the management focus of fisheries from managing individual target stocks for maximum sustainable yield to 

ecosystem-based fisheries management. This shift leads to a 

more holistic consideration of sustaining fishery yield, as well 

as maintenance of marine ecosystems and their function. Some 

fishery data were described in other questions of this document 

(see Questions 6 and 9 on pages 40 and 46 respectively) and 

that information should be considered along with the additional 

detail provided here. Generally, fishing can reduce ecosystem 

integrity in three ways: first, removing targeted species and 

killing non-target species (as bycatch) may result in cascading 

ecological effects (Frank et al. 2005). Second, because fishing 

is size-selective, concerns exist about ecosystem disruption 

by removal of ecologically important species such as top-level 

predators (e.g., groupers, snappers, sharks, jacks) and prey 

(e.g., shrimps, baitfish) of certain sizes. Third, fishing can stress 

all habitat types in the sanctuary in the form of physical impacts 

of fishing gear to the habitat and by introducing marine debris. 

For example, regular yet unintended trap loss in the lobster and 

stone crab trap fisheries results in trap ropes wrapping around 

coral heads and abrading or killing coral colonies. Combined, 

the two fisheries utilize approximately 815,000 traps per season 

in addition to an unknown number of recreational stone crab 

traps (five per person allowable with a Florida saltwater fishing 

license) have the same potential for habitat impact. In addition, 

lobster or stone crab traps can continue “fishing” even after they 

have been lost, which leads to continued mortality of marine organisms that are too large to escape the traps after capture.6

For the 1996 to 2006 period, Murray (2007) summarized 

various measures of fishing effort for Monroe County relative to 

“other Florida counties” (Table 2). Over this period, all measures 

of fishing effort declined more rapidly in Monroe County relative 

to all other counties in Florida, except for stone crab permits.

Table 2. Changes in commercial fishing effort in Monroe County between 1996 & 2006. (Source: in Murray 2007, data from FWC)

6 Plastic traps are required to have a degradable wooden panel; thus, there is a lifespan after which traps degrade (unlike other lost gear that may 

ghost fish for longer periods of time).

Effort Measure/Area 1996 2006 Change between 

1996 and 2006

Saltwater Product 

Licenses 2,895 1,636 -43.49 %

Commercial boats 4,194 2,921 -30.35 %

Commercial 

Fishing Trips 67,773 35,811 -47.16 %

Stone Crab Permits 1,198 459 -61.69 %

Lobster Permits 1,270 704 -44.57 %

Lobster Fishing Trips 29,039 14,278 -50.83 %

Generally, there is a very high exploitation rate in the Keys 

from both recreational effort and commercial effort. Trends in 

reef fish landings from 1981 to 1992 were reported for the Florida Keys by Bohnsack et al. (1994a). Depending on the year, 

recreational landings comprised between 40% and 66% of total 

landings. Reef fishes accounted for 58% of total fish landings, 

69% of recreational landings, and 16% of commercial landings. 

Commercial landings were dominated by invertebrates (Caribbean spiny lobster, shrimp, and stone crabs), which comprised 

63% of total landings. But trends in recreational and commercial 

fishing pressure in Monroe County/Florida Keys are in decline 

due to a number of fishery and extra-fishery factors, including 

stagnant ex-vessel values (the revenue the fisherman receives 

for his catch) resulting from low demand, higher landside prices 

such as cost of living, gear, crew, etc., and less waterfront space 

availability (Leeworthy and Wiley 1996, Leeworthy 1996, Lee-
State of Sanctuary Resources

50 Florida Keys CONDITION REPORT 2011

7 The Spiny Lobster Trap Certificate Program was established in 1990 to stabilize the spiny lobster fishery by reducing the total number of traps used in the 

spiny lobster fishery to the lowest number in order to increase the yield per trap and maintain or increase overall catch levels, promote economic efficiency 

in the fishery, and conserve natural resources. This program controls the number of traps in the lobster fishery using trap certificates that are issued to 

individual lobster fishers by the Fish and Wildlife Conservation Commission (FWC). Fishers receive one lobster trap tag for each certificate they own.

worthy et al. 2010, Leeworthy and Morris 2010, Murray 2007, 

Sharp et al. 2005). Commercial fishing catch declined from 21.8 

million pounds in 1995-1996 to 9.6 million pounds in 2008, a 

56% decrease. Fishing trips also declined 56% over this period, from 67,422 trips in 1995-1996 to 29,681 trips in 2008. 

This was a greater decline than what occurred across the entire 

state of Florida. Florida’s total catch declined about 34% during 

the same period, while trips declined about 47%. The decline 

was due in part to changes in fishery management designed to 

reduce overall fishing effort, as well as decreasing demand for 

Caribbean spiny lobsters, which is the dominant fishery in the 

Florida Keys. The Florida Keys historically account for 89% of 

commercial Caribbean spiny lobster catch. (FWRI 2010)

Ault et al. (1998) assessed the status of multiple reef fish 

stocks in the Florida Keys and determined that 13 of 16 groupers, seven of 13 snappers, one wrasse (hogfish) and two of 

five grunts were overfished, according to federal (NOAA Fisheries Service) standards (see Figure 31, page 46). They suggested that some stocks appeared to have been chronically 

overfished since the 1970s, and that the Florida Keys fishery 

exhibits classic “serial overfishing” in which the largest, most 

desirable species are depleted by fishing (Ault et al. 1998), followed by sequentially smaller species. Ault et al. (2001) found 

that the average size of adult black grouper (Mycteroperca bonaci) in the upper Keys was about 40% of its 1940 value, and 

that the spawning stock for this species is now less than 5% of 

its historical, unfished maximum. In subsequent analyses, Ault 

et al. (2005a, 2005b) determined that, of 34 species within the 

snapper-grouper complex for which sufficient data were available, 25 were experiencing overfishing. Another game fish that 

has declined in numbers is the bonefish (Albula vulpes), which 

is at approximately 5% of historic levels primarily because of 

habitat and food loss (Ault 2008). Although additional, long-term 

monitoring is necessary to adequately understand the impacts 

of new fishery regulations, initial research has shown that certain fish species (e.g., black and red groupers, Epinephelus morio, and mutton snapper) have responded positively to the combination of stronger regulations and larger ecological reserves 

within the sanctuary. These results will be further detailed in the 

“Response” section of this document.

The commercial and recreational lobster fisheries are regulated by the FWC. Due to the Spiny Lobster Trap Certificate 

Program (370.142)7

 the total number of commercial lobster traps 

allowed in the fishery has declined from about 750,000 in 1993 

and 1994 to about 480,000 in 2010 (FWC Fishery Statistics). The 

Florida lobster trap fishery is unique in that it allows the use of 

sub-legal lobsters as a “live attractant.” The consequences of this 

practice are well-documented in literature and include increased 

stress and mortality from confinement to traps (SEDAR 8 2005) 

and potential spread of a lethal lobster virus (Behringer et al. 

2008). Fishery managers suspect that more protection for sublegal-sized lobsters should improve landings in Florida’s lobster 

fishery (Matthews 2001), and improve the fishery sustainability. 

The queen conch is a large, marine gastropod that inhabits 

the tropical western Atlantic including the Florida Keys. It once 

supported significant commercial and recreational fisheries in 

south Florida; however, the ease of capture and the desirability 

of the shell and meat resulted in a severe depletion of the local 

population to the point that a ban was instituted in 1985 in state 

waters and then in 1986 in federal waters. When the ban was 

established, less than 6,000 adult conch remained in the Florida 

Keys (Glazer and Delgado 2003). Since then, ongoing surveys 

have shown a slow and very limited recovery with an estimated 

33,500 adults in 2010 (FWC unpublished data). 

In addition to the traditional “hook and line” and trap fishing pressure, biodiversity in the sanctuary is also affected by the 

aquarium trade. The collection and sale of living corals and hard 

substrate with attached organisms (“live rock”) has been prohibited in state waters of Florida since 1995 and in federal waters 

since 1997. The state and federal government both regulate a 

small but viable fishery based in live rock aquaculture, where geologically unique limestone is placed on sandy, barren ocean floor 

areas and acts as a recruitment site for hard and soft corals and 

other marine invertebrates. This fishery remains commercial in 

nature because the mature live rock is sold in the aquarium trade. 

Similar to live rock aquaculture, the collection and sale of live 

reef species comprises a small but well-managed fishery, most 

notably in the Florida Keys. This fishery has been regulated by 

the FWC since 1991, and there is currently a moratorium on the 

issuance of new marine life endorsements (permits). Approximately 80 commercial endorsements were renewed for the live 

collection of ornamental vertebrates and invertebrates for sale 

in the aquarium industry in Monroe County during each year 

from 2006 to 2009. Combined commercial landings in the Keys 

during the same time period included 291,672 total finfish and 

14,584,831 individual invertebrates (e.g., polychaete worms, tu-
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 51

nicates, crabs, sea stars and anemones) (source: FWC). Florida 

Keys commercial fishermen have initiated regulations for their 

fishery, recognizing fluctuations in the variety of species they fish. 

Concerned fishermen of the Keys continue to work with the FWC 

to suggest rule changes to ensure sustainability of the marine life 

fishery. However, there is also a recreationally allowable “catch” 

of marine life, and there is no way to account for the level of effort 

or extraction this sector represents at the current time. Lastly, but 

most importantly, there have been no stock assessments of any 

of the species collected, thus it is impossible to determine whether this fishery is environmentally sustainable over the long term. 

In a recent study by Rhyne et al. (2009), the Florida Marine 

Life Fishery landing data from 1994 to 2007 was analyzed for all 

invertebrate species, and it was discovered that of the 9 million 

individuals collected in 2007, 6 million were grazers. The results 

suggest the number of grazers greatly exceeds the number of 

specimens collected for ornamental purposes, representing a 

significant categorical shift, positioning the invertebrate ornamental fishery for a collapse. More targeted research would 

help managers determine what effect both sectors of the marine 

life fishery are having on ecosystem biodiversity and integrity to 

help more effectively manage these resources.

Although seabirds are an integral component of the food 

web, more studies are needed to better assess fishing impacts 

on prey availability in coastal and seabird populations. Many bird 

species forage in or around the marine environment where they 

can become entangled in fishing gear, hooks and line to the extent that they are unable to feed or move about freely. Bird rescue organizations regularly treat cormorants, pelicans, herons 

and gulls that have become entangled or injured by fishing gear. 

Shrimp are important in the diet of a wide range of species 

including many fish and bird species; however, they are also exploited by both recreational and commercial fisheries. Recreational 

“shrimping” usually occurs during the wintertime, but the effort and 

harvest levels associated with this sector are not known. Commercially, shrimp are harvested for both food (the pink shrimp Farfantepenaeus duorarum) and as bait for the recreational fisheries. For 

example, commercial landings of pink shrimp in the Florida Keys 

averaged 1,165,120 lbs in the years 2006-2010 (FWC statistics). 

Though landings have fluctuated over the last five years, it is generally not known how shrimp fishing impacts ecological sustainability.

11. What is the status of non-indigenous species and

how is it changing? Although the threats of introduced 

aquatic species to habitats they colonize is often unknown beforehand, some can have serious detrimental impacts, including 

competition with native species for food and space, alteration of 

habitat, predation on native species, and introduction of diseases 

to which native species have no resistance (Ruiz-Carus 2006). 

Non-indigenous species in the sanctuary are occurring with increasing frequency and may inhibit full community development 

and function and may cause measurable but not severe degradation of ecosystem integrity; therefore, this question is rated 

“fair” and “declining.” More than 30 species of non-native marine 

fishes have been documented in Florida waters (Schofield et al. 

2009), with more than 18 species of non-native marine fish being 

documented in Miami/Dade, Broward and Palm Beach counties 

in southeast Florida (REEF database 2006). Aquarium “dumping” has been identified as the likely source of these introductions 

given that most of the species are popular ornamental fish. 

The sanctuary has been witness to the non-indigenous Pacific orbicular batfish (Platax orbicularis), which was controlled, 

and the Indo-Pacific red lionfishes, which are presently the only 

non-native marine fish species known to be established along the 

coast of Florida (Schofield et al. 2009) (Figure 33). Red lionfish, 

formerly residents of the western Pacific, Red Sea, and eastern 

Indian Oceans only, were first reported in the 1980s along south 

Florida and are now well established along the Southeast U.S. 

and the Caribbean (Ruiz-Carus 2006, Morris et al. 2009). Reports 

of lionfish in the sanctuary began in January 2009, and between 

January 2009 and July 2010 there were approximately 500 reported lionfish sightings in the Florida Keys (250 of those were 

confirmed and removed from sanctuary waters) (Morris and Whitfield 2009). Since then, sighting and removal efforts have been 

continuously increasing. Juvenile lionfish (approximately 30 milFigure 33. The venomous lionfish, which is normally found in the Pacific and Indian Oceans, is a non-native fish that has established itself 

in the Atlantic. 

Photo: REEF
State of Sanctuary Resources

52 Florida Keys CONDITION REPORT 2011

Figure 34. The non-indigenous orange cup coral (Tubastrea coccinea) has 

expanded its range and can now be found in portions of the sanctuary.

Photo: Joyce and Frank Burek

Figure 35. The Red-tipped Sea Goddess (Glossodoris sedna), a nudibranch 

native to the tropical Pacific, is now well established in the Florida Keys.

Photo: NOAA/FKNMS

limeters in length) were observed in spring 2010 at several locations in Florida Bay (C. McHan, FWC, pers obs. and M. Butler, Old 

Dominion University, pers. comm.), suggesting a pervasive invasion is occurring across all the habitats of the Florida Keys ecosystem. The increasing abundance and wider distribution of lionfish in 

the South Atlantic Bight, Bermuda, Florida, and the Bahamas indicates that lionfish are the first marine fish species to successfully 

establish a breeding population in the tropical western Atlantic.

The venomous protective spines of lionfish, combined 

with their feeding habits, unique reproduction and few predators, contribute to their successful invasive abilities. Lionfish are 

ambush predators, can threaten local ecosystems by altering 

the structure of native reef fish communities by out-competing 

native reef organisms and reducing forage fish biomass (Morris 

and Whitfield 2009). Impacts from lionfish could include direct 

competition with groupers for food and predation on reef fish and 

crustaceans (Ruiz-Carus 2006, Albins and Hixon 2008, Morris 

and Akins 2009). Also, lionfish pose a danger to divers and fishermen – stings from the venomous spines of the fish may result 

in pain, swelling, numbness and sometimes more severe effects 

including paralysis and systemic effects. 

One coral species is invasive and could potentially impact 

ecological integrity. The range of the non-indigenous orange cup 

coral (Tubastraea coccinea) (Figure 34), has expanded since 

it was first observed offshore of Key Largo in 1999 and now 

includes the Gulf of Mexico, South Florida, and the Florida Keys, 

including the sanctuary (Fenner and Banks 2004, Ferry 2009, 

Shearer 2010). Observations in the Caribbean and the Gulf of 

Mexico show that this species inhabits natural reef substrates 

and can cause tissue necrosis and partial mortality of native 

corals (Creed 2006). However, in general, orange cup coral appears primarily on artificial substrates such as submerged steel 

wrecks (Fenner and Banks 2004, Ferry 2009, Shearer 2010). It 

is suspected that these artificial structures played a major role in 

the spread of this species. A study by Ferry (2009) indicates that 

orange cup coral has not yet become established in the lower 

Florida Keys. However, the potential for this species to impact 

reef communities is high due to high proliferation rates resulting 

from the production of asexual larvae, the ability to out-compete 

native species and limit substrate available for recruitment of 

native species, plus the lack of a natural predator. 

The Red-tipped Sea Goddess, (Glosssodoris sedna), a nudibranch native to the tropical Pacific (Figure 35), has become 

well-established in the Florida Keys (K. Nedimyer, Coral Restoration Foundation, pers. comm.). Over the last three to four 

years it has become seasonally abundant in a variety of habitats. Although they have become well established, it is unknown 

if they pose a threat to any resources in the sanctuary.

12. What is the status of key species and how is it changing? The key species or taxa in the sanctuary selected for use in 

this report include stony corals, seagrasses, queen conch, Caribbean spiny lobster, long-spined sea urchin, the snapper-grouper 

complex and sea turtles. These species are important for their 

ecological roles, and long-term datasets are available for assessing changes for these species. With the exception of seagrasses, 
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 53

historical data for each of these groups show substantial declines 

in abundance. Therefore, the status of key species in the sanctuary is rated as “poor” because the reduced abundance of selected keystone species has caused, or is likely to cause, severe 

declines in ecosystem integrity; or selected key species are at 

severely reduced levels and recovery is unlikely. The trend is rated 

as “not changing” because of the reduced abundance of a limited 

number of key species in each habitat type. Although there are 

very encouraging results of increased sizes and density of select 

species within certain sanctuary marine zones, forecasting how 

these changes will affect their long-term status is challenging.

Stony Corals

As discussed in earlier questions, long-term monitoring of 

nearshore coral habitats indicates a decline in both species richness and coral cover at the stations surveyed, and no significant 

recruitment has occurred since the monitoring program began in 

1996 (Ruzicka et al. 2010). The declines in abundance of two of 

the principal Caribbean reef-building corals, staghorn and elkhorn 

coral, are often-cited as examples of the changes in western Atlantic reefs that have occurred over the past several decades (Aronson and Precht 2001, Gardner et al. 2003). The causes of these 

declines, which began in the late 1970s, include large-scale factors such as coral bleaching and disease, especially white-band 

disease, as well as smaller-scale effects resulting from storms and 

predation by corallivorous snails and damselfishes. Both staghorn 

and elkhorn corals were under consideration for addition to the 

U.S. Endangered Species List since the early 1990s and were 

formally added as threatened in 2006 based on Caribbean-wide 

population declines and poor recovery (Williams et al. 2008). The 

more recent declines of the massive star corals (Montastraea spp.) 

have also led to the overall loss of coral cover both in the Florida 

Keys (Ruzicka 2010) and in other parts of the Caribbean (Hughes 

and Tanner 2000, Edmunds and Elahi 2007). As of July 2010, the 

NOAA Fisheries Service was conducting a status review of 82 additional coral species for ESA consideration, seven of which occur 

in the Caribbean and in the sanctuary (Agaricia lamarcki, Dendrogyra cylindrus, Dichocoenia stokesii, Montastraea annularis, 

Montastraea faveolata, Montastraea franksi, Mycetophyllia ferox).

Seagrass

Long-term monitoring of seagrass has shown changes in 

coverage and nutrient composition at some monitoring stations. 

These changes are consistent with model predictions of nutrient-induced changes of these systems. Although no significant 

overall loss of seagrass coverage in the sanctuary has occurred 

since monitoring began, there have been significant changes in 

the composition of the seagrass species found in benthic communities (Fourqurean 2009). Furthermore, shallow seagrass 

beds are regularly subject to injury by vessel groundings. 

Queen Conch

Although queen conch densities are relatively high within 

the sanctuary, the modest spatial extent of the aggregations 

results in low estimates of overall abundance. Queen conch 

populations are showing signs of gradual recovery from their 

low abundance estimates in the 1980s. Scientists from the Fish 

and Wildlife Research Institute are currently investigating the 

cause of chronic reproductive failure of nearshore aggregations. 

Although queen conch have been protected from fishing since 

1985, in both federal and state of Florida waters, poaching still 

occurs on a regular basis (G. Delgado, FWC, pers. comm.). 

Caribbean Spiny Lobster

Caribbean spiny lobster in the Florida Keys experience 

intense fishing pressure within Florida Keys National Marine 

Sanctuary, both from a heavily capitalized commercial fishery 

and a recreational fishery that is the most intensive such fishery 

on the globe (Sharp et al. 2005). In addition to the direct removal 

of lobsters by the fishery, each fishing sector also directly affects 

the survival rates of Caribbean spiny lobster before they recruit 

to the fishery. The commercial lobster trap fishery’s practice of 

confining sub-legal-sized lobsters within traps to serve as attractants results in an estimated 10% mortality rate among these 

lobsters (SEDAR 8 2005). The recreational fishery results in the 

catch-and-release of a large number of lobsters below the legal 

size limit, causing injuries that result in increased mortality (Parsons and Eggleston 2007). 

Although the no-take zones within the sanctuary were not 

designed as a fishery management tool, results from an FWC 

five-year monitoring project concluded that Sanctuary Preservation Areas (SPAs) were too small to protect Caribbean spiny 

lobsters from the fishery, but the larger Western Sambo Ecological Reserve (WSER) did function to some degree as a fishery 

reserve (Cox and Hunt 2005). There, the mean size of legalsized lobsters and the frequency of occurrence of lobsters were 

significantly larger than those commonly encountered within the 

fished areas of the sanctuary, having increased steadily after 

WSER establishment. Cox and Hunt (2005) also concluded the 

increased frequency of encountering atypically large lobsters 

in the areas adjacent to the WSER (including the nearby fishery-exploited areas) suggested lobsters were likely emigrating 

from the WSER, thus this zone may serve to some degree to 

enhance fishery landings. The WSER does not encompass all 
State of Sanctuary Resources

54 Florida Keys CONDITION REPORT 2011

of the habitats utilized by adult Caribbean spiny lobsters during their life 

history, and inclusion of the adjacent 

outlier reef would serve to protect 

lobsters from fishery exploitation (Cox 

and Hunt 2005).

Long-spined sea urchins

The long-spined sea urchin Diadema antillarum was considered a 

most important herbivore (grazer) because it helped to control the amount 

of algae on Western Atlantic coral 

reefs (Lessios et al. 2001). The demise of this once-ubiquitous echinoid 

is considered one of several factors 

responsible for the changes observed 

on Florida Keys reefs. Historical surveys of D. antillarum prior 

to the 1983 and 1984 Caribbean-wide mass mortality event are 

limited for the Florida Keys and consist of data collected at a few 

seagrass and fore-reef sites, mostly from Indian Key to reefs 

offshore of Key Largo. However, the available data indicate that 

densities were at least as high as four or five individuals per 10 

square feet (one square meter) (Chiappone et al. 2008). The 

Caribbean-wide mass mortality began in the Florida Keys during 

the summer of 1983 and presumably led to a 90% or greater 

reduction in population size. From 1983 to 1990, there were 

no published studies of D. antillarum density and size structure. Surveys carried out in the early 1990s suggested that the 

population was recovering, with densities on shallow spur and 

groove reefs approaching one-tenth (i.e., 0.5-0.6 individuals per 

10 square feet) of their pre-1983 level, and a size distribution 

dominated by larger (>2 inches, or 5 centimeters) TD) individuals (Forcucci 1994). In contrast to other wider Caribbean reef 

ecosystems, a second mortality event struck the Florida Keys D. 

antillarum population beginning in April 1991, with similar morbidity symptoms as the 1983 event that reduced the population 

to one-hundredth of its pre-1983 level (Forcucci 1994). Surveys 

conducted within one year of the 1991 mortality indicate that 

very low densities (<0.1 per 10 square feet) and small test sizes 

(<1 inch, or 3 centimeters) in shallow fore-reef habitats characterized the D. antillarum population (Forcucci 1994), a pattern 

that continued for the next decade (Chiappone et al. 2002 b, c).

Although monitoring conducted over the past decade has 

detected increases in both the density and size structure of longspined sea urchins on patch reefs, a similar trend has not been 

detected on offshore reef habitats. Overall, there has been slow 

recovery of long-spined sea urchins compared to pre die-off densities (Miller et al. 2008). Over an 11-year period (1999-2010), 

researchers examined densities and test sizes of D. antillarum 

and other sea urchins at more than 1,100 Florida Keys sites 

spanning 217 miles (350 kilometers), encompassing multiple 

habitat types from inshore to the deeper fore-reef slope. Surveys 

since 1999 indicate that current densities are still well below one 

individual per square meter and the maximum site-level density 

recorded during the 11-year period was only 0.33 individuals per 

10 square feet (one square meter) (Figure 36). However, there 

has been a notable positive shift in their average and maximum 

size (Chiappone et al. 2008). Population recovery to pre-1983 

levels could take decades, if not longer. Algal assemblages, in 

most habitats, despite reduced D. antillarum, are dominated by 

diminutive algal turfs, crustose coralline, and to a lesser extent 

macroalgae, suggesting that herbivorous fish grazing is critical 

for maintaining low algal standing crop on Florida Keys reef. 

Moreover, observations of newly recruited juvenile long-spined 

sea urchins have been largely confined to reef-rubble zones. 

However, because of the highly dynamic nature of the substrate 

resulting from wave and storm surge in this habitat, the mortality 

rate of these recruits is potentially substantial.

Groupers and other fishes

Previous sections of this report review the status of select 

species of finfish (see Questions 9 and 10). Even though sanctuary zones were not established to protect individual species, 

there have been encouraging observations of increased abundance and sizes of select finfish inside Tortugas Ecological Reserve (a no-take zone). Groupers in the Florida Keys have been 

Figure 36. Temporal patterns in mean Diadema antillarum density on shallow spur and groove reefs 

in the Florida Keys. 

Data: Randall et al. 1964, McPherson 1968, Forcucci 1994, Bauer 1980, Chiappone et al. 2002b, c, 2008)
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 55

historically exploited, and in a study by Ault et al. (1998) it was determined that 13 of 16 grouper species were overfished according to NOAA Fisheries Service standards. As of 2010, the status 

of grouper species has improved and according to the NOAA 

Fisheries Service, only three species of grouper (snowy, red, and 

gag) are still considered to be overfished in the same area (NOAA 

Fisheries Service fourth quarter 2010 “overfished map”).

Specifically, the goliath grouper was targeted by commercial and recreational fishing since the late 1800s. They are extremely susceptible to exploitation due to a mixture of life history 

traits such as slow growth, long life, delayed sexual maturity, 

and the pattern of spawning aggregations. These characteristics, in association with escalating fishing pressure, led to the 

fishery closure in 1990 and the subsequent listing of goliath 

grouper as a candidate for the Species of Concern List under the 

U.S. Endangered Species Act. Fishery closures and designating 

some sanctuary zones as no-take have helped to increase the 

goliath grouper population as well as expand its geographic distribution. However, it is not clear as to when the population may 

be fully recovered, or when the fishery will be reopened if it were 

to be (Collins 2009, Porch et al. 2003, 2006). It is hoped that 

more examples of positive finfish responses to sanctuary zones 

continue, but the damaging ecological effects of the invasive red 

lionfishes could counteract management efforts.

Another study on the social structure of hogfish (e.g., harems) showed a difference between Western Sambo Ecological 

Reserve and the adjacent “fished” areas; spawning was only 

observed inside Western Sambo Ecological Reserve during a 

recent study (Muñoz et al. 2010).

Sea turtles

Sea turtle species frequenting the Florida Keys that are 

listed as endangered under the U.S. Endangered Species Act 

include the green, leatherback, hawksbill, and Kemp’s Ridley 

turtles. Green sea turtles were hunted for their meat to the brink 

of extinction during the late 1800s and early 1900s in south Florida, and their numbers in the Florida Keys continue to remain low 

today. Systematic monitoring of green turtle nests on islands of 

the Key West National Wildlife Refuge show nearly a doubling 

since 1990; however, the number of nests still remains low (USFWS unpubl. data). These low population numbers affect seagrass beds, as these reptilian herbivores serve an important role 

in maintaining seagrass habitat quality by keeping the organic 

matter from accumulating in the sediments through continuous 

grazing. Green sea turtles are also affected by fibropapillomatosis (FP), a disease that forms large tumors on soft and hard tissues of turtles (Herbst 1994, Ene et al. 2005). In the Indian River 

Lagoon, Florida Bay, and the Florida Keys, 50-70% of the green 

turtles are affected (Ene et al. 2005) and since the early 1980s, 

the percentage of green turtles stranded in Florida with FP has 

been increasing each year (Foley et al. 2005).

Loggerhead turtles, listed as threatened, also frequent the 

Florida Keys. However, an updated analysis of Florida’s long-term 

loggerhead sea turtle nesting data reveals that loggerhead nest 

counts have declined 25% over the last 10 years (Witherington 

et al. 2009). Systematic monitoring of loggerhead turtle nests on 

islands of the Key West National Wildlife Refuge indicates a more 

than 50% decline since 1990. This marked decline in the number 

of breeders and nests, low productivity, a high proportion of false 

crawls, tidal flooding coupled with ongoing beach erosion, and 

sea level rise collectively threaten the future of the nesting loggerhead turtle population in the sanctuary (USFWS unpubl. data). 

In 2010, NOAA Fisheries Service and the U.S. Fish and Wildlife 

Service proposed to list nine Distinct Population Segments (DPS) 

of loggerhead sea turtles under the U.S. Endangered Species 

Act. Under this proposal, the South Atlantic Ocean DPS is being 

considered to go from “Threatened” status to “Endangered”. 

In January 2010, the Florida Keys experienced record low 

temperatures, causing many sea turtles to become stunned by 

cold-water temperatures. More than 250 cold stunned turtles 

were recorded in January 2010, the majority of which were 

green turtles, with smaller numbers of loggerheads and Kemp’s 

Ridleys. NOAA and the FWC helped to coordinate the rescue 

of hundreds of sea turtles to help them recover from the cold 

shock. Rescued turtles from the Florida Keys were housed and 

rehabilitated at the Sea Turtle Hospital in Marathon. The hospital 

is a non-profit facility that has been in operation since 1986.

Seabirds

The populations of most of the state and federally listed 

seabird species seem to be stable. The least tern and roseate 

tern nesting populations are stable but low in numbers. The 

roseate tern population dropped drastically after the 2005 hurricanes but has since rebounded. This was notably due to the 

disappearance of Pelican Shoal in the lower Keys. That site was 

a coral-rubble and sand island where roseate and bridled terns 

were nesting and the island is now underwater. The birds have 

shifted to nesting on roofs of large buildings in the Keys. There 

are no similar ground nesting sites (islands) throughout sanctuary boundaries (R. Zambrano, FWC, pers. comm.). 

Manatees

The West Indian manatee includes two distinct subspecies, the 

Florida manatee (Trichechus manatus latirostris) and the Antillean 
State of Sanctuary Resources

56 Florida Keys CONDITION REPORT 2011

manatee (Trichechus manatus manatus). The Florida manatee’s 

range is confined to the southeastern U.S., while Antillean manatees are found throughout the Caribbean. Due to a variety of human 

activities, like coastal development, this important herbivore has declined in numbers and their distribution is patchy throughout Florida.

A U.S. Fish and Wildlife Service survey estimated there were 

at least 3,800 Florida manatees in 2009. Even though this population number is low compared to historic records, the population is 

stable due to effective management of human-related threats (e.g., 

establishing watercraft speed limits to prevent propeller strikes). 

However, the Florida manatee population was negatively affected 

by the prolonged cold event in January 2010, when 244 deaths (13 

of which were newborns) were recorded statewide (FWC statistics).

13. What is the condition or health of key species and

how is it changing? The condition and health of key species 

in the sanctuary is rated as “fair/poor” because the comparatively 

poor condition of selected key resources makes prospects for their 

recovery uncertain. For example, the effect of diseases on hard 

and soft corals has caused substantial declines in coral cover (biomass) over the last two decades, yet there has been no significant 

coral recruitment recorded at any long-term monitoring station. 

Likewise, long-spined sea urchins have yet to recover from a 

1980s Caribbean-wide disease outbreak. Generally, the health of 

selected key species has been compromised by factors including 

exposure to algal blooms (including harmful algal blooms), fishing, 

entanglement in active and lost fishing gear, ingestion of marine 

debris, and disease. Due to persistence, and accumulating effects 

of these problems, the trend is considered to be “declining.”

Large, persistent phytoplankton blooms resulting in part from 

eutrophic conditions have been associated with fish kills and sponge 

and seagrass die-offs (Butler et al. 1995, Fourqurean and Robblee 

1999, Hunt and Nuttle 2007). Cyanobacterial blooms have been especially prevalent in central Florida Bay during the past two decades 

and at times have been carried by the tidal currents to the ocean 

side of the Keys. Blooms are not necessarily triggered or sustained 

by a single change in nutrient load; rather, a combination of multiple 

biotic and abiotic factors contribute to their intensity and duration. 

Unfortunately, there is currently insufficient data to predict cyanobacterial bloom initiation or longevity, thus there is a need to integrate 

existing biological, climatological, and oceanographic research efforts so that predictive models can be further developed and refined.

A health concern for key species in the sanctuary, including marine mammals, seabirds, sea turtles and corals, is interaction with 

active and lost fishing gear. Results from a recent study on marine 

debris prevalence in the sanctuary showed “marine debris, most of 

which is derelict angling and trap gear, is ubiquitous in the sanctuary, 

even within no-take zones. The sheer amount of debris recovered 

is testament to an increasingly visited and exploited marine ecosystem” (Miller et al. 2008). Marine debris poses entanglement threats 

not only to highly migratory species (e.g., sea turtles and manatees) 

but also to sessile species (e.g., coral and sponges). Lost fishing 

gear can wrap around coral heads and cause injury, mainly from 

abrasion caused by wave action. Likewise, sponges can be literally 

cut in half by the combination of derelict gear and wave energy. In 

addition, ingestion of plastic marine debris is a health concern for a 

number of sea turtle and seabird species in the sanctuary. Although 

there are no quantitative studies on the frequency and severity of 

this occurring, it is well known that sea turtles will ingest plastic bags 

and balloons, mistaking the debris as prey items. 

Corals throughout the Caribbean and Atlantic region have suffered from numerous diseases over the past several decades, and 

disease has been implicated in the demise of a number of reef-building species. Studies in the Florida Keys track disease prevalence at 

monitoring stations throughout the archipelago. For example, the 

Fish and Wildlife Research Institute’s Coral Reef Evaluation and 

Monitoring Project has shown the prevalence of diseases to vacillate 

over time, and from 2002 to 2006 generally decreased at monitored 

stations within the sanctuary and at the Dry Tortugas. The number 

of stations affected with white diseases peaked to more than 80% 

in 2002, subsided to 35% in 2005, then increased again to 50% in 

2006. The number of stations affected with “other” diseases peaked 

to 90% in 2001, but declined to 57% by 2006 (Ruzicka et al. 2009). 

A second study, which was conducted in August 2006, focused on 

diseases affecting two species of coral (elkhorn and staghorn coral) 

that had been recently listed as threatened on the U.S. Endangered 

Species List. One hundred and seven sites along approximately 29 

miles (46 kilometers) of coastline in the upper Keys were surveyed, 

and no evidence of white-band or any other diseases affecting either species was observed (Miller et al. 2008). Though they are the 

best datasets available to resource managers, it should be noted 

that these types of annual surveys do not necessarily capture the 

real trends of disease impacts (or trends thereof) to coral populations because of the acute nature of the disease outbreaks. 

Other diseases8

 impacting key species include fibropapillomatosis and PaV1. Fibropapillomatosis (FP) most commonly af8 Researchers from the Florida State University are also tracking the prevalence of a common tumor in Grey snapper (Lutjanus griseus), but as of 

2010 no peer reviewed information had been published.
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 57

fects juvenile green turtles in nearshore habitats. It is estimated 

that 50% to 70% of the green turtles in the Indian River Lagoon, 

Florida Bay, and the Florida Keys are affected and since the 

early 1980s, the percentage of green turtles stranded in Florida 

with FP has been increasing 1.2% each year (Ene et al. 2005, 

Foley et al. 2005). Another key species impacted by disease is 

Caribbean spiny lobster, which is susceptible to the Panulirus 

argus virus 1 (PaV1 (Behringer et al. 2006).

Studies on queen conch have shown nearshore populations 

are no longer reproductive. Nearshore water quality is suspected 

to be the cause of nearshore individuals experiencing rapid loss 

of gonadal tissue (Delgado et al. 2004, Spade et al. 2010).

The condition or health of seabirds is unknown, although 

their populations seem to be stable. However, as previously 

mentioned, birds are as susceptible to contaminants (e.g., oil, 

plastic, heavy metals), as are fish and corals. Impacts to small 

fish will obviously reduce food for terns and thereby reduce 

nesting productivity (R. Zambrano, FWC, pers. comm.).

During January and February 2010, the Florida Keys and 

the rest of Florida experienced severe, extended cold periods 

that caused drastic drops in seawater temperatures, especially 

in nearshore waters of Florida and Biscayne Bays. Such bouts 

of extreme cold are uncommon, but have occurred in the recent 

past (1977). The cold fronts during this time period moved in 

rather quickly, causing fish kills in nearshore waters and coldwater bleaching of corals that resulted in nearly 100% mortality 

of the colonies at the locations surveyed. Results from remote 

sensing data (NOAA and USF) and in-water surveys (managed 

by the Nature Conservancy) indicated that the coldest water 

was in the bays and flowed to the ocean side. Mid-channel 

reefs in Hawk Channel were particularly affected by cold-water 

stress and underwent extensive bleaching. Studies have shown 

that these same reefs are known to be more resilient to summertime warm-water bleaching events than many other coral 

communities within the sanctuary (see Response section, under climate change). Many sea turtles, manatees, and American crocodiles were also affected and suffered mortality. The 

long-term impacts of the loss of these animals, along with the 

numerous fish and coral losses, are unknown at the time of this 

writing and somewhat difficult to predict. 

14. What are the levels of human activities that may 

influence living resource quality and how are they

changing? Human activities affect the quality of living resources in the sanctuary directly and indirectly. Direct impacts to 

living resource quality include commercial and recreational fishing, vessel grounding, anchoring, propeller scarring, disposal of 

marine debris, and disturbance from recreational diving, snorkeling, or boating. Indirect activities result in nonpoint source 

pollution and illegal discharges.

Many activities, such as those related to vessel groundings, caused or are likely to cause severe impacts to sanctuary resources, and cases to date suggest a pervasive problem. 

Therefore, the response to this question is rated as “fair/poor.” 

However, the trend is rated as “not changing” because all waterbased human activities, whether engaged in by residents or by 

visiting tourists, have been decreasing in Florida Keys National 

Marine Sanctuary since the 1990s (Leeworthy 1996, Leeworthy 

et al. 2010, Leeworthy and Morris 2010).

Despite the human population decrease and overall reduction in fishing in the Florida Keys since the 1990s, heavy 

recreational and commercial fishing pressure continues to suppress biodiversity, affecting the abundance and distribution of 

key species (see Question 12). Fishing stress can disrupt living 

resource quality by removing ecologically important top-level 

predators and, therefore, shifting reef ecosystem dynamics 

(Frank et al. 2005). 

Fishing methods can also impact living resource quality. 

For example, damage to the benthos can result when traps or 

mobile fishing gear, such as trawls, are used. Marine debris, in 

the form of derelict fishing gear, can destroy benthic organisms 

and entangle mobile fauna, including endangered species, such 

as manatees and sea turtles (Donohue et al. 2001). When combined with high wave energy, lost, or, “ghost” crab and lobster 

traps can damage corals, and sever sponges (Chiappone et 

al. 2005) over a large area due to trap movement in high-windinduced wave events (Lewis et al. 2009). In a recent report by 

Miller et al. (2010), a survey in the Florida Keys generally found 

similar or greater amounts of marine debris, especially derelict 

fishing gear, in no-take zones, when compared to baseline data 

from 2000, 2001 and 2008. Entanglement and vessel strikes 

also pose a threat to marine mammals (such as dolphins and 

manatees) and sea turtles because they often inhabit overlapping fishing areas. 

In addition to fishing threats, vessel groundings occur 

regularly within the sanctuary, causing measurable impacts to 

living resources. Since 1998, almost all groundings have involved small (<50 feet, or 15 meters), privately owned vessels. 

Groundings often result in significant injury to corals, seagrasses, and other benthic organisms (NOAA 2007). Furthermore, 

vessels that try to “power off” the grounding site can cause 

significantly more injury. 

In the Florida Keys, the number of reported vessel groundings decreased annually from 2002 to 2006 (from 721 ground-
State of Sanctuary Resources

58 Florida Keys CONDITION REPORT 2011

ings in 2002 to 301 in 2006), but it is not possible to determine 

if this trend is a result of fewer boaters using the resource 

because of higher fuel costs, increased boater awareness of 

the sensitivity of the environment, or a reduced willingness 

to call for assistance if boaters run aground. Generally, there 

has been no proportional shift in impact to different living resource types: approximately 14% of groundings impact coral, 

an estimated 85% impact seagrasses, and about 1% impact 

hard-bottom habitat (Donahue et al. 2008). Because corals and 

seagrasses grow in shallow water they are also susceptible 

to a variety of other direct impacts from smaller commercial 

and recreational vessels such as damage from the propeller, 

hull, engine, and anchoring. Despite the fact that the number of 

reported vessel groundings in the Florida Keys is decreasing, 

anchor damage, groundings, and propeller scarring still occur 

frequently and often result in immediate resource devastation 

with long-term impacts (Farrer 2010).

From the beginning of 1994 through 2010, the Florida Department of Environmental Protection reported approximately 

2,500 incidents of spills in the Florida Keys. The annual mean 

number of petroleum and chemical spills was around 150 over 

the same period, with diesel fuel, motor oil, and gasoline representing 49% of these incidents, collectively. Spills in the sanctuary can have an impact on living resource quality. Whether 

associated with fuel discharges from small vessel groundings, 

or larger oil or chemical spills resulting from offshore shipping 

traffic, offshore drilling operations, or land-based sources, spills 

have the potential to adversely impact corals, foraging birds, 

marine mammals, fishes, seagrasses and mangroves. 

Diver impacts from recreational snorkeling or scuba diving 

can negatively impact corals in locations that are heavily utilized. 

Other ecotourism activities in the Florida Keys, such as dolphinwatching boats, can disrupt natural activities of these animals. 

Even though the human population recently decreased in the 

Florida Keys, indirect impacts from urbanization and use of coastal areas will continue to impact living resource quality. Runoff from 

nonpoint sources of pollution diminishes water quality. Illegal discharges (e.g., discharging or depositing sewage into all waters) 

can also create excessive amounts of nutrients, stimulating the 

rapid growth of algae, which in turn smother and kill live coral. 

Both direct and indirect impacts can adversely affect living resource quality in the Florida Keys. However, over the 

long term, localized direct impacts may be overwhelmed by the 

adverse and wide-ranging indirect effects of anthropogenically 

caused climate change resulting in sea level rise, abnormal air 

and water temperatures, and changing ocean chemistry.
State of Sanctuary Resources

CONDITION REPORT 2011 Florida Keys 59

Living Resources Status & Trends

# Issue Rating Basis for Judgment Description of Findings

9 Biodiversity ▼

Relative abundance across a spectrum of species has been substantially 

altered, with the most significant being large reef-building corals, largebodied fish, sea turtles, and many invertebrates, including, the long-spined 

sea urchin. Recovery is questionable.

Selected biodiversity loss has caused or is likely to 

cause severe declines in some but not all ecosystem 

components and reduce ecosystem integrity.

10 Extracted Species ?

Historical effects of recreational and commercial fishing and collection of 

both targeted and non-targeted species; it is too early to determine ecosystem effects of new fishery regulations and new ecosystem approaches to 

fishery management.

Extraction has caused or is likely to cause severe 

declines in some but not all ecosystem components and 

reduce ecosystem integrity.

11 Non-Indigenous 

Species ▼

Several species are known to exist; lionfish have already invaded and will 

likely cause ecosystem level impacts; impacts of other non-indigenous 

species have not been studied.

Non-indigenous species may inhibit full community 

development and function, and may cause measurable 

but not severe degradation of ecosystem integrity.

12 Key Species — Reduced abundance of selected key species including corals (many species), queen conch, long-spined sea urchin, groupers and sea turtles.

The reduced abundance of selected keystone species 

has caused or is likely to cause severe declines in ecosystem integrity; or selected key species are at severely 

reduced levels, and recovery is unlikely.

13 Health of Key 

Species ▼

Hard coral and gorgonian diseases and bleaching frequency and severity 

have caused substantial declines over the last two decades; long-term 

changes in seagrass condition; disease in sea turtles; sponge die-offs; low 

reproduction in queen conch; cyanobacterial blooms; lost fishing gear and 

other marine debris impacts on marine life.

The comparatively poor condition of selected key 

resources makes prospects for recovery uncertain.

14 Human Activities —

Despite the human population decrease and overall reduction in fishing 

in the Florida Keys since the 1990s, heavy recreational and commercial 

fishing pressure continues to suppress biodiversity. Vessel groundings 

occur regularly within the sanctuary. Annual mean number of reported 

petroleum and chemical spills were around 150 during that time period, 

with diesel fuel, motor oil, and gasoline representing 49% of these 

incidents collectively. Over the long term, localized direct impacts may be 

overwhelmed by the adverse and wide-ranging indirect effects of anthropogenic climate change resulting in sea level rise, abnormal air and water 

temperatures, and changing ocean chemistry.

Selected activities have caused or are likely to cause 

severe impacts, and cases to date suggest a pervasive 

problem.

Status: Good Good/Fair Fair Fair/Poor Poor Undet.

Trends: Improving (p), Not Changing (–), Declining (q), 

Undetermined Trend (?), Question not applicable (N/A)

NOTE: Judging an ecosystem as having “integrity” implies the

relative wholeness of ecosystem structure and function, along

with the spatial and temporal variability inherent in these characteristics, as determined by the ecosystem’s natural evolutionary history. Ecosystem integrity is reflected in the system’s

ability to produce and maintain adaptive biotic elements. Fluctuations of a system’s natural characteristics, including abiotic

drivers, biotic composition, complex relationships, and functional processes and redundancies are unaltered and are either

likely to persist or be regained following natural disturbance.
State of Sanctuary Resources

60 Florida Keys CONDITION REPORT 2011

Maritime Archaeological Resources

The following information provides an assessment by sanctuary 

staff and experts in the field of the status and trends pertaining to the 

current state of sanctuary maritime archaeological resources:

15. What is the integrity of known maritime archaeological resources and how is it changing? There is some uncertainty regarding the integrity of submerged maritime archaeological resources in the Florida Keys sanctuary. Organic, ferrous, and 

other manmade materials associated with maritime archaeological 

resources (wood, iron, copper, brass, leather, twine, and fabric) are 

non-renewable resources. To varying extents, they are all subject 

to deterioration from corrosive and chemical reactions involving 

seawater (e.g., salts and oxygen), movement caused by storms, 

and marine life impacts (e.g., sea turtles scratching or cleaning their 

carapaces, stone crabs eating wood). Sediment movement can 

also affect resources by subjecting them to shifting foundations, exposure, or abrasion. Storms such as hurricanes can also influence 

resource integrity by covering or uncovering resources with sediment. In addition, looters have been taking artifacts from archaeological sites in the Keys for many years. Because of these factors, 

the rating for this question is “fair/poor” because the diminished 

condition of selected archaeological resources has substantially 

reduced their historical, scientific or educational value and is likely 

to affect their eligibility for listing in the National Register of Historic 

Places. The trend rating is “declining” because anecdotal evidence 

suggests human impacts to maritime archeological resources has 

increased in the form of recreational and commercial fishing gear 

entanglement and multiple reported vessel groundings that occur 

on or near maritime archeological resources.

16. Do known maritime archaeological resources pose an

environmental hazard and how is this threat changing? No environmentally dangerous levels of hazardous material 

leakages have occurred in association with any maritime archeological resources in the sanctuary; however, some maritime archeological resources have been dislodged and fragmented during storm 

events. These fragments and pieces have the potential to come 

into contact with and impact the surrounding habitat. Therefore, our 

rating for this question is “good/fair” because selected maritime archaeological resources may pose isolated or limited environmental 

threats, but substantial or persistent impacts are not expected. Furthermore, there is no evidence to suggest that the environmental 

threat of sanctuary maritime archeological resources is changing.

17. What are the levels of human activities that may 

influence maritime archaeological resource quality and how are they changing? Volunteers with Florida 

Keys National Marine Sanctuary Submerged Resources and 

Maritime Archaeological Resources Status & Trends

# Issue Rating Basis for Judgment Description of 

Findings

15 Integrity ▼

Resources are nonrenewable and are 

subject to deterioration or loss resulting 

from looting, 

chemical processes, 

shifting sediments, 

marine life, fishing 

gear entanglement 

and vessel groundings (the last two 

are increasing in 

frequency).

The diminished 

condition of selected 

archaeological 

rezsources has substantially reduced 

their historical, 

scientific, or educational value and it 

likely to affect their 

eligibility for listing 

in the National 

Register of Historic 

Places.

16 Threat to 

Environment —

Movement of 

sunken vessels 

during storm 

threatens nearby 

resources.

Selected maritime 

archaeological 

resources may 

pose isolated or 

limited environmental threats, 

but substantial or 

persistent impacts 

are not expected.

17 Human Activities ▼

Reports of looting 

and vessel grounding cases involving 

potential resources 

are increasing.

Selected activities 

have caused or 

are likely to cause 

severe impacts, 

and cases to date 

suggest a pervasive 

problem.

Status: Good Good/Fair Fair Fair/Poor Poor Undet.

Trends: Improving (p), Not Changing (–), Declining (q), 

Undetermined Trend (?), Question not applicable (N/A)

Inventory Team have documented more than 400 underwater 

historical sites in the sanctuary, and it is assumed there are many 

resources yet to be discovered and documented. More than 300 

vessel groundings are reported in the sanctuary every year and 

some may impact maritime archaeological resources. In addition, 

the availability of inexpensive, off-the-shelf underwater technologies now affords the public the opportunity to locate and visit archaeological resources, thus increasing the potential for looting 

and other unauthorized human activities that can further affect 

the rate of deterioration and scientific value of maritime archaeological resources in the sanctuary. In addition, hook-and-line and 

commercial fishing tackle are also regularly found on submerged 

resources. Because reports of looting and vessel grounding 

cases involving potential maritime archaeological resources are 

increasing, the response to this question is rated “fair/poor” as 

these activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem. Although 

the intensity of these impacts varies year-to-year, the resulting 

trend suggests that conditions appear to be “declining.”
Response to Pressures

CONDITION REPORT 2011 Florida Keys 61

The sanctuary was created and exists under federal law. It became effective in state waters with the consent of the Board of 

Trustees of the Internal Improvement Trust Fund of the state of 

Florida, which is comprised of the governor and cabinet. It is administered by NOAA and is jointly managed with the state of Florida under a co-trustee agreement, specifically through the Florida 

Department of Environmental Protection (FDEP). In addition, the 

Florida Fish and Wildlife Conservation Commission (FWC) enforces sanctuary regulations in partnership with sanctuary managers 

and the NOAA Office of Law Enforcement (NOAA 2007).

Regulations are an integral component of the sanctuary management process. They make up an important part of sanctuary 

management by regulating certain activities on a sanctuary-wide 

basis and others depending on how an area of the sanctuary has 

been categorized or zoned. Permitting, authorization, notification 

and review processes allow certain activities that are otherwise 

prohibited to take place under carefully controlled circumstances 

(NOAA 2007).

An enforcement presence in sanctuary waters is necessary in 

order to protect and conserve resources. Sanctuary law enforcement has traditionally been accomplished through a Cooperative 

Enforcement Agreement between NOAA and the state of Florida. 

Beginning in 1981, NOAA and the state entered into an agreement in 

which the Florida Park Service, previously responsible for managing 

the John Pennekamp Coral Reef State Park, continued to provide 

management services to NOAA, including enforcement of sanctuary 

regulations. The state, now in the form of the FWC, continues as 

the sanctuary’s primary enforcement arm. A recent example of this 

cooperative enforcement agreement includes two of Florida’s largest illegal lobster fishing cases on record that took place in 2009. In 

these cases, divers were caught and later convicted of taking more 

than 10,000 pounds of lobsters off of illegal artificial structures known 

as casitas in the Great White Heron National Wildlife Refuge. These 

two separate cases were built by NOAA Fisheries Service agents 

and the U.S. Fish and Wildlife Service Office of Law Enforcement, 

and FWC played an important role in executing the resulting search 

and seizure warrants9

.

In addition to traditional law enforcement activities, the sanctuary relies heavily on “interpretive enforcement,” which seeks voluntary compliance primarily through education. The goal of interpretive enforcement is to gain the greatest level of compliance through 

understanding and public support of sanctuary goals. Interpretive 

enforcement emphasizes informing the public through educational 

messages and literature about responsible behavior before resources can be adversely impacted. Sanctuary law enforcement officers, 

staff and volunteers talk directly with users and distribute brochures 

in the field and throughout the community. Such encounters allow 

officers to make direct, informative contact with visitors and local 

residents while conducting routine enforcement activity. Preventive 

enforcement is achieved by maintaining sufficient presence within 

the sanctuary to deter violations. Successful enforcement relies on 

frequent water patrols and routine vessel boardings and inspections. 

Water patrols ensure that sanctuary users are familiar with regulations in order to deter willful or inadvertent violations and provide 

quick response to violations and emergencies (NOAA 2007).

The following section describes current or proposed management 

responses to pressures impacting sanctuary resources.

Marine Zoning

Marine zoning10 is being employed in the sanctuary to assist in 

the protection of the biological diversity of the marine environment 

in the Keys. Zoning is critical to achieving the sanctuary’s primary 

goal of resource protection. Its purpose is to protect and preserve 

sensitive components of the ecosystem by regulating activities within 

the zoned areas, while facilitating activities compatible with resource 

protection. Zoning ensures that areas of high ecological importance 

will evolve in a natural state, with minimal human influence. Zoning 

also promotes sustainable use of the sanctuary resources, and pro9 It is illegal to catch lobster from artificial structures in Florida waters, except from fishing gear allowed by FWC, FDEP or Army Corps on permitted artificial reefs (e.g. Duane, Eagle, Thunderbolt). Furthermore, sanctuary regulations (§922.163 (a)(3)) prohibit “...placing or abandoning any 

structure, material, or other matter on the seabed.”

10 Marine zone efficacy is currently being evaluated by sanctuary staff and partners. Results are expected to be released to the public in 2012.

Response to Pressures

F

lorida Keys National Marine Sanctuary uses an ecosystem approach to comprehensively address the variety of impacts, pressures, 

and threats to the Florida Keys marine ecosystem. It is only through this inclusive approach that the complex problems facing 

the sanctuary can be adequately addressed. The goal of the sanctuary is to protect the marine resources of the Florida Keys by 

interpreting the marine environment for the public and facilitating human uses of the sanctuary that are consistent with the primary 

objective of sanctuary resource protection.
Response to Pressures

62 Florida Keys CONDITION REPORT 2011

tects areas that represent diverse habitats and areas important for 

maintaining natural resources (e.g., fishes, invertebrates, etc.) and 

ecosystem functions.

In 1997, the sanctuary implemented its management plan that created special areas of varying sizes and purposes, and prohibited extractive activities within them. These areas were designated as types 

of marine zones in order to reduce pressures in heavily used areas, 

protect critical habitats and species, and reduce user conflicts. The 

efficacy of the marine zones is monitored sanctuary-wide under the 

Research and Monitoring Action Plan. The implementing regulations 

for this system of marine zones were instituted in the sanctuary in 1997. 

Three of the zone types (Sanctuary Preservation Areas, Ecological 

Reserves, and Special-use areas) are fully protected no-take areas, 

where all consumptive activities (e.g., lobstering, fishing, spearfishing, 

shell collecting) are prohibited. In July 2001, the 151-square-nauticalmile (518 square kilometers) Tortugas Ecological Reserve was implemented and is the largest of the sanctuary’s fully protected zones. All 

fully protected no-take zones combine to protect 6% of sanctuary waters, and encompass 65% of the spur and groove shallow coral reef 

habitat (Figure 37). 

The zone types within the Sanctuary include:

■ Areas to Be Avoided (ATBA) – These areas prohibit the operation of a tank vessel or vessels greater than 50 meters in registered length, with a few exceptions (e.g., national defense, law 

enforcement, responses to emergencies). Some ATBA boundaries buffer those of the sanctuary (Figure 37). 

■ Existing Management Areas (EMA) – These areas were 

established either by NOAA or another federal agency prior to 

1997 when sanctuary zoning regulations went into effect. EMAs 

delineate the existing jurisdictional authority of other agencies 

and have their own protections and restrictions above and beyond those that apply sanctuary-wide. Examples include Looe 

Key National Marine Sanctuary, Key Largo National Marine SancFigure 37. A map of many (not all) of the jurisdictions and zones in south Florida and the Florida Keys.

Source: NOAA /FWC
Response to Pressures

CONDITION REPORT 2011 Florida Keys 63

tuary, Key West National Wildlife Refuge, and Great White Heron 

National Wildlife Refuge. 

■ Wildlife Management Areas – These areas minimize disturbance to especially sensitive wildlife populations and their habitats. 

Examples of such areas include bird nesting, resting, or feeding areas and turtle nesting beaches. Regulations governing access are 

designed to protect endangered or threatened species or their habitats, while providing opportunities for public use. Access restrictions 

can include no-access buffer zones, no-motor zones, idle speed 

only/no wake zones, and closed zones. There are 27 wildlife management areas, 20 of which are under the management of the U.S. 

Fish and Wildlife Service as units of the National Wildlife Refuge 

System. These areas are located within the Great White Heron, Key 

West, Key Deer, and Crocodile Lake National Wildlife Refuges.

■ Ecological Reserves – These areas encompass large, contiguous and diverse habitats. They provide natural spawning, 

nursery, and permanent residence areas for the replenishment 

and genetic protection of marine life and to protect and preserve 

all habitats and species, particularly those not protected by fishery 

management regulations. Two ecological reserves protect areas 

that represent the full range of diversity of resources and habitats 

found throughout the sanctuary. These areas limit consumptive 

activities, while continuing to allow activities that are compatible 

with resource protection. This provides the opportunity for these 

areas to evolve in a natural state, with minimal human influence.

■ Sanctuary Preservation Areas (SPA) – These areas protect shallow reefs along the reef tract. SPAs encompass discrete, 

biologically important areas that help sustain critical marine species and habitats. Regulations for this zone type are designed 

to limit consumptive activities and to separate users engaged in 

different kinds of activities. Diving, snorkeling and boating are allowed inside these zones. SPAs have mooring buoys for boaters 

to use in order to prevent anchor damage to corals. The actual 

size and location of these zones was determined by examination 

of user patterns, aerial photography, and ground-truthing of specific habitats. Some SPAs allow limited baitfishing by permit only. 

■ Special-use Areas – These areas are set aside for scientific research, restoration, and monitoring. They can be used for specific 

uses such as long-term research and monitoring and/or minimizing 

the adverse environmental effects of high-impact activities. Currently, 

there is only one type of Special-use Area being utilized in the sanctuary; there are four small Research-Only areas (totaling less than three 

square nautical miles) located between Key West and Key Largo.

■ Tortugas Bank “No Anchor Area” – Vessels 50 meters in 

length are prohibited from anchoring on the portion of Tortugas 

Bank within the sanctuary west of Dry Tortugas National Park and 

south of Tortugas Ecological Reserve (North). 

■ General-use Area –Though not specifically identified in the 

sanctuary management plan, this zone includes the (remaining) 

areas in which general sanctuary regulations apply.

Research and Monitoring

The marine ecosystem of the Florida Keys is diverse and complex, 

and many of its ecological processes and their interrelationships are not 

well known. Although many resource impacts are obvious and severe, 

they are often not documented or quantified, and in addition, their causes 

may be unknown. As a result, the goal of the Florida Keys National Marine Sanctuary Research and Monitoring Action Plan (NOAA 2007) is to 

provide the knowledge necessary to make informed management decisions concerning the protection of the sanctuary’s resources. Monitoring 

enables the establishment of baseline information on natural resources 

and other components of the ecosystem, and allows for the measurement of changes over time. As monitoring studies gather data, they have 

the potential to detect significant changes in natural resources that result 

from management actions or from other causes. The findings of research 

projects must also help managers and scientists identify cause-and-effect 

relationships that generate ecological patterns and trends, and stressors 

and other factors that threaten the health of the coral reef ecosystem.

A few examples of monitoring programs that provide sanctuary 

managers with basic information about the state of the Florida Keys 

coral reef ecosystem include:

■ Water Quality Protection Program – since 1995, has conducted comprehensive, long-term monitoring of three ecosystem 

components: water quality, coral reefs and hard bottom communities, and seagrasses.

■ Ecological Research and Monitoring Program – detects 

status and trends of various ecological parameters (e.g., habitats 

such as coral reef and hard-bottom communities, seagrasses, and 

mangroves; episodic events such as algal blooms and fish kills; 

ecosystem indicators such as sedimentation rates and turbidity) 

in order to discern local and system-wide effects of human and 

natural disturbances on natural resources and to assess the overall 

health of the ecosystem.

■ Marine Zone Monitoring Program – documents the effectiveness of 24 marine zones established in 1997 and 2001, including 

the Tortugas Ecological Reserve, that are protected from consump-
Response to Pressures

64 Florida Keys CONDITION REPORT 2011

tive activities (“no-take zones”). Monitoring projects document 

trends in ecological processes, reef fishes, Caribbean spiny lobster, 

queen conch, other invertebrates, and benthic community structure 

within fully protected marine zones and nearby reference areas.

■ Social and Economic Monitoring – documents the levels 

of use and changes in those levels of use and researches the socioeconomic impacts of management decisions on user groups, 

including determining the knowledge, attitudes, and perceptions 

of sanctuary management strategies and regulations by commercial fishermen, dive shop owners and operators, and members of 

local environmental groups. The 2007-2008 study on recreation 

and tourism in the Florida Keys/Key West extended this to all residents and visitors, however the results are not yet available.

Management Responses to Water Quality Pressures

Point and Nonpoint Sources of Pollution

The sanctuary, in partnership with the EPA and the FDEP, has implemented a Water Quality Protection Program aimed at addressing 

point and nonpoint sources of pollution in order to restore and maintain the chemical, physical, and biological integrity of the sanctuary. 

This includes restoration and maintenance of a balanced, indigenous 

population of corals, shellfish, fish, and wildlife, along with recreational activities in and on the water. A variety of research has been 

and is being conducted under the Water Quality Protection Program 

umbrella. Most studies have been funded by EPA, but funding has 

also been provided by the US Fish and Wildlife Service and FDEP. 

Some of these are special studies designed to document the fate 

and ecological impacts of non-wastewater pollutants originating from 

sources such as permitted discharges, stormwater runoff, groundwater leachates, and marinas. Pollutants may include hydrocarbons, 

heavy metals, and pesticides (NOAA 2007). The research also includes wastewater pollutants and ecological studies, eutrophication 

gradient studies, comparative studies of impacted and non-impacted 

sites, historical studies, and use of sewage tracers (NOAA 2007).

Further efforts to address water quality issues reached a significant 

milestone in 1999, when the state of Florida requested a No Discharge 

Zone (NDZ) for city of Key West waters out to 600 feet (183 meters) from 

shore, prohibiting discharge of treated or untreated sewage from vessels, and the EPA concurred with this request. At the recommendation 

of the Water Quality Protection Program Steering Committee and the 

request of the Florida governor, in 2002 the EPA and the state of Florida 

established a NDZ for state waters within the sanctuary. The Steering 

Committee requested NOAA establish a similar zone for federal waters 

of sanctuary. As of December 2010, NOAA amended the sanctuary 

regulations to prohibit discharge or deposit of sewage from marine sanitation devices (MSDs) within the boundaries of the sanctuary and would 

require MSDs be secured to prevent sewage discharge or deposit.

Sanctuary educators have incorporated messages about water 

quality into their presentations and programs in the community and 

have reached out to local media to publicize this information as part 

of an annual water quality awareness campaign. 

Lastly, Monroe County and local municipalities are undergoing extensive upgrades in wastewater infrastructure that provide advanced 

wastewater treatment, significantly reducing wastewater impacts and 

pressures in the area. As part of this upgrade, old plants are being 

closed down and the new plants use deep-well injection or shallowwater injection instead of nearshore outfalls. All residences and businesses in the Florida Keys will be connected to central sewer by 2015.

Swimming Advisories

The Florida Department of Health has been monitoring beach 

water quality in the Florida Keys since 2000, as part of the “Florida 

Healthy Beaches Program.” This program tests on a weekly basis for 

the presence of fecal coliform and enterococci bacteria in beach water. 

High concentrations of these bacteria may indicate the presence of 

microorganisms that could cause disease, infections or rashes. When 

high levels of these bacteria are detected a “swimming advisory” is 

issued. The cause of each advisory is normally unknown; however, 

possible sources of pollution have been determined for most beaches 

in the state. The passage of new state legislation in the summer of 

2009 requires the FDEP to investigate public wastewater treatment 

facilities within one mile of a beach when an advisory is issued for that 

beach. There are currently 17 beaches tested every week in Monroe 

County, five of which are within the city of Key West. 

External Input

The sanctuary is partnering with the EPA and the FDEP to conduct research to understand the effects of water transported from 

Florida Bay on water quality in the sanctuary. Specifically, circulation 

studies have been conducted to estimate present-day, long-term net 

transport and episodic transport from Florida Bay to the sanctuary. 

In addition, studies have also been conducted to document any ecological impacts of Florida Bay water on sanctuary communities and 

potentially endangered or threatened species. 

Harmful Algal Blooms

The sanctuary provides support and coordination to Mote Marine 

Lab’s Tropical Research Center’s Marine Ecosystem Event Response 

and Assessment (MEERA) Project. The MEERA Project is designed to 

provide early detection and assessment of biological events occurring 

in the Florida Keys and surrounding waters. The goal is to help the scientific community better understand the nature and causes of events, 
Response to Pressures

CONDITION REPORT 2011 Florida Keys 65

such as coral bleaching and disease outbreaks, fish kills, harmful algal 

blooms, “red tides,” and other events that adversely affect marine organisms. Understanding the events will help scientists and managers 

determine if they are natural or linked to human activities. The project 

relies on observations made by people who are frequently on the water, 

such as charter boat captains, recreational boaters, environmental professionals, and law enforcement personnel (NOAA 2007).

Marinas and Boats

It has been documented that nutrients being introduced into nearshore waters have resulted in water quality degradation. One source of 

these nutrients is sewage discharge from boats and live-aboard vessels. 

As a result, in 2002 all state waters in the sanctuary were designated as 

“no-discharge” zones for sewage (treated or untreated) from all vessels. 

This designation was made by the EPA under the Clean Water Act. This 

designation requires that all boats store their sewage in a holding tank, 

to be pumped out at an approved facility. Mobile pump-out facilities were 

established to support compliance with this designation (NOAA 2007). 

Furthermore, NOAA initiated a rule in December 2010 that prohibits boaters from discharging or depositing sewage into both state and federal 

waters of the sanctuary. Pump-out locations have been identified in the 

Upper Keys Boater Guide (published by FWC and Monroe County) and 

a sanctuary one-page science summary that explains the new 2010 rule.

The sanctuary has also worked with the city of Key West and 

Reef Relief to develop and implement a “Pump It, Don’t Dump It!” 

boater-education program.

Cruise Ships

Cruise ships started visiting the Port of Key West in the late 1980s 

and by 2008, 346 ships arrived with nearly 740,000 passengers (Leeworthy et al. 2010). At the peak, cruise ship passengers exceeded 1 

million passengers, but this concerned the Key West local government. Local officials felt the city was too dependent on the cruise ship 

industry for their revenues, and they were concerned about the impact 

on the quality of life in Key West (Leeworthy et al. 2010). As a result, 

the Key West Port Authority has since attempted to restrict cruise ship 

visitation to fewer than 750,000 passengers per year.

Although large cruise vessels are the equivalent of small cities 

in regard to waste production, they are not subject to the strict environmental regulations and monitoring requirements imposed on 

land-based facilities, such as obtaining discharge permits, meeting 

numerous permit conditions and monitoring discharges while at sea. 

Though all ocean-going carriers (cruise ships included) are subject 

to numerous international and federal waste disposal regulations, 

such as the Act to Prevent Pollution from Ships (APPS), the International Convention for the Prevention of Pollution from Ships (MARPOL) and the Marine Plastic Pollution Research and Control Act, it is 

a legal option for any large ship to dispose of blackwater (sewage), 

graywater (waste from showers, sinks, laundries and kitchens), and 

most other solid waste except plastics while at sea.

The Florida Keys Sanctuary Advisory Council formed a Large 

Vessel Working Group, which was tasked with investigating the 

impacts of cruise ships on sanctuary resources (NOAA 2007). The 

working group collaborated closely with the cruise ship industry and 

ultimately agreed to support the city of Key West’s effort to develop 

fair and effective environmental practices for large ships. The working group also supported the expansion of the No Discharge Zone 

into all sanctuary waters for all vessels, including cruise ships. 

Petroleum (hydrocarbons) or Chemical Spills

A ban on oil drilling and hard mineral mining was established when 

the sanctuary was created. Also, in November 2002, the United Nations International Maritime Organization approved designation of the 

Florida Keys as a Particularly Sensitive Sea Area (PSSA). PSSAs 

are areas that need special protection because of their significance 

for recognized ecological, socioeconomic or scientific reasons, and 

which may be vulnerable to damage by international maritime activities. Such designation is not accompanied by additional rules and regulations, but rather seeks to elevate public awareness of the threat of 

oil spills and hazardous materials to sensitive marine environments.

Despite these measures, the potential for spills still poses a signifiIn order to manage discharge into the sanctuary, a

new NOAA rule, initiated in December 2010, prohibits boaters from discharging or depositing sewage into

both state and federal sanctuary waters.

The Deepwater Horizon (DWH) Oil Spill in 2010 was

of an unprecedented magnitude and beyond the scope

and design of local ACPs. It also posed an ecological

and economic threat to the Florida Keys. During the

oil spill response, sanctuary staff and SCAT (Shoreline

Cleanup and Assessment Technique) teams monitored

shorelines for tarballs. Because the Loop Current never connected to the spill area in the Gulf of Mexico,

there was no evidence that any DWH related pollution

or contaminants reached the Florida Keys. However,

long-term impacts to the overall area, if they occur,

will remain unknown for some time.
Response to Pressures

66 Florida Keys CONDITION REPORT 2011

cant threat to sanctuary resources. Spill response is structured via the 

Incident Command System (ICS) for the legal protection of the trustees 

of the resource, as well as the “responsible party.” As such, the general 

public is usually not directly involved in the response process, with few 

exceptions. Response to significant spills is led by the U.S. Coast Guard 

and the FDEP, with NOAA’s Office of Response & Restoration and the 

sanctuary participating at their request to provide relevant spill trajectory 

information and to assess damage to marine resources. The primary 

guidance documentation used by all parties during a spill is the local Area 

Contingency Plan, which for Sector Key West (includes the Florida Keys) 

can be found on line at http://ocean.floridamarine.org/ACP/KWACP. This 

document was developed as a result of the Oil Pollution Act of 1990, has 

been in place since 1996, and has been regularly updated. 

In an effort to streamline communications between responding and 

trust agencies, NOAA initiated “Safe Sanctuaries 2005” in the sanctuary, which simulated a tanker grounding within the sanctuary that injured 

coral habitat and historical artifacts and spilled oil that threatened other 

sanctuary resources. This exercise provided training in emergency response management, including sanctuaries-specific training in the use 

of the Sanctuaries Hazardous Incident Emergency Logistics Database 

System (SHIELDS) and in the Incident Command System (ICS); this 

hypothetical spill scenario was the most realistic at the time (i.e., one 

tanker spilling a known quantity of a known material). The exercise involved more than 150 people, including representatives from the U.S. 

Coast Guard, the U.S. Department of the Interior, the FDEP, the FWC, 

Monroe County, and various NOAA programs. In addition, in February 

2010 staff from the sanctuary participated in the Coast Guard Sector 

Key West’s “Combined Preparedness for Response Exercise Program 

Full Scale Oil Spill Drill.” Sanctuary personnel provided natural resource 

expertise and guidance to the various response teams, helping identify 

and prioritize marine habitats in need of protection during the drill. In 

turn, exercises such as these helped the sanctuary and its agency partners during the response to the Deepwater Horizon oil spill April – July 

2010. For smaller spill events and vessels, the sanctuary has often assumed a lead role in ensuring that fuel, oil, and vessel debris is removed 

to minimize further damage to sanctuary resources. The sanctuary has 

a dedicated team of biologists that handle these occurrences.

Commercial and Recreational Fishing

Florida Keys National Marine Sanctuary does not manage any 

aspect of commercial or recreational fisheries. Fisheries management agencies with jurisdiction in sanctuary waters are FWC, Gulf 

of Mexico and South Atlantic Fishery Management Councils, and 

NOAA Fisheries Service. Current involvement of the sanctuary in 

issues related to fishing is primarily through use of marine zones.

Marine fishes depend on healthy habitats to survive and reproduce. Throughout their lives, fishes use many types of habitats 

including seagrass, salt marsh, coral reefs, kelp forests and rocky 

intertidal areas, among others. Various activities on land and in the 

water constantly threaten to alter, damage, or destroy these habitats. NOAA’s Fisheries Service, regional fishery management councils, and federal and state agencies work together to address these 

threats by identifying Essential Fish Habitat (EFH) and Habitat Areas 

of Particular Concern (HAPC) for each federally managed fish species and developing conservation measures to protect and enhance 

these habitats. Productive commercial and recreational fisheries are 

inextricably linked to healthy marine habitats; protecting these habitats will help support fishing communities now and for generations to 

come. Federal agencies that fund, permit, or carry out activities that 

may adversely affect seagrass, mangrove, coral, live/hard-bottom, or 

other habitats that are designated EFH or HAPC by the South Atlantic Fishery Management Council are required to consult with NOAA 

Fisheries Service regarding the potential impacts of their actions on 

these areas. Through this consultation requirement, NOAA Fisheries 

Service may recommend measures to avoid, minimize, mitigate or 

otherwise offset adverse effects on EFH. The South Atlantic Fishery 

Management Council has designated Florida Keys National Marine 

Sanctuary as HAPC for coral, coral reef and live/hard-bottom, and 

areas within the sanctuary as HAPC for coastal migratory pelagic 

species, such as mackerel and cobia.

The regional fisheries councils and state of Florida have prohibited destructive or wasteful fishing gear, established minimum size 

and bag limits, as well as seasonal closures, and restricted the take 

of some species. As mandated by the Florida Keys National Marine 

Sanctuary and Protection Act (public law 101-605), six types of marine zones were established throughout the sanctuary to reduce user 

group conflicts and protect resources. These zones were designed 

to reduce damage to resources and threats to environmental quality, 

while allowing uses that are compatible with resource protection. The 

zones protect habitats and species by limiting consumptive or conflicting user activities, allowing resources to evolve in a natural state, 

with minimal human influence. Exploited species have shown positive responses in these areas (e.g., yellowtail snapper, mutton snapper, black grouper), but monitoring and appropriate regulation must 

be maintained to prevent overfishing. Distribution of fishing rules and 

information about marine zones and their regulations is a regular 

component of the sanctuary’s education and outreach program, especially at events and festivals and presentations in the community.

As mentioned in Question 12 in the “State of Sanctuary Resources” section of this report, the no-take zones within the sanctuary 

were not designed as a fishery management tool; however, at the 

sanctuary’s urging, the FWC’s Fish and Wildlife Research Institute 

initiated a long-term monitoring project designed to assess if and to 

what degree these areas served to provide protection of Caribbean 
Response to Pressures

CONDITION REPORT 2011 Florida Keys 67

spiny lobsters from fishery exploitation. The project was designed 

to compare the abundance and size-structure of Caribbean spiny 

lobster observed within the protected area with those encountered at 

adjacent “reference” sites that were subject to fishing pressure. The 

general expectation was that if these reserves provided protection 

from fishing, then the abundance and size-structure of the lobsters 

encountered within the reserves should increase relative to the adjacent reference sites. The initial five-year monitoring effort concluded 

that the SPAs were too small to adequately protect Caribbean spiny 

lobsters from the fishery, but the larger Western Sambo Ecological 

Reserve (WSER) did function to some degree as a fishery reserve 

(Cox and Hunt 2005). There, the mean size of legal-sized lobsters 

and the frequency of occurrence of lobsters significantly larger than 

those commonly encountered within the fished areas of the sanctuary increased steadily after its establishment. 

Continued monitoring of lobsters within the WSER, a smaller adjacent protected area, and nearby fishery-exploited areas found these 

atypically large lobsters in the areas adjacent to the WSER with increased frequency, suggesting that they were likely emigrating from 

the WSER. Additional research using acoustic marking to examine the 

movement patterns of Caribbean spiny lobsters within WSER revealed 

that Caribbean spiny lobsters do indeed commonly move across the 

boundaries of the WSER. The increased abundance of these large 

lobsters within the exploited areas of the sanctuary suggests that the 

WSER may serve to some degree to enhance fishery landings. Additionally, this study also revealed that female Caribbean spiny lobsters 

commonly cross the boundary of the WSER to the outlier reef lying 

seaward of the offshore bank reef to spawn. Although these reproductive-related movement patterns occur primarily during the fishery’s 

spawning season closure, these findings revealed that the WSER 

does not encompass all of the habitats utilized by adult Caribbean 

spiny lobsters during their life history, and inclusion of the adjacent 

outlier reef would serve to enhance lobsters from fishery exploitation.

Lastly, as the Federal agency responsible for ensuring the long-term 

sustainability of our nation’s ocean resources, NOAA continually evaluates the quality of recreational fishing data collected and reported. Considering the ever more detailed uses of NOAA’s data in stock assessments and fisheries management decision-making, in 2006 the National 

Research Council of the National Academy of Sciences recommended 

an overhaul of NOAA’s data program in order to provide more detailed 

and timely information to managers, fishermen and other stakeholders. 

One of the NRC’s recommendations was the creation of a universal 

“phone book” - or registry - of current saltwater anglers. This system will 

replace the previous method of randomly dialing coastal households, 

providing a far more efficient and effective way to determine the number 

of people fishing and the number of trips they take, or what is known as 

the overall fishing effort. That information is a crucial part of our ability 

to estimate the health of fish stocks, and to check that protections put 

in place to preserve fisheries will be fair, effective, and based on sound 

science. Registration is also a way for NOAA and anglers to work together to help ensure the long-term future of saltwater fishing. As the 

first comprehensive accounting of the scope of recreational saltwater 

fishing in the U.S., the registry will help to more fully demonstrate anglers’ economic, conservation and marine stewardship impacts. More 

information about the NRC’s recommendations and how NOAA is working to implement them can be found at www.countmyfish.noaa.gov. 

Climate Change, Bleaching Events, and 

Weather Disturbances

Extreme water temperature fluctuations in the sanctuary have 

been linked to bleaching and disease in reef corals and mass mortality of seagrass in Florida Bay. Beginning in 1989, recording thermographs have been deployed by the sanctuary in strategic areas 

throughout the Florida Reef Tract to monitor water temperature over 

the long term, and make that information available to management 

and research user groups. In addition to these thermographs, other 

state and academic researchers collect in-situ water temperature 

data and efforts are currently underway by the sanctuary and FWC 

to build a website that facilitates data sharing and collaboration.

With support from the Mote Marine Laboratory a program was created and modeled after the Great Barrier Reef Marine Park Authority’s 

“Bleach Watch” program. The Florida Keys “Bleach Watch” Program 

utilizes volunteers to provide reports from the reef on the actual condition of corals throughout the bleaching season. These field observations help to monitor for signs of coral bleaching. There are two 

facets to the program: the Professional Program and the Community 

Program. The Professional Program is for divers who visit a particular reef on a regular schedule and can provide weekly monitoring of 

the reefs to help gauge the pre-bleaching coral composition and help 

determine the susceptibility of a site to bleaching. The Community 

Program is designed for observers who make occasional reef trips or 

do not frequent the same reef sites. Information gathered from both 

programs is compiled into a “Current Conditions Report” that provides 

a comprehensive overview of current conditions throughout the sanctuary (see http://isurus.mote.org/Keys/current_conditions.phtml). 

As mentioned in the “Harmful Algal Blooms” section of this report, the sanctuary also provides support and coordination to Mote 

Marine Lab’s Tropical Research Center’s Marine Ecosystem Event 

Response and Assessment (MEERA) Project. One of the goals of 

the MEERA Project is to provide early detection and assessment of 

coral bleaching events in the sanctuary (NOAA 2007).

Sanctuary staff have also supported the Ocean Conservancy 

and the EPA in implementing the Reef Ecosystem Condition Monitoring Program (RECON). The RECON program trains volunteer 
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68 Florida Keys CONDITION REPORT 2011

divers to collect information about the reef environment, the health 

of stony corals, the presence of key reef organisms and obvious 

human-induced impacts. The goals of RECON are to broaden the 

scope of available information about bottom-dwelling organisms on 

coral reefs, to alert local researchers and managers of changing 

reef conditions such as coral bleaching and nuisance algal blooms, 

and to increase public understanding of these threats to coral reef 

ecosystems (NOAA 2007).

The sanctuary is also a partner in the Florida Reef Resilience 

Program (FRRP). This program is managed by The Nature Conservancy, with support from the state of Florida, NOAA and the Great 

Barrier Reef Marine Park Authority. A parallel program is in progress 

at Australia’s Great Barrier Reef, and the two programs are designed 

to complement one another and to inform coral-reef conservation 

around the globe. Specific to the field component of FRRP, sanctuary 

staff participate in the disturbance response monitoring efforts, which 

rapidly assess coral condition and health along the Florida Reef Tract 

during peak annual water temperatures, as well as after disturbances 

like the cold-water event of January 2010 (see Question 13). 

Diseases of Marine Organisms

The Florida Keys sanctuary has been collaborating with partners 

to better understand and document diseases plaguing the ecosystem. For example, a collaboration between EPA, NOAA, and Mote 

Marine Lab began epizootiological assessments of coral disease along 

the Florida Reef Tract in 1998. This research is ongoing, and aims to assess the prevalence of coral diseases as a function of time, the location 

within the Florida Reef Tract, and the reef type. Nine disease conditions 

described in the literature, two additional syndromes and “other disease” 

affecting scleractinian coral species and sea fans, are used in these assessments. Santavy et al. (2005) describes the epizootiological trends of 

coral disease from the first four years of this project, and a more comprehensive analysis of similar trends from 2005 to 2009 are in preparation.

In 2009, NOAA awarded The Nature Conservancy and its partners 

$3.3 million to support threatened coral recovery and restoration in 

Florida (including the Keys) and the U.S. Virgin Islands. The goal of 

this project is to recover one acre of coral reefs in each of eight distinct areas of the Caribbean by growing Acropora coral in seafloor 

nurseries and transplanting them to depleted reef sites (Figure 38). 

Figure 38. A diver performs regular maintenance on Acropora cervicornis fragments at a permitted coral nursery funded by the American Reinvestment 

and Recovery Act. 

Photo: Ken Nedimyer
Response to Pressures

CONDITION REPORT 2011 Florida Keys 69

This project will provide significant and tangible ecological impacts 

through an increase in local biodiversity, as well as enhanced ecosystem services for various user groups, including recreational divers and snorkelers, commercial dive tour operators, commercial fishers and recreational anglers. This funding is a direct result of the 

American Recovery and Reinvestment Act of 2009. 

In response to the large die-off of long-spined sea urchins in the 

1980s, husbandry techniques are currently being refined to produce laboratory-reared individuals to increase sea urchins densities 

throughout the Florida Keys. Experimental manipulations are also 

being conducted to compare the behavior of these individuals to wild 

D. antillarum. The goal of this work is to produce large numbers of 

ecologically competent hatchery-reared D. antillarum that can be 

released into the wild as part of a comprehensive reef restoration 

effort. This is a collaborative effort with Mote Marine Laboratory, and 

the FWC’s Fish and Wildlife Research Institute.

Vessel Use

In 1990, as part of the sanctuary management plan, several 

areas were declared off-limits to tankers and other vessels over 

164 feet (50 meters) in length. The Areas to Be Avoided (ATBAs) 

were developed in response to the region’s many historical groundings, and large vessels have been discouraged from operating in 

those located along the Florida Reef Tract. Four ATBAs account 

for 1,561 square nautical miles (5,354 square kilometers) of waters 

within and adjacent to the sanctuary. In addition, sanctuary staff 

use a database to assess trends in vessel groundings, identify “hot 

spots” where education and outreach activities can be enhanced, 

and determine what solutions, such as waterway marking, may be 

appropriate. The sanctuary is authorized to assess civil penalties 

and recover the cost of response, assessment, and restoration from 

the responsible parties. The sanctuary has Damage Assessment, 

Restoration and Resource Protection (DARRP) teams in the upper 

Keys and the lower Keys. In conjunction with sanctuary education 

and outreach staff, managers, and law enforcement personnel, 

DARRP staff develop grounding prevention measures, minimize impacts, assess impacts, repair injuries where possible, and support 

the associated legal processes. DARRP team members also conduct seagrass restoration using techniques developed by NOAA’s 

National Centers for Coastal Ocean Science. 

Since 1981, mooring buoys have been installed and maintained 

throughout the sanctuary with the intent to reduce vessel damage 

to sensitive marine habitats, specifically coral reef formations and 

seagrass beds, and to submerged archeological resources. There 

are currently nearly 500 mooring buoys within the boundaries of the 

sanctuary. While mooring buoys are excellent management tools, 

other management programs must accompany a mooring buoy program, including education, outreach, research and monitoring. The 

Mooring Buoy Action Plan, part of the 2007 Florida Keys National 

Marine Sanctuary Management Plan (NOAA 2007), establishes a 

methodology for identifying areas appropriate for mooring buoys 

and managing boating activities near coral reefs so that detrimental 

impacts are minimized. By allowing or directing access at selected 

locations, a Mooring Buoy Program can limit resource use conflicts 

and damage to the resources. In addition, sanctuary staff travels 

worldwide, assisting groups with mooring buoy installations that protect natural resources from anchor damage.

The state of Florida and the sanctuary have also been educating boaters to limit risks and improve navigation in coral reef areas. 

Large vessel avoidance and Racon beacons in lighthouses have 

resulted in declines in large vessel groundings. State and sanctuary 

officials have improved their response to grounding events and improved their restoration methods of damaged sites, thereby reducing 

the extent of damage. Reef restoration is a fertile field of study necessary to determine effective and efficient ways to restore degraded 

coral reef ecosystems. 

Sanctuary education and outreach efforts include resource and 

safety education for boaters in sanctuary waters. Education is accomplished through information booths at outdoor events and festivals; presentations given to boating, fishing and community clubs 

and organizations; distribution of boater education materials to businesses in the Keys; and many other programs. FWC provides some 

of the boater education materials that are distributed. Media outreach 

on vessel injury prevention and shallow-water boating techniques 

is accomplished through the Seagrass Outreach Partnership. The 

partnership is an interagency group that began in the Keys under 

sanctuary education and outreach leadership, but now has partners 

statewide. The sanctuary implemented a grant through the Coastal 

Zone Management Program that identified sensitive areas in need 

of additional marking by spar buoys to prevent vessel injuries and 

installed the needed spar buoys in conjunction with Monroe County. 

Coastal Development

Hydrology

Today, the South Florida Water Management District is responsible for operating and maintaining the Project to continue to provide 

for urban and agricultural development in coordination with flood 

and water supply protection (NOAA 1996). To address the priorities 

of returning more natural water flows to the Everglades and restoring the varied habitats from Kissimmee Chain of Lakes through the 

Florida Keys, Congress established the South Florida Ecosystem 

Restoration Task Force in 1996. Task force members include federal, state, local and tribal representatives who coordinate numerous 
Response to Pressures

70 Florida Keys CONDITION REPORT 2011

restoration initiatives. At the forefront of these undertakings is the 

Comprehensive Everglades Restoration Plan, a hydrologic plan that 

hopes to reverse the unintended consequences resulting from the 

original flood control project of the U.S. Army Corps of Engineers. 

Restoration projects, guided by task force strategic planning and 

success criteria, include land acquisition, invasive species management, water storage, and stormwater treatment, among others. Restoration projects are expected to take 40 to 50 years to accomplish. 

Sanctuary staff regularly participate in task force-related committees 

and actively track the progress of water management and restoration 

projects designed to restore freshwater flows to two important estuaries adjacent to sanctuary waters: Florida Bay and Biscayne Bay.

Nearshore Construction and Dredging

The U.S. Army Corps of Engineers, FDEP, South Florida Water 

Management District (SFWMD) and NOAA Fisheries Service serve 

lead roles in reviewing projects for nearshore construction that trigger 

federal and state dredge and fill regulations, including the Clean Water Act (33 U.S.C. §1344), Rivers and Harbors Act (33 U.S.C. §403), 

and Section 373 and Section 403 Florida Statutes of the MagnusonStevens Fishery Conservation and Management Act (16 U.S.C. 

§1801 et seq.). Waters of Monroe County have also been designated 

as Outstanding Florida Waters (62-302.700 Florida Administrative 

Code), which provides additional protections to water quality. Furthermore, the majority of dredge and fill projects associated with coastal 

residential and commercial development are regulated under Florida 

Statutes Chapter 37, while dredging and construction related to deepwater ports is also addressed in Chapters 161 and 403 FS. Construction projects that are not exempted by the sanctuary regulations 

(those not listed at 15 CFR 922.163(a)(3)(i) – (v)) or that trigger other 

sanctuary prohibitions are reviewed by the sanctuary. Conditions requiring avoidance of certain species during construction (e.g., stony 

corals), modification of project design to reduce impacts, or removal 

of sensitive organisms from the site may be included in any given 

permit or authorization that the sanctuary issues for a project. To the 

extent possible, DEP, SFWMD, NOAA Fisheries Service, U.S. Army 

Corps of Engineers, and sanctuary staff work collaboratively to comprehensively review projects and provide consistent determinations. 

NOAA also participates in the Naval Air Station Key West Partnering Team, an interagency group formed in 2004 to review large-scale 

projects, including continued maintenance of water depths in Key 

West Harbor, which support Navy and Homeland Security operations.

The sanctuary Coral Rescue and Nursery Program was developed 

in 2003 in response to repairs by the U.S. Navy at Key West Truman 

Harbor Mole Pier, which threatened thousands of stony corals growing on the wharf. Sanctuary staff have developed protocols for coral 

risk assessment, rescue and transplantation when corals are found 

growing on government or private structures that are slated for repair. 

Preferentially, corals removed from construction sites are transplanted 

back to the area once activities are complete, or are moved to a nearby 

location to preserve functional resource value. In instances where onsite relocation is not a viable option, corals are placed in the sanctuary coral nursery at the Dr. Nancy Foster Florida Keys Environmental 

Complex in Key West or at an offshore nursery managed by Mote Marine Laboratory. Corals receive routine husbandry until such time that 

they can be used for beneficial projects, including educational display 

and exhibition, basic and applied research, and restoration of damaged areas. Use of rescued corals for research purposes reduces the 

pressure on natural habitats, providing scientists with an alternate and 

viable source of samples. Rescued corals are also used in management-directed research that will help protect coral reefs in the future. 

Beach Nourishment

Similar to other nearshore construction projects, beach nourishment or restoration in the Florida Keys is regulated by U.S. Army 

Corps of Engineers and Florida DEP Bureau of Beaches and Coastal 

Systems (BBCS). BBCS has developed strict metrics for sediment 

grain composition, turbidity allowances, toe of fill effects, and time 

of year restrictions for these projects. These metrics are outlined in 

Chapter 161 of Florida Statutes, which addresses beach nourishment and protection structures. Through their permit process, the 

Army Corps is required to consult with the U.S. Fish and Wildlife Service and NOAA Fisheries Service and consider impacts of proposed 

beach nourishment on species and habitats managed by those 

agencies, including sea turtles, manatees and essential fish habitat.

Non-Indigenous Species

Eradication of introduced species is difficult and often impossible, 

and management practices focus largely on prevention of introductions. However, in one successful example of eradicating an invasive 

exotic finfish, four Pacific orbicular batfish were captured at Molasses 

Reef and given to the New England and Florida Aquariums for display. 

In June 2008, representatives from approximately 30 state, federal and non-profit institutions met during a workshop to develop an 

early detection and rapid response (ED/RR) program for non-native 

marine fish introductions in south Florida. This program identified 

ED/RR processes from sighting to removal. Since then, staff from 

NOAA’s Office of National Marine Sanctuaries and NOAA’s National 

Centers for Coastal Ocean Science (NCCOS) have been partnering with the U.S. Geological Survey (USGS), Reef Environmental 

Education Foundation (REEF), and Mote Marine Lab to test and further refine ED/RR protocols for South Florida (Morris and Whitfield 

2009). As part of this endeavor, Florida Keys sanctuary staff recently 

collaborated with REEF and NCCOS to develop an action plan for 
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CONDITION REPORT 2011 Florida Keys 71

the control and management of lionfish within sanctuary waters. This 

plan outlines a detection, control and management strategy for lionfish that will control the densities and impacts of invasive lionfish in 

the sanctuary (Morris and Whitfield 2009). Between January 2009 

and July 2010, there were more than 500 reported sightings and 250 

confirmed removals. 

As part of the effort to increase detection, reporting and response, 

REEF has worked with the sanctuary to conduct public workshops 

and training sessions for on–-water professionals. The sanctuary 

has issued permits to these professionals to remove lionfish in Sanctuary Preservation Areas (no-take zones). Additional workshops continue to train and engage local communities in collecting and handling techniques in efforts to effect successful removals. In addition 

to tracking done by USGS, sightings of non-native marine fishes are 

also being tracked through the REEF Volunteer Fish Survey Project 

in partnership with federal and state agencies in the hope of preventing additional successful invasions in Florida’s marine waters.

To help prevent the establishment of new non-native fishes in 

Florida’s marine waters, NOAA’s NCCOS, the USGS and REEF recently published the “Field Guide to Nonindigenous Marine Fishes 

of Florida” as part of their efforts to detect and remove non-native 

marine fishes as soon as they are discovered. The guide provides 

descriptions and illustrations of non-native marine fish species that 

have been seen along Florida’s coasts, and includes maps of the 

sightings. It is hoped that divers, fishermen, and others will use the 

guide to report non-native species immediately in order to help prevent their rapid establishment (Schofield et al. 2009).

Wildlife Disturbance

Until recently, the combination of the sanctuary’s marine zones 

(see Figure 37 on page 62) and its general regulations were the primary tools used to minimize wildlife disturbance. In an effort to augment these regulatory tools, two education and outreach programs 

were developed and implemented specifically to promote responsible 

visitor usage of sanctuary resources: the Dolphin SMART and the 

Blue Star programs.

A special area of the sanctuary is home to a resident group of 

bottlenose dolphins (Tursiops truncatus). It is also where many 

businesses conduct dolphin tours in a small geographic area. This 

may cause unnecessary stress to the local dolphin population by 

disrupting their natural behaviors. Therefore, conservation agencies 

including NOAA’s Office of National Marine Sanctuaries and NOAA 

Fisheries Service, the Dolphin Ecology Project, and the Whale and 

Dolphin Conservation Society, as well as local businesses and members of the public, teamed up in 2007 to launch the Dolphin SMART 

program — a unique, multifaceted program encouraging responsible 

viewing of wild dolphins and recognizing businesses that participated. Program participation is intended for commercial businesses 

conducting wild dolphin tours, or any commercial vessel that may 

opportunistically view wild dolphins. Dolphin SMART offers participation incentives for businesses that follow the program criteria and 

educate their customers about the importance of minimizing wild dolphin harassment. It also includes an important research component 

that provides insight about the daily lives of the local, wild dolphin 

populations. The acronym “SMART” in Dolphin SMART is a reminder 

of the basic principles of dolphin watching: Stay at least 150 feet 

(45 meters) from dolphins; Move away slowly if the dolphins seem 

disturbed; Always put your vessel engine in neutral when dolphins 

are near; Refrain from feeding, touching or swimming with wild dolphins; and Teach others to be Dolphin SMART. The program has 

recognized five operators in the Keys, as well as operators in other 

areas in southwest Florida and Alabama. A list of Dolphin SMART 

operators also is available online at http://sanctuaries.noaa.gov/dolphinsmart/welcome.html.

The Blue Star Program, launched in 2009, was established by 

the sanctuary to reduce the impact of divers and snorkelers on the 

local coral reef ecosystem. Blue Star is a voluntary education and 

recognition program for commercial dive and snorkel operators who 

are committed to coral reef conservation and education. By forming 

a partnership with commercial operators to educate their customers 

about the fragile nature of the coral reef ecosystem, the purpose and 

goals of the sanctuary, and diving and snorkeling etiquette individuals 

can use to make a difference. Specific goals of the program include:

■ Reduce the amount of damage to coral reefs caused by divers 

and snorkelers by emphasizing proper etiquette and empowering 

individual divers with the right information.

■ Increase knowledge among divers, snorkelers, and charter boat 

owners and staff about the purpose, goals and objectives of Florida Keys National Marine Sanctuary and engage them as partners 

in coral reef conservation.

■ Educate the public about the importance of responsible diving 

and snorkeling in the coral reef ecosystem.

In 2010, British researcher Emma Camp conducted a study analyzing diver interactions with coral reefs, documenting how divers 

either purposely or incidentally come into contact with coral. Touching coral has been shown to have a cumulative damaging effect on 

coral polyps. Camp observed more than 80 divers diving with four 

different dive shops. One of the conclusions of her study indicates 

that increased conservation education, such as that offered by the 

Blue Star program, can significantly reduce these diver touches and 

incidental interactions with the coral reef (Camp 2011).
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72 Florida Keys CONDITION REPORT 2011

Artificial Reefs

NOAA supports a precautionary approach when considering the 

deployment of artificial reefs, and will continue to emphasize the 

protection, restoration, and enhancement of natural habitats, as opposed to constructing artificial habitats, as a general matter of policy 

consistent with the Coral Reef Conservation Act, Magnuson-Stevens 

Fishery Conservation and Management Act, and the National Marine Sanctuaries Act when reviewing related permit applications. The 

sanctuary recognizes that additional research is needed to better understand both the socioeconomic and coral reef ecosystem impacts 

of artificial reefs. 

In 2006 research was done by NOAA to investigate the hypothesis that the introduction of the USS Spiegel Grove as an artificial reef 

off Key Largo would alter use patterns on the surrounding natural 

reefs. The results showed a 13% reduction in diver use on the surrounding natural reefs, a 160.5% increase in artificial reef use, and a 

net increase in total artificial and natural reef use of 9% (Leeworthy 

et al. 2006). This represents a positive increase in total business, 

while reducing pressure on the natural reefs. Concurrently, REEF 

implemented a five-year monitoring plan to document fish species, 

sighting frequency and estimated abundance over time at the Spiegel Grove site and at seven nearby natural and artificial reef sites. 

The primary goal of the monitoring was to document fish recruitment 

to the artificial reef, detect changes over time in the assemblage and 

compare patterns of select species between sites. Though the final 

report does not compare the change in abundance of all species 

surveyed between natural habitat and artificial structures over time, 

it does document that the Spiegel Grove had a slightly lower species 

richness than six of the other seven study sites by the end of the 

five-year project, which could be related to the impact of Hurricane 

Dennis in 2005. Similar research is underway by NOAA and REEF 

for the USS Vandenberg, which was sunk off Key West in 2009.

The revised sanctuary management plan also outlines a strategy related to researching the impacts of artificial reefs. In this strategy, there are three activities that must be carried out by the artificial reef permit holders with oversight from sanctuary staff. The first 

activity will guide the assessment of effects of artificial reefs on fish 

and invertebrate abundance and community composition and on 

other sanctuary resources. Further, the longevity of artificial reefs 

composed of different materials will be evaluated, and appropriate 

artificial reef locations will be determined, based in part on these 

findings. The second activity complements the first; information on 

habitat modifications caused by artificial reefs is a necessary element of evaluating consistency of artificial reefs with sanctuary 

goals and objectives. Soft sediments may be altered during installation of artificial reefs, and water flows around these structures 

are likely to continue to modify soft sediments and their associated 

communities. Nearby hard-bottom habitats may also experience 

modifications as a result of altered flows and other factors associated with artificial reefs, thus these factors need to be adequately 

studied. The third activity will assess and develop regulations for 

artificial reef construction and evaluate habitat suitability for artificial reef placement.

Marine Debris

Since 1994, the sanctuary has helped to organize the Adopt-aReef Program, an annual volunteer reef cleanup effort. The program 

targets recreational divers and provides data placards for recording 

debris collected at designated locations, usually popular dive sites, 

coordinated through local dive shops. The types of data collected 

include date and location of the cleanup, diver name, bottom time, 

number of trash bags filled, a rank-order of the five most important 

debris items, and an estimated weight of debris collected. From 1994 

to 2000, 866 divers collected 16,535 pounds (7,500 kilograms) of 

debris, with hook-and-line gear, aluminum cans, plastic, cardboard, 

wood, and rope from lobster pots constituting the most common 

items. The materials removed from the sanctuary are prevented from 

causing further impact to sanctuary resources and the data collected 

regarding the type and distribution of debris are being used by sanctuary staff for other marine debris response activities. 

Shoreline and water cleanups are a regular part of the sanctuary’s education and outreach Team OCEAN program. Significant 

amounts of marine debris have been retrieved from sanctuary waters over the years by volunteers and student groups using kayaks 

to collect debris from shallow waters and larger, recreational vessels to transport it back to shore. Since the sanctuary began tracking the amount removed from this effort (2007), more than 30,000 

pounds (13,608 kilograms) of marine debris have been hauled to a 

land-based solid waste facility. Lost fishing gear, polypropylene rope, 

Styrofoam buoys, plastic traps, and plastic trap throats constitute the 

majority of the debris collected by sanctuary staff and volunteers.

The sanctuary has also worked with Monroe County and FWC to 

identify derelict vessels for removal, and has administered funds for 

this purpose. 

During the 2005 hurricane season, the Florida Keys were subjected to several major storms that mobilized and damaged commercial lobster and stone crab traps, making it practically impossible 

for fishermen to locate and retrieve their fishing gear. Florida state 

regulations (Chapter 68B-55 FAC), which normally prohibits removal 

of commercial traps by anyone other than their owner or law enforcement officers, threatened to hinder removal efforts. Ultimately, 

the state of Florida partnered with Monroe County to recover more 

than 45,000 traps from Monroe County waters, at a cost of more 

than $1.8 million. Marine debris removal also occurs on a smaller 
Response to Pressures

CONDITION REPORT 2011 Florida Keys 73

scale, as community coastal cleanup events are regularly organized 

throughout the year. These non-sanctuary-sponsored events help 

eliminate trap-related debris that has washed onto mangrove islands 

and beaches. 

Summer 2009 also marked the end of a three-year debris removal project in which remote sensing was used to locate illegal lobsterattracting structures, called “casitas.” The NOAA Fisheries Service 

Restoration Center, with support from the NOAA Marine Debris Program, the sanctuary and other state and federal agencies, oversaw 

the identification and removal from sanctuary waters of 89 tons of 

casita material placed illegally.

Lastly, marine debris removal efforts have been directed as part 

of compensatory restoration in vessel grounding settlements.

Military Use

Military activities that were specifically identified in the Environmental Impact Statement (EIS) and management plan for the sanctuary 

are exempt from sanctuary regulations. For new activities, or activities 

that were not identified in the EIS and management plan, the military 

is required to consult with the sanctuary (as directed by Section 304(d) 

of the NMSA) to ensure that the proposed activities are carried out in a 

manner that minimizes impacts to sanctuary resources.

The most significant military activity occurring in the sanctuary 

since its designation has been ongoing maintenance of the Key West 

harbor by the U.S. Navy. In 2003, the sanctuary consulted with the 

U.S. Army Corps of Engineers, EPA and Florida DEP when the Navy 

proposed maintenance dredging in the Key West harbor, shipping 

channel and turning basins. The removal of approximately 1 million cubic yards of sediment was permitted by the Army Corps in 

July 2003 to restore the charted depth and facilitate safe transit of 

deeper-draft Navy vessels through the area, and has been successful in reducing sediment plumes created by the propellers of these 

and other larger vessels such as cruise ships. Sanctuary conditions 

requiring avoidance of known coral areas, and dredge effect monitoring, among others, were incorporated into the Army Corps permit to protect resources. Additional dredging was conducted by the 

Navy in 2007 to address sedimentation that occurred as a result of 

the hurricane seasons of 2004 and 2005. The Naval Air Station Key 

West Natural Resources and Environmental Compliance Partnering 

Team, an interagency group that includes the sanctuary, was formed 

in 2004 by the Navy to review large-scale projects, including continued maintenance of the Key West harbor. 

The U.S. Coast Guard Sectors Key West and Miami coordinate 

with the sanctuary on multiple initiatives and provide significant protection to the marine environment of the Florida Keys. Coast Guard 

maintained navigation aids, including warning markers, delineate 

popular reef sites, many of which are protected by the sanctuary as 

Sanctuary Preservation Areas, Ecological Reserves, and Special Use 

Areas. The Coast Guard works with the sanctuary and other federal, 

state and local jurisdictions to develop interagency response plans to 

oil spills or other environmental threats, which includes participation in 

the National Preparedness for Response Exercise Program (NPREP). 

This program was developed to establish a workable exercise schedule meeting the requirements of the Oil Pollution Act of 1990 and the 

Clean Water Act. The NPREP sets forth exercise requirements ranging from small internal or external notification exercises to full-scale, 

area-wide exercises involving personnel and equipment from federal, 

state, and local government and industry. The Coast Guard also consults the sanctuary for geographic information system (GIS) support 

during actual pollution response activities, migrant interdiction operations, and to assist with the development of map products for inclusion 

in Area Contingency Plans or other response planning documents. 

More recently, Coast Guard personnel led the Unified Command for 

intergovernmental response to the Deepwater Horizon MC252 oil 

spill. The Coast Guard also coordinates closely with the sanctuary 

through their marine event permitting program, ensuring that authorized events (such as boat races, regattas, fireworks displays and 

other public and private activities) comply with the sanctuary regulations and include conditions for resource protection.

Management Responses to Pressures Impacting 

Maritime Archaeological Resources

Proactive management of submerged archaeological resources in 

sanctuary waters occurs through a Programmatic Agreement involving 

the sanctuary, the state of Florida, and the Advisory Council on Historic 

Preservation. This partnership is responsible for managing cultural 

resources in the sanctuary consistent with the Federal Archaeology 

Program, the Abandoned Shipwreck Act of 1987 and the National HisTeam OCEAN is an on-the-water education and information program aimed at protecting the natural

marine resources of the Florida Keys, while enriching

the experiences of visitors to Florida Keys National

Marine Sanctuary. It involves the stationing of trained

volunteer teams at heavily visited reef sites throughout the Keys during peak recreational boating seasons to serve as educators and inform other boaters

about the unique nature of the coral reef habitat, share

their knowledge of the best approach to certain areas,

demonstrate the use of a mooring buoy, and distribute

safety information.
Response to Pressures

74 Florida Keys CONDITION REPORT 2011

toric Preservation Act. Maritime heritage resources in the sanctuary 

encompass a broad historical range. Because of the Keys’ strategic 

location on early European shipping routes, the area’s shipwrecks 

reflect the history of the entire period of discovery and colonization. 

Currently, 14 shipwrecks within the sanctuary are listed on the National 

Register of Historic Places. This richness of historical resources brings 

a corresponding responsibility to protect and preserve resources of 

national and international interest. Long-term protection requires a 

precautionary approach to historical resource management, particularly when information or artifacts may be destroyed or lost through 

direct or indirect activities. Accordingly, the resources are managed for 

public benefit and enjoyment, while the historical and cultural heritage 

is preserved for the future. As with all sanctuary resources, submerged 

archaeological resources are managed to facilitate multiple uses that 

are compatible with resource protection. (NOAA 2007)

It is an integral part of the sanctuary mission to protect and preserve 

maritime heritage resources for the public trust while still allowing for the 

private salvage of publicly owned historical resources. This is accomplished through a rigorous permit system which adheres to the Federal 

Archaeology Program guidelines. The three-tiered permit system allows 

for the private sector and institutions such as universities to survey, inventory, research, and recover maritime heritage resources in the sanctuary. The three types of permits available are the Survey and Inventory Permit, the Research and Recovery Permit, and the Deaccession/

Transfer Permit. Proper standards of conservation, cataloguing, display, 

curation and publication must be assured before permitting disturbance 

of any maritime heritage resources. Such projects are expensive and 

labor-intensive, sometimes requiring specialists in the fields of archaeology, conservation, museum work, historic shipwreck research, and 

recovery. Sanctuary staff continues to explore public and private partnerships for management and consider private-sector implementation, 

when appropriate. A comprehensive GIS database is used to track and 

monitor permits as well as other maritime heritage resources. 

Commercial salvage in the sanctuary can be allowed by permit for 

abandoned shipwrecks in federal waters. For wrecks in state waters, 

the state of Florida must be consulted due to their jurisdiction over 

abandoned shipwrecks through the Abandoned Shipwreck Act. There 

will be no commercial salvage of maritime archaeological resources of 

high historical significance, however commercial salvage for objects of 

low-to-moderate historical significance in areas relatively devoid of significant natural resources can be permitted. The recording and reporting 

of recovery operations, as well as the curation of representative samples 

of artifacts, must be consistent with the Programmatic Agreement for 

Maritime Archaeological Resources Management, as well as the Federal Archaeological Program or equivalent standards. The federal program 

was developed by the National Park Service by Presidential Order, and 

includes a collection of historical and archaeological resource-protection 

laws to which federal managers are required to adhere. The National 

Historic Preservation Act (NHPA) requires federal agencies to develop 

programs to inventory and evaluate historic resources. NHPA Section 106 requires review of each recovery permit by the State Historic 

Preservation Office and the Advisory Council on Historic Preservation. 

Permits within the scope of, and which adhere to all provisions of, the 

Programmatic Agreement need not go through an additional NHPA 106 

review process. The Abandoned Shipwreck Act requires that state’s 

management practices protect shipwrecks, natural resources and habitat areas, and guarantee recreational access to shipwreck sites. Sanctuary management also preserves selected shipwrecks in the sanctuary 

for research and recreation whereas some artifacts are recovered and 

preserved in museums with public access (NOAA 2007).

The sanctuary also has an extensive education and volunteer program in maritime heritage resources. Volunteers on the Submerged 

Resources Inventory Team have documented more than 400 underwater historical sites in the sanctuary. The three-volume inventory 

entitled “Underwater Resources of the Florida Keys National Marine 

Sanctuary” is available in public libraries throughout the Florida Keys. 

The education team has also developed a historic Shipwreck Trail 

which highlights nine historic vessels that sank in sanctuary waters 

and represents three broad periods of Florida Keys maritime history: 

European Colonial, American, and Modern. Brochures and underwater site guides for each vessel have been distributed to area dive 

operators and are also available in two sanctuary offices. The sites 

on the trail are marked with spar buoys and offer mooring buoys to 

eliminate damages from anchoring. The sanctuary also manages 189 

Collection-type Heritage Assets, and by way of a Curatorial Services 

Agreement, more than 100 of these artifacts are on loan to various 

organizations including the Mel Fisher Maritime Heritage Society and 

Historical Museum in Key West, the Florida Keys Land and Sea Trust/

Crane Point Museum and Nature Center in Marathon, and the Key 

Largo Chamber of Commerce. Of the remaining artifacts, some can 

be viewed on display in the Florida Keys National Marine Sanctuary 

Upper Region Office.
Concluding Remarks

CONDITION REPORT 2011 Florida Keys 75

This is the first attempt to comprehensively describe the status, pressures and trends of resources in the sanctuary. At its core, this 

document is an executive-level summary of research that describes the status and condition of sanctuary resources and should 

be used in conjunction with the more detailed summaries of the individual monitoring and research programs (e.g., zone monitoring program, water quality protection program, etc.). Additionally, this report helps identify strengths in current monitoring efforts, 

as well as causal factors that may require monitoring and potential remediation in the years to come. The data discussed will enable resource 

managers and stakeholders not only to acknowledge prior changes in resource status, but will provide guidance for future management 

challenges. For example, this report supports the need for additional management actions that address the degraded conditions of some key 

habitats and living resources in the sanctuary. 

In this era of significant decline of coral reefs throughout the world, resilience is the key to survival of this critical ecosystem. It has been 

estimated that coral cover on reefs in the Caribbean has declined by an average of 80% in the last three decades (Gardner et al. 2003). It is 

generally agreed that these declines are not due to a single cause, but have resulted from multiple stressors acting together to alter ecosystem conditions and resulting in widespread deterioration. In turn, resource “managers may be able to increase the resilience of the system to 

climate change...by reducing impacts of local- and regional-scale stressors, such as fishing, input of nutrients, sedimentation and pollutants, 

and degraded water quality” (Keller et al. 2009). Many areas within the sanctuary, especially patch reefs and the deeper, fore-reef environment, continue to exhibit relatively high cover (>25%) by reef-building corals, and this may provide important insight in understanding resilience and other factors that sustain coral reef vitality. Therefore, it is more important than ever to protect remaining healthy reefs from impacts 

that can be addressed through management actions, both for their own sake and in order to help us promote the recovery of other coral reefs.

Because of the recreational and commercial importance of the marine resources of the Florida Keys, protecting these sanctuary resources is 

valuable not only for the environment but also for the economy. The special marine resources of the region, which led to the area’s designation as a national marine sanctuary, contribute to the high quality of life for residents and visitors. Without these unique marine resources, the 

quality of both life and the economy of the Keys would decline. 

Concluding Remarks
Acknowledgements

76 Florida Keys CONDITION REPORT 2011

Acknowledgements

The staff of Florida Keys National Marine Sanctuary would like to acknowledge the assistance and efforts of

subject area experts who, by participating in meetings in March 2008, provided responses to questions that

guided the drafting of the “State of Sanctuary Resources” section of this report: Alejandro Acosta (FWC), Lad

Akins (REEF), Jerald Ault (UM-RSMAS), Erich Bartels (MML), James Bohnsack (NOAA Fisheries Service),

Joseph Boyer (FIU), Joseph Cavanaugh (REEF), Leda Cunningham (REEF), Bob Glazer (FWC), John Hunt

(FWC), G. Todd Kellison (NOAA Fisheries Service), Tom Matthews (FWC), Margaret Miller (NOAA Fisheries

Service), Steven Miller (UNCW), and Cory Walter (MML). The authors would also like to recognize the extensive contributions of Mark Chiappone (UNCW) to this document.

The report benefited significantly from the following individuals who either provided a preliminary review of

the report or contributed comments, content, images and data: Lad Akins (REEF), Jerry Ault (RSMAS), Carrie

Backlund (Naval Air Station, Key West), Edward Barham (Naval Air Station, Key West), Rick Beaver (FWC),

Cathy Becky (USGS Sirenia Project), Donald Behringer (UFL), Heather Blough (NOAA NMFS), Geoffrey Bock

(Dept. of Primary Industries & Fisheries), Jim Bohnsack (NOAA NMFS), Theo Brainerd (NOAA NMFS), Mark

Chiappone (UNCW), Gabriel Delgado (FWC), Michael Feeley (FWC), Roland Ferry (Wetlands, Coastal and

Oceans Branch, EPA, Region 4), Megan Forbes (NOAA Marine Debris Program), Karen Fox (Clancy Environmental Consultants, Inc., a Tetra Tech Company), Todd Hitchins (NOAA), John Hunt (FWC), Bill Kiene

(ONMS Southeast Region), William Kruczynski (Special Studies, EPA, Region 4), Gang Liu (NOAA Coral Reef

Watch Program), Jerry Lorenz (Audubon Society), Margaret Miller (NMFS), Anne Morkill (FWS), Ken Nedimyer (Coral Restoration Foundation), David Polk (Florida Department of Health), Rob Ruzicka (FWC), Joe

Schittone (formerly of ONMS), David A. Score (NOAA Corps), William Sharp (FWC), Tonya Shearer (Georgia Institute of Technology), Manoj Shivlani (RSMAS), and Ricardo Zambrano (FWC). Current and former

staff of Florida Keys National Marine Sanctuary also provided preliminary reviews of the report or contributed comments, content, images and data: Brenda Altmeier, Jeff Anderson, Michael Buchman, Karrie Carnes,

Joanne Delaney, Nancy Diersing, Kent Edwards, Alicia Farrer, Lilli Ferguson, William Goodwin, John Halas,

Todd Hitchins, J. Harold Hudson, Robert Keeley, Lauri MacLaughlin, Sean Morton, William Precht, Benjamin

Sniffen, Steve Werndli, and Fiona Wilmot.

Finally, our sincere thanks are extended to the peer reviewers of this document: John F. Bruno, Ph.D. (Associate

Professor, University of North Carolina at Chapel Hill), Richard E. Dodge, Ph.D. (Dean, Nova Southeastern

University Oceanographic Center), Paul Sammarco, Ph.D. (Professor, Louisiana Universities Marine Consortium), and Rob van Woesik, Ph.D. (Professor, Florida Institute of Technology).
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Additional Resources

92 Florida Keys CONDITION REPORT 2011

Biscayne National Park: http://www.nps.gov/BISC

Coral Restoration Foundation: http://www.coralrestoration.org

Dry Tortugas National Park: http://www.nps.gov/drto

Encyclopedia of the Florida Keys: http://www8.nos.noaa.gov/onms/park/Parks/?pID=8 

Everglades National Park: http://www.nps.gov/EVER 

Florida Department of Environmental Protection: http://www.dep.state.fl.us/coastal/sites/keys 

Florida Fish and Wildlife Conservation Commission: http://www.myfwc.com

Florida Keys Commercial Fishermen’s Association: http://fkcfa.org/default.aspx

Florida Keys National Marine Sanctuary: http://floridakeys.noaa.gov

Florida Keys National Marine Sanctuary Shipwreck Trail: http://floridakeys.noaa.gov/shipwrecktrail/welcome.html 

Florida Keys Online Guide: http://www.florida-keys.fl.us/history.htm

Florida Keys Sanctuary Science Summaries: http://floridakeys.noaa.gov/scisummaries/welcome.html 

John Pennekamp Coral Reef State Park: http://www.pennekamppark.com

Marine Ecosystem Event Response and Assessment (MEERA) http://isurus.mote.org/Keys/meera.phtml 

National Key Deer Refuge: http://www.fws.gov/nationalkeydeer

Naval Air Station (NAS) on Boca Chica: http://www.globalsecurity.org/military/facility/key_west.htm

Naval Air Station Key West: http://www.navy.mil/local/naskw

NOAA Coral Reef Watch: http://coralreefwatch.noaa.gov 

NOAA Marine Debris Program: http://marinedebris.noaa.gov

NOAA National Marine Fisheries Service: http://www.nmfs.noaa.gov

NOAA National Ocean Service: http://oceanservice.noaa.gov

NOAA Office of National Marine Sanctuaries: http://sanctuaries.noaa.gov

Reef Environmental Education Foundation: http://www.reef.org

Reef Relief: http://reefrelief.org 

Sanctuary Friends Foundation of the Florida Keys: http://www.sanctuaryfriends.org 

State of Florida: http://www.myflorida.com

U.S. Coast Guard: http://www.uscg.mil

U.S. Fish and Wildlife Service: http://www.fws.gov

University of Miami Rosenstiel School of Marine and Atmospheric Science: http://www.rsmas.miami.edu

Additional Online Resources
Appendix A: Rating Scheme for System-Wide Monitoring Questions

CONDITION REPORT 2011 Florida Keys 93

The purpose of this appendix is to clarify the 17 questions and possible responses used to report the condition of sanctuary resources 

in “Condition Reports” for all national marine sanctuaries. Individual staff and partners utilized this guidance, as well as their own 

informed and detailed understanding of the site to make judgments about the status and trends of sanctuary resources. 

The questions derive from the National Marine Sanctuary System’s mission, and a system-wide monitoring framework (NMSP 2004) developed to 

ensure the timely flow of data and information to those responsible for managing and protecting resources in the ocean and coastal zone, and to 

those that use, depend on and study the ecosystems encompassed by the sanctuaries. They are being used to guide staff and partners at each 

of the 14 sites in the sanctuary system in the development of this first periodic sanctuary condition report. Evaluations of status and trends may be 

based on interpretation of quantitative and, when necessary, non-quantitative assessments and observations of scientists, managers and users.

Judging an ecosystem as having “integrity” implies the relative wholeness of ecosystem structure and function, along with the spatial and 

temporal variability inherent in these characteristics, as determined by the ecosystem’s natural evolutionary history. Ecosystem integrity is 

reflected in the system’s ability to produce and maintain adaptive biotic elements. Fluctuations of a system’s natural characteristics, including 

abiotic drivers, biotic composition, complex relationships, and functional processes and redundancies are unaltered and are either likely to 

persist or be regained following natural disturbance. 

Following a brief discussion about each question, statements are presented that were used to judge the status and assign a corresponding 

color code. These statements are customized for each question. In addition, the following options are available for all questions: “ N/A” - the 

question does not apply; and “Undet.” - resource status is undetermined.

Symbols used to indicate trends are the same for all questions: “▲” - conditions appear to be improving; “▬” - conditions do not appear to 

be changing; “▼” - conditions appear to be declining; and “?” – trend is undetermined. 

This is meant to capture shifts in condition arising from certain changing physical processes and anthropogenic inputs. Factors resulting 

in regionally accelerated rates of change in water temperature, salinity, dissolved oxygen, or water clarity, could all be judged to reduce water 

quality. Localized changes in circulation or sedimentation resulting, for example, from coastal construction or dredge spoil disposal, can affect 

light penetration, salinity regimes, oxygen levels, productivity, waste transport, and other factors that influence habitat and living resource 

quality. Human inputs, generally in the form of contaminants from point or non-point sources, including fertilizers, pesticides, hydrocarbons, 

heavy metals, and sewage, are common causes of environmental degradation, often in combination rather than alone. Certain biotoxins, such 

as domoic acid, may be of particular interest to specific sanctuaries. When present in the water column, any of these contaminants can affect 

marine life by direct contact or ingestion, or through bioaccumulation via the food chain.

[Note: Over time, accumulation in sediments can sequester and concentrate contaminants. Their effects may manifest only when the sediments 

are resuspended during storm or other energetic events. In such cases, reports of status should be made under Question 7 – Habitat contaminants.]

Good Conditions do not appear to have the potential to negatively affect living resources or habitat quality.

Good/Fair Selected conditions may preclude full development of living resource assemblages and habitats, but are not likely to cause 

substantial or persistent declines.

Fair Selected conditions may inhibit the development of assemblages, and may cause measurable but not severe declines in 

living resources and habitats.

Fair/Poor Selected conditions have caused or are likely to cause severe declines in some but not all living resources and habitats.

Poor Selected conditions have caused or are likely to cause severe declines in most if not al, living resources and habitats.

Appendix A:

Rating Scheme for System-Wide Monitoring Questions

Water

Stressors 1. Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water quality and how are they changing?
Appendix A: Rating Scheme for System-Wide Monitoring Questions

94 Florida Keys CONDITION REPORT 2011

Nutrient enrichment often leads to planktonic and/or benthic algae blooms. Some affect benthic communities directly through space 

competition. Overgrowth and other competitive interactions (e.g., accumulation of algal-sediment mats) often lead to shifts in dominance 

in the benthic assemblage. Disease incidence and frequency can also be affected by algae competition and the resulting chemistry along 

competitive boundaries. Blooms can also affect water column conditions, including light penetration and plankton availability, which can alter 

pelagic food webs. Harmful algal blooms often affect resources, as biotoxins are released into the water and air, and oxygen can be depleted.

Good Conditions do not appear to have the potential to negatively affect living resources or habitat quality.

Good/Fair Selected conditions may preclude full development of living resource assemblages and habitats, but are not likely to cause 

substantial or persistent declines.

Fair Selected conditions may inhibit the development of assemblages, and may cause measurable but not severe declines in 

living resources and habitats.

Fair/Poor Selected conditions have caused or are likely to cause severe declines in some but not all living resources and habitats.

Poor Selected conditions have caused or are likely to cause severe declines in most if not all living resources and habitats.

Human health concerns are generally aroused by evidence of contamination (usually bacterial or chemical) in bathing waters or fish intended for consumption. They also emerge when harmful algal blooms are reported or when cases of respiratory distress or other disorders 

attributable to harmful algal blooms increase dramatically. Any of these conditions should be considered in the course of judging the risk to 

humans posed by waters in a marine sanctuary.

Some sites may have access to specific information on beach and shellfish conditions. In particular, beaches may be closed when criteria 

for safe water body contact are exceeded, or shellfish harvesting may be prohibited when contaminant loads or infection rates exceed certain 

levels. These conditions can be evaluated in the context of the descriptions below. 

Good Conditions do not appear to have the potential to negatively affect human health.

Good/Fair Selected conditions that have the potential to affect human health may exist but human impacts have not been reported.

Fair Selected conditions have resulted in isolated human impacts, but evidence does not justify widespread or persistent concern.

Fair/Poor Selected conditions have caused or are likely to cause severe impacts, but cases to date have not suggested a pervasive 

problem.

Poor Selected conditions warrant widespread concern and action, as large-scale, persistent, and/or repeated severe impacts are 

likely or have occurred.

Water

Eutrophic 

Condition 

2. What is the eutrophic condition of sanctuary waters and how is it changing?

3. Do sanctuary waters pose risks to human health and how are they changing?

Water

Human Health 
Appendix A: Rating Scheme for System-Wide Monitoring Questions

CONDITION REPORT 2011 Florida Keys 95

Among the human activities in or near sanctuaries that affect water quality are those involving direct discharges (transiting vessels, visiting 

vessels, onshore and offshore industrial facilities, public wastewater facilities), those that contribute contaminants to stream, river, and water 

control discharges (agriculture, runoff from impermeable surfaces through storm drains, conversion of land use), and those releasing airborne 

chemicals that subsequently deposit via particulates at sea (vessels, land-based traffic, power plants, manufacturing facilities, refineries). In 

addition, dredging and trawling can cause resuspension of contaminants in sediments.

Good Few or no activities occur that are likely to negatively affect water quality.

Good/Fair Some potentially harmful activities exist, but they do not appear to have had a negative effect on water quality.

Fair Selected activities have resulted in measurable resource impacts, but evidence suggests effects are localized, not widespread.

Fair/Poor Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Poor Selected activities warrant widespread concern and action, as large-scale, persistent, and/or repeated severe impacts have 

occurred or are likely to occur.

Habitat loss is of paramount concern when it comes to protecting marine and terrestrial ecosystems. Of greatest concern to sanctuaries 

are changes caused, either directly or indirectly, by human activities. The loss of shoreline is recognized as a problem indirectly caused by human activities. Habitats with submerged aquatic vegetation are often altered by changes in water conditions in estuaries, bays, and nearshore 

waters. Intertidal zones can be affected for long periods by spills or by chronic pollutant exposure. Beaches and haul-out areas can be littered 

with dangerous marine debris, as can the water column or benthic habitats. Sandy subtidal areas and hardbottoms are frequently disturbed 

or destroyed by trawling. Even rocky areas several hundred meters deep are increasingly affected by certain types of trawls, bottom longlines, 

and fish traps. Groundings, anchors, and divers damage submerged reefs. Cables and pipelines disturb corridors across numerous habitat 

types and can be destructive if they become mobile. Shellfish dredging removes, alters, and fragments habitats.

The result of these activities is the gradual reduction of the extent and quality of marine habitats. Losses can often be quantified through 

visual surveys and to some extent using high-resolution mapping. This question asks about the quality of habitats compared to those that 

would be expected without human impacts. The status depends on comparison to a baseline that existed in the past - one toward which 

restoration efforts might aim.

Good Habitats are in pristine or near-pristine condition and are unlikely to preclude full community development.

Good/Fair Selected habitat loss or alteration has taken place, precluding full development of living resource assemblages, but it is 

unlikely to cause substantial or persistent degradation in living resources or water quality. 

Fair Selected habitat loss or alteration may inhibit the development of assemblages, and may cause measurable but not severe 

declines in living resources or water quality.

Fair/Poor Selected habitat loss or alteration has caused or is likely to cause severe declines in some but not all living resources or water 

quality.

Poor Selected habitat loss or alteration has caused or is likely to cause severe declines in most if not all living resources or water quality.

4. What are the levels of human activities that may influence water quality and how 

are they changing?

Water

Human Activities 

5. What are the abundance and distribution of major habitat types and how are they 

changing?

Habitat

Abundance &

Distribution
Appendix A: Rating Scheme for System-Wide Monitoring Questions

96 Florida Keys CONDITION REPORT 2011

Many organisms depend on the integrity of their habitats and that integrity is largely determined by the condition of particular living organisms. Coral reefs may be the best known examples of such biologically-structured habitats. Not only is the substrate itself biogenic, but the 

diverse assemblages residing within and on the reefs depend on and interact with each other in tightly linked food webs. They also depend 

on each other for the recycling of wastes, hygiene, and the maintenance of water quality, among other requirements. 

Kelp beds may not be biogenic habitats to the extent of coral reefs, but kelp provides essential habitat for assemblages that would not 

reside or function together without it. There are other communities of organisms that are also similarly co-dependent, such as hard-bottom 

communities, which may be structured by bivalves, octocorals, coralline algae, or other groups that generate essential habitat for other 

species. Intertidal assemblages structured by mussels, barnacles, and algae are another example, seagrass beds another. This question is 

intended to address these types of places, where organisms form structures (habitats) on which other organisms depend.

Good Habitats are in pristine or near-pristine condition and are unlikely to preclude full community development.

Good/Fair Selected habitat loss or alteration has taken place, precluding full development of living resources, but it is unlikely to cause 

substantial or persistent degradation in living resources or water quality.

Fair Selected habitat loss or alteration may inhibit the development of living resources, and may cause measurable but not severe 

declines in living resources or water quality.

Fair/Poor Selected habitat loss or alteration has caused or is likely to cause severe declines in some but not all living resources or water 

quality.

Poor Selected habitat loss or alteration has caused or is likely to cause severe declines in most if not all living resources or water quality.

This question addresses the need to understand the risk posed by contaminants within benthic formations, such as soft sediments, hard 

bottoms, or biogenic organisms. In the first two cases, the contaminants can become available when released via disturbance. They can also 

pass upwards through the food chain after being ingested by bottom dwelling prey species. The contaminants of concern generally include 

pesticides, hydrocarbons, and heavy metals, but the specific concerns of individual sanctuaries may differ substantially.

Good Contaminants do not appear to have the potential to negatively affect living resources or water quality.

Good/Fair Selected contaminants may preclude full development of living resource assemblages, but are not likely to cause substantial 

or persistent degradation. 

Fair Selected contaminants may inhibit the development of assemblages, and may cause measurable but not severe declines in 

living resources or water quality.

Fair/Poor Selected contaminants have caused or are likely to cause severe declines in some but not all living resources or water quality.

Poor Selected contaminants have caused or are likely to cause severe declines in most if not all living resources or water quality.

6. What is the condition of biologically structured habitats and how is it changing? Habitat

Structure

7. What are the contaminant concentrations in sanctuary habitats and how are they 

changing?

Habitat

Contaminants
Appendix A: Rating Scheme for System-Wide Monitoring Questions

CONDITION REPORT 2011 Florida Keys 97

Human activities that degrade habitat quality do so by affecting structural (geological), biological, oceanographic, acoustic, or chemical characteristics. Structural impacts include removal or mechanical alteration, including various fishing techniques (trawls, traps, dredges, longlines, and 

even hook-and-line in some habitats), dredging channels and harbors and dumping spoil, vessel groundings, anchoring, laying pipelines and cables, 

installing offshore structures, discharging drill cuttings, dragging tow cables, and placing artificial reefs. Removal or alteration of critical biological 

components of habitats can occur along with several of the above activities, most notably trawling, groundings, and cable drags. Marine debris, particularly in large quantities (e.g., lost gillnets and other types of fishing gear), can affect both biological and structural habitat components. Changes 

in water circulation often occur when channels are dredged, fill is added, coastal areas are reinforced, or other construction takes place. These 

activities affect habitat by changing food delivery, waste removal, water quality (e.g., salinity, clarity and sedimentation), recruitment patterns, and a 

host of other factors. Acoustic impacts can occur to water column habitats and organisms from acute and chronic sources of anthropogenic noise 

(e.g., shipping, boating, construction). Chemical alterations most commonly occur following spills and can have both acute and chronic impacts.

Good Few or no activities occur that are likely to negatively affect habitat quality.

Good/Fair Some potentially harmful activities exist, but they do not appear to have had a negative effect on habitat quality.

Fair Selected activities have resulted in measurable habitat impacts, but evidence suggests effects are localized, not widespread.

Fair/Poor Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Poor Selected activities warrant widespread concern and action, as large-scale, persistent, and/or repeated severe impacts have 

occurred or are likely to occur.

This is intended to elicit thought and assessment of the condition of living resources based on expected biodiversity levels and the interactions between species. Intact ecosystems require that all parts not only exist, but that they function together, resulting in natural symbioses, 

competition, and predator-prey relationships. Community integrity, resistance and resilience all depend on these relationships. Abundance, 

relative abundance, trophic structure, richness, H’ diversity, evenness, and other measures are often used to assess these attributes. 

Good Biodiversity appears to reflect pristine or near-pristine conditions and promotes ecosystem integrity (full community development and function).

Good/Fair Selected biodiversity loss has taken place, precluding full community development and function, but it is unlikely to cause 

substantial or persistent degradation of ecosystem integrity.

Fair Selected biodiversity loss may inhibit full community development and function, and may cause measurable but not severe 

degradation of ecosystem integrity.

Fair/Poor Selected biodiversity loss has caused or is likely to cause severe declines in some but not all ecosystem components and 

reduce ecosystem integrity.

Poor Selected biodiversity loss has caused or is likely to cause severe declines in ecosystem integrity.

8. What are the levels of human activities that may influence habitat quality and how 

are they changing?

Habitat

Human Activities

9. What is the status of biodiversity and how is it changing? Living Resources

Biodiversity
Appendix A: Rating Scheme for System-Wide Monitoring Questions

98 Florida Keys CONDITION REPORT 2011

Commercial and recreational harvesting are highly selective activities, for which fishers and collectors target a limited number of species, 

and often remove high proportions of populations. In addition to removing significant amounts of biomass from the ecosystem, reducing its 

availability to other consumers, these activities tend to disrupt specific and often critical food web links. When too much extraction occurs (i.e. 

ecologically unsustainable harvesting), trophic cascades ensue, resulting in changes in the abundance of non-targeted species as well. It also 

reduces the ability of the targeted species to replenish populations at a rate that supports continued ecosystem integrity. 

It is essential to understand whether removals are occurring at ecologically sustainable levels. Knowing extraction levels and determining 

the impacts of removal are both ways that help gain this understanding. Measures for target species of abundance, catch amounts or rates 

(e.g., catch per unit effort), trophic structure, and changes in non-target species abundance are all generally used to assess these conditions.

Other issues related to this question include whether fishers are using gear that is compatible with the habitats being fished and whether 

that gear minimizes by-catch and incidental take of marine mammals. For example, bottom-tending gear often destroys or alters both benthic structure and non-targeted animal and plant communities. “Ghost fishing” occurs when lost traps continue to capture organisms. Lost 

or active nets, as well as lines used to mark and tend traps and other fishing gear, can entangle marine mammals. Any of these could be 

considered indications of environmentally unsustainable fishing techniques.

Good Extraction does not appear to affect ecosystem integrity (full community development and function).

Good/Fair Extraction takes place, precluding full community development and function, but it is unlikely to cause substantial or persistent degradation of ecosystem integrity.

Fair Extraction may inhibit full community development and function, and may cause measurable but not severe degradation of 

ecosystem integrity.

Fair/Poor Extraction has caused or is likely to cause severe declines in some but not all ecosystem components and reduce ecosystem 

integrity.

Poor Extraction has caused or is likely to cause severe declines in ecosystem integrity.

Non-indigenous species are generally considered problematic, and candidates for rapid response, if found, soon after invasion. For those 

that become established, their impacts can sometimes be assessed by quantifying changes in the affected native species. This question allows 

sanctuaries to report on the threat posed by non-indigenous species. In some cases, the presence of a species alone constitutes a significant 

threat (certain invasive algae). In other cases, impacts have been measured, and may or may not significantly affect ecosystem integrity.

Good Non-indigenous species are not suspected or do not appear to affect ecosystem integrity (full community development and 

function).

Good/Fair Non-indigenous species exist, precluding full community development and function, but are unlikely to cause substantial or 

persistent degradation of ecosystem integrity.

Fair Non-indigenous species may inhibit full community development and function, and may cause measurable but not severe 

degradation of ecosystem integrity.

Fair/Poor Non-indigenous species have caused or are likely to cause severe declines in some but not all ecosystem components and 

reduce ecosystem integrity.

Poor Non-indigenous species have caused or are likely to cause severe declines in ecosystem integrity.

10. What is the status of environmentally sustainable fishing and how is it changing?

Living Resources

Extracted 

Species

11. What is the status of non-indigenous species and how is it changing?

Living Resources

Non-Indigenous 

Species
Appendix A: Rating Scheme for System-Wide Monitoring Questions

CONDITION REPORT 2011 Florida Keys 99

Certain species can be defined as “key” within a marine sanctuary. Some might be keystone species, that is, species on which the 

persistence of a large number of other species in the ecosystem depends - the pillar of community stability. Their functional contribution to 

ecosystem function is disproportionate to their numerical abundance or biomass and their impact is therefore important at the community or 

ecosystem level. Their removal initiates changes in ecosystem structure and sometimes the disappearance of or dramatic increase in the 

abundance of dependent species. Keystone species may include certain habitat modifiers, predators, herbivores, and those involved in critical symbiotic relationships (e.g. cleaning or co-habitating species).

Other key species may include those that are indicators of ecosystem condition or change (e.g., particularly sensitive species), those 

targeted for special protection efforts, or charismatic species that are identified with certain areas or ecosystems. These may or may not meet 

the definition of keystone, but do require assessments of status and trends.

Good Key and keystone species appear to reflect pristine or near-pristine conditions and may promote ecosystem integrity (full 

community development and function).

Good/Fair Selected key or keystone species are at reduced levels, perhaps precluding full community development and function, but 

substantial or persistent declines are not expected.

Fair The reduced abundance of selected keystone species may inhibit full community development and function, and may cause 

measurable but not severe degradation of ecosystem integrity; or selected key species are at reduced levels, but recovery is 

possible.

Fair/Poor The reduced abundance of selected keystone species has caused or is likely to cause severe declines in some but not all 

ecosystem components, and reduce ecosystem integrity; or selected key species are at substantially reduced levels, and 

prospects for recovery are uncertain. 

Poor The reduced abundance of selected keystone species has caused or is likely to cause severe declines in ecosystem integrity; 

or selected key species are a severely reduced levels, and recovery is unlikely.

For those species considered essential to ecosystem integrity, measures of their condition can be important to determining the likelihood 

that they will persist and continue to provide vital ecosystem functions. Measures of condition may include growth rates, fecundity, recruitment, age-specific survival, tissue contaminant levels, pathologies (disease incidence tumors, deformities), the presence and abundance of 

critical symbionts, or parasite loads. Similar measures of condition may also be appropriate for other key species (indicator, protected, or 

charismatic species). In contrast to the question about keystone species (#12 above), the impact of changes in the abundance or condition 

of key species is more likely to be observed at the population or individual level, and less likely to result in ecosystem or community effects.

Good The condition of key resources appears to reflect pristine or near-pristine conditions.

Good/Fair The condition of selected key resources is not optimal, perhaps precluding full ecological function, but substantial or persistent declines are not expected.

Fair The diminished condition of selected key resources may cause a measurable but not severe reduction in ecological function, 

but recovery is possible.

Fair/Poor The comparatively poor condition of selected key resources makes prospects for recovery uncertain.

Poor The poor condition of selected key resources makes recovery unlikely.

12. What is the status of key species and how is it changing? Living Resources

Key Species

Living Resources

Health of Key 

Species

13. What is the condition or health of key species and how is it changing?
Appendix A: Rating Scheme for System-Wide Monitoring Questions

100 Florida Keys CONDITION REPORT 2011

Human activities that degrade living resource quality do so by causing a loss or reduction of one or more species, by disrupting critical 

life stages, by impairing various physiological processes, or by promoting the introduction of non-indigenous species or pathogens. (Note: 

Activities that impact habitat and water quality may also affect living resources. These activities are dealt with in Questions 4 and 8, and many 

are repeated here as they also have direct effect on living resources). 

Fishing and collecting are the primary means of removing resources. Bottom trawling, seine-fishing, and the collection of ornamental species 

for the aquarium trade are all common examples, some being more selective than others. Chronic mortality can be caused by marine debris 

derived from commercial or recreational vessel traffic, lost fishing gear, and excess visitation, resulting in the gradual loss of some species.

Critical life stages can be affected in various ways. Mortality to adult stages is often caused by trawling and other fishing techniques, cable 

drags, dumping spoil or drill cuttings, vessel groundings, or persistent anchoring. Contamination of areas by acute or chronic spills, discharges by vessels, or municipal and industrial facilities can make them unsuitable for recruitment; the same activities can make nursery habitats 

unsuitable. Although coastal armoring and construction can increase the availability of surfaces suitable for the recruitment and growth of hard 

bottom species, the activity may disrupt recruitment patterns for other species (e.g., intertidal soft bottom animals) and habitat may be lost.

Spills, discharges, and contaminants released from sediments (e.g., by dredging and dumping) can all cause physiological impairment and 

tissue contamination. Such activities can affect all life stages by reducing fecundity, increasing larval, juvenile, and adult mortality, reducing 

disease resistance, and increasing susceptibility to predation. Bioaccumulation allows some contaminants to move upward through the food 

chain, disproportionately affecting certain species. 

Activities that promote introductions include bilge discharges and ballast water exchange, commercial shipping and vessel transportation. 

Releases of aquarium fish can also lead to species introductions.

Good Few or no activities occur that are likely to negatively affect living resource quality.

Good/Fair Some potentially harmful activities exist, but they do not appear to have had a negative effect on living resource quality.

Fair Selected activities have resulted in measurable living resource impacts, but evidence suggests effects are localized, not 

widespread.

Fair/Poor Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Poor Selected activities warrant widespread concern and action, as large-scale, persistent, and/or repeated severe impacts have 

occurred or are likely to occur.

14. What are the levels of human activities that may influence living resource quality 

and how are they changing?

Living Resources

Human Activities
Appendix A: Rating Scheme for System-Wide Monitoring Questions

CONDITION REPORT 2011 Florida Keys 101

The condition of archaeological resources in a marine sanctuary significantly affects their value for science and education, as well as the 

resource’s eligibility for listing in the National Register of Historic Places. Assessments of archaeological sites include evaluation of the apparent levels of site integrity, which are based on levels of previous human disturbance and the level of natural deterioration. The historical, 

scientific and educational values of sites are also evaluated, and are substantially determined and affected by site condition.

Good Known archaeological resources appear to reflect little or no unexpected disturbance.

Good/Fair Selected archaeological resources exhibit indications of disturbance, but there appears to have been little or no reduction in 

historical, scientific, or educational value.

Fair The diminished condition of selected archaeological resources has reduced, to some extent, their historical, scientific, or 

educational value, and may affect the eligibility of some sites for listing in the National Register of Historic Places. 

Fair/Poor The diminished condition of selected archaeological resources has substantially reduced their historical, scientific, or educational value, and is likely to affect their eligibility for listing in the National Register of Historic Places.

Poor The degraded condition of known archaeological resources in general makes them ineffective in terms of historical, scientific, 

or educational value, and precludes their listing in the National Register of Historic Places.

The sinking of a ship potentially introduces hazardous materials into the marine environment. This danger is true for historic shipwrecks 

as well. The issue is complicated by the fact that shipwrecks older than 50 years may be considered historical resources and must, by federal 

mandate, be protected. Many historic shipwrecks, particularly early to mid-20th century, still have the potential to retain oil and fuel in tanks 

and bunkers. As shipwrecks age and deteriorate, the potential for release of these materials into the environment increases.

Good Known maritime archaeological resources pose few or no environmental threats.

Good/Fair Selected maritime archaeological resources may pose isolated or limited environmental threats, but substantial or persistent 

impacts are not expected.

Fair Selected maritime archaeological resources may cause measurable, but not severe, impacts to certain sanctuary resources 

or areas, but recovery is possible.

Fair/Poor Selected maritime archaeological resources pose substantial threats to certain sanctuary resources or areas, and prospects 

for recovery are uncertain.

Poor Selected maritime archaeological resources pose serious threats to sanctuary resources, and recovery is unlikely.

15. What is the integrity of known maritime archaeological resources and how is it 

changing?

Maritime 

Archaeological Resources

Integrity

16. Do known maritime archaeological resources pose an environmental hazard and 

how is this threat changing?

Maritime 

Archaeological Resources

Threat to 

Environment
Appendix A: Rating Scheme for System-Wide Monitoring Questions

102 Florida Keys CONDITION REPORT 2011

Some human maritime activities threaten the physical integrity of submerged archaeological resources. Archaeological site integrity is 

compromised when elements are moved, removed, or otherwise damaged. Threats come from looting by divers, inadvertent damage by 

scuba diving visitors, improperly conducted archaeology that does not fully document site disturbance, anchoring, groundings, and commercial and recreational fishing activities, among others. 

Good Few or no activities occur that are likely to negatively affect maritime archaeological resource integrity.

Good/Fair Some potentially relevant activities exist, but they do not appear to have had a negative effect on maritime archaeological 

resource integrity.

Fair Selected activities have resulted in measurable impacts to maritime archaeological resources, but evidence suggests effects 

are localized, not widespread.

Fair/Poor Selected activities have caused or are likely to cause severe impacts, and cases to date suggest a pervasive problem.

Poor Selected activities warrant widespread concern and action, as large-scale, persistent, and/or repeated severe impacts have 

occurred or are likely to occur.

17. What are the levels of human activities that may influence maritime archaeological 

resource quality and how are they changing?

Maritime 

Archaeological Resources

Human Activities
Appendix B: Consultation with Experts and Document Review

CONDITION REPORT 2011 Florida Keys 103

The process for preparing condition reports involves a combination of accepted techniques for collecting and interpreting information gathered from subject matter experts. The approach varies somewhat from sanctuary to sanctuary in order to accommodate 

differing styles for working with partners. The Florida Keys National Marine Sanctuary approach was closely related to the Delphi 

Method, a technique designed to organize group communication among a panel of geographically dispersed experts by using 

questionnaires, ultimately facilitating the formation of a group judgment. This method can be applied when it is necessary for decision-makers 

to combine the testimony of a group of experts, whether in the form of facts or informed opinion, or both, into a single useful statement. 

The Delphi Method relies on repeated interactions with experts 

who respond to questions with a limited number of choices to arrive 

at the best supported answers. Feedback to the experts allows them 

to refine their views, gradually moving the group toward the most 

agreeable judgment. For condition reports, the Office of National Marine Sanctuaries uses 17 questions related to the status and trends 

of sanctuary resources, with accompanying descriptions and five 

possible choices that describe resource conditions. 

In order to address the 17 questions, sanctuary staff selected and 

consulted outside experts familiar with water quality, living resources, habitat, and maritime archaeological resources. Phone calls and 

one-on-one meetings were convened where experts participated in 

discussions with sanctuary staff about each of the 17 questions. Experts represented various affiliations including Florida Fish and Wildlife Conservation Commission, Florida International University, Florida Keys National Marine Sanctuary, Mote Marine Laboratory, NOAA 

National Marine Fisheries Service, Reef Environment Education 

Foundation, University of Miami Rosenstiel School of Marine and Atmospheric Science, and the University of North Carolina Wilmington. 

During each consultation, experts were introduced to the questions 

and asked to provide recommendations and supporting arguments 

for their suggested rating. The ratings and text found in the report are 

intended to summarize the opinions and uncertainty expressed by 

the experts, who based their input on knowledge and perceptions of 

local conditions. Comments and citations received from the experts 

were included, as appropriate, in text supporting the ratings. 

The first draft of the document was sent to various subject matter 

experts and important partners in research and resource management for what was called an Invited Review. Individuals included 

representatives from Audubon Society, Coral Restoration Foundation, Department of Primary Industries and Fisheries, Environmental 

Protection Agency (Wetlands, Coastal and Oceans Branch and Special Studies), Florida Department of Health, Florida Fish and Wildlife 

Conservation Commission, Florida Keys National Marine Sanctuary, 

Georgia Institute of Technology, Naval Air Station Key West, NOAA 

Corps, NOAA National Marine Fisheries Service, Reef Environmental Education Foundation, University of Miami Rosenstiel School of 

Appendix B:

Consultation with Experts and Document Review

Marine and Atmospheric Science, and the University of North Carolina Wilmington. Individuals were asked to review the technical merits of resource ratings and accompanying text, as well as to point out 

any omissions or factual errors. The comments and recommendations of invited reviewers were received, considered by sanctuary 

staff, and incorporated, as appropriate, into a final draft document. 

A draft final report was then sent to John F. Bruno, Ph.D. (Associate Professor, The University of North Carolina at Chapel Hill), 

Richard E. Dodge, Ph.D. (Dean, Nova Southeastern University 

Oceanographic Center), Paul Sammarco, Ph.D. (Professor, Louisiana Universities Marine Consortium), and Rob van Woesik, Ph.D. 

(Professor, Florida Institute of Technology) who served as external 

peer reviewers. This External Peer Review is a requirement that 

started in December 2004, when the White House Office of Management and Budget (OMB) issued a Final Information Quality Bulletin 

for Peer Review (OMB Bulletin), establishing peer-review standards 

that would enhance the quality and credibility of the federal government’s scientific information. Along with other information, these standards apply to Influential Scientific Information, which is information 

that can reasonably be determined to have a “clear and substantial 

impact on important public policies or private sector decisions.” The 

Condition Reports are considered Influential Scientific Information, 

and for this reason, are subject to the review requirements of both the 

Information Quality Act and the OMB Bulletin guidelines. Therefore, 

following the completion of every condition report, they are reviewed 

by a minimum of three individuals who are considered to be experts 

in their field, were not involved in the development of the report, and 

are not Office of National Marine Sanctuaries employees. Comments 

from these peer reviews are incorporated into the final text of the 

report. Furthermore, OMB Bulletin guidelines require that reviewer 

comments, names, and affiliations be posted on the agency website: 

http://www.cio.noaa.gov/Policy_Programs/prplans/PRsummaries.

html. Reviewer comments, however, are not attributed to specific individuals. Reviewer comments are posted at the same time as with 

the formatted final document. Following the External Peer Review, 

the comments and recommendations of the reviewers were considered by sanctuary staff and incorporated, as appropriate, into a final 
Appendix B: Consultation with Experts and Document Review

104 Florida Keys CONDITION REPORT 2011

draft document. In some cases sanctuary staff reevaluated the status 

and trend ratings and when appropriate, the accompanying text in the 

document was edited to reflect the new ratings. The final interpretation, ratings, and text in the draft condition report were the responsibility of sanctuary staff, with final approval by the sanctuary manager. To 

emphasize this important point, authorship of the report is attributed 

to the sanctuary alone. Subject experts were not authors, though their 

efforts and affiliations are acknowledged in the report.
Florida Keys National Marine Sanctuary

CONDITION REPORT 2011 Florida Keys 105

Notes
The National Marine Sanctuary System

The Office of National Marine Sanctuaries, part of the National Oceanic and Atmospheric Administration, serves as the trustee for a system of 14 marine protected areas encompassing more than 150,000 square miles of ocean and Great Lakes waters. The 13 national marine 

sanctuaries and one marine national monument within the National Marine Sanctuary System represent areas of America’s ocean and Great 

Lakes environment that are of special national significance. Within their waters, giant humpback whales breed and calve their young, coral 

colonies flourish, and shipwrecks tell stories of our maritime history. Habitats include beautiful coral reefs, lush kelp forests, whale migrations 

corridors, spectacular deep-sea canyons, and underwater archaeological sites. These special places also provide homes to thousands of 

unique or endangered species and are important to America’s cultural heritage. Sites range in size from less than one to almost 140,000 

square miles and serve as natural classrooms, cherished recreational spots, and are home to valuable commercial industries.

The Office of National 

Marine Sanctuaries

is part of NOAA’s 

National Ocean Service.

Vision - People value 

marine sanctuaries as treasured 

places protected for future 

generations.

Mission - To serve as the 

trustee for the nation’s system of 

marine protected areas to conserve, protect and enhance their 

biodiversity, ecological integrity 

and cultural legacy.

National Marine Sanctuary System