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SIMM Report #1

Seagrass Integrated Mapping and Monitoring

for the State of Florida

Mapping and Monitoring Report No. 1

Edited by

Laura A. Yarbro and Paul R. Carlson Jr.

Florida Fish and Wildlife Conservation Commission

Fish and Wildlife Research Institute

St. Petersburg, Florida

March 2011
Yarbro and Carlson, Editors

SIMM Report #1
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SIMM Report #1

Table of Contents

Authors, Contributors, and SIMM Team Members..................................................................3

Acknowledgments ....................................................................................................................4

Abstract .....................................................................................................................................5

Executive Summary..................................................................................................................7

Introduction.............................................................................................................................31

How this report was put together ...........................................................................................36

Chapter Reports......................................................................................................................41

Perdido Bay...........................................................................................................................41

Pensacola Bay ......................................................................................................................45

Santa Rosa Sound and Big Lagoon.......................................................................................50

Choctawhatchee Bay.............................................................................................................56

St. Andrew Bay......................................................................................................................62

St. Joseph Bay ......................................................................................................................68

Franklin County Coastal Waters ............................................................................................75

Northern Big Bend.................................................................................................................81

Southern Big Bend ................................................................................................................89

Suwannee Sound, Cedar Keys, and Waccasassa Bay..........................................................96

Springs Coast......................................................................................................................102

Western Pinellas County .....................................................................................................109

Tampa Bay..........................................................................................................................113

Sarasota Bay and Lemon Bay .............................................................................................119

Charlotte Harbor Region......................................................................................................127

Estero Bay...........................................................................................................................137

Rookery Bay........................................................................................................................145

Ten Thousand Islands .........................................................................................................150
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Chapter Reports, continued

Florida Keys National Marine Sanctuary..............................................................................156

Florida Bay ..........................................................................................................................161

Biscayne Bay.......................................................................................................................168

Lake Worth Lagoon .............................................................................................................175

Southern Indian River..........................................................................................................182

Northern Indian River ..........................................................................................................191

Appendix

A. Acronyms and abbreviations used in this report ..............................................................200
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Authors, Contributors, and Team Members

Many authors, contributors, collaborators, and Seagrass Integrated Mapping and Monitoring 

(SIMM) team members made this project possible. SIMM team members from the Florida Fish 

and Wildlife Research Institute are Paul Carlson, Rene Baumstark, Christi Santi, Dave 

Palandro, Kathleen O’Keife, Harry Norris, Paul Julian, Makenzie Marsh, and Laura Yarbro. 

Authors and contributors to each chapter patiently responded to repeated requests for 

interviews, data, information, figures, text, and editing during the creation of this report. The list 

of authors and contributors below is arranged in an order similar to that of the chapters, i.e., 

geographically from the Florida Panhandle to the northern Indian River on Florida’s east coast. 

A number of authors contributed to more than one chapter. In addition to the chapter authors 

and contributors listed below, Brad Peterson (State University of New York, Long Island 

campus), Doug Scheidt (Kennedy Space Center), Seth Blitch (Apalachicola National Estuarine 

Research Reserve), Greg Blanchard (Manatee County), Ben Russell (Northwest Florida 

Department of Environmental Protection), Cindy Meyer (Pinellas County), Darlene Saindon 

(University of Florida), Lisa Schwenning and Judy Ashton (Florida Department of Environmental 

Protection), and Chris Gudeman (formerly of the Fish and Wildlife Commission Division of 

Habitat Species and Conservation) provided extensive information during telephone interviews 

in the early phases of this project. Affiliations and contact information for authors and 

contributors can be found at the end of each chapter.

Chapter Authors and Contributors

Ken Heck, Perdido Bay Judy Ott, Charlotte Harbor National Estuary Program

Dottie Byron, Perdido Bay Heather Stafford, Charlotte Harbor region

Shelley Alexander, Panhandle estuaries Peter Doering, Southwest Florida estuaries

Michael Lewis, Pensacola Bay Stephanie Erickson, Estero Bay

Amy Baldwin Moss, Santa Rosa Sound and Big Lagoon Victoria Vasquez, Rookery Bay

Larry Handley, Panhandle estuaries Jill Schmid, Rookery Bay

Alison McDowell, Choctawhatchee Bay Jim Fourqurean, Florida Keys National Marine Sanctuary

Linda Fitzhugh, St. Andrew Bay Penny Hall, Florida Bay, Biscayne Bay

Kim Wren, St. Joseph Bay Steve Blair, Biscayne Bay

Ron Mezich, Franklin County Chris Avila, Biscayne Bay

Kent Smith, Franklin County Pamela Sweeney, Biscayne Bay

Melissa Charbonneau, Big Bend, Cedar Key Sarah Bellmund, Biscayne Bay

Paul Carlson, Big Bend Paul Davis, Lake Worth

Laura Yarbro, Big Bend Eric Anderson, Lake Worth

Keith Kolasa, Springs Coast Becky Robbins, Southern Indian River

Kris Kaufman, Tampa, Sarasota Bays, Charlotte Harbor Mary Ridler, Southern Indian River

Melissa Harrison, Western Pinellas County Lorene Bachmann, Southern Indian River

Walt Avery, Tampa Bay Lori Morris, Northern Indian River

Jon Perry, Sarasota Bay Lauren Hall, Northern Indian River

Mindy Brown, Charlotte Harbor, Estero Bay

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Acknowledgments

This report culminates the successful collaboration of hundreds of people. Some provided data 

or wrote chapters for this report. Amber Whittle carefully edited the final draft, while Bland 

Crowder of FWRI and the Community Relations Office of FWC copy edited and produced the 

final document. Others provided and managed grant funds. Still others laid the groundwork for 

the Seagrass Integrated Mapping and Monitoring program and similar efforts to collate, 

summarize, and share data on seagrasses in Florida’s coastal waters. Efforts in Tampa Bay and 

the Indian River Lagoon were especially critical in demonstrating the need for regular 

assessment of seagrass cover, the link between water quality and the abundance of seagrass, 

and the effectiveness of seagrass mapping and monitoring in assessing improvements in water 

quality. Hundreds of scientists and managers participated in those efforts over decades. 

Regrettably, only the current project participants are listed in individual chapters, but they stand, 

as does the SIMM team, on the shoulders of those who came before.

This report was funded, in part, through a grant agreement from the Florida Department of 

Environmental Protection, Florida Coastal Management Program, by grants provided by the 

Office of Ocean and Coastal Resource Management under the Coastal Zone Management Act 

of 1972, as amended, National Oceanic and Atmospheric Administration (NOAA) Award 

Numbers NA09NOS4190076, NA07NOS4190071, and NA08NOS4190415 . Specific grants are 

CZ820, CZ920, and CM023. The views, statements, findings, conclusions, and 

recommendations expressed herein are those of the authors and do not necessarily reflect the 

views of the State of Florida, NOAA, or any of their subagencies.

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Abstract

This report is the first comprehensive effort of the Seagrass Integrated Mapping and Monitoring 

(SIMM) program to provide both mapping and monitoring information for seagrasses throughout 

Florida’s coastal waters. We have inventoried mapping and monitoring programs, identified 

spatial gaps in coverage by these programs, identified emergent metrics of seagrass 

distribution, abundance, and health, summarized mapping data, and produced this report using 

contributions of data, graphics, and text from many collaborators. We found that seagrass 

monitoring programs were collecting data in most of the estuaries and nearshore waters around 

the state. We have identified 34 active (and 4 inactive) monitoring projects or programs that we 

hope will be able to collaborate for the monitoring portion of SIMM. Three of the inactive projects 

are in St. Andrew Bay, the Pensacola Bay region, and the Apalachicola National Estuarine 

Research Reserve in the Panhandle region. There are planned projects in Choctawhatchee Bay

and the Ten Thousand Islands. Along Florida’s east coast, seagrasses along the Volusia 

County coastline are not monitored. A variety of agencies conducts monitoring programs in 

Florida coastal waters, including the Florida Department of Environmental Protection, the 

Florida Fish and Wildlife Research Institute, water management districts, counties, cities, 

universities, colleges, and contractors for military bases.

Monitoring programs measure the presence or absence of seagrasses and document the 

species composition of seagrass beds. Some include identification and assessment of 

macroalgae, and most measure seagrass abundance using the Braun-Blanquet scale or 

percentage cover in replicate quadrats at each site. Sampling methods are basically variations 

of two types: sampling along transects, often perpendicular to the long axis of seagrass beds, 

and point sampling, either fixed or varying, random or nonrandom, in design. Most programs 

conduct field monitoring at least once a year, but the time of year varies between summer and 

fall. Indicators that can be reported for most seagrass monitoring programs include seagrass 

(and macroalgal) abundance, species composition and diversity, and depth distribution of 

seagrass species.

We found that our current statewide set of seagrass maps includes 27 geographic information 

system datasets based primarily on aerial photography collected from 1992 to 2010. The goal of 

SIMM is to reduce the mapping cycle time to a minimum of six years for those regions that are 

not now routinely mapped. The primary indicators derived from mapping projects are seagrass 

areal coverage and habitat texture (i.e., continuous or patchy). Secondary indicators of 

seagrass condition and health determined by mapping projects are change analyses of gains 

and losses in cover and changes in texture determined from analyses of at least two sequential 

sets of imagery having the same spatial extent. Where successive imagery data sets are 

available, we have included changes in seagrass acreage.

Based on the most recent mapping data available for each region, we estimate that there are 

about 2,179,000 acres of seagrass in nearshore Florida waters. Most are located in southern 

Florida (1,300,000 acres) or in the Big Bend and Springs Coast region (618,000 acres). The 

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western Panhandle has 39,200 acres of seagrass, and that acreage is in decline. In recent 

years, seagrass acreage has increased along the west coast of Florida from Pinellas 

County/Tampa Bay to the Charlotte Harbor region. Seagrass acreage is probably stable in the 

Florida Keys and Florida Bay and is increasing on the east coast.

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Executive Summary

Florida seagrass beds are an extremely valuable natural resource. Approximately 2.2 million 

acres of seagrass have been mapped in estuarine and nearshore Florida waters (Carlson and 

Madley 2007), and they provide ecological services worth more than $20 billion a year

(Costanza et al. 1997; Orth et al. 2006). Many economically important fish and shellfish species 

depend on seagrass beds for critical stages of their life history, and seagrasses also play a role 

in the global carbon cycle, nutrient cycles, sediment stabilization, and the maintenance of 

coastal biodiversity. Seagrasses provide food and shelter for endangered mammal and turtle 

species (Orth et al. 2006; Waycott et al. 2009). 

Unfortunately, seagrasses are vulnerable to many direct and indirect human impacts, especially 

eutrophication and other processes that reduce water clarity. Although in some Florida 

estuaries, concerted efforts to improve water quality have resulted in increases in seagrass 

coverage, total seagrass coverage in Florida’s coastal waters is less than it was in the 1950s, 

and coverage is still declining in some areas. The Seagrass Integrated Mapping and Monitoring 

(SIMM) program was developed to protect and manage seagrass resources in Florida by 

providing a collaborative vehicle for seagrass mapping, monitoring, and data sharing. Given the 

budget problems that many agencies are facing, our efforts are directed at leveraging resources 

as well as decreasing and sharing costs for seagrass mapping and monitoring.

Elements of the SIMM program include: 1) ensuring that all seagrasses in Florida waters are 

mapped at least every six years; 2) monitoring seagrasses throughout Florida annually; and 3) 

publishing a comprehensive report every two years that combines site-intensive monitoring data 

and trends with statewide estimates of seagrass cover and maps showing seagrass gains and 

losses. This publication is our first such report. 

We hope that this report and the SIMM program will inform and support a number of state, 

federal, and local programs. For example, permitting agencies can now draw on contacts and 

data available for their area of interest. As we begin to serve data online, stakeholders will be 

able to download recent mapping and monitoring data on seagrass cover and species 

composition. Because in many Florida estuaries, seagrass communities represent significant 

resource management metrics, we hope that SIMM data will also be used by the Florida 

Department of Environmental Protection (FDEP) and the U.S. Environmental Protection Agency 

(EPA) to support the Total Maximum Daily Load (TMDL) Program and for the development of 

numeric nutrient and transparency criteria in Florida estuaries. Reaction to the SIMM concept 

has been positive; 27 agencies and 39 investigators have drafted chapters or contributed data 

for this report.

Data collated by the SIMM program have already proved invaluable in the state and federal 

response to the 2010 Deepwater Horizon oil spill disaster. Because of previous SIMM efforts 

supported by FDEP, we were able to immediately provide National Oceanic and Atmospheric 

Agency (NOAA) Natural Resource Damage Assessment (NRDA) staff draft chapters detailing 

seagrass resources in all Panhandle counties.

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Data Collation Methods: The Florida Fish and Wildlife Conservation Commission/Florida Fish 

and Wildlife Research Institute (FWC/FWRI) are committed to developing, implementing, and 

maintaining the SIMM program. Our first steps, supported by the FDEP Coastal Zone 

Management Program, have been the following:

1. An inventory of active mapping and monitoring programs

2. Identification of spatial gaps in mapping and monitoring programs

3. Identification of emergent metrics of seagrass distribution, abundance, and health that can be 

collated from disparate monitoring programs

4. Production of the first comprehensive mapping and monitoring report using contributions of 

data, graphics, and text from many collaborators.

We carried out these tasks by:

1. Sifting through active and inactive monitoring program databases

2. Interviewing dozens of scientists, agency employees, consultants, and managers conducting

seagrass monitoring programs around the state

3. Reviewing recent and historical seagrass mapping geographic information system (GIS) files 

and imagery datasets collected across the state.

Current Status of Seagrass Monitoring: We found that seagrass monitoring programs were 

collecting data in most of the estuaries and nearshore waters in Florida. We have identified 34 

active (and 4 inactive) monitoring projects or programs that we hope will be able to collaborate 

in the monitoring portion of SIMM (see Table ES-1). Three of the inactive projects are in St. 

Andrew Bay, the Pensacola Bay region, and the Apalachicola National Estuarine Research 

Reserve (NERR) in the Panhandle region. Another is expected to begin this summer in 

Choctawhatchee Bay. On Florida’s east coast, seagrasses along the Volusia County coastline 

are not being monitored.

We invited staff from each monitoring program to contribute to a chapter for their area, and for 

most areas we received excellent summaries, graphics, and data analyses. For a few regions, 

the editors downloaded monitoring data and produced summaries and graphics. Gaps in 

monitoring coverage exist in the Panhandle from Perdido Bay to Choctawhatchee Bay, in 

Waccasassa Bay, the southern Springs Coast, portions of the inshore Ten Thousand Islands, in 

Volusia County, and for large areas offshore of Florida’s Big Bend and the Ten Thousand 

Islands. Three inactive projects in Pensacola Bay, Santa Rosa Sound, and Apalachicola and 

Ochlockonee bays could be funded and resumed to fill most of the coverage gap in Panhandle 

waters. Oil impact sampling is still under way in seagrass beds in the western Panhandle and 

will probably provide some information where routine monitoring has been lacking. Seagrass 

monitoring in the Ten Thousand Islands poses a logistical challenge, but we are exploring 

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mapping and monitoring techniques that might work in these remote, sparse seagrass 

ecosystems in highly turbid waters. A greater challenge exists in monitoring deeper seagrasses 

offshore in federal waters. However, our overall assessment is that a statewide network of 

seagrass monitoring programs is feasible and that monitoring results for estuarine and 

nearshore waters can be collated and reported biennially, if not annually. 

Figure ES-1. Agencies conducting monitoring programs in Florida coastal waters.

A variety of agencies conducts monitoring programs in Florida coastal waters (Table ES-1, 

Figure ES-1). Of the 38 projects, 19 are carried out by State of Florida staff, primarily from 

FWC/FWRI and FDEP (Figure ES-1). Five monitoring programs are carried out by county 

agencies and four by city agencies. Universities or colleges conduct two programs, one in 

Florida Bay by Florida International University (FIU) and one in St. Andrew Bay by Gulf Coast 

Community College (GCCC). Seagrasses in coastal areas near Eglin Air Force Base and Cape 

Canaveral are monitored by federal contractors. The St. Johns River Water Management 

District (SJRWMD) and the South Florida Water Management District (SFWMD) monitor 

seagrasses in the Indian River Lagoon and tidal tributaries such as the St. Lucie Estuary. Local 

governments such as the Loxahatchee River District (Loxahatchee Estuary) and Palm Beach 

County Environmental Resources Management (Lake Worth Lagoon) also conduct seagrass 

monitoring. Many projects report to their water management district. A project in Sarasota Bay 

uses volunteer anglers to report presence or absence of seagrasses.

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TABLE ES-1. METRICS USED BY SEAGRASS MONITORING PROGRAMS IN FLORIDA

Estuary or Subregion Lead Agency

Sampling 

Frequency

B/B1 or 

% Cover

Species 

Comp2

Shoot 

Counts Biomass

Perdido Bay Dauphin Island Sea Laboratory* Event-driven Yes Yes Yes Yes

Big Lagoon Dauphin Island Sea Laboratory* Event-driven Yes Yes Yes Yes

Pensacola Bay Dauphin Island Sea Laboratory* Event-driven Yes Yes Yes Yes

Pensacola Bay Northwest FDEP Restoration monitoring only

Santa Rosa Sound Dauphin Island Sea Laboratory* Event-driven Yes Yes Yes Yes

Choctawhatchee Bay FWRI (2009 only) Annual Yes Yes No No

St. Joseph Bay FWRI Annual Yes Yes No No

St. Joseph Bay FDEP/CAMA Annual Yes Yes Yes Yes

St. Andrew Bay Gulf Coast Community College Annual No Yes Yes No

St. Andrew Bay Northwest FDEP Restoration monitoring only

Apalachicola Bay Apalachicola NERR Inactive program

St. Georges Sound FWC Habitat, Species Conserv. Annual Yes Yes No No

Franklin County FWC Habitat, Species Conserv. Annual Yes Yes No No

Ochlockonee Bay None None

St. Marks FWRI Annual Yes Yes No No

St. Marks FDEP/CAMA Annual Yes Yes Yes Yes

Big Bend FWRI Annual Yes Yes No No

Steinhatchee FDEP/CAMA Annual Yes Yes Yes Yes

Cedar Key FDEP/CAMA Annually Yes Yes Yes Yes

Waccasassa Bay None None

St. Martins Marsh FDEP/CAMA Annually Yes Yes Yes Yes

Homosassa FWRI (2008 only) Sporadic Yes Yes No No

Homosassa FDEP/CAMA Annually Yes Yes Yes Yes

Springs Coast None None

Western Pinellas Pinellas County Annually Yes Yes Yes No

Tampa Bay City of Tampa Annually Yes Yes Yes No

Sarasota Bay Sarasota County Twice a year No Yes No No

Sarasota Bay FDEP/CAMA Annually Yes Yes No No

Lemon Bay Sarasota County Twice a year Yes Yes No No

Lemon Bay FDEP/CAMA Annually Yes Yes Yes No

Charlotte Harbor FDEP/CAMA Annually Yes Yes Yes No

Estero Bay FDEP/CAMA Twice a year Yes Yes Yes No

Rookery Bay Rookery Bay NERR Inactive Yes Yes Yes No

Ten Thousand Islands US Geological Survey/NOAA Unknown Yes Yes ?? ??

Florida Bay FWRI Twice a year Yes Yes Yes Yes

Florida Keys NMS Florida International University Quarterly Yes Yes No Some

Biscayne Bay FWRI, through 2008 Twice a year Yes Yes Yes Yes

Biscayne Bay Miami-Dade County Annually Yes Yes Yes Yes

Palm Beach Palm Beach County Annually Yes Yes Yes No

South Indian River South Florida WMD Bimonthly Yes Yes Yes No

North Indian River St. Johns River WMD Twice a year Yes Yes Yes No

1Braun-Blanquet. 2composition. *Oil spill–targeted sampling, May 2010

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The Tampa Bay, Sarasota Bay, Charlotte Harbor, Florida Bay, Biscayne Bay, and Indian River 

estuarine systems receive intensive scrutiny from a number of agencies and multiple programs. 

A large database exists for these systems, often dating back 10 to 20 years. For many systems, 

monitoring data complement and support frequent, routine seagrass mapping efforts by aiding 

in interpretation of aerial photographs. Some projects have easily accessible data and websites: 

FIU’s Florida Bay project, the Charlotte Harbor National Estuary Program (CHNEP), and the 

Tampa Bay Estuary Program (TBEP) are excellent examples.

All monitoring programs measure presence or absence of seagrasses and species composition 

of seagrass beds. Some include identification and assessment of macroalgae, and most 

measure seagrass abundance using the Braun-Blanquet scale or percentage cover in replicate 

quadrats at each site (Table ES-1). Many programs determine shoot counts, and a few collect 

samples for biomass and morphometric 

analyses. Some collect optical and 

nutrient water quality data, and most 

sample at least once a year, generally 

during the summer or fall. 

Sampling methods are basically 

variations of two types: transect and point 

(Figure ES- 2). FDEP Coastal and Marine 

Assessment (CAMA) programs and 

programs administered by the Southwest 

Florida Water Management District 

(SWFWMD), SJRWMD, and SFWMD use 

established transects that evaluate the 

presence or absence of seagrass and the 

extent of cover by a variation of the 

Braun-Blanquet procedure. In addition, 

transects are frequently used in narrow 

coastal systems where determination of 

the location of the deep edge of seagrass 

beds is a high priority. The number and 

location of transects vary among projects. 

Point sampling, either fixed or varying, random or nonrandom, is commonly used in larger 

systems like Florida Bay, Biscayne Bay, and the Big Bend region. Some coastal regions are 

monitored by the use of both transect and point sampling (Florida Bay, Biscayne Bay, Tampa 

Bay, Lake Worth Lagoon, Southern Indian River Lagoon). Many programs are beginning to use 

probabilistic point sampling.

Figure ES-2. Seagrass monitoring methods.

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Most programs conduct field monitoring at least once a year, but the time of year varies 

between summer and fall. Some programs conduct field monitoring twice a year, in fall and 

spring or in winter and midsummer. A few programs collect data bimonthly or monthly. 

We found that the following indicators can be reported for most seagrass monitoring programs:

1. Seagrass (and macroalgal) abundance

2. Seagrass (and macroalgal) species composition and diversity

3. Depth distribution of seagrass species.

These three indicators can identify changes in seagrass ecosystems due to natural and 

anthropogenic stressors. For example, the combined impacts of the 2004 and 2005 hurricanes 

and heavy runoff in winter 2005 resulted in significant losses in seagrass cover, as well as in 

thinning and changes in species composition in surviving seagrass beds in portions of the Big 

Bend (Carlson et al. 2010). Although other indicators, such as tissue chemical composition 

(nitrogen, phosphorus, carbohydrate content, and stable nitrogen isotope ratios) and 

reproductive effort can be useful, seagrass abundance, species composition, and depth 

distribution represent the most accessible, cost-effective, and comparable indicators for today’s

monitoring programs. Possibly more important than the indicators themselves is the 

comparability of data from year to year and between projects of differing designs, i.e., fixed point 

and transects versus spatially distributed random sampling points.

Information available from monitoring programs varies across Florida. Each chapter in this 

report includes a monitoring assessment and data summary, but the intensity and frequency of 

monitoring, the number of agencies conducting monitoring in an estuary or subregion, and the 

availability of data and data analysis differ with area. In some chapters monitoring data from two 

or more agencies may be presented separately and in different ways. Where data are available, 

we present the most recent assessment of the frequency of occurrence by seagrass species for 

each estuary. 

We combined estuary- or region-specific data on seagrass species from monitoring projects and 

reported seagrass species composition from telephone interviews to summarize the most 

common seagrass species found in each estuary or region of coastal Florida (Table ES-2). 

Of the seven seagrass species that occur in Florida waters, only widgeon grass (RM; Ruppia 

maritima) was never observed as the most abundant species within a region or estuary. Three 

species were most abundant in only a few locations: Johnson’s seagrass (HJ; Halophila 

johnsonii) in central and southern Lake Worth Lagoon; star grass (HE; H. engelmannii) at some 

locations in Rookery Bay (but also common in other coastal areas along Florida’s west coast); 

and paddle grass (HD: H. decipiens) in Naples Bay, Lake Worth Lagoon (along with Johnson’s 

seagrass), and the southern Indian River Lagoon. Paddle grass was observed at other locations 

in Rookery Bay, in the Florida Keys National Marine Sanctuary, and near the St. Lucie Inlet in 

the southern Indian River Lagoon. Shoal grass (HW; Halodule wrightii) and turtle grass (TT; 

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Thalassia testudinum) were the most abundant seagrass species at 45% of all the areas 

surveyed, but only in a few locations did they co-occur in similar abundance. Shoal grass was 

more frequently most abundant in the Panhandle, along the west coast of Florida from western 

Pinellas County through Rookery Bay, and along the east coast from the Lake Worth Lagoon 

through the northern Indian River Lagoon. Turtle grass was most abundant at many locations 

throughout Florida coastal waters but especially in southern Florida and the Big Bend region. 

Manatee grass (SF; Syringodium filiforme) was most abundant at about 25% of locations in 

coastal waters and was most often found in the Big Bend region, where it often occurred with 

turtle grass. Manatee grass was also most abundant along the Gulf side of the Upper Florida 

Keys and in northern Biscayne Bay, and it occurred with shoal grass at several locations in the 

Indian River Lagoon. 

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TABLE ES-2. MOST ABUNDANT SEAGRASS SPECIES FOUND IN FLORIDA ESTUARIES. (HW = HALODULE 

WRIGHTII; TT = THALASSIA TESTUDINUM; SF = SYRINGODIUM FILIFORME; RM = RUPPIA MARITIMA; HE = 

HALOPHILA ENGELMANNII; HD = HALOPHILA DECIPIENS; HJ = HALOPHILA JOHNSONII)

Most Abundant Species Most Abundant Species

Estuary First Second Third Estuary First Second Third

Perdido Bay HW Sarasota and Lemon Bays

Pensacola Bay Sarasota Bay/Roberts Bay TT HW, SF

 Main none Little Sarasota/ Blackburn HW SF

 Escambia Bay brackish Lemon Bay HW, TT SF

 East Bay brackish Charlotte Harbor Region HW TT, SF

Big Lagoon HW TT Estero Bay HW, TT

Santa Rosa Sound Rookery Bay

 Fort Pickens HW TT, SF Cape Romano TT, HW, HE SF, HD

 Gulf Breeze TT HW Johnson Bay TT, HW, HE SF, HD

 East TT Cocohatchee River HW

Choctawhatchee Bay HW Naples Bay HW, HD, HE

St. Andrew Bay TT HW SF Ten Thousand Islands TT, SF HW, HE

St. Joseph Bay TT HW Florida Keys NMS

Franklin County Atlantic Upper Keys TT SF

 Alligator Harbor HW TT Atlantic Lower Keys TT SF HW

 Dog Island HW SF TT Gulf Upper Keys SF TT HW, HD

 St. George Sound HW Gulf Lower Keys TT SF

 Carabelle River TT, SF, HW Tortugas/Marquesas TT SF HW, HD

 Lanark River SF HW TT Florida Bay

 Turkey Point SF TT HW Northeast TT HW

Northern Big Bend East Central TT HW

 Steinhatchee North TT, SF North Central TT HW SF

 Keaton Beach SF TT South TT

 Fenholloway SF HW, HE TT West TT SF, HW

 Econfina SF TT HW, HE Biscayne Bay

 Aucilla TT,SF HW,HE Card Sound TT HW

 St. Marks SF TT South Biscayne Bay TT HW

 North Biscayne Bay SF TT, HW

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Table ES-2. MOST ABUNDANT SEAGRASS SPECIES FOUND IN FLORIDA ESTUARIES. (HW = HALODULE WRIGHTII; 

TT = THALASSIA TESTUDINUM; SF = SYRINGODIUM FILIFORME; RM = RUPPIA MARITIMA; HE = HALOPHILA 

ENGELMANNII; HD = HALOPHILA DECIPIENS; HJ = HALOPHILA JOHNSONII) (CONTINUED)

Most Abundant Species Most Abundant Species

Estuary First Second Third Estuary First Second Third

Southern Big Bend Lake Worth Lagoon

 Suwannee TT, SF North SF, TT, HW

 Horseshoe East TT SF, HW Central HJ, HD, HW

 Horseshoe West TT, SF HW South HJ, HD, HW

 Steinhatchee South TT SF HW South Indian River Lagoon

Suwannee Sound SF IR14-15 HW

Cedar Keys TT SF, HW IR16-20 HW

Waccasassa Bay Unknown IR21 HW

Springs Coast IR22 HW, SF

 St. Martins Keys TT SF HW IR23 HW, SF

West Pinellas County IR24 HD HW

 St. Joseph Sound TT HW IR25 HD HW

 Clearwater Harbor HW TT North Indian River Lagoon

 Boca Ciega Bay HW TT Mosquito Lagoon HW RM, SF

Tampa Bay Banana River HW RM

 Hillsborough Bay HW Melbourne HW

 Old Tampa Bay HW Sebastian Inlet HW SF

 Apollo Beach HW Vero Beach HW

 Mid-Bay TT SF Fort Pierce HW, SF RM, HJ

 Lower Bay TT SF St. Lucie Inlet HW, SF HJ, HD

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Seagrass Mapping 

Efforts: We found that our 

current statewide set of 

seagrass maps included

27 GIS datasets (Figure 

ES-3; Table ES-3) based 

primarily on aerial 

photography collected 

from 1987 to 2008—21

years! For other estuaries, 

however (e.g., Indian 

River Lagoon, Tampa 

Bay, Sarasota Bay, and 

Charlotte Harbor) imagery 

is collected every two 

years. SIMM’s goal is to 

reduce the mapping cycle 

time to 10 years at most 

and ideally to 6 years for 

coastal areas that do not 

have a regular mapping 

program. Imagery 

datasets collected in the 

1980s, 1990s, and early 

2000s were acquired with 

film cameras. More recent 

imagery has been acquired with digital cameras and so may be georectified and 

photointerpreted digitally. However, change analyses using older film imagery might require that 

those datasets be scanned and georeferenced. Interviewees have expressed considerable 

interest in historical imagery, so we are beginning to collect and scan older aerial photos and we 

will serve them on the Web. 

The primary indicators derived from mapping projects are seagrass areal coverage (see Table 

ES-4, below) and habitat texture (whether continuous or patchy; discussed in many of the 

chapters). However, with improving bathymetry data around the state, broader-scale information 

on depth distribution of seagrasses might also be obtained from mapping projects. Secondary 

indicators of seagrass condition and health determined by mapping projects are change 

analyses of gains and losses in area and changes in texture determined from analyses of at 

least two sequential sets of imagery. These analyses are useful in a broad context, but they are 

prone to artifacts, including seasonal changes in seagrass biomass (and, therefore, visual 

signatures) and differences in water clarity between successive imagery sets. But even with its 

limitations, mapping allows us to assess seagrass abundance over much larger areas than can 

Figure ES-3. Status of seagrass mapping efforts.

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be monitored on the ground. We report change analyses where successive mapping data sets 

with the same spatial extent are available.

TABLE ES-3. SEAGRASS IMAGERY AND MAPPING STATUS FOR FLORIDA

Imagery Collection

Estuary Most Recent Agency Most Recent Maps

Perdido Bay 2010 NASA, NOAA 2003

Big Lagoon 2010 NASA, NOAA 2003

Pensacola Bay System 2010 FWC/FWRI, NOAA 2003

Santa Rosa Sound 2010 FWC FWRI 2003

Choctawhatchee Bay 2010 FWC/FWRI SIMM 2003

St. Andrew Bay 2010 GCCC 2003

St. Joseph Bay 2010 FDEP CAMA 2006

Franklin County 2010 FWC/FWRI SIMM 1992

Big Bend Region 2006 FWC/FWRI SIMM 2006

Cedar Keys and Waccasassa 2001 SRWMD 2001

Springs Coast 2007 SWFWMD 2007

Tampa Bay 2010 SWFWMD 2010

Sarasota Bay 2010 SWFWMD 2010

Lemon Bay 2010 SWFWMD 2010

Charlotte Harbor North 2010 SWFWMD 2010

Pine Island Sound 2008 SFWMD 2006

Matlacha Pass 2008 SFWMD 2006

Caloosahatchee Estuary 2008 SFWMD 2006

Estero Bay 2008 SFWMD 2006

Rookery Bay 2009

SFWMD; Rookery Bay 

NERR 2003/2005

Ten Thousand Islands 2009

SFWMD; Rookery Bay 

NERR partial, 2005

Florida Bay 2004 FWC/FWRI SIMM 2004

Gulf Upper Keys 2006 NOAA NCCOS* 1992

Gulf Lower Keys, Marquesas 2006 NOAA NCCOS* 1992

Tortugas 2006 NOAA NCCOS* 1992

Atlantic Lower Keys 2006 NOAA NCCOS* 1992

Atlantic Upper Keys 2006 NOAA NCCOS* 1992

Biscayne Bay 2005 FWC/FWRI SIMM 2005

Lake Worth Lagoon 2009 SFWMD 2007

Southern Indian River Lagoon 2009 SFWMD 2007

Northern Indian River Lagoon 2009 SJRWMD 2007

*NCCOS = National Centers for Coastal Ocean Science

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Of the estuaries or subregions of coastal Florida, all have aerial imagery available obtained 

within the past 10 years, with the oldest imagery being that taken of the Cedar Keys and

Waccasassa Bay in 2001 (Table ES-3). However, photointerpretation, mapping, and mapping 

data have not been developed from the most recent imagery for many locations. In the 

Panhandle, imagery was collected in 2010 and awaits photointerpretation. The Southwest 

Florida Water Management District has just released mapping data from imagery collected in 

2010 for Tampa Bay south through the northern portions of Charlotte Harbor. In a few cases, 

imagery was collected but it is not likely that photointerpretation will take place due to largescale problems with glare or turbidity (Ten Thousand Islands) or insufficient funding (Florida 

Keys). As a result, for some locations, the most recent mapping data are from the early 1990s

(Franklin County, the Florida Keys National Marine Sanctuary); for others, data are not available 

(Rookery Bay, Ten Thousand Islands). One of the highest priorities of the SIMM program is to 

acquire or facilitate acquisition of imagery and mapping data for all coastal regions so that no 

more than six years separates consecutive mapping efforts.

At a recent workshop convened by FDEP, dozens of seagrass scientists also pointed out areas 

where mapping is prohibitively difficult because of water depth, persistent turbidity, or tanninstained waters. These areas include the Ten Thousand Islands, Hawk Channel in the Florida 

Keys, the northeast corner of the Big Bend Region, and portions of several estuaries in the 

Panhandle. In the immediate short term we will use monitoring data with sufficient density to 

create point distribution maps for these areas. Acoustic techniques, such as sidescan sonar,

have been used successfully to map seagrasses in some areas with turbid or tannin-stained 

waters (Shirley et al. 2006) and are worthy of continued development.

Areas too deep or too far offshore to map with conventional aerial photography also present a 

challenge. There are possibly 7 million acres of seagrass habitat in federal waters off Florida, 

more than three times that mapped in state waters. Areas where the continental shelf is shallow 

enough for seagrass growth include the Southwest Florida Shelf (the area between Cape 

Romano and Key West), the Springs Coast (between Anclote Key and Cedar Keys), and the Big 

Bend proper (from the Suwannee River to Alligator Point). Beds in deeper waters are dominated 

by paddle grass and star grass, both small plants that are difficult to detect remotely. These 

areas are important seagrass habitat because they provide migration corridors for species that 

spend their juvenile stages in estuaries and live offshore as adults. The productivity of these 

extensive beds (primarily paddle grass) is important in sustaining offshore snapper and grouper 

fisheries (Kammerstrom et al. 2006).

Off the Springs Coast and Big Bend, the water is so clear that seagrasses may be mapped as 

far offshore as 20 miles, so satellite imagery may be the most cost-effective way to map 

seagrasses there. Acquisition of WorldView 2 satellite imagery of the Springs Coast and Big 

Bend is anticipated in fall 2011. Nevertheless, paddle grass, which is common offshore, is small 

and has a dubious optical signature in deep water, so mapping these beds in the deeper waters 

of the Big Bend and the southwest Florida Shelf will be technically challenging.

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We have summarized the most recent mapping data for all Florida estuaries or regions and 

calculated an annual percentage change in seagrass area where two data sets having the same 

spatial extent were available for a region (Table ES-4). We used percentage annual change as 

the trend indicator because the time between mapping data sets ranges from 2 to 13 years.

However, as the time increases between mapping efforts, trend analysis becomes more general 

and cannot capture annual variation that could result from natural stressors, such as El Niño 

weather patterns and tropical cyclones, or short-term anthropogenic factors, such as dredging 

or changes in boat access. Also, methods of image acquisition and photointerpretation might

vary temporally and spatially. More detailed information on methods and seagrass acreage 

gains and losses is located in each chapter. These data are also summarized on a larger 

regional basis (Table ES-5; Figure ES-4).

The Panhandle has the lowest acreage of seagrass (39,192 acres, 1.8% of the total), and three 

estuaries in the Panhandle showed losses greater than 3% per year between 1992 and 2002–

03. Santa Rosa Sound and St. Andrew Bay had small annual percentage increases in 

seagrasses over the same time. As suggested by three years of monitoring data, seagrass 

acreage in Franklin County coastal waters is probably declining. Photointerpretation of imagery 

acquired in the fall of 2010 will provide updated information for all Panhandle estuaries.

About 28% (617,921 acres) of Florida seagrasses are found in the area from the northern Big 

Bend through the Springs Coast (Table ES-5). Change analysis was possible only for the Big 

Bend regions: Southern Big Bend showed a 1.2% annual loss in seagrass area from 2001 

through 2006, while Northern Big Bend showed an annual loss in area of less than 0.1% for the 

same period, indicating that seagrass cover was stable in that region. 

Seagrasses along Florida’s southwest coast (from Western Pinellas County through Rookery 

Bay) cover 137,914 acres or 6.3% of all the seagrass mapped along Florida’s coast. We have 

included 2010 mapping data very recently released by SWFWMD (Kaufman 2011). Substantial 

seagrass gains have occurred from Western Pinellas County through the Charlotte Harbor 

region. Estero Bay, on the other hand, lost seagrass acreage between 2004 and 2006 at the 

annual rate of 1.3%. 

More than half of all seagrasses (1,301,936 acres, or 59.7%) in Florida are located in south 

Florida, including the Florida Keys National Marine Sanctuary, Florida Bay, Biscayne Bay, and 

adjacent Atlantic waters. Change analyses were possible only for Florida Bay and Biscayne Bay 

and showed a probably negligible 0.07% annual loss in Florida Bay and small annual gains 

(0.28%) in Biscayne Bay. 

Seagrasses along the east coast of Florida cover 82,182 acres, 3.8% of all seagrasses in 

Florida waters. Seagrass cover is increasing on the east coast, with large annual increases 

observed in the Indian River Lagoon—6.7% and 4.7% per year in the southern and northern 

Indian River Lagoon, respectively.

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TABLE ES-4. MAPPING ESTIMATES OF SEAGRASS ACREAGE IN ESTUARINE 

AND COASTAL WATERS OF FLORIDA

Mapping data

Previous Most Recent Change

Estuary/Region Year Acres Year Acres (%/yr)

Perdido Bay 1987 642 2002 125 –5.4

Pensacola Bay System 1992 892 2003 511 –3.9

Big Lagoon 1992 538 2003 544 0.10

Santa Rosa Sound 1992 2,760 2003 3,032 0.90

Choctawhatchee Bay 1992 4,261 2003 2,623 –3.5

St. Andrew Bay 1992 9,832 2003 11,233 1.3

St. Joseph Bay 1993 8,170 2006 6,672 –1.4

Franklin County 1992 14,452 n/a

Northern Big Bend region 2001 149,840 2006 149,140 –0.093

Southern Big Bend region 2001 59,674 2006 56,146 –1.2

Suwannee, Cedar Keys, Waccasassa 2001 33,625 n/a

Springs Coast 2007 379,010 n/a

Western Pinellas County 2006 23,943 2008 25,880 4.0

Tampa Bay 2008 29,647 2010 32,897 5.5

Sarasota Bay 2008 12,641 2010 12,692 0.20

Lemon Bay 2008 2,863 2010 3,039 3.1

Charlotte Harbor region 2004 57,213 2006 58,849 1.4

Estero Bay 2004 3,625 2006 3,529 –1.3

Ten Thousand Islands n/a n/a n/a

Rookery Bay Aquatic Preserve 2003/05 1,028 n/a

Florida Keys National Marine Sanctuary 1992 856,355 n/a

Florida Bay 1992 146,615 2004 145,308 –0.074

Biscayne Bay 1992 153,827 2004/05 159,363 0.28

Atlantic side Biscayne 1992 140,910 n/a

Lake Worth Lagoon 2001 1,647 2007 1,688 0.41

Southern Indian River Lagoon 2005 7,808 2007 8,848 6.7

Northern Indian River Lagoon 2005 65,520 2007 71,646 4.7

Total Seagrass Acreage 2,179,145

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Of the 30 systems shown in Figure ES-4, seagrass acreage increased in 11 estuaries or 

subregions, with especially large increases in western Pinellas County, Tampa Bay, Lemon 

Bay, and the Indian River Lagoon. Smaller increases were detected in Santa Rosa Sound, St. 

Andrew Bay, Sarasota Bay, the Charlotte Harbor region, Biscayne Bay, and Lake Worth 

Lagoon. Acreage of seagrass beds is probably stable in Big Lagoon in western Florida, northern 

Big Bend, the Florida Keys National Marine Sanctuary, Florida Bay, and the nearshore Atlantic 

waters adjacent to Biscayne Bay. Change analyses were not available for Franklin County 

coastal waters, Suwannee Sound, Cedar Keys, Waccasassa Bay, the Springs Coast, Rookery 

Bay, the Ten Thousand Islands, the Florida Keys National Marine Sanctuary, or the nearshore 

Atlantic waters near Biscayne Bay.

We anticipate revising change analysis data using more recent mapping data for many areas, 

and this will strengthen our confidence in the observed trends. Digital color imagery was 

obtained in fall of 2010 for most of the Florida Panhandle, and photointerpretation and mapping 

of these images is under way. In addition, satellite imagery of the Big Bend region will be 

acquired in 2011.

Figure ES-4. Seagrass cover in Florida coastal waters and 

trends in seagrass acreage.

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TABLE ES-5. SEAGRASS ACREAGE FOUND IN FIVE 

COASTAL REGIONS OF FLORIDA

Seagrass

Region of Florida Acres % of total

Panhandle 39,192 1.8%

Big Bend to Springs 617,921 28.4%

Southwest Florida 137,914 6.3%

South Florida 1,301,936 59.7%

East Coast 82,182 3.8%

Total 2,179,145 100.0%

Figure ES-5 Distribution of seagrass acreage in Florida coastal waters.

Core Indicators for Seagrass Monitoring and Mapping: Based on the data and information 

available to us and from discussions with collaborators, we recommend, for a statewide 

seagrass mapping and monitoring network, that the following core indicators be used to assess 

seagrass health and that they be reported regularly to legislators and managers:

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Monitoring indicators

1. Seagrass (and macroalgal) abundance

2. Seagrass (and macroalgal) species composition and diversity

3. Depth distribution of seagrass species

Desirable, but optional, monitoring indicators include:

4. Optical water quality measurements (chlorophyll, turbidity, color, total suspended solids,

transparency)

5. Reproductive effort (flowering, fruiting, seedling production)

Mapping indicators

6. Seagrass areal coverage and texture

7. Time-series change analyses of areal coverage and texture

The Future of SIMM: Development of the SIMM program has been generously funded by the 

Florida Department of Environmental Protection Coastal Management Program (CMP).

However, the future of SIMM requires a sustained funding source. Increasing budget constraints 

at state, local, and federal levels require that costs be cut to absolute minimum levels. Recent 

technological developments and the ability to leverage costs among agencies provide several 

options for optimizing the use of available funds. Some tasks, such as imagery acquisition, 

might be less expensive if carried out by a single agency or as a pooled effort among agencies, 

while monitoring programs will likely be less expensive if carried out locally by partners 

throughout coastal Florida. 

Mapping Costs: In our first annual report (Carlson and Yarbro 2009), we reviewed mapping 

project costs (Table ES-6), separating imagery acquisition costs from photointerpretation and 

map production costs. In seven projects carried out from 2004 to 2008, imagery acquisition 

costs ranged from 6 to 19 cents per acre, with an average cost of 11 cents per acre.

Photointerpretation costs for those same projects ranged from 4 to 52 cents per acre, with an 

average cost of 23 cents per acre. The total combined costs for imagery acquisition and 

photointerpretation ranged from 11 to 63 cents per acre and averaged 34 cents per acre.

Because seagrass beds are surrounded by other habitats on the bottom of estuaries and bays

that are included in mapping projects, the total statewide estimate of seagrass area of 2.2 

million acres cannot be used to estimate statewide mapping costs. Using an estimate of 4.0 

million acres of nearshore bottom habitat, the total cost of mapping seagrass for the entire state 

of Florida one time using digital aerial imagery and conventional photointerpretation would be 

about $1.36 million. Spread over a six- year mapping cycle, the annual cost of mapping alone 

would be $227,000. With staff salary costs added, the total annual cost would be approximately 

$290,000 for mapping alone.

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TABLE ES-6. COMPARISON OF THE COSTS OF IMAGERY ACQUISITION AND MAPPING FOR SEVERAL PROJECTS IN 

FLORIDA

Project: Florida Bay 

SFWMD/FWRI 

2004

Biscayne Bay 

SFWMD/FWRI 

2005

Western 

Everglades 

2006

Springs Coast 

SWFWMD 

2005

Tampa Bay 

SWFWMD 

2006

Tampa Bay 

SWFWMD 

2008 

Indian River 

SJRWMD 

2007

Average 

Cost

Area of Study (acres) 815,854 557,222 1,061,091 528,640 1,553,757 1,504,718 224,065 –

Imagery Type Natural color 

film

Zeiss DMC 

digital

Zeiss DMC 

digital

Leica 

ADS40

Zeiss DMC 

digital

Zeiss DMC 

digital

Zeiss DMC 

digital –

Acquisition Cost $51,066 $55,588 $133,985 $99,946 $97,291 $170,545 $25,380 

Acquisition Cost 

per acre

$0.06 $0.10 $0.13 $0.19 $0.06 $0.11 $0.11 $0.11 

Photointerpretation 

and Mapping Costs $107,687 $142,498 $334,963 $170,000 $67,609 $77,346 $116,833 

Photointerpretation 

and Mapping Cost 

per acre

$0.13 $0.25 $0.32 $0.32 $0.04 $0.05 $0.52 $0.23 

Total Cost $158,753 $198,086 $468,948 $269,946 $164,900 $247,891 $142,213 

Total Cost per acre $0.19 $0.35 $0.44 $0.51 $0.11 $0.16 $0.63 $0.34 

Mapping: Imagery

Cost Ratio 2.1 2.6 2.5 1.7 0.69 0.45 4.6 2.1 

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Mapping costs can be reduced in three ways: by obtaining imagery for multiple purposes,

allowing several agencies or programs to share costs; by using satellite imagery in regions

where high spatial resolution is not required; and by using supervised software classification 

techniques to automate a significant portion of the photointerpretation process.

Cost-sharing for imagery acquisition is highly desirable, but it requires a large amount of 

coordination, and some partners might not receive imagery that fully meets their needs. For 

example, photography over land areas for tax assessment or infrastructure mapping is often 

carried out in winter, when cold fronts provide cloud-free skies. Moreover, long shadows are not 

desirable, so imagery is generally acquired between 10 a.m. and 2 p.m. For seagrass imagery 

acquisition, high sun elevation angles at midday can often create unacceptable levels of glare 

on the water surface, and cold fronts bring high winds that can cause sediment resuspension 

and turbid conditions. Furthermore, seagrass biomass is generally much lower in winter than in 

summer, so shallow and sparse seagrass beds might not be visible in winter photography. With 

patience and communication, however, the needs of all project partners can be met. We have 

had great success working with aerial photo contractors to acquire seagrass imagery in 

conjunction with land-area flights for other purposes. Most contractors are able to fly coastal and 

estuarine flight lines under conditions desirable for seagrass imagery, leaving flight lines over 

land for windy days and high sun elevation angles. Imagery acquisition costs are still in the 

vicinity of 12 cents per acre, however, so conventional aerial imagery is best used in areas 

where high spatial resolution is required.

For larger areas such as Florida’s Big Bend, Springs Coast, Biscayne Bay, Florida Bay, and the 

Florida Keys, satellite imagery can provide a significant cost savings for imagery acquisition. 

Over the course of SIMM’s development, the resolution of satellite imagery has greatly

improved and costs have decreased. Resolution, the minimum size of an area that can be 

discerned by a photointerpreter, of four-band (red, green, blue, and near-infrared) satellite 

imagery has improved considerably and now approaches 2 m2. Digital aerial imagery has a 

resolution of 1 ft2 which is about 10 times better than that of satellite imagery, but for most 

seagrass mapping projects where the minimum mapping unit is 0.25 ha, the 2-m

2

resolution of 

satellite imagery is more than adequate. Satellite imagery has been expensive in the past, but 

costs are dropping. Using an estimate of 8 cents per acre, a 33% savings over conventional 

aerial photography can be obtained.

On average, photointerpretation costs twice as much as imagery acquisition, so the ability to 

automate a portion of the mapping process would also result in significant savings. Using 

supervised software classification, our goal is to reduce interpretation costs more than 50%,

from an average of 23 cents per acre to 10 cents per acre. The uniform density and seamless 

acquisition of satellite imagery combined with software classification make this goal possible.

Total project costs using satellite imagery and software classification in conjunction with 

traditional photointerpretation reduces costs from an average of 34 cents per acre to 18 cents 

per acre, a savings of almost 50%. Statewide mapping costs would drop from $1.4 million to 

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$740,000. Over a six-year mapping cycle, annual mapping costs and project administration 

would drop from $290,000 to about $150,000. 

Monitoring Costs: The fundamental perspective of SIMM is that seagrass mapping and 

monitoring are complementary and that both are needed to effectively protect, manage, and 

restore seagrass resources. Seagrass monitoring can provide information on seagrass density, 

species composition, and health that cannot be extracted from aerial or satellite imagery.

Furthermore, monitoring can be carried out each year, and data can be analyzed within a few 

months of collection while the turnaround time for mapping data is considerably longer.

The costs of seagrass monitoring depend primarily on logistics and on the indicators measured.

Local agencies can monitor seagrass communities in their backyard less expensively than state 

or federal agency staff traveling long distances from their home offices. Inexpensive and basic 

indicators are seagrass and macroalgal species composition and abundance. Biomass 

sampling adds costs for sample collection, storage, and processing. Optical water quality 

measurements and chemical analysis of seagrass tissue and water samples also raise costs. 

Successful seagrass monitoring programs in the Indian River Lagoon, Florida Keys National 

Marine Sanctuary, Florida Bay, Biscayne Bay, and Big Bend provide a basis for calculating 

monitoring costs, and, depending on the parameters measured and analyses performed, we 

estimate that single per-site costs range from $100 to $400. These costs include vehicle and 

boat maintenance, fuel, travel, salary costs for staff, and analytical costs for chemical indicators.

Using a middle estimate of $250 per site and assuming sampling of 2000 sites yearly 

throughout the state, the annual cost of seagrass monitoring for the entire state will be

$500,000. However, the economic value of the ecological services provided by 2.2 million acres 

of seagrass is approximately $40 billion (Costanza et al. 1997), resulting in an annual cost–

benefit ratio of 0.125% 

Challenges and Opportunities:

Although it will be challenging to find a stable funding source for SIMM, we are optimistic that 

the program’s value will generate support among participating agencies. As the program 

continues, we will focus on a number of key tasks:

Compare monitoring results collected using different sampling designs (fixed points and 

transects vs. spatially distributed random sampling points). With the assistance of 

University of Florida staff, we are evaluating the comparability of data collected using 

fixed-transect, fixed-point, and probabilistic designs. SIMM will deal with this issue as the 

program develops, with the goal of implementing spatially distributed, random sampling 

throughout the state.

Report seagrass status and trends in Florida. By building upon the collaboration 

established during the creation of this first report and by assisting other monitoring 

programs logistically or monetarily, we hope to create seagrass monitoring report cards 

at least every two years.

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Optimize data management, statistical analyses, and Web sharing. Many monitoring 

programs are uncertain as to how to store and analyze monitoring data. Some data sets 

are stored in Web-accessible databases; others reside on hard-copy field-data sheets.

One of SIMM’s near-term goals is to provide data management and analysis support to 

monitoring programs that need it. In the longer term, we hope to build a Web-accessible 

database for seagrass monitoring data using our data initially and inviting other agencies 

to contribute either data or a link to their own Web database.

Close spatial gaps in monitoring programs. Gaps in program coverage exist in the 

Panhandle, Springs Coast, Ten Thousand Islands, and Volusia County. Because some 

programs elsewhere depend on grants, continued statewide seagrass monitoring 

coverage is dependent on stable funding, and we will continue to explore funding 

sources and work with other agencies to monitor seagrasses. We are currently assisting 

FWC, FDEP, the Northwest Florida Water Management District and local agency staff in 

setting up monitoring programs in Panhandle estuaries. 

Achieve consistency in mapping cycle times. Seagrass mapping cycles range from 2

years to more than 15 years, depending on the estuary or area. Detecting changes in 

seagrass area and density based on long cycle times has limited value. We have 

determined that it is highly feasible to link seagrass aerial photography to the triennial 

aerial photography carried out by the Florida Department of Revenue (FDOR). Narrow 

water bodies such as the Indian River Lagoon are frequently included in the FDOR 

imagery acquisition program. A number of issues, such as imagery collection conditions, 

added costs, and imagery collection schedules, remain to be resolved. In estuaries with 

two- and three-year mapping cycles, those schedules should be maintained. In estuaries 

for which no ongoing mapping programs exist, we hope the mapping cycle time will be

six years. 

Cut the lag times for seagrass mapping projects. The time between the collection of 

imagery and the distribution of GIS maps can be as long as five years. Where possible, 

we will reduce the processing time by finding funds to interpret imagery immediately

after collection. In the slightly longer term, mapping costs and turnaround time might be 

reduced by use of remote sensing and image analysis software for seagrass mapping 

instead of conventional photointerpretation.

Address the limitations of conventional aerial photography. Large areas of seagrass 

habitat important to fisheries in the northeastern Gulf of Mexico cannot be mapped by 

conventional aerial photography. Gains and losses can occur without our knowledge. 

We are presently investigating alternative techniques for assessing deep water seagrass 

beds, such as underwater photography or videography. Other developing technologies 

include sidescan sonar and hyperspectral imagery.

Provide data support for management actions. Where degraded water quality has been 

implicated in seagrass loss or thinning or changes in seagrass species composition, we 

hope that information from this and future SIMM reports will support opportunities for 

management actions found in TMDL, Outstanding Florida Waters (OFW), numeric 

nutrient criteria, and water quality criteria regulations administered by FDEP.

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Data Use for Damage Assessment from the 2010 Deepwater Horizon Oil Spill: Release of 

the final version of this report was delayed because of our involvement in the Natural Resources 

Damage Assessment (NRDA) of seagrass ecosystems in the northern Gulf of Mexico following 

the 2010 Deepwater Horizon oil spill. Nevertheless, the final draft chapters and summary 

information for Florida Panhandle estuaries provided vital information for NOAA’s Submerged 

Aquatic Vegetation Technical Working Group (SAV TWG). SIMM mapping and monitoring 

information allowed the SAV TWG to design data-acquisition efforts to fill data gaps and to 

devise statistically defensible sampling designs in the assessment of oiling and resource 

damage. Extensive and ongoing aerial imagery acquisition associated with damage 

assessment, and monies provided for the monitoring of Panhandle seagrass beds, might

provide mapping and monitoring data for estuaries for which, before the spill, mapping and 

monitoring programs were not current. However, another consequence related to the oil spill 

has been potentially destructive impacts to seagrass beds from response activities, such as 

booming, construction of barriers, and propeller scarring from vessels of opportunity (VOOs). 

Damage assessment of the direct oiling of seagrass beds and of response activities in 

Panhandle estuaries will continue at least through 2011. BP and its contractors, as well as 

federal and state agencies, have used a number of aerial and remote-sensing platforms to 

collect terabytes of imagery data. We hope some of this imagery and the effort spent to analyze 

it will realize benefits for future seagrass mapping efforts in Florida.

LITERATURE CITED

CARLSON, P. R., and K. MADLEY

2007. Statewide summary for Florida. Pp. 99–114 in L. Handley et al., eds. Seagrass status 

and trends in the northern Gulf of Mexico, 1940–2002. United States Geological Survey 

Scientific Investigations Report 2006-5287 and U.S. Environmental Protection Agency 855-R04-003, Washington, D.C. 267 p.

CARLSON, P. R., AND L. A. YARBRO

2009. SIMM: Seagrass Integrated Mapping and Monitoring for the state of Florida: inventory of 

recent and current seagrass mapping and monitoring programs, year 1 annual report. Florida 

Department of Environmental Protection Coastal Zone Management Grant Number CZ820. 

Tallahassee, Florida. 44 p.

CARLSON, P. R., L. A. YARBRO, K. K. KAUFMAN, and R. A. MATTSON. 2010. Vulnerability 

and resilience of west Florida seagrass communities to hurricane impacts. Hydrobiologia 649: 

39–53. 

COSTANZA, R., R. D’ARGE, R. DE GROOT, S. FARBER, M. GRASSO, B. HANNON, S. 

NAEEM, K. LIMBURG, J. PARUELO, R. V. O’NEILL, et al.

1997. The values of the world’s ecosystem services and natural capital. Nature 387: 253–260.

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KAMMERSTROM, K. K., W. J. KENWORTHY, M. S. FONSECA, and P. E. WHITFIELD

2006. Seed bank, biomass, and productivity of Halophila decipiens, a deep water seagrass on 

the west Florida continental shelf. Aquatic Botany 84: 110–120. 

KAUFMAN, K. A.

2011. SWIM 2010 seagrass mapping, PowerPoint presentation, 18 January 2011 Meeting of the 

Southwest Florida Seagrass Working Group. 

ORTH, R. J., et al. 

2006. A global crisis for seagrass ecosystems. Bioscience 56: 987–996.

SHIRLEY, M. A., S. D. LOCKER, and J. L. SCHMID

2006. A comparison of side scan sonar and aerial photography for submerged aquatic 

vegetation mapping. Final Report, Rookery Bay National Estuarine Research Reserve, Naples, 

Florida. 20 p.

WAYCOTT, M., C. M. DUARTE, T. J. B. CARRUTHERS, R. J. ORTH, W. C. DENNISON, S. 

OLYARNIK, A. CALLADINE, J.W. FOURQUREAN, K. L. HECK JR., A. R. HUGHES et al.

2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. 

Proceedings of the National Academy of Sciences of the United States of America 106: 12377–

12381.

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Introduction

Florida seagrass beds are an extremely valuable natural resource. Approximately 2.2 million 

acres of seagrass have been mapped in estuarine and nearshore Florida waters (Table I-1, 

after Carlson and Madley 2007), Seagrasses provide habitat for fish, shellfish, marine mammals 

and sea turtles that translate into a value of more than $20 billion each year (Costanza et al. 

1997). More seagrass exists in water too deep for conventional mapping, and the total area of 

seagrasses in Florida’s estuarine and coastal waters may be as great as 3 million acres. Many 

economically important fish and shellfish species depend on seagrass beds for critical stages of 

their life history, and seagrasses also play a role in the global carbon cycle, nutrient cycles, 

sediment stabilization, and the maintenance of coastal biodiversity and provide food and shelter 

for endangered mammal and turtle species (Orth et al. 2006; Waycott et al. 2009).

TABLE I-1. ESTIMATES OF MAPPED AND POTENTIAL 

SEAGRASS AREA IN FLORIDA WATERS (FROM 

CARLSON AND MADLEY 2007)

Hectares Acres

STATEWIDE TOTAL 913,231 2,256,594

Panhandle 16,942 41,864

Big Bend 247,699 612,064

Gulf Peninsula 43,341 107,096

Atlantic Peninsula 30,132 74,456

South Florida 575,117 1,421,114

POTENTIAL SEAGRASS

Big Bend 1,415,028 3,496,534

Southwest Florida Shelf 1,433,127 3,541,257

Unfortunately, seagrasses are vulnerable to many direct and indirect human impacts, especially 

eutrophication and other processes that reduce water clarity (Orth et al. 2006). Although 

concerted efforts to improve water quality have resulted in increases in seagrass area in some 

Florida estuaries, the area of seagrasses in some of the state’s coastal waters continues to

decline (Carlson et al. 2010). In order to identify areas of seagrass loss, to stem and reverse 

seagrass losses, and to monitor recovery of seagrasses, regular mapping and monitoring of this 

valuable resource are required.

Until now there has been no coordinated statewide program for the regular assessment of the 

abundance and health of seagrasses. Seagrasses in some estuaries—Indian River Lagoon, 

Tampa Bay, Sarasota Bay, and Charlotte Harbor, for example—are regularly mapped every two 

years by the St. Johns River Water Management District, the Southwest Florida Water 

Management District, and the South Florida Water Management District, respectively. However, 

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other estuaries and seagrass beds have been mapped using opportunistic grants with no 

consistent frequency, resulting in gaps of 8–12 years between mapping efforts. The last 

statewide reporting effort used a collection of seagrass maps produced over a period of 10

years. Comparing data from such disparate mapping projects often requires that the data be 

reworked into a standard format for computation of area estimates and ignores the potential for 

significant changes in seagrass cover between start and finish of data collection over such long 

periods. Comparisons of seagrass cover among regions and analysis of regional trends are also 

compromised.

Furthermore, when standard photointerpretation methods are used, there is a lag time of 18–36 

months between the collection of imagery and the production of seagrass maps in geographic 

information system (GIS) software. These lags, added to the sometimes lengthy interval 

between mapping efforts for an area, result in a poor ability to detect seagrass losses quickly 

and prevent further losses.

To provide more accurate estimates of changes in seagrass area and to provide greater spatial 

resolution and information on seagrass species composition, the Seagrass Integrated Mapping 

and Monitoring (SIMM) program integrates seagrass mapping and monitoring across Florida.

Monitoring programs provide greater spatial resolution and information on seagrass and algal 

species composition much faster than do mapping projects alone (Table I-2). Changes in 

seagrass abundance or species composition can be detected in a few months rather than over 

several years. Many agencies and groups are monitoring or have monitored seagrasses, and 

this offers the opportunity to link existing monitoring programs via a reporting network. However, 

doing so presents several challenges including gaps in spatial coverage, temporal gaps in 

monitoring data, and identification of key indicators, appropriate field methods, and statistical

techniques for analyzing disparate data sets.

TABLE I-2. SEAGRASS MAPPING AND MONITORING ARE 

COMPLEMENTARY

Characteristic Mapping Monitoring

Spatial Coverage Large: hundreds of km2 Small: hundreds of m2

Spatial Resolution Coarse: 0.2 ha Fine: 1 m2

Classification Coarse: 2−3 categories Fine: scalar

Species Composition None Complete

Revisit Interval Long: 2−10 years Short: 6−12 months

Data Lag Time Long: 12−24 months Short: 1−2 months

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The SIMM program was developed to protect and manage seagrass resources by linking 

seagrass mapping and monitoring programs across Florida and by filling gaps where necessary. 

Elements of this program include: 1) mapping of all seagrasses in Florida waters at least every 

six years for those regions for which a routine mapping program does not exist; 2) monitoring 

seagrasses throughout Florida annually; and 3) publication of a comprehensive report every two

years, combining site-intensive monitoring data and trends with statewide seagrass cover 

estimates and maps showing seagrass gains and losses.

The Florida Fish and Wildlife Conservation Commission/Fish and Wildlife Research Institute 

(FWC/FWRI) staff are committed to developing, implementing, and maintaining the SIMM

program. Our first steps, supported by the Florida Department of Environmental Protection 

(FDEP) Coastal Management Program, have been to:

1. Inventory existing mapping and monitoring programs 

2. Identify spatial gaps in mapping and monitoring programs

3. Collate and evaluate seagrass monitoring techniques

4. Identify emergent metrics of seagrass distribution, abundance, and health that can be 

obtained from disparate monitoring programs

5. Analyze seagrass phenology and the seasonal climatology of water clarity to determine the 

optimal times for mapping seagrass in Florida coastal waters

6. Develop an online imagery database (Marine Resources Aerial Imagery Database [MRAID]) 

to serve imagery for seagrass mapping projects

7. Carry out seagrass monitoring and mapping in areas for which our inventory identified gaps

8. Evaluate the feasibility of using satellite imagery instead of conventional aerial photography in 

seagrass mapping

9. Develop collaboration with the Florida Department of Revenue to add seagrass aerial 

imagery to scheduled land imagery collection in coastal counties

As the SIMM program continues, we will leverage resources among local, state, and federal 

agencies to make seagrass mapping and monitoring programs effective while saving money on 

imagery acquisition, photointerpretation, mapping, and monitoring costs. Ultimately, we hope to 

make all seagrass mapping and monitoring data accessible on the Web. SIMM program data 

provide or could provide:

1. Baseline data against which natural and human-caused disasters could be evaluated

2. Background data for permitting efforts in general and the Uniform Mitigation Assessment 

Method (UMAM) of FDEP in particular

3. Quantitative data to support Total Maximum Daily Load (TMDL) efforts and Basin 

Management Action Plans (BMAP) in estuaries

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4. Quantitative metrics for developing and monitoring the effectiveness of numeric nutrient 

criteria and numeric transparency criteria.

History and vision of the SIMM program: The roots of the SIMM program extend back to the 

1970s when the importance of seagrass habitat and its dependence on water quality were 

recognized in Tampa Bay and other estuaries. The Florida Water Resources Act of 1972 

established five water management districts across the state to manage water resources.

Citizen initiatives resulted in the funding of advanced wastewater treatment and control of pointsource pollution in Tampa Bay and other Florida estuaries. But by the mid-1980s it was 

apparent that nonpoint-source pollution also played an important role in estuarine eutrophication 

and seagrass loss. In 1987 the Florida Legislature created the Surface Water Improvement and 

Management Program (SWIM) to reduce nonpoint-source pollution in Florida waters. Three 

water management districts—St. Johns River Water Management District (SJRWMD), South 

Florida Water Management District (SFWMD), and Southwest Florida Water Management 

District (SWFWMD)—began mapping seagrasses in estuaries within their jurisdictional waters.

The first seagrass maps for the Indian River Lagoon were produced in 1987 by SJRWMD and 

SFWMD. SWFWMD began seagrass mapping from Tampa Bay through northern Charlotte 

Harbor in 1988 and has continued mapping every two years. When the Tampa Bay National 

Estuary Program was established in 1991, seagrasses were designated as critical habitat, 

seagrass restoration goals were set, water quality goals were established to support seagrass 

recovery, and the SWFWMD biennial seagrass maps became the primary means of assessing 

seagrass gains and losses in Tampa Bay, Sarasota Bay, Lemon Bay, and northern Charlotte 

Harbor. The efforts in Tampa Bay and the Indian River lagoon were critical in demonstrating the 

need for regular assessment of seagrass cover and the effectiveness of seagrass mapping.

The roots of seagrass monitoring and probabilistic sampling also extend back to the 1980s. The 

U.S. Environmental Protection Agency established the Environmental Monitoring and 

Assessment Program (EMAP) in the late 1980s in an effort to move beyond point-sourcedischarge monitoring. EMAP’s initial vision was to ―monitor the condition of the Nation’s 

ecological resources, to evaluate the cumulative success of current policies and programs, and 

to identify emerging problems before they become widespread or irreversible‖ (Messer et al. 

1991). Over 20 years of operation, EMAP has developed and validated two concepts that are 

key to any ecological assessment: 1) the success of ecological monitoring depends on 

development of reliable, scientifically defensible indicators for measuring ecological health, 

integrity, and change, and 2) the success of ecological monitoring depends on logistically 

feasible and statistically valid sampling designs capable of quantifying error, bias, and predictive 

value (USEPA 1997). Seagrass scientists have taken to heart EMAP’s emphasis on reliable 

indicators of community health, and many have also adopted the spatially distributed randomsampling (SDRS) design that EMAP developed. The advantages of the SDRS design are 1) that

it prevents clumping of sample points by distributing them in an array of tessellated hexagons 

laid over the study area while 2) locating sampling points randomly within each hexagon, 

permitting the use of parametric statistics. The first seagrass monitoring programs to adopt the 

EMAP probabilistic sampling strategy were the FWRI seagrass monitoring program in Florida 

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Bay and Florida International University’s monitoring program for the newly created Florida Keys 

National Marine Sanctuary.

In light of the groundswell of interest in seagrass monitoring and the development of practical 

sampling designs, in June 2000 Ken Haddad, director of Florida FWRI, held a workshop on 

seagrass mapping and monitoring with the purpose of fostering collaboration among all 

agencies carrying out seagrass mapping and monitoring in the state. FWRI staff prepared an 

inventory of seagrass mapping and monitoring programs for the workshop. This inventory 

showed that mapping projects were carried out at different intervals and depended heavily on 

the availability of grant funds and that methodologies varied among monitoring programs.

The 2000 workshop led to the development of the Florida Seagrass Conservation Information 

System (SCIS; http://research.myfwc.com/seagrass/), an online database of seagrass mapping 

and monitoring projects hosted on the FWRI website (http://myfwc.com/research/). Almost 200 

seagrass-related projects were logged into the SCIS database from 2000 through 2003.

Projects included mapping and monitoring efforts as well as projects addressing restoration, 

education, tissue culture, and boating impacts. The workshop also led to the publication of the 

Seagrass Managers Toolbox, an effort carried out by Gerald Morrison, Ronald Phillips, and Bill 

Sargent.

Also in 2000, Gil McRae, now director of FWRI, received a five-year grant from EPA to develop 

a probabilistic monitoring program for Florida estuarine and coastal waters. The Inshore 

Monitoring and Assessment Program (IMAP) incorporated two important elements: spatially

distributed random sampling (SDRS) and nondestructive visual estimation of seagrass 

abundance. Over the course of the IMAP program, seagrass and macroalgal species 

composition and abundance were measured at more than 500 sites around the state, 

demonstrating the inferential power of spatially distributed random sampling designs. In 2002 

FWRI investigators Paul Carlson and Laura Yarbro and Suwannee River Water Management 

District staff (Rob Mattson and Louis Mantini) began a collaborative mapping and monitoring 

program for Florida’s Big Bend Region using the SDRS design. In 2004, Carlson supervised the 

collection of aerial imagery of Florida Bay to serve as a benchmark dataset against which 

changes resulting from the Comprehensive Everglades Restoration Program (CERP) might be 

measured. In 2005, Kevin Madley of FWRI supervised collection of a similar imagery set for 

Biscayne Bay. 

Finally, in 2007, Larry Handley, Diane Altsman, and Richard DeMay produced a report titled 

Seagrass Status and Trends in the Northern Gulf of Mexico: 1940–2002 (Handley et al. 2007).

This report described seagrass mapping data for 15 estuarine and lagoonal systems from Texas 

to Florida and serves as the structural model for the SIMM report.

For the report by Handley et al., Carlson and Madley summarized recent trends in seagrass 

cover in estuaries of Florida’s west coast (Carlson and Madley 2007). They reported that, of 13 

estuaries and nearshore seagrass beds assessed for the status and trends effort, eight reported 

seagrass losses over the preceding decade, three reported gains, and two had insufficient 

mapping data to allow reliable assessment. The need for a coordinated statewide seagrass 

mapping and monitoring program was obvious, and the FDEP Coastal Management Program

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(CMP) provided start-up funds for the development of the SIMM program. With FDEP-CMP 

funds over the past three years we interviewed staff and collected data from more than 30 

mapping and monitoring programs across Florida. These programs vary considerably in their 

resources and scope, but all the participants see the value of contributing their information to 

this statewide effort. Because this report is a preliminary synthesis of seagrass mapping and 

monitoring data contributed by many individuals and agencies, there are bound to be errors and 

omissions. However, this report will be issued every two years and will provide an opportunity to 

continuously correct and improve our assessments.

How this report was put together:

Development of the SIMM program at the Fish and Wildlife Research Institute began in 2007 

with information gathering about the agencies, researchers, and programs addressing the 

health and acreage of seagrasses in the coastal waters of Florida. Telephone interviews 

followed so that we could become acquainted with our collaborators and learn what was being 

done by scientists and managers involved in assessing seagrass status and trends. Then we 

began gathering data and information to produce a chapter for each region or estuary along the 

coast of Florida. This effort allowed us to pursue the long-term goals of SIMM, which include 1) 

providing a snapshot of seagrass conditions in a statewide report issued annually, with 

contributions from researchers and managers; 2) establishing a statewide program of routine 

mapping occurring at least every six years and annual monitoring for all of Florida’s seagrass 

ecosystems by partnering with the many agencies and researchers who work on seagrass 

ecosystems; and 3) eliminating gaps in monitoring and mapping, through collaboration and 

funding where possible.

This first report compiles available information on seagrasses and any omissions or gaps are 

the responsibility of the editors. For each region or estuary, we asked our contributors to provide 

text, graphics, tables, and any other materials they thought appropriate for this report. As a 

result, some chapters are organized slightly differently from others, some chapters have a great 

deal of information while regions receiving less scrutiny have less, and each chapter has a 

different flavor and emphasis, depending on the status of seagrasses and their stressors. There 

is overlap among chapters in the Pensacola and Charlotte Harbor regions. For these chapters 

this may reflect jurisdictional and research boundaries of different organizations whose staff 

contributed information, or it may result from editorial decisions for which we are solely 

responsible. We hope that readers and contributors will continue to provide us with additional 

and updated information so that we might provide a more accurate report in the next edition. In 

the future, we also hope to include in each chapter 1) more information on management 

priorities and actions; 2) information on nutrient and optical water quality where such data are 

available; and 3) summaries of seagrass species occurrence and distribution. We have limited 

information for a few subregions along Florida’s coastline for which no monitoring and mapping 

program is now under way; these gaps include the Ten Thousand Islands region in southwest 

Florida and Apalachicola and Ochlockonee bays in the Panhandle. Aerial photography of 

seagrasses in the Panhandle was completed in late 2010 and we anticipate acquiring imagery 

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for the Ten Thousand Islands in 2011. We anticipate expanding or including chapters on these 

regions as part of our next edition. As we prepare to publish this report, damage assessment 

from the 2010 Deepwater Horizon oil spill continues, and the next edition will include the 

information available on oil spill impacts.

This report is organized to provide information to a wide range of readers. Each chapter 

provides information on an estuary or subregion of Florida coastal waters, and the chapters are 

in geographical order, beginning in the western Panhandle and ending with the northern Indian 

River Lagoon on Florida’s east coast. Beneath the title of each chapter are listed the names of 

the primary contacts and information providers for that estuary or subregion. Contact 

information (e-mail addresses and telephone numbers) for these contributors is provided at the 

end of the chapter. A thumbnail map at the top of the first page of each chapter shows the 

location of the estuary or subregion along the coast of Florida. Within each chapter, content 

includes a concise and general overall assessment and color-coded ―report card‖ of seagrass 

status, as well as a map of the distribution of seagrass beds in the estuary or subregion, created 

using the latest available mapping product. 

The report card graphic provides a general assessment of the health of seagrasses and the 

nature and extent of stressors. The colored boxes convey the following:

 Green—Healthy, improving, stable conditions

 Yellow—Declining, some stress present, some threats to ecosystem health

 Orange—Measureable declines, moderate stressors or declines in seagrass cover

 Red—Large negative changes in seagrass health and stressors, either acutely over a 

short period of time, or chronically over a period of years.

A reader wanting a quick snapshot of seagrass ecosystem status within a particular estuary or 

region could use the general assessment and the first status graphic presented on the first page 

of each chapter.

Following this summary information, the geographic extent covered by the chapter is outlined, 

followed by a map showing the most recent seagrass coverage, if available, and a brief list of 

mapping, monitoring, management, and restoration recommendations. We then provide more 

in-depth information on the status and trends of seagrasses, including another color-coded 

graphic addressing seagrass status indicators, such as cover, bed texture, species composition, 

and overall status, and seagrass stress indicators, such as water clarity, nutrients, 

phytoplankton, propeller scarring, and natural and anthropogenic events. The information in this 

status graphic varies from chapter to chapter and reflects differences in seagrass ecosystems 

and stressors among Florida estuaries and coastal waters.

Using mapping data from the two most recent mapping efforts (where available) having the 

same areal extent, we provide data on the overall acreage of seagrasses and changes in areal 

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cover, along with a short discussion of what factors might be effecting these changes. In some 

chapters, acreages and change analysis are broken down by location within the estuary or bay, 

or by the texture (continuous or patchy) of seagrass beds. Using information, graphics, and 

tables provided by our contributors, we provide an assessment from ongoing monitoring 

programs. Our contributors articulated mapping, monitoring, management and restoration 

recommendations, and these are discussed in greater detail than outlined at the beginning of 

the chapter. We provide information on how the most recent mapping and monitoring data and 

aerial imagery were obtained and analyzed and where the imagery, maps, and data may be 

accessed. Any pertinent technical or scientific reports or peer-reviewed publications are listed,

along with general references, websites, and additional information. 

LITERATURE CITED

CARLSON, P. R., and K. MADLEY

2007. Statewide summary for Florida. Pp. 99–114 in L. Handley et al., eds. Seagrass status 

and trends in the northern Gulf of Mexico, 1940–2002. United States Geological Survey 

Scientific Investigations Report 2006-5287 and U.S. Environmental Protection Agency 855-R04-003, Washington, D.C. 267 p.

CARLSON, P. R., L. A. YARBRO, K. K. KAUFMAN, and R. A. MATTSON. 2010. Vulnerability 

and resilience of west Florida seagrass communities to hurricane impacts. Hydrobiologia 649: 

39–53. 

COSTANZA, R., R. D’ARGE, R. DE GROOT, S. FARBER, M. GRASSO, B. HANNON, S. 

NAEEM, K. LIMBURG, J. PARUELO, R. V. O’NEILL, et al.

1997. The values of the world’s ecosystem services and natural capital. Nature 387: 253–260.

HANDLEY, L., D. ALTSMAN, and R. DEMAY

2007. Seagrass status and trends in the northern Gulf of Mexico, 1940–2002. United States 

Geological Survey Scientific Investigations Report 2006-5287 and U.S. Environmental 

Protection Agency 855-R-04-003, Washington, D.C. 267 p.

MESSER, J. J., R. A. LINTHURST, and W. S. OVERTON 

1991. An EPA program for monitoring ecological status and trends. Environmental Monitoring 

Assessment 17: 67–78.

ORTH, R. J., et al. 

2006. A global crisis for seagrass ecosystems. Bioscience 56: 987–996.

[USEPA] U.S. ENVIRONMENTAL PROTECTION AGENCY

1997. Environmental Monitoring and Assessment Program: research strategy. EPA/620/R98/001. Office of Research and Development, U.S. EPA, Washington, D.C. 18 p.

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WAYCOTT, M., C. M. DUARTE, T. J. B. CARRUTHERS, R. J. ORTH, W. C. DENNISON, S. 

OLYARNIK, A. CALLADINE, J.W. FOURQUREAN, K. L. HECK JR., A. R. HUGHES et al.

2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. 

Proceedings of the National Academy of Sciences of the United States of America 106: 12377–

12381.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Perdido Bay

Contacts: Ken Heck and Dorothy Byron, Dauphin Island Sea Laboratory, 

and Shelley Alexander, Northwest Florida Department of Environmental 

Protection (Monitoring)

General Assessment: Seagrasses in Perdido Bay are primarily shoal grass (Halodule wrightii) 

and diminished in area 80% between 1987 and 2002. In 2002 approximately 125 acres of 

seagrass remained. The 2004 storm season showed few short-term effects on seagrasses. The 

Deepwater Horizon oil spill affected the bay, particularly near the inlet on the eastern side.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining 82% loss, 1987-2002

Water clarity No information

Geographic Extent: Perdido Bay is the westernmost estuary of the Florida Panhandle and is 

located inside the barrier bar adjacent to the Gulf of Mexico. The study area begins at the 

Alabama–Florida state line to the west, extends east to Sunset Pass, and wraps around to 

include Kees Bayou and Russell Bayou along the northern section of the bay.

Figure 1. Seagrass map of Perdido Bay.

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Mapping and Monitoring Recommendations

• As part of damage assessment of the Deepwater Horizon oil spill, high-resolution aerial 

photography was acquired for the entire northern Gulf coast in October 2010. 

Photointerpretation of the imagery is under way, and the new mapping data will be used to

conduct change analysis and assessment of seagrass trends. 

• A monitoring program should be implemented to evaluate seagrass beds annually.

Management and Restoration Recommendations

• Damage that resulted from the Deepwater Horizon oil spill should be evaluated.

• If necessary, a restoration plan should be drafted and implemented. 

• Seagrass beds in high-use areas should be monitored for propeller scarring.

Summary Assessment: Mapping data from 1987 and 2002 show large-scale losses (80%) of 

seagrasses in Perdido Bay (Table 1). In 2002, only 125 acres of seagrass were mapped, and 

most of the beds were composed of shoal grass. A study of the short-term effects of the 2004 

hurricane season found that seagrasses tolerated these storms well. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining 80% loss, 1987-2002

Seagrass meadow texture Stable?

Seagrass species composition Variable Runoff from storms

Overall seagrass trends Declining

Seagrass Stressors Intensity Impact Explanation

Water clarity

Nutrients

Phytoplankton

Natural events Hurricanes; 2010 El Niño

Propeller scarring

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Seagrass Mapping Assessment: Most of the seagrass beds surveyed in 1987 had 

disappeared by 2002. Interpretation of aerial photography acquired in 2010 will evaluate current 

trends in seagrass cover. 

TABLE 1. SEAGRASS ACREAGE IN

PERDIDO BAY IN 1987 AND 2002

1987 2002 Change % Change

642 125 −517 −80.5

Monitoring Assessment: No monitoring program is in place. Some seagrass transplant sites 

are monitored by the Northwest Florida Department of Environmental Protection (NW FDEP). 

Mapping and Monitoring Recommendations

• An annual monitoring program should be established. 

• Aerial imagery of seagrass beds should be routinely acquired and photointerpreted.

Management and Restoration Recommendations

• Damage that resulted from the Deepwater Horizon oil spill should be evaluated.

• If necessary, a restoration plan should be drafted and implemented. 

• Seagrass beds in high-use areas should be monitored for propeller scarring.

Mapping Data and Imagery: In 2002, the Mobile Bay National Estuary Program surveyed 

submerged aquatic vegetation (SAV) using photointerpreted and ground-truthed aerial imagery, 

producing a map of SAV habitat. 

Monitoring Data: No routine monitoring program has been established, but the NW FDEP

continues to monitor seagrass transplant sites in the bay. 

Deepwater Horizon Oil Spill Addendum: The mouth of Perdido Bay and some areas in the 

eastern portion of the bay received repeated onslaughts of weathered oil, mousse, tar paddies, 

and tar balls during summer 2010. In particular, a location just inside and to the west of the inlet 

has persistent submerged oil (Shelley Alexander, personal communication). Perdido Bay, along 

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with Pensacola Bay and Santa Rosa Sound, continues to be evaluated for impacts of the oil 

spill, and beaches and shores along these bays are closely monitored for oil-related materials 

and are subject to clean-up operations.

Pertinent Reports and Scientific Publications

BYRON, D., and K. L. HECK. 2006. Hurricane effects on seagrasses along Alabama’s Gulf 

coast. Estuaries and Coasts 29: 939–942.

VITTOR AND ASSOCIATES INC. 2004. Mapping of submerged aquatic vegetation in Mobile 

Bay and adjacent waters of coastal Alabama. Final report to the Mobile Bay National Estuary 

Program. Mobile, Alabama. 30 p.

General References and Additional Information

FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION, NORTHWEST DISTRICT.

Seagrass Restoration Data and Maps, 

http://www.floridadep.org/northwest/ecosys/section/seagrassmaps.htm, accessed March 2011.

Contacts 

Monitoring:

Ken Heck and Dottie Byron, Dauphin Island Sea Laboratory, 251-861-2141, kheck@disl.org and 

dbyron@disl.org.

Shelley Alexander, Northwest Florida office of the Department of Environmental Protection, 850-

983-5359, Shelley.alexander@dep.state.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Pensacola Bay and Santa Rosa Sound

Contacts: Michael Lewis, U.S. Environmental Protection Agency, Gulf 

Breeze, Florida (Monitoring and Mapping)

General Assessment: Between 1950 and 1980, about 95% of seagrass habitat was lost in this 

coastal region of the far western Panhandle of Florida. In 2003, mapped seagrass covered 511 

acres in the Pensacola Bay System and 3,032 acres in Santa Rosa Sound. Seagrass mapping 

data from 1992 and 2003 show a loss of seagrass acreage of about 43% in the Pensacola Bay 

System and a gain of almost 10% in Santa Rosa Sound. During recent surveys, seasonal 

hypoxia was found to affect as much as 25% of the bottom area. Portions of the bay, particularly 

those in the vicinity of Pensacola Pass and Gulf Breeze, were repeatedly exposed to Deepwater 

Horizon oil product during summer 2010. Damage assessment is ongoing.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Declining Losses, hypoxia

Seasonal hypoxia Continuing Natural phenomena

Geographic Extent: The Pensacola Bay System is located in the western Florida Panhandle. It 

includes Escambia Bay, East Bay, and Pensacola Bay. Santa Rosa Sound is the lagoon south 

of the Pensacola Bay System. 

Mapping and Monitoring Recommendations

• Implement a regular monitoring program. 

• Photointerpret and map photographs taken to evaluate effects of the Deepwater Horizon oil 

spill. High-resolution aerial photography was obtained in October 2010. Photointerpretation is 

under way, and the new mapping data will be used to conduct change analysis and assessment 

of seagrass trends. 

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Figure 1. Seagrass cover in Pensacola Bay and Santa Rosa Sound, 2003.

Management and Restoration Recommendations

• Assess the extent and effects of seasonal hypoxia and the long-term effects of salinity 

changes in the upper regions of the Pensacola Bay System. 

• Evaluate injury to seagrasses caused by to the 2010 Deepwater Horizon oil spill and plan 

restoration. 

Summary Assessment: Significant losses in seagrass acreage have occurred in the past 60 

years. Between 1992 and 2003, the Pensacola Bay System lost approximately 43% of its 

seagrass area, while seagrass area in Santa Rosa Sound increased almost 10%. However, 

significant species changes occurred in Escambia Bay because higher salinities eliminated 

beds of American eelgrass (Vallisneria americana) and widgeon grass (Ruppia maritima). 

Seagrass beds in Santa Rosa Sound are dominated by turtle grass (Thalassia testudinum) and 

with some shoal grass (Halodule wrightii) present, but beds appear stunted and sparse. 

Seasonal hypoxia, with resulting elevated levels of sediment sulfides, is considered a 

contributing factor to ongoing losses and poor seagrass bed texture.

The decline in seagrass acreage between 1950 and 1980 has been attributed to poor water 

quality due to industrial pollution and perhaps harbor dredging (Olinger et al. 1975). However, 

since 2000 water clarity has been relatively high, and nutrient concentrations and chlorophyll 

levels have been low. Koch (2001) reported that seagrasses were absent from many locations 

where light was sufficient for their growth. 

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Losses, hypoxia

Seagrass meadow texture Poor growth Mortality, stunted, sparse

Seagrass species 

composition Little change Salinity changes, high sulfide levels

Overall seagrass trends Declining Salinity changes, high sulfide levels

Seagrass Stressors Intensity Impact Explanation

Water clarity Some improvement Poor in some areas

Nutrients Good Low levels, little runoff

Phytoplankton Good Low levels

Natural events N/A

Propeller scarring N/A

Seasonal hypoxia Continuing High sulfide levels

Seagrass Mapping Assessment: Between 1992 and 2003, total seagrass cover for the 

Pensacola Bay System declined 43%, from 894 to 511 acres, all in the upper reaches of 

Escambia Bay and East Bay, primarily due to increased salinity (Table 1). Losses in the upper 

system were partly offset by a gain of 91 acres in southern Pensacola Bay. Between 1992 and 

2003, seagrass beds in Santa Rosa Sound increased by 272 acres, to 3,032 acres, an increase 

of almost 10%. These beds are composed primarily of turtle grass along with some shoal grass, 

but seagrasses are sparse and stunted. 

TABLE 1. ACREAGE OF SEAGRASS HABITAT AREA (ACRES)

Basin 1992 2003 Change % Change

Total Pensacola Bay System 892 511 −381 −43

Escambia Bay 440 111 −329 −75

East Bay 170 27.2 −143 −84

Pensacola Bay 282 373 91 32

Santa Rosa Sound 2,760 3,032 272 9.9

Monitoring Assessment: Routine monitoring is not being conducted in this region. The City of 

Gulf Breeze has contracted Heather Reed, of Ecological Consulting Services Inc., to conduct 

seagrass restoration and follow-up monitoring near Deadman’s Island in Pensacola Bay.

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Mapping and Monitoring Recommendations

• Implement a routine monitoring program. 

• Obtain aerial photography and mapping data, particularly for evaluation of impacts of the 

2004–05 hurricanes and the 2010 Deepwater Horizon oil spill. 

Management and Restoration Recommendations 

• Assess the extent and effects of seasonal hypoxia and the long-term effects of salinity 

changes in the upper regions of the Pensacola Bay System. 

• Evaluate nutrient levels and inputs, particularly since any additional stress due to increased 

light attenuation or excessive nutrients could exacerbate seagrass losses. 

• Assess damage due to the 2010 Deepwater Horizon oil spill; plan and carry out restoration as 

needed.

Mapping Data and Imagery: Seagrass acreage data from photointerpretation of aerial imagery 

were obtained from the U.S. Geological Survey National Wetlands Research Center, Lafayette, 

Louisiana.

Monitoring Data: None are available.

2010 Deepwater Horizon Oil Spill Addendum: Oil and oil product from the spill impacted 

Pensacola Bay beginning in mid-June 2010 and continued through most of July. Portions of the 

bay near Pensacola Pass, the Gulf Breeze shoreline areas, Barrancas Beach, and Fort Pickens 

Park received oil impacts. In addition, certain responses to the spill, such as booming and 

vessel use, may have damaged seagrass beds, particularly those near the Pass.

Pertinent Reports and Scientific Publications

HAGY, J. D., J. C. KURTZ, and R. M. GREENE. 2008. An approach for developing numerical 

nutrient criteria for a Gulf coast estuary, U.S. Environmental Protection Agency, Office of 

Research and Development, National Health and Environmental Effects Research Laboratory, 

Research Triangle Park, North Carolina. EPA/600/R-08/004. 44 p. 

KOCH, E. W. 2001. Beyond light: physical, geological, and geochemical parameters as possible 

submersed aquatic vegetation habitat requirements. Estuaries 24(1): 1–17.

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LEWIS, M. A., R. DEVEREUX, and P. BOURGEOIS. 2008. Seagrass distribution in the 

Pensacola Bay System, northwest Florida. Gulf and Caribbean Research 20: 21–28.

OLINGER, L. W., R. G. ROGERS, P. L. FORE, R. L. TODD, B. L. MULLINS, F. T. 

BISTERFIELD, and L. A. WISE. 1975. Environmental and recovery studies of Escambia Bay 

and the Pensacola Bay System, Florida. U.S. Environmental Protection Agency, Atlanta, 

Georgia. 904/9-76-016. 468 p.

SCHWENNING, L., T. BRUCE, and L. W. HANDLEY. 2007. Pensacola Bay. Pp. 129–142 in:

Handley, L., D. Altsman, and R. DeMay (eds.). Seagrass status and trends in the northern Gulf 

of Mexico: 1940–2002. U.S. Geological Survey Scientific Investigations Report 2006-5287 and 

U.S. Environmental Agency 855-R-04-003. 267 p.

General References and Additional Information

Pensacola Bay, GulfBase.org: http://www.gulfbase.org/bay/view.php?bid=pensacola, accessed 

March 2011.

Pensacola Bay Watershed, Florida’s Water Ours to Protect: 

http://www.protectingourwater.org/watersheds/map/pensacola/, accessed March 2011.

Project Greenshores Phase 1 nears completion, City of Pensacola: 

http://www.ci.pensacola.fl.us/live/pages.asp?pageID=1671, accessed March 2011.

Seagrass Restoration Data and Maps, Northwest District FDEP: 

http://www.dep.state.fl.us/northwest/ecosys/section/seagrassmaps.htm, accessed March 2011.

Contacts

Mapping: Michael Lewis, U.S. Environmental Protection Agency, Gulf Ecology Division, Gulf 

Breeze, Florida, 850-934-9382, lewis.michael@epa.gov.

Monitoring (and 2010 Deepwater Horizon oiling information): Heather Reed, Ecological 

Consulting Services Inc., Pensacola, Florida, 850-417-7008, 

hreed@ecoconsultingservices.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Santa Rosa Sound and Big Lagoon

Contacts: Amy Baldwin Moss, Florida Department of Environmental 

Protection, Northwest District (Monitoring and Mapping)

General Assessment: Seagrass beds in Santa Rosa Sound and Big Lagoon appear stable in 

area. In 2003, mapping from aerial photography found 3,032 acres of seagrass in Santa Rosa 

Sound and 543 acres in Big Lagoon. Seagrass beds in southern Santa Rosa Sound/Big Lagoon 

[along the Gulf Islands National Seashore (GINS)] are prone to sediment burial from 

unconsolidated sand carried in from nearby barrier islands. In 2009, the Florida Department of 

Environmental Protection’s (FDEP) Ecosystem Restoration Program (ERS) found that as much 

as 9 cm of sand had been deposited (timeframe unknown) on monitored transplanted plots 

adjacent to Johnson’s Beach (GINS). The FDEP ERS maintains in the area an active seagrass 

salvage program that relocates seagrasses about to be destroyed by marine construction to 

areas in which seagrasses are in need of restoration. Areas of Big Lagoon and Santa Rosa 

Sound near Pensacola Pass were repeatedly exposed to oil product from the Deepwater 

Horizon spill during the summer of 2010. Damage assessment of seagrass beds is ongoing. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Stable

Water clarity Good

Nutrients Good Low levels, little runoff

Phytoplankton Good Low levels

Propeller scarring

Geographic Extent: Big Lagoon covers approximately 18 sq. mi. and connects Perdido and 

Pensacola bays. Santa Rosa Sound is east of Big Lagoon and is approximately 27,160 acres in 

area. It connects Choctawhatchee Bay to the east and Pensacola Bay to the west. Big Lagoon 

and Santa Rosa Sound are separated by Pensacola Pass, which is open to the Gulf of Mexico. 

County political boundaries separate Big Lagoon in Escambia County and Santa Rosa Sound in 

Santa Rosa and Okaloosa counties.

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Figure 1. Seagrass cover in Santa Rosa Sound, 2003.

 Figure 2. Seagrass cover in Big Lagoon, 2003.

Mapping and Monitoring Recommendations

• Establish an annual monitoring program to assess changes in nutrient loads in northern Santa 

Rosa Sound, which receives urban runoff.

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Management and Restoration Recommendations

• Assess the relationship between development pressures and storm runoff, scarring, 

sedimentation, and construction activities.

• Restore hurricane-related sediment-burial areas along the southern shoreline of Santa Rosa 

Sound (off Pensacola Beach).

• Restore vegetation of adjoining nonvegetated dune areas on the barrier islands.

• Continue assessing damage from the 2010 Deepwater Horizon oil spill, and initiate restoration 

program.

Summary Assessment: Seagrass beds in Santa Rosa Sound and Big Lagoon are considered 

stable, based on the limited information available. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Stable

Seagrass meadow texture Stable

Seagrass species composition Stable

Overall seagrass trends Stable

Seagrass Stressors Intensity Impact Explanation

Water clarity Good Improving

Nutrients Good Low levels, little runoff

Phytoplankton Good Low levels

Natural events Possible Hurricanes

Propeller scarring

Seagrass Mapping Assessment: Based on mapping data from aerial photography in 1992 and 

2003, the area of seagrass beds in Santa Rosa Sound and Big Lagoon has increased. In 1992, 

there were 2,760 acres of seagrass in Santa Rosa Sound; by 2003 acreage had increased to 

3,032 acres, or 9.9% (Table 1). In 1992, Big Lagoon had 537 acres of seagrass; in 2003, 543 

acres were mapped, an increase of 6 acres, or 1%. 

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TABLE 1. SEAGRASS ACREAGE IN SANTA ROSA SOUND 

AND BIG LAGOON IN 1992 AND 2003

1992 2003 Change % Change

Santa Rosa Sound

Total 2,760 3,032 272 9.9%

Big Lagoon

Continuous 372 401 29 7.9%

Patchy 166 143 −23 −13.7%

Total 538 544 7 1.3%

Monitoring Assessment: There is no monitoring program at present, but Paul Carlson 

collected field and seagrass percentage cover data from portions of Big Lagoon and Santa 

Rosa Sound in June 2010 as part of the baseline sampling effort associated with the Deepwater 

Horizon oil spill. This sampling effort targeted seagrass beds near the Pensacola inlet, which 

are parallel to the northern and southern shores of these bays. Therefore, seagrass beds in 

western Big Lagoon and eastern Santa Rosa Sound were not evaluated. Turtle grass (Thalassia 

testudinum) was the most common species of seagrass in eastern Big Lagoon, and shoal grass 

(Halodule wrightii) was the most common species at the Fort Pickens and Gulf Breeze sites in 

Santa Rosa Sound near the Pensacola inlet. Manatee grass (Syringodium filiforme) was the 

least common at all three sites; however, drift red algae were present in 15–45% of all sampling 

locations.

Figure 3. Percentage

occurrence of seagrasses 

in Big Lagoon and near 

Fort Pickens and Gulf 

Breeze in Santa Rosa 

Sound, June 2010.

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Mapping and Monitoring Recommendations

• Implement a routine monitoring program, which is acutely needed in light of oil impacts from 

the 2010 Deepwater Horizon spill. Monitoring data were collected from 1999–2001 to produce a 

seagrass management plan, and some monitoring was conducted in 2002 as well. 

• Photointerpret aerial photography acquired in 2009 and 2010 to update seagrass maps and 

acreage estimates.

Management and Restoration Recommendations

• Address potential increases in nutrients in coastal waters and sources of nutrients. 

• Minimize propeller scarring and conduct restoration efforts in areas with the greatest impacts. 

• Address sedimentation from unconsolidated sand on adjacent GINS barrier island areas 

through vegetative restoration of dunes. 

• Continue assessment of damage from the 2010 Deepwater Horizon oil spill, especially for 

seagrass beds near Pensacola Pass (Fort Pickens, south shore of Gulf Breeze, Robertson 

Island).

Mapping Data and Imagery: Seagrass data were derived from interpretation of color infrared 

photography taken in 2003. These images were mapped at 1:12,000 scale on hard copies that 

were rectified to U.S. Geological Survey (USGS) digital orthophoto quarter quadrangle base 

maps and were digitized at the USGS National Wetlands Research Center (NWRC). The 

seagrass beds were classified according to a USGS NWRC-derived classification scheme 

based on the Coastal Change Analysis Project (C-CAP) Coastal Land Cover Classification 

system of the National Oceanic and Atmospheric Administration. In assessing damage from the 

2010 Deepwater Horizon oil spill, high-resolution aerial photography of the entire northern Gulf 

coast was obtained in October 2010. This area will be reflown in April 2011. 

Monitoring Data: Project specific monitoring in 1999–2001 and 2002; no current monitoring 

program. 

2010 Deepwater Horizon Oil Spill Addendum: Portions of western Santa Rosa Sound were 

affected by weathered oil entering Pensacola Pass during the summer of 2010. The southern 

and western shores of Gulf Breeze were oiled several times. The far eastern portions of Big 

Lagoon also received oil, particularly those near Robertson Island. Assessment of the impacts is 

ongoing.

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Pertinent Reports and Scientific Publications

JOHNSON, M. W., K. L, HECK JR., and J. W. FOURQUREAN. 2006. Nutrient content of 

seagrasses and epiphytes in the northern Gulf of Mexico: evidence of phosphorus and nitrogen 

limitation. Aquatic Botany 85: 103–111.

LORES, E. M., E. PASKO, J. M. PATRICK, R. L. QUARLES, J. CAMPBELL, and J. 

MACAULEY. 2000. Mapping and monitoring of submerged aquatic vegetation in EscambiaPensacola Bay system, Florida. Gulf of Mexico Science 18: 1–14.

General References and Additional Information

Seagrass Management Plan for Big Lagoon and Santa Rosa Sound (2001):

http://www.epa.gov/gmpo/habitat/seagrassplan.html, accessed March 2011.

Flora and Fauna of Northwest Florida: http://uwf.edu/rsnyder/ffnwf/seagras/seagras.html,

accessed March 2011.

Seagrass Management Plan for Big Lagoon and Santa Rosa Sound, GulfBase.org: 

http://www.gulfbase.org/project/view.php?pid=smpfblasrs, accessed March 2011.

Contacts

Mapping and Monitoring: Amy Baldwin Moss, Florida Department of Environmental Protection, 

Northwest District, 850-595-8300, amy.baldwin@dep.state.fl.us.

2010 Deepwater Horizon Oil Spill Information: Heather Reed, Ecological Consulting Services 

Inc., Pensacola, Florida, 850-417-7008, hreed@ecoconsultingservices.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Choctawhatchee Bay

Contacts: Alison McDowell, Choctawhatchee Bay Alliance, Northwest Florida State College, 

and Paul Carlson, Fish and Wildlife Research Institute (Monitoring); Larry Handley, U.S. 

Geological Survey (Mapping); and Shelley Alexander, Florida Department of Environmental

Protection (Management)

General Assessment: In 1992, seagrasses covered 4,261 acres in Choctawhatchee Bay. In 

2003, total seagrass cover had decreased to 2,623 acres, a loss of 38%. In 2003, only 2% of 

the bay’s total bottom area of 133,300 acres was covered with seagrass. Of the seagrass 

mapped in Choctawhatchee Bay in 1992, 83% was located in the western bay. In 2003, that 

percentage was even greater. No seagrass was observed in the eastern segment during 

mapping in 2003. In 1992, the submerged aquatic vegetation (SAV) in the eastern segment was 

largely composed of brackish species—widgeon grass (Ruppia maritima) and tape grass 

(Vallisneria americana)—and these species are vulnerable to fluctuations in salinity and turbidity 

related to rainfall and runoff. Heavy winter rainfall in 2009 caused significant animal mortality 

and also may have affected seagrasses. Heavy rainfall also occurred in fall 2009 and winter 

2010, associated with an El Niño.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Declining Losses, storm runoff

Water clarity Declining?

Natural events Impacts Hurricanes, El Niño

Propeller scarring Negligible Little impact

Geographic Extent: The eastern half of Choctawhatchee Bay is in Walton County, and the 

western half is in Okaloosa County. The bay is divided by bridges into three segments: the 

western segment, which lies west of the U.S. 293 bridge crossing the middle of the bay; the 

eastern segment, which lies east of the SR331 bridge; and the middle segment, which lies 

between the two bridges. Roughly 75% of the seagrass mapped in Choctawhatchee Bay in 

1992 was located in the western segment.

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Mapping and Monitoring Recommendations 

• Continue the regular monitoring program begun in 2009 by the Fish and Wildlife Research 

Institute (FWRI). 

• Photointerpret aerial photographs of seagrass acquired in spring 2010 and, as part of oil spill 

damage assessment, in October 2010. Photointerpretation and mapping of the spring 2010 

photography began in early 2011.

Figure 1. Seagrass cover in Choctawhatchee Bay, 2003.

Management and Restoration Recommendations

• Continue to monitor water quality in the bay and in rivers and streams contributing runoff to the 

bay.

• Work with regional and state agencies to evaluate and institute controls of quantity and quality 

of storm runoff entering the bay. 

Summary Assessment: Based on seagrass data from 1992 and 2003, 38% of seagrass beds 

were lost from Choctawhatchee Bay during this 11-year period, and most of the remaining 

seagrass beds are located in the western bay. Losses in the western portions of the bay are 

attributed to hurricane and storm overwash and high wave energy. Submerged aquatic 

vegetation species mapped in 1992 in the eastern bay grow in brackish regions and are 

sensitive to variations in salinity and to storm runoff. In addition, increased colored dissolved 

organic matter (CDOM) in stream runoff has reduced water clarity and continues to contribute to 

seagrass losses in the eastern bay. Heavy rainfall associated with the 2009–10 El Niño may 

have resulted in further reductions in seagrass cover in this system.

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Losses, storm runoff

Seagrass meadow texture Declining?

Seagrass species composition Significant 

change Salinity changes

Overall seagrass trends Declining Salinity changes, storm runoff

Seagrass Stressors Intensity Impact Explanation

Water clarity Declining? Storm runoff

Nutrients Good

Phytoplankton Good Low levels

Natural events Impacts Hurricanes, El Niño

Propeller scarring Negligible Little impact

Seagrass Mapping Assessment: Seagrass acreage decreased from 1992 through 2003, 

especially in the eastern portions of the bay, where freshwater runoff caused almost complete 

losses of the brackish-water widgeon grass and tape grass (Table 1). Impacts from hurricanes 

and El Niño may continue this trend. 

TABLE 1.SEAGRASS ACREAGE IN

CHOCTAWHATCHEE BAY IN 1992 AND 2003

1992 2003 Change % Change

4,261 2,623 −1,638 −38.4

Monitoring Assessment: Monitoring was begun in summer 2009. Where seagrass is present, 

shoal grass (Halodule wrightii) is the most abundant seagrass in Choctawhatchee Bay. Turtle 

grass (Thalassia testudinum) occurs at a few sites near the western end of the bay and at the 

entrance to Santa Rosa Sound. In 2009, 493 0.25-m

2

quadrats were evaluated for the presence 

of seagrasses. Of those, 76% were bare, and shoal grass was found in the remaining 24%. As 

shown in Figure 2, below, seagrass, for the most part, is limited to the western half of

Choctawhatchee Bay. This pattern of distribution could be related to a strong, corresponding 

gradient in water clarity. Seagrasses are also limited to shallow water in Choctawhatchee Bay. 

We found shoal grass near many locations for which seagrass was mapped in 2003, and we did 

not find seagrass where it was not mapped in 2003. There is one large continuous seagrass

bed immediately inside the inlet at Destin and another at the west end of the bay along the 

Intracoastal Waterway entrance to Santa Rosa Sound. Other beds within the bay are very 

patchy.

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Figure 2. Location of seagrasses and water clarity in Choctawhatchee Bay, 2009.

Mapping and Monitoring Recommendations

• Continue the monitoring program begun in the summer of 2009. 

• Photointerpret spring 2010 imagery for mapping to evaluate impacts of the 2004–05 

hurricanes and the 2009–10 El Niño. 

Management and Restoration Recommendations

• Assess the effects of storm-related reductions in salinity and increases in CDOM on survival of 

brackish-water seagrass in the eastern bay. 

Mapping Data and Imagery: Seagrass data were derived from interpretation of color infrared 

photography taken in 2003. These images were mapped at 1:12,000 scale, rectified to U.S. 

Geological Survey (USGS) digital orthophoto quarter quadrangle base maps, and digitized at 

the USGS National Wetlands Research Center (NWRC). The seagrass beds were classified 

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according to a USGS NWRC-derived classification scheme based on the Coastwatch Change 

Analysis Project Coastal Land Cover Classification system of the National Oceanic and 

Atmospheric Administration. 

Monitoring Data: Monitoring was initiated in summer 2009 by FWRI staff, and data are 

available by contacting Paul Carlson. 

2010 Deepwater Horizon Oil Spill Addendum: Fortunately, Choctawhatchee Bay was not 

directly affected by oil or oil products from the spill, except for occasional tar balls washing into 

the inlet of the bay. However, as in all estuaries along the northern Gulf coast, response 

activities were extensive, and impacts from oil containment booms and vessels are being 

evaluated. 

Pertinent Reports and Scientific Publications

RUTH, B., and L. R. HANDLEY. 2006. Choctawhatchee Bay. Pp. 143–153 in Handley, L., D. 

Altsman, and R. DeMay (eds.). Seagrass status and trends in the northern Gulf of Mexico: 

1940–2002. U.S. Geological Survey Scientific Investigations Report 2006-5287 and U.S. 

Environmental Agency 855-R-04-003. 267 p.

LEWIS, M. A., D. D. DANTIN, C. A. CHANCY, K. C. ABEL, and C. G. LEWIS. 2007. Florida 

seagrass habitat evaluation: a comparative survey for chemical quality. Environmental Pollution 

146: 206–218.

General References and Additional Information

Seagrass Habitat in the Northern Gulf of Mexico: 

http://gulfsci.usgs.gov/gom_ims/pdf/pubs_gom.pdf.

Choctawhatchee Basin Alliance, http://www.basinalliance.org/, accessed March 2011.

Proposed Nutrient Criteria for Choctawhatchee Bay, by Ashley O’Neal, FDEP: 

http://www.dep.state.fl.us/water/wqssp/nutrients/docs/estuarine/tallahassee/choctawhatchee_ba

y_082410.pdf, accessed March 2011.

Seagrass Restoration Data and Maps, Northwest District FDEP: 

http://www.dep.state.fl.us/northwest/ecosys/section/seagrassmaps.htm, accessed March 2011.

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Contacts

Mapping: Larry Handley, Ph.D., U.S. Geological Survey National Wetland Research Center, 

Lafayette, Louisiana, 318-266-8691, larry_handley@usgs.gov.

Monitoring: Alison McDowell, Choctawhatchee Basin Alliance, 850-729-6423, 

mcdowel2@nwfstatecollege.edu; Shelley Alexander, Florida Department of Environmental 

Protection, 850-983-5359; shelley.alexander@dep.state.fl.us. 

Management: Shelley Alexander (see above)

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for St. Andrew Bay

Contacts: Linda Fitzhugh, Gulf Coast Community College (Monitoring); 

Larry Handley, U.S. Geological Survey (Mapping); and Shelley 

Alexander, Florida Department of Environmental Protection (Management)

General Assessment: In 2003, seagrasses covered 11,232 acres in St. Andrew Bay, and 

between 1992 and 2003 seagrass acreage increased 14%. Cover increased throughout the 

bay, but the greatest areal and fractional increases occurred in West Bay (585 acres, 30%). 

Based on aerial photos taken in 1953 and 1992, however, West Bay lost 49% of its seagrasses, 

or 1,853 acres over a 49 year period. Heavy winter rainfall in 2009 caused significant animal 

mortality and may also have affected seagrasses. Heavy rainfall associated with an El Niño 

event also occurred in fall 2009 and winter 2010.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing Throughout bay

Water clarity Variable

Nutrients Variable Low levels, except West Bay

Phytoplankton Variable Low levels, except West Bay

Propeller scarring Significant All shallow areas

Geographic Extent: St. Andrew Bay is located in Bay County in the Florida Panhandle. It 

consists of five segments: West Bay, North Bay, St. Andrew Bay proper, East Bay, and St. 

Andrew Sound. 

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Figure 1. Seagrass cover in St. Andrew Bay, 2003.

Mapping and Monitoring Recommendations

• Interpret aerial photography completed in spring 2010 and high-resolution aerial images 

obtained in October 2010 as part of damage assessment following the 2010 Deepwater Horizon 

oil spill. Photointerpretation of the spring 2010 imagery began in 2011. 

• Continue and expand seagrass and water-quality monitoring. Monitoring occurs in the fall in 

two main areas of the bay: St. Andrew Bay (SAB), behind Shell Island, and in West Bay Bowl 

(WBBOWL), below the Intracoastal Waterway. Five permanent transects are sampled in SAB, 

and four permanent transects are sampled in WBBOWL. The St. Andrew Bay Resource 

Management Association also has three permanent transects in West Bay Arm (WBARM), two 

between Crooked and Burnt Mill creeks and a third on the opposite side of the bay, and annual 

monitoring will eventually incorporate these stations. Most of the sites in SAB and WBBOWL 

have been monitored since 2000. Water quality has been monitored in the entire St. Andrew 

Bay system since 1990, and data analysis comparing the water quality of WBBOWL, WBARM, 

and SAB has been completed. Increasing the number of permanent transects in the St. Andrew 

Bay system would help determine the impacts of upland development on this pristine 

ecosystem. Upland development in the West Bay watershed will be substantial in the next 

several decades as approximately 35,000 acres of forest and wetlands are converted to 

residential, commercial, and industrial use. 

Management and Restoration Recommendations

• Assess changes in nutrient loads in WBBOWL once wastewater effluent is removed 

(scheduled for winter of 2010).

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• Assess changes in seagrass coverage in West Bay, especially WBARM, with the completion 

of the new international airport. The drainage system of the new airport feeds into Crooked and 

Burnt Mill creeks. 

• Facilitate a joint project between the St. Andrew Bay Resource Management Association and 

the Florida Department of Environmental Protection, Pensacola office, to study transplantation 

into WBBOWL of seagrasses salvaged from dock construction sites.

• Continue assessment of damage to seagrass beds, particularly those located near the inlet to 

the Gulf of Mexico, as a result of the response (booming, barrier construction, vessel transits) to

the 2010 Deepwater Horizon oil spill. This work is being done by the National Oceanic and 

Atmospheric Administration (NOAA).

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing Throughout bay

Seagrass meadow texture Stable Hurricanes, tropical storms

Seagrass species composition Stable Changing over time

Overall seagrass trends Increasing Possible winter storm impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Variable

Nutrients Variable Low levels, except West Bay

Phytoplankton Variable Low levels, except West Bay

Natural events Possible Winter rains

Propeller scarring Significant All shallow areas

Summary Assessment: Based on data gathered in 1992 and 2003, seagrasses increased in 

cover in St. Andrew Bay (Table 1). However, tropical storms in 2004 and 2005 and increasing 

watershed development may have impacted seagrasses since the last mapping effort. In 

particular, the West Bay may be most vulnerable to increasing nutrient inputs due to changes in 

watershed use and ensuing phytoplankton blooms. Propeller scarring is extensive in all shallow 

areas in the bay system.

Seagrass Mapping Assessment: Seagrass beds in St. Andrew Bay expanded during the 

period from 1992 to 2003, with most of the increase creating continuous beds (2,205 acres). 

Patchy seagrass beds, however, decreased in size (804 acres). On a percentage basis, the 

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greatest increase occurred in West Bay, and continuous beds increased by 1,495 acres. Areas 

showing the least change in seagrass were North Bay and St. Andrew Sound. In East Bay in 

particular, mapping data indicate that about half of the continuous beds in 1992 were patchy in 

2003. Aerial photography scheduled for 2010 will provide an update on seagrass acreage and 

the effects of the storms of 2004 and 2005 and increasing development on seagrasses. 

TABLE 1. SEAGRASS ACREAGE IN ST. ANDREW BAY IN 1992 and 2003

East Bay North Bay

St. Andrew 

Sound

St. Andrew 

Bay West Bay Total

2003

Continuous 960 1,638 247 1,862 1722 6,429

Patchy 1,763 338 690 1,197 815 4,803

All seagrass 2,724 1,975 937 3,060 2,537 11,232

1992

Continuous 1,631 988 54 1,324 227 4,224

Patchy 890 877 857 1,258 1,725 5,607

All seagrass 2,521 1,866 912 2,582 1,952 9,832

Percentage 

change 1992–

2003 8.1% 5.9% 2.7% 18.5% 30.0% 14.2%

Monitoring Assessment: Monitoring occurs in the fall in two main areas of the bay: St. Andrew 

Bay (SAB), behind Shell Island, and in West Bay Bowl (WBBOWL), below the Intracoastal 

Waterway. Five permanent transects are sampled in SAB; four permanent transects are 

sampled in WBBOWL. The St. Andrew Bay Resource Management Association also has three 

permanent transects in West Bay Arm (WBARM), two between Crooked and Burnt Mill creeks 

and a third on the opposite side of the bay, and annual monitoring will eventually incorporate 

these stations. Most of the sites in SAB and WBBOWL have been monitored since 2000. Water 

quality has been monitored in the entire St. Andrew Bay system since 1990, and data analysis 

comparing the water quality of WBBOWL, WBARM, and SAB has been completed. Increasing 

the number of permanent transects in the St. Andrew Bay system will help determine the impact 

of upland development on this pristine ecosystem. Upland development in the West Bay 

watershed will be substantial in the next several decades as approximately 35,000 acres of 

forest and wetlands will be converted to residential, commercial, and industrial use. 

Mapping and Monitoring Recommendations

• Increase the number of transects in the monitoring program. 

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• Photointerpret spring 2010 aerial photography and map seagrass beds, particularly to evaluate 

impacts of upland development. 

Management and Restoration Recommendations

• Evaluate nutrient levels and inputs, particularly since any additional stress due to increased 

light attenuation or excessive nutrients could exacerbate seagrass losses. 

• Continue assessment of damage due to response efforts from the 2010 Deepwater Horizon oil 

spill. 

Mapping Data and Imagery: Seagrass data were derived from interpretation of color infrared 

photography taken in 2003. These images were mapped at 1:12,000 scale as hard copies that 

were rectified to U.S. Geological Survey (USGS) digital orthophoto quarter quadrangle base 

maps and were digitized at the USGS National Wetlands Research Center (NWRC). The 

seagrass beds were classified according to a USGS NWRC-derived classification scheme 

based on the Coastwatch Change Analysis Project Coastal Land Cover Classification system of 

NOAA. 

Monitoring Data: St. Andrew Bay Seagrass Monitoring, Report by Linda Fitzhugh, February 

2010. 

2010 Deepwater Horizon Oil Spill Addendum: St. Andrew Bay was not directly impacted by 

the oil spill, but certain responses to the spill, including placement and removal of booms, the 

partial construction of a corrugated metal barrier across the inlet to the Gulf of Mexico, and 

vessel activities, may have impacted seagrass beds, particularly near the inlet. Damage 

assessment is ongoing.

Pertinent Reports and Scientific Publications

BRIM, M. S., and L. R. HANDLEY. 2006. St. Andrew Bay. Pp. 155–169 in: Handley, L., D. 

Altsman, and R. DeMay (eds.). Seagrass status and trends in the northern Gulf of Mexico: 

1940–2002. U.S. Geological Survey Scientific Investigations Report 2006-5287 and U.S. 

Environmental Agency 855-R-04-003. 267 p.

FITZHUGH, L. M. 2010. Seagrasses in West Bay: historical overview and future impacts, 

presentation: http://www.sabrma.org/images/Seagrasses_in_West_Bay_2-18-10.pdf, accessed 

March 2011.

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General References and Additional Information

Florida’s Water, St. Andrew Bay Watershed: 

http://www.protectingourwater.org/watersheds/map/choctawhatchee_st_andrew/standrew/, 

accessed March 2011.

St. Andrew Aquatic Preserve: http://www.dep.state.fl.us/coastal/sites/standrews/info.htm, 

accessed March 2011.

St. Andrew Bay Resource Management Association Inc.: http://www.sabrma.org/baywatch.html, 

accessed March 2011.

The St. Andrew Bay Watershed, Northwest Florida Water Management District: 

http://www.nwfwmd.state.fl.us/pubs/big_picture/st_andrew_bay.pdf, accessed March 2011.

Watershed Database and Mapping Projects/St. Andrew Bay (Florida) NOAA Office of Response 

and Restoration: http://response.restoration.noaa.gov/book_shelf/117_StAndrew_508.pdf, 

accessed March 2011.

Contacts

Mapping: Larry Handley, U.S. Geological Survey National Wetland Research Center, Lafayette, 

Louisiana, 318-266-8691, Larry_Handley@usgs.gov. 

Monitoring: Linda Fitzhugh, Gulf Coast Community College, Panama City, Florida, 850-769-

1551, ext. 2863, lfitzhugh@gulfcoast.edu.

Management: Shelley Alexander, Northwest Florida Department of Environmental Protection, 

850-983-5359, shelley.alexander@dep.state.fl.us. 

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for St. Joseph Bay

Contacts: Kim Wren, Florida Department of Environmental Protection, 

Coastal and Marine Assessment (Monitoring and Mapping)

General Assessment: Seagrasses covered 6,672 acres in St. Joseph Bay in 2006, based on 

hyperspectral imagery acquired at that time. Seagrass cover and species composition appear to 

be stable in St. Joseph Bay, but there are questions about declines observed when aerial 

imagery from 1992 and 1995 are compared with the 2006 hyperspectral imagery. This 

difference may be related to the use of better technology and measurement techniques or to 

deteriorating water quality. Baseline hyperspectral imagery collected in 2006 has proved to be 

an important resource management tool, and this survey should be repeated to evaluate 

changes in the amount and condition of the bay’s submerged habitats. 

Collection of high-resolution imagery in 2010–11 will allow Coastal and Marine Assessment 

(CAMA) staff to monitor changes in physical and biological conditions over the four to five years 

since the most recent survey and to detect any effects of declining water quality. CAMA staff will 

overlay the images from 2006 and 2010 to analyze changes in seagrass species, coverage, 

depth, propeller scarring, and water quality. The newly acquired imagery will allow staff to 

identify areas in the bay where increased management emphasis under the 2008 management 

plan may be necessary. 

Increased propeller scarring is also evident in St. Joseph Bay. 

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Declining Losses, 1995–2006

Water clarity Improving Affected by runoff, storms

Natural events Minimal impact Hurricanes

Propeller scarring Extensive

Geographic Extent: St. Joseph Bay is located in the central Florida Panhandle in Gulf County

(Figure 1). The bay is bounded on the eastern shoreline by the city of Port St. Joe and St. 

Joseph Bay State Buffer Preserve lands and on the west by the St. Joseph Peninsula and St. 

Joseph Peninsula State Park. The total surface area of the bay at mean high water is 

approximately 43,872 acres (Hemming et al. 2002). 

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Mapping and Monitoring Recommendations

• Acquire coastal imagery using the Worldview satellite and compare it with hyperspectral 

imagery collected in 2006. 

• Continue annual on-ground monitoring and mapping efforts with more focus on deeper (> 3 ft) 

areas. A regular monitoring program has been ongoing since 2002. Monitoring has evolved from 

five fixed-transect sites to 25 fixed-point stations. Monitoring four 1-m

2

quadrats at each station 

results in the analysis and mapping of 100 stations in the bay. 

Management and Restoration 

Recommendations

• Assess the effects of development 

pressures on storm runoff.

• Decrease propeller scarring.

Summary Assessment: Seagrass cover 

and species composition in St. Joseph Bay 

are stable; however, propeller scarring has 

increased in the southern portion of the bay 

(Figure 2). Monthly nutrient monitoring at 

seven sites in the bay has also indicated 

increased nitrogen in the bay which may be 

the cause of increased algal growth and 

epiphyte coverage on seagrass blades. 

Figure 1. Seagrass cover in St. Joseph Bay, 1992.

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Losses, 1995–2006

Seagrass meadow texture Stable

Seagrass species composition Stable

Overall seagrass trends Declining Epiphyte loading, scarring

Seagrass Stressors Intensity Impact Explanation

Water clarity Improving Affected by runoff, storms

Nutrients Relatively low Affected by runoff, storms

Phytoplankton Relatively low Affected by runoff, storms

Natural events Minimal impact Hurricanes

Propeller scarring Extensive

Seagrass Mapping Assessment: Seagrass acreage in St. Joseph Bay appears to have 

decreased between 1992 and 2006, from 9,740 acres to 6,672 acres (Table 1); however, the 

acreage estimates are based on data collected using two methods. In 1992 and 1993, cover 

estimates were made using aerial photography; in 2006, hyperspectral imagery was interpreted 

to estimate seagrass cover. Hyperspectral imagery collected in 2010 will provide another 

assessment of trends. In 1992–93, about half of all seagrass beds (4,840 acres) exhibited 

propeller scarring (Figure 2). By 2006, scarred areas had been reduced to 1,900 acres, but 

moderately scarred areas had increased by 900 acres. 

TABLE 1. SEAGRASS ACREAGE IN ST. JOSEPH BAY IN 1992, 1993,

AND 2006

Category 1992 1993 2006

Change 

1993--2006

Percent 

Change

All seagrass 9,740 8,170 6,672 −1,498 −18.3

 Lightly scarred 4,200 448 −3,752 −89.3

 Moderately scarred 530 1,430 900 170

 Severely scarred 110 21 −89 −80.9

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Figure 2. Hyperspectral imagery interpreted to show propeller scarring in 1992 and 2006.

Monitoring Assessment: St. Joseph Bay 

seagrass beds were monitored by Florida 

Department of Environmental Protection 

(FDEP) CAMA staff twice a year from 2002 

through 2008 at fixed locations (Figure 3). 

Since 2009, seagrass monitoring has been 

conducted annually. In recent years, 

seagrass beds appear stable in size and 

species composition. Turtle grass 

(Thalassia testudinum) is the dominant 

species found in the bay and occurs at 

depths to 9 ft. Manatee grass (Syringodium 

filiforme) occurs frequently with turtle grass 

and is predominantly located in areas along 

the eastern shoreline of the bay. Epiphyte 

loads on seagrass blades are increasing, 

presumably due to increasing nutrients in 

the water column, and propeller scarring 

continues to affect seagrass beds. 

Figure 3. Seagrass monitoring sites in St. Joseph Bay.

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Mapping and Monitoring Recommendations

• Continue annual on-ground monitoring. 

• Regularly obtain satellite imagery and mapping data to assess changes in habitat. 

• Secure assistance with data analysis, including comparing transect data with fixed-point data. 

• Analyze hyperspectral imagery to determine the extent of patchy seagrass vs. continuous 

seagrass. 

• Assess propeller scarring from 2010 satellite imagery. 

Management and Restoration Recommendations

• Address potential increases in nutrients in the bay and determine nutrient sources. 

• Minimize propeller scarring and investigate funding opportunities for restoration efforts in areas 

with the most damage.

Mapping Data and Imagery: In 1992, seagrass distribution for the Gulf Coast of Florida from 

Anclote Key to the Alabama–Florida line was interpreted from natural color aerial photographs 

(1:24,000 scale). The joint National Wetlands Research Center/National Oceanic and 

Atmospheric Administration seagrass mapping protocol was used, and the abundance of 

seagrasses in St. Joseph Bay was estimated at 9,740 acres. Sargent et al. (1995) used the 

1992 and 1993 aerial photography of St. Joseph Bay to estimate the total area of seagrass beds

in the bay. Habitat coverage was estimated at 8,170 acres; of this, 4,200 acres were lightly 

scarred, 530 acres were moderately scarred, and 110 acres were severely scarred. Overall,

4,840 acres of habitat showed some amount of propeller scarring. In the fall of 2006, a 

hyperspectral spectroradiometer with high resolution was used to acquire imagery of the bay. 

Areal extent, abundance and productivity of seagrass meadows, as well as shallow-water (< 2

m) bathymetry were quantified and mapped using a combination of algorithms and models. 

Seagrass beds were distinguished from surrounding sand and optically deep water using unique 

reflectance characteristics in the near infrared. Retrieved bathymetry and modeled watercolumn optical properties were then used to estimate the absolute reflectance of seagrass. 

Statistical relationships between reflectance, leaf area index, and biomass were then used to 

calculate total seagrass productivity in St. Joseph Bay. The areal extent of seagrass in the bay 

was estimated to be 27 km2, or 6,672 acres, which is 17% of the total footprint of the bay. 

Between 1993 and 2006, St. Joseph Bay lost approximately 6 km2 (1,498 acres) of seagrass 

habitat. This might be due to deterioration of water quality or could reflect differences in 

measurement techniques, i.e., radiometrically calibrated images vs. aerial photographs where 

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darker areas of sand could be identified as seagrass, the spatial resolution of the hyperspectral 

sensor as compared with aerial photography, or errors in calculating areas by drawing polygons 

around beds of identified seagrass. There may also be interannual variability in seagrass growth 

that is not measured because aerial surveys are not performed annually.

Monitoring Data: Seagrasses have been monitored in St. Joseph Bay each year since 2002 by 

FDEP CAMA staff. Seagrass and macroalgal cover are estimated by species for four quadrats 

at 25 fixed sites throughout the bay (Figure 3). Other data collected include canopy height, 

epiphyte coverage and type, sediment type, other organisms present, biomass samples (taken 

occasionally), epiphyte samples for laboratory analysis, underwater photographs or video, and 

depth. Water quality parameters include dissolved oxygen, temperature, salinity, pH, turbidity, 

Secchi depth, and light attenuation. 

2010 Deepwater Horizon Addendum: While oil and oil products from the 2010 spill did not 

directly affect St. Joseph Bay, booms were placed across the opening on the north side of the 

bay during the incident, and seagrass may have been damaged by booms and vessels.

Pertinent Reports and Scientific Publications

Preserve staff is analyzing seagrass data for the Central Panhandle Aquatic Preserves (Alligator 

Harbor, Apalachicola Bay, and St. Joseph Bay). Plans include the development of a seagrass 

technical report for the area as well as a State of the Coast report for CAMA. 

HEMMING, J. M., M. BRIM, and R. B. JARVIS. 2002. Survey of dioxin and furan compounds in 

sediments of Florida Panhandle bay systems. U.S. Fish and Wildlife Service Publication number 

PCFO-EC 02-01, Panama City, Florida. 92 p. 

PETERSON, B. J., and K. L. HECK JR. 2001. Positive interactions between suspensionfeeding bivalves and seagrass—a facultative mutualism. Marine Ecology Progress Series 213: 

143–155.

SARGENT, F. J., T. J. LEARY, D. W. CREWZ, and C. R. KRUER. 1995. Scarring of Florida’s 

seagrasses: assessment and management options. Florida Marine Research Institute Technical 

Report TR-1, Florida Department of Environmental Protection, St. Petersburg, Florida. 37 p. + 

appendices.

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General References and Additional Information

Central Panhandle Aquatic Preserves: 

http://www.dep.state.fl.us/water/wqssp/nutrients/docs/estuarine/apalachicola/st_joe_bay_overvi

ew.pdf, accessed March 2011.

Resource database for Gulf of Mexico research: St. Joseph Bay: 

http://www.gulfbase.org/bay/view.php?bid=sjb, accessed March 2011.

St. Joseph Bay Aquatic Preserve management plan, September 2008 through August 2018: 

http://www.dep.state.fl.us/COASTAL/sites/stjoseph/pub/StJosephBay_2008.pdf, accessed 

March 2011. 

St. Joseph Bay Aquatic Preserve: 

http://www.dep.state.fl.us/COASTAL/sites/stjoseph/science/seagrass.htm, accessed March 

2011.

Contacts: Mapping and Monitoring: Kim Wren, Florida Department of Environmental Protection, 

Coastal and Marine Assessment, 850-670-4783, ext. 104, kim.wren@dep.state.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Franklin County Coastal Waters

Contacts: Ron Mezich and Kent Smith, Habitat Species Conservation, 

Fish and Wildlife Conservation Commission (Monitoring); Paul Carlson, Fish and Wildlife 

Research Institute, Fish and Wildlife Conservation Commission (Mapping)

General Assessment: The most recent seagrass mapping effort in the coastal waters of the 

Florida Panhandle’s Franklin County was completed from aerial photography taken in 1992. At 

that time, Franklin County waters contained approximately 14,450 acres of seagrass, almost 

half of which was located near Dog Island Reef (Figure 1). The size of seagrass beds appears 

to be decreasing, but species composition remains fairly stable. However, increasing 

development within the watershed raises concerns about decreasing water clarity and quality. 

Some areas are affected by propeller scarring, and epiphyte loading on seagrass blades is quite 

heavy in some locations. Runoff from the Ochlockonee and Apalachicola rivers contributes 

considerable freshwater, color, and turbidity to this region during stormy periods. Excessive 

runoff from the 2009–10 El Niño may have had impacts on seagrasses. 

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Stable

Water clarity Good Affected by runoff, storms

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Localized

Geographic Extent: Franklin County coastal waters extend from Alligator Harbor in the east to 

St. Georges Sound, ending at the causeway on the western side of St. Georges Island, and 

include St. Vincent Sound, Apalachicola Bay, St. Georges Sound, Dog Island Reef, and

Alligator Harbor and shoal. 

 

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Figure 1. Seagrass cover in Franklin County coastal waters, 1992.

Mapping and Monitoring Recommendations

• Continue seagrass monitoring. Fish and Wildlife Conservation Commission (FWC) staff have

monitored seagrasses each summer since 2006. 

• Photointerpret the high-resolution aerial photography obtained in October 2010 as part of 

damage assessment following the Deepwater Horizon oil spill. 

Management and Restoration Recommendations

• Assess the effects of development on storm runoff.

• Decrease propeller scarring.

 

Summary Assessment: In 1992, Franklin County coastal waters contained 14,452 acres of 

seagrass, with 6,937 acres found at Dog Island Reef, 3,562 acres in St. Georges Sound, 3,146 

acres in Apalachicola Bay, 755 acres in Alligator Harbor and associated shoal, and 52 acres in 

St. Vincent Sound (Table 1). Aerial photography was completed in 2010. Monitoring 

assessment indicates that, overall, seagrass coverage is decreasing, except near Dog Island 

Reef. Optical water quality measurements indicate that water clarity is declining, probably a 

result of storm runoff from heavy to extreme winter rain events in 2008 and 2009. 

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Runoff, nutrients

Seagrass meadow texture Fairly stable No significant changes

Seagrass species composition Fairly stable No significant changes

Overall seagrass trends Declining Potential nutrient impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Declining Affected by runoff, storms

Nutrients Increasing Affected by runoff, storms

Phytoplankton Increasing Affected by runoff, storms

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Localized

Seagrass Mapping Assessment: See the summary above. Mapping of photography obtained 

in 2010 should provide trend and change data. 

TABLE 1. SEAGRASS ACREAGE IN 

FRANKLIN COUNTY COASTAL WATERS

IN 1992

 St. Vincent Sound 52

 Apalachicola Bay 3,146

 St. George Sound 3,562

 Dog Island Reef 6,937

 Alligator Harbor and Shoal 755

 Total 14,452

Monitoring Assessment: Annual monitoring has been conducted during the summer since 

2006. Seagrass beds are decreasing in size but stable in species composition. Epiphyte loads 

on seagrass blades are increasing, presumably due to increasing nutrients in the water column. 

Propeller scarring continues to affect seagrass beds. In 2009, seagrasses were least abundant 

in Alligator Harbor and near St. Georges Island, where more than 80% of the quadrats surveyed 

were bare of seagrasses (Figure 2). In waters near St. Georges Island, shoal grass (Halodule 

wrightii) was the only seagrass observed, and it was the only seagrass species found in every 

subregion of Franklin County coastal waters. In the other six subregions, manatee grass 

(Syringodium filiforme) occurred in 5–45% of the quadrats surveyed, and turtle grass (Thalassia 

testudinum) occurred in 7–33% of quadrats surveyed.

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. 

Figure 2. Occurrence of seagrasses and drift algae in quadrats evaluated in subregions of Franklin 

County coastal waters, 2009.

Mapping and Monitoring Recommendations

• Continue annual routine monitoring program. 

• Obtain aerial photography and mapping data on a regular schedule. 

• Photointerpret high-resolution aerial photography obtained in October 2010 as part of damage 

assessment following the Deepwater Horizon oil spill.

Management and Restoration Recommendations

• Address potential increases in nutrients in coastal waters and determine the sources of 

nutrients. 

• Evaluate effects of winter storm runoff from the Apalachicola and Ochlockonee rivers on 

available light during the following spring. 

• Minimize propeller scarring and conduct restoration efforts in highly impacted areas.

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Mapping Data and Imagery: The northwest Florida seagrass mapping data set, using imagery 

obtained in December 1992 and early 1993, was created by the U.S. Geological Survey (USGS) 

Biological Resources Division at the National Wetlands Research Center in Lafayette, 

Louisiana. The study area was from Anclote Key to Perdido Bay on the Alabama–Florida state 

line and includes the coastal waters of Franklin County. Imagery was natural color at 1:24,000 

scale. Aerial photographs were interpreted and delineated by USGS, then transferred to a base 

map using a zoom transfer scope. The maps were digitized into ArcInfo software. 

Photointerpretation of imagery acquired in 2010 is under way. 

Monitoring Data: Since 2006, a spatially distributed, random sampling design has been used to 

monitor seagrasses in each of seven subregions of Franklin County coastal waters during the 

summer. At each sampling site, seagrass cover is estimated using a modification of the BraunBlanquet technique. Species composition of seagrasses and macroalgae and optical water 

quality parameters (light attenuation, color, turbidity, total suspended solids, chlorophyll-a

concentrations) are measured as well. For more information, contact Ron Mezich, FWC Habitat 

and Species Conservation, or Paul Carlson at the Fish and Wildlife Research Institute. 

2010 Deepwater Horizon Oil Spill Addendum: While this region of the northern Gulf coast did 

not receive direct impacts from the oil spill, extensive response efforts (booms, vessel activity) 

may have affected seagrass beds. 

Pertinent Reports and Scientific Publications

CHANTON, J., and F. G. LEWIS. 2002. Examination of coupling between primary and 

secondary production in a river-dominated estuary: Apalachicola Bay, Florida, U.S.A. Limnology 

and Oceanography 47: 683–697.

HAYS, C. G. 2005. Effect of nutrient availability, grazer assemblage and seagrass source 

population on the interaction between Thalassia testudinum (turtle grass) and its algal 

epiphytes. Journal of Experimental Marine Biology and Ecology 314: 53–68.

General References and Additional Information

Central Panhandle Aquatic Preserves: 

http://www.dep.state.fl.us/water/wqssp/nutrients/docs/estuarine/apalachicola/st_joe_bay_overvi

ew.pdf, accessed March 2011.

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Contacts

Mapping: Paul Carlson, Fish and Wildlife Research Institute, Florida Fish and Wildlife 

Conservation Commission, 727-896-8626; paul.carlson@myfwc.com.

Monitoring: Ron Mezich, FWC Habitat and Species Conservation, 850-922-4330, 

ron.mezich@myfwc.com; Kent Smith, FWC Habitat and Species Conservation, 850-922-4330, 

kent.smith@myfwc.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Northern Big Bend Region

Contacts: Laura Yarbro (Monitoring) and Paul Carlson (Mapping), Fish 

and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission

General Assessment: The northern Big Bend region contained 149,140 acres of seagrass in 

2006. Seagrass cover in northern Big Bend is stable, although slight declines were noted 

between the St. Marks and Ochlockonee rivers. Seagrass species composition also appears to 

be stable. Fragmentation of continuous seagrass beds into patchy beds is cause for concern.

Stressors include nutrients, phytoplankton, and turbidity. These stressors were elevated after 

the 2004 and 2005 hurricane seasons, but they have returned to background levels. Heavy 

propeller scarring is evident around the St. Marks River mouth, Keaton Beach, and 

Steinhatchee but is minimal elsewhere.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Fairly stable Slight gains, 2001–06

Water clarity Good Affected by runoff, storms

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Localized St. Marks, Keaton Beach

Geographic Extent: This region extends from the mouth of the Ochlockonee River in the west 

(shown at far left, Figure 1) to the mouth of the Steinhatchee River in the southeast (right,

Figure 1). Dark and light green polygons show the extent of mapped continuous and patchy 

seagrass, respectively. Seagrass beds extend a considerable distance into deeper water but 

are not shown in Figure 1.

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Figure 1. Seagrass cover in the northern Big Bend, 2006.

Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Map the entire region again in 2011–12.

• Continue annual on-ground monitoring.

• Establish a monitoring program near the mouth of the Ochlockonee River.

• Monitor the effects of improved quality of freshwater discharged from the Fenholloway River 

on seagrass beds located offshore.

Management and Restoration Recommendation

• Assess changes in nutrient loads in Ochlockonee, St. Marks, Aucilla, Econfina, Fenholloway, 

and Steinhatchee rivers.

Summary Assessment: Seagrass cover in northern Big Bend is stable, although slight losses

were noted between the St. Marks and Ochlockonee rivers. Seagrass species composition also 

appears to be stable. However, mapping data suggest that as much as 2,720 acres of 

continuous seagrass beds converted to patchy beds between 2001 and 2006, which is cause 

for concern. Stressors include nutrients, phytoplankton, and turbidity; increases in these water 

quality parameters decrease light available to seagrass beds. These stressors were elevated 

after the 2004 and 2005 hurricane seasons, but they returned to background levels. After the 

extreme storm events of the 2009–10 winter, phytoplankton and turbidity were still elevated in 

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July 2010, especially in the Econfina subregion. Heavy propeller scarring is evident around the 

St. Marks River mouth, Keaton Beach, and Steinhatchee but is minimal elsewhere.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Fairly stable Slight gains, 2001–06

Seagrass meadow texture Fragmenting St. Marks, Steinhatchee

Seagrass species composition Fairly stable No significant changes

Overall seagrass trends Fairly stable Potential nutrient impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Relatively low Affected by runoff, storms

Nutrients Relatively low Affected by runoff, storms

Phytoplankton Relatively low Affected by runoff, storms

Natural events Minimal impact 2004, 2005 Hurricanes

Propeller scarring Localized St. Marks, Keaton Beach

Seagrass Mapping Assessment: Between 2001 and 2006, total seagrass cover for northern 

Big Bend (excluding the area immediately offshore of the mouth of the Fenholloway River) 

declined from 149,840 acres to 149,140 acres, a decrease of 700 acres, or 0.5% (Table 1). This

represents a loss of 840 acres near the Ochlockonee River and marginal gains elsewhere in the 

region. Most (95%) of the seagrass beds in the northern Big Bend are large and continuous.

However, during this five-year period patchy seagrass area increased 61%, from 4,490 acres to 

7,210 acres, as continuous seagrass area declined by 3,420 acres (2.3%), from 145,350 acres 

to 141,930 acres. Fragmentation of beds is cause for concern, especially in the St. Marks East 

and Steinhatchee North subregions. However, some of the fragmentation may have resulted 

from the 2004 and 2005 hurricanes.

The 2001 and 2006 mapping efforts did not extend far enough offshore to capture the deep 

edge of seagrass beds in the northern Big Bend. Furthermore, there are extensive, but sparse,

beds of paddle grass (Halophila decipiens) offshore that cannot be mapped with conventional 

aerial photography. These beds probably serve as a bridge for grouper and other important fish 

and shellfish species as they migrate inshore and offshore.

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TABLE 1. SEAGRASS ACREAGE IN NORTHERN BIG BEND IN 2001 AND 2006

Habitat Type

St. 

Marks 

West

St. 

Marks 

East Aucilla Econfina

Keaton 

Beach

Stein* 

North

All 

Regions

Acres in 2001

Patchy 230 760 920 140 1,220 1,220 4,490

Continuous 15,710 15,610 24,550 28,510 38,080 22,890 145,350

All seagrass 15,940 16,370 25,470 28,650 39,300 24,110 149,840

Acres in 2006

Patchy 1,180 1,780 1,150 280 1,220 1,600 7,210

Continuous 13,920 14,630 24,360 28,390 38,100 22,530 141,930

All seagrass 15,100 16,410 25,510 28,670 39,320 24,130 149,140

Change 2001–06

Patchy 950 1,020 230 140 0 380 2,720

Continuous −1,790 −980 −190 −120 20 −360 −3,420

All seagrass −840 40 40 20 20 20 −700

*Steinhatchee

Monitoring Assessment: Big Bend seagrass beds are monitored each summer by Fish and 

Wildlife Commission (FWC) staff and collaborators. The number of samples each year has 

varied between 450 and 600, so results in Table 2 are expressed as the percentage of samples 

in which each seagrass species was found.

TABLE 2. OCCURRENCE (%) OF SEAGRASS SPECIES

IN NORTHERN BIG BEND

No Star Shoal Manatee Turtle Widgeon Drift

Year Seagrass Grass Grass Grass Grass Grass Algae

2004 17.9 8.7 29 55.2 35.7 4.8 34.5

2005 13.1 7.5 30.3 50.3 46.7 0.3 15.8

2008 23.5 15.4 17.3 56.4 33.7 0 29.2

2009 23.5 10.0 15.0 61.0 42.7 0.9 17.4

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Figure 2. Percentage occurrence of seagrass species in the subregions of northern Big Bend, 2009.

Manatee grass (Syringodium filiforme) occurs at more sampling locations than turtle grass

(Thalassia testudinum), but the two species frequently occur together (Table 2). Both of these 

seagrasses increased in occurrence in 2009 above levels observed in the previous five years. 

The number of sampling locations with shoal grass (Halodule wrightii) appears to have declined 

over the past five years—a potentially disturbing trend because 1) shoal grass often occurs at 

the deep edge of seagrass beds, and 2) it is subject to light stress if water clarity deteriorates. 

Star grass (Halophila engelmannii) occurred in 7.5–15% of all sampling locations from 2004 

through 2009. The occurrence of widgeon grass (Ruppia maritima) dropped off sharply from 5% 

in 2004 and has remained at low levels since. The number of samples with no seagrass 

increased between 2005 and 2008 and remained unchanged in 2009 (23.5%). It is unclear 

whether this seagrass loss will continue. However, in 2009, drift red macroalgae occurred at 

nearly 2005 levels (17.4% of sites evaluated), down from 29% in 2008.

In 2009, seagrasses were present in more than 70% of sampling locations, with greatest 

occurrence in the Fenholloway and Econfina subregions (Figure 2). Manatee grass occurred 

more than 50% of the time at all subregions except Aucilla. Turtle grass was the second most 

abundant seagrass at all sites except Fenholloway, where turtle grass and star grass were 

equally abundant and occurred at nearly 40% of the sites. Shoal grass and star grass were 

found more frequently in Fenholloway and Econfina than in other areas of the northern Big 

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Bend. The Aucilla and St. Marks subregions had the greatest occurrence (> 30%) of bare 

quadrats. 

Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and map the entire region again in 2011–12.

• Continue annual on-ground monitoring, especially near Ochlockonee River.

• Monitor the effects of improved water quality in the Fenholloway River discharge on offshore 

areas.

Management and Restoration Recommendation

• Assess changes, if any, in nutrient loads in Ochlockonee, St. Marks, Aucilla, Econfina, 

Fenholloway and Steinhatchee rivers.

Mapping Data and Imagery: In 2001, natural color aerial photography of the Big Bend region 

was flown at 1:24,000 scale for the Suwannee River Water Management District (SRWMD) by 

U.S. Imaging. The location of the original negatives is not known, but copies are housed at 

SRWMD headquarters in Live Oak, Florida. Benthic habitats were classified and mapped from 

this dataset by Avineon Inc. using the Florida Land Use Cover Classification System (Florida 

Department of Transportation, 1999). ArcMap shapefiles of benthic habitats are distributed on 

the Fish and Wildlife Research Institute (FWRI) Marine Resources Geographic Information 

System (MRGIS) website (http://ocean.floridamarine.org/mrgis/). In 2006, the Florida 

Department of Transportation acquired digital aerial imagery of Big Bend seagrass beds taken 

with a Zeiss DMC digital camera. Digital 3-band color imagery is available from Paul Carlson, 

FWRI, and from the Marine Resources Aerial Imagery Database (MRAID) website 

(http://myfwc.com/research/gis/data-maps/marine/mraid/). Benthic habitats were classified and 

mapped from 2006 imagery by Photoscience Inc. (Contact: Richard Eastlake). ArcMap

shapefiles of benthic habitats based on the 2006 imagery are also distributed on the FWRI 

MRGIS website.

Monitoring Data: Seagrass monitoring has been conducted in the northern Big Bend each 

summer since 2002 by FWC staff and collaborators. Seagrass and macroalgal cover are 

estimated by species for 8–10 0.25 m2quadrats at approximately 120 spatially distributed, 

randomly selected sites throughout the region. Optical water quality measurements (light 

attenuation, turbidity, color, total suspended solids, and chlorophyll-a concentration) are made 

at every site as well. 

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2010 Deepwater Horizon Oil Spill Addendum: While the northern Big Bend was spared 

impacts from oil and oil products from the 2010 oil spill, response activities, including placement 

of booms and heightened vessel activity, occurred in the St. Marks subregion. Damage 

assessment is under way. 

Pertinent Reports and Scientific Publications

CARLSON, P. R., L. A. YARBRO, K. K. KAUFMAN, and R. A. MATTSON. 2010. Vulnerability 

and resilience of west Florida seagrass communities to hurricane impacts. Hydrobiologia 649: 

39–53. 

DAWES, C. J., R. C. PHILLIPS, and G. MORRISON. 2004. Seagrass communities of the Gulf 

coast of Florida: status and ecology. Florida Fish and Wildlife Conservation Commission Fish 

and Wildlife Research Institute and the Tampa Bay Estuary Program. St. Petersburg, Florida. iv 

+ 74 p.

http://www.sarasota.wateratlas.usf.edu/upload/documents/Seagrass-Communities-Status-andEcology.pdf, accessed March 2011.

HALE, J. A., T. K. FRAZER, D. A. TOMASKO, and M. O. HALL. 2004. Changes in the 

distribution of seagrass species along Florida’s central Gulf coast: Iverson and Bittaker revisited. 

Estuaries and Coasts 27: 36–43.

HAMMERSTROM, K. K., W. J. KENWORTHY, M. S. FONSECA, and P. E. WHITFIELD. 2006. 

Seed bank, biomass, and productivity of Halophila decipiens, a deep water seagrass on the 

west Florida continental shelf. Aquatic Botany 84: 110–120.

IVERSON, R. L., and H. F. BITTAKER. 1986. Seagrass distribution and abundance in eastern 

Gulf of Mexico coastal waters. Estuarine, Coastal and Shelf Science 22: 577–602.

MATTSON, R. A. 2000. Seagrass ecosystem characteristics and research and management 

needs in the Florida Big Bend. Pp. 259-277 in Bortone, S. A. (ed.) Seagrasses: monitoring, 

ecology, physiology, and management, Boca Raton, Florida. 318 p.

MATTSON, R. A., T. K. FRAZER, J. HALE, S. BLITCH, and L. AHIJEVYCH. 2007. Florida Big 

Bend. Pp. 171–188 in L. Handley et al., eds. Seagrass status and trends in the northern Gulf of 

Mexico, 1940–2002. United States Geological Survey Scientific Investigations Report 2006-

5287 and U.S. Environmental Protection Agency 855-R-04-003, Washington, D.C. 267 p.

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General References and Additional Information

Big Bend Seagrasses Aquatic Preserve: 

http://www.dep.state.fl.us/coastal/sites/bigbend/info.htm, accessed March 2011.

Faunal Communities in Seagrass Meadows: 

http://www.marinelab.fsu.edu/faculty/seagrass.aspx, accessed March 2011.

Contacts 

Mapping: Paul Carlson, Florida Fish and Wildlife Research Institute, 727-896-8626, 

paul.carlson@fwc.state.fl.us.

Monitoring: Laura Yarbro, Florida Fish and Wildlife Research Institute, 727-896-8626, 

laura.yarbro@fwc.state.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Southern Big Bend Region

Contacts: Laura Yarbro (Monitoring) and Paul Carlson (Mapping), 

Florida Fish and Wildlife Research Institute, Fish and Wildlife Conservation Commission

General Assessment: Seagrass cover in the southern Big Bend region declined between 2001 

and 2006, and historical change analyses indicate that losses have been occurring for more 

than 25 years. In 2006, seagrasses covered 56,146 acres, mostly as continuous beds (44,109 

acres). Between 2001 and 2006, the southern Big Bend experienced a net loss of about 3,500 

acres (6%) of its seagrass, which reflects the deterioration of 7,100 acres of continuous beds 

into only 3,600 acres of patchy beds. Most seagrass beds are located in the Steinhatchee and 

Horseshoe West subregions, and declines were greatest in the Horseshoe West subregion.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Declining Significant losses, 2001–06

Water clarity Poor Affected by runoff, storms

Natural events Serious impact 2004, 2005 hurricanes

Propeller scarring Localized Horseshoe Beach

Geographic Extent: This region extends from the mouth of the Suwannee River north to the 

mouth of the Steinhatchee River (Figure 1). Dark and light green polygons show extent of 

mapped continuous and patchy seagrass, respectively. Seagrass beds also extend a 

considerable distance into deeper water, where conventional mapping techniques cannot be 

used; these deepwater beds are not shown in Figure 1.

Figure 1. 

Seagrass 

cover in the 

southern 

Big Bend 

region in 

2006.

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Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and map the entire region again in 2011–12.

• Continue annual on-ground monitoring from the mouth of the Suwannee River to the mouth of 

the Steinhatchee River. 

• Implement regular water quality monitoring. 

Management and Restoration Recommendations 

• Assess changes in nutrient loads in the Suwannee River, and evaluate the effects of changing 

coastal optical water quality on the extent and location of seagrass beds. 

• Assess potential impacts of herbicides used for control of hardwood species in pine 

plantations.

Summary Assessment: Seagrass cover in the southern Big Bend declined significantly 

between 2001 and 2006 (Table 1). Mapping data from 1984 suggest that seagrass loss has 

been occurring for more than 25 years. Conversion of continuous seagrass beds to patchy beds 

is also cause for concern. Stressors include nutrients, phytoplankton, and turbidity associated 

with runoff from the Suwannee River, and these stressors, in turn, increase light attenuation in 

the water column. Impacts of river discharge extend as far as 40 km north and west of the river 

mouth and probably contribute to the observed decrease in acreage and species occurrence 

between the northern and southern Big Bend regions. Seagrass species shifts attributable to 

light stress have also been observed.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Significant losses, 2001–06

Seagrass meadow texture Fragmenting Steinhatchee, Horseshoe West

Seagrass species composition Declining Less manatee, shoal grass

Overall Seagrass Trends Declining Storms, runoff impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Poor Affected by runoff, storms

Nutrients Relatively high Affected by runoff, storms

Phytoplankton Relatively high Affected by runoff, storms

Natural events Serious impact 2004, 2005 hurricanes

Propeller scarring Localized Horseshoe Beach

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Seagrass Mapping Assessment: Between 2001 and 2006, total seagrass cover for the 

southern Big Bend region decreased from 59,674 acres to 56,146 acres, or 5.9% (Table 1). 

However, continuous seagrass cover decreased 14%, from 51,244 to 44,109 acres. Some of 

the bed fragmentation might have resulted from the 2004 and 2005 hurricanes. Most (84%) of 

the region’s seagrass beds occur in the Steinhatchee South and Horseshoe West subregions, 

and the least extensive beds (973 acres) are found near the mouth of the Suwannee River. 

Between 2001 and 2006, most of the seagrass losses occurred in the Horseshoe West 

subregion, but the Suwannee subregion had small gains (126 acres). Water clarity, however, 

may affect mapping accuracy in coastal waters near the mouth of the Suwannee River. 

Extensive, but sparse, beds of paddle grass (Halophila decipiens) offshore cannot be mapped 

with conventional aerial photography. These beds probably serve as a corridor for grouper and 

other important fish and shellfish species as they migrate inshore and offshore.

TABLE 1. SEAGRASS ACREAGE IN SOUTHERN BIG BEND IN 2001 AND 2006

Habitat Type

Steinhatchee 

South

Horseshoe 

West

Horseshoe 

East Suwannee Total

Acres in 2001

Patchy 2,500 4,468 1,070 390 8,428

Continuous 20,840 22,893 7,054 457 51,244

All seagrass 23,341 27,361 8,124 848 59,674

Acres in 2006

Patchy 3,429 2,919 4,850 839 12,037

Continuous 20,101 20,991 2,883 134 44,109

All seagrass 23,530 23,910 7,733 973 56,146

Change 2001–06

Patchy 929 −1,549 3,780 449 3,609

Continuous −739 −1,902 −4,171 −323 −7,135

All seagrass 190 −3,451 −391 126 −3,528

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Monitoring Assessment: Big Bend’s seagrass beds are monitored each year by Fish and 

Wildlife Conservation Commission (FWC) staff and collaborators. The number of samples each 

year has varied between 450 and 600, so the results shown in Table 2 are expressed as the 

percentage of the total number of sample locations at which each seagrass species was found. 

Since 2004, the average occurrence of bare bottom has ranged from 40% to 50% of sample 

locations throughout the southern Big Bend. This is twice the frequency of bare bottom found in 

the northern Big Bend. The most commonly occurring seagrasses are turtle grass (Thalassia 

testudinum) and manatee grass (Syringodium filiforme), and occurrence of these two species 

dropped 21–24% after the storms of 2004 and 2005. Shoal grass (Halodule wrightii), however, 

decreased sharply in occurrence in 2005 and has not recovered. Star grass (Halophila 

engelmannii), on the other hand, has increased in occurrence, albeit only slightly, since 2005.

The occurrence of drift red macroalgae dropped sharply between 2004 and 2005 and has also 

remained low. Compared with those at the northern Big Bend, all seagrass species except turtle 

grass and drift macroalgae occurred half as frequently in the southern Big Bend region. The 

difference in occurrence between regions for turtle grass was less and may reflect less light 

stress because of the shallow depths at which turtle grass grows. 

TABLE 2. OCCURRENCE (%) OF SEAGRASS SPECIES

IN SOUTHERN BIG BEND

No Star Shoal Manatee Turtle Widgeon Drift

Year Seagrass Grass Grass Grass Grass Grass Algae

2004 44.4 1.7 11.2 32.8 32.5 2.2 28.1

2005 40 0.4 6.6 36.3 43 0 6.5

2008 48.5 6.8 5.8 27.5 34.1 0 10.3

2009 49.5 3.4 5.7 28.4 35.4 0.5 8.4

In 2009, nearly 90% of all sample locations were bare in the Suwannee subregion, and the 

percentage of bare sample locations dropped off sharply along the south-to-north gradient 

(Figure 2). Seagrasses occurred in more than 70% of sampling locations in the Horseshoe West 

and Steinhatchee South subregions. Turtle grass was the most common seagrass in all 

subregions and occurred most frequently in Horseshoe West and Steinhatchee South. Manatee 

grass was the second most common seagrass species and often occurred with turtle grass. 

Both the occurrence and diversity of seagrasses increased with distance from the mouth of the 

Suwannee River. 

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Figure 2. Percentage occurrence of seagrass species in the subregions of southern Big Bend, 2009.

Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and map the entire region again in 2011–12.

• Continue annual on-ground monitoring, especially near the Suwannee River. 

Management and Restoration Recommendation

• Assess the effects of Suwannee River discharge on seagrass beds.

Mapping Data and Imagery: In 2001, natural color aerial photography of the entire Big Bend 

region was flown at 1:24,000 scale for the Suwannee River Water Management District 

(SRWMD) by U.S. Imaging. Location of the original negatives is uncertain, but copies of 

diapositives are housed at SRWMD headquarters in Live Oak, Florida. Benthic habitats were 

classified and mapped by Avineon Inc. using the Florida Land Use Cover Classification System 

(from the Florida Department of Transportation, 1999). ArcMap shapefiles of benthic habitats 

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are distributed on the Fish and Wildlife Research Institute (FWRI) Marine Resources 

Geographic Information System (MRGIS) website (http://ocean.floridamarine.org/mrgis/). In 

2006, the Florida Department of Transportation acquired digital aerial imagery of Big Bend 

seagrass beds taken with a Zeiss DMC digital camera. Digital 3-band color imagery is available 

from Paul Carlson, FWRI, and from the Marine Resources Aerial Imagery Database (MRAID) 

website (http://myfwc.com/research/gis/data-maps/marine/mraid/). Benthic habitats were 

classified and mapped from the 2006 imagery by Photoscience Inc. ArcMap shapefiles of 

benthic habitats based on the 2006 imagery are also distributed on the FWRI MRGIS website.

Monitoring Data: Seagrass monitoring has been conducted in the northern Big Bend region 

each summer since 2002 by FWC staff and collaborators. Seagrass and macroalgal cover are 

estimated by species for 8–10 0.25-m

2

quadrats at approximately 120 spatially distributed, 

randomly selected sites throughout the region. Optical water quality measurements (light 

attenuation, turbidity, color, total suspended solids, and chlorophyll-a concentration) are made 

at every site as well. 

Pertinent Reports and Scientific Publications

CARLSON, P. R., L. A. YARBRO, K. K. KAUFMAN, and R. A. MATTSON. 2010. Vulnerability 

and resilience of west Florida seagrass communities to hurricane impacts. Hydrobiologia 649: 

39–53.

DAWES, C. J., R. C. PHILLIPS, and G. MORRISON. 2004. Seagrass communities of the Gulf 

coast of Florida: status and ecology. Florida Fish and Wildlife Conservation Commission Fish 

and Wildlife Research Institute and the Tampa Bay Estuary Program. St. Petersburg, Florida, iv 

+ 74 p. http://www.sarasota.wateratlas.usf.edu/upload /documents/Seagrass-CommunitiesStatus-and-Ecology.pdf, accessed March 2011.

HALE, J. A., T. K. FRAZER, D. A. TOMASKO, and M. O. HALL. 2004. Changes in the 

distribution of seagrass species along Florida’s central Gulf coast: Iverson and Bittaker revisited. 

Estuaries and Coasts 27: 36–43.

HAMMERSTROM, K. K., W. J. KENWORTHY, M. S. FONSECA, and P. E. WHITFIELD. 2006. 

Seed bank, biomass, and productivity of Halophila decipiens, a deep water seagrass on the 

west Florida continental shelf. Aquatic Botany 84: 110–120.

IVERSON, R. L., and H. F. BITTAKER. 1986. Seagrass distribution and abundance in eastern 

Gulf of Mexico coastal waters. Estuarine, Coastal and Shelf Science 22: 577–602.

MATTSON, R. A. 2000. Seagrass ecosystem characteristics and research and management 

needs in the Florida Big Bend. Pp. 259-277 in Bortone, S. A. (ed.) Seagrasses: monitoring, 

ecology, physiology, and management, Boca Raton, Florida. 318 p.

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MATTSON, R. A., T. K. FRAZER, J. HALE, S. BLITCH, and L. AHIJEVYCH. 2007. Florida Big 

Bend. Pp. 171–188 in L. Handley et al., eds. Seagrass status and trends in the northern Gulf of 

Mexico, 1940–2002. United States Geological Survey Scientific Investigations Report 2006-

5287 and U.S. Environmental Protection Agency 855-R-04-003, Washington, D.C. 267 p.

General References and Additional Information

Big Bend Seagrasses Aquatic Preserve: 

http://www.dep.state.fl.us/coastal/sites/bigbend/info.htm, accessed March 2011.

Faunal Communities in Seagrass Meadows: 

http://www.marinelab.fsu.edu/faculty/seagrass.aspx, accessed March 2011.

Contacts

Mapping: Paul Carlson, Florida Fish and Wildlife Research Institute, 727-896-8626, 

paul.carlson@fwc.state.fl.us. 

Monitoring: Laura Yarbro, Florida Fish and Wildlife Research Institute, 727-896-8626, 

laura.yarbro@fwc.state.fl.us. 

Melissa Charbonneau (for Steinhatchee area), Big Bend Seagrasses Aquatic Preserve, 352-

563-0450, melissa.charbonneau@dep.state.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Suwannee Sound, Cedar Keys, and

Waccasassa Bay Region

Contacts: Melissa Charbonneau, Florida Department of Environmental Protection, Coastal and 

Marine Assessment (Monitoring), and Paul Carlson, Fish and Wildlife Research Institute, Fish 

and Wildlife Conservation Commission (Mapping)

General Assessment: In 2001, 33,625 acres of seagrasses were mapped in Suwannee Sound, 

Cedar Keys, and Waccasassa Bay with 72% of the seagrass beds occurring in Waccasassa 

Bay (24,184 acres). Suwannee Sound had 1,652 acres of seagrasses, located along the 

offshore reef west and south of the mouth of the Suwannee River. In the Cedar Keys region, 

7,789 acres of seagrass were mapped. Of the total seagrass area, 72%, or 24,296 acres, were 

continuous beds. Seagrass cover in the Cedar Key region appears to be stable. Seagrass 

species composition also appears to be stable. However, conversion of continuous seagrass 

beds to patchy beds is cause for concern. Stressors include nutrients, phytoplankton, and 

turbidity, which reduce water clarity. These stressors were elevated after the 2004 and 2005 

hurricane seasons, but they have returned to background levels. Localized, direct impacts from 

propeller scarring are evident in this region, especially between North Key and Seahorse Key in 

the Cedar Keys. Less information is available for Suwannee Sound and Waccasassa Bay.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Decreasing River impacts in Suwannee

Water clarity Variable Poor in Suwannee Sound

Natural events Minimal impact 2009–10 El Niño, tropical storms

Propeller scarring Localized Cedar Keys area

Geographic Extent: This region extends south from the mouth of the Suwannee River to just 

south of the mouth of the Waccasassa River. Seagrasses are limited to the offshore reef near 

the mouth of the Suwannee but become much more common south and east of the Cedar Keys. 

This area is characterized by a mixture of hard bottom, reefs, sands, and seagrass beds. 

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Figure 1. Seagrass cover in Suwannee Sound, Cedar Keys, and Waccasassa Bay, 2001.

Mapping and Monitoring Recommendations

• Establish a seagrass monitoring program in the Waccasassa Bay estuary and in Suwannee 

Sound. 

• Acquire and map aerial or satellite imagery of seagrass beds in 2011–12 in the Cedar Keys 

and Waccasassa Bay subregions, where poor optical properties of the water have prevented 

photointerpretation of recently collected imagery.

Management and Restoration Recommendations 

• Reduce nutrient levels in the Suwannee River. This will partly address the negative impacts of 

river discharge, but episodic high runoff associated with tropical storms and El Niño events will 

continue to affect seagrasses in this region.

• Survey and evaluate propeller scarring in the Cedar Keys region and develop a proactive 

program for reducing impacts. The current strategy includes distribution of and publicity about 

the new boater guide for the Nature Coast region to increase boaters’ awareness of seagrass 

beds in the region. FDEP staff have posted at public boat ramps signs advising boaters of 

penalties for the propeller scarring of seagrass beds. Law enforcement will educate the public 

for a year before it begins to issue citations for scarring by boaters. 

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Summary Assessment: Nutrients and poor water clarity in the highly colored and turbid 

discharge from the Suwannee River continue to impact seagrass beds close to the mouth of the 

river. Seagrass beds are very limited in Suwannee Sound and occur mostly near the reef 

offshore and to the south of the river mouth. In recent years turbidity and resulting light 

attenuation have made it impossible to map seagrasses near Cedar Key and in Waccasassa 

Bay and might also be causing seagrass losses. However, without mapping data or a 

monitoring program, the status of seagrasses in Waccasassa Bay cannot be assessed. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Decreasing River impacts in Suwannee

Seagrass meadow texture Unknown

Seagrass species composition Stable

Overall seagrass trends Fairly stable Potential nutrient impacts

Seagrass Stressors Intensity Impact Assessment, Causes

Water clarity Variable Poor in Suwannee Sound

Nutrients Variable High near Suwannee River

Phytoplankton Relatively low

Natural events Minimal impact 2009–10 El Niño, tropical storms

Propeller scarring Localized Cedar Keys area

Seagrass Mapping Assessment: Based on aerial photography obtained in 2001, most of the 

seagrasses in this region are found in continuous beds, with nearly 75% of all seagrass acreage 

found in Waccasassa Bay (Table 1). Suwannee Sound has the smallest area of seagrasses 

(1,652 acres), but more than half the beds (905 acres) are continuous. Seagrasses in the Cedar 

Keys (7,789 acres) are also predominantly found in continuous beds (79%). 

TABLE 1. SEAGRASS ACREAGE IN SUWANNEE SOUND, CEDAR KEYS, AND

WACCASASSA BAY IN 2001

Habitat Type

Suwannee 

Sound Cedar Keys

Waccasassa 

Bay

 All 

Regions

Patchy 747 1,643 6,939 9,329

Continuous 905 6,146 17,245 24,296

 All Seagrass 1,652 7,789 24,184 33,625

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Monitoring Assessment: Staff of the Big Bend Seagrasses Aquatic Preserve have been 

monitoring seagrass beds at 25 sites in the Cedar Keys area since 2006 using fixed transects 

and Braun-Blanquet assessment of 1-m

2

quadrats. Turtle grass (Thalassia testudinum) is 

usually the most common seagrass species found near Cedar Key, but in September 2006, 

shoal grass (Halodule wrightii) was most common and occurred in more than 50% of the 

quadrats (Figure 2). Manatee grass (Syringodium filiforme) and star grass (Halophila 

engelmannii) occurred less frequently among quadrats but were present to some extent during 

every sampling effort. Very few quadrats in Cedar Key were bare of seagrass. Evaluation of 

total seagrass cover (all species) by Braun-Blanquet score indicates a decline in seagrass 

density near Cedar Key from 2006 through 2009 (Figure 3). 

Figure 2. Percentage occurrence of seagrasses and drift algae in the Cedar Key subregion, May 2006–

September 2008.

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Figure 3. Mean seagrass cover (using Braun-Blanquet scores) in the Cedar Key subregion, 

2006–2009.

Mapping and Monitoring Recommendations

• Photograph and map this region in 2011–12. Continue to map seagrasses every 5–6 years. 

• Continue the monitoring program in the Cedar Key subregion and expand it to include 

Suwannee Sound and Waccasassa Bay.

Management and Restoration Recommendations

• Continue efforts to reduce propeller scarring of seagrass beds near the Cedar Key subregion. 

• Acquire imagery and map Waccasassa Bay to allow trend analysis. 

• Continue to assess impacts from river runoff to seagrasses near the mouth of the Suwannee 

River.

Mapping Data and Imagery: Seagrass data were photointerpreted from 2001 natural color 

aerial photography acquired at 1:24,000 scale and classified using the South Florida Water 

Management District modified Florida Land Use Cover Classification System (FLUCCS, from 

the Department of Transportation, 1999). Features were stereoscopically interpreted from the 

aero-triangulated aerial photography, and vector data were compiled using analytical 

stereoplotters. Extensive field reconnaissance and seagrass bed monitoring were conducted to 

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resolve classification and boundary problems encountered during photointerpretation. The 

minimum mapping unit for classification was 0.5 acre.

Monitoring Data: Data are available for the Cedar Key subregion from staff of the Big Bend 

Seagrasses Aquatic Preserve, Melissa Charbonneau, manager. No monitoring program is in 

place for Waccasassa Bay or Suwannee Sound.

Pertinent Reports and Scientific Publications

JACKSON, J. B., and D. J. NEMETH. 2007. A new method to describe seagrass habitat 

sampled during fisheries-independent monitoring. Estuaries and Coasts 30: 171–178.

MATTSON, R. A. 2000. Seagrass ecosystem characteristics and research and management 

needs in the Florida Big Bend. Pp. 259-277 in: Bortone, S. A. (ed.) Seagrasses: Monitoring, 

ecology, physiology, and management, Boca Raton, Florida. 318 p.

General References and Additional Information:

Big Bend Seagrasses Aquatic Preserve: http://www.dep.state.fl.us/coastal/sites/bigbend/,

accessed March 2011.

Resource Database for Gulf of Mexico Research: Suwannee River: 

http://www.gulfbase.org/bay/view.php?bid=suwaneeriver, accessed March 2011.

Contacts 

Mapping: Paul Carlson, Fish and Wildlife Research Institute, 727-896-8626; 

paul.carlson@myfwc.com .

Monitoring: Melissa Charbonneau, Florida Department of Environmental Protection, Coastal and 

Marine Assessment, 352-563-0450, Melissa.charbonneau@dep.state.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Springs Coast

Contacts: Melissa Charbonneau, Florida Department of Environmental 

Protection, Coastal and Aquatic Managed Areas (Monitoring); and Keith Kolasa, Southwest 

Florida Water Management District (Mapping)

General Assessment: The Springs Coast 

region contained 379,010 acres of seagrass in 

2007. Seagrass cover in the Springs Coast 

region appears to be stable or increasing 

slightly, based on a rough comparison 

between data collected in 1999 and 2007.

Seagrass species composition also appears to 

be stable. Conversion of continuous seagrass 

beds to patchy beds is a cause for concern.

Stressors include nutrients, phytoplankton, and 

turbidity which in turn affect light available to 

seagrasses. These were elevated after the 

2004 and 2005 hurricane seasons, but they 

have returned to background levels. Heavy 

propeller scarring is evident around the mouth 

of Pithlachascotee River, St. Martins marker 

shoal (10 nmi off Pasco County), and Anclote 

Key, but is less extensive elsewhere.

Figure 1. Seagrass cover along the Springs Coast,

2007.

Geographic Extent: The Springs Coast extends from the mouth of the Crystal River south to 

Anclote Key, with a total project area of 494,403 acres. In Figure 1, dark green areas show 

extent of mapped continuous seagrass beds, and light green and bright green areas show 

locations of sparse and patchy seagrass, respectively. Seagrass beds extend a considerable 

distance beyond the mapped area into deeper water.

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Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Increasing Steady gains

Water clarity Good Affected by runoff, storms

Natural events Minimal impact 1998 El Niño, 2004, 2005 hurricanes

Propeller scarring Localized Anclote Key, Pithlachascotee River

Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and map the entire region again in 2011–12.

• Continue the monitoring program in the St. Martins Keys area (south of the mouth of the 

Crystal River through Homosassa Bay) by staff of the Florida Department of Environmental 

Protection (FDEP) Coastal and Managed Areas (CAMA)

• Continue water quality monitoring of the Homosassa, Pithlachascotee, Crystal, Weeki 

Wachee, and Withlacoochee rivers, their associated estuaries, and adjacent coastal marine 

waters.

• Investigate mapping techniques needed for monitoring trends in the expansion of drift 

macroalgae and its associated impacts on seagrass communities.

Management and Restoration Recommendations

• Monitor the impact of propeller scarring, with the goal of developing a proactive strategy for 

reducing impacts.

• Identify which seagrass beds around the St. Martins Keys are most prone to impacts from 

improper boat navigation and develop a boater’s guide for this shallow-water region.

• Use the recently completed boater’s guide for the St. Joseph Bay region (which includes 

Anclote Key) to improve boater education and awareness of seagrass beds around Anclote Key

and to reduce propeller scarring.

Summary Assessment: Seagrass cover in the Springs Coast appears stable, with a similar 

total area of seagrass mapped between 2007 and 1999, when the same project boundary is 

used (Table 1). Seagrass species composition also appears to be stable. Conversion of 

continuous seagrass beds to patchy beds is cause for concern. Stressors include increased 

nutrients, phytoplankton, and turbidity. These were elevated after the 1998 El Niño event and 

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the 2004 and 2005 hurricane seasons, but they have returned to background levels. Heavy 

propeller scarring is evident around the mouth of the Pithlachascotee River, St. Martins marker 

shoal, and Anclote Key but is less evident elsewhere.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Fairly stable Slight gains, 1999–2007

Seagrass meadow texture

Seagrass species composition Fairly stable No significant changes

Overall seagrass trends Fairly stable Potential nutrient impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Good Affected by runoff, storms

Nutrients Relatively low Affected by runoff, storms

Phytoplankton Relatively low Affected by runoff, storms

Natural events Minimal impact 1998 El Niño; 2004, 2005 hurricanes

Propeller scarring Localized Anclote Key, Pithlachascotee River

Seagrass Mapping Assessment: Total seagrass cover for the Springs Coast region in 2007

was 379,010 acres (77% of the total 494,402 acres mapped), with dense seagrass comprising 

272,772 acres, medium to sparse seagrass comprising 87,393 acres, and patchy seagrass 

comprising 18,850 acres (Table 1). 

TABLE 1. SEAGRASS ACREAGE IN THE SPRINGS COAST REGION IN 2007

Habitat Type

Anclote–

Pithlachascotee 

Aripeka–

Hernando 

Beach

Weeki Wachee–

Chassahowitzka

Homosassa–

Crystal River

All 

Regions

Patchy 5,903 4,138 4,401 4,408 18,850

Continuous 40,422 94,316 137,526 87,896 360,160

 All seagrass 46,325 98,454 141,927 92,304 379,010

A comparison of the seagrass coverage in 2007 to that in 1999 was completed using the 

footprint of the 1999 mapping area as the common base. A smaller project area was mapped in 

1999 with only the nearshore region included. Although different sets of habitat categories and 

techniques were used between the 2007 and 1999 projects, a similar total area of seagrass 

coverage was found, with 229,000 acres of seagrass mapped in 1999 and 226,500 acres 

mapped in 2007 (Table 2). 

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TABLE 2. ACRES OF SEAGRASS ALONG

THE SPRINGS COAST, 1999 AND 2007

Habitat Type 1999 2007

Dense 71,000 155,500

Sparse 44,000 58,000

Medium 114,000 Not used

Patchy Not used 13,000

All Seagrass 229,000 226,500

The 1999 and 2007 mapping efforts in this region did not extend far enough offshore to capture 

the deep edge of seagrass beds. Furthermore, there are extensive, but sparse, beds of paddle 

grass (Halophila decipiens) offshore that cannot be mapped with conventional aerial 

photography. These beds probably serve as a bridge for groupers and other important fish and 

shellfish species during migration inshore or offshore.

Monitoring Assessment: Since 1997, FDEP staff have monitored 25 sites in the St. Martins 

Keys area each summer. Data are reported as percentage occurrence of seagrass in 100 

randomly placed quadrats (Figure 2). For 2004, 2005, and 2008, turtle grass (Thalassia 

testudinum) was most common, found in 70–84% of quadrats (Table 3). Manatee grass 

(Syringodium filiforme) and shoal grass (Halodule wrightii) followed, with percentage occurrence 

ranging from 41% to 48% for manatee grass and from 24% to 39% for shoal grass. Star grass 

(Halophila engelmannii) and widgeon grass (Ruppia maritima) were found in fewer than 10% of 

quadrats. For the period 1997--2009, the occurrence of turtle grass and manatee grass is 

increasing, while the occurrence of shoal grass has decreased sharply in the most recent 

sampling efforts. 

TABLE 3. OCCURRENCE (%) OF SEAGRASS SPECIES

IN THE ST. MARTINS KEYS AREA

No Star Shoal Manatee Turtle Widgeon Drift

Year Seagrass Grass Grass Grass Grass Grass Algae

2004 0 9 39 41 81 2 25

2005 0 5 31 42 84 9 35

2008 3 2 24 48 70 4 7

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Figure 2. Occurrence of seagrass species in the St. Martins Keys, 1997–2009.

Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and map the entire region again in 2011–12.

• Continue seagrass monitoring program and continue water quality monitoring of the coastal 

rivers (Homosassa, Pithlachascotee, Crystal, Weeki Wachee, and Withlacoochee) and their 

associated estuaries, as well as coastal marine waters. 

• Investigate mapping techniques needed to monitor trends in the expansion of drift macroalgae 

and its impacts to seagrass communities. 

• Continue water quality monitoring programs such as Project Coast (Southwest Florida Water 

Management District and University of Florida) to assess changes in nutrient loads in the 

Homosassa, Pithlachascotee, Crystal River, Weeki Wachee, and Withlacoochee rivers.

Management and Restoration Recommendations

• Monitor propeller scarring impacts within the St. Martins marker shoal (1,500-acre shallowwater offshore seagrass bed located 9 nmi offshore of Pasco County) toward development of a 

proactive strategy for reducing further impacts. 

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• Use the recently completed boater’s guide for the St. Joseph Bay region (including Anclote 

Key) to improve boater education and awareness of seagrass beds around Anclote Key. 

• Identify the seagrass beds around the St. Martins Keys prone to impacts from improper boat 

navigation and develop a boater’s guide for this shallow-water region. 

Mapping Data and Imagery: In April 2007, digital aerial imagery of the Springs Coast region 

was flown at 1:12,000 scale for the Florida Wildlife Research Institute (FWRI) and the 

Southwest Florida Water Management District (SWFWMD). The imagery was collected using a 

Z/I Digital Mapping Camera (DMC) with position determined using airborne GPS procedures 

and an Applanix Inertial Measurement Unit (IMU). 

Benthic habitats were classified and mapped from this dataset by Avineon Inc., using the Florida 

Land Use Cover Classification System. ArcMap shapefiles of benthic habitats are distributed on 

the Geographic Information Systems database at SWFWMD and are available upon request. 

The digital imagery is available from FWRI from the Marine Resources Aerial Imagery Database 

(MRAID) (http://myfwc.com/research/gis/data-maps/marine/mraid/).

Monitoring Data: FDEP staff have conducted annual seagrass surveys in the St. Martins Keys 

region of the Springs Coast since 1997. Staff use 1-m

2

quadrats to survey 25 fixed-position 

sites. Species composition and percentage cover for seagrass and macroalgae are estimated 

using four randomly placed quadrats at each site, totaling 100 samples.

Pertinent Reports and Scientific Publications

AVINEON. 2009. Final project report for the 2007 Springs Coast Seagrass Mapping Project, 

Southwest Florida Water Management District, Brooksville, Florida.

DAWES, C. J., R. C. PHILLIPS, and G. MORRISON. 2004. Seagrass communities of the Gulf 

coast of Florida: status and ecology. Florida Fish and Wildlife Conservation Commission Fish 

and Wildlife Research Institute and the Tampa Bay Estuary Program. St. Petersburg, Florida. iv 

+ 74 p.

DIXON, L. K., and E. D. ESTEVEZ. 2001. Summary of information: water quality and 

submerged aquatic vegetation in the Chassahowitzka National Wildlife Refuge, 1996–2001, 

Mote Marine Laboratory Technical Report Number 759, Sarasota, Florida. 47 p.

KOLASA, K. V., and V. CRAW. 2009. Improving Seagrass Maps of Florida’s Springs Coast 

Through Digital Imagery. Proceedings of the American Society of Photogrammetry and Remote 

Sensing (ASPRS) 2009 Annual Conference, Baltimore, Maryland. 946 p.

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General References and Additional Information

CONTINENTAL SHELF ASSOCIATES INC. and MARTEL LABORATORIES INC. 1985.

Florida Big Bend seagrass habitat study narrative report. A final report by Continental Shelf 

Associates Inc. submitted to the Minerals Management Service, Metairie, Louisiana. Contract 

No. 14-12-0001-39188. 114 p.

District completes Springs Coast Seagrass Mapping project: 

http://www.swfwmd.state.fl.us/news/article/1380/, accessed March 2011.

Florida Department of Environmental Protection, Florida’s Water: 

http://www.protectingourwater.org/watersheds/map/springs_coast/, accessed March 2011.

Seagrass beds grow along Gulf coastline despite increasing pollution. Tampa Tribune, 

November 18, 2009: http://www2.tbo.com/content/2009/nov/18/seagrass-beds-growing-alonggulf-coastline-despite/, accessed March 2011.

FRAZER, T. K., and J. A. HALE. 2001. Changes in abundance and distribution of submersed 

aquatic vegetation along Florida’s Springs Coast: 1992–1999. Final report. Southwest Florida 

Water Management District, Brooksville, Florida. 10 p.

Contacts

Mapping: Keith Kolasa, Southwest Florida Water Management District, 800-423-1476, ext. 

4236, Keith.Kolasa@swfwmd.state.fl.us. 

Monitoring: Melissa Charbonneau, Big Bend Seagrasses Aquatic Preserve and St. Martins 

Marsh Aquatic Preserve, 352-563-0450, Melissa.Charbonneau@dep.state.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Western Pinellas County 

Contacts: Melissa Harrison, Pinellas County Environmental Management 

(Monitoring), and Kristen Kaufman, Southwest Florida Water Management 

District (Mapping)

General Assessment: In 2008, 25,880 acres of seagrass were mapped in Boca Ciega Bay, 

Clearwater Sound, and St. Joseph’s Sound, with St. Joseph’s Sound accounting for almost 50% 

of the mapped acreage. Between 2006 and 2008, seagrass acreage increased 8.1% for the 

entire region, but seagrass area in Boca Ciega Bay decreased 504 acres, or 5.6%. Many 

seagrass beds in this urban county are greatly affected by storm runoff. In addition, propeller 

scarring affects seagrass beds in some areas. Water quality is affected by storm runoff and 

large-scale events such as El Niño.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing

All areas except 

Boca Ciega Bay

Water clarity Locally poor Boca Ciega Bay

Nutrients Increasing Storm runoff

Phytoplankton Variable Low levels

Propeller scarring Regional Near high-use areas

Geographic Extent: This region includes the shallow waters of Boca Ciega Bay, Clearwater 

Harbor, Shell Key, and St. Joseph’s Sound along the Gulf coast of Pinellas County.

Mapping and Monitoring Recommendations

• Continue annual monitoring formerly conducted by the Pinellas County Department of 

Environmental Management. 

• Continue biennial imagery acquisition and interpretation.

Management and Restoration Recommendations

• Reduce storm runoff into Boca Ciega Bay.

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• Decrease propeller scarring in areas of greatest 

boat use.

Summary Assessment: Seagrass beds in 

western Pinellas County are increasing in size in 

all areas except Boca Ciega Bay based on 

mapping data from 2006 and 2008. Acreage 

increased in St. Joseph’s Sound by 20% during 

this two-year period. All coastal waters receive 

storm runoff from the highly urban Pinellas 

peninsula, and this poses a threat to water clarity 

and quality. Propeller scarring, especially in areas 

of greatest boat use near the Intracoastal 

Waterway, continues to fragment seagrass beds. 

Seagrass Mapping Assessment: In the coastal 

waters of western Pinellas County, almost half the 

seagrass beds are found in St. Joseph’s Sound in 

the northwestern portion of this region (Figure 1). 

Seagrass acreage increased 20%, or 2,093 acres, 

in St. Joseph’s Sound between 2006 and 2008

(Table 1). Seagrass beds also increased in size in 

Clearwater Sound during the same period, by 

about 8%. However, Boca Ciega Bay lost 504 

acres between 2006 and 2008, a 5.6% decline.

Figure 1. Seagrass cover in Western Pinellas 

County, 2008.

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing All areas except 

Boca Ciega Bay

Seagrass meadow texture Stable

Seagrass species composition Stable

Overall seagrass trends Stable Urban runoff is a concern

Seagrass Stressors Intensity Impact Explanation

Water clarity Locally poor Boca Ciega Bay

Nutrients Increasing Storm runoff

Phytoplankton Variable Low levels

Natural events Low El Niño

Propeller scarring Regional Near high-use areas

Monitoring Assessment: Seagrass assessment and monitoring suggest that seagrass beds 

are stable in Boca Ciega Bay, Clearwater Harbor, and St. Joseph’s Sound. Seagrass species 

include shoal grass (Halodule wrightii), manatee grass (Syringodium filiforme), and turtle grass 

(Thalassia testudinum). Some transects showed a temporary decrease in density from 2004 to 

2005, most likely an effect of tropical storms (Meyer and Hammer Levy 2008).

TABLE 1. WESTERN PINELLAS COUNTY SEAGRASS ACREAGE

IN 2006 AND 2008

Bay Segment 2006 2008 Change % Change 

Clearwater North 3,522 3,784 262 7

Clearwater South 914 1,000 86 9

St. Joseph's Sound 10,546 12,639 2,093 20

Boca Ciega Bay 8,961 8,457 −504 −6

 Total 23,943 25,880 1,937 8.1

Mapping Data and Imagery: The Southwest Florida Water Management District (SWFWMD) 

has acquired aerial imagery of submerged aquatic vegetation in the Tampa Bay region every 

two years since 1988. The most recent set of photographs was acquired in 2010. In 2006 and 

2008, seagrass imagery was photointerpreted from 1:24,000 scale natural color aerial 

photography and classified using the SWFWMD modified Florida Land Use Cover Classification 

System. The minimum mapping unit for classification was 0.5 acre.

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Monitoring Data: Seagrass beds are monitored as part of a regional program administered by 

the Tampa Bay Estuary Program. Seagrass cover is evaluated by the Braun-Blanquet method 

using quadrats located along fixed transects. There are 11 fixed transects in Boca Ciega Bay 

and 14 in Clearwater Harbor and St. Joseph Sound. Staff of the Pinellas County Department of 

Environmental Management have been responsible for field assessment each fall, and their 

data are reported to the Tampa Bay Estuary Program. 

Pertinent Reports and Scientific Publications

MEYER, C. A., and K. HAMMER LEVY. 2008. Pinellas County Seagrass Resource 

Assessment & Monitoring Program: Status Report 1998–2007, Pinellas County Environmental 

Management, Clearwater, Florida. 129 p. 

General References and Additional Information

Pinellas County Wateratlas: http://www.pinellas.wateratlas.usf.edu, accessed March 2011.

Tampa Bay Estuary Program: http://tbep.org; http://tbeptech.org, accessed March 2011.

Surveys Show Record Gains for Tampa Bay Seagrasses (January 21, 2011), Tampa Bay 

Estuary Program: http://www.tbep.org/news/whatsnew.shtml , accessed March 2011.

Contacts

Mapping: Kris Kaufman, Southwest Florida Water Management District, 813-985-7481, 

Kristen.kaufman@swfwmd.state.fl.us. 

Monitoring: Melissa Harrison, Pinellas County Department of Environmental Management, 727-

464-4425, mharrison@co.pinellas.fl.us.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Tampa Bay

Contacts: Walt Avery (retired), City of Tampa, and Ed Sherwood, 

Tampa Bay Estuary Program (Monitoring); Kristen Kaufman, Southwest Florida Water 

Management District (Mapping)

General Assessment: Seagrasses covered 29,647 acres of Tampa Bay in 2008. Seagrass 

acreage has increased steadily since 1999, up 4.8%, or 1,350 acres, from 2006 to 2008, with 

the greatest gains in Middle Tampa Bay and modest gains in Hillsborough Bay and Old Tampa 

Bay. Some of these gains were offset by a loss of 1,010 acres of seagrass in the lower 

subregions of Tampa Bay. Seagrass species composition also appears to be stable. Stressors 

include diminished light availability, which results from frequently elevated phytoplankton and 

turbidity. A continuing effort to reduce nitrogen inputs and thus limit phytoplankton productivity is 

challenged by nonpoint sources from the highly urban watershed. Runoff resulting from the 

1997–98 El Niño in particular fueled phytoplankton blooms and resulted in losses of slightly 

more than 2,000 acres of seagrass. With improving water quality, seagrass cover had 

rebounded to pre–El Niño levels by 2004. 

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Increasing Steady gains

Water clarity Improving Affected by runoff, storms

Natural events Minimal impact 1997−98 El Niño

Propeller scarring Extensive

Geographic Extent: This region extends from the mouth of Tampa Bay north and includes the 

tidal portions of the Manatee River, Terra Ceia Bay, and Boca Ciega Bay. Boca Ciega Bay runs 

between the Pinellas peninsula and the barrier islands along the Gulf of Mexico.

Mapping and Monitoring Recommendations

• Continue biennial imagery acquisition and mapping. The most recent mapping effort occurred 

in 2008, and the most recent aerial photography was acquired in 2010. 

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• Continue seagrass monitoring 

completed annually or quarterly by 

several agencies, including the 

Southwest Florida Water 

Management District (SWFWMD), 

Pinellas County, Manatee County, 

the City of Tampa, the Florida 

Department of Environmental 

Protection, and the Fish and 

Wildlife Research Institute. 

Management and Restoration 

Recommendations

• Continue reducing nitrogen in 

runoff to limit phytoplankton 

productivity. 

• Focus on trouble areas where 

seagrass cover is not increasing. 

• Continue efforts to reduce 

propeller scarring. 

Summary Assessment: Seagrass cover in Tampa Bay is steadily increasing in area. Seagrass 

species composition and meadow texture appear to be stable. Stressors include light limitation, 

phytoplankton, turbidity, and propeller scarring. Heavy runoff resulting from El Niño events 

elevates phytoplankton levels and reduces light availability to seagrasses. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing Steady gains

Seagrass meadow texture Stable No significant changes

Seagrass species composition Stable No significant changes

Overall seagrass trends Improving Improving water quality

Figure 1. Seagrass cover in Tampa Bay, 2008.

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Seagrass Stressors Intensity Impact Explanation

Water clarity Improving Affected by runoff, storms

Nutrients Relatively low Affected by runoff, storms

Phytoplankton Medium Affected by runoff, storms

Natural events Minimal impact 1997−98 El Niño

Propeller scarring Extensive

Seagrass Mapping Assessment: Between 2006 and 2008, total seagrass cover for Tampa 

Bay increased by 1,349 acres, from 28,300 acres to 29,650 acres, or 4.8% (Table 1). Most of 

this increase occurred in Middle Tampa Bay, with small losses occurring in lower portions of the 

bay. Some of the losses might be due to differences in map interpretation, because turbidity in 

waters in the southern bay often obscures the bottom in aerial photographs. On a percentage 

basis, Hillsborough Bay had the greatest gain in seagrass cover, a 95% increase between 2006 

and 2008. Seagrass cover increased 7.3% in Old Tampa Bay and 31% in Middle Tampa Bay. 

The restoration goal for Tampa Bay is a total of 40,400 acres, the estimated seagrass area in 

1950. At press time, the Tampa Bay Estuary Program released 2010 mapping data for Tampa 

Bay: 32,897 acres, an increase of 3,250 acres (11%) since 2008. 

TABLE 1. SEAGRASS ACREAGE IN TAMPA BAY

Change

Segment 1950 1982 1996 1999 2004 2006 2008 2006−08

Hillsborough Bay 2,300 0 193 192 566 415 810 395

Old Tampa Bay 10,700 5,943 5,763 4,395 4,636 5,434 5,829 395

Middle Tampa Bay 9,600 4,042 5,541 5,639 6,269 5,089 6,659 1,570

Lower Tampa Bay 6,100 5,016 6,381 5,847 6,319 6,578 6,322 −256

Boca Ciega Bay 10,800 5,770 7,699 7,464 7,731 8,961 8,457 −504

Terra Ceia Bay 700 751 973 929 1,055 1,007 932 −75

Manatee River 200 131 366 375 448 814 638 −176

Total 40,400 21,653 26,916 24,841 27,024 28,299 29,647 1,349

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Monitoring Assessment: Tampa Bay seagrass beds are monitored by the Tampa Bay 

Interagency Seagrass Monitoring Program with participants assessing an average of 1,550 1-m 

× 1-m quadrats annually. Results are expressed as the percentage frequency of occurrence for 

each seagrass species.

Shoal grass (Halodule wrightii) is the dominant Tampa Bay species, found in all Tampa Bay 

subregions (Table 2). Turtle grass (Thalassia testudinum), the dominant lower Tampa Bay 

species, and manatee grass (Syringodium filiforme) are also common. The frequency of 

occurrence of shoal grass and manatee grass increased during 1998–2008; however, turtle 

grass has remained relatively stable, with slight interannual variations. An alga, Caulerpa sp., 

has been a major contributor to Tampa Bay submerged aquatic vegetation (SAV), especially in 

the upper portions of Tampa Bay. The number of quadrats having no seagrasses has steadily 

decreased, from 50% in 1999 to almost 38% in 2008. 

TABLE 2. PERCENTAGE FREQUENCY OF OCCURRENCE OF SEAGRASS

SPECIES AND CAULERPA SPP. IN TAMPA BAY

Star Shoal Manatee Turtle Widgeon Caulerpa

Year Bare Grass Grass Grass Grass Grass Alga

1998 49.3 0.0 33.9 4.7 18.4 1.9 1.7

1999 50.4 0.5 35.7 4.9 17.8 0.1 1.7

2000 50.5 0.4 31.0 7.5 18.5 0.8 1.5

2001 47.1 0.2 34.6 7.0 17.3 0.3 2.3

2002 44.1 0.1 38.2 9.0 14.8 0.6 3.2

2003 46.7 0.0 32.0 9.7 19.4 2.0 2.6

2004 46.7 0.3 34.7 9.7 15.4 2.4 4.6

2005 36.0 0.3 39.7 10.6 16.7 5.5 9.6

2006 39.7 0.2 37.7 12.4 18.2 1.5 2.5

2007 36.9 0.1 37.5 12.3 19.0 0.7 4.6

2008 38.3 0.2 39.7 12.5 16.8 0.2 6.0

Mapping and Monitoring Recommendations

• Continue biennial mapping and the annual monitoring program. 

• Evaluate methods for comparing cover data obtained using transects with data collected at 

fixed sampling points.

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Management and Restoration Recommendations

• Continue improvement in water quality and light transmission to the bay bottom.

• Increase control of nonpoint-source pollution. 

• Remediate and prevent propeller scarring. 

Mapping Data and Imagery: SWFWMD has obtained aerial imagery of SAV communities 

within Tampa Bay every two years since 1988. The most recent set of photographs was 

obtained in 2010. In 2008, seagrass imagery was photointerpreted from 1:24,000 scale natural 

color aerial photography and classified using the SWFWMD modified Florida Land Use Cover 

Classification System. The minimum mapping unit for classification was 0.5 acre.

Monitoring Data: Seagrasses have been monitored in the Tampa Bay region annually since 

1986 by regional agency staff and collaborators. The monitoring program is coordinated by the 

Tampa Bay Estuary Program. Seagrass and macroalgal cover are estimated by species 

annually in 1,550 quadrats located every 10–25 m on approximately 62 transects and quarterly 

at 21 fixed locations. These sampling locations are distributed throughout the bay. 

Pertinent Reports and Scientific Publications

GREENING, H., and A. JANICKI. 2006. Toward reversal of eutrophic conditions in a 

subtropical estuary: water quality and seagrass response to nitrogen loading reductions in 

Tampa Bay, Florida, USA. Environmental Management 38: 163–178.

HU, C., Z. CHEN, T. D. CLAYTON, P. SWARZENSKI, J. C. BROCK, and F. E. MULLERKARGER. 2004. Assessment of estuarine water-quality indicators using MODIS mediumresolution bands: initial results from Tampa Bay, FL. Remote Sensing of Environment 93: 423–

441.

TAMPA BAY ESTUARY PROGRAM. 2010. Data summary from the Tampa Bay Interagency 

Seagrass Monitoring Program through year 2008. Technical Report #01-10. Prepared by the 

City of Tampa Bay Study Group (Walt Avery and Roger Johansson), St. Petersburg, Florida.

TOMASKO, D. A., C. A. CORBETT, H. S. GREENING, and G. E. RAULERSON. 2005. Spatial 

and temporal variation in seagrass coverage in southwest Florida: assessing the relative effects 

of anthropogenic nutrient load reductions and rainfall in four contiguous estuaries. Marine 

Pollution Bulletin 50: 797–805.

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General References and Additional Information

Tampa Bay Estuary Program: http://tbep.org; http://tbeptech.org, accessed March 2011.

Surveys Show Record Gains for Tampa Bay Seagrasses (January 21, 2011), Tampa Bay

Estuary Program: http://www.tbep.org/news/whatsnew.shtml, accessed March 2011.

Contacts

Mapping: Kris Kaufman, Surface Water Improvement and Management Program, Southwest 

Florida Water Management District, 813-985-7481; Kristen.kaufman@swfwmd.state.fl.us. 

Monitoring: Walt Avery (retired from the City of Tampa), wmave@msn.com; Ed Sherwood, 

Tampa Bay Estuary Program, 727-893-2765, esherwood@tbep.org.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Sarasota Bay and Lemon Bay

Contacts: Jon Perry, Sarasota County, Judy Ashton and Melynda 

Brown, Florida Department of Environmental Protection (Monitoring); Kristen Kaufman, 

Southwest Florida Water Management District (Mapping); Jay Leverone, Sarasota Bay Estuary 

Program, and Judy Ott, Charlotte Harbor National Estuary Program (Resource Management 

Coordination)

General Assessment: In 2008, seagrass covered 12,641 acres in Sarasota Bay and 2,863 

acres in Lemon Bay. Acreage has been steadily increasing since 1999. Between 2006 and 

2008, seagrasses increased 28%, or 2,787 acres, in Sarasota Bay and 5.5%, or 149 acres, in 

Lemon Bay. The greatest gains occurred in Upper Sarasota Bay in Manatee County (1,844 

acres), with smaller gains in Sarasota Bay in Sarasota County (850 acres). These gains were 

offset by a loss of 104 acres of seagrass in Roberts Bay and Blackburn Bay. Seagrass species 

composition appears to be stable. Stressors include light availability, which is limited in turn by 

occasionally elevated phytoplankton and turbidity. Seagrass acreage in Sarasota Bay now 

exceeds the estimated coverage in 1950. Seagrass-based water quality targets have been 

developed for both bays based on seagrass light requirements, depth at deep edge, and recent 

or historical acreage.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Increasing Large gains, 2006−08

Water clarity Good Affected by runoff, storms

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Localized

Geographic Extent: Greater Sarasota Bay extends from Anna Maria Sound in Manatee County 

south through Blackburn Bay and includes Roberts and Little Sarasota bays. Seagrass 

resources of Greater Sarasota Bay are managed by the Sarasota Bay Estuary Program. Lemon 

Bay begins south of Venice and extends south into Charlotte County. Lemon Bay, along with 

Lyons, Dona and Roberts bays (coastal Venice) are managed by the Charlotte Harbor National 

Estuary Program (CHNEP). Lemon Bay is also managed as a Florida Aquatic Preserve.

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Figure 1. Seagrass cover in Sarasota Bay and Lemon Bay, 2008.

Mapping and Monitoring Recommendations

• Continue to map seagrass cover every two years to evaluate trends in seagrass acreage. 

• Continue to monitor changes in species composition, abundance, and deep edge, conducted 

by several agencies, including the Southwest Florida Water Management District (SWFWMD), 

Manatee County, Sarasota County, CHNEP, and Florida Department of Environmental 

Protection (FDEP).

• Update the 2003 propeller scarring map of Lemon Bay prepared for CHNEP by Sargent et al. 

(2005) to assess trends in scarring and recovery. Assess scarring in Sarasota Bay using similar 

methods. 

Management and Restoration Recommendations

• Evaluate water quality and light attenuation annually using region-specific models and tools 

available as part of regional Comprehensive Conservation and Management Plans. For more 

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accurate assessment and management, bay waters are divided into segments having generally 

homogeneous water quality and seagrass conditions. Sarasota Bay is divided into several 

subestuaries, including Palma Sola Bay (Upper Sarasota Bay), Roberts Bay, Little Sarasota 

Bay, and Blackburn Bay (Figure 2), while the Lemon Bay region is divided into Upper and Lower 

Lemon bays (Figure 3). Within each segment, water quality results are evaluated together with 

seagrass mapping and monitoring data every two years. 

• Assess development pressures on storm runoff.

• Continue efforts to reduce propeller scarring. 

Summary Assessment: Seagrass cover in Sarasota Bay and Lemon Bay increased during the 

past four to five years (Table 1). Seagrass species composition and meadow texture appear 

stable. Stressors include light limitation and propeller scarring. Seagrass cover decreased by 

1,085 acres in 1999, following the 1997–98 El Niño. However, optical water quality has 

improved since then, and increases in seagrass acreage were observed in 2006. Seagrass 

acreage in Sarasota Bay mapped in 2008 (12,641 acres) exceeded by 29% the target of 9,797 

acres. At the same time, steady increases in the extent of continuous seagrass beds have been 

observed (State of the Bay 2010, Sarasota Bay Estuary Program). Seagrasses in Lemon Bay 

increased by 149 acres between 2006 and 2008, with 2,863 acres mapped in 2008. 

Figure 2. Estuary segments of Sarasota Bay 

used in seagrass and water quality data 

analyses.

Figure 3. Estuary segments of Lemon Bay 

and Charlotte Harbor used in seagrass and 

water quality data analyses.

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing Large gains, 2006−08

Seagrass meadow texture Fairly stable No significant changes

Seagrass species composition Fairly stable No significant changes

Overall seagrass trends Improving Potential nutrient impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Good Affected by runoff, storms

Nutrients Relatively low Affected by runoff, storms

Phytoplankton Relatively low Affected by runoff, storms

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Localized

Seagrass Mapping Assessment: Between 2006 and 2008, total seagrass cover for the 

Sarasota Bay region increased by 2,787 acres, from 9,854 acres to 12,641 acres, an increase 

of 28% (Table 1). Most of the increase occurred in Upper Sarasota Bay in Manatee County 

(1,844 acres). Seagrasses cover small areas in Roberts Bay and Blackburn Bay, and these 

subregions lost 25 and 79 acres, respectively, from 2006 to 2008. Seagrass acreage in the 

Sarasota Bay region in 2008 exceeded the target acreage, based on estimates of cover in 1950, 

by 2,844 acres, or 29%. Seagrass acreage in Lemon Bay increased 5.5%, or 149 acres, 

between 2006 and 2008, from 2,714 acres to 2,863 acres. 

TABLE 1. SEAGRASS ACREAGE IN SARASOTA BAY AND LEMON BAY

Change

Segment 1988 1996 1999 2004 2006 2008 2006–08

Upper Sarasota Bay–Manatee Co. 5,469 6,278 5,714 5,493 5,829 7,673 1,844

Upper Sarasota Bay–Sarasota Co. 1,909 2,578 2,060 2,153 2,637 3,487 850

Roberts Bay 331 358 330 368 324 299 −25

Little Sarasota Bay 532 717 770 762 640 837 197

Blackburn Bay 410 401 373 468 424 345 −79

Total Acres in Sarasota Bay 8,651 10,332 9,247 9,244 9,854 12,641 2,787

Lemon Bay 2,714 2,863 149

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Monitoring Assessment: Seagrass beds throughout this region are stable or increasing in 

area for the most part. Recent seagrass losses observed in Roberts Bay near Venice coincided 

with a dramatic increase in the cover of the green attached alga Caulerpa prolifera. Turtle grass 

(Thalassia testudinum) is most common in Sarasota Bay, and shoal grass (Halodule wrightii) is 

dominant in Roberts Bay, Little Sarasota Bay, and Blackburn Bay to the south (Figure 4). In 

Lemon Bay, shoal grass is the most common seagrass in the northern reaches, and turtle grass 

is most common in the southern portion. The average deep edge of seagrass beds in Lemon 

Bay varied by location and year from 1999 to 2006, ranging from 1.4 m to 1.6 m, based on 

FDEP transect data. 

Figure 4. Occurrence of seagrass in Sarasota Bay and Roberts Bay (left), Little Sarasota Bay and 

Blackburn Bay (middle), and Lemon Bay (right). (Data from the Sarasota County monitoring program.)

Management and Restoration Assessment: Seagrass acreage targets for each segment of 

Sarasota Bay and Lemon Bay were established by the Sarasota Bay Estuary Program (SBEP) 

and the CHNEP, respectively, using the maximum historical extent and interannual variability of 

seagrass cover. In turn, seagrass target acreages were used to establish water quality targets

for each estuarine segment. Using aerial photography, persistence of seagrass locations 

(Figure 5) and historical acreages were determined for Dona, Roberts, and Lemon bays.

Seagrass targets for Sarasota Bay are: Palm Sola, 1,031 acres; Sarasota Bay, 7,269 acres; 

Roberts Bay, 348 acres; Little Sarasota Bay, 702 acres; and Blackburn Bay, 447 acres. For 

Lemon Bay, seagrass targets are: Dona/Roberts Bay, 110 acres; Upper Lemon Bay, 1,010 

acres; and Lower Lemon Bay, 2,880 acres, for a total of 4,000 acres. Progress toward seagrass 

and water quality targets will be evaluated annually.

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Other management goals include continual improvement of water quality and light transmission 

to the bay bottom, increasing control of nonpoint-source pollution, assessment of the impacts of 

diverting freshwater from tributaries into Roberts Bay, and remediation and prevention of 

propeller scarring. 

Figure 5. Persistence of seagrass locations in Dona/Roberts and Lemon bays, 1988–2006.

Mapping and Monitoring Recommendations

• Continue biennial mapping and the twice-yearly monitoring program. 

• Update the 2003 propeller scarring maps of Lemon Bay produced by Sargent et al. (2005), 

and produce scarring maps for Sarasota Bay. 

Management and Restoration Recommendations

• Evaluate water quality and light attenuation annually using available region-specific models 

and tools.

• Twice a year, compare water quality and seagrass maps and monitoring data to assess 

progress in meeting seagrass acreage targets.

• Continue efforts to reduce propeller scarring.

Mapping Data and Imagery: SWFWMD has acquired aerial imagery in Sarasota Bay and 

Lemon Bay every two years since 1988. The most recent set of photographs was obtained in 

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2010. In 2008, seagrass imagery was photointerpreted from 1:24,000 scale natural color aerial 

photography and classified using the SWFWMD modified Florida Land Use Cover Classification 

System. The minimum mapping unit for classification was 0.5 acre.

Monitoring Data: Seagrass monitoring has been conducted in the Sarasota Bay region 

annually in the fall since 1999 by FDEP staff. In Lemon Bay, seagrasses have been monitored 

since 2001 in the fall in a program coordinated by CHNEP. Both monitoring programs evaluate 

seagrasses along established transects, and seagrass and macroalgal cover are estimated by 

species. In addition, both programs assess epiphyte loads, seagrass blade length, and 

sediment quality. Sarasota County staff coordinate a twice-yearly (August and February) 

monitoring program using volunteers from the fishing community. 

Pertinent Reports and Scientific Publications

CORBETT, C. A., and J. A. HALE. 2006. Development of water quality targets for Charlotte 

Harbor, Florida, using seagrass light requirements. Florida Scientist 69: 36–50.

SARGENT, F. J., T. J. LEARY, D. W. CREWZ, and C. R. KRUER. 1995. Scarring of Florida’s 

seagrasses: assessment and management options. Florida Marine Research Institute Technical 

Report TR-1, Florida Department of Environmental Protection, St. Petersburg, Florida, 37 p. + 

appendices.

FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION CHARLOTTE HARBOR 

AQUATIC PRESERVES. 2007. Seagrass annual data summary from the Charlotte Harbor & 

Estero Bay Aquatic Preserves Seagrass Transect Monitoring Program, 1999–2006. Prepared 

by Celia Stearns. 50 p. 

http://www.dep.state.fl.us/coastal/sites/charlotte/research/Seagrass_Data_Summary.pdf, 

accessed March 2011.

TOMASKO, D. A., D. L. BRISTOL, and J. A. OTT. 2001. Assessment of present and future 

nitrogen loads, water quality, and seagrass (Thalassia testudinum) depth distribution in Lemon 

Bay, Florida. Estuaries and Coasts 24: 1559–2723.

TOMASKO, D. A., C. A. CORBETT, H. S. GREENING, and G. E. RAULERSON. 2005. Spatial 

and temporal variation in seagrass coverage in southwest Florida: assessing the relative effects 

of anthropogenic nutrient load reductions and rainfall in four contiguous estuaries. Marine 

Pollution Bulletin 50: 797–805.

CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM. 2009. Water quality target 

refinement project, task 1: harbor segmentation scheme, interim report 2, Janicki 

Environmental, Inc., St. Petersburg, Florida. 62 p., http://www.chnep.org; accessed March 2011. 

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CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM. 2009. Water quality target 

refinement project, task 2: seagrass target development, interim report 2. 

http://www.chnep.org/NEP/agendas2010/TAC/WQQOS_WQ%20Target%20Refine%20Report%202%20Seagrass%20targets.pdf, 

accessed March 2011. 

General References and Additional Information 

TAMPA BAY ESTUARY PROGRAM. 2011. Surveys show record gains for Tampa Bay

seagrasses, Jan. 21, 2011, http://www.tbep.org/news/whatsnew.shtml, accessed March 2011.

SARASOTA BAY ESTUARY PROGRAM. 2010. State of the bay 2010: Celebrating paradise, 

staying the course. 43 p. http://www.sarasotabay.org/documents/SOB2010forwebsite.pdf, 

accessed March 2011.

Sarasota Bay Estuary Program: http://www.sarasotabay.org/habitat-seagrass.html, accessed 

March 2011.

Lemon Bay Aquatic Preserve: http://www.dep.state.fl.us/coastal/sites/lemon/info.htm, accessed 

March 2011.

Sarasota County Wateratlas: http://maps.wateratlas.usf.edu/sarasota/index.asp; accessed 

March 2011.

The Charlotte Harbor National Estuary Program: http://www.chnep.org/, accessed March 2011.

Contacts 

Mapping: Kris Kaufman, Surface Water Improvement and Management Program, Southwest 

Florida Water Management District, 813-985-7481, Kristen.kaufman@swfwmd.state.fl.us. 

Monitoring: Jon Perry, Sarasota County, 941-861-0984, jsperry@scgov.net; Judy Ashton, FDEP 

Southwest District, 813-632-7600, judy.ashton@dep.state.fl.us; Mindy Brown, Charlotte Harbor 

Aquatic Preserves, 941-575-5861, melynda.a.brown@dep.state.fl.us.

Resource Management Coordination: Judy Ott, Charlotte Harbor National Estuary Program, 

239-338-2556, jott@swfrpc.org; Jay Leverone, Sarasota Bay Estuary program, 941-955-8085, 

jay@sarasotabay.org.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Charlotte Harbor, Cape Haze, Pine Island 

Sound, and Matlacha Pass 

Contacts: Heather Stafford and Melynda Brown, Charlotte Harbor Aquatic Preserves, Florida 

Department of Environmental Protection (Monitoring); Kristen Kaufman, Southwest Florida 

Water Management District, and Peter Doering, South Florida Water Management District 

(Mapping); Judy Ott, Charlotte Harbor National Estuary Program (Resource Management 

Coordination)

General Assessment: Seagrass acreage in Charlotte Harbor, Cape Haze, Pine Island Sound, 

and Matlacha Pass has been stable or increasing in recent years (Figures 1 and 2). Acreage 

has increased since 2004, with recovery from the 2004/2005 hurricanes. In 2004, 57,213 acres 

were mapped throughout the region, and in 2006, 58,849 acres were mapped, an increase of 

1,636 acres, or 2.9%. Seagrass-based water quality targets have been developed throughout 

the Charlotte Harbor region based on seagrass light requirements, water depth at the deep 

edge of seagrass beds, and acreage. Human development, with the resulting impacts of 

increasing nutrients and turbidity in coastal waters, is a threat to seagrass beds. Propeller 

scarring continues to impact seagrass beds throughout this region; beds in Pine Island Sound 

and Matlacha Pass in Lee County have experienced the most severe damage. In these two 

regions, 21,507 acres of seagrass beds have been scarred by propellers. 

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Increasing Improved since 2004−05

Water clarity Local declines Affected by runoff, storms

Natural events Moderate impact 2004, 2005 hurricanes

Propeller scarring Increasing Increased boating

Geographic Extent: This chapter includes Charlotte Harbor, Gasparilla Sound, Cape Haze, 

Pine Island Sound, Matlacha Pass, San Carlos Bay, and the tidal Caloosahatchee and Peace 

rivers. The region is managed through both the Aquatic Preserve Program of the Florida 

Department of Environmental Protection (FDEP) and the Charlotte Harbor National Estuary 

Program (CHNEP). The Gasparilla Sound/Charlotte Harbor Aquatic Preserves extend from the 

tidal Peace and Myakka rivers through Lemon Bay to Pine Island Sound and Matlacha Pass. 

The CHNEP includes these estuaries, plus Lemon Bay to the north, all of Charlotte Harbor, and 

Estero Bay to the south. In addition, the northern estuaries of this region (those in Charlotte and 

Sarasota counties, including Lemon Bay, Upper Charlotte Harbor, Peace River, Myakka River, 

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Gasparilla Sound, and Cape Haze) fall within the jurisdiction of the Southwest Florida Water 

Management District. The southern estuaries (in Lee County, including Lower Charlotte Harbor, 

Pine Island Sound, Matlacha Pass, San Carlos Bay, and the tidal Caloosahatchee River) are 

within the jurisdiction of South Florida Water Management District.

Mapping and Monitoring Recommendations

• Continue biennial aerial photography, photointerpretation, and mapping by the Southwest 

Florida Water Management District (SWFWMD) for northern Charlotte Harbor and by South 

Florida Water Management District (SFWMD) for southern Charlotte Harbor to evaluate trends 

in seagrass acreage. 

• Continue annual fall monitoring by staff of the Gasparilla Sound/Charlotte Harbor Aquatic 

Preserves to evaluate changes in species composition, abundance, and water depth at the 

deep edge of seagrass beds.

• Update the map of propeller scarring in Charlotte Harbor (Sargent et al. 2005) to assess trends 

in scarring and recovery.

Figure 1. Seagrass in northern 

Charlotte Harbor, 2008.

Figure 2. Seagrass in southern 

Charlotte Harbor, 2008.

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Management and Restoration 

Recommendations

• As part of the regional management 

plan, evaluate water quality and light 

attenuation annually using available 

region-specific models and tools. For 

more accurate assessment and 

management, bay waters are divided into 

segments having generally 

homogeneous water quality and 

seagrass conditions (Figure 3). Within 

each segment, water quality results are 

compared with seagrass mapping and 

monitoring data on a biennial basis. 

• Assess effects of development on 

storm runoff.

Figure 3. Estuary segments used for seagrass water 

quality analyses.

• Implement a region-wide program with the goal of decreasing propeller scarring and evaluate 

the effectiveness of the No Internal Combustion Motor Zones in Pine Island Sound and 

Matlacha Pass and the Pole and Troll zone near Blind Pass, once they are in place.

Summary Assessment: Overall, seagrass acreage has declined from historical levels due to 

development and dredge-and-fill operations in coastal waters. More recently, seagrass acreage 

has been recovering, despite episodic runoff from hurricanes and tropical storms in 2004. From 

2004 to 2006, seagrass acreage throughout the subestuaries of the Charlotte Harbor region 

increased from 57,213 acres to 58,849 acres, or 2.9%. However, monitoring studies indicate 

that seagrass meadow texture and species composition vary, especially between subestuaries. 

Overall, the abundance of shoal grass (Halodule wrightii) and turtle grass (Thalassia

testudinum) is probably declining, and the number of monitored quadrats that are devoid of 

seagrasses has increased. Factors that affect water clarity, such as turbidity, color, and 

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chlorophyll-a concentration, are a concern in some subestuaries and watersheds. Propeller 

scarring is present throughout the study area and is particularly severe in Pine Island Sound

and Matlacha Pass, where 44% of the 21,507 propeller-scarred acres are classified as severely 

impacted. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Increasing Runoff, nutrients

Seagrass meadow texture Changing Increasing bare areas

Seagrass species composition Fairly stable Increase in shoal grass

Overall seagrass trends Improving Drought before 2010

Seagrass Stressors Intensity Impact Explanation

Water clarity Local declines Affected by runoff, storms

Nutrients Increasing Affected by runoff, storms

Phytoplankton Increasing Affected by runoff, storms

Natural events Moderate impact 2004, 2005 hurricanes

Propeller scarring Increasing Increased boating

Seagrass Mapping Assessment: From 2004 to 2006, seagrass acreage increased by 1,636 

acres throughout the Charlotte Harbor region (Table 1). In Upper Charlotte Harbor, seagrass 

cover increased in all estuary segments except the Cape Haze area, which lost 553 acres of 

seagrass (a 7.4% loss). The largest percentage gains occurred along the West Wall of Charlotte 

Harbor and in the tidal portions of the Myakka and Peace rivers. In 2006, there were 16,650 

acres of seagrass in the northern segments. In 2006, the Lower Charlotte Harbor estuary 

segments contained almost 2.5 times as many acres of seagrass as Upper Charlotte Harbor, 

and most of this acreage was in Pine Island Sound. All estuary segments in Lower Charlotte 

Harbor had gains in seagrass area between 2004 and 2006, and these gains (1,494 acres), 

which occurred mostly in Pine Island Sound, accounted for 91% of the increase in seagrass 

acreage for the entire Charlotte Harbor region. 

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TABLE 1. SEAGRASS ACREAGE IN THE CHARLOTTE HARBOR REGION

Change % Change

1999 2004 2006 2004–06 2004–06

A. Upper Charlotte Harbor (SWFWMD)

Tidal Myakka River 539 331 375 44 13.3

Tidal Peace River 302 295 341 46 15.6

West Wall 1,993 1,784 2,121 337 18.9

East Wall 3,587 3,275 3,382 107 3.3

Cape Haze 6,709 7,464 6,911 −553 −7.4

Bokeelia 3,101 3,359 3,520 161 4.8

Total 16,231 16,508 16,650 142 0.9

B. Lower Charlotte Harbor (SFWMD)

Pine Island Sound 25,941 28,034 29,204 1,170 4.2

Matlacha Pass 6,055 7,479 7,619 140 1.9

San Carlos Bay 3,709 5,192 5,376 184 3.5

Total 35,705 40,705 42,199 1,494 3.7

C. Total Charlotte Harbor Region

51,936 57,213 58,849 1,636 2.9

Monitoring Assessment: Monitoring has been conducted each fall since 1999 using 50 fixed 

transects. Evaluation of data from 1999 through 2009 suggests that, overall, seagrass beds are 

increasing or stable in size and in species composition (Table 2), with no changes in depth 

distribution (data not shown). Six species of seagrass are found in the Charlotte Harbor region: 

turtle grass (T. testudinum), shoal grass (H. wrightii), and manatee grass (Syringodium filiforme) 

are the most common, and widgeon grass (Ruppia maritima), paddle grass (Halophila

decipiens), and star grass (H. engelmannii) are ephemeral. From 1999 to 2005, the abundance 

of shoal grass, turtle grass, and manatee grass declined, based on Braun-Blanquet quadrat 

assessments. At the same time, the number of bare quadrats increased from 10% to 24%. 

Greenawalt-Boswell et al. (2006) also found a significant increase in the number of quadrats 

having no seagrass. After 2005, shoal grass rebounded in percentage occurrence, and the 

fraction of bare quadrats decreased. However, the percentage abundance of turtle grass and

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TABLE 2. PERCENTAGE OCCURRENCE OF SEAGRASS SPECIES 

IN QUADRATS WITHIN THE CHARLOTTE HARBOR AQUATIC 

PRESERVES AREA 

No Shoal Turtle Manatee Widgeon Star 

Year Seagrass Grass Grass Grass Grass Grass

1999 10 46.5 31.5 9.2 1.9 0.8

2000 11.9 47.8 30.4 9.3 0.7 0

2001 16.2 40.5 32 9.5 1.4 0.4

2002 15.5 44.5 31.7 8.3 0 0

2003 19.9 41.3 29.9 8.9 0 0

2004 19.9 41.6 30.1 8.4 0 0

2005 24.3 41 26.5 8.2 0 0

2006 20.3 44.5 27.2 7.9 0 0

2007 15.8 47.4 26.8 9.3 0 0.7

2008 16 47 25.4 8.7 2.8 0

2009 12.5 51.2 27.5 8.8 0 0

manatee grass has remained near 2005 levels. Within the Charlotte Harbor region, GreenawaltBoswell et al. (2006) found net losses of seagrasses in the Peace River, Myakka River, and 

North Charlotte Harbor. Pine Island Sound, San Carlos Bay, and Matlacha Pass were stable in 

seagrass cover, while Southern Charlotte Harbor and Gasparilla Sound had increases. 

Figure 4. Average deep edge of 

seagrass growth.

Figure 5. Mean total abundance of all 

seagrasses in the Charlotte Harbor 

Aquatic Preserves, reported by BraunBlanquet score, 1999-2006.

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The average water depth at the deep edge of seagrass beds varied by subestuary based on 

FDEP transect monitoring data from 1999 to 2006, ranging from approximately 70 cm in the 

Myakka River to 180 cm in San Carlos Bay (Figure 4). Mean total abundance of all seagrasses 

in the Charlotte Harbor region has steadily increased since 2005 (Figure 5). Propeller scarring in 

Pine Island Sound, increased nutrient inputs due to watershed development, and increases in 

the amount of suspended particles in the water continue to impact seagrass beds. 

Management and Restoration 

Assessment: Seagrass acreage targets for 

each subestuary of Charlotte Harbor (Table 

3) were established by CHNEP, using the 

maximum historical extent and inter-annual 

variability of seagrass cover. In turn, 

seagrass target acreages were used to 

establish water quality targets for each 

estuarine segment (CHNEP 2009). Based on 

aerial photography, persistence of seagrass 

locations and acreage was determined for 

each estuary segment. An example is shown 

in Figure 6 for Pine Island Sound.

Figure 6. Persistence of seagrass locations from 

1999-2006 in Pine Island Sound.

TABLE 3. SEAGRASS PROTECTION AND 

RESTORATION TARGETS FOR THE 

CHARLOTTE HARBOR REGION

Target

Estuarine Segment (acres)

Tidal Peace and Myakka rivers 1,430

Charlotte Harbor 9,350

Cape Haze 7,000

Pine Island Sound 26,840

Matlacha Pass 9,320

San Carlos Bay 4,370

Tidal Caloosahatchee River 90

Total 58,400

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Mapping and Monitoring Recommendations

• Continue biennial mapping and annual monitoring programs. 

• Update the 2003 propeller scarring maps of Charlotte Harbor produced by Sargent et al. 

(2005) to assess trends in scarring and to evaluate areas where severe propeller scarring 

continues.

Management and Restoration Recommendations

• Evaluate water quality and light attenuation annually using available region-specific models 

and tools. 

• Address levels of nutrient inputs, and identify sources of nutrients and other factors that reduce 

water clarity. 

• Minimize propeller scarring and evaluate the effectiveness of the No Internal Combustion 

Motor Zones in Pine Island Sound and Matlacha Pass and the Pole and Troll zone near Blind 

Pass, once they are in place.

Mapping Data and Imagery: SWFWMD is responsible for mapping seagrasses in the northern 

portion of the Charlotte Harbor Aquatic Preserves, and aerial photography is obtained every two 

years. In 2008, seagrass imagery was photointerpreted from 1:24,000 scale natural color aerial 

photography and classified using the SWFWMD modified Florida Land Use Cover Classification 

System (FLUCCS). The minimum mapping unit for classification was 0.5 acre. Lower Charlotte 

Harbor, Pine Island Sound, Matlacha Pass, and the Caloosahatchee Estuary are under the 

jurisdiction of SFWMD. For these subregions, seagrass data were photointerpreted from 2006 

1:24,000 scale natural color aerial photography and classified using SFWMD modified FLUCCS. 

Features were stereoscopically interpreted from the aero-triangulated aerial photography, and 

vector data were compiled using digital stereo plotters. The minimum mapping unit for 

classification was 0.5 acre. 

Monitoring Data: Seagrass beds in the Charlotte Harbor Aquatic Preserves are monitored 

each fall using 50 transects from shore to deep edge. Total abundance and species abundance 

are assessed in 1 m × 1 m quadrats using the Braun-Blanquet method (1: < 5%, 2: 6–25%, 3: 

26–50%, 4: 51–75%, 5: 76–100%). Shoot counts, blade lengths, and epiphyte loading on 

seagrass blades are evaluated as well. Data summaries and reports are available on the 

Charlotte Harbor Aquatic Preserves website: 

(http://www.dep.state.fl.us/coastal/sites/charlotte/research/Seagrass_Data_Summary.pdf). 

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Pertinent Reports and Scientific Publications

CHAMBERLAIN, R. H., P. H. DOERING, B. ORLANDO, and B. M. SABOL. 2009. Comparison 

of manual and hydroacoustic measurement of seagrass distribution in the Caloosahatchee 

Estuary, Florida. Florida Scientist 72: 386–405.

CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM. 2009. Water quality target 

refinement project, task 1: harbor segmentation scheme. Interim Report 1, Janicki 

Environmental, Inc., St. Petersburg, Florida. 33 p., http://www.chnep.org; accessed March 2011. 

CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM. 2009. Water quality target 

refinement project, task 2: seagrass target development. Interim Report 2, Janicki 

Environmental, Inc., St. Petersburg, Florida. 62 p., http://www.chnep.org/NEP/agendas2010/TAC/WQQOS_WQ%20Target%20Refine%20Report%202%20Seagrass%20targets.pdf; 

accessed March 2011. 

CORBETT, C. A. 2006. Seagrass coverage changes in Charlotte Harbor, Florida. Florida 

Scientist 69: 7–23.

CORBETT, C. A., and J. A. HALE. 2006. Development of water quality targets for Charlotte 

Harbor, Florida, using seagrass light requirements. Florida Scientist 69: 36–50.

GREENAWALT-BOSWELL, J. M., J. A. HALE, K. S. FUHR, and J. A. OTT. 2006. Seagrass 

species composition and distribution trends in relation to salinity fluctuations in Charlotte Harbor, 

Florida. Florida Scientist 69: 24–35.

OTT, J. A., R. M. DUFFEY, S. E. ERICKSON, K. S. FUHR, B. A. RODGERS, and M. A. 

SCHNEIDER. 2006. Comparison of light limiting water quality factors in six Florida aquatic 

preserves. Florida Scientist 69: 73–91.

SARGENT, F. J., T. J. LEARY, D. W. CREWZ, and C. R. KRUER. 1995. Scarring of Florida’s 

seagrasses: assessment and management options. Florida Marine Research Institute Technical 

Report TR-1, Florida Department of Environmental Protection, St. Petersburg, Florida. 37 p. 

plus appendices.

FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION CHARLOTTE HARBOR 

AQUATIC PRESERVES. 2007. Seagrass annual data summary from the Charlotte Harbor & 

Estero Bay Aquatic Preserves Seagrass Transect Monitoring Program, 1999–2006. Prepared 

by Celia Stearns. 50 p. 

http://www.dep.state.fl.us/coastal/sites/charlotte/research/Seagrass_Data_Summary.pdf; 

accessed March 2011. 

WESSEL, M. R., and C. A. CORBETT. 2009. Assessing the performance of an optical model 

used in setting water quality targets in Lemon Bay, Charlotte Harbor and Estero Bay, Florida. 

Florida Scientist 72: 367–385.

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General References and Additional Information

Charlotte Harbor Aquatic Preserves: http://www.dep.state.fl.us/coastal/sites/charlotte/info.htm; 

accessed March 2011.

Charlotte Harbor National Estuary Program: http://www.chnep.org/; accessed March 2011.

Sarasota County Wateratlas: http://www.sarasota.wateratlas.usf.edu/; accessed March 2011.

Contacts 

Monitoring: Heather Stafford or Melynda Brown, Charlotte Harbor Aquatic Preserves, Florida 

Department of Environmental Protection, 941-575-5861, heather.stafford@dep.state.fl.us, 

melynda.a.brown@dep.state.fl.us.

Mapping: Kris Kaufmann, Surface Water Improvement and Management Program, Southwest 

Florida Water Management District, 813-985-7481, Kristen.Kaufman@swfwmd.state.fl.us; Peter 

Doering, South Florida Water Management District 561-682-2772, pdoering@sfwmd.gov.

Resource Management Coordination: Judy Ott, Charlotte Harbor National Estuary Program, 

239-338-2556, jott@swfrpc.org.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Estero Bay

Contacts: Stephanie Erickson, Estero Bay Aquatic Preserve, Florida 

Department of Environmental Protection (Monitoring); Peter Doering, South Florida Water 

Management District (Mapping); Judy Ott, Charlotte Harbor National Estuary Program 

(Resource Management Coordination)

General Assessment: In 2006, there were 3,529 acres of seagrass in Estero Bay, a 2.6% 

decrease since 2004. Between 2007 and 2009, density of seagrass shoots also decreased 

slightly. Long-term abundance of turtle grass (Thalassia testudinum) and shoal grass (Halodule 

wrightii) is stable, with expected seasonal fluctuations, but occurrence of manatee grass

(Syringodium filiforme), paddle grass (Halophila decipiens), and star grass (H. engelmannii) 

varies from year to year. Recently, widgeon grass (Ruppia maritima) has been observed in the 

central portion of the bay near New Pass (Schmid 2009). Seasonal increases in the abundance 

of macroalgae decrease light availability to seagrasses and can diminish seagrass productivity. 

Seagrass-based water quality targets have been developed for Estero Bay based on seagrass 

light requirements, bed depth at deep edge, and historical acreage. Development with the 

resulting impacts of increasing nutrients and turbidity in coastal waters threatens seagrass beds. 

Propeller scarring continues to impact seagrasses in the bay.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Declining Runoff, turbidity

Water clarity Impacted Runoff, turbidity

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Significant Baywide

Geographic Extent: Estero Bay extends from south of Matanzas Pass to Bonita Beach Road in 

Lee County. There are extensive seagrass beds in the central region of the bay, particularly 

along the eastern shoreline. Estero Bay is managed by the Estero Bay Aquatic Preserve and as 

part of the Charlotte Harbor National Estuary Program (CHNEP) and is in the jurisdiction of the 

South Florida Water Management District (SFWMD).

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Mapping and Monitoring 

Recommendations

• Continue biennial aerial photography, 

photointerpretation, and mapping by the 

SFWMD. 

• Continue monitoring seagrasses twice a 

year by Estero Bay Aquatic Preserves 

staff. 

• Update the map of propeller scarring in 

Estero Bay (Sargent et al. 2005) to 

assess trends in scarring and recovery. 

Management and Restoration Recommendations

• Continue to evaluate water quality and light attenuation of Estero Bay waters. Estero Bay is 

managed as one of several regions in the Charlotte Harbor National Estuary Program (Figure 

2). Under the regional management plan, water quality and light attenuation of bay waters are 

evaluated annually using available region-specific models and tools. These water quality data 

are compared biennially to seagrass maps and monitoring data. 

• Increase efforts to eliminate propeller scarring 

• Increase efforts to minimize urban runoff and turbidity. 

Figure 1. Seagrass cover in 

Estero Bay, 2006.

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Runoff, turbidity

Seagrass meadow texture Fairly stable No significant changes

Seagrass species composition Fairly stable Shoal grass, turtle grass

Overall seagrass trends Declining Water clarity, macroalgae

Seagrass Stressors Intensity Impact Explanation

Water clarity Impacted Turbidity, runoff

Nutrients Impacted Affected by runoff, storms

Phytoplankton Local impacts Affected by runoff, storms

Natural events Minimal impact 2004, 2005 hurricanes

Propeller scarring Significant Baywide

Summary Assessment: Seagrass acreage decreased 2.6% from 2004 to 2006, and losses 

may have resulted from short-term impacts of the 2004–05 storm seasons (Table 1). 

Photointerpretation of 2008 aerial photography will provide data that will allow better 

assessment of storm effects and recovery. Monitoring data indicate that seagrass bed texture 

and species composition are stable over the long term, with shoal grass and turtle grass most 

Figure 2. Estuary segments used for 

seagrass and water quality analyses.

Figure 3. Estuary segments used for 

seagrass beds affected by propeller 

scarring in Estero Bay.

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common. Occurrence of star grass, paddle grass, and manatee grass are variable. Propeller 

scarring remains a significant concern throughout the bay (see Figure 3). 

Seagrass Mapping Assessment: Seagrass acreage in Estero Bay decreased by 96 acres, or 

2.6%, from 2004 to 2006 (Table 1). Photointerpretation of 2008 aerial photography will provide 

updated information. 

TABLE 1. ACREAGE OF SEAGRASSES

IN ESTERO BAY

2004 2006 Change % Change

3,625 3,529 −96 −2.6

Monitoring Assessment: Staff of the Florida Department of Environmental Protection (FDEP) 

Estero Bay Aquatic Preserves have monitored seagrasses twice a year since 2002. Since 2006, 

species composition and abundance have varied by season and year, with abundance greater 

in summer (Figure 4). Over the past two years, total species abundance within seagrass beds 

during the summer monitoring period has declined slightly. The average deep edge of seagrass 

also varied by year, ranging from about 120 cm in 2003 and prior to the severe storm seasons 

of 2004–05 to 75 cm in 2006. (Figure 5). Turbidity due to resuspension of bottom sediments in 

this very shallow system continues to affect water clarity, as do seasonal increases in

macroalgae. 

Figure 4. Seagrass abundance in Estero Bay, based on 

Braun-Blanquet scores.

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Management and Restoration Assessment: 

Propeller scarring is a significant problem in Estero 

Bay and No Internal Combustion Motor Zones were 

recently established (Figure 6). A restoration target of 

3,660 acres for Estero Bay was established by the 

CHNEP, using the maximum historical extent and 

interannual variability of seagrass cover. In turn, the 

seagrass target acreage was used to establish water 

quality targets for the bay (CHNEP 2009). Using

aerial photography, persistence of seagrass locations 

and acreage were determined for each estuary 

segment (Figure 7).

Figure 5. Average depth of the deep 

edge of seagrass beds in Estero Bay.

Figure 6. Location of no internal 

combustion motor zones in Estero Bay.

Figure 7. Persistence of seagrass 

locations in Estero Bay, 1999-2006.

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Mapping and Monitoring Recommendations

• Continue monitoring by the Estero Bay Aquatic Preserves and biennial mapping by SFWMD. 

• Update the 2003 FWRI propeller scarring maps of Estero Bay produced by Sargent et al. 

(2005) to assess trends in scarring and evaluate areas where propeller scarring remains severe.

Management and Restoration Recommendations

• Repair areas with propeller scarring, and eliminate or minimize new impacts. 

• Evaluate the effectiveness of the No Internal Combustion Motor Zones near Big Carlos Pass 

and New Pass once they have been implemented. 

• Minimize impacts of storm runoff. 

• Evaluate progress toward seagrass and water quality targets annually. 

• Address potential increases and determine the sources of nutrients and other factors that 

contribute to decreased water clarity.

Mapping Data and Imagery: Seagrass mapping data were acquired from photointerpretation of 

1:24000 scale natural color aerial photography taken in 2006 and then classified using the 

SFWMD modified Florida Land Use Cover Classification System. Features were 

stereoscopically interpreted from the aero-triangulated aerial photography, and vector data were 

compiled using digital stereoplotters. The minimum mapping unit for classification was 0.5 acre. 

Monitoring Data: Seagrass beds are monitored twice a year by staff of the Estero Bay Aquatic 

Preserves in coordination with the Charlotte Harbor Aquatic Preserves monitoring program. 

Seagrasses are evaluated along five transects, where species composition, species abundance, 

total seagrass abundance, blade length, shoot counts, and epiphyte loading are assessed. 

Other recorded parameters include sediment type, water depth, dissolved oxygen (DO), Secchi 

depth, salinity, and water temperature. Data summaries and reports are available through the 

Charlotte Harbor Aquatic Preserves website 

(http://www.dep.state.fl.us/coastal/sites/charlotte/research/seagrass.htm).

Pertinent Reports and Scientific Publications

BYRNE, M. J., and J. N. GABALDON. 2008. Hydrodynamic characteristics and salinity 

patterns in Estero Bay, Lee County, Florida. U.S. Geological Survey Scientific Investigations 

Report 2007-5217. 33 p. http://pubs.usgs.gov/sir/2007/5217/, accessed March 2011.

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CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM. 2009. Water Quality Target 

Refinement Project, task 1: harbor segmentation scheme, Interim Report 1, Janicki 

Environmental, Inc., St. Petersburg, Florida. 33 p.

CHARLOTTE HARBOR NATIONAL ESTUARY PROGRAM. 2009. Water Quality Target 

Refinement Project, task 2: seagrass target development, Interim Report 2, Janicki 

Environmental, Inc., St. Petersburg, Florida. 62 p. 

CORBETT, C. A. 2006. Seagrass coverage changes in Charlotte Harbor, Florida. Florida 

Scientist 69: 7–23.

CORBETT, C. A., and J. A. HALE. 2006. Development of water quality targets for Charlotte 

Harbor, Florida, using seagrass light requirements. Florida Scientist 69: 36–50.

ESTERO BAY AGENCY ON BAY MANAGEMENT. 2009. State of the bay update. 

http://www.sfwmd.gov/org/exo/ftmyers/report-text/index.html, accessed March 2011.

FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION CHARLOTTE HARBOR 

AQUATIC PRESERVES. 2007. Seagrass annual data summary from the Charlotte Harbor & 

Estero Bay Aquatic Preserves Seagrass Transect Monitoring Program, 1999–2006. Prepared 

by Celia Stearns. 50 p. 

http://www.dep.state.fl.us/coastal/sites/charlotte/research/Seagrass_Data_Summary.pdf; 

accessed March 2011.

GREENAWALT-BOSWELL, J. M., J. A. HALE, K. S. FUHR, and J. A. OTT. 2006. Seagrass 

species composition and distribution trends in relation to salinity fluctuations in Charlotte Harbor, 

Florida. Florida Scientist 69: 24–35.

OTT, J. A., R. M. DUFFEY, S. E. ERICKSON, K. S. FUHR, B. A. RODGERS, and M. A. 

SCHNEIDER. 2006. Comparison of light limiting water quality factors in six Florida aquatic 

preserves. Florida Scientist 69: 73–91.

SARGENT, F. J., T. J. LEARY, D. W. CREWZ, and C. R. KRUER. 1995. Scarring of Florida’s 

seagrasses: assessment and management options. Florida Marine Research Institute Technical 

Report TR-1, Florida Department of Environmental Protection, St. Petersburg, Florida. 37 p. 

plus appendices.

SCHMID, J. R. 2009. Ecological assessment and calibration of water quality in Estero Bay, 

Florida. Final Report to the Environmental Protection Agency Gulf of Mexico Program Office.

100p.

WESSEL, M. R., and C. A. CORBETT. 2009. Assessing the performance of an optical model 

used in setting water quality targets in Lemon Bay, Charlotte Harbor and Estero Bay, Florida. 

Florida Scientist 72: 367–385.

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General References and Additional Information

Estero Bay Aquatic Preserve: http://www.dep.state.fl.us/coastal/sites/estero/info.htm, accessed 

March 2011.

FLORIDA DEPARTMENT OF NATURAL RESOURCES. 1983. Estero Bay Aquatic Preserve 

Management Plan, Tallahassee, Florida. 126 p. 

http://www.dep.state.fl.us/coastal/downloads/management_plans/aquatic/EsteroBay.pdf, 

accessed March 2011.

The Charlotte Harbor National Estuary Program, http://www.chnep.org/, accessed March 2011.

Sarasota County Wateratlas, http://www.sarasota.wateratlas.usf.edu/; accessed March 2011.

Contacts

Monitoring: Stephanie Erickson, Florida Department of Environmental Protection, 239-463-

3240, Stephanie.erickson@dep.state.fl.us; Keith Kibbey, Lee County, kibbey.ka@leegov.org. 

Mapping: Peter Doering, South Florida Water Management District, 561-682-2772, 

pdoering@sfwmd.gov.

Resource Management Coordination: Judy Ott, Charlotte Harbor National Estuary Program, 

239-338-2556; jott@swfrpc.org.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Rookery Bay National Estuarine Research 

Reserve

Contacts: Victoria Vazquez and Jill Schmid, Rookery Bay National Estuarine Research 

Reserve (Monitoring and Mapping); Katie Laakkonen, City of Naples (Monitoring)

General Assessment: Approximately 1,028 acres of seagrass have been mapped using 

sidescan sonar within the Rookery Bay National Estuarine Research Reserve. The most 

extensive seagrass bed within the reserve is located on the Cape Romano shoals (680 acres) in 

the Ten Thousand Islands. Other regions in the reserve exhibit mostly patchy beds. Recently, 

seagrass beds appear to be declining. Research and monitoring are under way to determine 

causes of the decline and to determine whether seagrass beds are declining throughout the 

reserve.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Declining Undetermined cause

Water clarity Poor High to low turbidity

Geographic Extent: The research reserve includes coastal waters in Collier County from 

Gordon Pass, south of Naples, through the Ten Thousand Islands where the reserve borders 

Everglades National Park. The reserve has also been involved in monitoring efforts in the 

Cocohatchee River located in the Delnor-Wiggins State Park, north of the reserve. The turbid 

waters in the reserve and the patchiness of the seagrass there make mapping of submerged 

habitat difficult. Therefore, current locations of seagrass beds have not been well identified and 

need to be reassessed.

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Figure 1. Seagrass cover in the Rookery Bay National Research Reserve, 2002-2005.

Mapping and Monitoring Recommendations

• Remap and analyze changes in areas where seagrass was documented in the 1980s by 

Collier County and in the area near Cape Romano. 

• Map areas along the Ten Thousand Islands so that changes can be detected after hydrologic 

restoration efforts. 

• Expand monitoring efforts to include measurement of nutrients, light attenuation, and sediment 

accumulation rates.

Management and Restoration Recommendations

• Reduce propeller scarring.

• Determine which factors contribute to the seagrass decline.

Summary Assessment: Recent monitoring assessments suggest that seagrass cover is 

declining on Cape Romano shoals, the location of the most extensive seagrass beds in Rookery 

Bay Reserve. However, seagrass species do not appear to be changing. Water clarity is highly 

variable due to changing turbidity from suspended particles. Nutrients and phytoplankton are 

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usually low in Rookery Bay but increase in response to storm runoff. Propeller scarring is 

localized near Cape Romano, but burial of seagrass beds by sedimentation or shifting sands is 

of concern at Cape Romano, Johnson Bay, and Cocohatchee River. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Declining Losses, 2007–09

Seagrass meadow texture Sparse

Seagrass species composition Stable

Overall seagrass trends Declining? Unknown extent

Seagrass Stressors Intensity Impact Explanation

Water clarity Poor High turbidity

Nutrients Relatively low Affected by runoff, storms

Phytoplankton Relatively low Affected by runoff, storms

Natural events Minimal impact Hurricane Wilma, 2005

Propeller scarring Localized Cape Romano

Sedimentation/shifting sand Localized Ongoing

Seagrass Mapping Assessment: During 2002–05, several areas within the reserve were 

mapped using sidescan sonar. The only area with continuous seagrass was the Cape Romano 

seagrass bed (345 acres); the remaining areas all had patchy seagrass beds (Table 1). 

Extensive propeller scars were also mapped at Cape Romano. Recently, reserve staff members 

have observed a decrease in seagrass coverage. Additional sidescan sonar mapping is needed 

for change analysis.

TABLE 1. SEAGRASS ACREAGE IN THE ROOKERY BAY AQUATIC PRESERVE, 2003-2005

Seagrass 

Beds

Henderson 

Creek

Hall 

Bay

Rookery 

Bay

Cape 

Romano

Pumpkin 

Bay

Faka

Union Bay

Fakahatchee 

Bay Total

Patchy 41 31 95 335 80 0 101 683

Continuous 0 0 0 345 0 0 0 345

Total 41 31 95 680 80 0 101 1,028

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Monitoring Assessment: Seagrass beds near Cape Romano are declining and impacted by 

propeller scarring. Turtle grass (Thalassia testudinum), shoal grass (Halodule wrightii), and star 

grass (Halophila engelmannii) were the dominant species at the Cape Romano and Johnson 

Bay sites. Manatee grass (Syringodium filiforme) and paddle grass (Halophila decipiens) also

occurred at low levels at Cape Romano and Johnson Bay. Shoal grass was the only seagrass 

species observed at the Cocohatchee River site. Channel markers were installed in 2008 by 

Collier County Coastal Zone Management in an effort to minimize boating impacts. A sand bar 

in Johnson Bay is shifting, to the detriment of seagrass coverage. Seagrass in Cocohatchee

River is declining. The City of Naples monitors seagrass beds in three locations in Naples Bay. 

These beds consist of sparse patches of shoal grass, paddle grass, and star grass.

Mapping Data and Imagery: Sidescan sonar data were collected and interpreted by Stan 

Locker of the University of South Florida, College of Marine Science, during 2002–05. In 2003, 

aerial photography of coastal southwest Florida was collected at a 1:24,000 scale by the South 

Florida Water Management District and georeferenced by reserve staff. In 2005, aerial 

photography of the Cape Romano shoals was collected by U.S. Imaging Inc. (Bartow, FL) at a 

1:24,000 scale and georeferenced by reserve staff. This effort was done in conjunction with the 

collection of sidescan sonar data to compare the accuracy of the two seagrass mapping 

techniques.

Monitoring Data: Several areas within the reserve have been monitored annually or quarterly 

using a fixed-transect modified Braun-Blanquet methodology. Johnson Bay was monitored from 

2000 to 2009, Cape Romano from 1998 to 2005, and Cocohatchee River from 2001 to 2003 

and in 2005 and has been monitored since 2007. Plans are under way to resume monitoring at 

Cape Romano. A graduate student is comparing seagrasses at Cape Romano and Round Key, 

and results of this study will help determine which factors are leading to seagrass losses. In 

Naples Bay, seagrass beds have been monitored along five transects in spring and fall since 

2006; measurements include water depth, seagrass species, abundance (Braun-Blanquet), 

blade length, total percentage cover, epiphyte density, sediment type, shoot density, light 

attenuation, and water quality parameters.

Pertinent Reports and Scientific Publications

LOCKER, S. D. 2005. Establishing baseline benthic habitat coverages in Faka Union and 

Fakahatchee bays for present and future environmental studies. Final Report to South Florida 

Water Management District, Big Cypress Basin Board, Contract No. DG040614. 60 p.

LOCKER, S. D. 2006. Mapping submerged aquatic vegetation using sidescan sonar, Cape 

Romano Shoals, Florida. Final Report, College of Marine Science, University of South Florida, 

St. Petersburg, Florida. 18 p.

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LOCKER, S. D., and A. K. WRIGHT. 2003. Benthic habitat mapping for habitat suitability 

modeling in Rookery Bay National Estuarine Research Reserve. Final Report, College of Marine 

Science, University of South Florida, St. Petersburg, Florida. 84 p.

SHIRLEY, M. A., S. D. LOCKER, and J. L. SCHMID. 2006. A comparison of side scan sonar 

and aerial photography for submerged aquatic vegetation mapping. Final Report, Rookery Bay 

National Estuarine Research Reserve, Naples, Florida. 20 p.

General References and Additional Information

Rookery Bay National Estuarine Research Reserve: http://www.rookerybay.org/, accessed 

March 2011.

Rookery Bay and Cape Romano–Ten Thousand Islands Aquatic Preserves: 

http://www.dep.state.fl.us/coastal/sites/caperomano/, accessed March 2011.

Cocohatchee River estuary, Estuary Conservation Association Inc.: 

http://estuaryconservation.org/, accessed March 2011.

Contacts

Mapping and monitoring: Victoria Vazquez, Research Coordinator, 239-417-6310, ext 402, 

Victoria.vazquez@dep.state.fl.us; and Jill Schmid, GIS Specialist, Rookery Bay National 

Estuarine Research Reserve, 239-417-6310, ext. 406, jill.schmid@dep.state.fl.us.

Monitoring: Katie Laakkonen, City of Naples, 239-213-7122, klaakkonen@naplesgov.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for the Ten Thousand Islands

Contacts: Victoria Vazquez and Jill Schmid, Rookery Bay National Estuarine Research 

Reserve (Mapping and Monitoring), Paul Carlson, Florida Fish and Wildlife Research Institute 

(Mapping)

General Assessment: With the exception of beds in the Cape Romano area, seagrasses in the 

Ten Thousand Islands region of southwest Florida are difficult to assess. Overlying waters 

remain turbid and darkly colored most of the year, preventing remote sensing of seagrasses, 

and the remoteness of the area has slowed monitoring efforts. However, aerial photography in 

2009 produced imagery that will allow seagrass mapping of approximately 60% of the region. A 

monitoring program is also being developed. Seagrasses are generally sparse but include turtle 

grass (Thalassia testudinum), shoal grass (Halodule wrightii), and star grass (Halophila 

engelmannii). 

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Very sparse Runoff, turbidity

Water clarity Poor Runoff, turbidity

Natural events Moderate 2004, 2005 hurricanes

Propeller scarring Localized Cape Romano

Geographic Extent: The Ten Thousand Islands is a shallow coastal region off Collier and 

Monroe counties, on Florida’s far southwest coast (Figure 1). The region gets its name from the 

many islands and mangrove marshes that extend from the mainland. Coastal waters receive 

drainage from the Big Cypress and Everglades areas through the Turner and Chatham rivers, 

as well as the Faka Union canal. 

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Figure 1. Turbidity in the Ten Thousand Islands following Hurricane Wilma in 2005 (Ikonos satellite 

imagery).

Mapping and Monitoring Recommendations

• Supplement aerial imagery flown in 2006 and 2009, and develop a mosaic map from these 

sources. Seagrasses of the nearshore Cape Romano region were mapped by sidescan sonar in 

2003–05. Seagrass beds in the Ten Thousand Islands need to be mapped again, but nearly 

constant high turbidity makes use of traditional aerial photography and mapping techniques 

difficult. 

• Evaluate alternative mapping techniques, such as underwater videography. 

• Continue development of projects for evaluating seagrass cover, optical water quality 

conditions, and forage available for manatees. This work has been undertaken by several 

investigators (Daniel Sloane, U.S. Geological Survey, Jud Kenworthy, National Oceanographic 

and Atmospheric Administration, Penny Hall and Paul Carlson, Fish and Wildlife Research 

Institute) 

• Implement a monitoring program for identification of seagrass beds that uses a spatially 

distributed, random sampling design (Figure 3).

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Management and Restoration Recommendations

• Investigate causes of ongoing turbidity.

• Assess water quality impacts on seagrasses of water entering the estuary from canals.

Summary Assessment: Seagrass maps produced by sidescan sonar in 2003–05 show 680 

acres of seagrass near Cape Romano; half of it existed as continuous beds (Shirley et al. 2006). 

A mapping project for the entire Ten Thousand Island region is under way using imagery from 

several sources, and this product will fill a large data gap. Monitoring assessments of nearshore 

Cape Romano seagrasses by staff of the Rookery Bay National Estuarine Research Reserve 

(NERR) from 1998 to 2005 indicated that seagrass beds were declining and had been scarred 

by propellers. Turtle grass, shoal grass, and star grass were dominant species. A preliminary 

monitoring effort in October 2010 by Fish and Wildlife Research Institute (FWRI) staff showed 

that seagrasses were very sparse. Species included turtle grass, manatee grass (Syringodium 

filiforme), and star grass. A monitoring program will be implemented in 2011 to evaluate 

seagrass cover, species composition, and optical water quality.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Very sparse Runoff, turbidity

Seagrass meadow texture Fairly stable

Seagrass species composition Fairly stable Turtle, manatee, shoal, 

star grasses

Overall seagrass trends Declining?? Water clarity

Seagrass Stressors Intensity Impact Explanation

Water clarity Poor Turbidity, runoff

Nutrients Impacted Canals, runoff, storms

Phytoplankton Impacted Canals, runoff, storms

Natural events Moderate 2004, 2005 hurricanes

Propeller scarring Localized Cape Romano

Seagrass Mapping Assessment: Sidescan sonar measured 680 acres of seagrass in the 

nearshore Cape Romano area in 2003–05. Figure 2 shows the area of the two sets of imagery

to be used for mapping seagrass in the Ten Thousand Islands. The area of the 2009 imagery is

shown in blue, and the area of the 2006 imagery is shown in red. The bold black line indicates 

the northwestern boundary of Everglades National Park. Supplemental collections of imagery for 

seagrass mapping will be obtained by using the Worldview 2 satellite in 2011. 

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 Figure 2. Imagery data sets for the Ten Thousand Islands, 2006 and 2009.

Monitoring Assessment: Monitoring data from 1998–2005 indicated that seagrass beds near 

Cape Romano were in decline and had been scarred by propellers. Turtle grass, shoal grass, 

and star grass were common species near Cape Romano. A preliminary field effort in October 

2010 provided limited information on seagrass cover (cover was generally very sparse), optical 

water quality, and seagrass species present. Turtle grass, manatee grass, shoal grass, and star 

grass were observed but were of very sparse density. Turbidities were high, but color and 

chlorophyll-a values were low. 

Figure 3. Proposed

seagrass monitoring grid for 

the Ten Thousand Islands.

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Mapping Data and Imagery: Sidescan sonar data were collected and interpreted by Stan 

Locker of the University of South Florida College of Marine Science during 2002–05 to produce 

seagrass maps for the nearshore Cape Romano area. Imagery interpretation and acquisition 

are ongoing.

Monitoring Data: Seagrasses near Cape Romano were monitored annually or quarterly from 

1998 to 2005 by staff of the Rookery Bay NERR using a fixed-transect modified Braun-Blanquet 

methodology. Paul Carlson (FWRI) began reconnaissance sampling for development of a 

seagrass monitoring program in the Ten Thousand Islands in spring 2011. We anticipate that 

Everglades National Park and Rookery Bay NERR staff will collaborate in the monitoring effort, 

and our initial project will sample a 1-km

2

grid extending from Cape Romano and the Everglades 

City/Chokoloskee area. At a randomly chosen sampling point within each grid cell, we will 

determine seagrass and macroalgal cover and abundance in eight quadrats. We will also 

measure optical water quality parameters (turbidity, color, chlorophyll-a, and light extinction 

coefficients) at a subset of 30 sites that will be chosen to achieve representative coverage.

Pertinent Reports and Scientific Publications

BOYER, J. N. 2006. Shifting N and P limitation along a north-south gradient of mangrove 

estuaries in South Florida. Hydrobiologia 569: 167–177.

HEIL, C. A., M. REVILLA, P. M. GLIBERT, and S. MURASKO. 2007. Nutrient quality drives 

differential phytoplankton community composition on the southwest Florida shelf. Limnology and 

Oceanography 52: 1067–1078.

MAIE, N., J. N. BOYER, C. YANG, and R. JAFFE. 2006. Spatial, geomorphological, and 

seasonal variability of CDOM in estuaries of the Florida Coastal Everglades. Hydrobiologia 569: 

135–150.

SHIRLEY, M. A., S. D. LOCKER, and J. L. SCHMID. 2006. A comparison of side scan sonar 

and aerial photography for submerged aquatic vegetation mapping. Final Report, Rookery Bay 

National Estuarine Research Reserve, Naples, Florida. 20 p.

General References and Additional Information

Rookery Bay and Cape Romano—Ten Thousand Islands Aquatic Preserves: 

http://www.dep.state.fl.us/coastal/sites/caperomano/, accessed March 2011.

Rookery Bay National Estuarine Research Reserve: http://www.rookerybay.org/, accessed 

March 2011.

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Contacts 

Mapping and Monitoring: Victoria Vazquez, Research Coordinator, Rookery Bay National 

Estuarine Research Reserve, 239-417-6310, ext 402, Victoria.vazquez@dep.state.fl.us, and Jill 

Schmid, GIS Specialist, Rookery Bay National Estuarine Research Reserve, 239-417-6310, ext. 

406, jill.schmid@dep.state.fl.us.

Mapping: Paul Carlson, Florida Fish and Wildlife Conservation Commission, 727-896-8626, 

paul.carlson@myfwc.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for the Florida Keys National Marine Sanctuary

Contacts: Jim Fourqurean, Florida International University (Monitoring); 

Paul Carlson, Florida Fish and Wildlife Conservation Commission (Mapping)

General Assessment: The Florida Keys National Marine Sanctuary (FKNMS) includes some of 

the largest expanses of seagrasses in Florida coastal waters. In 1992, 856,360 acres of 

seagrass habitat was mapped in the sanctuary (Figure 1). Seagrass beds covered 131,620 

acres on the Atlantic side of the Upper Keys and 144,875 acres on the Atlantic side of the Lower 

Keys. On the Gulf of Mexico side, seagrasses covered 115,860 acres near the Upper Keys and 

453,000 acres near the Lower Keys and the Marquesas Keys; 11,000 acres of seagrasses 

surrounded the Dry Tortugas. Seagrass cover in the Florida Keys National Marine Sanctuary is 

probably stable, but significant changes in seagrass species composition continue in many

locations in response to alterations in water quality.

Seagrass Status and 

Stressors Status Trend Assessment, Causes

Seagrass cover Stable

Water clarity Locally poor Phytoplankton blooms

Nutrients Increasing?

Phytoplankton Increasing?

Propeller scarring Local Near high-use areas

Geographic Extent: The Florida National Marine Sanctuary includes the waters adjacent to the 

Florida Keys from Key Largo to Key West and out to the Dry Tortugas. 

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Figure 1. Seagrasses in the Florida Keys National Marine Sanctuary, 1992.

Mapping and Monitoring Recommendations

• Map the 2004 aerial photography. 

• Obtain new aerial imagery. 

• Continue the long-term monitoring program by staff from the Florida International University. 

Management and Restoration Recommendations

• Continue to assess changes in seagrass beds associated with changing nutrient conditions in 

the water column.

Summary Assessment: Seagrass cover in the FKNMS is probably stable, but 

photointerpretation of 2004 aerial photography is needed to confirm this. Despite generally 

stable acreage, the texture and species composition of seagrass beds continue to change in 

response to changing water quality. Nutrient content in seagrass tissues indicates that more 

nutrients are available to these ecosystems. Increased nutrient availability in the past 20 years 

is altering the relative abundance and dominance of seagrasses and macroalgae. Where 

nutrients have been elevated for some time, long-term increases in phytoplankton populations 

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have been observed, which increases light attenuation in the water column and thus harms 

seagrass beds. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Stable

Seagrass meadow texture Some changes Species changes

Seagrass species composition Changing Water quality

Overall seagrass trends Changing Altered water quality

Seagrass Stressors Intensity Impact Explanation

Water clarity Locally poor Phytoplankton blooms

Nutrients Increasing? Northeastern region

Phytoplankton Increasing? Northeastern region

Natural events Low Hurricanes

Propeller scarring Local Near high-use areas

Seagrass Mapping Assessment: Photointerpretation of aerial photography taken in 1992 

showed that approximately 856,300 acres of seagrasses covered shallow bottom of the 

sanctuary from the Upper Keys to the Dry Tortugas (Table 1). Seagrass beds on the Gulf of 

Mexico side of the Lower Keys accounted for 52% of the total acreage in the sanctuary. Imagery 

is available from 2004, and photointerpretation is under way.

TABLE 1.SEAGRASS ACREAGE IN THE FLORIDA KEYS

NATIONAL MARINE SANCTUARY IN 1992

Upper 

Keys

Lower 

Keys Tortugas Total

Atlantic Ocean side 131,620 144,875 276,495

Gulf of Mexico side 115,860 453,000 568,860

Total 247,480 597,875 11,000 856,355

Monitoring Assessment: Florida Keys seagrass beds are monitored annually by staff of 

Florida International University (FIU) and collaborators. Using 2004 data from the FIU database, 

we calculated the frequency of occurrence of seagrasses in subregions of FKNMS (Figure 2). 

Turtle grass (Thalassia testudinum) occurred at 80% of sampling locations in seagrass beds

along the Atlantic side of the Upper Keys and was first or second in abundance in the other 

subregions. Manatee grass (Syringodium filiforme) was also common and was the most 

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abundant species along the Gulf side of the Upper Keys. Shoal grass (Halodule wrightii) and 

paddle grass (Halophila decipiens) were less common but were found in all subregions. 

Figure 2. Mean (plus two standard error) frequency of occurrence of seagrasses in the FKNMS in 2004

(data from FKNMS/FIU database).

Mapping and Monitoring Recommendations

• Photointerpret 2004 aerial photography. 

• Acquire and photointerpret new imagery.

Management and Restoration Recommendations

• Continue assessment of the effects of nutrient enrichment on seagrass ecosystems.

Mapping Data and Imagery: The South Florida Geographic Information System benthic habitat 

data set includes areal extent of seagrass beds, interpreted from 1:48,000 scale natural color 

aerial photography taken in 1992. The FKNMS photography was digitized by a 

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photogrammetrist and stereo analytical plotters made available by the National Oceanographic 

and Atmospheric Administration. IKONOS satellite imagery from 2006 is being interpreted.

Monitoring Data: Seagrass monitoring has been conducted in the FKNMS quarterly and 

annually since 1996. Summary reports and monitoring data are available on the FIU FKNMS 

Seagrass website (http://serc.fiu.edu/seagrass/!CDreport/DataHome.htm).

Pertinent Reports and Scientific Publications

COLLADO-VIDES, L., V. G. CACCIA, J. N. BOYER, and J. W. FOURQUREAN. 2007. Tropical 

seagrass-associated macroalgae distributions and trends relative to water quality. Estuarine, 

Coastal and Shelf Science 73: 680–694.

HERBERT, D. A., and J. W. FOURQUREAN. 2009. Phosphorus availability and salinity control 

productivity and demography of the seagrass Thalassia testudinum in Florida Bay. Estuaries 

and Coasts 32: 188–201.

KIRSCH, K. D., K. A. BARRY, M. S. FONSECA, P. E. WHITFIELD, S. R. MEEHAN, J. W. 

KENWORTHY, and B. E. JULIUS. 2005. The mini-312 program: an expedited damage 

assessment and restoration process for seagrasses in the Florida Keys National Marine 

Sanctuary. Journal of Coastal Research 40: 109–119.

LAPOINTE, B. E., P. J. BARILE, and W. R. MATZIE. 2004. Anthropogenic nutrient enrichment 

of seagrass and coral reef communities in the Lower Florida Keys: discrimination of local versus 

regional nitrogen sources. Journal of Experimental Marine Biology and Ecology 308: 23–58.

General References and Additional Information

Florida Keys National Marine Sanctuary Seagrass Status and Trends Monitoring Data: 

http://serc.fiu.edu/seagrass/!CDreport/DataHome.htm, accessed March 2011.

Contacts

Mapping: Paul Carlson, Florida Fish and Wildlife Research Institute, 727-896-8626; 

paul.carlson@fwc.state.fl.us.

Monitoring: Jim Fourqurean, Florida International University, 305-348-4084; 

jim.fourqurean@fiu.edu.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Florida Bay

Contacts: Penny Hall (Monitoring) and Paul Carlson (Mapping), Florida 

Fish and Wildlife Research Institute

General Assessment: In 2004, approximately 145,300 acres of seagrass were mapped in 

Florida Bay (Figure 1). Seagrass area decreased slightly since 1992 when 146,600 acres of 

seagrass were mapped. Seagrass cover in western Florida Bay suffered significant losses in the 

late 1980s and early 1990s as the result of a massive, apparently natural die-off. Seagrasses

appear to have recovered from this event, based on data from the most recent (2004) imagery. 

In 2005, Hurricanes Katrina and Wilma passed directly over Florida Bay with serious impacts on 

mangroves and aboveground communities. Seagrasses, however, appear to have been less 

affected. Thick phytoplankton blooms occurred in the eastern basins in 2007 and 2008, but they 

abated in 2009. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover and species Fairly stable

Water clarity Local Phytoplankton blooms 

(eastern bay)

Nutrients Good

Phytoplankton Variable High in eastern bay

Propeller scarring Local Within Everglades Park

Geographic Extent: Florida Bay lies at the southern end of the Florida peninsula. The total 

area of Florida Bay within the boundaries of Everglades National Park is approximately 395,000 

acres, or 615 sq. mi. 

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Figure 1. Seagrass cover in Florida Bay, 2004. The blue area in the middle of the Bay was 

uninterpretable because of suspended sediment.

Mapping and Monitoring Recommendations

• Continue aerial photography and mapping of the north half of Florida Bay at least every 5 

years and the entire bay every 10 years. 

• Continue twice-yearly on-ground monitoring.

Management and Restoration Recommendations

• Continue the program initiated by Everglades National Park staff to reduce propeller scarring 

in the park. 

• Continue monitoring programs for collection of data that will allow prediction of the impacts of 

changing hydrology due to planned restoration of the Everglades.

Summary Assessment: Seagrass beds are generally stable across Florida Bay in terms of 

both acreage and species composition. Persistent phytoplankton blooms in the northeastern 

portion of the bay may be affecting seagrasses, particularly turtle grass (Thalassia testudinum). 

Recent hurricanes (for example, Wilma in 2005) had minimal impact on seagrass beds in the 

bay. Propeller scarring of shallow banks near boat channels in Everglades National Park affects 

some seagrass beds. 

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Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Stable

Seagrass meadow texture Stable

Seagrass species composition Stable

Overall seagrass trends Stable Phytoplankton blooms

Seagrass Stressors Intensity Impact Explanation

Water clarity Local Northeastern bay

Nutrients Good

Phytoplankton Variable High in eastern bay

Natural events Low Hurricanes

Propeller scarring Local Within Everglades Park

Seagrass Mapping Assessment: Mapping assessments from interpretation of aerial 

photography have shown little change in total seagrass area in Florida Bay. In 1992, 146,615 

acres of seagrass covered Florida Bay, and in 2004, 145,308 acres of seagrass were mapped, 

a loss of 1,307 acres, or 0.9%. 

Monitoring Assessment: As part of the Florida Bay Fisheries Habitat Assessment Program 

(FHAP), staff of the Florida Fish and Wildlife Research Institute (FWRI) monitor seagrass 

ecosystems twice a year, in May and October. This monitoring program has been under way 

since 1996. Throughout Florida Bay, turtle grass is the dominant seagrass, occurring in at least 

75% of the sampling locations in all subregions of the bay. In 2005, abundance of turtle grass 

exceeded 80% in all regions of Florida Bay (Figure 2); in 2008, turtle grass abundance had 

dropped to 75% in the northeastern bay, perhaps reflecting effects of an ongoing phytoplankton 

bloom there. Shoal grass (Halodule wrightii) was the second most abundant seagrass and was 

most abundant in the north central bay and the western bay in both 2005 and 2008. Manatee 

grass (Syringodium filiforme) was abundant only in the western bay. In 2008, star grass 

(Halophila engelmannii) was found in the north central bay but was absent across the bay in 

2005. The occurrence of bare sampling locations was greatest in the northeastern bay and 

showed a sharp increase from 2.5% to 10% between 2005 and 2008 in the south region of 

Florida Bay.

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Figure 2. Mean frequency of occurrence of seagrasses in Florida Bay, 2005 and 2008 (data from 

FWRI FHAP).

Seagrass abundance information obtained during monitoring in 2009 demonstrates the predominance of turtle grass in Florida Bay (Figure 3) and its greater abundance in western 

portions of the bay. Shoal grass was less abundant in the western bay in 2009 compared with 

earlier years and showed its greatest abundance in the north central bay (Rankin Lake and 

Whipray Basin) and in areas near the Keys in the northeastern bay (Barnes and Blackwater 

sounds). Manatee grass was much less common than turtle grass or shoal grass and was most 

abundant in the western bay in 2005, 2008, and 2009. 

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Figure 3. Abundance of seagrass species across Florida Bay, 2009 (data from FHAP).

Mapping and Monitoring Recommendations

• Acquire aerial photography or satellite imagery of the northern half of the bay every 5 years 

and the entire bay every 10 years. 

• Continue FHAP and Florida International University monitoring programs to assess long-term 

changes and provide background information before the planned hydrologic restoration of the 

Everglades.

Management and Restoration Recommendations

• Evaluate potential impacts of changing hydrology due to Everglades restoration.

• Assess nutrient inputs from increasing development in the Florida Keys.

• Mitigate and minimize propeller scarring on banks adjacent to channels in the Everglades 

National Park.

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Mapping Data and Imagery: The South Florida Water Management District (SFWMD) acquired 

aerial photography in the spring of 2004, and images were photointerpreted and ground-truthed. 

Benthic habitats were defined using the Habitat Classification Categories for Florida Bay 

Benthic Habitat Mapping—2004/2005, Version 3-23-05.

Monitoring Data: Monitoring data are available from the Florida Bay Fisheries Habitat 

Assessment Program (FWRI, Penny Hall), funded by SFWMD; and the Florida Keys National 

Marine Sanctuary Seagrass Status and Trends Monitoring Data (Florida International University, 

James Fourqurean).

Pertinent Reports and Scientific Publications

HACKNEY, J. W., and M. J. DURAKO. 2004. Size-frequency patterns of morphometric 

characteristics of the seagrass Thalassia testudinum reflect environmental variability. Ecological 

Indicators 4: 55–71.

HALL, M. O., M. J. DURAKO, J. W. FOURQUREAN, and J. C. ZIEMAN. 1999. Decadal 

changes in seagrass distribution and abundance in Florida Bay. Estuaries and Coasts 22: 445–

459.

HALL, M. O., K. MADLEY, M. J. DURAKO, J. C. ZIEMAN, AND M. B. ROBBLEE. 2006. 

Florida Bay. Pp. 242–253 in L. Handley, D. Altsman and R. DeMay (eds.). Seagrass status and 

trends in the northern Gulf of Mexico, 1940–2002, Scientific Investigations Report 2006-5287, 

U.S. EPA 855-R-04-003. 267 p.

MADDEN, C. J., D. T. RUDNICK, A. A. MCDONALD, K. M. CUNNIFF, and J. W. 

FOURQUREAN. 2009. Ecological indicators for assessing and communicating seagrass status 

and trends in Florida Bay. Ecological Indicators 9(6, Supplement 1): S68–S82.

General References and Additional Information

Florida Keys National Marine Sanctuary Seagrass Status and Trends Monitoring Data: 

http://serc.fiu.edu/seagrass/!CDreport/DataHome.htm, accessed March 2011.

2010 Everglades Seagrass Workshop, Everglades National Park, 

http://www.nps.gov/ever/naturescience/2010seagrassworkshop.htm, accessed March 2011.

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Contacts

Monitoring: Penny Hall, Florida Fish and Wildlife Research Institute, 727-896-8626; 

penny.hall@myfwc.com, and James Fourqurean, Florida International University, 305-348-

4084; jim.fourqurean@fiu.edu.

Mapping: Paul Carlson, Florida Fish and Wildlife Research Institute, 727-896-8626; 

paul.carlson@myfwc.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for Biscayne Bay

Contacts: Steve Blair and Chris Avila, Miami–Dade County Department of Environmental 

Resource Management, Penny Hall, Fish and Wildlife Research Institute, and Pamela 

Sweeney, Biscayne Bay Aquatic Preserves (Monitoring); Paul Carlson, Fish and Wildlife 

Research Institute (Mapping)

General Assessment: Seagrasses cover extensive areas (159,363 acres, from aerial 

photography acquired in 2004 and 2005) in the Biscayne Bay region (Figure 1). Mapping data 

from 1992 indicate that seagrass beds in the adjacent nearshore Atlantic Ocean accounted for 

an additional 104,910 acres. Most of the seagrass acreage in the Biscayne Bay region (120,756 

acres) occurs in Biscayne Bay proper, as continuous beds. Turtle grass (Thalassia testudinum)

is the dominant seagrass species in Card Sound and southern Biscayne Bay, while northern 

Biscayne Bay has more diverse seagrass beds, the most common species being manatee 

grass (Syringodium filiforme). 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover and species Stable Cover is increasing

Water clarity Good

Nutrients Good

Phytoplankton Variable High in Card Sound

Propeller scarring Local Near high-use areas

Geographic Extent: The Biscayne Bay region includes North Biscayne Bay, Biscayne Bay 

proper, Card Sound, and Barnes Sound and extends from the Oleta River north of Miami Beach 

on the east coast of Florida south through Biscayne National Park, Card Sound, and Barnes 

Sound to the U.S. Highway 1 bridge to the Keys. 

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Figure 1. Seagrass cover in the Biscayne Bay region, from photography collected in 2004 and 

2005.

Mapping and Monitoring Recommendations

• Map the region’s seagrass every six years. 

• Continue and expand seagrass-monitoring programs. Monitoring has been conducted by staff 

of several agencies. The Fisheries Habitat Assessment Program (FHAP) of the Fish and Wildlife 

Research Institute (FWRI) conducted monitoring twice a year from 2005 through 2009 at 

randomly selected sampling points. Staff of the Miami–Dade County Department of 

Environmental Resource Management (Miami–Dade DERM) sample 100 probabilistic randomly 

chosen sites and 12 nonrandom fixed sites each June.

Management and Restoration Recommendations

• Evaluate the response of seagrass beds to anticipated hydrological changes associated with 

restoration of the Everglades. 

• Evaluate nutrient loading from land runoff, the greatest threat to seagrass health in Biscayne 

Bay. 

• Continue to monitor phytoplankton populations in Card Sound, where they have been 

elevated.

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Summary Assessment: Seagrass cover is extensive (159,363 acres) in the Biscayne Bay 

region and increased in area in all subregions of the bay from 1992 to 2005 except North 

Biscayne Bay, which lost 660 acres, or 11% (Table 1). Species composition is generally stable. 

Comparison of monitoring data from 2005 and 2007 (see Figure 2) showed few differences 

between years. However, there are substantial differences in seagrass species composition 

among the regions of Biscayne Bay. Turtle grass (T. testudinum) dominates beds in Card 

Sound and southern Biscayne Bay, while in northern Biscayne Bay seagrass beds are more 

diverse, with manatee grass (S. filiforme) occurring most frequently. The proportion of bay 

bottom that is bare also increases from south to north. Nutrient loading from the watershed, 

changing hydrologic regimes, and boating are likely stressors to seagrass beds. 

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass cover Stable Cover is increasing

Seagrass meadow texture Stable

Seagrass species composition Stable

Overall seagrass trends Stable Urban runoff

Seagrass Stressors Intensity Impact Explanation

Water clarity Good

Nutrients Good

Phytoplankton Variable High in Card Sound

Natural events Low Hurricanes

Propeller scarring Local Near high-use areas

Seagrass Mapping Assessment: Mapping of aerial photography acquired in 2004 and 2005 

showed that seagrasses covered 159,363 acres in the Biscayne Bay region and that most of the 

acreage (120,756 acres, or 76%) was found in Biscayne Bay proper (Table 1). The classification 

system used for seagrass cover from the 1992 imagery differed from that for the 2004–05 

imagery sets. Change analysis between 1992 and 2004–05, therefore, is useful only for total 

seagrass area. We conducted change analysis in ArcMap software, using identical polygons or 

spatial extents for 1992 and 2004–05 for the Biscayne Bay region. Cover was least in North 

Biscayne Bay (5,208 acres) and had decreased from the 5,868 acres mapped in 1992. Barnes 

and Card sounds showed small increases in seagrass acreage in 2004, with seagrass covering 

18,793 and 14,606 acres that year, respectively. Overall, seagrasses increased by 5,536 acres, 

or 3.60%, between 1992 and 2004–05. In 2004–05, 92% of seagrass beds in the Biscayne Bay

region were classified as continuous seagrass. In addition, in 1992, 104,910 acres of seagrass 

were mapped along the margin of the nearshore Atlantic Ocean outside the boundaries of 

Biscayne Bay. 

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TABLE 1. SEAGRASS ACREAGE IN THE BISCAYNE BAY REGION

IN 1992 AND 2004–2005

A. Acreage in 1992

Habitat Type Barnes 

Sound

Card 

Sound

Biscayne Bay 

Proper

Northern 

Bay

Biscayne 

Bay Total

Nearshore 

Atlantic

Continuous seagrass 14,733 11,672 56,464 3,846 86,715 79,296

Hardbottom/seagrass 3,107 1,634 42,842 0 47,583 7,605

Patchy seagrass 795 1,106 15,606 2,022 19,529 18,009

 All seagrass 18,635 14,412 114,912 5,868 153,827 104,910

B. Acreage in 2004–2005

Year Imagery Acquired: 2004 2004 2005 2005 2004–05

Habitat Type Barnes 

Sound

Card 

Sound

Biscayne Bay 

Proper

Northern 

Bay

Biscayne 

Bay Total

Nearshore 

Atlantic

Continuous seagrass 18,479 14,388 109,440 4,277 146,584 n/a

Patchy seagrass 314 218 11,316 931 12,779 n/a

 All seagrass 18,793 14,606 120,756 5,208 159,363 n/a

C. Change in acreage for all seagrass

2004 2004 2005 2005 2004–05

Barnes 

Sound

Card 

Sound

Biscayne Bay 

Proper

Northern 

Bay

Biscayne 

Bay Total

Acres 158 194 5,844 −660 5,536

% Change 0.85% 1.35% 5.09% −11.2% 3.60%

Monitoring Assessment: The Fisheries Habitat Assessment Program (FHAP), supervised by 

Penny Hall, monitored seagrasses in Biscayne Bay twice a year from 2005 through 2009. 

Monitoring assessments were conducted each May and October using fixed sampling points 

and Braun-Blanquet assessment of 0.25-m

2

quadrats. In 2005 and in 2007 (see Figure 2, 

below), turtle grass occurred most frequently in Card Sound and southern Biscayne Bay (> 80% 

frequency of occurrence). Manatee grass occurred most frequently in northern Biscayne Bay 

during both years (52–57% frequency of occurrence). Shoal grass (Halodule wrightii) occurred 

in all segments of Biscayne Bay but generally at < 30% frequency of occurrence. The number of 

bare quadrats increased from south to north and was > 20% frequency of occurrence in 

northern Biscayne Bay in 2007, where seagrass cover decreased from 1992 to 2005. Significant 

changes in species distributions or occurrence were not observed between the two years.

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Figure 2. Mean frequency of occurrence of seagrasses in Biscayne Bay, 2005 and 2007 (data from 

FHAP/FWRI).

Mapping and Monitoring Recommendations

• Acquire and interpret new imagery every six years. 

• Continue and expand monitoring programs.

Management and Restoration Recommendations

• Evaluate the response of seagrass beds to anticipated hydrological changes associated with 

restoration of the Everglades. 

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• Evaluate nutrient loading from land runoff, the greatest threat to seagrass health in Biscayne 

Bay. 

• Continue to monitor phytoplankton populations in Card Sound, where they have been 

elevated.

Mapping Data and Imagery: Aerial imagery acquired in 1992 is part of the GIS data set of 

benthic habitats of South Florida archived at the Fish and Wildlife Research Institute. The 

presence of seagrass beds, classified as either continuous beds, mixed hard bottom and 

seagrass, or patchy seagrass, was interpreted from 1:48,000 scale natural color aerial 

photography. The photographs were digitized by Greenhorne and O’Mara (West Palm Beach, 

FL) using stereo analytical plotters. Imagery acquired in 2004 and 2005 was interpreted by 

PhotoScience Inc.(St. Petersburg, FL) using a modified Florida Land Use Cover Classification 

System in which seagrasses were classified as continuous or patchy in extent. ArcMap shape 

files of benthic habitats are distributed on the Fish and Wildlife Research Institute (FWRI) 

Marine Resources Geographic Information System (MRGIS) website 

(http://ocean.floridamarine.org/mrgis/). 

Monitoring Data: Data summaries of monitoring programs are available from the Fisheries 

Habitat Assessment Program (FWRI, Penny Hall), funded by the South Florida Water 

Management District for 2005 through 2009 and from the Miami-Dade Department of 

Environmental Resource Management. 

Pertinent Reports and Scientific Publications

LIRMAN, D., and W. P. CROPPER. 2003. The influence of salinity on seagrass growth, 

survivorship, and distribution within Biscayne Bay, Florida: field, experimental, and modeling 

studies. Estuaries and Coasts 26: 131–141.

General References and Additional Information

Miami–Dade County Department of Environmental Resource Management: 

http://www.miamidade.gov/derm; accessed March 2011.

Biscayne Bay Aquatic Preserve: http://www.dep.state.fl.us/coastal/sites/biscayne/info.htm; 

accessed March 2011.

Biscayne National Park: http://www.nps.gov/bisc/index.htm; accessed March 2011.

South Florida Information Access: http://sofia.usgs.gov/virtual_tour/biscaynebay/index.html; 

accessed March 2011.

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Contacts

Monitoring:

Steve Blair and Chris Avila, Miami–Dade County Department of Environmental Resource 

Management, 305-372-6853, blairs@miamidade.gov; 305-372-6861, avilac@miamidade.gov. 

Penny Hall, Fish and Wildlife Research Institute, 727-896-8626, penny.hall@myfwc.com.

Pamela Sweeney, Biscayne Bay Aquatic Preserves, 305-795-3486, 

Pamela.sweeney@dep.state.fl.us.

Sarah Bellmund, Biscayne National Park, 786-335-3624, sarah_bellmund@nps.gov.

Mapping: 

Paul Carlson, Fish and Wildlife Research Institute, 727-896-8626, paul.carlson@myfwc.com. 

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Florida Seagrass Integrated Mapping and Monitoring 

Program 

Summary Report for Lake Worth Lagoon 

Contacts: Paul Davis and Eric Anderson; Palm Beach County 

Department of Environmental Resource Management (Mapping 

and Monitoring) 

General Assessment: Based on interpretation of aerial photographs, seagrass cover in Lake 

Worth Lagoon (LWL) between 2001 and 2007 was generally stable, with a slight increase in 

2007. Approximately 1,688 acres of seagrass were mapped in the lagoon in 2007. Most of the 

increase can be attributed to greater areas of patchy seagrass beds throughout the lagoon.

Most of the seagrass (65%) is found in North LWL near Singer Island in Riviera Beach. The 

dominant species in North LWL are manatee grass (Syringodium filiforme), turtle grass 

(Thalassia testudinum), and shoal grass (Halodule wrightii). The least coverage by seagrasses 

occurs in the central (12%) and southern (23%) portions of the lagoon; dominant species are 

Johnson’s seagrass (Halophila johnsonii), paddle grass (H. decipiens), and shoal grass.

Seagrass species composition also appears to be stable in all sections of the lagoon. Annual 

transect monitoring indicated decreases in cover and density after the 2004, 2005, and 2006 

hurricanes. Record high levels of seagrass cover and density were noted in 2007, but slight 

decreases were observed in 2008 and 2009. Stressors include nutrients, suspended sediments, 

and turbidity associated with stormwater discharges from three major canals (C-51, West Palm 

Beach Canal; C-16, Boynton Canal; and C-17, Earman River). Freshwater discharge was

elevated after the 2004, 2005, and 2006 hurricanes, but they have returned to background 

levels. Minor propeller scarring is evident around South Lake Worth (Boynton) Inlet and Lake 

Worth (Palm Beach) Inlet but is minimal elsewhere.

Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Stable? Little change, 2001−07

Water clarity Declining Affected by runoff, storms

Nutrients, turbidity Increasing Affected by runoff, storms

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Mapping and Monitoring Recommendations

• Map and monitor seagrasses in areas where conventional aerial photography is not effective 

(where water is too deep, visibility through the water column is poor, and diminutive species

such as paddle grass and Johnson’s seagrass are dominant).

• Collect aerial photography for the entire region again in 2011–12. 

• Continue annual fixed-transect monitoring.

• Evaluate the effectiveness of patch scale 

monitoring and continue if effective.

Management and Restoration 

Recommendations

• Assess proposed changes in freshwater 

discharges, nutrient loads, and sediment 

loads from the canals that empty into LWL.

• Evaluate nutrient and suspended sediment 

loading from the agricultural areas (L8 basin) 

and identify the most cost-effective 

management options.

Summary Assessment: Seagrass acreage 

in Lake Worth Lagoon remained relatively 

stable between 2001 and 2007, although 

some increases in patchy cover were 

observed (Table 1). From 1990 to 2001, 484 

acres of seagrass, or 23%, were apparently 

lost, but different mapping methods were 

used in the 1990 assessment, which may 

account for some of this difference. Annual 

fixed transect monitoring has shown 

fluctuations in seagrass cover over the nine 

years of the project: years of poor water 

quality due to increased freshwater releases 

(2004, 2005, and 2006) coincided with

Figure 2. Seagrass beds in Lake Worth Lagoon, 

2007.

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widespread reductions in seagrass cover. Monitoring programs documented increases in

seagrasses in 2001, 2002, 2007, 2008, and 2009, when water quality was better.

However, it is very difficult to provide an accurate estimate of seagrass habitat within the lagoon 

because of poor water quality, limited visibility through the water column, and the very small size 

and limited optical signature of Johnson’s seagrass and paddle grass. Stressors include 

increased freshwater inputs to the lagoon, nutrients, sedimentation, turbidity, and phytoplankton 

blooms associated with runoff from urban stormwater and the regional canal discharges.

Impacts of regional canal discharges extend throughout the Lagoon but are most severe in the 

central portions adjacent to the C-51 canal. The hurricanes of 2004, 2005, and 2006 also 

affected seagrass beds. 

Seagrass Mapping Assessment: Between 2001 and 2007, total seagrass cover for the LWL

region increased from 1,647 acres to 1,688 acres, or 2.5% (Table 1). The majority of the 

increase resulted from a greater area of patchy seagrass beds throughout the lagoon. Seagrass 

cover varies throughout the lagoon, with the most seagrass found in the northern end (65%),

compared with 12% in the central segment and 23% in the southern segment. Comparing the 

2001 maps to the 2007 maps revealed a 59-acre decrease in seagrass cover in the northern 

segment, a 9-acre increase in the central segment, and a 91-acre increase in the southern 

segment. The results are considered an underestimate of seagrass cover because areas of the 

lagoon have poor visibility and the tiny and thus difficult to assess Johnson’s seagrass and 

paddle grass are dominant. As a result, mapping efforts may not have accurately identified 

seagrass cover. Mapping efforts identified only seagrass beds that were 0.25 acre or more in 

size and were designed to detect large-scale changes.

Seagrass Status Indicators Status Trend Assessment, Causes

Seagrass abundance Stable Slight increase, 2001−07

Seagrass species composition Poor

Overall seagrass trends Stable Stormwater runoff impacts

Seagrass Stressors Intensity Impact Explanation

Water clarity Poor Affected by runoff, storms

Nutrients Relatively high Affected by runoff, storms

Phytoplankton Relatively high Affected by runoff, storms

Natural events Serious impacts 2004-06 hurricanes

Propeller scarring Localized Near inlets

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TABLE 1. SEAGRASS ACREAGE IN LAKE WORTH LAGOON

Regions of Lagoon

Habitat type North Central South Total

2001

Patchy 13 1 0 14

Continuous 1,136 195 302 1,633

 All seagrass 1,149 196 302 1,647

2007

Patchy 21 21 10 52

Continuous 1,069 184 383 1,636

 All seagrass 1,090 205 393 1,688

Change 2001-2007

Patchy 8 20 10 38

Continuous −67 −11 81 3

 All seagrass −59 9 91 41

Percent change −5.1% 4.6% 30.1% 2.5%

Monitoring Assessment: In 2000, the Palm Beach County Department of Environmental 

Resource Management (PBC DERM) initiated a long-term seagrass monitoring program that

included the establishment and annual assessment of nine fixed transects throughout LWL

(Figure 3). With improving water quality and clarity, seagrasses are expected to grow at greater 

depths or to increase in density and diversity. To test this hypothesis, transects were located in 

areas where the lagoon bottom increased in depth by 1–2 ft. within 50–100 ft. of the edge of an 

existing seagrass bed. The first five years of surveys showed fluctuations in seagrass cover with 

no obvious pattern of increase or decrease—until the hurricanes of 2004. The survey conducted 

in June 2005 and 2006 showed a major decrease in seagrass cover in most areas of the 

lagoon. This loss is believed to be the result of increased turbidity and suspended sediments 

caused by runoff from the hurricanes and discharges from Lake Okeechobee, as well as burial 

and scour from wave action. Areas suffering the least severe impact were shallow sites and 

sites closer to inlets, where water quality was least affected. The 2007 survey reported record 

highs in terms of total number of sampling locations at which seagrass was observed and of 

percentage cover at the sampling locations. The 2007, 2008, and 2009 surveys documented not 

only increases in seagrass cover but also the expansion of beds into deeper water.

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Figure 3. Seagrass occurrence along monitoring transects, 2000–09. In 2000, the project consisted of 

only five transects (15 stations). In 2001–05 and 2007–09, it consisted of nine transects (27 stations). In 

2006, poor water clarity allowed for the monitoring of only 4 transects (12 stations). In 2006, the number 

shown is the average of 2005 and 2007 values.

Management and Restoration Recommendations

• Assess proposed changes in freshwater discharges, nutrient loads, and sediment loads from 

the canals that empty into LWL.

• Evaluate nutrient and suspended sediment loading from the agricultural areas (L8 basin), and

identify the most cost-effective management options.

Mapping Data and Imagery: In 2001 and 2007, natural color aerial photography of the Lake 

Worth Lagoon region was flown at 1:10,000 scale for Palm Beach County by U.S. Imaging

(Bartow, FL). The original negatives and copies of diapositives are housed at PBC DERM. 

Benthic habitats were classified and mapped from this dataset by Avineon Inc. (Clearwater, FL)

using the Florida Land Use Cover Classification System. ArcMap shape files of benthic habitats 

are available on the Fish and Wildlife Research Institute Marine Resources Geographic 

Information System (MRGIS) website (http://ocean.floridamarine.org/mrgis/) or by contacting 

PBC DERM.

Monitoring Data: A variety of groups and agencies monitors seagrass in the Lake Worth 

Lagoon (Table 2). Since 2000, PBC DERM has been monitoring seagrass annually along nine

transects (27 stations) throughout LWL with the Fixed Transect Monitoring Project (FTMP).

Since 2006 the Fish and Wildlife Research Institute (FWRI) and the National Oceanic and 

Atmospheric Administration (NOAA) have been monitoring Johnson’s seagrass (H. johnsonii) at 

8 locations and 33 stations in the lagoon for the H. johnsonii Recover Team. And in 2009, the 

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South Florida Water Management District (SFWMD) and the U.S. Army Corps of Engineers

(USACOE) began bimonthly monitoring at five locations (with 30 stations at each) for the 

Comprehensive Everglades Restoration Plan (CERP)/Restoration, Coordination and Verification 

(RECOVER) Seagrass Monitoring Section. 

TABLE 2. MONITORING PROGRAMS IN LAKE WORTH LAGOON

Program Agency Frequency Number of 

locations

Number of

stations per 

location

Annual total 

of stations

LWL FTMP PBC DERM Annually 9 3 27

Johnson’s 

Recovery FWRI/NOAA Annually 9 33 297

CERP/ 

RECOVER 

SFWMD/ 

USACOE Bimonthly 5 30 900

Pertinent Reports and Scientific Publications

CRIGGER, D. K., G. A. GRAVES, and D. L. FIKE. 2005. Lake Worth Lagoon conceptual 

ecological model. Wetlands 25: 943–954.

PALM BEACH COUNTY DEPARTMENT OF ENVIRONMENTAL RESOURCES 

MANAGEMENT IN CONJUNCTION WITH DAMES AND MOORE. 1990. Lake Worth Lagoon 

natural resources inventory and resource enhancement study, West Palm Beach, Florida. 226 

p.

PALM BEACH COUNTY DEPARTMENT OF ENVIRONMENTAL RESOURCES 

MANAGEMENT AND STATE OF FLORIDA DEPARTMENT OF ENVIRONMENTAL 

PROTECTION, SOUTHEAST DISTRICT. 1998. Lake Worth Lagoon management plan, West 

Palm Beach, Florida. 257 p.

PALM BEACH COUNTY DEPARTMENT OF ENVIRONMENTAL RESOURCES 

MANAGEMENT. 2008. Palm Beach County Mangrove and Seagrass Mapping Project. Final 

report prepared by Avineon Inc., West Palm Beach, Florida. 18 p.

PALM BEACH COUNTY DEPARTMENT OF ENVIRONMENTAL RESOURCES 

MANAGEMENT. 2009. Lake Worth Lagoon: fixed transect seagrass monitoring cumulative 

report 2000–2008. Final report prepared by Applied Technology and Management Inc., West 

Palm Beach, Florida.

REstoration COordination and VERification. 2007. Final 2007 system status report. Section 

5 Northern Estuaries Module, Comprehensive Everglades Restoration Plan. 11 p.

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REstoration COordination and VERification. 2010. 2009 system status report draft. Section 4 

Northern Estuaries Module, Comprehensive Everglades Restoration Plan. 91 p., see also: 

http://www.evergladesplan.org/pm/ssr_2009/hc_ne_sav_results_lake_worth.aspx; accessed 

March 2011.

General References and Additional Information

KING, JOE. 2010. Numerical nutrient criteria for the Lake Worth Lagoon. Palm Beach County 

Department of Environmental Resources Management, March 2010: 

http://www.dep.state.fl.us/water/wqssp/nutrients/docs/estuarine/ftpierce/lake_worth_lagoon.pdf; 

accessed March 2010.

Palm Beach County: http://www.pbcgov.com/erm/lakes/seagrasses/.

Contacts

Mapping and Monitoring: Paul Davis, Palm Beach County Department of Environmental 

Management, 561-233-2509, pdavis@pbcgov.org; Eric Anderson, Palm Beach County 

Department of Environmental Management, 561-233-2514, eanderson1@pbcgov.org.

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0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

10,000

1999 2001 2003 2005 2006 2007 Acres

Year

Southern Indian River Lagoon Seagrass Acreage (1999 - 2007)

Florida Seagrass Integrated Mapping and Monitoring 

Program

Summary Report for the Southern Indian River Lagoon

Contact: Becky Robbins, South Florida Water Management District (Mapping and Monitoring); 

Bud Howard and Lorene Bachmann, WildPine Ecological Laboratory, Loxahatchee River District 

(Mapping and Monitoring), and Penny Hall, Fish and Wildlife Research Institute (Monitoring)

General Assessment: Seagrass cover in Southern Indian River Lagoon (SIRL) increased 

between 1999 (7,808 acres) and 2007 (8,848 acres). However, SIRL seagrasses, particularly in 

the vicinity of the St. Lucie River, experienced significant impacts from hurricanes and 

associated freshwater discharges in 2004 and 2005. Impacts included decreases in cover and 

density and, to a lesser extent, burial by shifting bottom sediments. Seagrass status is 

improving, as documented by increases in mapped acreage, recruitment into areas left bare 

following the hurricanes, and transition from the diminutive Johnson’s seagrass (Halophila 

johnsonii) and paddle grass (Halophila decipiens) to the more robust, canopy-forming shoal 

grass (Halodule wrightii) and manatee grass (Syringodium filiforme). A 13% increase in mapped 

seagrass acreage occurred from 2005 to 2007, probably the result of continued post-hurricane 

recovery and drought, which encouraged more favorable salinities and increased water clarity.

Figure 1. Seagrass cover in the southern Indian River Lagoon, 1999-2007.

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Seagrass Status and Stresses Status Trend Assessment, Causes

Seagrass cover Increasing

Recovery following hurricane 

impacts; favorable salinities and 

improved water clarity due to 

drought conditions

Water clarity Improving

Apparent decline in total 

suspended solids , chlorophyll-a, 

and color, 1992–2008; recent 

improvements probably tied to 

drought conditions

Natural events

Significant 

localized impacts 

(vicinity of St. 

Lucie Inlet); 

recovery under 

way

2004, 2005 hurricanes 

Geographic Extent: The SIRL lies along the east coast of Florida from the St. Lucie/Indian 

River County line south to Jupiter Inlet. The IRL Surface Water Improvement and Management 

Plan (SWIM) identified 26 seagrass management units, or segments, throughout the lagoon 

(Steward et al., 2003). Five of the segments (22–26) lie within the SIRL; segment 22 is between 

the Indian River County line and the Fort Pierce Inlet, segments 23 and 24 are located between 

the Fort Pierce Inlet and the St. Lucie Inlet, and segments 25 and 26 occur between the St. 

Lucie Inlet and Jupiter Inlet. IRL SWIM efforts focus on improving water quality to restore and 

protect seagrasses. Therefore, the SIRL seagrass segment boundaries primarily follow the 

boundaries of five water quality zones (areas of relatively homogeneous water quality). Other 

factors, such as physical configuration and land use in the area, also support this segmentation 

scheme.

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Figure 2. Location of seagrass beds in the southern Indian River lagoon, 2006.

Mapping and Monitoring Recommendations

• Implement landscape-scale seagrass mapping projects and patch-scale, species-specific 

mapping and monitoring. Landscape-scale seagrass maps, based on aerial photographs and 

ground-truthing, have been produced for the SIRL every two to three years since 1986. These 

maps provide an overall understanding of changes in seagrass cover and distribution. However, 

they do not provide information about seagrass species distribution. Understanding seagrass 

species distribution is important for water management, because seagrass species found in the 

SIRL have species-specific salinity tolerance thresholds (Irlandi 2006). Species shifts may occur 

as a result of restoration projects, and these changes cannot be detected from aerial 

photographs. 

Management and Restoration Recommendations

• Improve management of water discharges from the watersheds surrounding the SIRL. The 

largest tributaries of the SIRL are the St. Lucie River/Estuary and the C-25 canal, which 

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discharges near the Fort Pierce Inlet. Managing the quality, quantity, and timing of these 

releases is needed for seagrass restoration in the St. Lucie Estuary and SIRL. 

• Restore natural water flows and improve water quality in the watershed. These efforts are part 

of the Comprehensive Everglades Restoration Plan (CERP), which is tasked with improving 

water delivery to tributaries.

Summary Assessment: Seagrass cover in the SIRL is increasing. Seagrass species 

composition and meadow texture are recovering in areas affected by hurricanes. Major 

stressors include light limitation and salinity extremes.

Seagrass 

Status 

Indicators

Status Trend Assessment, Causes

Seagrass 

cover

Increasing Recovery following hurricane impacts; favorable salinities 

and improved water clarity due to drought

Seagrass 

meadow 

texture

Improving

Recovery following hurricane impacts, colonization of 

bare bottom, and species shifts from diminutive to more 

robust (canopy-forming) species

Seagrass 

species 

composition

Improving

In areas impacted by hurricanes, bare areas were first 

typically colonized by Halophila spp. and continue to 

trend toward canopy-forming species

Overall 

seagrass 

trends

Improving Improving water clarity 

Seagrass 

Stressors Intensity Impact Explanation

Water clarity Improving Affected by runoff, storms

Nutrients Relatively 

low Affected by runoff, storms

Phytoplankton Relatively 

low Affected by runoff, storms

Natural events Localized 

impacts Hurricanes

Seagrass Mapping Assessment: Robbins and Conrad (2001) provide a detailed analysis of 

SIRL seagrass map data from 1986 to 1999. A detailed change analysis for subsequent data 

(through 2009) is being done by the South Florida Water Management District (SFWMD) and is 

expected to be completed in 2010. Because trends observed for the SIRL as a whole may not 

reflect seagrass trends for individual segments, the 2010 evaluation will look in detail at 

changes in acreage and distribution by lagoon segment. In general, the acreage of dense 

seagrass decreased in most segments following the 2004–05 hurricanes. All segments showed 

an increase in overall cover from 2005 to 2007 except segment 26, in which no appreciable 

change was noted (Table 1). The increase in acreage from 2005 through 2007 is probably due 

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0

10

20

30

40

50

60

70

80

90

100 Percent Occurrence/Cover

Date

Percent Occurrence/Cover of Syringodium filiforme

(Mean ± SE)

Percent Occurrence - SFIL Percent Cover SFIL (New Methods) Hurricane

to a combination of post-hurricane recovery and drought, which provided favorable salinities and 

clear water. The portion of the SIRL most affected by water management practices is the area 

that receives discharges from the St. Lucie Estuary. Accordingly, seagrasses in the portion of 

the lagoon adjacent to the estuary mouth were mapped to the species level (using detailed 

ground-truthing and GPS technology) in 2007–08 (Avineon 2008). Species-specific maps have 

been produced for the St. Lucie Estuary for 1997 (URS Greiner Woodward Clyde, 1999) and 

2007 (Ibis Environmental Inc., 2007).

TABLE 1.SEAGRASS ACREAGE IN THE SOUTHERN INDIAN RIVER LAGOON SYSTEM

Segment 1940 1992 1996 1999 2003 2005 2007 Change 

2005–07

Segment 22 764 2,310 2,649 2,978 2,910 2,806 2,978 172

Segment 23 3,244 4,273 5,187 2,856 3,238 3,335 4,081 746

Segment 24 2,754 1,513 1,589 1,520 1,342 1,189 1,299 110

Segment 25 358 413 136 134 167 156 172 16

Segment 26 548 365 303 320 234 322 318 −4

Total 7,668 8,874 9,864 7,808 7,891 7,808 8,848 1,040

Monitoring Assessment: Monitoring provides species-specific information for assessing SIRL 

seagrass resources. Preliminary results of monthly transect monitoring and a new method of bimonthly patch-quadrat monitoring indicate that sites near the mouth of the St. Lucie River 

Figure 3. Percentage occurrence of manatee grass (S. filiforme) in the southern Indian River Lagoon, 

2002—2009.

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previously dominated by manatee grass were significantly affected (grasses lost or eliminated) 

following the 2004 and 2005 hurricanes. Recovery toward pre-hurricane conditions is being 

documented by monitoring. An example of the hurricane impacts and recovery process is 

shown in Figure 3 for a SIRL monitoring site located near the influence of the St. Lucie River. 

Additional data analysis by the SFWMD is planned for completion in 2010. Using probabilistic, 

post-2004 hurricane monitoring data collected in 2005 by Penny Hall’s team at the Fish and 

Wildlife Research Institute, we examined the frequency of occurrence of seagrass species by 

estuarine segment in the southern Indian River Lagoon (Figure 4). Seagrasses were found in 3–

68% of the quadrats, and overall, shoal grass was the most common species. In segments 22 

and 23, shoal grass and manatee grass were equally common. From segment 21 south, the 

number of bare quadrats increased sharply, with more than 96% of quadrats in segment 25 

having no seagrass. Halophila spp. were much less common, and of these, H. decipiens

(paddle grass) was most commonly observed and occurred in 26% of quadrats in segment 23. 

The threatened H. johnsonii (Johnson’s seagrass) was most frequent in segments 14 and 15, 

south of the SIRL. 

Mapping and Monitoring 

Recommendations

• Continue landscape-scale 

mapping from aerial photographs or 

ground recording every two to three 

years.

• Continue bimonthly patch-scale 

monitoring.

• Continue biannual transect 

monitoring. 

• Continue data evaluation.

Figure 4. Occurrence of seagrass 

species by estuarine segment in the 

SIRL and Lake Worth Lagoon, 2005. 

(Data from FWRI, Penny Hall, 2005).

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Management and Restoration Recommendations

• Continue to fund state and federal IRL restoration programs. Florida’s SWIM Program, the 

U.S. Environmental Protection Agency National Estuary Program, and the U.S. Army Corps of 

Engineers’ CERP Restoration Coordination and Verification (RECOVER) Monitoring and 

Assessment Plan (MAP) have identified seagrass ecosystems as critical habitats in the SIRL 

and have committed substantial resources toward restoration and protection. 

Mapping Data and Imagery: The SWIM Plan directs the St. Johns River Water Management 

District (SJRWMD) and SFWMD to map seagrasses in the IRL at two- to three-year intervals. 

Accordingly, SIRL seagrass maps have been prepared for the following years: 1986 (partial), 

1989 (partial), 1992, 1994, 1996, 1999, 2001, 2003, 2005, 2006, 2007, and 2009. SIRL 

seagrass mapping is based on interpretation of 1:24,000 and 1:10,000 aerial photographs by an 

outside contractor. In most cases, features on the aerial photographs were identified by means 

of photointerpretation keys and ground-truthing. Features are classified according to 

SJRWMD/SFWMD modified Florida Land Use Cover Classification System codes. Interpretation 

of aerial photographs and subsequent stereoscopic analysis of digital images were used to 

delineate the features and transfer the polygons into GIS data. An accuracy assessment report 

has been provided for the later surveys (since 1999). Species-specific, landscape-scale 

mapping of the Loxahatchee River Estuary was conducted by the Loxahatchee River District for 

SFWMD in 2007 and 2010 using 9m2quadrats and GPS.

Monitoring Data: Seagrass monitoring using transect methods has been conducted in the SIRL 

Lagoon twice a year (in winter and summer) since 1994 by regional agency staff and 

collaborators. The monitoring program is coordinated by the SJRWMD. Seagrass and 

macroalgal cover are estimated in 1-m

2

quadrats located every 5–10 m along 18 transects. A 

new (since 2007) seagrass patch-quadrat monitoring methodology is being used bimonthly at 

10 sites within the SIRL and is coordinated by the SFWMD. The new method includes 

haphazardly deploying 30 1-m

2

quadrats within specified boundaries. Percentage occurrence of 

seagrass species and macroalgal functional groups are determined within 25 subsections of the 

large quadrats. Additionally, seagrass canopy height is measured and quadrat location is 

recorded. Water quality monitoring has been conducted in the SIRL by the SFWMD since 1990. 

From October 1990 through July 1999, 40 stations were monitored quarterly. Beginning in 

January 2000, water quality stations were established along seagrass transects, and monitoring 

frequency was increased to seven times a year. 

Pertinent Reports and Scientific Publications

ARRINGTON, D. A. 2008. Spatial and temporal dynamics of seagrass in the Loxahatchee River 

estuary during the period October 2007–September 2008. Prepared for the South Florida Water 

Management District. West Palm Beach, Florida. Report from the Loxahatchee River District.

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AVINEON INC. 2008. Species specific SAV mapping test project (Phase II). Final project report 

for contract ST061300-WO05 for South Florida Water Management District, West Palm Beach, 

Florida. 24 p.

AVINEON INC. 2010. Final project report Saint Johns River Water Management District/South 

Florida Water Management District 2009 Indian River Lagoon seagrass mapping, May 2010. 49 

p.

IBIS ENVIRONMENTAL INC. 2007. 2007 St. Lucie Estuary submerged aquatic vegetation 

mapping study. Prepared for the South Florida Water Management District. West Palm Beach, 

Florida. 7 p.

IRLANDI, E. 2006. Literature review of salinity effects on submerged aquatic vegetation (SAV) 

found in the southern Indian River Lagoon and adjacent estuaries. South Florida Water 

Management District, West Palm Beach, Florida. 30 p.

RECOVER. 2009. 2009 System status report. Restoration Coordination and Verification 

Program, U.S. Army Corps of Engineers, Jacksonville, Florida, and South Florida Water 

Management District, West Palm Beach, Florida. 765 p., 

http://www.evergladesplan.org/pm/ssr_2009/ssr_main.aspx.

RIDLER, M. S., R. C. DENT, and L. R. BACHMAN. 2003. Viability and variability of seagrass 

communities in the Loxahatchee estuary and associated reach of the Indian River Lagoon 1998, 

2000, 2002, Report from the WildPine Ecological Laboratory, Loxahatchee River District, 17 p. + 

appendices. 

ROBBINS, R., and C. CONRAD. 2001. Southern Indian River Lagoon seagrass change 

analysis (1986–1999). South Florida Water Management District, West Palm Beach, Florida. 32 

p.

SIME, P. 2005. St. Lucie Estuary and Indian River Lagoon conceptual ecological model. 

Wetlands 25: 898–907.

STEWARD, J. S., R. BROCKMEYER, R. VIRNSTEIN, P. GOSTEL, P. SIME, and J. 

VANARMAN. 2003. Indian River Lagoon Surface Water Improvement and Management 

(SWIM) Plan, 2002 update. St. Johns River Water Management District, Palatka, Florida, and 

South Florida Water Management District, West Palm Beach, Florida. 272 p.

URS GREINER WOODWARD CLYDE. 1999. Distribution of oysters and submerged aquatic 

vegetation in the St. Lucie Estuary. Final report to the South Florida Water Management District 

(Contract No. C-7779). 91 p.

General References and Additional Information

CREAN, D. J., R. M. ROBBINS, and N. IRICANAN. 2007. Water quality target development in 

the southern Indian River Lagoon. Florida Scientist 70: 522–531.

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Loxahatchee River District: http://www.loxahatcheeriver.org/reports.php.(accessed March 

2011). This website provides historical reports on seagrass, maps, and the 2007 shape file of 

landscape-scale mapping data.

RECOVER. 2004. CERP Monitoring and assessment plan, Part 1: monitoring and supporting 

research. Restoration Coordination and Verification Program, U.S. Army Corps of Engineers, 

Jacksonville, Florida, and South Florida Water Management District, West Palm Beach, Florida; 

http://www.evergladesplan.org/pm/recover/recover_map_2004.aspx, accessed July 2011.

REY, J. R., and C. R. RUTLEDGE. 1985. Seagrass beds of the Indian River Lagoon., 

University of Florida, Institute of Food and Agricultural Sciences: http://edis.ifas.ufl.edu/in189.

Southeast Florida Aquatic Preserves: http://www.dep.state.fl.us/coastal/sites/indianriversouth/, 

accessed March 2011.

Contacts

Mapping and Monitoring: Becky Robbins, South Florida Water Management District, 561-753-

2400, Ext. 4710, brobbins@sfwmd.gov.

Bud Howard and Lorene Bachmann, WildPine Ecological Laboratory, Loxahatchee River 

District, 561-747-5700, Bud.Howard@loxahatcheeriver.org, 

Lorene.Bachman@loxahatcheeriver.org.

Monitoring: Penny Hall, Fish and Wildlife Research Institute, 727-896-8626, 

penny.hall@myfwc.com.

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Florida Seagrass Integrated Mapping and Monitoring Program

Summary Report for the Northern Indian River Lagoon 

System

Contact: Lori Morris, St. Johns River Water Management District (Mapping and Monitoring)

General Assessment: Seagrass area in the Northern Indian River Lagoon (NIRL) system has 

been increasing steadily since 1996. In 2007, mapping estimated a total of 71,646 acres of 

seagrass in the NIRL, an increase of about 9% over 2005. The increase is the result of depthlimit expansion of seagrasses, which appears to be a response to modest increases in light 

availability (reduction in light attenuation since 1997). Seagrass species composition and bed 

texture (patchiness) have been generally stable throughout the system. However, despite the 

expansion of seagrass area, percentage cover (seagrass density) has decreased, most 

markedly during 2004–05 in the southern NIRL following the 2004 hurricanes, probably as a 

result of persistently low salinity. Propeller scarring is not a widespread problem, but it is 

extensive in the south-central Mosquito Lagoon and, to a lesser degree, near the Sebastian 

Inlet. Seagrass recovery is occurring in both locations: in the Mosquito Lagoon due to new 

troll/no-motor zones and near the Sebastian Inlet because of improved channel marking.

TABLE 1. SUMMARY OF SEAGRASS STATUS, TRENDS, AND POSSIBLE CAUSES

Seagrass Status Indicator Status Trend Assessment, Possible Causes

Seagrass acreage 

 

Recent 

increases

Steady depth-limit expansion due to 

increased light availability

Species composition

 

Stable with 

intermittent 

localized impacts

Salinity variability

Seagrass density Recent 

decreases

Frequent, prolonged reductions in 

salinity

Seagrass Stressor Status Trend Assessment, Possible Causes

Light limitation (turbidity)

Yellow

Modest 

improvements Droughts, point-source reductions

Salinity Localized 

impacts

Frequent, heavy stream discharges 

(interbasin, urban, etc.)

Propeller scarring

Localized 

impacts with 

improving 

conditions

Motor boat regulations

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Geographic Extent: The 

NIRL system includes three 

sub-lagoons, Mosquito 

Lagoon, Banana River 

Lagoon, and Indian River 

Lagoon (Figure 1), extending 

110 miles (177 km) from 

Ponce de Leon Inlet in 

northern Mosquito Lagoon to 

the southern Indian River 

County line.

Figure 1. Seagrass beds in the 

northern Indian River Lagoon 

system.

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Mapping and Monitoring Recommendations

• Continue mapping seagrass acreage. Mapping is done approximately every two years; the 

most recent (2009) mapping effort is under way. The entire NIRL system is scheduled to be 

mapped again in 2011. 

• Continue seagrass monitoring program. Monitoring has been conducted each winter and 

summer for 15 years by the St. Johns River Water Management District (SJRWMD), with 

selected stations monitored monthly during the last 4 years. 

• Continue water quality monitoring, which has been implemented to assess potential stressors, 

including attenuators of light (turbidity/total suspended solids [TSS]), monthly near seagrass 

monitoring locations. Water quality monitoring has been ongoing since 1989. Information from 

the combined seagrass and water quality monitoring programs provides a rich data set of 

historical importance that has assisted in addressing management goals, including the 

establishment of seagrass depth-limit targets and total maximum daily loads (TMDLs) of total 

nitrogen and total phosphorus for rivers and canals discharging into the NIRL. 

• Improve spatial and temporal monitoring as needed to meet changing resource management 

goals by periodically reviewing monitoring programs. These reviews will include evaluation of

our ability to detect change at appropriate spatial resolutions.

Management and Restoration Recommendations

• Continue coordination of state and federal Indian River Lagoon restoration programs. Florida’s 

Surface Water Improvement and Management Program (SWIM), the U.S. Environmental 

Protection Agency National Estuary Program, and the U.S. Army Corps of Engineers’ North 

Indian River Lagoon Feasibility Study have identified seagrass as critical habitat in this system 

and have committed substantial resources toward its restoration and protection. 

• Determine water quality benchmarks (e.g., nutrient, TSS, transparency, and salinity levels) 

concomitant with seagrass depth limits, acreage, and seagrass density targets. Establishment 

of such restoration targets provides the basis for specific pollutant load reduction goals (e.g., 

TSS) and TMDLs (nutrients), which, in turn, are applied toward the development of design 

details for watershed runoff storage and treatment facilities and other remediation strategies 

(U.S. Army Corps of Engineers and SJRWMD 2002; Steward et al. 2003). The targets will also 

be used to gauge multiyear trends in seagrass coverage and the effects of management actions

on those trends. 

The establishment of seagrass depth-limit targets by Steward et al. (2005) provides an example 

of a management strategy. A segment that achieves its light-at-depth target will have attained a 

water transparency condition equivalent to or better than that segment’s historical best, based 

on historical seagrass coverage maps and water transparency models. If transparency targets

are achieved but seagrass area and depth-limit targets are not met, then factors other than light 

may be influencing the depth limit of seagrasses and should be investigated.

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Seagrass Cover and Meadow Metrics

Year Acres

0

10000

20000

30000

40000

50000

60000

70000

80000 Percent Cover ( %)

0

5

10

15

20

25

30

35

40

45

50

55

60 Transect Length (m)

0

25

50

75

100

125

150

175

200

225

Unmapped Seagrass Acreage (estimated) in the Mosquito Lagoon Mapped Seagrass Acreage (aerial photographic survey)

Seagrass Percent Cover (measured during transect monitoring)

Transect Length (measured from shore to edge of seagrass bed) 

1996

1994

1992

1989

2003 2006

1999 2005 2007

1986

1943

• Continue to evaluate propeller scarring in affected areas of the NIRL using ground 

observations and aerial photography to locate scars, using the management strategy of Schaub 

et al. (2009). New photointerpretation tools have been developed to measure severity of 

scarring. Troll/no-motor zones have been established to encourage seagrass-bed recovery in 

the most damaged locations. Continuation of aerial surveys will help in assessing restoration 

success and management potential for additional areas as needed.

Summary Assessment: Table 2 and Figure 2 depict the steady increase in seagrass area 

since 1996, probably a consequence of modest decreases in average light attenuation, or Kd

(especially in Banana River Lagoon: Kd(’90–’96) = 1.02; Kd(’97–’07) = 0.91; and southern NIRL 

from Sebastian through Vero Beach: Kd(’90–’96) = 1.31, Kd(’97–’07) = 1.17). In 2007, 

seagrasses covered 71,646 acres, and most of the acreage (55,906 acres, or 78%) was located

from Titusville north through the southern Mosquito Lagoon (Canaveral segment) and in the 

Banana River Lagoon (Table 2). The 2007 coverage represents 82% of available lagoon bottom 

that could support seagrass (Steward et al. 2005). Heavy turbid runoff caused by a quick 

succession of hurricanes in 2004 promoted substantial decreases in seagrass area in the fall 

and winter of 2004–05, with most of the loss occurring in the Rockledge to Melbourne reach. 

However, recovery was complete by the next growing season. In contrast, the systemwide 

average density of seagrass has decreased in recent years and is below the pre-2005 average 

(Figure 2). This decline is believed to be the result of persistently low salinities (< 20 ppt), 

primarily in the central reaches of the NIRL.

Figure 2. Average seagrass area (total acres) in the NIRL per mapping year; average percentage

coverage (bed density) along the transect; and the corresponding average length of monitoring 

transects to the seagrass deep edge.

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TABLE 2. MAPPED SEAGRASS AREA (ACRES) IN THE NORTHERN INDIAN RIVER LAGOON USING AERIAL 

PHOTOGRAPHY

Change Area

Segment 1943 1992 1996 1999 2003 2005 2007 ’07–’05 Target

Mosquito Lagoon–New Smyrna 822 330 19 59 67 72 94 22 1,003

Mosquito Lagoon–Oak Hill 2,974 2,668 2,350 2,810 2,736 2,760 2,765 5 3,427

Mosquito Lagoon–Canaveral 14,511 13,326 13,459 13,339 13,460 13,362 13,964 602 15,926

Banana River–NASA 6,719 9,824 9,962 10,479 11,861 11,843 12,182 339 11,767

Banana River–Port Canaveral 1,975 1,837 1,909 2,239 2,315 2,153 3,061 908 2,592

Banana River–Cocoa Beach 4,497 4,578 3,406 4,663 4,328 4,495 5,384 889 5,448

Banana River–Newfound Harbor 2,795 1,374 1,287 2,280 2,530 2,439 2,926 487 2,834

Banana River–Satellite Beach 406 173 159 210 221 219 458 239 531

NIRL–Titusville 14,035 14,961 14,399 13,938 14,516 14,556 15,072 516 19,274

NIRL–Cocoa/Rockledge 5,404 2,167 3,085 4,816 4,914 4,855 5,016 161 7,596

NIRL–Melbourne/Palm Bay 3,633 705 1,913 2,563 2,774 2,757 3,134 377 4,183

NIRL–Sebastian 1,325 2,671 3,500 3,165 3,306 3,409 3,783 374 4,776

NIRL–Vero Beach 3,047 1,558 1,950 2,523 2,586 2,600 3,807 1,207 4,082

Total 62,143 56,172 57,398 63,084 65,614 65,520 71,646 6,126 83,439

Note: green high-lighted acreages have exceeded area targets.

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TABLE 3. AVERAGE DEPTH (M) OF SEAGRASS DEEP EDGE BY NIRL SEGMENT

Change Depth

Segment 1943 1992 1996 1999 2003 2005 2007 2005–07 Target

Mosquito Lagoon–New Smyrna 1.39 1.29 NA NA NA 0.5 0.49 −0.01 NA

Mosquito Lagoon–Oak Hill 0.84 0.71 0.68 0.71 0.71 0.62 0.62 0 0.8

Mosquito Lagoon–Canaveral 1.14 0.87 0.93 0.87 0.9 0.87 0.9 +0.03 1.3

Banana River–NASA 1.02 1.48 1.32 1.54 1.67 1.69 1.81 +0.12 1.8

Banana River–Port Canaveral/ Cocoa Beach 1.39 1.11 1.11 1.14 1.11 1.11 1.26 +0.15 1.6

Banana River–Newfound Harbor 1.39 1.02 0.96 1.51 1.51 1.51 1.55 +0.04 1.6

Banana River–Satellite Beach 1.23 1.26 0.93 1.07 1.02 0.99 1.23 +0.24 1.4

NIRL–Titusville 1.17 1.14 1.26 1.05 1.17 1.08 1.23 +0.15 1.6

NIRL–Cocoa/Rockledge 1.2 0.93 1.11 1.29 1.29 1.29 1.35 +0.06 1.5

NIRL–Melbourne/Palm Bay 1.29 1.05 1.26 1.26 1.32 1.29 1.42 +0.13 1.5

NIRL–Sebastian 0.91 1.15 1.21 1.18 1.18 1.21 1.27 +0.06 1.3

NIRL–Vero Beach 1.15 0.88 1.03 1.12 1.15 1.18 1.27 +0.09 1.3

Note: Depths highlighted in green have exceeded area targets.

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Seagrass Mapping Assessment: Between 2005 and 2007, total seagrass area increased 

9.3%. All segments showed an increase (Table 2), with the greatest gains in the Banana River 

Lagoon (2,862 acres) and in the Vero Beach reach of the NIRL (1,207 acres). Systemwide 

seagrass area in 2007 exceeded the 1943 estimate by 9,503 acres. However, since 1943, 

Mosquito Lagoon has lost nearly 1,500 acres of seagrass, mostly in its northernmost segments 

(near New Smyrna Beach). Seagrass area in the Sebastian segment has almost tripled since 

1943, primarily a consequence of the permanent opening at Sebastian Inlet, which has been 

maintained since 1948. The northern half of Banana River Lagoon is close to meeting its 

multiyear area and depth-limit targets (Table 2 and Table 3). If the 2009 mapping data support 

this trend, and if high seagrass densities are maintained, then this segment (which is in waters 

under control of the National Aeronautics and Space Administration)) may be the first segment 

in the NIRL system to be considered restored. In order for a segment to be considered restored 

with respect to areal seagrass cover, it must achieve its area target in at least four out of seven 

mapping years. Sebastian and Vero Beach were the only other segments to attain their depthlimit targets in 2007 (Table 3). 

Monitoring Assessment: As shown with mapped areas (acreage and deep-edge depths), 

transect lengths (the distance from shore edge to deep edge) are increasing in many locations.

(Figure 2). Unfortunately, as seagrass beds expand, they are decreasing in percentage cover 

(bed density). This is particularly evident in the Melbourne/Palm Bay reach, which has 

experienced persistent periods (up to one year) of low salinity (< 20 ppt).

Mapping Data and Imagery: The SWIM Plan directs the SJRWMD and South Florida Water 

Management District (SFWMD) to map seagrasses in the IRL at two- to three-year intervals. 

Accordingly, in addition to the 1943 maps, IRL seagrass maps have been prepared for the 

following years: 1986, 1989, 1992, 1994, 1996, 1999, 2001 (partial), 2003, 2005, 2006, and 

2007. Seagrass mapping is based on interpretation by an outside contractor of 1:24,000 (and to 

a lesser extent 1:10,000) aerial photos. In most cases, features on the aerial photographs are 

identified by means of photointerpretation keys and ground-truthing. Features are classified 

according to SJRWMD/SFWMD-modified Florida Land Use Cover Classification System codes.

Interpretation of aerial photographs and subsequent stereoscopic analysis of digital images

were used to delineate the features and transfer the polygons into GIS coverage. An accuracy 

assessment report has been provided for the surveys since 1999. 

Monitoring Data: Field monitoring of seagrass has been conducted in the NIRL twice a year 

since 1994 by regional agency staff and collaborators. The monitoring program is coordinated 

by the SJRWMD. Seagrass and macroalgal cover are estimated by species in 1-m

2

quadrats 

placed every 10 m along each transect. Currently, there are 98 transects located throughout the 

NIRL; of these, 74 transects have been monitored since 1994. Transects are randomly 

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distributed throughout the system, and each transect is located within 3 km of a water quality 

monitoring station.

Water quality monitoring has been conducted by a multiagency team since 1989. Major 

modifications of the water quality monitoring network occurred in 1996: all samples have been 

processed and analyzed by a single laboratory, and consistent methodology for the collection of 

field data and water samples has been established. These modifications improved quality 

control for the sake of data precision and accuracy. 

Pertinent Reports and Scientific Publications

AVINEON INC. 2010. Final project report Saint Johns River Water Management District/South 

Florida Water Management District 2009 Indian River Lagoon seagrass mapping, May 2010. 49 

p.

MORRIS, L. J., and R. W. VIRNSTEIN. 2004. The demise and recovery of seagrass in the 

Northern Indian River Lagoon, Florida. Estuaries 27: 915–922.

MORRIS, L. J., R. W. VIRNSTEIN, J. D. MILLER, and L. M. HALL. 2000. Monitoring seagrass 

changes in Indian River Lagoon, Florida using fixed transects. Pp. 167–176 in: S. A. Bortone 

(ed.), Seagrasses monitoring, ecology, physiology and management, CRC Press, Boca Raton, 

Florida.

SCHAUB, R., D. M. SCHEIDT, C. M. GARREAU, and C. R. HALL. 2009. Quantitative 

assessment of seagrass scarring in the southern Mosquito Lagoon and Northern Indian River of 

Brevard and Volusia counties, Florida. U.S. Fish and Wildlife Service, Merritt Island National 

Wildlife Refuge, Florida, Contract no. GS10F0237R, and St. Johns River Water Management 

District, Palatka, Florida. 39 p.

STEWARD, J. S., R. BROCKMEYER, R. VIRNSTEIN, P. GOSTEL, P. SIME, and J. 

VANARMAN. 2003. Indian River Lagoon surface water improvement and management (SWIM) 

plan, 2002 Update. St. Johns River Water Management District, Palatka, Florida, and South 

Florida Water Management District, West Palm Beach, Florida. 272 p.

STEWARD, J. S., R. W. VIRNSTEIN, L. J. MORRIS, and E. F. LOWE. 2005. Setting seagrass 

depth, coverage, and light targets for the Indian River Lagoon system, Florida. Estuaries 28: 

923–935.

U.S. ARMY CORPS OF ENGINEERS and ST. JOHNS RIVER WATER MANAGEMENT 

DISTRICT. 2002. Central and Southern Florida Project, project management plan: Indian River 

Lagoon North feasibility study. June 18, 2002. USACE Southeast District, Jacksonville, Florida, 

and St. Johns River Water Management District, Palatka, Florida, 63 p. + appendices.

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General References and Additional Information

St. Johns River Water Management District: http://www.sjrwmd.com/irlinsert/index.html, 

accessed March 2011.

Indian River National Estuary Program: 

http://www.epa.gov/region4/water/watersheds/documents/indian_river_lagoon.pdf, accessed 

March 2011.

Contacts 

Mapping and Monitoring: Lori Morris, St. Johns River Water Management District, Palatka 

Headquarters, 386-329-4544, lmorris@sjrwmd.com; Lauren Hall, St. Johns River Water 

Management District, Palm Bay Service Center, 321-409-2118, lhall@sjrwmd.com. 

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Appendix A: Acronyms and abbreviations used in this report

Acronym or 

Abbreviation Full Name

BMAP Basin Management Action Plans

CAMA Coastal and Marine Assessment

C-CAP Coastwatch Change Analysis Project 

CDOM colored dissolved organic matter

CERP Comprehensive Everglades Restoration Plan

CHNEP Charlotte Harbor National Estuary Program

CMP Coastal Management Program

DMC digital mapping camera

EMAP Environmental Monitoring and Assessment Program

ENP Everglades National Park

ERP Ecosystem Restoration Program

FDEP Florida Department of Environmental Protection

FDOR Florida Department of Regulation

FHAP Fisheries Habitat Assessment Program

FIU Florida International University

FKNMS Florida Keys National Marine Sanctuary

FLUCCS Florida Land Use Cover Classification Systems

FTMP Fixed Transect Monitoring Project

FWC/FWRI Fish and Wildlife Commission/Fish and Wildlife Research 

Institute

FWRI Fish and Wildlife Research Institute

GCCC Gulf Coast Community College

GINS Gulf Islands National Seashore

GIS geographic information system

IMAP Inshore Monitoring and Assessment Program

IMU inertial measurement unit

IRL Indian River Lagoon

LWL Lake Worth Lagoon

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Acronym or 

Abbreviation Full Name

Miami-Dade DERM Miami-Dade County Department of Environmental Resource 

Management

MMS Mineral and Mining Service

MRAID Marine Resources Aerial Imagery Database

MRGIS Marine Resources Geographic Information System

NASA National Aeronautics and Space Administration

NCCOS National Centers for Coastal Ocean Science

NEP National Estuary Program

NERR National Estuarine Research Reserve

NGO nongovernmental organization

NIRL Northern Indian River Lagoon

NOAA National Oceanic and Atmospheric Administration

NRDA Natural Resources Damage Assessment

NWFWMD Northwest Florida Water Management District

NWRC National Wetlands Research Center

OFW Outstanding Florida Waters

PBC DERM Palm Beach County Department of Environmental Resource 

Management

RECOVER Restoration Coordination and Verification

RSOWQ Remotely sensed optical water quality

SAB St. Andrew Bay

SAV submerged aquatic vegetation

SAV TWG Submerged Aquatic Vegetation Technical Working Group

SBEP Sarasota Bay Estuary Program

SCIS Seagrass Conservation Information System

SDRS spatially distributed random sampling

SFWMD South Florida Water Management District

SIMM Seagrass Integrated Mapping and Monitoring

SIRL Southern Indian River Lagoon

SJRWMD St. Johns River Water Management District

SRWMD Suwannee River Water Management District

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Acronym or 

Abbreviation Full Name

SWFWMD Southwest Florida Water Management District

SWIM Surface Water Improvement and Management Program

TMDL total maximum daily load

TSS total suspended solids

UMAM Uniform Mitigation Assessment Method

U.S. EPA United States Environmental Protection Agency

USACOE United States Army Corps of Engineers

USGS United States Geological Survey

VOO vessel of opportunity

WBBOWL West Bay Bowl (in St. Andrew Bay)

WBARM West Bay Arm (in St. Andrew Bay)

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