Yarbro and Carlson, Editors

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 2011Yarbro and Carlson, Editors

SIMM Report #1Yarbro and Carlson, Editors

SIMM Report #1



## Table of Contents

Authors, Contributors, and SIMM Team Members

................................ ................................ .. 3

Acknowledgments

................................ ................................ ................................ .................... 4

Abstract

................................ ................................ ................................ ................................ ..... 5

Executive Summary

................................ ................................ ................................ .................. 7

Introduction

................................ ................................ ................................ ............................. 3 1

How this report was put together

................................ ................................ ........................... 3 6

Chapter Reports

................................ ................................ ................................ ...................... 4 1

Perdido Bay

................................ ................................ ................................ ........................... 4 1

Pensacola Bay

................................ ................................ ................................ ...................... 4 5
Santa Rosa Sound and Big Lagoon

................................ ................................ ....................... 5 0

Choctawhatchee Bay

................................ ................................ ................................ ............. 5 6

St. Andrew Bay

................................ ................................ ................................ ...................... 6 2

St. Joseph Bay

................................ ................................ ................................ ...................... 68

Franklin County Coastal Waters

................................ ................................ ............................ 7 5

Northern Big Bend

................................ ................................ ................................ ................. 8 1
Southern Big Bend

................................ ................................ ................................ ................ 8 9

Suwannee Sound, Cedar Keys

, and Waccasassa Bay

................................ .......................... 9 6
Springs Coast

................................ ................................ ................................ ...................... 10 2

Western Pinellas County

................................ ................................ ................................ ..... 10 9

Tampa Bay

................................ ................................ ................................ .......................... 11 3

Sarasota Bay and Lemon Bay

................................ ................................ ............................. 1 19
Charlotte Harbor Region

................................ ................................ ................................ ...... 12 7

Estero Bay

................................ ................................ ................................ ........................... 13 7

Rookery Bay

................................ ................................ ................................ ........................ 14 5

Ten Thousand Islands

................................ ................................ ................................ ......... 15 0Yarbro and Carlson, Editors

SIMM Report #1

Chapter Reports , c ontinued

Florida Keys National Marine Sanctuary

................................ ................................ .............. 15 6

Florida Bay

................................ ................................ ................................ .......................... 16 1

Biscayne Bay

................................ ................................ ................................ ....................... 16 8

Lake Worth Lagoon

................................ ................................ ................................ ............. 17 5

Southern Indian River

................................ ................................ ................................ .......... 18 2

Northern Indian River

................................ ................................ ................................ .......... 19 1

Appendi x

A . Acronyms and abbreviations used in this report

................................ .............................. 20 0Yarbro and Carlson, Editors

SIMM Report #1



## 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, Chri sti Santi, Dave Palandro, Kathleen O’Keife, Harry Norris, Paul Julian, Makenzie Marsh, and Laura Yarbro.

Authors and contributors to e ach 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 cont ributors 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 contr ibuted 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

3Yarbro and Carlson, Editors

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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 S eagrass I ntegrated M apping and M onitoring 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 L agoon were especially critical in demonstrating the need for regular

as sessment of seagrass cover, the link between water quality and the abundance of seagrass, and the effectiveness of seagrass mapping and monitoring in assess ing 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 do es the SIMM team, on the shoulders of those who came before.

This report was funded, in part, through a grant agreement from the Flor ida 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 Administra tion (NOAA) Award

N umbers 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

.

4Yarbro and Carlson, Editors

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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, i dentified spatial gaps in coverage by these programs , identified emergent metrics of seagrass distribution, abundance, and health, summarized mapping data, and produced th is report using contributions of data, graphics, and text from many collaborators

. We found that seagrass monitoring pr ograms 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 N ational E stuarine

R esearch R eserve in the Panhandle region. There are planned project s in Choctawhatchee Bay

and the Ten Thousand Islands . Along Florida’s east coa st, seagrasses along the Volusia County coastline are not monitored. A variety of agencies conduct s 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 ident ification and assessment of

m a croalgae, and most measure seagrass abundance using the Braun

- Blanquet scale or percent age cover in replicate quadrats at each site

. Sampling methods are basically va riations of two types: sampling along transects, often perpe ndicular 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 b e reported for most seagrass monitoring programs include s eagrass (and macroalgal) abundance

, species composition and diversity , and d epth distribution of seagrass species

.
We found that our current statewide set of seagrass maps includes 27 geographic inf ormation system datasets based primarily on aerial photography collected from 19 92 to 20 1 0

. 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

. T he primary indicators derived f rom 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 eac h 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

5Yarbro and Carlson, Editors

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western Panhandle has 39,200 acres o f seagrass, and that acreage is in declin e . 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 B ay and is increasing on the east coast.

6 6Yarbro and Carlson, Editors

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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 $ 2 0 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 h istory , 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; Waycot t 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 declin ing 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 a re directed at leveraging resources
as well as decreasing and sharing costs for seagrass mapping and monitoring.

Elements of th e SIMM program include: 1) ensuring that all seagrasses in Florida waters are mapped at least every six years ; 2) monitoring sea grasses throughout Florida annually ; and 3) publi shing a comprehensive report every two years that combin es 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 h ope 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 ) P rogram and for the development of
numeric nutrient and tran sparency 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 N ational O ceanic an d A tmospheric

A gency (NOAA) Natural Resource Damage Assessment (NRDA) staff draft chapters detailing seagrass resources in all Panhandle counties.

7Yarbro and Carlson, Editors

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Data Collation Methods: The Florida Fish and Wildlife Conservation Commission/Florida Fish
and Wildlife Resea rch Institute (FWC/FWRI) are committed to developing, implementing, and

m aintaining the SIMM program. Our first steps, supported by the FDEP Coastal Zone Management Program, have been the following:

1. An i nventory of active mapping and monitoring programs

2. Identif ication of spatial gaps in mapping and monitoring programs

3. Identif ication 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 o f 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 coll aborate

in the monitoring portion of SIMM (see Table ES

- 1). Three of the inactive projects are in St. Andrew Bay, the Pensacola Bay r egion, 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

, a nd 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 Choctawhat chee Bay, in Waccasassa Bay

, t he 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 b ays c ould be funded and resumed to fill most of the coverage gap in Panhandle

waters

. O il impact sampling is still under way in seagrass beds in t he western Panhandle and

will probably p rovide some information where routine monitoring has been lacking

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

8Yarbro and Carlson, Editors

SIMM Report #1

mapping and monitoring techniques that might work in these remote, sparse seagrass ecosyst ems 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 estu arine and nearshore waters can be collated and reported biennial ly , if not annual ly

.

Figure ES

- 1. Agencies conductin g monitoring programs in Florida coastal waters.

A variety of agencies conduct s 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 F DEP (Fig ure 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 F lorida I nternational U niversity (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.

9Yarbro and Carlson, Editors

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TABLE ES

- 1. METRICS USED BY SEAGRASS MONITORING PROGRAMS IN FLORIDA

Estuary or Subregion Lead Agency Sampling Frequency B/B 1 or

% Cover Species

Comp 2 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

1 Braun

- Blanquet. 2 composition. *Oil spill

– targeted sampling, May 2010

10Yarbro and Carlson, Editors

SIMM Report #1

The Tampa Bay, Sarasota Bay, Charlotte Harbor, Florida Bay, Biscayne Bay, and Indian River
estuarine system s 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 f requent, 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 N ational E stuary P rogram (CHNEP) , and the Tampa Bay Estuary Program (TBEP) are excellent example s

.

All monitoring programs measure presence or absence of seagrasses and species composition of seagrass beds. Some include identification and assessment of m a croalgae, and most measure seagrass abundance using the Braun

- Blanquet scale or percent age cover in replicate quadrats at each site (Table ES

- 1). Many p rograms determine shoot counts

, and a few collect samples for biomass and morphometric analys e s

. 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

estab lished 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.

P oint 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 us e probabilistic point sampling. Figure ES

- 2. Seagrass monitoring methods.

11Yarbro and Carlson, Editors

SIMM Report #1

M ost 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 i ndicators can be reported for most seagrass monitoring programs:

1. Seagrass (and macroalgal) abundance

2. Seagrass (and macroalgal) species composition and diversity

3. Dept h distribution of seagrass species

.

T hese three indicators c a n identify change s 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 project s of diffe ring designs , i.e., fixed point
and transects v er s us 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 se parately 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 widge on 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 w ith 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; Ha lodule wrightii ) and turtle grass (TT;

12Yarbro and Carlson, Editors

SIMM Report #1

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 wa s 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 c oastal 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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T ABLE ES

- 2. MOST ABUNDANT SEA GRASS 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 SEA GRASS 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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S eagrass Mapping
Efforts: We found that our
current statewide set of

seagrass maps include d 27 GIS datasets (Figure
ES

- 3 ; Table ES

- 3 ) based primarily on aerial photography collected
from 19 87 to 200 8

— 21 years! For o ther estuaries,

h owever (e.g., Indian River Lagoon, Tampa Bay, Sarasota Bay, and
Charlotte Harbor ) imagery
is collected every two

yea rs. 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

. I magery datasets collected in the 1980s, 1990s, and early 2000s were acquired with
film cameras. Mo re 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 W eb.

T he primary indicators derived from mapping projects a re 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 projec ts. 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 as sess seagrass abundance over much larger areas than can Figure ES

- 3. Status of seagrass mapping efforts.

16Yarbro and Carlson, Editors

SIMM Report #1

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

17Yarbro and Carlson, Editors

SIMM Report #1

Of the estuaries or subregions of coastal Florida, all have aerial imagery available obtained
within the p ast 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 pl ace due to large

scale 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 year s 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 tannin

stained waters. These area s 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 be en 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 s tate waters. Areas where the cont inental 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 sustain ing 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

. A cquisition of WorldView 2 satellite imagery of the Springs Coast and Big

Bend i s anticipated in fall 2011. Ne vertheless, p addle grass

, which is common offshore

, is small
and has a dubious optical signature in deep water , so m apping these beds in the deeper waters of the Big Bend and the s outhwest Florida Shelf will be technically challenging.

18Yarbro and Carlson, Editors

SIMM Report #1

We have summarized the most recent mapping data for all Florida estuaries or regions and calculated an annual percent age change in seagrass area where two data sets having the same spatial extent were available for a region (Table ES

- 4). W e used percent age annual change as
the trend indicator because t he 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 natur al stressors, such as El Ni ñ o 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 m ight vary temporally and spatially. More deta iled information on methods and seagrass acreage gains and losses is located in each chapter. Th e s e 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 show ed losses greater than 3% per year between 1992 and 2002

– 0 3. Santa Rosa Sound and St. Andrew Bay had small annual percent age increases in seagrasses over the same time. As suggested by three years of monitor ing 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 a re 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 wa s stable in th at 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 Wes tern 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

F lorida, 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 L agoon

— 6.7% and 4.7% per year in the southern and northern Indian River Lagoon, respectively.

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SIMM Report #1

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

20Yarbro and Carlson, Editors

SIMM Report #1

O f 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 . S maller 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 B ay

. 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 ne ar 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.

21Yarbro and Carlson, Editors

SIMM Report #1

TABLE ES

- 5. SEAGRASS A CREAGE 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 regular ly to legislators and managers:

22Yarbro and Carlson, Editors

SIMM Report #1

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. T ime

- 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 req uires 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 opt ions for optimiz ing 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 1 1 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 combin ed costs for imagery acquisition and photointerpret ation 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, t he 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 b ottom 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.

23Yarbro and Carlson, Editors

SIMM Report #1

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

24Yarbro and Carlson, Editors

SIMM Report #1

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 m ight 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 level s 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 acquir e seagrass imagery in conjunction with land

- area flights for other purposes. Most contractors are able to fly coastal and estuarine flight lines under con ditions 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
whe re 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 great ly 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 m 2

. Digital aerial imagery has a
resolution of 1 ft 2 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 resolu tion 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, p hotointerpret ation 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 t han 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 sof tware 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

25Yarbro and Carlson, Editors

SIMM Report #1

$740,000. Over a six

- year map ping 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 effectivel y 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 y ear, 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 s eagrass 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 add s 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 Natio nal 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%

Ch allenges 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 :

Compar e 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 col lected 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.

26Yarbro and Carlson, Editors

SIMM Report #1

Optimize d ata management

, statistical analyses , and Web sharing

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

are stored in W eb

- accessible databases ; o ther s 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 othe r agencies
to contribute either data or a link to their own Web database.
Close s patial gaps in monitoring program s . Gaps in program coverage exist in the Panhandle, Springs Coast, Ten Thousand Islands, and Volusia County. Because some programs elsewhere d epend 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 Florid a 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. D etectin g changes in seagrass area and density based on long cycle t imes 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 Revenu e (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 imag ery 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 l ag times for seagrass mapping projects . The time between the collection of imagery and the distribution of GIS map s can be as long as five years. Where possible,
we will reduce the process ing time by finding funds to interpr et 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
ha bitat 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 l oss or thinning or changes in seagrass species composition, we hope that information from this and future SIM M reports will support opportunities for management action s found in TMDL, O utstanding F lorida W aters (OFW)

, numeric nutrient criteria, and water q uality criteria regulations administered by FDEP.

27Yarbro and Carlson, Editors

SIMM Report #1

Data Use for Damage Assessment from the 2010 Deepwater H orizon 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 Deep w ater Horizon oil spill. Nevertheless , the fin al 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

- acqui sition efforts to fill data gaps and to devise statistically defensible sampling designs in the assessment of oiling and resource damage. E xtensive and ongoing aerial imagery acquisition associated with damage assessment, and monies provided for the monito r ing 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 i mpacts to seagrass beds from response activities, such as booming, construction of barriers, and prop eller scarring from v essels of o pportunity (VOOs). Damage assessment of the direct oiling of seagrass beds and of response activities in
Panhandle estuarie s 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 anal yze 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

- R

04

- 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: i nventory of

r ecent and c urrent s eagrass m apping and m onitoring p rograms, y ear 1 a nnual r eport. Florida Department of Environmental Protection Coastal Zone Management Grant Number CZ820

. Tallahassee, F lorida. 4 4 p.

CARLSON, P. R., L. A . YARBRO, K. K. KAUF MAN, and R. A. MATTSON. 2010. Vulnerability and resilience of west Florida seagrass communities to hurricane impacts. Hydrobiologia 649:

39

– 53.

COSTANZA, R., R. D’A RGE, R. DE GROOT, S. FARBER, M. GRASSO, B . HANNON, S. NAEEM, K. LIMBURG, J . PARUELO, R. V. O’N EILL, 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. S eed 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. D UARTE, T. J. B. CARR UTHERS, R. J. ORTH, W. C. DENNISON, S. OLYARNIK, A. CALLADI NE, J.W. FOURQUREAN, K. L. HECK JR., A. R . HUGHES et al.

2009. Accelerating loss of seagrasses a cross 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 provid e habitat for fish, shellfish, marine mammals
and sea turtles that translate into a value of more than $ 2 0 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 impor tant 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
declin e (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 ha s been no coordinated statewide program for the regular assessment of the
abundance and health of seagrass es

. 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,

31Yarbro and Carlson, Editors

SIMM Report #1

other estuaries and seagrass beds have been mapped using opportunistic grants with no consistent frequency, resulting in gaps of 8

– 12 year s 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 p otential 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, w hen standard photointerp retation methods are used, there is a lag time of 18

– 36
months between the collection of imagery and the production of seagrass maps in g eographic

i nformation s ystem (GIS) software. These lags, added to the sometimes lengthy interval between mapping effort s for a n area, result in a poor ability to detect seagrass losses quickly and prevent further losses.

To provide more accurate estimates of change s in seagrass area and to provid e greater spatial
resolution and information on seagrass species composition, the S eagrass I ntegrated M apping
and M onitoring (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 m apping 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 includ ing 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 km 2 Small: hundreds of m 2

Spatial Resolution Coarse: 0.2 ha Fine: 1 m 2

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

32Yarbro and Carlson, Editors

SIMM Report #1

The SIMM program was developed t o 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 maintaini ng the SIM M

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 optim al times for mapping seagrass in Florida coasta l waters

6. Develop an online imagery database (Marine Resources Aerial Imagery Database [ MRAID ] ) to serve imagery for seagrass mapping projects

7. Carry out seagrass mo nitoring 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 W eb. SIMM program data provide or could provide:

1. Baseline data against which natural an d 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

33Yarbro and Carlson, Editors

SIMM Report #1

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 b ack 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 wa ter resources. Citizen initiatives resulted in the funding of advanced wastewater treatment and control of point

source pollution in Tampa Bay and other Florida estuaries. But by the mid

- 1980s it was apparent that nonpoint

- source pollution also played an i mportant 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. Joh ns 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 lo sses in Tampa Bay, Sarasota Bay, Lemon Bay, and northern Charlotte
Harbor. The e fforts 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

- source

discharge 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 s uccess of ecological monitoring depends on development of reliable, scientifically defensible i ndicators for measuring ecological health, integrity, and change

, and 2 ) the s uccess of ecological monitoring depends on logistically feasible and statistically valid sampling designs capable of quantifying error

, bias

, and predictive value ( US EPA 1997). S eagrass scientists have taken to heart EMAP’s emphasis on reliable indicators of community health, and man y have also adopted the spatially distributed random

sampling (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

3 4Yarbro and Carlson, Editors

SIMM Report #1

Bay and F lorida I nternational U niversity ’s monitoring program for the newly created Florida Keys
National Marine Sanctuary.

In light of the gro undswell of interest in seagrass monitoring and the development of practical sampling designs, in June 2000 Ken Haddad, director of F lor ida FWRI, held a workshop on seagrass mapping and monitoring with the purpose of foster ing collaboration among all

agenc ies carrying out seagrass mapping and monitoring in the state. FWRI staff prepared an inventory of seagrass mapping and monitoring programs for the workshop. Th is inventory showed that mapping projects were carried out at different intervals and depended h eavily on the availability of grant funds and that method ologie s varied among monitoring programs.

The 2000 workshop led to the development of the Florida Seagrass Conservation Information System ( SCIS; ht tp://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 (I MAP) 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 Loui s 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 re port titled Seagrass Status and Trends in the Northern Gulf of Mexico: 1940

– 2002 (Handley et al. 200 7 )

. This report describ e d seagrass mapping data for 15 estuarine and lagoonal systems from Texas

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

For the report by Handley et al.

, Carlson and Madley summarized recent trends in seagrass
cover in estuaries of Florida’s w est c oast (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

35Yarbro and Carlson, Editors

SIMM Report #1

(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 d ata 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 cor rect and improve our assessments.



### How this report was put together:

D evelopment of the SIMM program at the Fish and Wildlife Research Institute began in 2007 with information gathering about the agencies, researchers, and programs address ing the health and acreage of seagrasses in the coastal waters of Florida. Telep hone 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 a nd trends. Then we began gathering data and information to produce a chapter for each region or estuary along the
coast of Florida . This effort allow ed us to pursue the long

- term goals of SIMM, which include 1) providing a snapshot of seagrass conditions i n a statewide report issued annually, with contributions from researchers and managers; 2) establish ing a statewide program of routine mapping occurring at least every six years and annual monitoring for all of Florida’s seagrass ecosystems by partnering w ith the many agencies and researchers who work on seagrass ecosystems; and 3) eliminat ing gaps in monitoring and mapping, through collaboration and funding where possible.

This first report compiles available information on seagrasses and any omissi ons or gaps are the responsibility of the editors. For each region or estuary, w e 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 s olely 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, w e 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 Ochlock o nee b ays in the Pa nhandle. Aerial photography of seagrasses in the Panhandle was completed in late 2010 and we anticipate acquiring imagery

36Yarbro and Carlson, Editors

SIMM Report #1

for the Ten Thousand Islands in 2011. W e anticipate expanding or including chapters on these regions as part of our next edition. As w e prepare to publish this report , damage assessment
from the 2010 D eep w ater H orizon 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 re aders. 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 thu mbnail 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

stat us , 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 stres sors. The colored boxes convey the following:



###  Green

— H ealthy, improving, stable conditions



###  Yellow

— D eclining, some stress present, some threats to ecosystem health



###  Orange

— M easureable declines, moderate stressors or declines in seagrass cover



###  Red

— L arge 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 t he general assessment and the first status graphic presented on the first page of each chapter

.
Following this summary information, t he geographic extent covered by the chapter is outlined, followed by a map showing the most recent seagrass coverage, if av ailable, and a brief list of mapping, monitoring, management

, and restoration recommendations

. W e then provide more

in

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

- coded graphic addressing seagrass status indicators, su ch 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 var ies 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 a r e al

37Yarbro and Carlson, Editors

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cover, along with a short discussion o f what factors m ight be e ffecting 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, managemen t 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 th e 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 8 55

- R

04

- 003, Washington, D.C. 267 p.

CARLSON, P. R., L. A . YARBRO, K. K. KAUF MAN, and R. A. MATTSON. 2010. Vulnerability and resilience of west Florida seagrass communities to hurricane impacts. Hydrobiologia 649:

39

– 53.

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

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

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

– 260.

HANDLEY, L., D. ALTS MAN, and R. DEMAY 2007. Seagrass status and tr ends 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. ENVIRON MENTAL PROTECTION AG ENCY

1997. Environmental M onitoring and Assessment Program : research strategy. EPA/620/R

98/001 . Office of Research and Development, U.S. EPA, Washington, D.C. 18 p.

3 8Yarbro and Carlson, Editors

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WAYCOTT, M., C. M. D UARTE, T. J. B. CARR UTHERS, R. J. ORTH, W. C. DENNISON, S. OLYARNIK, A. C ALLADINE, J.W. FOURQ UREAN, 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.

39Yarbro and Carlson, Editors

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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 seag rasses. 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

G eographic 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 wr aps around to include Kees Bayou and Russell Bayou along the northern section of the bay.

Figure 1. Seagrass map of Perdido Bay

.

41Yarbro and Carlson, Editors

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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 Statu s 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 Ni ñ o

Propeller scarring

42Yarbro and Carlson, Editors

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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. S EAGRASS A CREAGE IN P ERDIDO B AY 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

43Yarbro and Carlson, Editors

SIMM Report #1

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.

Pe rtinent 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 ASSOCIATE S 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 O F ENVIRONMENTAL PROT ECTION, NORTHWEST DI STRICT.

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 sh ow 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 t he 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 mapp ing data will be used to conduct change analysis and assessment of seagrass trends.

45Yarbro and Carlson, Editors

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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.

S umm ary 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 test udinum ) 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.

T he 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 concentra tions 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 1 992 and 200 3 , total seagrass cover for the Pensacola Bay System declined 43%, from 8 94 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 p rimarily of turtle grass along with some shoal grass, but seagrasses are sparse and stunted.

TABLE 1. A CREAGE OF S EAGRASS H ABITAT A REA ( 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, part icularly 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 up per 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 Br eeze 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 Scienti fic Publications

HAGY, J. D., J. C. K URTZ, 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, N orth C arolina . 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.

48Yarbro and Carlson, Editors

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LEWIS, M. A., R. DEV EREUX, 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.
BISTERFI ELD, and L. A. WISE

. 1975. Environmental and recovery studies of Escambia Bay and the Pensacola Bay System, Florida. U.S. Environmental Protection Agency, Atlanta,
G eorgia . 904/9

- 76

- 016. 468 p.

SCHWENNING, L., T. B RUCE, and L. W. HANDLEY. 2007. Pensacola B ay. 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 completi on, 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
Bree ze, 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: S eagrass beds in Santa Rosa Sound and Big Lagoon appear stable in area. In 2003, mapping from aerial photography found 3,032 acres of se agrass 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 ER S 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 rep eatedly 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 Sou nd 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 polit ical 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 pressur es 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 o n the barrier islands.

• Continue assessing damage from the 2010 Deepwater Horizon oil spill, and initiate restoration

program.

S ummary Assessment: Seagrass beds in Santa Rosa Sound and Big Lagoon are considered stable, based on the limited information av ailable.

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. S EAGRASS A CREAGE IN S ANTA R OSA S OUND
AND B IG L AGOON 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 par allel 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. Percent age occurrence of seagrasses in Big Lagoon and near
Fort Pickens and Gulf
Breeze in Santa Rosa Sound, June 2010.

53Yarbro and Carlson, Editors

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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.

• Min imize 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 f rom 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

seag rass 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 southe rn 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. PAS KO, J. M. PATRICK, R . L . QUARLES, J. CAMPBE LL, and J.
MACAULEY. 2000. Mapping and monitoring of submerged aquatic vegetation in Escambia

Pensacola Bay system, Florida. Gulf of Mexico Science 18: 1

– 14.

General References and Additional Information

Seagrass Management Plan for Bi g 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@ecoconsu ltingservices.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 cov ered 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 runof f. 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

east ern 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 Recommendat ions

• 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 damag e 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.

S ummary 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 an d 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 ru noff 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. S EAGRASS A CREAGE IN C HOCTAWHATCHEE B AY IN 1992 AND 2003

1992 2003 Change % Change

4,261 2,623 −1,638 −38.4

Monit oring 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 b ay 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 s eagrass 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 ve ry 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 survi val 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 Na tional 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 Atmospheri c 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 extensi ve, 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/cho ctawhatchee_ba y_082410.pdf , accessed March 2011.

Seagrass Restoration Data and Maps, Northwest District FDEP: http://www.dep.state.fl.us/northwest/ecosys/section/seagrassmap s.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

b etween 1992 and 2003 sea grass 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 ac res 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 Stat us 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 th e 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 cre eks 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 sinc e 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 sys tem 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

int o 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

S ummary 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 nut rient 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 s eagrass acreage and the effects of the storms of 2004 and 2005 and increasing development on seagrasses.

TABLE 1. S EAGRASS A CREAGE IN S T . A NDREW B AY 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 WBBO WL. 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
thes e 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. Inc reasing 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 approxim ately 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 interpre tation 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 Wetla nds 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 Seagras s 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 constru ction 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.

Pe rtinent 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.
Environment al 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_i n_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.protectingour water.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 Resto ration: 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 ac res 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 co mpared 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 d etect any e ffects of de clining water quality . CAMA staff will overlay the images from 2006 and 2010 to analy ze changes in seagrass species, coverage,
de pth, prop eller scar ring , and water quality. T he ne wly 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 i s approximately 43,872 acres (Hemming et al. 2002).

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M apping 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 map ping 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.

M anagement and Restoration
Recommendations

• Assess the effects of development pressures on storm runoff.

• Decrease propeller scarring.

S ummary 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 th e 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.

69Yarbro and Carlson, Editors

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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 20 06, 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 2 006, scarred areas had been reduced to 1,900 acres, but moderately scarred areas had increased by 900 acres.

TABLE 1. S EAGRASS A CREAGE IN S T . J OSEPH B AY 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 freque ntly 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 se agrass 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 N ational W etlands R esearch C enter /N ational O ceanic and Atmospheric Administration s eagrass 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 est imate 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 th e b a y

. 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 water

colum n 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 b ay was estimated to be 27 km 2 , or 6,672 acres, which is 17% of the total footprint of the bay.

Between 1993 and 2006, St. Joseph Bay los t approximately 6 km 2 (1,4 98 acres) of seagrass

habitat. This m ight 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 area s 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 h eight, 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, temper ature, 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. B RIM, 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 suspension

feeding 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

sea grasses: 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

Centra l 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, Septe mber 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 Pr otection, 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 i n 1992 . At that time, Franklin County waters contained approximately 14,450 acres of seagrass, almost
half of whic h 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 qualit y. 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 Alliga tor 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.

S ummary 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

a ssessment 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. S EAGRASS A CREAGE IN
F RANKLIN C OUNTY C OASTAL W ATERS

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: A nnual 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 th e 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 S t. 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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.

F igure 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 t he 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 Braun

Blanquet technique. Species composition of seagrasses and macroalgae and optical water quality parameters (light attenuation, colo r, 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

CHANTO N, 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/estu arine/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 n orthern 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 Oc hlockonee r ivers. Seagrass species composition also appears to

be stable. F ragmentation of continuous seagrass beds in to patchy beds is cause for concern. Stressors include nutrients, phytoplankton

, and turbidity. These stressors were elevated after
the 20 04 and 2005 hurricane seasons, but they have returned to background levels. Heavy

p ropeller 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

s eagrass, 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 n orthern 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 r ivers. 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 r eturned 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 p ropeller scarring is evident around the
St. Marks River mouth

, Keaton Beach , and Steinhatchee but is minimal elsewhere

.

Seagrass Status Indicators Status Trend Assessment, Cau ses

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 149,8 40 acres to 149 ,140 acres, a decrease of 700 acres, or 0.5% (Table 1)

. Th is represents a loss of 84 0 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 p atchy seagrass area increased 61 %

, from 4,490 acres to

7 ,210 acres
, as continuous seagrass area declined by 3,420 acres (2.3 % ), from 1 4 5 ,350 acres to 1 41,930 acres. Frag mentation of beds is cause for concern, especially in the St. Marks East
and Steinhatchee North sub regions. 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 th e northern Big Bend

. Furthermore, there are extensive, but sparse

, beds of paddle grass ( Halophila decipiens ) offshore that can no t 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 in shore and offshore.

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TABLE 1. S EAGRASS A CREAGE IN N ORTHERN B IG B END 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 F ish and

W ildlife C ommission (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 percent age of samples
in which each seagrass species was found.

TABLE 2. O CCURRENCE (%) OF SEAGRASS SPECIES

IN NORTHERN B IG B END

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 o ccurrence of seagrass species in the subregions of n orthern Big Bend , 2009

.

Manatee grass ( Syringodium filiforme ) occurs at more sampl ing 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 sampl ing locations with shoal grass ( Halodule wrightii ) appears to have declined over the past five years

— a potenti ally disturbing tr end 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
thro ugh 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 uncle ar 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.

• Acqui re imagery and m ap 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 Restor ation 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 1:2 4,000 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

th is dataset by Avineon Inc. using the Florida Land Use Cover Classification System (Florida Department of Transportation, 1999). Arc M ap shapefiles of benthic habitats are distributed on the Fish and Wildlife Research Institute (FWRI) Marine Resources Geogra phic 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/researc h/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 m 2 quadrats at approximately 120 spatially d istributed, 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.

86Yarbro and Carlson, Editors

SIMM Report #1

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 wa y.

Pertinent Reports and Scientific Publications

CARLSON, P. R., L. A . YARBRO, K. K. KAUF MAN, 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. Peters burg, Florida. iv + 74 p.

http://www.sarasota.wateratlas.usf.edu/upload/documents/Seagrass

- Communities

- Status

- and

Ecology.pdf

, accessed March 2011.

HALE, J. A., T. K. F RAZER, 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

w est 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

– 1 88 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.

8 7Yarbro and Carlson, Editors

SIMM Report #1

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.f l.us

.

88Yarbro and Carlson, Editors

SIMM Report #1



### 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 sou thern 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 a cres, 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 patch y 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 can not be used; these deepwater beds are not shown in Figure 1.

F igure 1. Seagrass

cover in the
southern Big Bend region in

2006

.

89Yarbro and Carlson, Editors

SIMM Report #1

Mapping and Monitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and m ap 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 contro l 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. Conv ersion 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 col umn. 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 th e northern and souther n Big Bend regions. Seagrass species shifts attribut able 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

90Yarbro and Carlson, Editors

SIMM Report #1

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, o r 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 a nd 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.

E xtensive, bu t sparse

, beds of paddle grass ( Halophila decipiens ) offshore can not 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 in shore and offshore.

TABLE 1. S EAGRASS A CREAGE IN SOUTHERN B IG B END 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

91Yarbro and Carlson, Editors

SIMM Report #1

Monitoring Assessment: Big Bend ’s seagrass beds are monitored each year by F ish and

W ildlife Conservation C ommission (FWC) staff and collaborators. The number of samples each year has varied between 450 and 600, so the results shown in T able 2 are expressed as the percent age of the total number of sample locations at which each seagrass species was found. Since 2004, the average occurrence of bare bot tom has ranged from 40% to 50% of sample
locations throu ghout the southern Big Bend. This is twice the frequency of bare bottom found in
the n orthern 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 o f drift red macroalgae dropped sharply between 2004 and 2005 and has also remained low. Compared with those at the nort hern 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 gro ws.

TABLE 2. O CCURRENCE (%) OF SEAGRASS SPECIES

IN SOUTHERN B IG B END

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 occurr ed with turtle grass. Both the occurrence and diversity of seagrasses increased with distance from the mouth of the
Suwannee River.

92Yarbro and Carlson, Editors

SIMM Report #1

Figure 2. Percentage o ccurrence of seagrass species in the subregions of s outhern Big Bend

, 2009.

Mapping and Mo nitoring Recommendations

• Map and monitor seagrasses in water too deep for conventional aerial photography.

• Acquire imagery and m ap 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 Suwann ee 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). Arc M ap shapefiles of benthic habitats

93Yarbro and Carlson, Editors

SIMM Report #1

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/mr aid/ ). Benthic habitats were classified and mapped from the 2006 imagery by Photoscience Inc. Arc M ap 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 Gul f 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

- and

- Ecology.pdf , accessed March 2011.

HALE, J. A., T. K. F RAZER, D. A. TOMASKO

, and M. O. HALL. 2004. Changes in th e 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 Ha lophila decipiens, a deep water seagrass on the

w est 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

.

94Yarbro and Carlson, Editors

SIMM Report #1

MATTSON, R. A., T. K. FRAZER, J. HALE, S. BLITCH, and L. AHIJEVYCH. 2007 . Florida Big
Bend. Pp. 171

– 1 88 in L. Handley et al., eds. Seagrass statu s 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 Seag rasses Aquatic Preserve, 352

- 563

- 0450, melissa.charbonneau@dep.state.fl.us

.

95Yarbro and Carlson, Editors

SIMM Report #1



### 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)

Ge neral 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
of fshore 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 stabl e. Seagrass species composition also appears to be stable. However, c onversion of continuous seagrass beds to patchy beds is cause for concern. Stressors include nutrients, phytoplankton

, and turbidity , which reduce water clarity . These stressors were elev ated 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 Ni ñ o, 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.

Thi s area is characterized by a mixture of hard bottom, reefs, sands, and seagrass beds.

96Yarbro and Carlson, Editors

SIMM Report #1

Figure 1. S eagrass cover in Suwannee Sound, Cedar Keys, and Waccasassa Bay, 2001.

M apping 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 wa ter 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 as sociated 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 th e 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.

97Yarbro and Carlson, Editors

SIMM Report #1

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 ree f 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 dat a 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 Ni ñ o, 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. S EAGRASS A CREAGE IN S UWANNEE S OUND , C EDAR K EYS

, AND W ACCASASSA B AY 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

98Yarbro and Carlson, Editors

SIMM Report #1

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 pres ent 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 (F igure 3).

Figure 2. Percent age occurrence of seagrasses and drift algae in the Cedar Key subregion, May 2006

– September 2008.

99Yarbro and Carlson, Editors

SIMM Report #1

F igure 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

100Yarbro and Carlson, Editors

SIMM Report #1

re solve 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 Pres erve, 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

.

101Yarbro and Carlson, Editors

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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 i n 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 sc arring is evident around the mouth
of Pithlachascotee River , St. Martins marker shoal ( 10 nm i off Pasco County), and Anclote Key, but is less extensive elsewhere.

Figure 1. Seagrass cover along the Springs Coast

, 2007.

G eographic Extent : Th e 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, d ark 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.

102Yarbro and Carlson, Editors

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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 Ni ñ o, 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 m ap 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 Departme nt of Environmental Protection (FDEP) Coastal and Managed Areas (CAMA)

• C ontinue 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 monitor ing trends in the expansion of drift

macro algae 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
reduc ing 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 C oast 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 caus e for concern. Stressors include increased nutrients, phytoplankton

, and turbidity. These were elevated after the 1998 El Ni ñ o 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 Ni ñ o; 2004, 2005 hurricanes

Propeller scarring Localized Anclote Key, Pithlachascotee River

Seagrass Mapping Assessment: T otal seagrass cover fo r 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 se agrass comprising 18,850 acres (Table 1)

.

TABLE 1. S EAGRASS A CREAGE IN THE S PRINGS C OAST R EGION 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. A CRES OF SEAGRASS ALONG
THE S PRINGS C OAST , 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 can no t 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 percent age occurrence of seagrass in 100 randomly placed quadrats (Figure 2)

. F or 2004, 2005

, and 2008

, turtle grass ( Thalassia
testudinum ) was m ost common, found in 7 0

– 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 maritim a ) 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. O CCURRENCE (%) OF SEAGRASS SPECIES IN THE S T . M ARTINS K EYS 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 m ap 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 shallow

water 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 co mpleted 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 naviga tion 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 ma pped from this dataset by Avineon Inc., using the Florida Land Use Cover Classification System. Arc M ap shapefiles of benthic habitats are distributed on the Geographic Information Systems database at SWFWMD and are available upon request. The digital image ry 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 percent age 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, F lorida

.
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. Peters burg, 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 AS SOCIATES INC. and MARTEL LABORATORIES INC. 1985. Florida Big Bend s eagrass h abitat s tudy n arrative r eport. A final report by Continental Shelf
Associates Inc. submitted to the Min erals Management Service, Metairie, L ouisiana . 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.

Seagr ass beds grow along Gulf coastline despite increasing pollution. Tampa Tribune, November 18, 2009: http://www2.tbo.com/content/2009/nov/18/seagrass

- be ds

- growing

- along

gulf

- coastline

- despite/ , accessed March 2011.

FRAZER, T. K., and J. A. HALE. 2001. Changes in a bundance and d istribution of s ubmersed

a quatic v egetation a long Florida ’ s Springs Coast: 1992

– 1999. Final report. Southwest Florida Water Manage ment 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 in c ludes 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

• Redu c e s torm 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 a n d 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 Ni ñ o

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. W ESTERN P INELLAS C OUNTY S EAGRASS A CREAGE 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, sea grass 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: Seagra ss 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 Scien tific 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, F lorida

. 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 (J anuary 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 nonpoin t 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 Ni ño

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 li ght 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 Ni ño

Propeller scarring Extensive

Seagrass Mapping Assessment: Between 200 6 and 200 8 , total seagrass cover for Tampa Bay increased by 1,349 acres, fr om 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 i n 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. S EAGRASS A CREAGE IN T AMPA B AY
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 monito red by the Tampa Bay Interagency Seagrass Monitoring Program with participants assessing an average of 1,550 1

- m
× 1

- m quadrats annually. R esults are expressed as the percen tage frequency of occurrence for
each seagrass species.

Shoal grass ( Halodule wrightii ) is the dominant Tampa Bay species, found in all Tampa Bay
sub regio ns (Table 2)

. Turtle grass ( Thalassia testudinum ), the dominant lower Tampa Bay species, and m a natee 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.
, h as 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. P ERCENTAGE FR EQUENCY OF OCCURRENCE OF SEAGRASS

SPECIES AND C

AULERPA SPP

. IN T AMPA B AY

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 scarr ing.

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 annual ly 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 tr ansects 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. SWARZ ENSKI, J. C. BROCK, and F. E. MULLER

KARGER. 2004. Assessment of estuarine water

- qu ality indicators using MODIS medium

resolution bands: initial results from Tampa Bay, FL. Remote Sensing of Environment 93: 423

– 441.

TAMPA BAY ESTUARY PR OGRAM. 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. GRE ENING, 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 acre s 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

exc eeds 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, C auses

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 so uth 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 p ropeller 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 an d 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 homogeneou s 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 9,7 97 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 i n 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 200 6 and 200 8 , total seagrass cover for the Sarasota Bay region increased by 2,787 acres, fr om 9,854 acres to 12,641 acres, a n increas e 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, respectivel y, 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 2,71 4 acres to 2,863 acres.

TABLE 1. S EAGRASS A CREAGE IN S ARASOTA B AY AND L EMON B AY 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 th e 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, sea grass 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 b ays. Seagrass target s 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, i ncreasing 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 map s 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 photograp hs 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 quali ty 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 R esearch Institute Technical Report TR

- 1, Florida Department of Environmental Protection, St. Petersburg, Florida, 37 p. + appendices.

FLORIDA DEPARTMENT O F ENVIRONMENTAL PROT ECTION CHARLOTTE HAR BOR
AQUATIC PRESERVES . 2007. Seagrass annual data summary fro m 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. GRE ENING, and G. E. RAULERSON. 2005. Spatial and temporal variation in seagrass coverage in southwest Florida: assessing the relative effects
of an thropogenic nutrient load reductions and rainfall in four contiguous estuaries. Marine
Pollution Bulletin 50: 797

– 805.

CHARLOTTE HARBOR NAT IONAL ESTUARY PROGRA M. 2009. Water quality target refinement project, task 1: harbor segmentation scheme, interim rep ort 2, Janicki Environmental, Inc., St. Petersburg, F lorida

. 62 p., http://www.chnep.org ; accessed March 2011.

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CHARLOTTE HARBOR NAT IONAL ESTUARY PROGRA M. 2009. Water quality target refinement project, task 2: seagrass target development, interim report 2. http://www.chnep.org/NEP/agendas

2010/TAC/WQQOS_WQ%20Target%20Refine%20Report%202%20Seagrass%20targets.pdf

, accessed March 2011.

General References and Additional Information

TAMPA BAY ESTUARY PR OGRAM. 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 Wate ratlas: http://maps.wateratlas.usf.edu/sarasota/index.asp ; accessed
March 2011.

The Charlotte Harbor National Estuary Program: http://www.chnep.org/ , access ed 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

.

Monit oring: 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

.

12 6Yarbro and Carlson, Editors

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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 th is 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

G eographic 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.

T he 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 Car los Bay, and the tidal Caloosahatchee River) are within the jurisdiction of South Florida Water Management District.

M apping 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, e valuate 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 (Fig ure 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 p lace.

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 comp osition 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 waters heds. 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 estuar y 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 gras s ( 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 CHARL OTTE 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, Greenawalt

Boswell 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 P ass 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 Braun

Blanquet 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 7 0 c m in the Myakka River to 18 0 c m 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 increas es 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 histori cal 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 acre age was determined for each estuary segment

. A n 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 HARBO R 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 sev ere 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 ar e 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 Pa ss, 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 stereoscop ically 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 Preser ves 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 leng ths, 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 NAT IONAL ESTUARY PROGRA M

. 2009. Water quality target refinement project, task 1: harbor segmentation scheme. Interim Report 1, Janicki Environmental, Inc., St. Petersburg, F lorida

. 33 p., http://www.chnep.org ; accessed March 2011.

CHARLOTTE HARBO R NATIONAL ESTUARY P ROGRAM

. 2009. Water quality target refinement project, task 2: seagrass target development. Interim Report 2, Janicki Environmental, Inc., St. Petersburg, F lorida

. 62 p., http://www.chnep.org/NEP/agendas

2010/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. DU FFEY, S. E . ERICKSON, K. S. FU HR, 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 O F 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 mo del 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, Kris ten.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 a bundance of turtle grass ( Thalassi a testudinum ) and shoal grass ( Halodule wrightii ) is stable , with expected seasonal fluctuations , but o ccurrence 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 (S chmid 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, b ed 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 seagrass es 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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Ma pping 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 effe cts 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

sca rring 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. A CREAGE OF SEAGRASSES
IN E STERO B AY

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 ha ve 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 spec ies 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. (Figur e 5). Turbidity due to resuspension of bottom sediments in this very shallow system continues to affect water clarity, as do seasonal increases in

m acroalgae.

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 acre age w ere 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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Map ping 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 Aquati c 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 NAT IONAL ESTUARY PROGRA M

. 2009. Water Quality Target Refinement Project, task 1: harbor segmentation s cheme, Interim Report 1

, Janicki Environmental, Inc., St. Petersburg

, F lorida

. 33 p.

CHARLOTTE HARBOR NAT IONAL ESTUARY PROGRA M

. 2009. Water Quality Target Refinement Project, task 2: seagrass target development, Interim Report 2, Janicki Environmental, Inc., St. Petersburg, F lorida

. 6 2 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 b ay u pdate. http://www.sfwmd.gov/org/exo/ftmyers/report

- text/index.html

, accessed March 2011

.

FLORIDA DEPARTMENT O F ENVIRONMENTAL PROT ECTION CHARLOTTE HAR BOR
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/ch arlotte/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. DU FFEY, 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. C REWZ, 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. pl us 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

E stero Bay Aquatic Preserve: http://www.dep.state.fl.us/coastal/sites/estero/info.htm , accessed
March 2011.

FLORIDA DEPARTMENT O F NATURAL RESOURCES. 1983. Estero Bay Aquatic Preserve Management Plan, Tallahassee, Flo rida. 126 p. http://www.dep.state.fl.us/coastal/downloads/management_plans/aquatic/EsteroBay.pdf

,
access ed March 2011.

The Charlotte Harbor National Estuary Program, http://www.chnep.org/ , accessed March 2011.

S arasota County Wateratlas, http://www.sarasota.wateratlas.usf.edu/ ; acces sed 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 seagras s 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 reserv e 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 Stresse s 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
Gord o n 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 Rese arch 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 Restorati on Recommendations

• R educe 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 shif ting 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 w ere 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. S EAGRASS ACREAGE IN THE R OOKERY B AY A QUATIC P RESERVE , 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 eng el

manni i ) 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 g rass , and s tar 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,

a erial photography of coastal southwest Florida was collected at a 1:24,000 scale by the South Florida Water Managem ent 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
coll ection of sidescan sonar data to compare the accuracy of the two seagrass mapping techniques.

Monitoring Data: Several areas within the r eserve have been monitored annually or quarterly using a fixed

- transect modified Braun

- Blanquet methodology. Johnson B ay 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, s eagrass species, abundance (Braun

- Blanquet)

, blade length, total percent age 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.

LO CKER, S. D. 2006. Mapping s ubmerged a quatic v egetation u sing s idescan s onar, 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 ha bitat 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 201 1.

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 Rese arch 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 mos t 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 pro gram 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).

M apping 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 n early 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, optic al 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

sever al 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 tur tle 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

S eagrass 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 ima gery 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 spe cies 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 o f South Florida College o f 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 Carls o n (FWRI) began reconnaissance sampling f or 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 th e monitoring effort,
and our i nitial project will sample a 1

- k m 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. REVI LLA, P. M. GLIBERT, and S. MURASKO. 2007. Nutrient quality drives differential phytoplankton community co mposition on the southwest Florida shelf. Limnology and Oceanography 52: 1067

– 1078.

MAIE, N., J. N. BOYE R, C. YANG, and R. JAFFE. 2006. Spatial, geomorphological, and seasonal variability of CDOM in estuaries of the Florida Coastal Everglades. Hydrobiologi a 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.

Ge neral 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 Rese arch 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 seagras ses 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 Monito ring 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 availabi lity 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 attenuatio n 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. S EAGRASS ACREAGE IN THE F LORIDA K EYS
N ATIONAL M ARINE S ANCTUARY 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

F lorida 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 wr ightii ) 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 digitiz ed 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 F KNMS 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. CAC CIA, 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. WHI TFIELD, 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. Seagrass es appear to have recovered from this event, based on data from the most recent (2004) imagery. In 2005, Hurricanes Ka trina 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
aba ted 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 b y E verglades N ational P ark 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.

S ummary 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 progr am 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. T he 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 pre

dominance 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 lo ng

- 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. MADL EY, M. J. DURAKO, J. C. ZIEMAN, AND M. B. ROBBLEE. 2006.

F lorida 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. MCDON ALD, 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 M apping 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 (15 9

, 363 acres, from aerial photography acquired in 2004 and 2005 ) in the Biscayne Bay region (Figure 1)

. Ma pping data
from 1992 indicate that s eagrass beds in the adjacent nearshore Atlantic Ocean accounted for an additional 104, 9 1 0 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 e xtends from the Oleta River north of Miami Beach on the east coast of Florida south through Biscayne National Park, Card Sound, a nd 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 th rough 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 Restora tion 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 ex cept 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 Ass essment, 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 sea grass 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

spa tial 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 seagra ss 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

– 20 05

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

– 20 05

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), t urtle 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

pr esence 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 Beac h, 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.floridamarin e.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 Dep artment 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/der m ; 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/biscay nebay/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

Contact s : Paul Davis and Eric Anderson; Palm Beach County Department of Environmental Resource Management (Mapping and Monitoring)

General Assessment: Based on interpretation of aerial photographs, s eagrass cover in Lake
Worth Lagoon (LWL) between 2001 and 2007 was generally st able

, 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 l agoon. 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 ( S yringodium filiforme ), turtle grass ( T halassia test u dinum ), and shoal grass ( H alodule wright

i i ). The least coverage by seagrasses

occurs in the central (12 %) and southern (23%) portions of the l agoon ; dominant species are Johnson’s seagrass ( H alophila j oh n sonii ), paddle grass ( H

. d

ecipiens ), and shoal grass

. Seagrass species composition also appears to be stable in all section s of the lagoon. Annual

transect monitoring indicated decreases in cover and density after the 2004, 2005, and 2006
hurricanes

. R ecord high levels of seagrass cover and density were noted in 2007 , but slight
decrease s 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). F reshwater 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 a nd Lake Worth (Palm Beach) Inlet but is minimal elsewhere.

Seagrass Status and Stresses Status Trend Assessmen t, 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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M apping 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 ent ire region again in 2011

– 12.

• Continue a nnual f ixed

- t ransect m onitoring.

• 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 e mpty into LWL

.

• Evaluate nutrient and suspended sediment loading from the agricultural areas ( L8 basin )
and i dentify 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
f ixed t ransect monitoring ha s shown
fluctuations in seagrass cove r 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 i ncreases 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 li mited 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 d ischarges. 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. S eagrass cover varies throughout t he lagoon, with the mo st seagrass found in the northern end ( 65% )

, compared with 12% in the central segment and 23% in the southern segment. C omparing the 2001 maps to the 2007 maps revealed a 5 9

- 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 ha ve poor visibility and the tiny and thus difficult to assess Johnson’s seagra ss and paddle grass are dominant

. As a result, mapping effort s may not have accurately identified

seagrass cover. Mapping efforts identified on ly seagrass beds that were 0.25 acre or more in
size and w ere designed to detect large

- scale changes.

Seagrass S tatus 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. S EAGRASS ACREAGE IN L AKE W ORTH L AGOON

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 P alm B each C ounty Department of E nvironmental

R esource M anagement (PBC DERM) initiated a long

- term seagrass monitoring pro gram t h at 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

– 1 00 ft. of the edge of an existing seagrass bed. The first five years of surveys showed fluctuation s 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 de crease 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 acti on. 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

pe rcent age 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 . I n 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 t ransects (12 stations)

. In 2006, the number
shown is t he 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 e mpty into LWL

.

• Evaluate nutrient and suspended sediment loading from the agricultural areas ( L8 basin ), and

i dentify 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 flow n at 1:10,000 scale for Palm Beach County by U.S. Imaging (Bartow, FL)

. T he original negatives and copies of diapositives are housed at PBC DE R M. Benthic habitats were classified and mapped from this dataset by Avineon Inc . (Clearwater, FL) using the F lori da L and U se C over C lassification S ystem

. ArcMap shape files of benthic habitats

are available on the F ish and W ildlife R esearch I nstitute Marine Resources G eographic

I nformation S ystem (MRGIS) website ( http://ocean.floridamarine.org/mrgis/ ) or by contacting
PBC D ERM.

Monitoring Data: A variety of groups and agencies monitor s seagrass in the Lake Worth Lagoon (Table 2)

. Since 2000, PBC DERM has been monitoring seagrass annually along nine

transec t s ( 27 stations ) throughout LWL with the Fixed Transect Monitoring Project (FTMP)

. S ince 2006 the F ish and W ildlife Research Institute (FWRI) and the N ational Oceanic and

A tmospheric A dministration ( NOAA) have been monitoring Johnson’s seagrass ( H. jo h nson i i ) at
8 locations and 33 stations in the lagoon for the H. joh n sonii Recover Team. And in 2009

, the

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S outh F lorida W ater M anagement D istrict (SFWMD) and the U

. S

. A rmy C orps of E ngineers (USACOE) began bimonthly monitoring at five locations ( with 30 station s at each) for the
C omprehensive E verglades R estoration P lan (CERP) / Restoration, Coordination and Verification (RECOVER) Seagrass Monitoring Section

.

TABLE 2. M ONITORING PROGRAMS IN L AKE W ORTH L AGOON

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

P ertinent 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 DE PARTMENT OF ENVIRONM ENTAL RESOURCES
MANAGEMENT IN CONJUN CTION WITH DAMES AND MOORE. 1990. Lake Worth Lagoon

n atural r esources i nventory and r esource e nhancement s tudy , West Palm Beach, F lorida. 226

p.

PALM BEACH COUNTY DE PARTMENT OF ENVIRONM ENTAL RESOURCES
MANAGEMENT AND STATE OF FLORIDA DEPARTMEN T OF ENVIRONMENTAL PROTECTION, SOUTHEAS T DISTRICT. 1998. Lake Worth Lagoo n m anagement p lan , West Palm Beach, F lorida. 257 p.

PALM BEACH COUNTY DE PARTMENT OF ENVIRONM ENTAL RESOURCES
MANAGEMENT. 2008. Palm Beach County Mangrove and Seagrass Mapping Project. Final report prepared by Avineon Inc. , West Palm Beach, F lorida. 18 p.

PA LM BEACH COUNTY DEPA RTMENT OF ENVIRONMEN TAL RESOURCES
MANAGEMENT. 2009. Lake Worth Lagoon: f ixed t ransect s eagrass m onitoring c umulative

r eport 2000

– 2008. Final report prepared by Applied Technology and Management Inc., West Palm Beach, F lorida

.

REstoration COordination and VERification. 2007. Final 2007 s ystem s tatus r eport. Section

5 Northern Estuaries Module , Comprehensive Everglades Restoration Plan

. 1 1 p.

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REstoration COordination and VERification. 2010. 2009 s ystem s tatus r eport d raft. Sectio n 4
Northern Estuaries Module

, Comprehensive Everglades Restoration Plan

. 9 1 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 M onitoring: 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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### 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 Ha ll, 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 ( H

alophila decipiens ) to the more robust, canopy

- forming s hoal 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 (Ste ward 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.

M apping 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 distri bution 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 effor ts 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

s tressors 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 expecte d 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

185Yarbro and Carlson, Editors

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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 w ere mapped to the species level (using detailed ground

- truthing and GPS technology) in 2007

– 08 (Avineon 2008). S pecies

- 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. S EAGRASS ACREAGE IN THE S OUTHERN I NDIAN RIVER L AGOON S YSTEM

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 bi

monthly 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. R ecovery 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. U sing 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 sharpl y, 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 (Johns on’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

yea rs.

• Continue bimonthly patch

- scale

m onitoring.

• Continue bi annual 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 Ve rification (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 Distric t for SFWMD in 2007 and 2010 using 9m 2 quadrats 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 monit oring 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 th e 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. Beginn ing 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 s pecific SAV m apping t est p roject (Phase II). Final p roject r eport
for contract ST061300

- WO05 for South Florida Water Management District, West Palm Beach,

F lorida

. 24 p.

AVINEON INC. 2010. Final project report Saint Joh ns River Water Management District/South Florida Water Management District 2009 Indian River Lagoon seagrass mapping, May 2010

. 49

p.

IBIS ENVIRONMENTAL I NC. 2007. 2007 St. Lucie Estuary submerged aquatic vegetation mapping study. Prepared for the South Florida Water Management District. West Palm Beach,

F lorida

. 7 p.

IRLANDI, E . 2006. Literature r eview of s alinity e ffects on s ubmerged a quatic v egetation (SAV)
found in the s outhern Indian River Lagoon and a djacent e stuaries. South Florida Water Management District, West Palm Beach, F lorida. 30 p.

RECOVER. 2009. 2009 System s tatus r eport. Restoration Coordination and Verification Program

, U.S. Army Corps of Engineers, Jacksonville, F lorida, and South Florida Water Management District, West Palm Beach, F lorida

. 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 Loxa hatchee 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 chang e analysis (1986

– 1999). South Florida Water Management District, West Palm Beach, F lorida

. 32

p.

SIME, P. 2005. St. Lucie Estuary and Indian River Lagoon conceptual ecological model.

Wetlands 25: 898

– 907.

STEWARD, J. S., R. B ROCKMEYER, R. VIRNST EIN, P. GOSTEL, P. S IME, and J.

VANARMAN. 2003. Indian River Lagoon Surface Water Improvement and Management (SWIM) Plan, 2002 u pdate. 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 r eport to the South Florida Water Management District (Contract No. C

- 77 79). 91 p.

General References and Additional Information

CREAN, D. J., R. M. ROBBINS, and N. IRICANAN. 2007. Water quality target development in
the s outhern 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.

RECOV ER. 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 depth

limit expansion of seagrasses, which appears to be a r esponse to modest increases in light availability (reduction in light attenuation since 1997). S eagrass species composition and bed

texture (patchiness) ha ve been generally stable throughout the system . However, despite the expansion of seagrass area, perc ent age cover (seagrass density) has decreased , most markedly during 2004

– 05 in the southern NIRL following the 2004 hurricanes , probably as a
result of persistent ly low salinity. Propeller scarring is not a widespread problem, but it is
extensive in the so uth

- central Mosquito Lagoon and, to a lesser degree, near the Sebastian
Inlet. S eagrass 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

S eagrass 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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M apping 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 w ater 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

t he combined seagrass and water quality monitor ing 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 ri vers and canals discharging into the NIRL

.

• I mprove spatial and temporal monitor i ng as needed to meet changing resource management goals by periodic ally reviewing monitor ing programs. Thes e reviews will includ e 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 Engineer s’ 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, transpare ncy, 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 t urn, 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 mul tiyear 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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• 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 se verity of scarring . Troll/no

- motor zones have been established to encourage sea grass

- bed recovery in the most damaged locations. Continuation of aerial surveys will help in assess ing restoration success and management potential for additional areas as need ed.

Summary Assessment: Table 2 and Figure 2 depict the steady incre ase in seagrass area since 1996, probably a consequence of modest decreases in average light attenuation

, or K d (especially in Banana R iver Lagoon: K d ( ’ 90

– ’ 96) = 1.02 ; K d ( ’ 97

– ’ 07) = 0.91; and southern NIRL
from Sebastian through Vero Beach: K d ( ’ 90

– ’ 96) = 1.31, K d ( ’ 97

– ’ 07) = 1.17). In 2007,

seagrasses covered 71,64 6 acres, and most of the acreage (55,90 6 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 cau sed 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 seaso n. 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 percent age 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 (2,86 2 acres) and in the Vero Beach reach of the NIRL (1,20 7 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
mult i year area and depth

- limit targets (Table 2 and Table 3) . If the 2009 map ping 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 seagr ass cover, it must achieve its area target in at least f our out of seven mapping years

. Sebastian and Vero Beach were the only other segments to attain their depth

limit 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 percent age cover (bed densi ty). 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 SJR WMD 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 photo interpretation keys and ground

- truthing. Features are classified according to SJRWMD/SFWMD

- modified F lorida L and U se C over C lassification S ystem 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 throug hout the

NIRL ; of these, 74 transects have been monitored since 1994

. T ransects are random ly

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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. MIL LER, and L. M. HALL. 2000. Monitoring seagrass changes in Indian River Lagoon, Florida using fixed transects. Pp. 167

– 176 in : S. A. Bortone (ed.), Seagra sses monitoring, ecology, physiology and management, CRC Press, Boca Raton,
Florida.

SCHAUB, R., D. M. SC HEIDT, C. M. GARREAU

, and C. R. HALL. 2009. Quantitative assessment of seagrass scarring in the southern Mosquito Lagoon and Northern Indian River of

B revard 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. B ROCKMEYER, R. VIRNST EIN, P. GOSTEL, P. S IME, and J.

VANARMAN. 2003. Indian River Lagoon s urface w ater i mprovement and m anagement (SWIM)

p lan, 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 E NGINEERS and ST. JOHNS RIVER WATE R 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 Manageme nt District, Palatka, Florida, 63 p. + appendices.

19 8Yarbro and Carlson, Editors

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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 Serv ice 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)

202