page 

150 Florida

The State of Coral Reef Ecosystems of Florida 

Edited by:

Katherine Andrews1

, Larry Nall1, Chris Jeffrey2, Simon Pittman2

Contributing Authors:

Ken Banks3

, Carl Beaver4, James Bohnsack5, Richard E. Dodge6,7, David Gilliam6,7, Walt Jaap4, Brian Keller8, V. Robert 

Leeworthy9, Tom Matthews4, Ramon Ruiz-Carus4, Deborah Santavy10, Richard Spieler6,7

Other Contributors:

Jerald Ault11

, Gabriel Delgado4, Fleur Ferro8, Carol R. Fretwell7, Bill Goodwin8, Doug Harper5, John Hunt4, Margaret 

Miller5, Christy Pattengil-Semmens12, Bill Sharp4, Steve Smith11, Jennifer Wheaton4, Dana Williams5

INTRODUCTION AND SETTING 

Florida is located at the convergence of the subtropical and temperate climate zones (Chen and Gerber, 

1990). The Gulfstream (a warm-water boundary current) has a major influence on water temperature and the 

transport of flora and fauna to the region (Jaap and Hallock, 1990). The Gulfstream intrudes into the Gulf of 

Mexico as the Loop Current and reverses flow to return to the Straits of Florida, joining the main body of the 

Florida Current before flowing in a northeasterly direction towards Europe. The influence of the Gulfstream 

together with the presence of a broad-shallow continental shelf around Florida and the absence of any major 

rivers have provided conditions for the development of extensive coral reefs (Figure 7.1). Most coral reefs are 

found in water less than 18 m deep. Rohmann et al. (in press) have estimated that 30,801 km2 of shallowwater inshore areas around Florida could potentially support coral reef ecosystems. In comparison, the area 

estimated was 16.4 km2 in Guam, 1,231.4 km2 in the Main Hawaiian Islands and 2,207.6 km2 in Puerto Rico. 

Florida Reef Tract 

The Florida Reef Tract, which extends from Soldier Key to Tortugas Banks, has coral reef characteristics similar to many areas in the Bahamas and Caribbean Basin (Vaughan, 1914). The undeveloped coastal fringe 

includes extensive mangrove forests and a mosaic of exposed rock and sediments. Elevated rock formations 

support coral reef development and the sediments support the most extensive seagrass beds in the world 

(Fourqurean et al., 2002). 

Three types of coral reef habitats found in the Florida Keys are hardbottom, patch reefs, and bank reefs (Table 

7.1). Hardbottom or live bottom habitat is the most extensive habitat type, found at a wide range of water 

depths and characterized by rock colonized with calcifying algae (e.g., Halimeda spp.), sponges, octocorals, 

and several species of stony coral. Local environmental conditions determine the composition of the communities that colonize the rock. Patch reefs typically consist of massive stony corals, with the boulder star coral 

(Montastraea annularis) being most dominant. Other common foundation-building species include Colpophyllia natans and Siderastrea siderea. Patch reefs are concentrated in north Key Largo, Hawk Channel between 

Marathon Key and Key West, and the area off Elliott Key. Species diversity and richness of stony corals are 

highest in patch reef habitats (Jaap et al., 2003). Bank reefs are the most seaward of coral reef habitats in 

the Florida Keys coastal ecosystem and are frequently visited by recreational scuba divers and snorkelers. 

Their principal unique feature is the spur-and-groove system, a series of ridges and channels built primarily by 

elkhorn coral (Acropora palmata) (Shinn, 1963). Spur-and-groove systems occur in depths ranging from a few 

centimeters to 10 m. In deeper waters, spur-and-groove formations may continue seaward as very low relief 

structures. Often, this type of habitat is referred to as the forereef and may continue to about 30 m in depth. 

Seaward, sediments separate the fore-reef from deeper reef formations at a depth of about 40 m. 

1 Florida Department of Environmental Protection 

2 NOAA, Center for Coastal Monitoring and Assessment, Biogeography Team 

3 Broward County Environmental Protection Department 

4 Florida Fish and Wildlife Conservation Commission 

5 NOAA Fisheries, Southeast Fisheries Science Center 

6 Nova Southeastern University Oceanographic Center 

7 National Coral Reef Institute 

8 Florida Keys National Marine Sanctuary 

9 NOAA Ocean Service, Special Projects Office 

10 U.S. Environmental Protection Agency, Gulf Ecology Division 

11 University of Miami, Rosenstiel School of Marine and Atmospheric Sciences 

12 Reef Environmental Education Foundation 
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The State of Coral Reef Ecosystems of Florida

Florida 

Figure 7.1. Locator map for Florida. Map: A. Shapiro. 

page 

151 

Tortugas Banks 

The Tortugas Banks are coral reefs that developed on a foundation of Pleistocene karst limestone at depths of 

20-40 m. The banks are extensive with low coral diversity, but high coral cover. The most conspicuous coral 

is Montastraea cavernosa, and black coral (Antipatharia) are common on the outer bank edges. The banks 

are also used by groupers and snappers that support a major fishery. 
The State of Coral Reef Ecosystems of Florida

The Southeastern Coast Table 7.1. Habitat area estimates for the Florida Reef Tract. Source: FMRI 1998. 

page 

152 FloridaThis reef system continues the Florida 

reef tract northwards and runs from 

northern Monroe County to Martin 

County in a series of discontinuous 

reefs paralleling the shore. Duane 

and Meisberger (1969) and Goldberg 

(1973) defined the habitat including 

corals at several locations. Moyer et 

al. (2003) investigated the ecological 

and spatial patterns of the benthos 

on various reefs of Southeast Florida 

(Broward County; Figure 7.2). 

In addition to nearshore hardbottom 

areas, there are generally three lines 

of reef – one that nominally crests in 

3-4 m of water (inner reef), another in 

6-8 m (middle reef), and a third in 15-

21 m (outer reef). A series of ridges 

that are not reefal in origin occur on 

the shoreward side of inner reef areas (Moyer et al., 2003). 

Inner reefs are characterized by macroalgae and numerous small octocorals. The substrate is relict reef of Anastasia Formation limestone and 

worm reef (Phragmatopoma spp.), with breaks and sediment pockets within the reef. Typical sessile organisms are lesser starlet coral (Siderastrea radians) and colonial zoanthids (Palythoa mammilosa and P. caribaeorum). In the past few years, vigorous recruitment of staghorn coral (Acropora cervicornis) have occurred, 

and some extensive aggregations are now present generally inshore of inner reefs in Broward County. Here, 

monospecific stands of coral form significant habitats (Vargas-Ángel et al., 2003). Spawning activity has been 

documented in late July to early August (Vargas-Ángel and Thomas, 2002; Vargas-Ángel et al., in prep.). 

Middle reefs have more relief and dissecting channels. Octocorals are most conspicuous, with densities of 

more than 30 per m2 in some areas. Abundant stony corals include great star coral (Montastraea cavernosa), 

massive starlet coral (Siderastrea siderea), and mustard hill coral (Porites astreoides) (Gilliam et al., 2003). 

The outer reef system often has stronger vertical relief and exhibits the highest diversity and abundance of 

sessile reef organisms. Octocorals and large barrel sponges (Xestospongia muta) are most conspicuous and 

visually dominate this reef. Stony corals are somewhat larger than those located on the middle reef. Moderate-sized colonies of star corals are common. 

The reef system at St. Lucie Inlet Preserve State Park (27°05 ́ to 27°09 ́ N) is the northern limit for subtropical 

coral reefs on the east coast of Florida. The topography is composed of Anastasia Formation limestone that 

is covered with reef biota. Diploria clivosa forms very large pancake-like colonies and provides the majority of 

the cover. Montastraea cavernosa also attains large sizes. The other species present - Siderastrea radians, 

Isophyllia sinuosa, Solenastrea bournoni, and Oculina diffusa - are not large. Stony corals accounted for 3-5% 

of benthic cover at two 100-m transects (Herren, 2004). 

TYPE OF REEF HABITAT HECTARES KM2 ACRES 

Hardbottom 82370 824 203540 

Patch Reef 3370 34 8330 

Bank Reef 29550 295 73010 

Total coral reef estimate 115290 1153 284880 

Seagrass 292520 2925 722840 

Figure 7.2. A reef profile along a shore-perpendicular transect of high resolution 

bathymetry data from 0-30m depth off central Broward County. The x-axis represents 

distance from shore in meters and y-axis represents elevation in meters. The seafloor 

of the profile is categorized in the sections below the profile line. The red line along 

the profile represents the three main shore-parallel reef tracts. Source: R. Dodge, 

National Coral Reef Institute, http://www.nova.edu/ocean/ncri/, Accessed 1/6/2005. 
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153Florida

The State of Coral Reef Ecosystems of Florida

ENVIRONMENTAL AND ANTHROPOGENIC STRESSORS

Coral reefs in Florida face a number of different stressors. These include coral bleaching, diseases, water pollution, physical impacts (such as groundings, dredging activities, and beach renourishment), tropical storms, 

and winter cold fronts. Other stressors of less concern in Florida include national security activities and trade 

in coral species.

Climate Change and Coral Bleaching

Coral bleaching due to exceptionally high water temperatures has been reported in Florida since the early 20th 

century (Vaughan, 1911; Mayer, 1918). Jaap (1979, 1984) also reported coral bleaching events in the Lower 

Keys following late summer doldrums 

when water temperatures exceeded 

31oC. Other significant and severe 

bleaching events on reefs throughout Florida occurred in 1987, 1990, 

and 1997-98 (Causey, 2001). These 

bleaching events have caused moderate mortality of the more sensitive 

stony corals, Millepora complanata 

and Agaricia agaricites. Bleaching 

episodes have become much more 

severe in space and time in the past 

few decades.

Coral bleaching assessments were 

made during the 1998 global bleaching event by the U.S. Environmental 

Protection Agency’s (EPA) Gulf Ecology Division, in collaboration with the 

National Oceanic and Atmospheric 

Administration’s (NOAA) Florida Keys 

National Marine Sanctuary (FKNMS), 

Mote Marine Laboratory’s Center for 

Tropical Research, and University of 

Georgia. Surveys were conducted 

in the Florida Keys, with sites in the 

Lower Keys, New Grounds, and Dry 

Tortugas. Details of the sampling 

design, approach, and methods are 

described in Santavy et al. (2001). 

Bleaching was scored if greater than 

50% of a coral colony had translucent 

white tissue present. Every species 

recorded in this assessment was observed to be bleaching. At least 50% 

of the colonies of the species Acropora palmata, Diploria labyrinthiformis, D. strigosa, Colpophyllia natans, 

Mycetophyllia danaana and Montastraea cavernosa were over 50% 

bleached (Figure 7.3). Reefs in the 

Lower Keys exhibited the greatest 

bleaching (43% ± 5.7 SE) compared 

to reefs in the Dry Tortugas and New 

Figure 7.3. Mean percentage of coral colonies that were greater than 50% bleached 

identified by species assessed in September 1998 in the Lower Keys and the Dry 

Tortugas sites. Error bars represent 1 SE. X axis legend: Acer: Acropora cervicornis; Apal: A. palmata; Cnat: Colpophyllia natans; Dlab: Diploria labyrinthiformis; Dsto: 

Dichocoenia stokesii; Dstr: Diploria strigosa; Mann. Montastraea annularis; Mcav: 

Montastraea cavernosa; Mdan: Meandrina danae; Mfer: Mycetophyllia ferox; Past: 

Porites astreoides; Sbou: Solenastrea bournoni; Smic: Stephanocoenia michelinii; 

Ssid: Siderastrea siderea. Source: Santavy et al., 2001. 

Figure 7.4. Mean percentage of coral colonies that were greater than 50% bleached 

assessed in September 1998 in the Dry Tortugas, Lower Keys, and New Grounds. 

Error bars represent 1 SE. Source: Santavy et al., 2001. 
The State of Coral Reef Ecosystems of Florida

page 

154 FloridaGrounds (Figure 7.4). Shortly after the assessments, Hurricane Georges passed over Key West as a Class 

3 hurricane which caused substantial physical destruction. The stress from intense bleaching and Hurricane 

Georges was responsible for significant coral mortality that occurred between surveys in late summer 1998 

and late spring 1999. Detailed information concerning bleaching distributions are reported in Santavy et al. 

(2001). 

Disease 

Surveys conducted along the Florida Keys Reef Tract during 1998-2002 assessed coral diseases for several 

applications. The first application was to determine the frequency and distribution of coral condition, using 

coral disease as the indicator to determine the overall health of corals. This approach was applied during the 

2000 survey. The second application was to compare coral diseases between geographical regions in the 

Dry Tortugas, New Grounds, Key West region, Lower Keys, Middle Keys, and Upper Keys. Coral diseases 

were assessed by scientists from EPA’s Gulf Ecology Division, FKNMS, and Mote Marine Laboratory’s Center 

for Tropical Research. In general, diseases were most abundant in 1998, with observed changes in species 

composition which suggest that corals are increasingly dying and not recovering. In extreme cases, there has 

been almost complete deterioration of several keystone species, most notably Acropora palmata (Patterson 

et al., 2002). Although it is clear that new diseases are emerging at an accelerated rate, cause and effect 

relationships are not well documented. Coral health and diseases have not been critically or thoroughly characterized, and few baseline studies have been conducted in this region. More information about the results of 

coral disease studies can be found in the ‘Benthic Habitats’ section. 

Tropical Storms 

Storms are a normal part of the 

South Florida ecosystem because 

of the close proximity of Florida to 

the Caribbean Basin, where intense 

hurricanes develop seasonally. Hurricanes that have impacted Florida 

since 1979 are shown in Figure 7.5. 

Tropical storms can be a major force 

structuring coral reef communities 

through processes such as direct 

physical impact, increased terrestrial 

runoff, sedimentation, and pollution. 

For example, Hurricane Georges 

(1998) broke and reduced to rubble 

many large branching elkhorn and 

staghorn corals which were already 

weakened by disease (USGS, 1998; 

AOML, 1999). In 2004, various parts 

of Florida’s coastline were hit by four 

major hurricanes (Charley, Francis, 

Ivan, and Jeanne). Hurricane Charley caused moderate damage to coral 

reefs at Dry Tortugas and off Broward. 

For instance, at the northeast side of 

Loggerhead Key, a patch of Acropora 

cervicornis was broken into small 

pieces and washed inshore; however, a month later surviving fragments 

appeared healthy. On Bird Key Reef, 

many large coral formations were dislodged and abundance of benthic algae was drastically reduced on most 

Figure 7.5. The paths and intensities of hurricanes in Florida, 1979-2004. Year of 

storm, hurricane name and storm strength on the Saffir-Simpson scale (H1-5) are 

indicated for each. Map: A. Shapiro. Source: NOAA Coastal Services Center. 
Sidebar

The State of Coral Reef Ecosystems of Florida 

of the reefs visited after the storm (W.C. Japp, pers. obs.). Hurricanes Francis and Jeanne caused damage 

to coral reefs off Palm Beach and Martin Counties (W.C. Japp, pers. obs.). 

Nevertheless, tropical storms may have beneficial effects on coral reef ecosystems off Florida’s southeast 

coastline. Florida Bay is very shallow (1 m), with a myriad of banks and shoals that quickly dissipate tidal exchanges and prevent regular flushing of the bay. Reduced tidal flushing has contributed to the accumulation 

of organic matter, sediments, and nutrients which promote phytoplankton blooms that decrease the amount 

of light available to seagrass beds (AOML, 1999). Increased storm surge and wave action from powerful hurricanes increase tidal flushing, reduce sedimentation and are thought to reduce phytoplankton blooms (AOML, 

1999). After Hurricane Georges (1998), however, water quality conditions were not significantly different than 

before because nutrient-enriched waters remained trapped within Florida Bay by broad, shallow banks in the 

central and western portions of the bay (AOML, 1999). Additionally, Lirman (2003) found that the abundance 

of A. palmata correlated positively with an increase in storm frequency from one storm every 15 years to one 

storm every two years, but declined with a further increase in storm frequency. Successful survivorship, reattachment, and growth of coral fragments after storm events may be the only means of propagation for A. palmata when sexual recruitment is limited (Lirman, 2003). However, the synergistic effects of multiple stressors 

(e.g., disease, coastal pollution, and overgrowth by algae) could prevent normal patterns of recovery in corals 

after storm events (USGS, 1998). 

Coastal Development and Runoff 

The reefs of mainland Southeast Florida, by virtue of their high latitude and proximity to shore, exist at the 

environmental extremes for corals. Natural phenomena, such as cold weather fronts; upwelling of cold, nutrient-rich waters; and freshwater runoff from land all contribute to “pushing the environmental limits” for corals 

and other reef-associated organisms. Anthropogenic activity that leads to a reduction in water quality may 

result in further physiological stress to corals and adversely impact coral reef ecosystems. 

Nonpoint sources of pollution include surface water runoff, storm water discharge, and groundwater seeps. 

The nonpoint-source pollution may be delivered to the reef directly, as in the case of runoff, through navigational inlets and passes, and through the porous limestone substrate underlying south Florida. Nutrient 

loading of nitrogen and phosphorus from inland agriculture to the coastal waters offshore of Palm Beach 

County (mainland Southeast Florida) via surface water discharge are 2,473 and 197 metric tons (mt) per year, 

respectively, and via submarine groundwater discharge are 5,727 and 414 (mt) per year, respectively (Finkl 

and Charlier, 2003; Finkl and Krupa, 2003). Studies have estimated that groundwater from the interior parts 

of South Florida can take five to eight decades to reach the nearshore zone (Finkl and Charlier, 2003). Furthermore, run-off from the Everglades via Florida Bay and the Keys has been found to impact water quality 

around the Keys (Boyer and Jones, 2002). 

Coastal Pollution 

The effects of coastal pollution on reef-associated communities are not entirely understood. One obvious impact, however, is an increase in the magnitude and persistence of macroalgal blooms, which have increased 

worldwide during the past several decades (Morand and Briand, 1996). There is evidence that blooms may 

be a result of nutrient loading from land-based sources (NRC, 2000). Lapointe (1997) and Lapointe and Barile 

(2001) linked nitrogen from land-based sewage to macroalgal blooms in Southeast Florida. In Southeast 

Florida, harmful macroalgal blooms have occurred extensively in the offshore waters of Palm Beach County 

during the past decade (Lapointe and Barile, 2003), and over the past two years the cyanobacterium (Lyngbya 

confervoides) has covered an extensive area of the middle reef tract offshore Broward County. These blooms 

have had a significant impact on reef-associated organisms (Lapointe, 1997). The impacts include smothering and resultant mortality, as well as substrates dominated by macroalgae that would naturally be colonized 

by other organisms, such as corals and sponges. Researchers in Barbados (Tomascik, 1991; Wittenberg 

and Hunte, 1992) reported decreased coral larval settlement on reefs in nutrient-rich waters. Other impacts 

of water pollution on reef communities include increased bioerosion rates (reviewed by Risk et al., 2001) and 

possible links to coral diseases. Patterson et al. (2002) identified the human fecal bacterium (Serratia marcescens) as the causal agent of white pox disease in corals in the Florida Keys, and Bruno et al. (2003) reported 

evidence of nutrient enrichment increasing the severity of disease in sea fans and some coral species. 

page 

155 Florida 
page 

156 Florida 

The State of Coral Reef Ecosystems of Florida 

An extensive water quality monitoring program for the Florida Keys and Florida Bay underway since 1995 

(Boyer and Jones, 2003) has reported elevated nitrogen levels in the nearshore areas of the Keys but not in 

the Tortugas region, suggesting a relationship with land-use patterns. No coastal water quality monitoring is 

underway for the mainland Southeast Florida region. There is a great need for such a monitoring program, 

particularly in light of the number of extensive macroalgal blooms that have occurred on mainland reefs in 

recent years. In addition to monitoring, further research to identify cause-and-effect relationships (i.e., water 

quality and reef community response) are needed. 

The most extensive program underway to reduce water pollution is the National Pollution Discharge Elimination System (NPDES), a Federal program to regulate pollution from point source and stormwater discharges 

into receiving waters. The NPDES program is mandated in the Federal Clean Water Act (33 U.S.C. § 1251 

et seq.) and is administered by the EPA and delegated to states, including Florida. Industrial, municipal, and 

other facilities must obtain permits if their discharges go directly to surface waters. Facilities discharging 

stormwater must meet appropriate treatment criteria and may not cause or contribute to a violation of water 

quality standards. The program has been effective in requiring many private small wastewater treatment 

plants to eliminate raw sewage discharges. All municipal wastewater treatment plants must attain minimum 

levels of effluent quality using secondary treatment, including facilities with ocean outfalls. Water quality standards need to be re-evaluated from a perspective that addresses impacts to coral reef systems. 

Wastewater in the Florida Keys is handled by approximately 200 treatment plants and numerous private septic 

tanks. Because of the low land elevation in the Keys, the septic tank drain fields are under tidal influence and 

nutrient-rich water leaches through the porous limestone into coastal waters. In order to decrease this nutrient 

loading, Monroe County is undertaking a study of the septic tank problem and consolidation of the wastewater 

plants into regional facilities. 

Tourism and Recreation 

Florida’s coral reefs are located near the four most densely populated counties of the state (U.S. Census 

Bureau, 2003). The combined population of these four counties is more than five million, with 2.3 million in 

Miami-Dade, 80,000 in Monroe, 1.7 million in Broward, and 1.2 million in Palm Beach County (U.S. Census 

Bureau, 2003). Tourism is Florida’s top industry and generates over $50 billion a year for the state’s economy. 

In 2003, Florida hosted over 74 million visitors who participated in reef-based recreation, generating $18 million annually in the Florida Keys (VISIT FLORIDA Year-in-Brief, 2003). Reef tourism is a significant economic 

asset in Palm Beach, Broward, Miami-Dade, and Monroe Counties, which are all on the list of top ten destination counties for tourists to Florida (Johns et al., 2001; VISIT FLORIDA Year-in-Brief, 2003). The primary 

tourism activities include snorkeling, scuba diving, fishing, glass bottom boat tours, boat rentals, dive training, 

and dive shop sales (Table 7.2). By far, the largest economic benefits generated by direct use of the reefs of 

Southeast Florida are related to recreation and tourist activities. For example, in the June 2000 to May 2001 

tourist season, tourism generated over $16 billion in output/sales, including local multiplier impacts. These 

sales, in turn, generated an estimated $6.2 billion in income, which supported over 251,000 full-time and parttime jobs. In Florida, the Monroe County economy is the most highly dependent on tourism, with 61% of all 

county employment related to tourist activity. 

Johns et al. (2001) estimated direct use of both the artificial and natural reefs and the associated market and 

non-market economic use values for Southeast Florida. For the four-county area, direct use of natural reefs 

by both residents and visitors was estimated at 18.4 million person-days of snorkeling, scuba diving, fishing, 

and viewing coral reefs from glass-bottom boats, which resulted in over $2.7 billion in output/sales (Table 7.2). 

This activity further generated over $1.2 billion in income that supported over 43,000 full-time and part-time 

jobs. Annual net direct user value of natural reefs was over $229 million. Residents and visitors to the Florida 

Keys (Monroe County) spent about 3.9 million person-days of diving, fishing, and viewing coral reefs and $373 

million in local sales, which generated about $107 million in income locally that supported over 7,600 jobs. In 

addition to these economic impacts, users received over $57 million in net annual user value, with an asset 

value of $1.9 billion. 

In Palm Beach County, users spent over 2.8 million person-days on the natural reefs off the coast of the county with economic impacts on the county of $354 million in sales, which generated $141 million in local income 
Sidebar

and supported 4,500 jobs. Reefs off 

Palm Beach County had a net annual 

user value of over $42 million, with 

an asset value of $1.4 billion. In Broward County, users spent about 5.4 

million person-days on the natural 

reefs, spent $1.1 billion, generated 

$547 million in local income, and supported about 18,600 jobs (Table 7.2). 

Reefs off Broward County had a net 

annual user value of about $83 million and an asset value of $2.8 billion. 

In Miami-Dade County, users spent 

over 6.3 million person-days on the 

natural reefs, generated $878 million 

in sales and $419 million in income 

locally, and supported about 12,600 

jobs. The reefs of Miami-Dade had a 

net annual user value of almost $47 

million, with an asset value of $1.6 

billion (Table 7.2). 

The State of Coral Reef Ecosystems of Florida 

Fishing 

Coral reefs provide the ecological foundation for important fisheries and a tourism-based economy in South 

Florida that generated an estimated 71,000 jobs and $6 billion of economic activity in 2001 (Johns et al., 

2001). Fishing is an important part of this activity and a human stressor on coral reefs. 

Florida’s reef fisheries are concentrated in South Florida and are complex (Bannerot and Alevizon, 1990; Chiappone and Sluka, 1996). Commercial and sport fisheries target adult reef fishes and spiny lobster for food 

and sport around bridges and on patch reefs and offshore bank reefs. Fisheries also target live fishes and invertebrates for marine aquaria. Pink shrimp, which are ecologically important as a principal prey item for many 

reef species, are also economically important and intensively exploited. Adult pink shrimp inhabiting soft and 

rubble bottoms near coral reefs are targeted by the commercial fishery as a food, and juvenile pink shrimp are 

targeted as live bait for the recreational fishery in coastal bays and near barrier islands. Finally, pre-spawning 

subadult pink shrimp are targeted by both food and sport fisheries as they emigrate from coastal bay nursery 

grounds to offshore spawning grounds. 

Total fishing activity reflects Florida’s population, which grew tenfold from 1.5 million people in 1930 to 16 

million in 2000. In 2000, over five million residents, nearly one-third of Florida’s population, lived in the five 

southern counties adjacent to coral reefs (Palm Beach, Broward, Miami-Dade, Monroe, and Collier Counties). 

Like residents, recreational fishing (i.e., sport angling and spear fishing) is a popular activity for tourists. Over 

three million tourists annually visit the Florida Keys alone (Leeworthy and Vanasse, 1999). 

Precise data on fishing effort on coral reefs do not exist, but are reflected by statewide fishing statistics. In 

2001, for example, an estimated 6.7 million recreational fishers took 28.9 million marine fishing trips in Florida, 

catching 171.6 million fish, of which 89.5 million (52%) were released or discarded (U.S. DOC, 2003). Although 

some measures of recreational fishing activity such as the annual number of anglers and fishing trips were unchanged between 1993 and 2002, other measures (e.g., annual totals of fishes caught, released, and landed) 

may have increased between 1997 and 2002 (Figure 7.6). Additionally, the number of registered recreational 

boats in five South Florida counties adjacent to coral reefs grew more than 500% between 1964 and 2002, 

although the number of registered vessels actually used for fishing is unknown (Figure 7.7). In comparison, 

the number of commercial vessel registrations grew at a much lower rate of about 150% (Figure 7.7). Besides 

an increased fleet size, average fishing power (the proportion of stock removed per unit of fishing effort) may 

Table 7.2. Estimates by county of area and monetary value of recreational and tourism-related activities occurring in coral reef ecosystems of Southeastern Florida, 

2000-2001. Source: Johns et al., 2001. 

ATTRIBUTE BROWARD MIAMI-DADE MONROE PALM 

BEACH 

Habitat area (x 1000 

hectares) 

8.3 7.2 115.3 12.0 

Person days of activity 

(millions of days) 

5.4 6.3 3.9 2.8 

Sales and Services 

(millions of $) 

1100 878 373 354 

Income 

(millions of $) 

547 419 107 141 

Number of jobs 18,600 12,600 7,600 4,500 

Asset value 

(millions of $) 

2,800 1,600 1,900 1,400 

Snorkeling 

(millions of $) 

0.8 1.5 1.5 0.4 

Scuba diving 

(millions of $) 

2 0.7 0.5 1.3 

Fishing 

(millions of $) 

2.6 4.1 1.8 1.1 

Glass-bottom boat 

rides (millions of $) 

0.04 0.01 0.07 0 

page 

157 Florida 
have quadrupled in recent decades 

because of technological advances in fishing tackle, hydroacoustics 

(depth sounders and fish finders), 

navigation (charts and global positioning systems), communications, 

and vessel propulsion (Mace, 1997; 

Bohnsack and Ault, 1996; Ault et al., 

1998, in press). 

Fishing can stress coral reefs by removing targeted species, killing nontarget species as bycatch, and causing habitat damage. Because fishing 

is size-selective, concerns exist about 

ecosystem disruption by removal of 

ecologically important keystone species, top predators (groupers, snappers, sharks, and jacks), and prey 

(e.g., shrimps and baitfish). Fishing 

stress is compounded when combined with other stressors such as 

pollution and habitat damage. From 

a fishery perspective, whether stocks 

decline from fishing or detrimental environmental changes, reducing fishing pressure is an appropriate fishery 

policy choice (Rosenberg, 2003). 

To balance increased fishing pressure, many new fishery regulations 

have been enacted since the 1980s 

in Florida state waters by the Florida 

Fish and Wildlife Conservation Commission (FFWCC; http://www.state. 

fl.us/gfc/marine) and in Federal waters by the South Atlantic Fishery 

Management Council (SAFMC, http:// 

www.safmc.net/fishid) and Gulf of 

Mexico Fishery Management Council 

(GMFMC, http://www.gulfcouncil.org/ 

about.htm). Their actions include: 

prohibiting destructive or wasteful 

fishing gear (e.g., roller trawls, explosives, wire fish traps); requiring 

reduced bycatch survival (e.g., vessel-holding requirements and limits on number of short lobster used as live bait in lobster traps, escape gaps 

and release hatches for lobster traps); establishing minimum size and bag limits on a number of reef species 

landed; establishing seasonal and spatial closures for certain fishing gears (e.g., spears, power heads, lobster 

diving) and breeding seasons (e.g., for amberjack and black grouper; Bohnsack et al., 1994); limiting or restricting fishing for some species; and limiting entry into certain fisheries. The FKNMS has numerous marine 

protected areas (MPAs), many of which restrict or eliminate fishing and diving (http://www.fknms. nos.noaa. 

gov, accessed 2/8/2005). Fisheries for Nassau grouper (Epinephelus striatus), goliath grouper (E. itajara), 

queen conch (Strombus gigas), and stony corals (Bohnsack et al., 1994) were closed in 1998 and remain 

closed today. 

Source: National Marine Fisheries Service SEFSC.

Figure 7.6. Florida total marine recreational fishing trips, angler fishing trips, total 

catch, and total landings for the period 1993 to 2002 estimated from the MRFSS database. 

page 

158 Florida 

The State of Coral Reef Ecosystems of Florida 

Figure 7.7. Time series of nominal fishing effort for commercial (open circles) and 

recreational (dark circles) fleets directed at South Florida reef fish from 1964 to 2002. 

Source: Ault et al. (2001, 2002). 
Sidebar

The State of Coral Reef Ecosystems of Florida

Trade in Coral and Live Reef Species 

The trade in coral and live reef species is not considered a major direct threat to coral reef ecosystems in 

Florida. 

Ships, Boats, and Groundings 

Many ship groundings have occurred on Florida’s coral reefs (Table 7.3). Federal and state rules and regulations protect the stony coral (Magnuson-Stevens Fishery Conservation and Management Act, FWC Rule 

68B-42.009) and there are specific laws and regulations regarding vessel groundings (16 U.S.C. § 1443 and 

1437, FS 253.001 and 253.04). Nevertheless, ship groundings and anchors can damage and destroy corals 

and other biota. According to the FFWCC’s law enforcement records, there are between 500 and 600 vessel 

groundings reported in the FKNMS annually. In addition, there are many unreported groundings that damage 

resources. FFWCC data indicate that approximately 12-15% (60 to 90) of groundings have involved injuries 

to coral reef habitat. 

Vessel groundings can be arbitrarily classified as small (<10 m length), medium (10 to 30 m), or large (greater 

than 30 m). Large vessel groundings often result in immediate and long-term damage. Although the vast maTable 7.3. Summary of vessel groundings in Florida. Source: compiled by staff from FFWCC, NSU, FKNMS, unpublished data. 

VESSEL NAME 

VESSEL SIZE: 

MEDIUM, LARGE 

YEAR OF 

INCIDENT LOCATION INJURED AREA (M2) 

Capt Allen M 1973 Middle Sambo, FKNMS Approximately 125 

M/V Lola L 1976 Looe Key, FKNMS Approximately 200 

M/V Wellwood L 1984 Molasses, FKNMS 1,282 

M/V Mini-Laurel L 1984 FKNMS 270 

M/V Alec Owen Maitland L 1984 FKNMS 661 

M/V Mavro Vetranic L 1989 Pulaski Shoal, Dry Tortugas 15,800 

M/V Elpsis L 1989 Elbow, FKNMS 2,605 

USS Memphis L 1993 Broward County 1,205 

M/V Ms Beholdin L 1993 Western Sambo, FKNMS ???? 

M/V Firat L 1994 Broward County, near Port Everglades 1,000 

R/V Columbus Iselin L 1994 Looe Key, FKNMS 345 

M/V Sealand Atlantic L 1994 Port Everlades entrance, Broward County Approximately 1000 

M/V Igloo Moon L 1996 Biscayne National Park 1,000 

M/V Houston L 1997 Maryland Shoal, FKMMS 7,107 

M/V Hind L 1998 Broward County, near Port Everglades 1000 

M/V Pacific Mako L 1998 Broward County, near Port Everglades 1000 

Lagniappe M 2001 Key West, FKNMS 35 

M/V Diego L 2001 Tortugas Banks 1,886 

M/V Alam Senang L 2003 Broward County, near Port Everglades 216 

M/V Puritan L 2004 Broward County 100 estimated 

M/V Eastwind L 2004 Broward County, near Port Everglades 11,000 preliminary 

Terresa Llyn M 2002 Dry Tortugas 50 estimated 

Captain Bozo M 2002 Dry Tortugas 50 estimated 

Blind Faith M 2002 Dry Tortugas 50 estimated 

Adaro M 2003 

Connected M Western Sambo, FKNMS 

Poetic Justice M 

High Queen and barge M 2002 St Lucie inlet ?? minimal 

Wave Walker M 2002 The Rocks, FKNMS 

Jacquelyn L M Western Sambo, FKNMS 

page 

159 Florida 
page 

160 Florida 

The State of Coral Reef Ecosystems of Florida 

jority of grounding incidents are caused by small, privately owned vessels often resulting in minimal resource 

damage to the resources, the cumulative impacts can be detrimental and long-lasting. Several large- and 

medium-sized vessel grounding incidents have occurred off the east and south coasts of Florida (Table 7.3). 

Large vessels often create injuries exceeding 1,000 m2. The majority of vessel groundings in Florida coral 

reefs are the result of operator error (poor navigating, lack of local knowledge, and inappropriate charts). 

Several groundings have occurred because of stormy weather or an inappropriate anchorage. Anchors and 

chains from large ships can also cause substantial damage, as occurred with the ships M/V Diego in 2001 

and M/V Puritan in 2004. Many of the reported incidents included damage from anchor and chain, as well 

as from the physical impact of the hull. Damage included crushed, broken, and dislodged organisms (e.g., 

sponges, Millepora spp., octocorals, scleractinian corals, zooanthids, anemones, and bryozoans). Large vessels pulverize the limestone reef substrata creating rubble deposits, fractured structure, and in some cases, 

canyons or trenches. Ships often attempt to free themselves from the reef by engaging the propeller. The 

propwash from the propeller mobilizes loose material and may create pits, trenches, and piles of sediment and 

rubble. Damage caused by a propwash can be more severe than the damage caused by hull contact alone. 

In Broward County, significant damage to coral reefs was caused by the grounding and subsequent propwash 

of the nuclear submarine USS Memphis (Banks et al., 1999). 

The type of impact depends upon grounding circumstances such as storm conditions; the ship’s cargo, which 

governs how much the ship draws; and the length of anchor chain or tug boat line used to tow the vessel off 

the reef. Many large vessel groundings have occurred near Port Everglades, Broward County (Table 7.3), 

where ships attempting to anchor or at anchor are driven inshore onto the reef by severe weather. In the Florida Keys, large ship groundings have occurred at Pulaski Shoal, Maryland Shoal, Looe Key, and Molasses, 

Elbow, and Carysfort reefs. Navigational error was the principal cause, although all of the large ships were 

equipped with advanced navigating technology, such as, global positioning system (GPS) receivers, radar, 

radio direction finders, and depth recorders. Often, foreign ships do not have local charts; for example, the 

Mavro Vetranic was found trying to navigate from the eastern Gulf of Mexico into the Straits of Florida with a 

chart that had coverage of the entire Atlantic Ocean at a scale that did not show local aids to navigation (e.g., 

lighthouses). 

Efforts to reduce the effects of vessel groundings have included installing mooring buoys on highly visited reefs 

in Monroe, Miami-Dade, and Broward Counties. This has reduced chronic effects from small boat anchoring. 

The State of Florida and FKNMS have published brochures and made information available on the internet to 

educate users on the risks and best ways to navigate in coral reef areas. The FKNMS has established large 

vessel avoidance areas and installed Racon beacons on lighthouses between Dry Tortugas and Key Largo. 

The beacon transmits a unique signal that is received on active radar receivers identifying the reef lighthouse. 

There is an active effort to find a better anchorage for Port Everglades. Projected future efforts to reduce 

groundings include extending vessel avoidance zones, prohibiting the use of Port Everglades anchorage 

when the wind speed exceeds 25 knots, and enhancing management of the Port Everglades anchorage. 

Vessels that run aground because of negligent operation are held responsible by natural resource trustees 

including the State of Florida, NOAA, and National Park Service (NPS). The nominal responsibility of the 

shipping company-insurance carrier includes assessment, triage, direct restoration, compensatory restoration 

(and/or punitive actions), and post-restoration monitoring. Small boat owners are also held responsible for 

their negligent actions. Scaling for compensation and restoration is based on assessing the injury: defining 

the spatial extent using biological metrics (abundance and cover of coral) and determining the time necessary 

for recovery to pre-incident status for both the injured area and the compensatory action. The Habitat Equivalency Analysis method is a useful approach in determining compensation restoration (Fonseca et al., 2000; 

NOAA, 1997, 2000; Milon and Dodge, 2001). 

Restoration at grounding sites has taken a variety of forms in order to enhance recovery (Jaap, 2000). While 

it is impossible to instantly replace an injured coral reef resource, steps can be taken to promote recovery. 

The typical scenario is to salvage all detached coral and cache them for subsequent reattachment. It is desirable to remove loose injury-generated rubble to expose the reef foundation (limestone rock) and to eliminate 

a source of material that could be mobilized and create additional injury in future storm events. If the reef 

framework is fractured to a significant extent, concrete, native limestone boulders and fiberglass rods may be 
Sidebar

The State of Coral Reef Ecosystems of Florida 

needed and have been used to stabilize the fractured foundation. After the reef has been cleared of rubble 

and the foundation made stable, corals are reattached based on microhabitat requirements (e.g., orientation 

to light and waves). In cases where the reef was rendered flat by severe hull injuries, the topographic relief 

can be enhanced using native limestone, concrete and prefabricated rock structures. These are often secured 

with concrete and reinforcement rods. 

While there are few detailed studies comparing recovery of restored sites with unrestored injury areas, it is 

clear that there have been some successes. Coral reattachment has been a useful method. A number of 

monitoring studies off Broward County have demonstrated very high Scleractinian coral reattachment success 

(80-95%) (Continental Shelf Associates, 2000; Gilliam et al., 2001, 2003; Thornton et al., 2002). After approximately three years, recruitment of coral (octocoral and scleractinian corals) is very common. For example, 

there are restored areas off Miami-Dade County where measurements of percent cover, density, and diversity 

of sessile benthic organisms exceed those at a nearby reference site (Miami-Dade County, 2003). 

Marine Debris 

Lost and discarded lobster, stone crab, and blue crab traps are a common component of marine debris in 

Florida. Traps and the associated buoys and ropes are commonly lost during both routine fishing operations 

and when conflicts occur with other fishing gear and boats. Surveys suggest that, of the 500,000 lobster traps 

currently in the fishery, 20% of them are lost annually. No surveys have been conducted that estimate the 

number of lost stone crab and blue crap traps, but fishers report that they replace 20% of the 818,000 stone 

crab traps used annually, and anecdotal reports suggest that during 1998, 30-50% of the 360,000 blue crab 

traps were lost. Additional trap losses occur during tropical and severe winter storms. During the Ground Hog 

Day storm in 1998, approximately 80,000 lobster traps and 22,000 stone crab traps were lost in the Florida 

Keys. The combined effects of Hurricane Georges and Tropical Storm Mitch later that same year destroyed 

an estimated 111,000 lobster traps and a few thousand stone crab traps. 

Trap debris is distributed in coastal environments and underwater. One shoreline debris removal program 

conducted during 1999 removed 

12,700 kg of plastic trap debris and 

buoys, filling 1,445 50-gallon plastic 

bags along five miles of shoreline 

in the Florida Keys (Figure 7.8). An 

underwater survey conducted in the 

Florida Keys during 1993 estimated 

that there were 2.84 lost or discarded 

traps per ha. Trap debris on shorelines is a significant source of visual 

pollution, but probably poses little 

threat to marine life unless the material is reintroduced to the marine 

environment. However, submerged 

trap debris is known to cause the loss 

of vegetation from beneath the traps 

and may have more severe effects if 

moved during storms. The impact of 

trap debris on coral communities is 

currently being examined. 

Figure 7.8. A mountain of debris removed from the Florida Shoreline during 1999. 

Photo: T. Matthews. 

page 

161 Florida 

Aquatic Invasive Species 

Fish 

Within the United States the number of non-native fishes caught in the wild in Florida is second only to the 

number caught in California. At least 123 non-native fish species have been caught in Florida. Of these, 56 

are established in freshwater habitats and at least four are established in estuaries (FMRI, unpublished data; 
page 

162 Florida 

The State of Coral Reef Ecosystems of Florida 

USGS, 2003). Fifteen species of non-native tropical reef fishes, mainly angelfishes (Pomacanthus spp.), 

surgeonfishes (Zebrasoma spp.), and a serranid (Chromileptes altivelis), have been observed in southeastern Florida reefs (Semmens et al., 2004; USGS, 2003), but are not known to be established. The ecological 

impact of non-native species has been discussed by various authors (Taylor et al., 1984; Carlton and Geller, 

1993; Simberloff et al., 1997; Carlton, 2001; Kolar and Lodge, 2002). 

The red lionfish (Pterois volitans) is the only marine species that appears to have become established in 

Florida (Whitfield et al., 2002; Ruiz-Carus et al., in press). Six lionfish were freed into Biscayne Bay, Dade 

County on August 24, 1992, when Hurricane Andrew destroyed a large marine aquarium (Courtenay, 1995). 

Red lionfish were initially sighted on shallow-water reefs off Palm Beach in October 1992 (Courtenay, 1995). 

Reports of lionfish were sporadic from 1993 to 2001. In 2002, two voucher specimens were captured off St. 

Augustine and Jacksonville. Sightings were reported in Nassau, Palm Beach, and Miami-Dade Counties. 

Gonad histology of the voucher female lionfish showed that most likely it spawned in local waters; the male 

voucher showed a testis in the mid-maturation class (Ruiz-Carus et al., in press). Red lionfish are now found 

along the seaward edge of reefs and in lagoons, turbid inshore areas, and harbors (Schultz, 1986; Myers, 

1991). In the U.S., red lionfish were also observed at artificial reefs and in waters as deep as 79 m off North 

and South Carolina (Ruiz-Carus et al., in press). Red lionfish are often found during the day under ledges and 

crevices but may also hunt small fish, shrimps, and crabs in open water at night (Myers, 1991). The paucity 

of biological data on red lionfish brings new challenges to managers and researchers. 

The red lionfish could pose a threat to Florida’s fishers, divers, and wildlife inspectors because it is venomous. 

Furthermore, potential ecological effects include habitat alteration; water quality degradation; and introduction of diseases and parasites, competition, predation, hybridization, and replacement of native species. As 

introduction of non-native marine fishes is relatively rare, the effects of such introductions are not well documented. 

Both the accidental and purposeful introductions of non-native fishes into Florida waters reflect the rise in 

Florida’s consumption and production of tropical ornamental fishes (Ruiz-Carus et al., in press). It is likely 

that the number of marine species in the market will increase because of improvements in “mini-reef system” 

aquaria (Larkin and Degner, 2001), and greater access to remote areas where additional non-native species 

can be obtained (Larkin, 2003). 

Coral 

Orange cup coral (Tubastrea coccinea) is a solitary or cluster of tubes, usually less than 15 cm high and 2 cm 

in diameter. Larger clusters may include 50 or more bright orange tubes. The tentacles are orange and often 

extend outward from the top of the tube capturing food. 

Tubastrea coccinea is well known in the Pacific Ocean, Red Sea, and Indian Ocean. The species type was 

found off of Bora Bora by Lesson in 1829. The earliest report of T. coccinea in the Caribbean/western Atlantic 

is in 1943 from Puerto Rico and Curacao and it was subsequently sited throughout the Caribbean Basin (Jamaica-1955, Cuba-1982, Bahamas-1985, western Gulf of Mexico-1999). In Florida, the preferred habitat is on 

vertical steel structures (sunken ships and engineering platforms). Tubes are usually facing in the direction of 

the current. A good example is the sunken vessel, U.S. Coast Guard cutter Duane off Key Largo, where the 

southern facing deck structures are veneered with multiple colonies. T. coccinea was reported on the Duane 

in 1999 (J. Sprung, pers. comm.) and that it was well established there by March 2002 (W. Jaap, pers. obs.). 

In the Pacific, T. coccinea is often found in caves with swift water movement, usually below 15 m depth. 

The appearance of this coral in Florida indicates that some Indo-Pacific reef fauna can reproduce and survive 

in the western Atlantic. To date, there are no reports of T. coccinea replacing native species and it is only 

known to settle and grow on steel structures. Monitoring is recommended at selected locations to follow the 

status and trends in abundance and distribution for T. coccinea. 

Plants 

While non-native fishes and corals may threaten Florida’s coral reef, non-native plants pose the greatest 

risks. The world-wide spread of the algae, Caulerpa taxifolia, and its effects in the Mediterranean have 
Sidebar

The State of Coral Reef Ecosystems of Florida

been well documented (http://www.pbs.org/ 

wgbh/nova/algae/chronology.html). More recently, Caulerpa brachypus (Figure 7.9), native to the Pacific region, has been detected 

in Florida on nearshore reefs and in the Indian 

River Lagoon. The species was probably released from saltwater aquaria or from ships’ 

ballast water. In the absence of predators it 

grows unchecked and can smother corals and 

seagrass beds rapidly if sufficient nutrients are 

available (http://www.dep.state.fl.us/southeast/ 

hottopics/caulerpa/cbrachypusalertbulletin. 

pdf). Recent reports from divers and fishers indicate that the algae has now become so thick 

on reefs in Palm Beach County, that it is forcing lobsters and fish away. The species has 

also now been observed 100 km north at Fort 

Pierce, Florida, and Lapointe and Barile (2003) 

believe the rapid spread is enhanced by anthropogenic enrichment. 

Security Training Activities 

Security training activities are not recognized as a major threat to coral reef ecosystems in Florida. 

Offshore Oil and Gas Exploration 

There is currently no oil or gas drilling occurring in state waters. Florida law prohibits future leasing or drilling 

of the seabed within the state’s territorial sea for purposes of oil and gas exploration and development. Holders of any offshore drilling leases that were granted by the state prior to the enactment of the current law must 

obtain permits under state environmental laws and regulations prior to conducting any drilling activities. No 

leases exist in Florida areas where coral reef tracts are located. 

Other 

Subsea Engineering Projects: Fiber Optic Cables and Gas Pipelines 

In the past decade, multiple fiber optic cables have been installed off Miami-Dade, Broward, and Palm Beach 

Counties. The nominal construction included horizontal directional drilling from the coast to beyond the first 

reef terrace. After exiting from the bore hole, the cable was deployed eastward on the surface of the seafloor. 

During some cable installations, there were “frac-outs” (i.e., when drilling mud escapes from the bore hole 

through a crack or void in the rock). These incidents were not serious in terms of mortality or morbidity of 

marine fauna. 

In 1999, AT&T Corporation installed four cables off Hollywood Beach in Broward County. Two of the cable 

deployments resulted in injuries to numerous coral colonies (Table 7.4), and several large barrel sponges 

(Xestospongia muta) were amputated at their bases. The contracting firm paid for direct and compensatory 

restoration, which included installing mitigation modules (limestone boulders imbedded in a concrete base). 

Florida 

page 

163 

In April 2001, a second cable injury Table 7.4. Impacts to coral from AT&T incident. Source: PBS&J, 2000. 

occurred at the ARCOS-I cable deployment in Sunny Isles, Miami-Dade 

County. Injuries to corals are provided in Table 7.5. The injuries were 

repaired and compensatory mitigation included installing a boulder field 

Figure 7.9. The ‘green menace’, Caulerpa brachypus, was introduced to 

Florida from the Pacific. Anecdotal reports indicate that it is flourishing in 

Florida and poses a threat to native reef organisms. Photo: L. Nall. 

IMPACT CATEGORY AMERICAS II CABLE COLUMBUS III CABLE 

Cable overhanging coral 78 56 

Cable lying on top of coral 45 63 

Cable abrasion injury 12 29 

Totals 135 148 
The State of Coral Reef Ecosystems of Florida

near the cables. Subsequent to the Table 7.5. Impacts to coral from ARCOS incident. Source: PBS&J, 2003. 

page 

164 Floridacable installations in 1999-2001, the 

State of Florida directed cable companies to install all future cables in areas where there are gaps in the reefs 

to reduce resource injury risks. 

A 36-inch diameter gas pipeline (Gulfstream Gas Natural Gas System) 

was installed from Mobile Bay, Alabama to Port Manatee, Tampa Bay and began operating in May 2002. The 

pipeline was required to be buried three feet under the seafloor to a water depth of 200 ft; beyond 200 ft, the 

pipe was positioned on the seafloor. A trench was created with a submarine plow and the pipe was laid in the 

trench. In multiple areas in and offshore Tampa Bay, the trenching was impeded by dense-hard rock. In cases 

of partial pipe burial, the contractor used boulders to cover the pipe; in cases where the plow did not penetrate 

the rock, the contractor fastened the pipe to the rock with metal hardware. Trenching resulted in injuries to 

coral and other hardbottom resources within Tampa Bay and the Gulf of Mexico. Injuries also occurred from 

vessel and barge mooring anchors and cables. Injuries within Tampa Bay were compensated by mitigation 

projects. Two-hundred sponges and octocorals were moved from hardbottom areas in the pipeline corridor to 

mitigation structures and eight acres of habitat structures (at six mitigation sites) were installed. Each mitigation site provides 1.3-1.4 acres of limestone boulder-pyramids; each site includes 16 to 17 pyramids which are 

composed of 20 ft long by 24 ft wide, by 3-4 ft high boulders (ENSR International, 2002). Inspections reveal 

colonization of these structures by algae, sponges, octocorals, blue crabs, stone crabs, and schools of anchovies and spadefish. In the eastern Gulf of Mexico, the pipeline installation disturbed 27 acres of hardbottom, including sponges, octocorals, and stony coral communities. Installation of nine boulder fields and three 

pre-fabricated module sites mitigated the injuries. Approximately 49 acres of mitigation was provided at the 

12 locations seaward of Egmont Key, in depths ranging from 52 to 120 ft (Continental Shelf Associates, 2001; 

Sea Byte, 2001). Over 400,000 tons of boulders were deployed in discrete fields. The boulders (at least 3 ft in 

dimension) were deployed in multiple layers to provide refuge. Inspections of boulders and modules revealed 

colonization by algae, sponges, hydroids, snapper, schools of anchovies, nurse sharks, and goliath grouper. 

Additional gas pipeline projects on the east coast of Florida are currently being reviewed for permits. Two 

proposals from the Calypso-Tractebel and AES Ocean Express have advanced to the point that permitting 

may occur in 2005. Another pipeline proposed by El Paso is not as far along in the permitting process. These 

projects propose to install 24-inch diameter pipelines that would originate in the Bahamas, cross the Straits of 

Florida, and terminate near Port Everglades (Jupiter for El Paso). The draft environmental impact statements 

for the first two projects proposed the removal of rubber tires deployed in the 1960s as artificial reefs for mitigation of their impacts. These tires have become unbundled, have moved, and are injuring reef resources. 

Larger corals in known areas of impact will be relocated to non-impacted sites. The pipeline companies propose to avoid injuring reef habitat by drilling under the reefs and connecting the sections of pipe in non-reef 

areas. There are concerns regarding deployment of construction equipment, “frac-outs” from drilling, possible 

of a major storm events during drilling, and deployment of pipes in a major boundary current (Gulfstream or 

Florida Current) in extremely deep water. 

Construction of the pipeline projects will involve direct impacts to coral reef habitat from horizontal directional 

drilling and associated sump berms, trenching in areas where the pipeline will transit from horizontal directional drilling holes, sedimentation and turbidity associated with drilling and trenching, and possible “frac-outs” 

during drilling. In addition, some pipeline strings have to be laid out and pulled into horizontal directional drilling holes. Some pulling will occur over coral reef habitat, thereby causing injury from the dragging. 

ARCOS NORTH ACROS SOUTH 

IMPACT CATEGORY CABLE CABLE 

Cable overhanging coral 67 75 

Cable lying on top of coral 34 23 

Cable abrasion injury 8 16 

Totals 109 114 
Sidebar

The State of Coral Reef Ecosystems of Florida 

CORAL REEF ECOSYSTEMS—DATA-GATHERING ACTIVITIES AND RESOURCE CONDITION 

The FKNMS enabling legislation requires a comprehensive water quality status and trends monitoring program with three major components: water chemistry, seagrass, and coral reefs (U.S. DOC, 1996). The 

protocols and sampling strategies were developed in collaboration with EPA in 1994-95. Water chemistry and 

seagrass monitoring are conducted by Florida International University; coral reef monitoring is conducted by 

the FFWCC’s Fish and Wildlife Research Institute. The two institutions began collecting data in 1995-96. 

The waters of the FKNMS are characterized by complex water circulation patterns, with much of the spatial 

and temporal variability due to seasonal influences on regional circulation regimes. The Sanctuary is directly 

influenced by the Florida Current, Gulf of Mexico Loop Current, inshore currents of the southwestern Florida 

Continental Shelf (Shelf), discharge from the Everglades through the Shark River Slough, and tidal exchange 

with both Florida Bay and Biscayne Bay (Lee et al., 1994, 2002). Advection from these external sources has 

significant effects on the physical, chemical, and biological composition of waters within the Sanctuary, as may 

internal nutrient loading and freshwater runoff from the Keys themselves and episodic upwelling (Leichter et 

al., 2003). 

A spatial framework for water quality management was proposed on the basis of geographical variation of 

regional circulation patterns (Klein and Orlando, 1994). Quarterly sampling of more than 200 stations in the 

Sanctuary and on the Shelf, as well as and monthly sampling of 100 stations in Florida Bay, Biscayne Bay, 

and the mangrove estuaries of the southwestern Florida coast, provide a unique opportunity to explore the 

spatial variability in water quality measures in South Florida’s coastal waters (Figure 7.10). Details on water 

chemistry sampling strategy, field sampling methods, laboratory analyses, and data processing are available 

on-line at http://sefrc.fiu.edu/wqmnetwork/ (accessed 1/31/05). 

WATER QUALITY 

Methods 

Several variables were measured in situ and from grab samples at 54 fixed stations within the Sanctuary 

boundary beginning in March 1995 (Figure 7.10). Depth profiles of temperature, salinity, dissolved oxygen 

(DO), photosynthetically active radiation (PAR), in situ chlorophyll a 

(CHLa) specific fluorescence, optical 

backscatterance turbidity, depth, and 

density were measured by conductivity-temperature-depth (CTD) casts 

using a Seabird SBE 19 instrument 

(Table 7.6). Vertical light attenuation (kd

, per meter) was calculated at 

0.5 m intervals from PAR and depth 

(Kirk, 1994) and averaged over the 

depth of each station. Where it was 

too shallow to use a CTD, surface 

salinity and temperature were measured using a combined salinity-conductivity-temperature probe. DO was 

measured with an oxygen electrode 

corrected for salinity and temperature. PAR was measured with a LiCor irradiance meter. The extent of 

water stratification was calculated as 

the difference between surface and 

bottom density (∆δt), such that positive values denoted greater densities 

Figure 7.10. The Southeast Environmental Research Center (SERC) Water Quality 

Monitoring Network showing the distribution of fixed sampling stations (+) within the 

Florida Keys National Marine Sanctuary (red stations) and Florida Bay, Biscayne Bay, 

Whitewater Bay, Ten Thousand Islands, and Southwest Florida Shelf (blue stations). 

Source: Boyer and Jones, 2003. 

page 

165 Florida 
page 

166 Florida 

The State of Coral Reef Ecosystems of Florida

of bottom water relative to the surface and negative values indicated the opposite. A value of ∆δt >1 indicated 

weak stratification, whereas ∆δt >2 meant strong water stratification. 

Water samples were collected from approximately 0.25 m below the surface and at approximately 1 m from 

the bottom. Unfiltered water samples were analyzed for total organic carbon (TOC), total nitrogen (TN), total 

phosphorus (TP), silicate (Si(OH)4), alkaline phosphatase activity (APA), and turbidity. Fluorescences at initial 

and after two-hour incubation were measured using a spectrofluorometer (Jones, 1996). Filtrates were analyzed for nitrate+nitrite (NO -

x ), nitrite (NO -2 ), ammonium (NH +4 ), and soluble reactive phosphorus (SRP). 

Several parameters were not measured directly. Nitrate (NO -

3 ) was 

calculated as NO -

x - NO -2 , dissolved 

inorganic nitrogen (DIN) was determined as NO - + NH +

x 4 , and total organic nitrogen (TON) was defined as 

TN - DIN. DO saturation in the water 

column (DOsat) was calculated using 

the equations of Garcia and Gordon 

(1992). Stations were stratified according to water quality characteristics (i.e., physical, chemical, and biological variables) using multivariate 

statistical techniques, an approach 

that has been very useful in understanding the factors influencing nutrient biogeochemistry in Florida Bay, 

Biscayne Bay, and the Ten Thousand 

Islands (Boyer and Jones, 2003). 

Data from individual sites for the 

complete period of record were plotted as time series graphs to illustrate 

any temporal trends that might have 

occurred. Temporal trends were 

quantified by simple regression with 

significance set at P <0.05. 

Summary statistics for all water quality variables from all 29 sampling 

events through September 2002 are 

shown as median, minimum, maximum, and number of sample stations 

(Table 7.6). Overall, the region was 

warm and euhaline with a median 

temperature of 27.1°C and salinity of 

36.2 parts per thousand (ppt); DOsat 

was relatively high at 90.1%. On this 

coarse scale, the Sanctuary exhibited 

very good water quality with median 

NO -

, NH +

3 4 , and TP concentrations of 

0.09, 0.30, and 0.20 μM, respectively. 

NH + 

4 was the dominant DIN species 

in almost all of the samples (~70%). 

However, DIN comprised a small 

fraction (4%) of the TN pool with TON 

Table 7.6. Median, minimum (Min.), and maximum (Max.) values and the number of 

sample stations (n) for water quality variables measured in the Florida Keys National 

Marine Sanctuary between March 1995 and September 2002. Source: Boyer and 

Jones, 2003. 

VARIABLE DEPTH MEDIAN MIN. MAX. n 

Nitrate (μM) Surface 0.087 0 5.902 4386 

Bottom 0.08 0 5.01 2675 

Nitrite (μM) Surface 0.043 0 0.71 4396 

Bottom 0.038 0 1.732 2682 

Ammonium (μM) Surface 0.299 0 10.32 4395 

Bottom 0.268 0 3.876 2680 

Total Nitrogen (μM) Surface 10.83 1.707 211.1 4391 

Bottom 9.036 1.482 152.23 2661 

Total Organic Surface 10.261 0.389 210.78 4372 

Nitrogen (μM) Bottom 8.445 0 151.91 2641 

Total Phosphorus Surface 0.198 0 1.777 4394 

(μM) Bottom 0.185 0 1.497 2663 

Soluble Reactive Surface 0.013 0 0.297 4383 

Phosphorus (μM) Bottom 0.013 0 0.39 2674 

Alkaline Surface 0.06 0 5.616 4232 

Phosphatase 

Activity (μM h-1) 

Bottom 0.048 0 0.491 2520 

Chlorophyll a (μg 

l

-1) 

Surface 0.261 0.01 15.239 4394 

Total Organic Surface 199.69 83.77 1653.5 4393 

Carbon (μM) Bottom 171.6 89.38 883.1 2669 

Silicate (μM) Surface 0.701 0 127.11 4090 

Bottom 0.455 0 30.195 2491 

Turbidity (NTU) Surface 0.62 0 37 4349 

Bottom 0.52 0 16.9 2700 

Salinity Surface 36.2 26.7 40.9 4315 

Bottom 36.2 27.7 40.9 4287 

Temperature (oC) Surface 27.1 15.1 39.6 4322 

Bottom 26.6 15.1 36.8 4294 

Vertical Light 0.23 0.003 3.41 3050 

Attenuation 

Coefficient k (m-1) d

Dissolved Oxygen Surface 90.1 31.2 191.6 4286 

saturation (%) Bottom 89.9 19.3 207 4240 

Water Stratification 0.007 -4.42 6.64 4269 

(surface density -

bottom density, ∆δ ) t
Sidebar

The State of Coral Reef Ecosystems of Florida 

making up the bulk (median 10.3 μM). SRP concentrations were very low (median 0.013 μM) and comprised 

only 6% of the TP pool. CHLa concentrations were also very low overall (0.26 μg/L), but ranged from 0.01 to 

15.2 μg/L. TOC was 199.7, a value higher than open-ocean levels but consistent with coastal areas. Median 

turbidity was low (0.6 nephelometric turbidity units, or NTUs) as reflected in a low kd (0.23/m). This resulted in 

a median photic depth of approximately 22 m, which was within 1% of incident PAR. Molar ratios of nitrogen 

(N) to phosphorous (P) suggested that was P was limited in the water column (median TN:TP = 57), but observed ratios of N to P could have resulted because TN may not be biologically available. 

Principal component analysis identified five composite variables (hereafter refered to PC1, PC2, etc.) that accounted for 63.2% of the total variance. PC1 had high factor loadings for NO3

-

, NO2

-

, NH4

+, and SRP and was 

named the inorganic nutrient component. PC2 included TP, APA, CHLa, and turbidity and was designated as 

the phytoplankton component. The covariance of TP with CHLa implies that, in many areas, phytoplankton 

biomass may be limited by phosphorus availability. This is contrary to much of the literature on the subject, 

which usually ascribes nitrogen as the limiting factor for phytoplankton production in coastal oceans. TON and 

TOC were included in PC3 as the terrestrial organic component. Temperature and DO were inversely related 

in PC4. Finally, PC5 included salinity and TP, implying a source of TP from marine waters. 

Spatial distributions of the mean factor 

score for each station indicated that 

water quality varied over the study 

area (Figure 7.11). The inorganic 

nutrient component had two peaks 

in the Backcountry, and along the 

northern side (bayside) of the Middle 

Keys (Figure 7.11). The phytoplankton component described a north to 

south gradient in the Backcountry and 

Sluiceway that extended west across 

the northern Marquesas. The terrestrial organic component was highest 

in eastern Sluiceway extending into 

the Backcountry and was also distributed as a gradient away from land on 

the Atlantic side (oceanside) of the 

Keys. Temperature and DO showed 

a distribution heavily loaded in the 

oceanside. Finally, the salinity/TP 

component showed lower loadings in 

the nearshore Upper Keys and bayside Sluiceway extending through 

most Atlantic sites of the Middle and 

Lower Keys. 

Cluster analysis separated sampling 

sites (n=150) into eight clusters, with 

most stations grouped within clusters 1, 3, 5, 6, 7, and 8 (Figure 7.12). 

Statistically significant differences 

between clusters indicated a nutrient gradient throughout the Sanctuary (highest to lowest concentrations: 

clusters 7 & 8 > 1 > 5 > 6 > 3). Cluster 7 was composed primarily of stations located inside the Backcountry, 

Figure 7.11. Map of South Florida showing the boundary of the Florida Keys National 

Marine Sanctuary and geographic segments (names and numbers) used for site selection during routine water quality sampling for the period 1995 to 2003. Source: 

Boyer and Jones, 2003. 

8 

page 

167 Florida 

Figure 7.12. Map of sample stations forming distinct water quality groups represented by colored dots. Station groups were identified through objective classification 

analysis. Source: Boyer and Jones, 2003. 
The State of Coral Reef Ecosystems of Florida

page 

168 Floridabayside Middle Keys, and inshore sites off Lower Matecumbe Key. This group was highest in inorganic nutrients, especially NO3

-

, TOC, and TON. In the shallow Backcountry sites benthic flux of nutrients might be 

very important, whereas elevated DIN at inshore Lower Matecumbe sites may be the result of anthropogenic 

loading. Cluster 8 included the northernmost sites in the Sluiceway, Backcountry, and Marquesas, which had 

the highest TP, CHLa, and turbidity, but was low in inorganic nutrients, DON, and DOC. Water quality in this 

cluster probably was driven primarily by Shelf circulation patterns. 

Cluster 1 was composed of two sites in the northern Sluiceway and 12 sites in the northern Backcountry extending out to the Marquesas (Figure 7.12). This group was high in TP, CHLa, and turbidity. The main distinction between Clusters 1 and 8 was that Cluster 8 was higher in CHLa and lower in TOC. These clusters may 

be viewed as a gradient of high-TP Shelf water being attenuated by uptake of nutrients within the Backcountry 

and/or mixing with Atlantic Ocean waters. 

Clusters 5, 6, and 3 may be interpreted as representing an onshore-offshore nutrient gradient (Figure 7.12). 

Cluster 5 included most of the inshore sites of the Keys, excluding the northernmost and southernmost ones. 

They were elevated in DIN relative to Hawk Channel and reef tract sites. Cluster 6 was made up of sites in 

Hawk Channel of the Lower Keys and alongshore sites in the Upper Keys. This group was slightly lower in 

nutrients than Cluster 5. Cluster 3 was made up of outer reef tract and Tortugas stations. These sites had 

the lowest nutrients, CHLa, turbidity, and TOC in the Sanctuary. A clear gradient of elevated DIN, TP, TOC, 

and turbidity from alongshore to offshore was observed in the Keys, with the Upper Keys being lower than the 

Middle and Lower Keys. The elevated DIN in the nearshore zone of the Keys was not observed in the nearly 

uninhabited Tortugas, indicating an anthropogenic source. No significant onshore-offshore gradient was observed for CHLa. 

The highest concentrations of CHLa 

were observed on the southwestern 

Shelf (Figure 7.13), with a strong 

decreasing gradient toward the Marquesas and Tortugas. This pattern 

was likely caused by higher TP concentrations on the Shelf because of 

southward advection of water along 

the mainland coast. Most parameters 

were relatively consistent from year 

to year, with some seasonal excursions. The exceptions were statistically significant increases in TP and 

decreases in DO and TOC throughout the region (Figure 7.14). 

The local trends described in this 

study may occur across the whole region, although less pronounced. 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. Large changes have 

occurred in Sanctuary water quality over time, and some sustained monotonic trends have been observed 

(Figure 7.14). However, trend analysis is limited to the window of observation; trends may change, or even 

reverse, with additional data collection. 

The large scale of this monitoring program has allowed a holistic view of broad physical/chemical/biological interactions occurring over the South Florida region. Much information has been gained by inference 

from this type of data collection program; major nutrient sources have be confirmed, relative differences in 

Figure 7.13. Distribution of median concentrations of Chlorophyll a in Florida’s coastal waters for the period 1995 to 2003. Sampling stations are indicated with a + symbol. Source: Boyer and Jones, 2003. 
Sidebar

The State of Coral Reef Ecosystems of Florida

geographical determinants of water 

quality have been demonstrated, and 

large-scale transport via circulation 

pathways has been elucidated. In 

addition, this program demonstrates 

the importance of looking “outside 

the box” for questions asked within. 

Rather than thinking of water quality 

monitoring as a static, non-scientific 

pursuit, it should be viewed as a tool 

for answering management questions and developing new scientific 

hypotheses. 

Downloadable contour maps, timeseries graphs, and interpretive reports 

from the Southeast Environmental Research Center’s water quality 

network (which includes Florida Bay, 

Whitewater Bay, Biscayne Bay, Ten 

Thousand Islands, and Southwest 

Florida Shelf) are available at http:// 

serc.fiu.edu/wqmnetwork (Accessed, 

1/31/2005). 

Florida 

Figure 7.14. Distribution of significant increases in total phosphorus concentrations 

(top panel) and decreases in dissolved oxygen (middle panel) and total organic carbon (bottom panel). Sampling stations are indicated with a + symbol. Source: Boyer 

and Jones, 2003 

page 

169 
page 

170 Florida 

The State of Coral Reef Ecosystems of Florida 

BENTHIC HABITATS 

The Coral Reef Evaluation and Monitoring Project 

Methods 

The FFWCC’s Coral Reef Evaluation and Monitoring Project (CREMP) tracks the status and trends of stony 

corals and selected benthic biota at 53 stations across the Florida Reef Tract from Palm Beach through the 

Dry Tortugas. The project annually samples at 43 permanent sites in the Florida Keys and Dry Tortugas and 

10 sites off the Southeast Florida coast in Palm Beach, Broward, and Miami-Dade Counties. Habitat types 

include hardbottom, patch reef, shallow offshore, and deep offshore communities. Within stations, sampling 

consists of a station species inventory (SSI), video transects, and a bioeroding sponge survey. Diseased coral 

surveys, stony coral abundance surveys, and temperature surveys are also conducted at selected sites. Details on sampling strategy, field methods, and data processing and analyses may be accessed at http://www. 

floridamarine.org/corals (Accessed 2/8/05). 

Results and Discussion 

The inventory of coral species richness within FKNMS from 1996 through 2003 exhibited a trend of general 

decline in stony coral species richness in all reef types and geographic areas (Upper, Middle, and Lower 

Keys). The number of species observed declined at 74 stations (70%), increased at 21 stations (20%), and 

remained stable at 10 stations (10%). More coral species were seen at deep reef and patch reef stations than 

in shallow reef and hardbottom stations (Table 7.7). 

The number of stations where Acropora cervicornis and Scolymia lacera 

were present decreased significantly 

(P <0.05) while Copolphyllia natans, 

Madracis mirabilis, Porites porites, 

Siderastrea radians, Mycetophyllia 

ferox, and M. lamarkiana showed decreases (P <0.1). Only Siderastrea 

siderea was observed at a significantly greater number of stations in 

2001-2002 than in previous years. 

There were trends showing increases 

in the number of stations where coral 

Table 7.7. Change in coral species richness among benthic habitats and regions 

of the Florida Keys and Dry Tortugas between 1996 and 2003. Source: Jaap et al., 

2003. 

disease occurred, number of different types of disease, and number of coral species infected with disease. 

In 1996, diseased corals were seen at 20 stations, compared with 95 stations in 2003. Black band disease 

(BBD; Rützler and Santavy, 1983) was least common of the conditions monitored; the incidence of BBD was 

slightly higher in 1998 and has wavered at low levels in subsequent years. Colpophyllia natans, Montastraea annularis, Montastraea cavernosa and Siderastrea siderea were the species most infected by BBD. In 

1996, white band disease (WBD) was recorded at five stations; in 2002 it was present at 90 stations. WBD in 

Agaricia agaricites was not seen at any stations in 1996, but was seen at 33 stations in 2002. Montastraea 

annularis complex followed a similar pattern with no reports in 1996, but corals at 32 stations showed infection in 2002. Purple spot on Siderastrea siderea was also reported. Fourteen species exhibited an increase 

in diseases: Agaricia agaricites, Colpophyllia natans, Dichocoenia stokesii, Eusmila fastigiata, Favia fragum, 

Meandrina meandrites, Millepora alcicornis, Millepora complanata, Montastraea cavernosa, Montastraea annularis complex, Porites astreoides, P. porites, S. siderea, and Stephanocenia michelinii. 

Coral cover exhibited a significant decline for the period 1996-1999; there was no significant change from 

1999- 2003 (Figure 7.15). These changes were most likely related to bleaching episodes in 1997 and 1998 

and hurricanes in 1998 and 1999. The areas most influenced by these disturbances were shallow offshore 

sites. During bleaching events, temperatures were high enough to cause expulsion of zooxanthellae, thereby 

discoloring many of the zooanthids, fire coral, stony corals, and some octocorals such as Biareum spp. The 

organisms that exhibited the most bleaching were M. complanata and Palythoa mammillosa. These are senCATEGORY LOST TAXA GAINED TAXA UNCHANGED 

# % # % # % 

All stations 74 70 21 20 10 10 

Hard bottom 6 55 3 27 2 18 

Patch Reef 29 72 3 11 5 14 

Shallow offshore 28 72 10 26 1 3 

Deep offshore 26 73 5 15 2 6 

Upper Keys 23 77 2 7 5 17 

Middle Keys 20 69 7 24 2 7 

Lower Keys 31 67 12 26 3 7 

Dry Tortugas* 9 75 3 25 0 0 

*Database for Tortugas is 1999 – 2002. (gains + unchanged) 
Sidebar

tinel species; they bleach at a slightly lower threshold than many of the 

other corals. M. complanata cover 

decline was greatest from 1998 to 

1999 and has not recovered since 

then (Table 7.8). The percent cover 

and frequency of occurrence of corals improved slightly after 2001. The 

bleaching event in 1997 may have 

stressed M. complanata, and a second exposure to hypothermia in 1998 

may have been sufficient to reduce 

the population drastically. 

The golden sea mat (Palythoa mammillosa) is conspicuous in shallow 

reefs. The CREMP analysis pooled 

all zooanthids (Zoanthus spp., Palythoa spp., Ricordia spp.) into a single 

category. Virtually all zoanthids observed in the images were P. mammillosa. Unlike the fire coral, (M. 

complanata), P. mammillosa showed 

little change in cover after the bleaching disturbance (Table 7.9). A slight 

reduction in the mean percent cover 

of P. mammillosa occurred between 

1997 and 1998, although population 

levels equaled or exceeded the prebleaching period in 2000 and subsequent years. 

Florida 

The State of Coral Reef Ecosystems of Florida 

Hurricane Georges crossed the 

Straits of Florida near Key West on 

September 25, 1998. Sombrero Key 

C-MAN buoy recorded a maximum 

sustained wind of 82 knots with a 

peak gust to 92 knots at 1500 Universal Time on September 25 (Table 

7.10). Hurricane Georges’ greatest 

influence on coral reef communities 

was between Sombrero Key and 

Dry Tortugas. The hurricane’s impact was evidenced by the change 

in Acropora palmata cover, which 

decreased in range, mean, and frequency of occurrence after Hurricane 

Georges (Table 7.11). Sampling occurred before the hurricane struck in 

1998, thus the major decline is most 

noticeable in 1999 and subsequent 

years. A. palmata exhibited the highest pre-hurricane cover at Western 

Sambo station two: 15.28% in 1996 and 16.34% in 1997 (Table 7.11). Figure 7.16 provides evidence of the 

coral cover loss attributed to Hurricane Georges. 

Figure 7.15. Mean percent live coral cover in the Florida Keys National Marine Sanctuary between 1996 and 2003. Source: Jaap et al., 2003. 

Table 7.8. Descriptive statistics for annual percent cover of Millepora complanata in 

the Florida Keys National Marine Sanctuary between 1996 and 2002. Source: Jaap 

et al., 2003. 

YEAR 1996 1997 1998 1999 2000 2001 2002 

Range 0-15.71 0-17.33 0-16.44 0-1.88 0-1.19 0-0.85 0-0.49 

Mean 2.55 2.23 1.56 0.19 0.13 0.09 0.11 

Std.dev. 4.54 4.05 3.25 0.37 0.28 0.18 0.17 

Freq. 0.85 0.85 0.72 0.48 0.33 0.41 0.46 

Table 7.9. Descriptive statistics for annual percent cover of Palythoa mammillosa in 

the Florida Keys National Marine Sanctuary between 1996 and 2002. Source: Jaap 

et al., 2003. 

page 

171 

YEAR 1996 1997 1998 1999 2000 2001 2002 

Range 0-25.54 0-24.69 0-20.01 0-22.48 0-24.45 0-21.54 0-25.39 

Mean 4.36 4.97 4.4 4.25 4.61 4.48 5.3 

Std.dev. 5.4 5.74 4.95 5.11 5.67 5.6 6.32 

Freq. 0.92 0.97 0.92 0.94 0.92 0.92 0.89 

Table 7.10. Data on conditions during Hurricane Georges at C-MAN Stations in the 

Florida Keys, October, 1999. Source: NOAA National Hurricane Center, http://www. 

nhc.noaa.gov/abouttafb.shtml, Accessed: 2/14/2004. 

LOCATION PRESS. 

(mb) 

DATE/TIME 

(UTC) 

SUSTAINED 

WIND 

(kts) 

PEAK 

GUST 

(kts) 

DATE/ 

TIME 

(UTC) 

Lake Worth, FL 1010.0 25/1100 30 35 25/1400 

Fowey Rocks, FL 1006.3 25/1000 45 52 25/1000 

Molasses Reef, FL 1003.1 25/0800 46 53 25/1400 

Long Key, FL 1000.0 25/1000 47 58 25/1400 

Sombrero Key, FL 994.5 25/1300 81 92 25/1500 

Sand Key, FL 990.5 25/1300 56 71 25/1400 

Dry Tortugas, FL 976.3 25/2000 59 68 26/0000 
page 

172 Florida 

The State of Coral Reef Ecosystems of Florida 

The National Hurricane Center re- Table 7.11. Descriptive statistics for annual percent cover of Acropora palmata in the 

ported that Tropical Storm Irene Florida Keys National Marine Sanctuary between 1996 and 2002. Source: Jaap et 

reached hurricane status over the al., 2003. 

Florida Straits on October 14, 1999. 

The center moved over Key West 

on October 15 (Table 7.12). Most 

of the hurricane force winds were 

confined to the east of Irene’s center over the lower to middle Florida 

Keys. Irene made its fourth landfall 

near Cape Sable, Florida and then 

moved across southeast Florida before crossing the Keys, into the Everglades. Its sustained and peak wind 

gusts were less than those of Hurricane Georges (Table 7.10). The second hurricane in 13 months disturbed 

offshore shallow reefs, but since Hurricane Georges had already reduced 

populations of A. palmata and other 

organisms, Hurricane Irene’s influence was somewhat muted. 

Frequency and Distribution of 

Coral Diseases 

Methods 

A broad-scale survey to determine 

the frequency and distribution of coral 

disease in the Florida Keys was conducted in August 2000 and incorporated 30 sites from Key Biscayne to 

the Dry Tortugas. Sites were located 

in Biscayne National Park, FKNMS, 

New Grounds, and the Dry Tortugas 

National Park. A sampling protocol 

similiar to those used in EPA’s Environmental Monitoring and Assessment Program was used to select 

site locations (Summers et al., 1995; 

Santavy et al., 2001). The probabilistic sampling design was generated 

and implemented to estimate the 

baseline condition of reef corals to 

compare with future assessments. The survey will be repeated in August 2005. 

The study produced unbiased estimates of coral condition with a quantifiable level of uncertainty for the distribution and frequency of coral diseases in the Florida Keys. The distribution of coral disease was assessed 

as present or absent for each site. The frequency of coral disease was the percentage of diseased coral from 

each site. The area represented by the study was 41 km2 of the South Florida Keys Tract. The reef areas of 

the Florida Keys (Upper, Middle, and Lower Keys; New Grounds; and Dry Tortugas) that contained hard coral 

bottom were demarcated based on benthic habitat maps of the Florida Keys (FMRI, 1998). Habitat boundaries 

were redefined by experts to include areas known to have living corals and to eliminate areas that contained 

only dead or geological reef structure. The design was developed in three steps: (1) regional stratification, (2) 

overlay of a hexagonal grid on the sample frame, and (3) random selection of multiple sites within grid cells 

(Summers et al., 1995; Santavy et al., 2005). 

YEAR 1996 1997 1998 1999 2000 2001 2002 

Range 0-15.28 0-16.34 0-9.96 0-3.40 0-2.72 0-2.44 0-4.88 

Mean 2.97 2.91 1.79 0.4 0.33 0.27 0.4 

Std.dev. 4.6 4.55 3.2 0.9 0.73 0.58 0.98 

Freq. 0.44 0.44 0.38 0.28 0.3 0.28 0.28 

Figure 7.16. Loss of Acropora palmata along a video transect at Western Sambo, 

Florida Keys between 1996 and 2000. Source: Jaap et al., 2003. 

Table 7.12. Data on conditions during Hurricane Irene at C-MAN Stations in the 

Florida Keys, October, 1999. Source: NOAA National Hurricane Center, http://www. 

nhc.noaa.gov/abouttafb.shtml, Accessed: 2/14/2004. 

LOCATION PRESS. 

(mb) 

DATE/ 

TIME 

(UTC) 

SUSTAINED 

WIND 

(kts) 

PEAK 

GUST 

(kts) 

DATE/ 

TIME 

(UTC) 

Sombrero Key C-MAN 990.5 15/1700 57 69 15/1530 

Molasses Reef C-MAN 991.5 15/2100 53 64 15/2020 

Long Key C-MAN 988.7 15/2000 50 61 15/2000 

Sand Key C-MAN 987.0 15/1200 43 57 15/0610 

Dry Tortugas C-MAN 41 51 15/0850 

Key West Intl. Airport 987.6 15/1010 38 47 15/0518 
Sidebar

The State of Coral Reef Ecosystems of Florida

Results and Discussion 

The areal estimates of coral disease generated by the 2000 survey indicated that at least one coral colony affected by active disease was observed in 85% ± 9 (95% confidence intervals) of the area sampled. Coral disease was widely dispersed throughout the Florida Keys Reef Tract and did not seem to be confined to a particular region. While the presence or distribution of disease was widespread, the proportion of colonies affected 

by disease or disease prevalence at any particular location was significantly less. The maximum percent of 

coral colonies affected with disease or maximum prevalence of coral disease in South Florida at any one site 

during August 2000 was 13%, with 2.2% ± 4 (97 ha) of the sampling area containing this maximum level of 

coral disease (Figure 7.17). Approximately 15% ± 9 (662 ha) of the area sampled contained no coral disease, 

whereas 31% ± 14 (1,369 ha) of the area had between 0.4%- 2.2% of the colonies affected by coral disease. 

Approximately 28% ± 15 (1,236 ha) of the area had greater than 2% and no more than 4% of colonies affected 

by disease. Finally, 24% ± 4 (1,060 ha) of the sampled area had between 4% and 9% frequency of coral disease. By establishing this baseline, future surveys can examine changes and trends in the spatial and temporal distribution and frequency of coral disease in South Florida (Santavy et al., 2005). This approach will allow 

the condition of reefs to be classified 

generally from excellent to degraded, 

to better communicate their status to 

the public and policy makers. 

Regional Coral Disease Assessments 

Methods 

Coral disease prevalence was compared between different geographical regions in the Dry Tortugas, New 

Grounds, Key West region, Lower 

Keys, Middle Keys, and Upper Keys 

from 1998 to 2002 (Figure 7.18). All 

surveys were conducted using a radial arc transect method developed for 

the coral disease surveys (Santavy 

et al., 2001). If the location had sufficient coral coverage (>5%), a permanent installation was made and 

the site was surveyed. Only the 8-10 

m segment of the radial arc transect 

(113 m2) was necessary to estimate 

coral disease (Mueller et al., 1998; 

Santavy et al., 1999a, 2001). Twenty-two species of scleractinian corals 

and gorgonian sea fans were surveyed and only colonies greater than 

10 cm were counted. M. annularis, M. 

faveolata, and M. franksii, the three 

species of coral contained within the 

Montastraea annularis complex (Weil 

and Knowlton, 1994) were combined 

as a single taxon, M. annularis, for 

data analysis. Two gorgonian sea 

fan species were combined as Gorgonia spp. 

Only coral colonies containing active 

disease lesions were enumerated. 

page 

173 Florida 

Figure 7.17. Frequency of coral disease or percent area having 0-13% of colonies 

affected by coral diseases in South Florida Keys Tract. Error bars represent 95% 

confidence levels. Source: Santavy et al., 2005. 

Figure 7.18. Map of the coral disease assessment regions, in which all the sites 

were contained in this study, including areas in Dry Tortugas National Park, New 

Grounds, Key West, Lower Keys, Middle Keys, Upper Keys and Biscayne National 

Park. Source: Santavy et al., 2005. 
The State of Coral Reef Ecosystems of Florida

page 

174 FloridaThe diseases consistently assessed are listed in Table 7.13. Signs used to distinguish coral diseases were obtained from published literature (McCarty and Peters, 1998; Patterson et al., 2002; Santavy and Peters, 1997; 

Santavy et al., 1999a,b, 2001). No distinction was made between white plague type 1 and 2 (Dustan,1977; 

Richardson et al.,1998a,b). Additionally, a combination of 13 disease conditions obtained from published literature was used to identify seafan disease (Smith et al., 1996; Nagelkerken et al., 1997a, b; Santavy et al., 

2001; Kim and Harvell, 2002). 

Table 7.13. Diseases assessed in surveys with corresponding abbreviations and references detailing the signs used in assessing 

condition. Source: Santavy et al., 2005. 

DISEASE NAME DISEASE 

ABBREVIATION 

SPECIES AFFECTED IN TROPICAL WESTERN 

ATLANTIC 

REFERENCES 

Sea Fan Disease SD Gorgonia spp. Nagelkerken et al., 1997a, b; 

Smith et al., 1996. 

Black Band Disease BB Diploria strigosa, D. labyrinthiformis, Colpophyllia natans, Montastraea cavernosa, M. annularis, M. frankii, 

M. faveolata, Siderastrea siderea, Gorgonia spp. 

Antonius,1981; Rützler et 

al.,1983; Rützler & Santavy, 

1983. 

Dark Spot Disease DS C. natans, M. annularis (species complex), S. siderea, Stephanocoenia intersepta Garzón-Ferreira and Gil, 1998. 

Hyperplasia HP D. strigosa, Dichocoenia stokesii Peters et al., 1986. 

Patchy Necrosis/ 

White Pox 

PX Acropora palmata Bruckner and Bruckner, 1997; 

Patterson et al., 2002. 

Red Band Disease RB Gorgonia spp., C. natans Rützler and Santavy, 1983; 

Richardson, 1993. 

White Plague WP D. stokesii, Agaricia agaricites, A. lamarchi, C. 

natans, Dendrogyra cylindrus, D. labyrinthiformis, D. 

strigosa, Eusmilia fastigiata, Madracis decactis, M. 

mirabilis, Manicina areolata, Meandrina meandrites, 

M. annularis (species complex), M. cavernosa, S. 

siderea, Solenastrea bournoni, Stephanocoenia michilinii, and hydrocoral Millepora alcycornis. 

Richardson et al.,1998a, b. 

White Band Disease 1 WB1 A. cervicornis, A. palmata, A. prolifera Gladfelter, 1982; Peters, 1993. 

White Band Disease 2 WB2 A. cervicornis Ritchie and Smith, 1998. 

Yellow Blotch Disease YB M. faveolata, M. annularis Santavy et al.,1999b. 

Results and Discussion 

The percentage of diseased coral colonies ranged from 0-43% among all the sites surveyed during the four 

sampling periods. No geographic location was consistently identified as a ‘hotspot’ where a high level of disease was sustained at the same site for multiple survey periods. The greatest percentage of diseased colonies occurred at Looe Key back reef site during summer 1998; 42.9% of all the colonies were diseased, with 

white pox affecting 41.4% of them. Twelve sites had over 20% of the colonies diseased at a single sampling 

period, and six occurred during the summer 1998 sampling period (Table 7.14). Five of these six sites occurred in the Key West and Lower Keys regions, with white pox affecting the majority of these colonies. The 

other site was WH01 in the Dry Tortugas. These disease events co-occurred with the single most severe and 

massive bleaching event recorded in modern history. Table 7.15 shows the percentage of diseased corals 

encountered in each region. Each region was not assessed during each survey due to limitations based on 

level of support available. The 2001 survey was incomplete due to the termination of cruises after the events 

of September 11, 2001. 
Sidebar

The State of Coral Reef Ecosystems of Florida 

Table 7.14. Sites with at least 20% disease prevalence in a survey. Abbreviation for diseases: DS=Dark Spots Disease; PX=White Pox 

Disease; PX_WB=White Pox Disease and White Band Disease on same colony; SD=Seafan Disease; and WB=White Band Disease. 

Source: Santavy et al., 2005. 

REGION SITE YEAR PERIOD % DISEASED* PRIMARY 

DISEASE 

% PRIMARY 

DISEASE 

OTHER IMP. 

DISEASES 

Dry Tortugas White Shoals 2 1998 Summer 22.86 9 SD 17.14 DS, WB 

Dry Tortugas Bird Key 4 1999 Spring 28.33 6 PX 27.50 WB 

Dry Tortugas Bird Key 5 1999 Spring 27.37 8 PX 27.37 

Key West Rock Key 3 1998 Summer 27.27 8 PX 18.80 WB 

Key West Sand Key 2 1998 Summer 36.61 3 PX 16.94 WB, PX_WB 

Key West Sand Key 5 1998 Summer 27.78 7 PX 22.22 WB 

Lower Keys E. Sambo 3 1998 Summer 31.91 5 PX 31.91 

Lower Keys Looe Key 3 1998 Summer 42.86 1 PX 41.43 WB 

Middle Keys Alligator Reef 2 1998 Spring 22.22 10 SD 22.22 

Upper Keys Carysfort Reef 2 1998 Spring 20.00 11 SD 20.00 

Upper Keys Carysfort Reef 3 1998 Spring 32.29 4 SD 23.53 PX 

Upper Keys Carysfort Reef 3 1999 Spring 40.00 2 PX 25.00 WB, DS 

Table 7.15. Percent diseased colonies for each geographic region sampled from 

1998 to 2002. Source: Santavy et al., 2005. 

REGION YEAR PERIOD % DISEASED 

Dry Tortugas 1998 Spring 4.49 

1998 Summer 4.93 

1999 Spring 4.51 

2000 Summer 4.61 

2002 Summer 3.64 

New Grounds 1998 Spring 0.98 

1998 Summer 1.13 

2000 Summer 0.46 

Key West 1998 Spring 5.91 

1998 Summer 12.8 

1999 Spring 6.84 

2000 Summer 5.34 

2002 Summer 4.55 

Lower Keys 1998 Spring 6.81 

1998 Summer 21.19 

1999 Spring 6.41 

2002 Summer 4.55 

Middle Keys 1998 Spring 3.36 

1998 Summer 1.84 

1999 Spring 2.46 

2002 Summer 2.38 

Upper Keys 1998 Spring 14.17 

1998 Summer 9.8 

1999 Spring 4.23 

2002 Summer 3.22 

Biscayne National Park 1998 Spring 8.77 

1998 Summer 3.91 

1999 Summer 0.6 

page 

175 Florida 
page 

176 Florida 

The State of Coral Reef Ecosystems of Florida 

Acroporid Species in the Upper 

Keys 

Methods 

The surviving Acropora spp. populations in the Upper Florida Keys are 

scarce and highly patchy in distribution, requiring a focal monitoring approach. In 1998, annual monitoring 

of Acropora palmata populations and 

their snail predators (Coralliophila abbreviata) was initiated at four sites in 

the FKNMS. Annual surveys record 

data on size structure and condition 

of A. palmata colonies at each site as 

well as snail infestation, damselfish 

territories, and disease prevalence 

(see Miller et al., 2002 for complete 

methods). Since 2002, individual colonies of Acropora palmata and A. cervicornis have been monitored at four 

sites in the FKNMS and four sites in 

Biscayne National Park (BNP). Approximately 20 colonies at each site 

were chosen to reflect the range of 

conditions present at that site (e.g., 

health, disease, predation). Colonies 

were tagged, mapped, extensively 

photographed, measured (length, 

width, and height), assessed for condition, and re-surveyed at 4-5 month 

intervals. 

Results and Discussion 

The annual survey of A. palmata 

patches shows that a substantial 

decline occurred between 1998 and 

1999. This interval included two major disturbances: Hurricane Georges 

and a major bleaching event. Since 

then, abundance of live coral at these 

four sites has remained fairly stable 

but has not shown any recovery (Figure 7.19). The proportion of colonies 

infested by snail predators increased 

in 1999 following this decline in coral abundance, but has rebounded back to its previous (1998) level of about 

15-20% (Figure 7.20). A similar proportion of colonies are affected by three-spot damselfish biting, but a much 

smaller percentage of A. palmata colonies display signs of active disease (Figure 7.20). 

Over most of the study period, predation by snails appeared to be the condition posing greatest impact to recruits of both species in terms of both live tissue loss and decreased growth of individuals. Snail predation is 

also the most prevalent threat at the population level. However, in April 2003, this individual-based monitoring 

of Acropora spp. colonies led to the discovery of a coral disease outbreak at White Bank Dry Rocks (Figure 

7.21). In the observed outbreak, approximately 65% of the A. cervicornis colonies had significant or total 

Figure 7.19. Total live area (sum of length x width x % live cover) of Acropora palmata at fully censused sites off Key Largo, FL from 1998 to 2003. Source: Miller et 

al., 2002. 

Figure 7.20. Average prevalence of Acropora palmata surveyed from reefs (n = 6) 

in the Upper Florida Keys that were infested with snails (Coralliophila abbreviata) 

inhabited by three-spot damselfish (Stegastes planifrons) or displayed active signs 

of disease (including White Band Disease and White Pox/Patchy Necrosis). Surveys 

were conducted at 6 reefs including South Carysfort, Horse Shoe, Little Grecian, 

French, Pickles, and Molasses reefs. Source: Miller et al., 2002. 
Sidebar

The State of Coral Reef Ecosystems of Florida

tissue loss. The tagged population 

(n=19 colonies) showed a loss of 

mean colony live tissue coverage 

from 95% prior to the outbreak to 

less than 15% in a follow-up survey 

in February 2004. This event emphasizes the vulnerability of Acropora 

spp. recovery to stochastic events 

which are difficult, if not impossible to 

manage or mitigate. 

Florida 

Figure 7.21. An Acropora cervicornis colony displays rapid tissue loss at White Bank 

Dry Rocks, Florida Keys. During this outbreak in spring 2003, many colonies exhibited this condition at several other reef sites in the Florida Keys. Source: Miller et al., 

2002. 

page 

177 

ASSOCIATED BIOLOGICAL COMMUNITIES 

FISH 

Fishery-Dependent Monitoring 

Various programs that collect data directly from Florida fisheries are summarized in Table 7.16. 

Table 7.16. Florida fishery-dependent data collection programs. Source: J. Bohnsack, NOAA Fisheries, SEFSC. 

PROGRAM TARGET AGENCY DATE STARTED 

Marine Recreational Fishing 

Statistical Survey (MRFSS) 

Recreational fishing from shore, bridge, 

private, rental and charter boats 

NOAA Fisheries 1979 

NMFS Headboat Survey Recreational headboat landings and 

biostatistical sampling 

NOAA Fisheries 1978 

Recreational world record 

gamefish 

Largest fish landed by recreational angling by 

line class and rod type by men and women 

International Gamefish 

Association (IGFA) 

1939 

Recreational fishing licenses Recreational marine angling, spiny lobster 

diving 

Florida Fish & Wildlife 

Conservation Commission 

1990 

Florida Trip Ticket System Commercial food fish and invertebrate 

landings 

Florida Fish & Wildlife 

Conservation Commission 

1986 

Florida Trip Ticket System Commercial marine life fisheries Florida Fish & Wildlife 

Conservation Commission 

1990 

General Canvass Landings 

Statistics (GCLS) 

Commercial landings NOAA Fisheries 1967 

Trip Interview Program (TIP) Commercial biostatistical data NOAA Fisheries 1985 

Commercial Logbook Program Commercial fishing by fish traps, longlines NOAA Fisheries 1993 

Commercial vessel registrations Number of commercial vessels NOAA Fisheries 1985 

Biscayne National Park (BNP) 

Creel Census 

Recreational fishing within and adjacent to 

BNP 

Biscayne National Park 1976 

Everglades National Park 

(ENP) Creel Census 

Recreational fishing within and adjacent to 

ENP 

Everglades National Park 1972 
The State of Coral Reef Ecosystems of Florida 

Florida Fish and Wildlife Conservation Commission 

The FFWCC has collected commercial food fish landings since 1986 and commercial marine life fishery statistics since 1990. NOAA Fisheries (U.S. DOC, 2003) collects landings data for commercial and recreational 

food fisheries, and for recreational charter boats, headboats, private boats and shore fishing. Commercial and 

recreational spiny lobster fishing effort is reflected by the number of licenses issued (Figures 7.22 and 7.23). 

page 

178 Florida 

Figure 7.22. Commercial landings and license C-numbers for the spiny lobster fishery in Florida. Commercial landings include catch from traps and from diving. License numbers overestimate the number of vessels since some vessels may have 

more than one set of C-numbers. Landings for 2003-4 are preliminary. Source: 

Florida Fish and Wildlife Conservation Commission, unpublished data. 

Figure 7.23. Numbers of recreational licenses for the spiny lobster fishery in Florida 

(1991-2002). Source: Florida Fish and Wildlife Conservation Commission. 

Results and Discussion 

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., 1994; Bohnsack and Ault, 1996; Harper et al., 

2000). 

Fishery-dependent reef fish landings 

trends were reported for the Florida 

Keys (Bohnsack et al., 1994). Reef 

fishes accounted for 58% of fish 

landings. From 1981-1992, mean 

total annual landings from recreational reef fisheries in the Florida 

Keys (Monroe County) were 0.107 

x 106 kg for headboats in the Tortugas 0.201 x 106 kg for the rest of the 

Keys, and 1.79 x 106 kg for other recreational fisheries. In comparison, 

total commercial reef fishery landings 

were 2.12 x 106 kg for spiny lobster, 

1.25 x 106 kg for pink shrimp, 0.17 x 

106 kg for grouper, and 1.00 x 106 kg 

(using 1992 as a benchmark). In the 

1980s, pink shrimp landings declined 

to approximately 40% of previous 

levels while total grouper declined to 

less than half of previous levels. Increases in landings were reported for 

yellowtail snapper, amberjack, and 

various jacks. 

Harper et al. (2000) described trends 

in the recreational hook-and-line and 

diving fishery in the BNP from 1976-

1991 in which more than 170 taxa 

were recorded. Mean annual landings were 4.77 fish/angler/trip (ranging from 3.80 in 1991 to 5.83 in 1981) and dropped significantly in years 

following Florida’s adoption of new minimum size restrictions in 1985 and 1990. Spiny lobster landings averaged 8.02 per trip and releases averaged 5.73 per trip. Spearfishing accounted for 12% of trips and 10.3% of 

fish landed by numbers. 
Sidebar

In a report to the U.S. Congress 

(U.S. DOC, 2003) the SAFMC listed 

six Florida reef fishes (speckled hind, 

warsaw grouper, black grouper, red 

porgy, goliath grouper, and Nassau 

grouper) as either overfished (i.e., 

depleted below minimum standards) 

or undergoing overfishing (i.e., being fished at a rate that would lead 

to overfishing), four species were 

not overfished and 46 species were 

in unknown condition. The GMFMC 

listed two species, goliath and Nassau grouper, as either overfished 

or undergoing overfishing, while 26 

were in unknown condition. More recently hogfish (Lachnoliamus maximus) stocks were shown to be overfished and undergoing overfishing in 

the Florida Keys (Ault et al., 2003) 

although fishing mortality trends showed a gradual decrease following a fish trap prohibition in 1990 and establishment of minimum size regulations in 1993 (Figure 7.24). 

A yellowtail snapper (Ocyurus chrysurus) stock assessment (Muller et al., 2003) showed landing trends increased from 1000 mt in 1981 to 1643 mt in 1993, and then declined to 802 mt in 2001. Effort followed a 

similar trend as landings, increasing to a peak and then declining. Compliance with the 30.5 cm minimum size 

limit was high. Noncompliance, depending on the region, was 2% for commercial, 4-5% for recreational, and 

2-3% for headboat fisheries. Only 0.2% of anglers in the Atlantic region and 1.3% in the Keys exceed the 10 

fish per trip limit. The assessment concluded that the stock was neither undergoing overfishing or overfished 

(http://www.sefsc.noaa.gov/SEDAR2/yellowtailFinal.pdf, Accessed 02/09/05). 

Goliath grouper (Epinephelus itajara) fishing was closed in Florida and Atlantic waters in 1990 and in the Gulf 

of Mexico in 1992. In 2003, evidence indicated that the stock was rebuilding and had a 50% chance of being 

rebuilt by 2006 in its historical core habitat range in southern Florida (Porch et al., 2003). 

Fishery-Independent Monitoring 

Several monitoring programs collect resource data independent of Florida fisheries. 

NOAA Reef fish visual census 

Methods 

The NOAA Southeast Fisheries Science Center’s reef fish visual census (RVC) method has used non-destructive visual survey methods to assess reef fish communities and habitat associations in the Florida Keys since 

1979. The goals of the method are to monitor trends and habitat associations of the entire reef fish fauna, and 

to monitor changes in various MPAs and specifically in FKNMS marine reserves following their establishment 

in 1997 and 2001. A stationary, centrally located diver in a random 7.5 m-radius plot assesses reef fish composition, abundance (density), and size structure. All species observed for five minutes are listed, counted, 

and their sizes estimated. Habitat features and depth are also recorded. Details on reef fish monitoring field 

methods and data processing and analyses are published in Bohnsack and Bannerot (1986) and Bohnsack 

et al. (1999). 

Florida 

The State of Coral Reef Ecosystems of Florida 

Figure 7.24. Estimated total annual fishing mortality rates (1985-2000) for Florida 

hogfish showing commercial (light) and recreational (dark) contributions. Source: 

Ault et al., 2003. Fishing mortality rate 

page 

179 
page 

180 Florida 

The State of Coral Reef Ecosystems of Florida 

Results and Discussion 

The RVC database was used to assess condition and retrospective changes in reef fish stocks in the Florida 

Keys. Ault et al. (1998) showed that a total of 13 of 16 groupers, seven of 13 snappers, and two of five grunts 

were found to be below the 30% spawning potential ratio the Federal definition of overfishing at that time. 

Some stocks appeared to have been chronically overfished since the late 1970s. Thus, 65% of the 35 assessed exploited reef fish stocks were below the then-existing Federal standards for sustainability. 

Monitoring of Sanctuary Preservation Areas 

Methods 

In 1997, the FKNMS established multiple no-take marine reserves, or “sanctuary preservation areas.” Annual 

underwater visual surveys have been conducted to assess changes in reef fish populations in areas open and 

closed to fishing compared to baselines established between 1994 and 1997. 

Results and Discussion 

A gradient of fishing impacts in the Florida Keys was found - from a high near human population centers near 

Miami in the BNP (Ault et al., 2001; Harper et al., 2000) and decreasing to a low southwest to the Dry Tortugas 

(Ault et al., 2002). In the BNP, the average size fish within the exploited phase for 35 important fishery species has remained relatively constant for the last 25 years and is very close to minimum size of capture and 

not to the historically unfished population size (Ault et al., 2001). The average size of adult black grouper, for 

example, was estimated to be 40% of 

what it was in 1940, fishing mortality 

was several times the level needed 

to achieve optimum yield (Figure 

7.25), and the spawning stock is now 

less than 5% of its historical unfished 

maximum (Figure 7.25). 

Overall, 77% of the 35 stocks that 

could be analyzed were overfished 

by federal standards, including 13 of 

16 grouper species, 11 of 13 snapper, barracuda, and two of five grunt. 

In addition, stock biomass was below 

standards for most of the key targeted species within the reef fish fishery 

(Figure 7.26). 

Figure 7.25. Fishery assessment for black grouper, Mycteroperca bonaci, in Biscayne National Park and the Florida Keys. Source: Ault et al., 2001. 
Sidebar

The State of Coral Reef Ecosystems of Florida

Florida 

Figure 7.26. Fishery management benchmark spawning potential ratio (SPR) analyses for 35 exploited species of Biscayne National 

Park-Florida Keys reef fish, comprising groupers, snappers and hogfish, grunts and great barracuda. Filled bars indicate stock ‘overfishing’ and hatched bars indicate the stock is above the 30% SPR (U.S. Federal standard). Asterisk indicates estimate from headboat 

data outside BNP. The high SPR estimate for Nassau grouper is dubious. Source: Ault et al., 2001. 

page 

181 
The State of Coral Reef Ecosystems of Florida

page 

182 FloridaChanges in no-take and fished zones 

were assessed and compared to a 

four-year baseline (1994-1997) established before new zone regulations were implemented in 1997. 

Although no-take zones established 

in 1997 comprised only 0.5% of the 

FKNMS, they included about 5.5% 

of the reef habitat because no-take 

zones were preferentially selected 

to include reefs. Preliminary results 

showed a significant and dramatic increase in mean density of exploitablesized individuals, but no significant 

changes for two species not targeted 

by fishing. In no-take zones within 

the first three years (1998-2000), 

densities of economically important 

exploitable phase yellowtail snapper 

(Ocyurus chrysurus) (Figure 7.27) 

and combined grouper (Serranidae) 

increased significantly compared to 

baseline levels. In the fourth year, 

gray snapper (Lutjanus griseus) had 

also increased significantly. In comparison, average densities of two 

non-exploited species, striped parrotfish (Scarus croicensis) and stoplight 

parrotfish (Sparisoma viride), were 

essentially unchanged compared to 

baseline performance ranges. 

Figure 7.27. Changes in density for yellowtail snapper (Ocyurus chrysurus) inside 

and outside marine reserves in the FKNMS. Source: Ault et al., 2001. 
Sidebar

The State of Coral Reef Ecosystems of Florida

Ferro et al. (2003) used the RVC 

method to monitor reef fish trends 

and describe reef composition of the 

three reef tracts off Broward County, 

Florida from 1998-2002 (Figure 7.2). 

They collected 667 samples comprising 86,463 individuals of 208 species 

from 52 families and showed that reef 

fish abundance, total biomass and 

species richness increased from inshore to offshore reefs. 

Florida 

Figure 7.28. Mean fish species richness, abundance, and biomass (n = 667) on the 

three reef tracts off Broward County, Florida from 1998 to 2002. Source: Ferro et al. 

2003. 

page 

183 
page 

184 Florida 

The State of Coral Reef Ecosystems of Florida 

Reef Environmental Education 

Foundation Reef Fish Monitoring 

The Reef Environmental Education 

Foundation (REEF) is a nonprofit organization that trains amateur divers 

to conduct standardized volunteer 

surveys of reef fishes in an effort to 

monitor species distributions and 

changes in reef fish occurrence. 

Methods 

Volunteers used a roving diver technique (Schmitt and Sullivan, 1996) to 

develop a comprehensive species list 

from a dive site and multiple surveys 

to calculate percent frequency-of-occurrence from a dive site. For each 

dive, observed species are scored in 

abundance categories based on what 

a diver observed. Between 1994 and 

2004, over 55,595 individual surveys 

have been conducted in the Tropical 

Western Atlantic Ocean. A total of 

11,105 surveys were collected in the 

Florida Keys through 2002. Details of 

methods are available at http://www. 

reef.org/ (Accessed 01/23/05). 

REEF fish monitoring involves expert REEF divers (members of the 

Advanced Assessment Team) that 

visit certain sites to do repeated fish 

surveys. Figure 7.29 shows trends in 

sighting frequency for Nassau grouper at no-take reserves and comparable fished sites in the FKNMS. 

Figure 7.30 shows trends for four angelfish species. 

MACROINVERTEBRATES 

FFWCC Spiny Lobster Monitoring 

To test the hypothesis that no-take zones would sufficiently protect spiny lobster and that their average abundance and size would increase in protected zones compared to similar fished areas, the FFWCC undertook 

a lobster monitoring program. Methods included documenting the abundance and size of spiny lobster in 15 

no-take and fished reference areas in the FKNMS during the closed and open lobster fishing seasons starting 

in 1977. 

Figure 7.29. Changes in mean sighting frequency for Nassau grouper at 16 reefs in 

no-take marine reserves and 11 fished reference reefs in the Florida Keys National 

Marine Sanctuary. Source: Reef Environmental Education Foundation, http://www. 

reef.org/data/fknms_02.pdf, Accessed 5/3/05. 

Figure 7.30. Changes in mean abundance scores for four species of angelfish 

(Pomacanthidae) at 27 sites in the Florida Keys National Marine Sanctuary. Source: 

Reef Environmental Education Foundation, http://www.reef.org/data/fknms_02.pdf, 

Accessed 5/3/05. 
Sidebar

page

185Florida

The State of Coral Reef Ecosystems of Florida

FFWCC Queen Conch Monitoring in the Florida Keys

Methods

The FFWCC initiated a project to monitor the recovery of queen conch (Strombas gigas) in the Florida Keys 

and within no-take marine reserves. Divers conduct belt-transects in locations with conch aggregations, including marine reserves and adjacent reference areas. All conch within 1 m along each belt-transect (laid out 

across an aggregation) were counted and mapped. Density and area estimates were used to determine population abundance. More information on data collection methods can be found in Glazer and Delgado (2003).

Results and Discussion

Since Florida’s queen conch fishery was closed in 1986, there have been signs that adult queen conch have 

begun to recover (Glazer and Delgado, 2003; Figure 7.31). Within aggregations, overall conch density has increased to approximately 700 conch 

per ha and the area encompassed 

by the aggregations is approximately 

49.5 ha. Approximately 37,000 adult 

queen conch were observed within breeding aggregations in 2003. 

Whereas the recovery of conch stock 

is occurring fairly rapidly in back reef 

areas, the lack of spawning and poor 

recovery of conch aggregations in 

areas immediately adjacent to the 

islands remain concerns. The FFWCC, University of Florida, and NOAA 

have started a joint project to examine the effects of xenobiotics on the 

reproductive development and output 

of conch from those aggregations. 

Overall Conclusions and Summary of Analytical Results

Inventories of coral richness show a general decline in stony coral species richness in all reef types and 

geographic areas. Diseased coral colonies were widely found, although no consistent geographic ‘hotspot’ 

was identified. Acropora spp. in the Upper Keys declined substantially during 1998-99 due to hurricanes and 

bleaching; they remain scarce and have exhibited no comeback. Non-native corals and fish have been detected; Caulerpa brachypus – a macrophytic algae – is becoming widespread and is of considerable concern. 

Effects of coastal pollution on reef communities are not well understood. Elevated nitrogen levels have been 

detected in nearshore waters, may relate to land use patterns, and have resulted in macroalgal blooms including non-native algal species.

Trends in fisheries effort show a continual increase in the number of recreational anglers in South Florida. A 

number of key species have exhibited signs of fishing stress. Stocks of the goliath grouper, however, appear 

to be recovering after a decade of fishery closure.

Figure 7.31. Trends in the abundance of adult queen conch, Strombus gigas, in the 

Florida Keys, estimated from yearly monitoring of the breeding aggregations on the 

backreef. Source: Glazer and Delgado, 2003.
page 

186 Florida 

The State of Coral Reef Ecosystems of Florida 

CURRENT CONSERVATION MANAGEMENT ACTIVITIES 

Mapping 

Only about 50% of Florida’s coral reef and associated benthic habitats have been mapped. As a result, reliable estimates of the percentage of coral reef and related habitats, as well as the area protected by no-take 

provisions, cannot be accurately computed statewide. 

Mapping efforts were undertaken in the FKNMS in the 1990s. NOAA and FFWCC’s Florida Marine Research 

Institute (FMRI) published digital benthic habitat maps for the Florida Keys in 1998 (FMRI, 1998; Figure 7.32). 

Recently, the Dry Tortugas region was characterized (Schmidt et al., 1999). Also, Agassiz (1882) produced 

a remarkable baseline map of Dry Tortugas benthic habitats, which suggests a 0.4 km2 loss of elkhorn coral 

in a 100-year period (Davis, 1982). Mapping gaps exist for deeper regions of the Tortugas. The reefs along 

the Southeastern Florida coast are less well studied. In 1999, Nova Southeastern University’s National Coral 

Reef Institute (NCRI) and the Broward County Department of Planning and Environmental Protection (DPEP) 

initiated mapping of Broward County reefs. Together with the FMRI, NCRI is presently mapping the reefs of 

southern Palm Beach and northern Miami-Dade Counties. Maps still need to be completed for the remainder 

of Miami-Dade and Palm Beach Counties. Reef habitat mapping efforts are underway by the State of Florida 

and NCRI along the Southeast Florida coast using a variety of techniques including satellite remote sensing, 

laser-based bathymetry, acoustic bottom classification, and in situ diver assessment (Moyer et al., 2003). 

Figure 7.32. Benthic habitat map for the Florida Keys. Map: A. Shapiro. Source: CCMA-BT, http://sposerver.nos.noaa.gov/projects/ 

benthic_habitats/, Accessed 02/14/05. 

Improved mapping for specific projects has resulted from aerial photos of nearshore areas and laser-based 

bathymetry of the three reef tracts off Southeastern Florida. For example, detailed laser depth sounding bathymetry is complete for all of Broward County, offshore to 36 m. A smaller amount of the area is also mapped 

with multibeam bathymetry and side-scan sonar. Using acoustic seafloor discrimination, NCRI is mapping the 

distribution of benthic fauna over the reef tracts of Broward County, southern Palm Beach County, and northern Miami-Dade County. The goal is to provide maps that allow quantification of patterns, and thus information 

on underlying ecological processes. The work proceeds in collaboration with the Broward County DPEP and 

FMRI. 

Estimates of benthic cover are available from some monitoring programs. There is a coral reef distribution 

map in Jaap and Hallock (1990). No mapping of the Florida Middle Grounds has been conducted to date. 

Monitoring, Assessments, and Research 

In the FKNMS, a comprehensive research and monitoring program has been implemented to establish baseline information on the various components of the ecosystem and help ascertain possible causes and effects 
Sidebar

The State of Coral Reef Ecosystems of Florida

of changes. This way, research and monitoring can ensure the effective implementation of management 

strategies using the best available scientific information. 

Research and monitoring are conducted by many groups, including local, state, and federal agencies, public and private universities, private research foundations, environmental organizations, and independent researchers. Sanctuary staff facilitate and coordinate research by registering researchers through a permitting 

system, recruiting institutions for priority research activities, overseeing data management, and disseminating 

findings to the scientific community and the public. 

The Water Quality Protection Program (WQPP), which began in 1994 and is funded by the EPA and NOAA, is 

the most comprehensive, long-term monitoring program in the Florida Keys. The program includes monitoring of three components: water quality, seagrasses, and coral/hardbottom communities. Reef fishes, spiny 

lobster, queen conch, and benthic cover are also monitored throughout the Sanctuary. Water quality has been 

monitored at 154 fixed stations since 1995. Water samples are collected to measure salinity, temperature, 

DO, turbidity, relative fluorescence, and light attenuation. The water chemistry study focuses on detecting 

NO3

-

, NO2

-

, NH4

+, DIN, and SRP. Concentrations of TON, TOC, TP, and silicate are also measured, along with 

CHLA and APA (Jones and Boyer, 2001). 

Seagrass monitoring through the WQPP allows for the identification of seagrass the distribution and abundance within the Sanctuary and the tracking of changes over time. Quarterly monitoring is conducted at 30 

fixed stations and annual monitoring occurs at 206-336 randomly selected sites (Fourqurean et al., 2002). 

Permanent stations are co-located at 30 of the water quality monitoring sites to help discern relationships between seagrass health and water quality. This long-term monitoring is also invaluable for determining human 

impacts on the Sanctuary’s seagrass communities. 

The CREMP tracks the status and trends of coral and hardbottom communities throughout the Sanctuary 

(Jaap et al., 2001). The project’s 43 permanent sites include hardbottom, patch reef, shallow offshore reef, 

and deep offshore reef communities. Biodiversity, coral condition, and coral cover are recorded annually at 

four stations within each site, for a total of 172 stations. This project has recently been extended to reefs of 

Southeast Florida, adding 10 sites throughout Miami-Dade, Broward, and Palm Beach Counties (Gilliam et 

al., 2004b). 

Broward County’s Marine Biological Monitoring Program tracks the status and trends of coral and hardbottom 

communities in the county (Gilliam et al. 2004a). The program’s 25 permanent sites located on the nearshore 

and offshore reef terraces have been monitored yearly since 1997 by the Broward County DPEP and NCRI. 

Each site consists of one 30-m belt phototransect, two 30-m fish transects, one stationary fish point count, 

and a sediment trap. Along each belt phototransect, 40 0.75-m2 quadrat (framer) images are taken; stony 

coral species (Millepora and Scleractinia) presence, colony size, and condition (diseased or bleached) are recorded; and sponge and octocoral densities are recorded. Fish species abundance and size classes are also 

recorded along transects and during point counts. Sedimentation rate and grain size analysis is determined 

bimonthly. 

In addition to the WQPP, the FKNMS Zone Monitoring Program monitors the 24 discrete marine reserves located within the Sanctuary. Implemented in 1997, the goal of the program is to determine whether these fully 

protected zones effectively protect marine biodiversity and enhance human uses related to the Sanctuary. 

Parameters measured include the abundance and size of fish, invertebrates, and algae, as well as economic 

and aesthetic values of the Sanctuary and compliance with regulations. This program monitors changes in 

ecosystem structure (size and number of invertebrates, fish, corals, and other organisms) and function (coral 

recruitment, herbivory, predation). Human uses of zoned areas are also tracked. Lastly, continuous monitoring of certain physical parameters of seawater and ocean conditions are recorded by instruments (C-MAN stations) installed along the Florida Reef Tract as part of the Florida Keys Seascape program (SEAKEYS, 2002). 

There are six C-MAN stations from Fowey Rocks to the Dry Tortugas and one in Florida Bay. These stations 

gather data and periodically transmit to satellites, to provide near real-time reports available on the Internet. 

For the past 10 years, the Sanctuary has maintained a network of 27 thermographs located both inshore and 

offshore throughout the Keys that record water temperature every two hours. 

page 

187 Florida 
page 

188 Florida 

The State of Coral Reef Ecosystems of Florida 

As baselines are being documented, FKNMS managers are developing a comprehensive science plan outlining specific management objectives and their associated monitoring and research needs. This is an evolving, 

adaptive management approach to help ensure management decisions are supported by the best available 

science. The science plan will identify high-priority research and monitoring projects to help fill gaps in understanding the ecosystem and its responses to management actions. Recognizing the importance of an ecosystem approach to management, the Sanctuary engages agencies working on the Comprehensive Everglades 

Restoration Plan to achieve appropriate restoration goals for the entire ecosystem, including coral reefs and 

seagrasses. Active monitoring of natural resources is a Sanctuary priority in order to detect changes occurring 

as a result of water management regimes and restoration. 

Along Florida’s southeastern coast, much of the present monitoring originated as impact and mitigation studies for activities that had adverse impacts to specific sites (e.g., dredging, ship groundings, pipeline and cable 

deployments, and beach renourishment). In the past, such studies have been of limited duration (e.g., one 

to three years) and the focus has been largely on beach renourishment, restoration for grounding impacts, 

and some baseline data collection from reference areas. Monitoring has begun in Broward County at 25 fixed 

30-m2 sites for environmental conditions (sedimentation quantities and rates, water quality, and temperature), 

and coral, sponge, and fish abundance and/or cover (Figure 7.33). Assessment studies by NCRI scientists 

also identify the distribution, abundance, and disease condition of staghorn corals in Broward County. Research on the reproductive status and 

potential of Acropora cervicornis is 

also being conducted. There have 

been a number of discrete fish surveys on the reefs of Miami-Dade and 

Palm Beach Counties, most of which 

have been associated with beach renourishment projects or artificial reef 

management (Lindeman and Snyder, 

1999; P. Light, pers. comm.; Avila, 

2005). However, there is currently a 

concerted effort underway by NCRI 

scientists to complete a baseline survey of reef fishes off Broward County 

(Ettinger et al., 2001; Harttung et al., 

2001; Ferro et al., 2003). Initiated in 

1998, this NOAA-funded survey is 

recording fishes on the edges and 

crests of the three major reef lines. 

The initial survey was completed in 2003 and consists of more than 650 point-counts. In addition, during summer 2001, NCRI scientists inventoried fish on the first 30 m of the inshore reef at 158 m intervals for 25 km of 

shoreline using multiple visual techniques (point-count, 30 m transects, and 20 minute random swims) (Baron 

et al., 2001). Broward County now has a database comprised of more than 1,000 visual censuses from the 

shore to 30 m for reef fish. The NCRI inventory of reefs off Broward County is continuing with a NOAA-funded 

survey of the fishes in 30-150 m depths using a remotely operated vehicle. 

Figure 7.33. Researcher conducting reef monitoring offshore of Broward County, 

Florida. Photo: D. Gilliam. 
Sidebar

The State of Coral Reef Ecosystems of Florida

Researchers at NCRI are also currently involved in a multivariate, hypothesis-driven study of the interaction of fish, transplanted corals, coral 

recruits, and potential coral attractants or optimal substrates (Figure 

7.34). Research variables include 

four potentially different fish assemblages (determined by reef complexity) and biofilm and coral recruitment 

on settlement plates made of concrete, concrete and iron, concrete 

and quarry rock, or concrete and coral transplants. Results of this threeyear study should yield information 

critical to reef restoration. 

MPAs and Fully Protected Reserves 

As with monitoring, assessment, and 

research programs, coral reef conservation and management through the designation and implementation of MPAs varies widely. The largest 

and best-known MPA in Florida, the FKNMS, was designated in 1990, thereby placing 9,850 km2 of coastal 

waters and 1,381 km2 of coral reef area under NOAA and State of Florida management. Immediate protective 

measures were instituted as a result of Sanctuary designation, including prohibitions on oil and hydrocarbon 

exploration, mining, and other activities altering the seabed, as well as restrictions on large ship traffic. Coral 

reefs were protected by prohibiting anchoring on coral, touching coral, and harvesting or collecting coral and 

‘live rock.’ To address water quality concerns, discharges from within the Sanctuary and areas outside the 

Sanctuary that could potentially enter and affect local resources were also restricted. 

In addition, a network of marine zones was instituted in 1997 in the Sanctuary to address a variety of management objectives. Five types of zones were designed and implemented to achieve biodiversity conservation, 

wildlife protection, and the separation of incompatible uses, among other goals. Three of the zone types 

(sanctuary preservation areas, ecological reserves, and special use/research-only areas) are fully protected 

areas, or marine reserves, where lobstering, fishing, spearfishing, shell collecting, and all other consumptive 

activities are prohibited. 

The 1997 zoning plan established 23 discrete fully protected zones that encompass 65% of the Sanctuary’s 

shallow coral reef habitats. The largest zone at that time, the 30.8 km2 Western Sambo Ecological Reserve, 

protects offshore reefs as well as other critical habitats, including mangrove fringe, seagrasses, productive 

hardbottom communities, and patch reefs. In July 2001, the 517.9 km2 Tortugas Ecological Reserve was 

implemented (see Figure 7.1). It is now the largest of the Sanctuary’s fully protected zones. Located in the 

westernmost portion of the Florida Reef Tract, the Reserve conserves important deep-water reef resources 

and fish communities unique to this region of the Florida Keys. Together with the other fully protected zones, 

the Tortugas Ecological Reserve increased the total protected area of coral reefs within the Sanctuary to 

10%. 

The Tortugas Ecological Reserve is also significant because it adjoins a 157.8 km2 research natural area in the 

Dry Tortugas National Park, a zone where shallow seagrass, coral, sand, and mangrove communities are now 

conserved. Anchoring is prohibited in the research natural area, and scientific research and educational activities consistent with management of this zone require advance permits from the NPS. To protect important 

fish nursery and spawning sites, no fishing is allowed in the research natural area. Wildlife viewing, snorkeling, 

diving, boating and sightseeing are managed in this zone primarily through commercial tour guides. Together, 

the Sanctuary’s Tortugas Ecological Reserve and the Dry Tortugas National Park’s research natural area fully 

protect nearshore to deep reef habitats of the Tortugas region and form the largest, permanent marine reserve 

in the U.S. 

Florida 

Figure 7.34. Researcher assessing coral recruitment on experimental artificial reef 

modules offshore of Broward County, Florida. Photo: D. Gilliam. 

page 

189 
page 

190 Florida 

The State of Coral Reef Ecosystems of Florida 

Overall, the Sanctuary management regime uses an ecosystem-wide approach to comprehensively address 

the variety of impacts, pressures, and threats to Florida Keys marine ecosystems. It is only through this inclusive approach that the complex problems facing coral reefs can be adequately addressed. 

The BNP encompasses 683 km2 of waters just south of Miami, including the majority of Biscayne Bay and a 

substantial portion of the northern reef tract with 291 km2 of coral reefs. The Park is renowned for its productive coastal bay, nearshore, and offshore habitats, including islands, mangrove shorelines, seagrass beds, 

hardbottom communities, and coral reefs, which provide important recreational opportunities and spectacular 

scenic areas. The NPS is concerned about degradation of BNP resources in the face of coastal development, 

increases in the number of recreational boats visiting the Park, and fishing pressure. The Park is revising 

its general management plan to allow for management zones that would give greater protection to Park resources, including natural resources reserve areas where fish nurseries and spawning habitats would be 

protected from fishing and other disturbances. In addition, the BNP is developing a cooperative plan with the 

State of Florida to adopt a coordinated and seamless approach to protecting and restoring fishery resources 

both within and outside Park boundaries. 

The Key West National Wildlife Refuge and Great White Heron National Wildlife Refuge overlap with portions 

of the FKNMS in the backcountry of the lower Keys and an extensive area around the Marquesas Islands 

between Key West and the Dry Tortugas. The Refuges, established in 1908 and 1938, respectively, contain 

over 1,619 km2 of lush seagrass beds, reef tract, patch reefs, hardbottom communities, and pristine mangrove 

islets. A cooperative agreement between the U.S. Fish and Wildlife Service (USFWS) and State of Florida on 

the management of these submerged lands created a number of wildlife management zones in the refuges. 

These zones direct human activities away from sensitive wildlife and habitats, and help ensure their continued 

conservation. The USFWS, as administrator of the National Wildlife Refuge System, works cooperatively with 

the State and the FKNMS to protect these sites. 

Of the state parks in Southeast Florida, two are considered marine. One of the oldest marine parks in the world 

(acquisition began in 1959), the John Pennekamp Coral Reef State Park is located in Monroe County on Key 

Largo. It covers 249 km2 and has 461 km2 of coral reefs, seagrass beds, and mangrove swamps. The Lignum 

Vitae Key Botanical State Park, which includes Shell Key, is located in Monroe County, west of Islamorada. 

The Park’s submerged habitats are located in Florida Bay and the Atlantic Ocean, and include fringing mangrove forest, extensive seagrass beds, patch reef, and sand flats. 

Gaps in Monitoring and Conservation Capacity 

Current monitoring in the FKNMS has largely focused on detecting changes within the fully protected zones 

and determining Sanctuary-wide status and trends of water quality, seagrasses, and corals. While some 

trends are beginning to show and provide a source of hypotheses to be tested continued monitoring is critical. 

These data will facilitate the detection of long-term changes in communities locally and ecosystem-wide. 

Reef monitoring programs in southeastern Florida are limited by a lack of comprehensive inventories of the 

non-coral components of the marine communities. Baseline assessments of additional sites are needed. 

Furthermore, new monitoring programs should be developed at sites within counties in the region. The first 

step should be to develop a functional classification of the reef habitats. For effective selection of monitoring 

sites, this classification should incorporate criteria to ensure that both representative habitats and unique sites 

receive attention. 
Sidebar

The State of Coral Reef Ecosystems of Florida

The databases of reef fish in Broward, Miami-Dade, and Palm Beach 

Counties are based on visual survey 

techniques that can overlook a substantial number of cryptic species (as 

many as 37% in a recent Caribbean 

survey; Collette et al., 2001). Thus, 

intensive and broad-scale monitoring 

is necessary to obtain a complete record of resident ichthyofauna. In addition, fish assemblages below a depth 

of 30 m are poorly characterized, yet 

they are exploited by recreational 

fishers. Likewise, the structure and 

composition of reef fish communities 

in seagrass and mangrove habitats of 

Port Everglades and the Intracoastal 

Waterway remain a mystery to researchers. Such habitats can be important nursery sites for several reef 

associated fishes (Figure 7.35; Leis, 1991). Given the high level of human activity in these areas, monitoring 

of reef fish communities is necessary. 

In May 2002, Coleman and Jaap (W. Jaap, pers. obs.) mounted an expedition to the Florida Middle Grounds 

to sample sites surveyed by Hopkins in 1975. Data collected at most of the sample stations indicated that the 

sessile benthic community remained very similar to the status described by Hopkins et al. (1977). However, 

grouper and snapper populations were extremely depleted. Reefs along the southeast coast and the Middle 

Grounds banks should be fully mapped to develop map products including a reef atlas similar to that recently 

published for reef areas off Brazil. The Brazilian reef atlas includes high quality maps, aerial and satellite photographs, underwater habitat photos, and short descriptions of the reefs and resources. 

Government Policies, Laws, and Legislation 

When President George H. W. Bush signed the Florida Keys National Marine Sanctuary and Protection Act 

into law in 1990, the FKNMS became the first national marine sanctuary designated by Congress. Authority 

for the Sanctuary, along with the 12 other national marine sanctuaries, is established under the National Marine Sanctuaries Act of 1972 (16 U.S.C. 1431 et seq., as amended). The FKNMS is administered by NOAA 

under the U.S. Department of Commerce, and is managed jointly with the State of Florida under a co-trustee 

agreement because over half of the Sanctuary waters are state territorial waters. The co-trustees agreement 

commits the Sanctuary to periodically review the Sanctuary’s management plan. 

In 1997, a comprehensive management plan for the Sanctuary was implemented. It contains 10 action plans 

and associated strategies for conserving, protecting, and managing the significant natural and cultural resources of the Florida Keys marine environment. Largely non-regulatory, the plan’s strategies are to educate 

citizens and visitors, use volunteers to build stewardship for local marine resources, appropriately mark channels and waterways, install and maintain mooring buoys for vessel use, survey submerged cultural resources, 

and protect water quality. As previously described the Sanctuary management plan also designated five types 

of marine zones to reduce pressures in heavily used areas, protect critical habitats and species, and reduce 

use conflicts. A total of 24 fully protected zones were implemented in 1997 and 2001, covering approximately 

6% of the Sanctuary and protecting 65% of shallow bank reef habitats and about 10% of coral reefs. 

Most of the smaller zones (sanctuary preservation areas) are located along the offshore reef tracts and encompass the most heavily used spur-and-groove coral formations. In these areas, all consumptive activities 

are prohibited. The effectiveness of these zones and other biological and chemical parameters are monitored 

under the FKNMS Research and Monitoring Action Plan. 

Florida 

Figure 7.35. Mangrove prop roots serve as an important nursery area for some reef 

fish species. Photo: M. Kendall. 

page 

191 
page 

192 Florida 

The State of Coral Reef Ecosystems of Florida 

With guidance from the U.S. Coral Reef Task Force, the Florida Department of Environmental Protection and 

the FFWCC have coordinated formation of an interagency Southeast Florida Action Strategy Team (SEFAST) 

for coral reef conservation and management. This team is developing a local action strategy (LAS) to improve 

coordination of technical and financial support for the conservation and management of coral reefs from the 

southern Miami-Dade County line to Hobe Sound (Martin County). The Southeast Florida Coral Reef Initiative is targeting this region because the coral habitats are close to shore and co-exist with intensely urbanized 

areas that lack a coordinated management plan. 

SEFAST is made up of four workgroups: Awareness and Appreciation; Fishing, Diving and Other Uses; LandBased Sources of Pollution and Water Quality; and Maritime Industry and Coastal Construction Impacts. 

The workgroups are tasked with 1) outlining and presenting issues and threats at stakeholder workshops, 2) 

combining information from public input and technical advisory committees, 3) further defining threats to coral 

habitats, and 4) proposing projects to minimize harmful effects. The outcome will be a coordinated plan to 

address causes of coral degradation and provide a roadmap for successful management. 

Commercial fishing remains one of the largest industries in the Florida Keys, but it is regulated heavily by State 

and Federal fishery management councils. Regulations for most commercial invertebrates and finfish include 

annual catch quotas, closed seasons, and gear catch size restrictions. The State of Florida also collects 

landing information on approximately 400 kinds of fish, invertebrates, and plants to track species trends and 

evaluate regulations. The reefs of southeastern Florida are in state territorial waters and protected from some 

impacts by state laws and regulations. These include fishing regulations, dredging permits, and a law protecting corals from harvest, sale, or destruction. Broward County has a small boat mooring program intended to 

reduce anchoring impacts on reefs. 

OVERALL STATE CONCLUSIONS AND RECOMMENDATIONS 

Due to its high latitude and proximity to the continental U.S., reefs in Florida exist at the environmental extremes for coral. Natural phenomena such as cold fronts and freshwater run-off, as well as heavy use, introduction of non-native species, offshore and coastal construction activities, and water quality degradation are 

all stressors to Florida’s reefs. These factors provide challenges to Florida’s coral reef managers and emphasize the need for careful conservation of the resource. Overall, immediate action is needed to curtail alarming 

declines in coral reef condition throughout Florida. 

Habitat maps have been prepared for the Florida Keys and the Tortugas, but only about half of Florida’s coral 

reef and benthic resources have been mapped. Reefs on the southeastern Florida coast are not as well 

studied as those of the Keys. Broward County has begun a mapping program. NCRI has begun mapping 

programs in Broward, Palm Beach and Miami-Dade Counties. Mapping has been improved through the use 

of laser-based bathymetry. Detailed mapping of all benthic resources is essential. The distribution of non-native species - especially Caulerpa brachypus - should also be determined, and methods to restrict its spread 

must be examined. 

There are a considerable number of minor and major ship groundings on Florida’s reefs resulting in part 

from increased recreational and commercial boating activity. Groundings result in significant injury to coral, 

seagrass, and hardbottom resources. The majority of groundings is due to small vessels causing minor damage individually, but considerable cumulative effects. Installation of mooring buoys has reduced the chronic 

impacts of small boat anchoring. These efforts need to be expanded, especially for large vessels near ports. 

The State of Florida and the FKNMS have been educating boaters to limit risks and improve navigation in coral 

reef areas, and these efforts should be expanded. 

Large vessel avoidance and Racon beacons in lighthouses have resulted in declines in large vessel groundings. State and FKNMS 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. 

Effects of coastal pollution on reef communities are not well understood, however, there is evidence that it has 
Sidebar

The State of Coral Reef Ecosystems of Florida 

resulted in macroalgal blooms including non-native species. A comprehensive water quality monitoring program for Southeast Florida does not exist, but is necessary to establish a relationship between water quality 

and reef community response in the area. Permitting programs have been effective in reducing raw sewage 

discharges. Monroe County is undertaking a study of the septic tank problem and possible consolidation into 

regional facilities. Continued monitoring is critical to establish a relationship between coastal activities and 

coral resource conditions. 

Coral reefs provide the ecological foundation for a multibillion dollar fisheries and tourism-based economy 

in South Florida. Thus reducing fishing pressure is an appropriate goal. 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 taking of some species. Numerous MPAs have been established to restrict fishing. Exploitable species have shown significant increases in these areas. Monitoring and 

appropriate regulation must be maintained to prevent overfishing. 

Management programs in southeastern Florida are limited by a lack of comprehensive inventories. The State 

of Florida has formed the SEFAST to develop a LAS for coral reef conservation and management in the area. 

Such a plan is essential if these resources are to co-exist with the intensely urbanized area. 

Local communities that are culturally and economically supported by coral reefs are working to employ management strategies and to focus on alleviating controllable human impacts. For example, in southeastern 

Florida, the environmental impacts of fisheries, dredging, vessel anchorages, vessel groundings, freshwater 

management, and nutrient inputs should receive attention to maximize reef protection in this area. In the Florida Keys, the community is continuing to pursue solutions that address wastewater and stormwater problems, 

habitat degradation, and overfishing. 

Citizens, stakeholders, elected officials, and resource managers must work together to improve water quality, 

minimize physical impacts to corals and seagrasses, reduce nonpoint pollution, and increase education to 

instill a stronger sense of stewardship in Floridians for their coral reefs. 

page 

193 Florida 
page 

194 Florida 

The State of Coral Reef Ecosystems of Florida 

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Sidebar

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