FWRI Technical Report TR-11 2007

TECHNICAL REPORTS

Florida Fish and Wildlife

Conservation Commission

Florida Bay Science Program: 

A Synthesis of Research on Florida Bay

John Hunt and William Nuttle

Editors

FISH AND WILDLIFE RESEARCH INSTITUTE

TECHNICAL REPORTS

ISSN 1930-1448
Charlie Crist

Governor of Florida

Florida Fish and Wildlife Conservation Commission

Kenneth D. Haddad

Executive Director

The Fish and Wildlife Research Institute (FWRI) is a division of the Florida Fish and Wildlife

Conservation Commission (FWC). The FWC is “managing fish and wildlife resources for their

long-term well-being and the benefit of people.” The FWRI conducts applied research pertinent to managing marine-fishery resources and marine species of special concern in Florida.

Programs at the FWRI focus on resource-management topics such as managing gamefish and

shellfish populations, restoring depleted fish stocks and the habitats that support them,

protecting coral reefs, preventing and mitigating oil-spill damage, protecting endangered and

threatened species, and managing coastal-resource information.

The FWRI publishes three series: Memoirs of the Hourglass Cruises, Florida Marine Research Publications, and FWRI Technical Reports. FWRI Technical Reports contain information relevant to

immediate resource-management needs.

Gil McRae, FWRI Director

James F. Quinn, Jr., Science Editor

Judith G. Leiby, Copy Editor

Llyn C. French, Publications Production
Florida Bay Science Program: 

A Synthesis of Research on Florida Bay

John H. Hunt

Editor

Florida Fish and Wildlife Conservation Commission

Fish and Wildlife Research Institute

South Florida Regional Laboratory

2796 Overseas Highway, Suite 119

Marathon, Florida 33050 USA

William Nuttle

Editor

Eco-hydrology.com

Ottawa, Ontario

Canada K1S 4B6

Florida Fish and Wildlife Conservation Commission

FWRI Technical Report TR-11

2007
Cover Photographs

Center: The Crocodile Dragover pass, below Terrapin Bay and Madeira Bay (Bill Perry, Everglades 

National Park). Clockwise from upper left: Sampling in seagrass (Florida Fish and Wildlife Conservation

Commission); Anhinga with spotted sea trout, Florida Bay (Bill Perry, Everglades National Park); Florida

Bay hardbottom habitat (Florida Fish and Wildlife Conservation Commission); White Pelicans and 

Black Skimmers at low tide, Flamingo, Florida Bay (Bill Perry, Everglades National Park).

Copies of this document may be obtained from

Florida Fish and Wildlife Conservation Commission

Fish and Wildlife Research Institute

100 Eighth Avenue SE

St. Petersburg, FL 33701-5020 USA

Attention: Librarian

Document Citation

Hunt, J. H., and W. Nuttle, eds. 2007. Florida Bay Science Program: A Synthesis of Research on Florida

Bay. Fish and Wildlife Research Institute Technical Report TR-11. iv + 148 p.

Document Production

This document was composed in Microsoft Word® and produced using QuarkXPress® on Apple Macintosh®

computers.The headline font is Adobe® Avant Garde, the text font is Adobe® Palatino, and the cover headline

is Adobe® Gill Sans.

The cover and text papers used in this publication meet the minimum requirements of the American

National Standard for Permanence of Paper for Printed Library Materials Z39.48—1992.
Table of Contents

Chapter 1 Florida Bay Science ............................ 1

Chapter 2 Executive Summary ............................ 2

PURPOSE OF THIS REPORT ................................ 2

ECOSYSTEM HISTORY .................................. 3

PHYSICAL PROCESSES .................................. 4

NUTRIENT DYNAMICS .................................. 4

PLANKTON BLOOMS................................... 5

Northeast Region ..................................... 5

Central Region...................................... 5

West Region ....................................... 6

SEAGRASS ECOLOGY .................................. 6

HIGHER–TROPHIC–LEVEL SPECIES............................ 7

Chapter 3 Ecosystem History ............................. 9

INTRODUCTION ..................................... 9

Methodology ...................................... 9

Previous Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Summary of Ecosystem History and Paleoecology Research. . . . . . . . . . . . . . . . . . . . 12

SALINITY PATTERNS AND TRENDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

NUTRIENT PATTERNS AND TRENDS . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

OCCURRENCE AND PATTERN OF ALGAL BLOOMS . . . . . . . . . . . . . . . . . . . . 23

Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

SEAGRASS TRENDS AND PATTERNS . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

HIGHER–TROPHIC–LEVEL SPECIES. . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Chapter 4 Physical Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Research Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

DRIVING PROCESSES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Winds and Storms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Precipitation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Evaporation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Surface-Water Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Groundwater Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Sea Level and Tides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Boundary Currents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

i
ii

INFLUENCE OF DRIVING PROCESSES . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Salinity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Circulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Exchanges with Adjacent Waters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

PREDICTION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Fresh Water Inflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Exchanges with Adjacent Waters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Circulation Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Salinity Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

UNRESOLVED QUESTIONS AND ONGOING RESEARCH . . . . . . . . . . . . . . . . . . 48

Driving Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

System Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Hydrodynamic Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Chapter 5 Nutrient Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Summary of Knowledge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

PATTERNS AND TRENDS IN WATER QUALITY . . . . . . . . . . . . . . . . . . . . . . . 57

Period of Study. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Recent Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

EXOGENOUS SOURCES OF NUTRIENTS . . . . . . . . . . . . . . . . . . . . . . . . . 59

Nutrient Inputs from the Everglades: Taylor Slough–C-111 and Shark River. . . . . . . . . . . . . 60

Ground Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Atmospheric, Keys Waste Water, Keys Storm Water, and the Gulf of Mexico Nutrient Inputs . . . . . . 66

Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

INTERNAL NUTRIENT CYCLING . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Benthic Nutrient Fluxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Internal Nutrient Cycling: Carbonate–Phosphorus–Iron Relations . . . . . . . . . . . . . . . . . 67

Role of Sediment Resuspension in Phosphorus Cycling . . . . . . . . . . . . . . . . . . . . . 67

Nutrient Flux at the Sediment–Water Interface . . . . . . . . . . . . . . . . . . . . . . . . . 68

Seagrass Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

INFLUENCE OF FLORIDA BAY WATER QUALITY ON THE REEF TRACT . . . . . . . . . . . 69

Nutrient Export Through Keys Passes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

WATER–QUALITY MODELING . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

CURRENT AND ONGOING RESEARCH . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Unresolved Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Summary of Ongoing Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Chapter 6 Plankton Blooms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Regional Differences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Summary of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

EASTERN FLORIDA BAY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

CENTRAL FLORIDA BAY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Cause of Blooms in the Central Region . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

Domination by Cyanobacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85

WESTERN FLORIDA BAY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Chapter 7 Seagrass Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Seagrass Communities in Florida Bay . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Recent and Historical Changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Conceptual Models for Seagrass Die-off . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

Summary of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

EFFECT OF ECOSYSTEM CHARACTERISTICS ON GROWTH AND SURVIVAL . . . . . . . 101

Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

Salinity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Sulfide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Labyrinthula Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Sediment Characteristics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

EFFECT OF ECOSYSTEM CHARACTERISTICS ON COMMUNITY STRUCTURE 

AND DISTRIBUTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

Correlation with Patterns of Water Quality . . . . . . . . . . . . . . . . . . . . . . . . . 104

Geographic Variation in Seagrass Die-off . . . . . . . . . . . . . . . . . . . . . . . . . . 104

MODELING CHANGE IN BENTHIC COMMUNITIES . . . . . . . . . . . . . . . . . . . 106

CURRENT RESEARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Field Assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Experimental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Chapter 8 Higher-Trophic-Level Species . . . . . . . . . . . . . . . . . . . . . . 110

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110

Description of Higher-Trophic-Level Species in Florida Bay . . . . . . . . . . . . . . . . . . 110

Processes Driving Change in the Ecosystem . . . . . . . . . . . . . . . . . . . . . . . . . 113

Research Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Summary of Recent Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

DISTRIBUTION OF SPECIES AND PATTERNS OF ABUNDANCE . . . . . . . . . . . . . . 119

EFFECT OF ECOSYSTEM CHARACTERISTICS ON GROWTH AND SURVIVAL . . . . . . . 120

Effect of Salinity on Growth and Survival. . . . . . . . . . . . . . . . . . . . . . . . . . 120

Effect of Water Quality on Growth and Survival . . . . . . . . . . . . . . . . . . . . . . . 121

Effect of Benthic Habitat on Growth and Survival . . . . . . . . . . . . . . . . . . . . . . 122

Immigration, Growth, and Survival of Offshore-Spawning Fishes that Use Florida Bay as a Nursery . 122

EFFECT OF ECOSYSTEM CHARACTERISTICS ON SPECIES DISTRIBUTION AND 

COMMUNITY AND TROPHIC STRUCTURE . . . . . . . . . . . . . . . . . . . . . . 123

Effect of Salinity on Species Abundance and Community Structure . . . . . . . . . . . . . . . 123

Effect of Water Quality on Species Abundance and Community Structure . . . . . . . . . . . . . 124

Effect of Benthic Habitat on Species Abundance and Community Structure . . . . . . . . . . . . 124

VARIATION IN ECOSYSTEM CHARACTERISTICS . . . . . . . . . . . . . . . . . . . . 127

Effects of Animals on the Ecosystem . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Oceanographic Effects on Larval Transport and Recruitment . . . . . . . . . . . . . . . . . . 128

Effect of Human Activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

MODELING CHANGE IN HIGHER–TROPHIC–LEVEL SPECIES . . . . . . . . . . . . . . 134

Statistical Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Simulation Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

ONGOING RESEARCH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Projects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Unresolved Issues and Questions: Research Needs . . . . . . . . . . . . . . . . . . . . . . 138

LITERATURE CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

iii
About This Report

This report draws its material directly from syntheses compiled for the 2001 Florida Bay Science 

Conference. The Florida Bay Science Program organizes itself around five strategic research questions.

Topical teams associated with each question consist of modelers and researchers working in the Bay and

adjacent marine systems.These teams compiled the original synthesis documents.

In preparation for the 2003 Florida Bay Science Conference, the research teams have modified the

existing synthesis documents to bring them up to date and implement a more uniform, common format.

In some cases, entirely new documents have been drafted, such as the information here on ecosystem

history and on nutrient dynamics. The present report compiles these separate documents into one and

provides the reader with summary material as a guide to the contents.

Team Leaders

Ecosystem History

G. Lynn Wingard (USGS, Reston)

Physical Processes

Thomas Lee (University of Miami), Elizabeth Johns (NOAA/AOML), Peter Ortner and Dawn Boyer

(NOAA/AOML, PMC)

Nutrient Dynamics

Joseph Boyer (Florida International University), Brian Keller ( Florida Keys National Marine Sanctuary,

PMC)

Algal Blooms

Gary Hitchcock (University of Miami), Ed Phlips (University of Florida), Larry Brand (University of

Miami), Douglas Morrison (ENP, PMC)

Seagrass Ecology

Michael Durako (University of North Carolina at Wilmington), Joseph Zieman (University of Virginia),

Michael Robblee (USGS, PMC)

Higher-Trophic-Level Species

Joan Browder (NOAA/NMFS), John Lamkin (NOAA/NMFS, PMC)

Editors

William Nuttle (Eco-hydrology.com) and John Hunt (Florida FWC, PMC)

iv
Florida Bay lies between the southern tip of the Florida

mainland and the island chain known as the Florida

Keys. More than 85% of the bay’s 2,200-km2 area lies

within Everglades National Park, and the Florida Keys

National Marine Sanctuary contains much of the rest.

The bay includes more than 200 small islands, many

of which are rimmed with mangroves. Florida Bay

supports numerous protected species, including the

Roseate Spoonbill, the bottlenose dolphin, the American crocodile, the West Indian manatee, and several

species of sea turtles. Moreover, Florida Bay provides

critical habitat for commercially important species,

such as spiny lobsters, stone crabs, and many important finfish species. It also serves as the principal nursery for the offshore Tortugas pink shrimp, which

supports an important fishery.

Florida Bay is an important component of the

much larger south Florida region that is the focus of

the Comprehensive Everglades Restoration Plan

(CERP). The bay receives freshwater runoff from the

Everglades, a large portion of which is managed discharge from canals in the region. Decisions guiding the

restoration of the Everglades carry implications for

future conditions in Florida Bay, just as the development of the regional water management system over

the past fifty years influences present conditions. Although a specific restoration target has not yet been defined for Florida Bay, many expect that restoration of

more natural hydrologic conditions in the Everglades

will move the bay toward an ecological state more typical of the period prior to the time of engineered

changes imposed on the regional south Florida system.

Rapid ecological changes occurred in Florida Bay

between 1987 and 1991. These changes came at the

end of a multiyear drought that had elevated salinity

values in the central portion of the bay to nearly 70 practical salinity units (psu), almost double the typical

salinity of seawater. Large areas of seagrasses began

to die late in 1987. Concurrently, the shrimp harvest on

the Tortugas Grounds declined to record lows. In 1991,

turbidity and plankton concentrations increased dramatically, reducing the supply of light to the remaining seagrass beds through the previously “gin-clear”

bay waters. Mass mortality of sponges, which help to

filter the bay’s waters and provide habitat for juvenile

lobster, followed in the path of the plankton blooms.

By the end of 1991, there was widespread concern

among the public for the health of the Florida Bay

ecosystem, yet very little scientific information existed

that resource managers could use in response to this

concern.

The Florida Bay Science Program emerged in 1994

as a coordinated effort by state and federal agencies to

identify the mechanisms and underlying causes responsible for the recent ecological changes. Its objectives were to implement an interagency program of

research aimed at developing the knowledge needed

to guide ecosystem restoration and to communicate this

scientific knowledge to restoration managers, scientists,

policy makers, and the informed public. Currently 11

state and federal agencies participate in the program

through representatives on the Program Management

Committee. This committee formulated a Strategic

Plan, which was revised in 1997, to coordinate the research supported independently by the separate agencies.The committee also provides for occasional review

of the program by the independent Science Oversight

Panel and for dissemination of its findings through a

series of science conferences.This report is part of the

Strategic Plan’s effort.

The CERP was established in 2000 with the overarching goal of restoring and preserving the ecosystems

of south Florida, including Florida Bay.This plan relies

on scientific information to document the condition of

south Florida’s ecosystems and evaluate the effects of

human activities on them. Human activities influence

the structure and function of ecosystems both directly,

by altering the ecosystems themselves, and indirectly,

by altering the climatic, hydrologic, and geologic

processes that drive the ecosystems and maintain their

structure.This has probably occurred throughout history. However, the extent and intensity of human activities and their influence on ecosystems has increased

greatly with the expansion of agriculture and urban development in the past 100 years. In order to guide

restoration efforts, resource managers now require

scientific information on the bay’s ecosystem, how it has

changed during the past 100 years, how it works, and

how it likely will respond to planned restoration activities. Since its inception, the Florida Bay Science

Program has pursued the goal of developing this information and providing it to resource managers.

FWRI Technical Report TR-11 1

Chapter 1

Florida Bay Science
2 FWRI Technical Report TR-11

Purpose of This Report

This report documents the progress made toward the

objectives established in the Strategic Plan revised in

1997 for the agencies cooperating in the program.

These objectives are expressed as five questions (see

box below) that organized the research on the Florida

Bay ecosystem. Each question examines different characteristics of the Florida Bay ecosystem and the relation of these to the geomorphological setting of the bay

and to processes linking the bay with adjacent systems

and driving change.This report also examines the additional question of what changes have occurred in

Florida Bay over the past 150 years.

Preparation of this report coincided with the reevaluation of the strategy for organizing ecosystem research in Florida Bay around these five central

questions. This strategy originated in response to the

need by resource managers for basic information about

startling changes in the ecosystem that occurred in

the late 1980s and early 1990s. Since 1994, the program, focused by the central questions, has sought to

identify the underlying mechanisms and causes of

these decade-old events. Resource managers now ask

a different set of questions.The inception of the Comprehensive Everglades Restoration Plan (CERP) in

2000 signals a shift in resource management away

from the reactive stance of protecting natural resources

toward the proactive pursuit of restoring south Florida’s

ecosystems. In general, ecosystem restoration challenges us to look ahead.

Can we predict future conditions in the Florida Bay

ecosystem that will follow from resource-management

decisions made today? The 1997 Strategic Plan describes a set of interrelated predictive models for this

purpose, i.e., for circulation, water quality, and ecological models.This activity has been pursued at several levels. The most visible has been the ongoing

effort to identify and implement an appropriate set of

numerical simulation models to describe circulation

and water quality within the bay and the interaction

of the bay with the Everglades, the Florida Shelf, the

reef tract, and waters of the Florida Keys. Research

has spawned the development of other types of predictive models, i.e., historical analogs, correlative models, and mechanistically based empirical models. Some

of these models can be used to peer into the future, albeit through somewhat narrow windows focused on

specific elements of the bay.

The concluding chapter examines progress toward

answering the original central questions and explores

some of the new challenges for research on Florida Bay.

By maintaining focus on the central questions to serve

the programmatic purposes described above, this report addresses most directly past concerns of resource

managers. However, scientific information developed

by the Florida Bay Science Program is also relevant to

the present management goal of restoring the ecosysChapter 2

Executive Summary

Ecosystem History What was the Florida Bay ecosystem like 50, 100, and 150 years ago?

Question 1—Physical Processes How and at what rates do storms, changing freshwater flows, sea level

rise, and local evaporation and precipitation influence circulation and salinity patterns within Florida Bay and

exchange between the bay and adjacent waters?

Question 2—Nutrient Dynamics What is the relative importance of the influx of external nutrients and

of internal nutrient cycling in determining the nutrient budget for Florida Bay? What mechanisms control the

sources and sinks of the bay’s nutrients?

Question 3—Plankton Blooms What regulates the onset, persistence, and fate of planktonic algal blooms

in Florida Bay?

Question 4—Seagrass Ecology What are the causes and mechanisms for the observed changes in the seagrass community of Florida Bay? What is the effect of changing salinity, light, and nutrient regimes on these

communities?

Question 5—Higher Trophic Levels What is the relationship between environmental and habitat change

and the recruitment, growth, and survivorship of animals in Florida Bay?
tems of south Florida. For both the program and for efforts to restore Florida Bay, knowledge of the past offers the best perspective for looking ahead.

Ecosystem History

The alarming ecological changes witnessed in Florida

Bay during the late 1980s and early 1990s precipitated

a shift in natural-resource management in south

Florida that culminated in the CERP. For many in the

public-at-large, and among scientists as well, the

restoration of Florida Bay will mean a return to conditions remembered from immediately prior to these

changes—clear water, lush beds of seagrass, and good

fishing. Resource managers must be concerned with

whether these conditions can be sustained by the

ecosystem given the variety of processes driving change

in the ecosystem. Perhaps if viewed over a time span

longer than only the past twenty years, the natural

state of Florida Bay will be revealed as something

quite different from what is remembered.

An objective of the program shared across the five

central questions has been to construct a history of past

conditions in the bay based principally on objective,

quantitative data. Quantitative observations on the

state of the Florida Bay ecosystem date back to the

1950s, when systematic surveys were conducted by

Finucane, Dragovich, and Tabb. Although invaluable,

these observations provide an incomplete and biased

representation of the bay’s natural state. Major changes

had already occurred in the hydrology of the Everglades by the time these studies took place. Fortunately, through analysis of coral and sediment cores we

can read the history of the Florida Bay ecosystem

recorded in the skeletons of organisms that resided

here during the past 150 years.This work leads to the

following conclusions:

• Salinity in Florida Bay is more strongly correlated to

rainfall than any other single factor. A periodicity in

salinity and rainfall data suggests linkages to the El

Niño/Southern Oscillation climatic patterns. Although anthropogenic influences play a secondary

role to rainfall in determining salinity for Florida Bay

as a whole, they may be a factor in the magnitude of

salinity variations seen in recent times. Additionally,

anthropogenic factors may act on a local basis to

influence salinity patterns.

• Seagrass has been more abundant in the past 50

years than in the first half of the 20th century. Prior

to the mid-20th century, epiphytal ostracodes were

relatively rare at sites in central and northeastern

Florida Bay, suggesting a greater abundance and/or

density of seagrass over the past 50 years than in the

first half of the century. Epiphytal mollusks, although

not rare, increased significantly at most sites from approximately 1940 on.These data suggest that dense

and abundant seagrass beds may not have been the

long-term normal state of the ecosystem, and they

carry implications for restoration.

• Downcore profiles of dated cores from central Florida

Bay show that productivity events (i.e., blooms) have

occurred historically in Florida Bay. A large multidecadal productivity event characterized by greatly

elevated levels of organic carbon and nitrogen, dated

to about the mid 1700s, was observed in two cores

from Whipray Basin. Interestingly, total phosphorus

was not elevated during this time span.This time period (the Little Ice Age) may correspond to a period

of higher rainfall in the Everglades and more extensive land runoff into Florida Bay, which may have

triggered the productivity event.

• Sediments from northeastern Florida Bay (especially from sites near Pass Key and Russell Key banks)

show indications of recent nutrient (carbon, nitrogen,

and phosphorous) enrichment (1980 to present).

This nutrient enrichment could be related to recent

microalgal blooms and seagrass die-off within

Florida Bay.

• Northeastern Florida Bay appears to be a source of

nutrients to the mangrove zone at the southern end

of Taylor Slough. Uranium-isotope studies indicate

that the phosphorus contamination at the northern

end of Taylor Slough appears to be fertilizer-derived. However, phosphorus contamination in Taylor Slough diminishes to background by midslough;

therefore, Taylor Slough does not appear to be a

source of nutrients to northeastern Florida Bay.

• Macroalgae have increased. Relative abundance of

mollusks with a strong preference for Thalassia has

declined since approximately 1970 in northeastern

Florida Bay and since 1910 in Whipray, whereas

more generally epiphytic organisms have generally

increased. This may indicate an increase in the

amount of macrobenthic algae relative to Thalassia.

• At Bob Allen, seagrass abundance appears to have

been increasing since a recent minimum around

1960. Downcore profiles of lignin phenols from Pass

Key core show large variations in lignin-phenol distributions over short time intervals, reflecting the

proximity of this site to the mangrove zone along the

coast and the outlet of Taylor Creek.

• Changes also occurred in circulation and exchange

with adjacent waters during the early part of the

20th century. Geochemical changes recorded in coral

bands suggest that construction of the overseas railroad altered exchange by blocking passes between

the Keys. Other changes appear to be the result of

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 3

Executive Summary
Florida Bay Synthesis Hunt and Nuttle

4 FWRI Technical Report TR-11

decreased freshwater inflow from the Everglades

that resulted from “reclamation” activities on the

mainland.

Physical Processes

Research on physical processes aims to identify the

main external factors that control the movement of

water and solutes within Florida Bay and their exchange with the Everglades and adjacent marine systems.The difficulty is estimating the relative influence

of the various physical driving processes, even though

the identities of the physical processes themselves are

known from the study of other estuaries. The two

physical characteristics of Florida Bay that distinguish it from most other estuaries in the U.S. are the

restricted exchange across the shallow but otherwise

open boundary with the Florida Shelf and the relatively small amount of terrestrial freshwater discharge

to the bay.

• Historical data from the salinity-synthesis database

(Robblee et al., 2001) show that Florida Bay has behaved as a marine lagoon for the past several

decades. Salinity has reached as high as 70 in the central bay on a few occasions and typically exceeded

40 during drought years like 1989–1990. For example,

following the wet period of 1994–1995, salinity increased, tropical storms in 1999 induced a decrease,

and data from the drought years of 2000 and 2001 indicated another increase. More recent data from

2002 and early 2003 indicate another general freshening trend.

• The south Florida coastal region is surrounded by an

intense, large-scale, oceanic boundary current (the

Loop Current–Florida Current system) and its evolving eddies that link local coastal waters to remote

river discharges upstream in the Gulf of Mexico.

• Seasonal cycles in local wind-forcing produce seasonal patterns in circulation pathways, connecting

south Florida coastal waters through western Florida

Bay and transporting Everglades freshwater

discharges. Southward flows through the Keys passages predominate in winter and spring, north-northwest flows in summer, and southwest flow toward the

Tortugas in the fall. Large-volume, wind-forced flows

through the Keys passages provide linkage for gulfto-Atlantic exchange through the southwestern shelf

region adjacent to western Florida Bay.

• Seasonal cycles in south Florida coastal current systems provide seasonal pathways for local larval recruitment. They also furnish opportunities for

recruitment from remote sources.

• Shallow bank configurations that restrict water exchange tend to separate the bay’s interior into three

distinct regions with different salinity regimes.The

northeastern region is the most isolated from oceanic

influences, receives most of the surface runoff, and

has the largest seasonal cycle of salinity.The central

region receives little runoff and has the maximum

salinity. The basins in the western region have the

greatest oceanic exchange and the smallest seasonal

change in salinity.

• Variability of Florida Bay average salinity is directly

related to the net flux of fresh water from the combined influence of evaporation, precipitation, and

runoff. For the bay as a whole, on seasonal or annual

time scales, evaporation is approximately equal to

precipitation, and runoff is roughly 10% of either. Historical salinity data and salinity proxy data show

that Florida Bay salinity has commonly undergone

large changes on time scales of seasonal, interannual

(ENSO), decadal (NAO), and even longer periods that

are not understood.

• Stable-isotopic markers indicate that runoff from

the Everglades is the dominant source of fresh water

to the northeastern region of Florida Bay, whereas

for the western region, precipitation shows a strong

signal. In the central region, a mixture of runoff and

precipitation provides the fresh water.

• Since 1985, freshwater discharge from Taylor Slough

and the C-111 canal have increased as a consequence

of changes in water management.Trout Creek conveys the largest volume of fresh water to northeastern Florida Bay, varying from –6 to 32 m3

/s. By

contrast, the flow from each of another eight creeks

where discharge is metered ranges from –1.4 to 6

m3/s. Negative flows can occur during the dry season and during storm events.

• Low-salinity Shark River plume waters are advected

southward around Cape Sable to western Florida Bay

and the Keys reef tract by seasonal, wind-driven

coastal flows. For the Ten Thousand Island region of

the western Everglades, the mean annual river discharge is estimated to be 13.3 m3

/s for Harney River,

11 m3/s for Broad River, and 12.4 m3/s for Shark

River.

• Groundwater inflows are believed to be most influential along the northern boundary of the bay. However, estimates for the rate of groundwater discharge

are highly uncertain, ranging over four orders of

magnitude.

Nutrient Dynamics

In contrast to water movement and salinity, which reflect the influence of outside processes, both external

Executive Summary
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 5

and internal processes combine to determine characteristics of water quality. Research on this question

has concentrated on quantifying external sources and

sinks of nitrogen and phosphorus. More recently, the

focus has been on internal exchanges between the

sediment and the water column. The major external

sources of nutrients have proven difficult to quantify.

As a result it has been challenging to resolve the question of whether the seagrass die-off and subsequent

plankton blooms were triggered by the onset of eutrophication of Florida Bay.

• Over a thirteen-year period of record, temporal

trends have shown bay-wide declines in total phosphorus (P), total nitrogen (N), and chlorophyll a

(CHLA), with an overall increase in turbidity.

• Objective analysis shows that there are three zones

in Florida Bay that exhibit significant differences in

water-quality characteristics due to nutrient inputs,

tidal advection, and water residence time. These

zones correspond generally to the northeast, central,

and west regions, which are defined by variation in

other ecosystem characteristics. In general, dissolved

phosphorus concentrations increase and nitrogen

concentrations decrease from east to west, resulting

in a shift from phosphorous limitation to nitrogen

limitation. Central bay waters have high ammonium

concentrations, which may indicate a bottleneck in

the process of nitrification.

• Atmospheric input of nutrients is large relative to

other sources.

• There is a measurable effect of water management

on nutrient loading in the Taylor Slough system.Terrestrial nutrient loading fluctuates in phase with

freshwater flow; however, flow-weighted concentrations decrease with increasing flow. A serious

disconnect exists between upland/canal loading estimates and actual input to the bay because of unmeasured nutrient processing in the intervening

wetland/mangrove areas.

• High rates of organic carbon and nitrogen fluxes

occur, both into and out of sediments, over diel cycles.

Benthic denitrification is higher than predicted from

nitrogen-loading rates.There are times when benthic

N2 fixation in Florida Bay balances denitrification but

the system overall shows a net loss of nitrogen.

• Sediment flux of ammonium decreases with an increase in sediment chlorophyll a concentration,

which indicates that the microphytobenthos is important in regulating water column nitrogen concentrations.

• There is very little, if any, inorganic phosphorous flux

out of the sediments with the exception of the western bay/shelf area.

Plankton Blooms

For Florida Bay as a whole, plankton blooms can be

viewed as a distinct mode of variation in the ecosystem that arises from a consequence of external drivers

and internal processes. On a mechanistic level, plankton blooms form whenever plankton growth exceeds

the combined effect of grazing and dispersion (the

processes that reduce plankton concentrations). Studies of other estuaries link plankton blooms to increased

nutrient loads in runoff. Research on plankton blooms

in Florida Bay has been directed at describing the

combination of internal and external conditions associated with the onset, persistence and fate of blooms

in this ecosystem. Research to date indicates that there

are three ecologically distinct regions within the bay

from the standpoint of algal blooms: the Northeast

Region, the Central Region, and the West Region.The

nature and causes of blooms can be most appropriately

summarized within the context of these three regions.

Northeast Region

• Algal blooms are largely absent from the Northeast

Region of Florida Bay. The phytoplankton community of the Northeast Region is a diverse mixture of

cyanobacteria, dinoflagellates, diatoms, and microflagellates, none of which form blooms.

• The lack of algal blooms in the Northeast Region of

Florida Bay is largely attributable to the severe phosphorus limitation characteristic of the region. Despite

significant water inflows to the region from the Everglades, the very low phosphorus levels in these inputs combined with the calcium carbonate-rich

waters of the region result in nutrient-limited conditions.

Central Region

• Large algal blooms have been a common feature of

the central region since at least 1992.The focal point

for blooms is in the north-central part of the region,

extending from Rankin Basin and into Whipray

Basin.The greatest bloom activity is generally in the

summer and early fall, although blooms have been

observed in other seasons. In the fall and early summer, blooms originating in the north-central part of

the Central Region are pushed southward by the

prevailing, wind-driven circulation into the southern part of the Central region, where they can spread

out into the Atlantic reef tract through cuts in the

Florida Keys. The dominant bloom-forming alga in

the central region is the picoplanktonic cyanobacExecutive Summary
Florida Bay Synthesis Hunt and Nuttle

6 FWRI Technical Report TR-11

terium Synechococcus elongatus, although several

species of diatom and dinoflagellate do occasionally

occur in bloom proportions.

• Nutrient limitation of phytoplankton growth in the

central region appears to switch back and forth from

phosphorus to nitrogen.The nature of the sources of

nutrients for blooms in the central region has been

a subject of considerable debate, yielding several

hypotheses: 

° A significant supply of nutrients for algal production is available from the flocculent muddy

sediments within the region;

° A groundwater source of phosphorus is present

within the region that, in combination with nitrogen from the northeast region, feeds algal blooms;

° Nutrients from the shelf region west of the bay are

available to blooms in the central region via tidal

exchange;

° Atmospheric deposition is a significant source of

nutrients (particularly N) for algal primary production.

These hypotheses are not mutually exclusive, and

several mechanisms may be operational at the same

time.

• The domination of blooms in the Central Region by

Synechococcus elongatus is attributable to the unique

ecophysiological characteristics of this species of

cyanobacterium.These characteristics include 

° wide tolerance to salinity,

° superior ability to compete for phosphorus at low

concentrations,

° ability to regulate buoyancy and thereby take advantage of nutrients available in the sediments, and

° lower susceptibility to grazing losses.

West Region

• Algal blooms are also a common feature of the West

Region of Florida Bay.The West Region, in contrast

to the cyanobacterial blooms in the Central Region,

is dominated by diatoms.The blooms in the West Region are mainly Rhizosolenia spp., Chaetoceros spp.,

and pinnate diatoms, which dominate in terms of cellular biomass. Diatom blooms in the west region

begin in late summer and are advected into the bay

from shallow coastal waters off Cape Sable.

• The diatom-dominated blooms in western Florida

Bay are mainly limited in their growth by nitrogen,

either singly or in combination with phosphorus

and/or silicon supply. Temperature, salinity, and

light do not appear to be important factors in the initiation or maintenance of diatom blooms. Maximum

growth rates of the diatom community during bloom

initiation in the West Region range from 1 to 2 day–1

(first-order rate constant), based on increases in netplankton (>5 μm size fraction), chlorophyll a, or biogenic silica. The onset of diatom blooms on the

western Florida Shelf appears to be associated with

enhanced riverine outflow, predominantly from the

Shark River.The onset of increased diatom biomass

occurs within the riverine, low-salinity plume near

Cape Sable.

Seagrass Ecology

Seagrasses account for a major portion of the primary

production in the Florida Bay ecosystem.Therefore, it

is particularly important to understand the mechanism

for the die-off observed in the late 1980s and the relation of this event to the algal blooms that occurred

subsequently. The loss of seagrass observed in other

estuaries has been explained as a consequence of eutrophication increasing algal growth and reducing

the amount of light available to the seagrasses.The seagrass die-off in Florida Bay did not follow this pattern,

and its cause may be unique to Florida Bay. Research

on this topic has focused on the influence of both internal conditions and external driving factors on plant

growth and metabolism and on documenting the sequence and patterns of seagrass die-off and recovery

in Florida Bay.

• Geographic variation in patterns of seagrass loss

suggests multiple causes and a distinction between

primary die-off and secondary mortality.There is a

high spatial coincidence among the distribution of

Thalassia loss, Labyrinthula abundance, high sediment sulfide levels, and turbidity. Determining the

relative contributions of these factors to die-off versus secondary mortality has been problematic.

• Primary die-off is associated with high-density Thalassia beds. High-density beds result in conditions

that increase stress on Thalassia: high sediment sulfide levels (>2–4 mmol), self-shading of shoots, nighttime or early morning anoxia/hypoxia in meristems,

and increased susceptibility for leaf-to-leaf transmission of the Labyrinthula disease organism. Recent

die-off in the Barnes Key area occurred where Thalassia densities and standing crop were among the

highest in Florida Bay.

• Recent bay-scale changes in seagrass distribution and

abundance, following the region-scale primary seagrass die-off (1987–1991), are largely due to secondary mortality of Thalassia, which is associated

with areas of chronic turbidity (since 1994) in the West

Region. These changes are most likely due to light

limitation as indicated by stand-thinning in Thalassia beds and concommitant increases in low-lightExecutive Summary
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 7

adapted species such as Halodule wrightii and

Halophila engelmanii. There has also been a loss of

Thalassia in northern Little Madeira Bay, near the

mouth of the Taylor River, followed by recolonization

by Halodule and Ruppia.The cause of this loss is unknown. Primary acute die-off (rapidly developing

dead patches within dense beds) is known to be

currently occurring (initiated in 1999) only in the

high-density Thalassia beds of the Barnes Key area.

A chronic die-off is occurring in dense beds in Sunset Cove. However, the etiologies of these two sites

are different.

• In central basins that periodically have low salinities,

shallow sediments and low overall densities of Thalassia, there has been little net change in seagrass distribution since 1995. These conditions may reduce

density-related stresses and allow for development

of robust species communities. Low salinity may

also provide refugia from disease since Labyrinthula

has never been observed in Florida Bay in salinities

below 15 practical salinity units (psu).

• Unique characteristics of the Florida Bay ecosystem

make it susceptible to conditions that contribute to

primary die-off. Other marine areas with high Thalassia densities and carbonate sediments, such as

the Lakes Region of the Lower Keys, did not experience extensive die-off in the late 1980s. Relative to

these other areas, the central basins in Florida Bay

are isolated from tidal influences and are subject to

relatively high terrestrial influence.

• A statistical, disciminant-function model of seagrass

species occurrence has been developed.The model

predicts that an increase in freshwater delivery to

Florida Bay will result in an expansion of Ruppia

maritima and Halodule wrightii distribution into the

Northeast Region and a concomitant loss of Thalassia in this region.

Higher-Trophic-Level Species

The value placed on Florida Bay derives largely from

its role supporting ecologically and commercially important animal species. These species and the communities they create depend on and integrate the net

ecosystem metabolism at lower trophic levels. As well,

the structure of the ecosystem at higher trophic levels

can feed back to influence the structure and function

at lower levels, i.e., top-down control. Research in this

area focuses on the influence of internal conditions of

water quality and benthic habitat on both the growth

and survival of individual organisms and on whole

populations and communities. A key objective in this

work has been to formulate models that can predict how

valued species can be expected to respond to changes

in the supply of fresh water and water quality.

• Salinity patterns and variability directly affect recruitment, survival, and growth of many animals

that live in Florida Bay and that use Florida Bay as

a nursery ground.We have sufficient information on

about a dozen key species to predict how they will

respond to future salinity conditions that might arise

from altered freshwater inflow into Florida Bay.

• Habitat, tidal amplitude, freshwater inflow to Florida

Bay, and salinity were the most widely influential

variables explaining density in 11 forage species in

a meta-analysis of data from historical surveys. Seagrass density and tidal amplitude were significant for

10 species, seagrass type and freshwater inflow were

significant for nine species, and salinity was significant for seven species.

• Analysis of historical data indicates that water management affects the productive capacity of Florida

Bay. This information has been used to predict the

annual catch of pink shrimp in the Dry Tortugas

fishery based on upstream hydrologic conditions in

the Everglades.

• Recent findings discount earlier concerns that seagrass die-off and subsequent plankton blooms signaled a fundamental change in the food web. The

abundance of bay anchovy in the West Region, one

signal of a possible shift, has fluctuated since it

reached a maximum in 1995.The diversity and overall abundance of canopy-dwelling fauna has increased since 1995 without a return to the original

Thalassia-dominated seagrass canopy.

• Seagrass diversity may determine faunal density. A

principal components analysis suggested that faunal species have affinities to certain seagrass types—

Thalassia, Halodule, Syringodium, or macroalgae.

Seagrass type was significant in explaining a metaanalysis of faunal density in Florida Bay. Faunal density in relation to seagrass type varied differently

depending on faunal species. No species favored

pure Thalassia.

• Characteristics of the bottom and shoreline habitats

affect abundance and community composition. Mangrove prop root habitats in northeastern Florida Bay

have significantly more fish larvae than nearby,

open-water sites or nearshore areas without mangroves.

• Fishing affects fish populations. According to a comparison of the length-frequency distribution inside

and outside of an area in Everglades National Park

protected from recreational fishing affects the size

structure of gray snapper. Evidence of overfishing is

seen in gray snapper and other species on the reef

tract.

Executive Summary
• Spatial variation in influencing factors (e.g., freshwater inflow, tidal mixing) is reflected in distinct regional patterns of species distributions, community

composition, and trophic composition. Postlarval

shrimp enter the bay preferentially where tidal flows

are greatest. Peak concentrations of postlarval pink

shrimp are roughly an order of magnitude greater

in passes leading into the West Region from the

Gulf of Mexico than in channels to Florida Bay

through the Florida Keys.

• The food web shows the same regional structure as

seen in the variation of circulation, salinity, and

water quality. Based on stable isotope analyses, the

central region has a strongly seagrass-based trophic

structure, whereas the northwestern bay has a more

plankton-dominated trophic structure. The Northeast Region has a non-seagrass-based diet (more

likely water-column based). The trophic structure

of the southwestern bay is supported by macroalgae.

• Temporal variation in recruitment strength of spiny

lobster, snapper, and pink shrimp is related to regional oceanographic processes, especially the Tortugas gyres.

• High methylmercury in Florida Bay and its biota

may have a local source in the bay. Sources of elevated mercury concentrations in fish from northeastern Florida Bay include (1) methylmercury in

runoff from the Everglades and (2) in situ mercury

methylation in sediments from both the mangrove

transition zone and the open bay itself. Mercury

concentrations seem to be higher along a Taylor

River–Little Madeira Bay sampling transect than

along a C-111 canal–Joe Bay transect. These data

suggest that the urban and agricultural runoff that

more strongly influences the C-111 canal–Joe Bay

transect is not the most important source of mercury

to the bay and its biota.

Loss of sponges may have reduced water clarity

and affected seagrass recovery. Recovery of the largest

and most abundant species has been extremely slow

following a die-off in the early 1990s. Sponges are efficient filters of small (<5 μm) planktonic particles. At

pre-die-off (pre-1992) densities, sponges in Florida

Bay may have been capable of filtering the entire water

column in one day. At present densities, filtering takes

an estimated four days.

Florida Bay Synthesis Hunt and Nuttle

8 FWRI Technical Report TR-11

Executive Summary
FWRI Technical Report TR-11 9

Introduction 

Question—What was the Florida Bay ecosystem like 50,

100, and 150 years ago?

A critical part of understanding an ecosystem as a

whole is to understand the natural patterns and cycles

of change. However, changes in ecosystems take place

at many time scales, from diurnal to millennial, and it

is not practical or even possible to directly observe

change at the longer time scales. The ability to accurately understand natural conditions and cycles of

change within Florida Bay is crucial to successfully restore and preserve the bay and to meet the goals of the

Comprehensive Everglades Restoration Plan (CERP).

Information on the historical and current natural system allows restoration planners to establish realistic

baseline conditions, restoration goals, and performance measures; create predictive models; and monitor the success of restoration efforts. Understanding

past conditions and cycles of change also allows for better-informed planning, project implementation, and

land-management decisions.

Although the ecosystem history and paleoecology of Florida Bay was not specifically identified by the

Florida Bay Science Program as a strategic research

question, these types of studies contribute to all five

strategic questions. By their very nature, these studies

are multidisciplinary and integrate data to provide a

holistic picture of the environment over biologically significant time scales.This chapter summarizes ecosystem history research that has contributed to the Florida

Bay Science Program.

Methodology

The history of an ecosystem may be recorded in two

distinct modes: (1) human records, in the form of historical accounts, reports, or archived data; and (2) natural records preserved in the sediments. Both methods

can provide valuable information, but the sediment

record and associated paleoecologic data can be especially important because few monitoring programs

have been in place long enough to provide sufficient

data to establish the range of variability in ecosystem

parameters over a significant period of time. Furthermore, monitoring or experimental data are absent

prior to human influence on the environment. Ideally,

both human records and natural records are retrieved,

compiled, and compared to develop the most complete picture possible of the configuration of an ecosystem over time and of the spatial and temporal scale of

changes to the system.

HUMAN RECORDS

Significant efforts have been made by a number of individuals and groups to compile data sets and historical records for the south Florida ecosystem and Florida

Bay. It is not the purpose of this summary to list all of

these compilations, but the following illustrate the

variety of records available:

Robblee, M. B., et al. (2000, 2001)—A compilation of

more than 34,000 historical salinity measurements

from Florida Bay, beginning in 1947 and extending

through 1995.

DeMaria, K. (1996)—Changes in the Florida Keys

Marine Ecosystem Based upon Interviews with Experienced Residents—A compilation of “eyewitness”accounts of 75 individuals with more than 10 years’

experience on Florida Keys and Florida Bay waters.

Smith,T. J. (2002a and unpublished data)—Historical

reconstruction of vegetation from aerial photographs

of selected islands within Florida Bay, dating from

1927. Areas of interest include the entirety of Everglades NP, Big Cypress NP, and the Water Conservation Areas.

Smith,T. J., et al. (2002b)—Digitally compiled set of

scanned historical topographic sheets from the Everglades and south Florida available on CD–ROM.

SEDIMENT RECORDS

Retrieving historical information recorded in sediments involves basic principals of geology (principally

the laws of superposition and “the present is the key

to the past”) and using a number of paleoecological and

geochemical tools: 

Chapter 3

Ecosystem History

Lead Author G. Lynn Wingard (USGS, Reston)

Contributors Tom Cronin (USGS) and William Orem (USGS)
Florida Bay Synthesis Hunt and Nuttle

10 FWRI Technical Report TR-11

Assemblage analyses—the faunal and floral remains

found in a sediment core allow inferences to be made

about past environments, including salinity, substrate,

and water quality, based on analoguous data from

the present.

Biochemical analyses—organisms with calcareous

skeletons record information about the water in which

they secrete their skeletons. Stable isotope analyses and

metal:calcium ratios in shells or coral skeletons can provide information on salinities and sources of water.

Geochemical analyses—radiogenic isotopes are used

to determine the chronology of cores,and analyses of the

geochemistry of the sediments (carbon, nitrogen, sulfur,

and phosphorus, for example) provide data on changes

in nutrient supply and sediment influx over time.

Each of these methods is limited by the resolution

of the age model for sediment deposition. Typical

geochronologic methods used on late Holocene sediments involve analyses of 210Pb (lead), 137Cs (cesium), 7

Be (beryllium), and 14C (carbon) (see Holmes et al., 2001,

for explanation).The error term increases down-core,

so that a typical core from eastern Florida Bay with a

sedimentation rate of 1.0 cm/year and an error of ±0.08

cm/year will have an average age of 1900 years (±8

years) at a depth of one meter. Because of the error associated with increasingly older sediments, the annual banding of corals provides the most accurate age

control, but only a few large corals have been found

within Florida Bay that can be used to reconstruct past

conditions.

Analyses of sediment cores from Florida Bay have

been conducted principally by two different groups of

researchers during the past ten years (Table 3.1): (1) the

University of Miami/NOAA group ( C. A. Alvarez

Zarikian, P. L. Blackwelder,T. Hood,T. A. Nelson, P. K.

Swart, L. P. Tedesco, H. R. Wanless, et al.) and (2) the

USGS group (T. M. Cronin, G. S. Dwyer, R. B. Halley,

C. W. Holmes, J. K. Huvane, S. E. Ishman, W. Orem, E.

Shinn, D. A.Willard, G. L.Wingard, et al.). Both groups

have sought out areas of sediment accretion with minimal sediment disturbance; however, they diverge in

terms of benthic habitats (Holmes et al., 2001; Nelsen

et al., 2002).The University of Miami/NOAA group has

sought out cores from bare-bottom habitats in order

to ensure the presence of well-laminated sediments

undisturbed by roots. The USGS group has collected

cores from banks stabilized by seagrass beds because

these areas are subjected to minimal erosion during

storms, so that the organisms being analyzed are

trapped in situ. Both groups X-ray and physically examine the cores for signs of sediment disruption and

use the radiogenic isotope profiles as assurance of

minimal disturbance. These two divergent strategies

have been beneficial by providing data from different

regions and different environmental settings within

Florida Bay. A comparison of the findings and results

will be discussed below.

Previous Work 

Prior to 1990, few paleoecological analyses of sediment cores had been conducted in Florida Bay. The

Holocene core studies that had been done focused on

the sediments themselves and the diagenesis of the

sediments (Fleece, 1962), the mineralogy of the sediments (Taft and Harbaugh, 1964), and the origins of the

material composing the sediments (Enos, 1977). In

their study of the molluscan fauna of Florida Bay,Turney and Perkins (1972) examined cores to determine the

persistence of subenvironments over time.They discuss

the growth and migration of mudbanks based on their

analyses. Wanless and Tagett (1989) performed an extensive study of cores to determine the depositional history of the mudbanks within Florida Bay. All of these

studies provide important information on the sedimentation and geologic history of Florida Bay and

allow the history of the late Holocene ecosystem to be

more accurately interpreted.

Two studies were done in the 1980s on a coral from

Lignumvitae Basin. Hudson et al. (1989) compared the

growth of a 1-m-diameter Solenastrea to rainfall, temperature records, and human perturbations.They found

a significant correlation between poor coral growth and

construction of the Flagler Railroad. Smith et al. (1989)

investigated the relationship between the fluorescent

banding (a result of terrestrial runoff) of the same

Lignumvitae Basin coral and the flow of water in Shark

River and Taylor sloughs. A decline in freshwater flow

(as indicated by the fluorescence) began around 1912,

a date that corresponds to the construction of drainage

canals carrying water from Lake Okeechobee to the Atlantic. Smith et al. (1989) found a statistically significant

difference between mean fluorescence in the pre-canal

segment (pre-1932) of the coral and in the post-canal segment (post-1932) of the coral. In addition, Smith et al.

(1989) found evidence for a 4- to 6-year periodicity in the

historical annual flow regimes that was no longer apparent in the Shark River Slough flow record.This periodicity corresponds to south Florida rainfall records.

They concluded that prior to canal construction, the

flow of fresh water in Shark River Slough was controlled by rainfall, but that as early as 1940, flow through

the slough was reduced substantially and that the natural periodicity in flow regimes had been lost.

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 11

Table 3.1A List of sediment cores analyzed in Florida Bay between 1990 and present. Abbreviations in square brackets

following core location correspond to abbreviations on Figure 3.1 and were used by the original authors.

General Core Location Researchers Analyses Done Status/References

(Core ID)

1 Joe Bay [JB] Holmes 210Pb Geochronology Holmes et al., 1999;

Willard Pollen Assemblages Willard et al., 1997

Wingard Molluscan Assemblages

Ishman Foraminferal Assemblages

2 Taylor Creek [TC] Ishman Foraminferal Assemblages Brewster-Wingard

(T24) Wingard Molluscan Assemblages et al., 2001; Cronin 

(TC-1,TC-1a, Cronin Ostracode Assemblages et al., 2001; Dwyer

TC-2,TC2br) Holmes 210Pb Geochronology and Cronin, 2001;

Dwyer Ostracode Biochemistry Holmes et al., 2001;

Willard Pollen Assemblages Ishman et al., 1996

Edwards Dinoflagellate Assemblages

Orem Sediment Geochemistry

3 Pass Key [PAK] Wingard Molluscan Assemblages Brewster-Wingard

(PK17D, PK37) Cronin Ostracode Assemblages et al., 1998a; Brewster-

(FB-1 Pass Key) Ishman Foraminferal Assemblages Wingard et al., 2001;

Halley Molluscan Biochemistry Cronin et al., 2001;

Holmes 210Pb Geochronology Halley and Roulier,

Huvane Diatom Assemblages 1999; Huvane and

Willard Pollen Assemblages Cooper, 2001; Orem

Edwards Dinoflagellate Assemblages et al., 1999a

Orem Sediment Geochemistry

4 Russel Bank [RB] Wingard Molluscan Assemblages Brewster-Wingard and

(RB19A, RB19B) Cronin Ostracode Assemblages Ishman, 1999; Brewster-

(RB19C) (FB-2) Ishman Foraminferal Assemblages Wingard et al., 2001; 

Holmes 210Pb Geochronology Cronin et al., 2001; 

Dwyer Ostracode Biochemistry Cronin et al., 2002; 

Willard Pollen Assemblages Dwyer and Cronin,

Halley Molluscan Biochemistry 2001; Halley and 

Edwards Dinoflagellate Assemblages Roulier, 1999; Holmes

Orem Sediment Geochemistry et al., 2001; Huvane and

Cooper, 2001; BrewsterWingard et al., 1997;

Orem et al., 1999a

5 Park Key [PKK] Cronin, Dwyer Ostracode Biochemistry Cronin et al., 2001 

(PKK23A) Holmes 210Pb Geochronolgy Dwyer and Cronin, 2001; 

Holmes et al., 2001

6 Bob Allen [BA] Wingard Molluscan Assemblages Brewster-Wingard and

(BA6A) (FB-3) Cronin Ostracode Assemblages Ishman, 1999; BrewsterIshman Foraminferal Assemblages Wingard et al., 2001; 

Holmes 210Pb Geochronology Cronin et al., 2001;

Halley Molluscan Biochemistry Dwyer and Cronin, 2001;

Willard Pollen Assemblages Halley and Roulier,

Edwards Dinoflagellate Assemblages 1999; Wingard et al.,

Orem Sediment Geochemistry 1995; Orem et al., 1999a

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

12 FWRI Technical Report TR-11

Table 3.1A List of sediment cores analyzed in Florida Bay between 1990 and present. Abbreviations in square brackets

following core location correspond to abbreviations on Figure 3.1 and were used by the original authors. (continued)

General Core Location Researchers Analyses Done Status/References

(Core ID)

7 Whipray [WH] Wingard Molluscan Assemblages Trappe and Wingard,

(25B) (FB-4, FB-5) Cronin, Dwyer Ostracode Geochemistry 2001; Cronin et al., 2001;

Holmes 210Pb Geochronology Holmes et al., 2001; 

Orem Sediment Geochemistry Orem et al., 1999a

8 Rankin [RA] Wingard Molluscan Assemblages Unpublished data; report

Cronin, Dwyer Ostracode Geochemistry in progress

Holmes 210Pb Geochronology

Orem Sediment Geochemistry,

Lignin Phenols

Shinn, Reich Sediment Trace 

Element Geochemistry

9 Jimmy Key [JK] Wanless, Nelsen Sedimentology, Nelsen et al., 2002

Geochronology

(JK) Hood Foraminferal Assemblages

Zarikian Ostracode Assemblages,

Ostracode Geochemistry

Swart Stable Isotope Geochemistry

Trefry and Metz Geochemistry

Blackwelder, Capps

O’Neal, Garte,

Featherstone, Kang,

Ellis

10 Oyster Bay [OB] Wanless, Nelsen Sedimentology, Alvarez Zarikian et al.,

Geochronology 2001; Nelsen et al., 2002

(OB) Hood Foraminferal Assemblages

Zarikian Ostracode Assemblages,

Ostracode Geochemistry

Swart Stable Isotope Geochemistry

Tedesco Pollen Assemblages

Trefry and Metz Geochemistry

Blackwelder, Capps

O’Neal, Garte,

Featherstone, Kang,

Ellis

11 Coot Bay [CB] Wanless, Nelsen Sedimentology, Nelsen et al., 2002

Geochronology

Trefry and Metz Geochemistry

Blackwelder, Capps

O’Neal, Garte

Summary of Ecosystem History and 

Paleoecology Research

Following are the significant research findings to date

of the Ecosystem History-Paleoecology research

groups, organized into the five principal Florida Bay

research questions (Table 3.2).

Question 1—How and at what rates do storms, changing

freshwater flows, sea level rise, and local evaporation and

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 13

Table 3.1B List of corals analyzed in Florida Bay between 1990 and present. Numbers in parentheses following the 

location are shown in Figure 3.1 and were used by the original authors.

Location Researchers Analyses Done References

Lignumvitae (SFB-5) Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1996;

Fluorescence, trace elements Swart et al., 1999

(Ba)

Lignumvitae Basin Smith, Hudson Fluorescence, growth bands Smith et al., 1989; 

(referred to as Peterson Hudson et al., 1989

Key Basin by Smith et al.)

(SFB-6)

Blackwater Sound Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

(SFB-3)

Arsenicker Keys Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

(SFB-7)

Rabbit Key Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

(SFB-14)

Bob Allen Key Basin/ Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

Calusa Key (SFB-16)

Duck Key Basin/The Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

Bogies (SFB-23)

Lignumvitae Basin (SFB-40) Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

Lignumvitae Basin (SFB-42) Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

Manatee Key (SFB-45) Swart, Healy, et al. Stable isotopes (C and O) Swart et al., 1999

precipitation influence circulation and salinity patterns

within Florida Bay and outflows from the bay to adjacent

waters?

• Salinity in Florida Bay is more strongly correlated

with rainfall than with any other single factor, and

the periodicity in salinity and rainfall data suggests

linkages to El Niño/Southern Oscillation (ENSO)

climatic patterns.

• Anthropogenic influences play a secondary role to

rainfall in determining salinity for Florida Bay as a

whole, but they may be a factor in the magnitudes

of salinity variations seen in recent times. Additionally, anthropogenic factors may act on a local

basis to influence salinity patterns.

• Declines in diversity and increases in dominance of

salinity-tolerant species have occurred since the

1980s in several benthic invertebrate groups in different regions of Florida Bay.

Question 2—What is the relative importance of the influx

of external nutrients and of internal nutrient cycling in determining the nutrient budget for Florida Bay? What mechanisms control the sources and sinks of the bay’s nutrients? 

• Uranium isotope studies indicate that the phosphorus contamination at the northern end of Taylor

Slough appears to be fertilizer-derived. However,

phosphorus contamination in Taylor Slough diminishes to background by mid slough; therefore, Taylor Slough does not appear to be a source of nutrients

to eastern Florida Bay.

• Eastern Florida Bay does appear to be a source of nutrients to the mangrove zone at the southern end of

Taylor Slough.

• Sediments from eastern Florida Bay (especially from

sites near Pass Key and Russell Key banks) show indications of recent nutrient (carbon [C], nitrogen

[N], and phosphorus [P]) enrichment (1980 to present). This nutrient enrichment could be related to

recent microalgal blooms and seagrass die-off within

Florida Bay.

• Downcore profiles of dated cores from central Florida

Bay (Whipray Basin) show that productivity events

have occurred historically in Florida Bay.

• A large, multidecadal productivity event in the

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

14 FWRI Technical Report TR-11

Table 3.2 Summary of research on ecosystem history by topic.

Type of Analysis

Faunal and Floral Biochemical Geochemical

Research Questions Assemblage Analysis Analysis Analysis

1 How and at what rates Wingard et al., 1995; Smith et al., 1989; Holmes et al., 2001;

do storms, changing Ishman et al., 1996; Halley et al., 1994; Nelsen et al., 2002

freshwater flows, sea Brewster-Wingard et al., Healy, 1996; Swart 

levels, and local 1997; Brewster- et al., 1996; Halley and

evaporation/precipitation Wingard et al., 1998a,b; Roulier, 1999; Swart et

influence circulation and Brewster-Wingard and al., 1999; Alvarez

salinity patterns within Ishman, 1999; Zarikian et al., 2001;

Florida Bay and outflows Alvarez Zarikian Dwyer and Cronin,

from the bay to adjacent et al., 2001; Brewster- 2001; Cronin et al.,

waters? Wingard et al., 2001; 2002; Nelsen et al., 2002

Cronin et al., 2001; 

Huvane and Cooper,

2001; Trappe and

Wingard, 2001; Cronin

et al., 2002; Nelsen et

al., 2002

2 What is the relative Swart et al., 1999 Orem et al., 1997;

importance of the influx of Orem, 1998; Orem 

external nutrients and of et al., 1999a; Gough 

internal nutrient cycling in et al., 2000; Nelsen 

determining the nutrient et al., 2002

budget for Florida Bay? 

What mechanisms control 

the sources and sinks of 

the bay’s nutrients?

3 What regulates the Huvane and Cooper, Swart et al., 1999 Orem et al., 1999a

onset, persistence, and fate 2001 Holmes et al., 2001

of planktonic algal blooms 

in Florida Bay?

4 What are the causes Brewster-Wingard et al., Dwyer and Cronin, Orem et al., 1999a,

and mechanisms for the 1998b; Brewster- 2001 b; Holmes et al.,

observed changes in Wingard and Ishman, 2001

seagrass communities of 1999; BrewsterFlorida Bay? What are Wingard et al., 2001;

the effects of changing Cronin et al., 2001;

salinity, light, and Trappe and Brewsternutrient regimes on these Wingard, 2001

communities?

5 What are the Brewster-Wingard et al., Holmes et al., 2001

relationships between 2001 (mollusks only)

environmental and habitat 

changes and the 

recruitment, growth,

and survivorship of 

animals in Florida Bay?

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 15

mid-1700s, which was characterized by greatly elevated levels of organic carbon and nitrogen, was

observed in two cores from Whipray Basin. Interestingly, although organic carbon and total nitrogen were high, total phosphorus was not elevated

during this time span. This time period (the Little

Ice Age) may correspond to a period of higher rainfall in the Everglades and more extensive land

runoff into Florida Bay, which may have triggered

the productivity event.

• Organic carbon records from Jimmy Key indicate that

hurricanes help flush organic carbon out of Florida

Bay.

Question 3—What regulates the onset, persistence, and fate

of planktonic algal blooms in Florida Bay?

• Surface sediments from eastern Florida Bay show indications of nutrient (carbon, nitrogen, and phosphorus) enrichment from 1980 to the present, which

could be related to recent microalgal blooms within

Florida Bay.

• The multidecadal productivity event of the 1700s

noted in sediment geochemical analyses from

Whipray Basin cores may represent a period of extensive algal blooms.

• Downcore changes in abundance and assemblages

of dinoflagellates and diatoms have been examined

at some sites in Florida Bay. Additional studies of the

ecology of dinoflagellates and diatoms are needed

to interpret the findings in terms of bloom conditions.

Question 4—What are the causes and mechanisms for the

observed changes in seagrass community of Florida Bay?

What are the effects of changing salinity, light, and nutrient regimes on these communities?

• Frequent changes have occurred in the relative abundance of epiphytal species of ostracodes and mollusks over the past century.

• Prior to mid-20th century, epiphytal ostracodes were

relatively rare at sites in central and eastern Florida

Bay, suggesting a greater abundance and/or density

of subaquatic vegetation (SAV) over the past 50 years

than in the first half of the 20th century. Epiphytal

mollusks, although not rare, increased significantly

in relative abundance from approximately 1940 onward at most sites.These data raise the question of

whether dense and abundant seagrass beds are natural in Florida Bay; if the answer is no, these results

have very significant implications for restoration.

• A decline occurred in SAV-dwelling ostracodes and

mollusks in cores from Whipray, Russell, Bob Allen,

and Pass keys between the 1970s and 1980s.

• The relative abundance of mollusks with a strong

preference for Thalassia has declined since approximately 1970 in eastern Florida Bay and since 1910

in Whipray, whereas SAV generalists have increased.

These findings may indicate an increase in the

amount of macrobenthic algae relative to Thalassia.

• Downcore profiles of lignin phenols from a Pass Key

core show large variations in lignin phenol distributions over short time intervals.These variations reflect the proximity of this site to the mangrove zone

along the coast and the outlet of Taylor Creek.

• At Bob Allen Keys, the lignin-phenol distributions

show downcore variations in the abundance of seagrass over time. At Bob Allen, seagrass abundance

appears to have been increasing since a recent minimum around 1960.

Question 5—What are the relationships between environmental and habitat changes and the recruitment, growth,

and survivorship of animals in Florida Bay?

• Declines in molluscan faunal diversity have occurred

during the latter half of the 20th century.

Salinity Patterns and Trends

The majority of the ecosystem history-paleoecology research since 1994 has been focused on addressing the

question of salinity patterns and influx of fresh water

into Florida Bay.The most critical issue in the CERP is

to restore more natural patterns of freshwater flow

through the terrestrial ecosystem and into the estuaries and coastal areas. Restoring natural flow to Florida

Bay includes restoring the timing, delivery, quantity,

and quality of the water to the bay. In order to re-create natural freshwater flow patterns, it is essential to

understand both the natural patterns of freshwater

flow and the natural sources of water prior to significant human alteration of the system. Changing salinity patterns, whether natural or anthropogenically

induced, affect the fauna and flora of the bay.The first

step in restoration is to understand the natural patterns

and be able to set targets and performance measures

for restoration.

An important tool in the restoration effort is modeling the freshwater flow from the Everglades to Florida

Bay under different restoration scenarios.The “Natural

System Model” (NSM) of the South Florida Water

Management District (SFWMD) was developed in part

to meet these needs. The NSM is driven by rainfall.

Efforts to calibrate model-simulated freshwater flow in

the Everglades using historical rainfall records have

only been partially successful due to the lack of historical data on natural conditions prior to waterdiversion activities. A similar lack of long-term

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

16 FWRI Technical Report TR-11

instrumental records of salinity in adjacent Florida

Bay has limited our ability to set restoration targets for

aquatic ecosystems.

The research projects summarized below have addressed the lack of historical data on Florida Bay salinity and freshwater influx. One goal of these studies has

been to determine the natural patterns of salinity

change and freshwater influx. A second goal has been

to distinguish the natural patterns of change from

changes in the salinity regime caused by water diversion in the Everglades during the 20th century.This section summarizes the methodology applied and the

progress made towards these goals.

Methods

Both the University of Miami/NOAA and USGS research groups have used basic assemblage analyses

and biochemical analyses. They use these forms of

analysis to extract salinity information from sediment

cores dated using 210Pb and other methods of establishing chronology (Table 3.1). Interpretations of faunal and floral assemblages are based on observations

of the modern ecology of the organisms being studied.

These assemblages represent a death assemblage and

are therefore time-averaged. However, decadal-scale

resolution can be obtained from the assemblages because the Florida Bay environment has relatively rapid

sedimentation rates, little erosion, and low transport

of silt and sand-sized sediments (Turney and Perkins,

1972; Halley et al., 1997). Additional support that a

death assemblage accurately represents a life assemblage, and therefore a discrete environment, is obtained when several faunal groups are analyzed and

compared from a single sample and the condition of

the shell material is considered.

Biochemical methods are based on the analyses of

individual shells and therefore capture the salinity

record of the time during which that shell was secreted. Although these analyses can provide an almost instantaneous record, the data are still limited by

the temporal resolution of the dating-method for the

sample from which the shell was extracted.

Dwyer and Cronin (2001) and Cronin et al. (2001,

2002) have used the ratio of magnesium to calcium

(Mg:Ca) ions in ostracode shells to reconstruct salinity from Florida Bay cores. They have examined the

ecology and shell chemistry of modern ostracodes in

Florida Bay and have demonstrated that the Mg:Ca ratios in the calcium carbonate shells of ostracodes are

strongly influenced by the salinity and temperature in

which the organism secretes its shell.They have focused

the shell biochemical studies on the epiphytal species

Loxoconcha matagordensis, although in some cores, Peratocytheridea setipunctata is analyzed. Based on their

ecological studies, it appears that adult L. matagordensis secrete their shells principally during spring or

summer seasons (Cronin et al., 2001). In Florida Bay,

warm-season temperatures vary little over interannual timescales, so temperature is considered less important than salinity in influencing ostracode Mg/Ca.

However, additional research is warranted.

Alvarez Zarikian et al. (2001) and Nelsen et al.(2002)

have conducted stable isotopic analyses (δ18O and δ13C)

on ostracodes and benthic foraminifera to extract information on rainfall, freshwater influx, and evaporation to infer salinity conditions. Changes in δ18O can

be correlated to changes in salinity, and those in δ13C

can indicate changes in the influx of organic material.

Evaporation of marine and brackish water preferentially removes the lighter isotopes (16O) and enriches

the water with heavier isotopes (18O). An increase in

δ18O indicates increased evaporation and therefore,

increased salinity. In Florida Bay, however, interpretation of the δ18O value is complicated by the influx of

fresh water from the terrestrial Everglades. Interpretation of δ13C is also complicated in coastal waters.

Under normal marine conditions, the δ13C of calcareous organisms is principally controlled by physiological processes However, in areas where fresh and

marine waters mix, variations in the dissolved inorganic

carbon are probably the dominant factor. Freshwater

from the Everglades is typically isotopically depleted

in δ18O and δ13C, whereas the marine waters from the

gulf or Atlantic are enriched in δ18O and δ13C. By comparing and correlating δ18O to δ13C, researchers can interpret the relative influence of fresh and marine

waters at the core site. (See Halley et al., 1994; Swart et

al., 1996, 1999; and Alvarez Zarikian et al., 2001, for a detailed explanation of the environmental factors that influence δ18O and δ13C.) 

Stable isotopic analyses have also been used to analyze corals within Florida Bay (Healy, 1996; Swart et

al., 1996, 1999) and on a reef affected by Florida Bay waters (Halley et al., 1994).The annual banding of corals

provides a very accurate means of determining the

age of the isotopic samples being analyzed. Halley

and Roulier (1999) used whole mollusk shells (Brachidontes exustus and Transennella spp.) from radiometrically dated cores for δ18O and δ13C analyses.

Findings

The following summary is intended to synthesize

briefly the key results from paleoecologic studies completed in the past 10 years.The reader is referred to the

original papers for detailed results, methods, and evidence supporting the conclusions.

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 17

• Salinity in Florida Bay is more strongly correlated

with rainfall than with any other single factor, and

a periodicity in salinity and rainfall data suggests

linkages to El Niño/Southern Oscillation climatic

patterns.

Nelsen et al. (2002) and Alvarez Zarikian et al.(2001)

concluded on the basis of multidisciplinary studies of

cores from Oyster Bay and Jimmy Key (Table 3.1, Figure 3.1) that “anthropogenic influences play a secondary role to natural influences such as regional

rainfall”(Nelsen et al., 2002: 445).Their analyses showed

that salinity responded directly to regional rainfall

and that “microfaunal data also indicate direct correlation to rainfall patterns for temporal scales ranging

from decadal down to the limit-of-resolution of

geochronology”(Nelsen et al., 2002). Even at the mouth

of Shark River Slough they found rainfall to be the dominant driver.

Dwyer and Cronin (2001) compared downcore

salinity trends derived from Mg:Ca ratios from Russell

Bank, Park Key, and Bob Allen Key mudbank (Table 3.1;

Figure 3.1) to historical rainfall records. They found

good correspondence between rainfall and the paleosalinity data. In addition, they found four extreme lowsalinity periods that corresponded to strongly negative

values in the El Niño/Southern Oscillation (ENSO)

index.

Cronin et al. (2002) conducted time-series analyses

on ostracode Mg:Ca ratios and ostracode abundance

data from the Russell Bank core (Table 3.1, Figure 3.1).

They determined that based on the Mg:Ca ratio, a 5.6-

year salinity periodicity existed and that all salinity

proxy data analyzed showed 6- to 7-year, 8- to 9-year,

and 13- to 14-year periods of variability. They compared the paleosalinity data to climatic factors and

conducted a time-series analysis on south Florida winter rainfall and the Southern Oscillation Index (SOI),

which suggested ~5-, 6- to 7-, 8- to 9-, and 13- to 14-year

cycles. Paleoproxies and climate data were compared

using cross-spectral analyses.The results suggest “that

Figure 3.1 Location of sites within Florida Bay where cores and corals have been analyzed for paleoecologic information. Table 3.1 lists

details about the investigations. Sediment cores listed in Table 3.1A are identified as follows on the map: Bob Allen = BA; Coot Bay = CB;

Jimmy Key = JK; Joe Bay = JB; Oyster Bay = OB; Park Key = PKK; Pass Key = PAK; Rankin Basin = RA; Russell Bank = RB; Taylor Creek

= TC; Whipray Basin = WH. Coral collection sites (SFB) are listed in Table 3.1B.

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

18 FWRI Technical Report TR-11

regional rainfall variability influences Florida Bay salinity over interannual and decadal timescales and that

much of this variability may have its origin in climate

variability in the Pacific Ocean/atmosphere system.”It

may also be related to ENSO (Cronin et al., 2002).

Swart et al. (1999), in an analysis of coral records

from Florida Bay (Table 3.1), mentioned that “a superficial comparison between precipitation from the lower

east coastal region of south Florida appears to indicate

that periods of lowest rainfall relate to times when the

salinity was highest.”However, a comparison of the δ18O

of the coral skeleton from Lignumvitae Basin indicates no statistically significant correlation. Perhaps

this is due to miscalculations in the age of the coral

bands or to the lack of accurate rainfall data for that

basin.They conducted spectral analyses on the salinity values calculated from the corals and found three

statistically significant signals at 4–7 years, 28 years, and

12–14 years.They pointed out that the most significant

periodicity, the 4–7-year cycle, which accounts for

greater than 20% of the variance, may be related to

ENSO cycles (Swart et al., 1999: 392–393).

These short-term cycles in salinity that have been

found in recent research are consistent with the findings of Smith et al. (1989) in their examination of fluorescent banding in the Lignumvitae Basin coral.They

found “strong evidence for a regular 4- to 6-year periodicity in the historical annual flow regimes: years of

low flow alternated with years of high flow.”(Smith et

al., 1989: 280) 

• Anthropogenic influences play a secondary role to

rainfall in determining salinity for Florida Bay as a

whole, but they may be a factor in the magnitude of

salinity variations seen in recent times. Additionally,

anthropogenic factors may act on a local basis to

influence salinity patterns.

Dwyer and Cronin (2001) noted a shift to high-amplitude salinity oscillations after 1950 as indicated by

the Mg:Ca ratio from cores in eastern Florida Bay

(Table 3.1, Figure 3.1).These high-amplitude oscillations

corresponded to a period of increased variability in

rainfall, but human alteration of freshwater flow may

also have been a factor.

Brewster-Wingard and Ishman (1999) noted similar increases in the amplitude of salinity oscillations

after ~1940, as indicated by foraminiferal and molluscan assemblages in cores from Bob Allen and Russell

banks (also examined by Dwyer and Cronin; Table 3.1,

Figure 3.1). They did not conduct any statistical comparisons but they did note that the cause could be

meteorological patterns, anthropogenic changes to

freshwater flow, or a combination of factors.

Clear evidence of decreasing freshwater influence

during the 20th century was found in the northern

transition zone at the mouth of Taylor Creek and at Mud

Creek near Joe Bay by Holmes et al. (1999) and Willard

et al. (1997) (Table 3.1, Figure 3.1). The changes in the

molluscan assemblage from an oligohaline-mesohaline fauna to a predominantly polyhaline fauna could

be explained by the local alteration of flow through Taylor Slough, by changes in rainfall that ultimately affected the flow, or by a combination of both.

Alvarez Zarikian et al. (2001) and Nelsen et al.(2002)

presented evidence of the local effects of water-management practices in their detailed analyses of the

Oyster Bay core (Table 3.1, Figure 3.1). Several anthropogenic factors affected Oyster and Whitewater

bays during the 1980s: the beginning of SFWMD’s

“Rainfall Plan” for managing flow, the shift of water

from Shark River Slough basin into Taylor Slough

basin, and the closing of Buttonwood Canal. Alvarez

Zarikian et al. (2001) noted that a significant decline in

ostracode diversity and abundance occurred around

1980, which could have been linked to these anthropogenic changes or could have been due to the mid1980s drought. Nelsen et al. (2002) illustrated that

regardless of the cause of the faunal changes in Oyster Bay, a comparison of rainfall and flow records

showed that the most significant correlations were

prior to 1960, during the “pre-management period,”and

after 1983, during implementation of the Rainfall Plan.

• Declines in diversity and increases in dominance of

salinity-tolerant species have occurred since the

1980s in several benthic invertebrate groups in different regions of Florida Bay.

Alvarez Zarikian et al. (2001) and Nelsen et al.

(2002) saw two periods of reduced diversity in the benthic microfauna at Oyster Bay: mid-1930s to late 1940s

and late 1970s to the time of core recovery in 1994.

Nelsen et al. (2002: 444) related the faunal changes to

“the changing nature of the salinity field at Oyster

Bay after ~1980.”At Jimmy Key, the periods of reduced

diversity were from the mid to late 1930s and late 1970s

to core recovery in 1997, which they also related to

changes in the salinity field. Prior to 1950, declines in

ostracode abundance and diversity were followed by

rapid recovery. Following the crash in the late 1970s,

the population has not recovered. The ostracode and

foraminiferal faunas in the period from the late 1970s

on are dominated by individual species (Peratocytheridea

setipunctata and Ammonia parkinsoniana typica), interpreted as showing survivor-type dominance. Peratocytheridea setipunctata is known to tolerate extreme

salinity fluctuations from less than 5 practical salinity

units (psu) to 42 psu (Alvarez Zarikian et al., 2001: 140).

Brewster-Wingard et al. (2001) and Trappe and

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 19

Brewster-Wingard (2001) noted similar patterns in the

molluscan assemblages from cores in eastern and central Florida Bay. In every core examined, Brachidontes

exustus, a mollusk known to tolerate large salinity variations (10–44 psu measured in the field) and reduced

water quality, became the dominant species in the

upper portions of the cores from approximately 1980

on. The exception was in Whipray Key, where Brachidontes reached its peak in the late 1970s and then declined. In almost every core, with the exception of the

Taylor Creek core, increases in the relative abundance

of Brachidontes corresponded to declines in molluscan

diversity. Brewster-Wingard et al. (2001) interpreted this

as opportunistic dominance.

Status of Research

ACCOMPLISHMENTS AND 

QUESTIONS RESOLVED

• Most researchers have reached the consensus that

rainfall and climatic patterns are the strongest driving factor in determining Florida Bay salinity patterns. Anthropogenic influences play a secondary

role.

• An indication of an increasingly stressed system is

the dominance of species that tolerate extreme fluctuations in salinity.This pattern of dominance is unprecedented in cores prior to the latter quarter of the

20th century.

• Careful comparison of faunal data and biochemical

data to instrumental salinity records for the past 50

years has demonstrated the validity of using paleoecologic techniques to interpret downcore salinity

patterns that extend beyond instrumental data

records.

• Increasing the coverage of Florida Bay by adding new

cores will elucidate bay-wide trends.

• Increased refinement of proxy data has allowed

more accurate interpretation of downcore results.

RECENT ACCOMPLISHMENTS

• Ground-truthing of ostracode Mg:Ca-ratio-based

paleosalinity reconstruction with instrumental salinity records (1950–present) confirms that the Mg:Ca

method yields salinity values within 1–4 psu of salinity maxima and minima over the past 50 years.

• A method of reducing molluscan-assemblage data

to a single salinity value has been developed.

• The hypothesis that decadal patterns of salinity are

driven by climatological factors, including rainfall,

was supported by analyses of the sediment-core paleosalinity record from Rankin Lake. The Rankin

Lake paleosalinity record matches records obtained

in earlier studies of Russell Key and Bob Allen Key.

• The Rankin Lake core indicates the strong influence of freshwater at the site near the bottom of the

core.

Cronin and Dwyer (Cronin et al., 2003) have tested

the accuracy of their downcore salinity estimates based

on a comparison of the Mg:Ca ratios in ostracode shells

to historical instrumental salinity records from the

Russell Bank. These historical records date back to

Figure 3.2 Comparison between instrumental salinity (black

line) and salinity calculated from Mg/Ca ratios of ostracodes in Russell Bank core 19B (dashed gray line). Instrumental data from

Robblee et al. (2000, 2001). The measured instrumental salinity

curve was constructed by computing monthly mean values for

Whipray, Rankin, and Bob Allen Basins and then obtaining a

grand mean for the central region.

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

20 FWRI Technical Report TR-11

1947 and have been compiled by Robblee et al. (2000,

2001). Figure 3.2 compares the Mg:Ca paleosalinity

curve against the instrumental record of salinity for the

past 50 years. Both the instrumental records and the

paleosalinity curve show large decadal swings in salinity in central Florida Bay from salinities exceeding 50

psu to those in the low 20s. For salinity maxima during the early 1990s, late 1970s, and mid-1960s, the difference between paleosalinity and instrumental salinity

was approximately –1.1., 0.9, and 3 psu, respectively.The

differences in the four periods of Florida Bay salinity

mimima (1993–1995, the 1980s, the late 1960s to early

1970s, and near 1960) were 0.3 psu, 3.6 psu, 1.9 psu, and

0.8 psu, respectively. Given the temporal gaps in the

instrumental record, the error on the sediment core age

estimates, and the spatial and temporal averaging

used for both records, these comparisons provide a remarkable confirmation that the Mg:Ca-based shell

chemistry method yields accurate estimates of past

salinity to within less than 1–4 psu.

Wingard (unpublished report) has developed a

method to reduce the core samples to a single averaged

salinity value for molluscan faunal assemblage data.

Presence and absence data for live mollusks and for numerous environmental parameters, including salinity, have been recorded in Florida Bay since 1995

(http://sofia.usgs.gov/exchange/flaecohist/). These

salinity data have been compiled and examined statistically to determine the mean, median, minimum,

maximum, standard deviation, and confidence interval for each mollusk species observed live. Any species

with a confidence level above 5 or number of observations less than 15 were deleted from the modern

database. The modern salinity information was then

combined with data from a core sample. It was then

weighted based on the percent abundance of each

species present in the sample core assemblage, and a

cumulative average salinity value was produced for the

entire sample. This method has allowed the average

salinity value to be directly compared to instrumental

records of salinity and can be used by modelers.

A preliminary comparison (Wingard, unpublished

report) of the cumulative, weighted-average salinity

data from three cores and the instrumental records of

salinity compiled by Robblee et al. (2000, 2001) has

been completed. It is important to note that this method

is only as good as the modern data upon which it is

based. During the period of observations between

1995 and 2000, salinity values in excess of 48 psu were

never recorded, and only four site surveys were conducted in water exceeding 40 psu during the course of

the study (Brewster-Wingard et al., 2001, and unpublished data). This lack of high-salinity observations

means that the modern database is skewed toward

lower salinities. Despite this problem, the cumulative

weighted averages show downcore trends and can be

compared with the instrumental records because they

give a precise numerical value, unlike standard analyses of assemblage data.

ONGOING RESEARCH 

• Dwyer and Cronin are continuing to examine the

ecology of the ostracode Loxoconcha matagordensis

in order to refine their understanding of the role of

temperature versus salinity in the Mg:Ca ratios in the

shells.They also plan to examine the different magnesium ionic concentrations of fresh versus marine

waters.These studies may provide another way to determine past freshwater influx into Florida Bay.

• Wingard, Stamm, and Murray are conducting growth

experiments and calibrating water chemistry to shell

chemistry for the molluscan species Chione cancellata. These experiments should allow them to be

able to extract salinity data from the metal:Ca ratios

and stable isotopic ratios (18O and δ13C) in the individual growth increments of the shell.

• Wingard, Cronin, Dwyer, Orem, Holmes, and others

are completing analyses on cores from Rankin Lake.

Results will help determine whether hypersalinity

bull’s-eyes noted in this area over the past 15 years

are a recent phenomenon or if they existed under

natural flow conditions.

• Wingard, Stamm, and Murray are conducting salinity-stress tests on common molluscan species found

within modern Florida Bay. They are also testing

sediment cores in order to refine the average salinity values for each molluscan species used in the cumulative, weighted-sample, average-salinity method

discussed above.

UNRESOLVED QUESTIONS AND NEEDED 

RESEARCH

• How did salinity change in Florida Bay on a seasonal

basis prior to significant alteration of freshwater

flow into the bay? What were the extremes in seasonal change?

° Wingard and others are researching the biochemistry of individual molluscan growth increments to address this question.

• Did hypersalinity zones form in Florida Bay prior to

instrumental data recordings in the past two

decades? If so, how often, what was the duration, and

were these linked to natural climatic patterns or to

anthropogenic change?

° Examination of Rankin Core by USGS groups is

beginning to address these questions.

• Additional cores are needed from critical areas

within the bay, such as from transects along the

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 21

margins of northern and eastern Florida Bay and the

Cape Sable–Ten Thousand Islands area, where shortterm salinity oscillations are large.

• Attempts should be made to locate areas with records

extending back into the early 1800s in order to examine 50–100 years of salinity patterns prior to any

alteration of the environment.

• A better understanding of the controls on shell biochemistry should be developed, especially in coastal

areas where fresh and marine waters mix.This effort

should include refining our understanding of the

salinity and temperature effects on shell chemistry

by integrating trace elemental (principally Mg-Ca,

but also strontium [Sr] and barium [Ba]) analyses

with stable isotopic analyses.

° Zarikian and Swart plan to continue their stable

isotopic studies of water, ostracodes, and corals.

° Dwyer and Cronin are continuing their studies of

Mg-Ca in water and ostracodes.

° Swart, Zarikian, Dwyer, and Cronin hope to work

together on the same cores, examining both isotopic and trace elements in ostracode and

foraminifer shells.

• Knowledge of modern ecology of organisms being

used in downcore studies should be refined.

° Wingard and others are continuing tests in situ and

in the laboratory on mollusks to determine tolerance to salinity extremes.

• Examine modern data (Montague and Ley, 1993.

See discussion in Nelsen et al. (2002) to determine

whether mean salinity or standard deviation in salinity exerts more control over benthic fauna and flora.

• A carbon budget for Florida Bay should be developed

in order to contribute to a better understanding of

the carbon isotope record of the cores and provide

a better means for interpreting historical freshwater influx into the bay (Halley and Roulier, 1999).

• We need to perform additional “groundtruthing”of

paleosalinity methods (Mg:Ca in ostracodes; cumulative, weighted-sample average of mollusks) by

comparing the results of these methods on new,

short sediment cores from key sites with the fairly

continuous instrumental salinity record available

since 1985.

• Calibrate Mg:Ca ratios in other ostracode species and

apply them to new areas of study within the bay.

• Measured and reconstructed salinity and forcing

factors (rainfall, evaporation, groundwater, and discharge from sloughs) should undergo more rigorous

statistical analyses.

• Apply paleosalinity data to Natural System Model

simulations to test the model’s accuracy in predicting the trends determined from the paleorecord.

Begin with paleosalinity data that has been

“groundtruthed”by comparison with instrumental

records of Robblee et al. (2000, 2001).

Nutrient Patterns and Trends

Restoration efforts to reestablish natural rates of freshwater discharge into Florida Bay potentially could

cause additional harm to the bay if the quality of the

water entering the system is not considered. It is essential to understand the prealteration patterns of nutrient influx into the bay and nutrient cycling within

the bay in order to provide the baseline information for

nutrient modeling.

Methods

Sediments have been geochemically analyzed by both

research groups (University of Miami/NOAA and

USGS) to extract information from sediment cores

dated using 210Pb and other methods of dating (Table

3.1). Orem et al. (1999a) typically analyzed the sediments

for organic carbon, total nitrogen, and total phosphorus. Nelsen et al. (2002) analyzed organic carbon, total

aluminum, and lead. Swart et al. (1999) discussed the

possible use of trace elements in calcareous organisms as a proxy for nutrients.

Findings

LOWER TAYLOR SLOUGH AND MANGROVE

FRINGE

• Uranium isotope studies indicate that phosphorus

contamination at the northern end of Taylor Slough

appears to be fertilizer-derived. However, phosphorus contamination in Taylor Slough diminishes

to background by mid slough; therefore, Taylor

Slough does not appear to be a source of nutrients

to eastern Florida Bay.

• Eastern Florida Bay does appear to be a source of nutrients to the mangrove zone at the southern end of

Taylor Slough.

Orem et al. (1997, 1999a), Orem (1998), and Gough

et al. (2000) conducted detailed surveys of nutrients,

metals, and major ion geochemistries in Taylor Slough

and in eastern and central Florida Bay from 1996 to present. The study involved analyses of surface water,

sediment porewater, and solid phase sediments from

cores (Table 3.1, Figure 3.1; Taylor Slough cores are not

included because they are not within Florida Bay).

Cores were dated using 210Pb, 137Cs, and 14C. Results

from Taylor Slough showed that there is some degree

of nutrient contamination (phosphorus) at the head of

the slough. Uranium isotope studies indicated that

this phosphorus contamination appeared to be fertilEcosystem History
Florida Bay Synthesis Hunt and Nuttle

22 FWRI Technical Report TR-11

izer-derived.The phosphorus contamination in Taylor

Slough diminished to background levels by midslough, so Taylor Slough does not appear to be a source

of nutrients to eastern Florida Bay. Rather, Florida Bay

appears to be a source of nutrients to the mangrove

zone at the southern end of Taylor Slough.

EASTERN AND CENTRAL FLORIDA BAY

• Beginning in the mid 1980s, nutrification (increases

in nitrogen and phosphorus) has occurred in portions

of eastern and central Florida Bay as indicated by

abrupt shifts in organic carbon, total nitrogen, and

total phosphorus. Pass Key, located closest to terrestrial influx, showed the most pronounced shifts,

and Bob Allen Key, the most southerly site, showed

the least pronounced shifts.

• A large multidecadal-productivity event in the mid1700s, which was characterized by greatly elevated

levels of organic carbon and nitrogen, was observed

in two cores from Whipray Basin.

Orem et al. (1999a) conducted analyses on organic

carbon, total nitrogen, and total phosphorus from five

sites in eastern Florida Bay (Table 3. 1, Figure 3.1).They

found “sudden and dramatic shifts”indicating increased

nutrification that could not be explained by diagenetic

processes. The sediments at Pass Key showed two

episodes of increased nutrification in the mid-1970s

and after 1985. Nutrification at Bob Allen and Russell

banks began in the early 1980s. The shifts in nitrogen

and phosphorus occurred just prior to the reported

microalgal blooms and seagrass die-off events in 1987.

Two cores from Whipray Basin, which preserve a

long record dating back into the 1700s, were analyzed

by Orem et al. (1999a). Downcore profiles at these sites

illustrated a large productivity event that occurred in

the mid-1700s.This event was multidecadal and characterized by greatly elevated levels of organic carbon

and nitrogen, probably representing a period of extensive algal blooms. Interestingly, total phosphorus

was not elevated during this time span. This productivity event occurred during the Little Ice Age and

may correspond to a period of higher rainfall in the

Everglades. Higher rainfall would contribute to more

extensive land runoff into Florida Bay, which may have

triggered the productivity event.

WESTERN FLORIDA BAY–WHITEWATER BAY

AREA

• Organic carbon records from Jimmy Key indicate that

hurricanes help to flush organic carbon out of the bay.

Nelsen et al. (2002) analyzed and contrasted organic

carbon content in Oyster Bay, Jimmy Key, and Coot Bay

cores (Table 3.1; Figure 3.1).They found that organic carbon decreased by a factor of two from Oyster Bay to

Coot Bay and by a factor of four from Oyster Bay to

Jimmy Key. Aluminum was closely correlated to organic

carbon at Oyster Bay and Coot Bay because of erosion

and mixing of the mangrove peats, which contribute

the organic carbon and the associated clay and quartz,

which in turn contributes the aluminum. Storm deposits and subsequent dissolution then concentrate the

aluminum and organic carbon. Large organic carbon

excursions at Oyster Bay correspond to hurricane

events because of an increase in organic detritus.The

trend in organic carbon at Oyster Bay is towards a decline from the first to the second half of the 20th century. At Coot Bay, organic carbon increases upcore,

but at Jimmy Key it is segmented. The periods of organic carbon increase at Jimmy Key (1900 to mid 1930s

and after mid-1970) correspond to periods of decreased

hurricane activity, whereas the period of declining organic carbon (mid-1930s to mid-1970s) took place during a period of increased hurricane activity.These data

support the hypothesis that hurricanes contribute to

flushing of organic carbon from the bay (Nelsen et al.,

2002: 424, 442).

TRACE–ELEMENT ANALYSES OF CORAL

Swart et al. (1999) tested the use of barium (Ba) as a

proxy for nutrient enrichment.They found that Ba increased when salinity decreased, but they concluded

that the controls on barium were “enigmatic”and that

more research was necessary to understand the distribution of barium within the bay.

Status of Research

ACCOMPLISHMENTS AND QUESTIONS 

RESOLVED

• Multidecadal shifts in nitrogen and phosphorus

have been documented in sediments deposited prior

to anthropogenic change, illustrating that these shifts

occur naturally and can be of long duration.

• Recent dramatic increases in nitrogen, phosphorus,

and total carbon have occurred in eastern Florida Bay

and show decreasing amplitude with increasing distance from Taylor Slough.

ONGOING RESEARCH

• Orem et al. are currently working on analyses of

carbon, nitrogen, and phosphorus from a Rankin

Lake core.

UNRESOLVED QUESTIONS AND NEEDED 

RESEARCH

• Certain trace elements within calcareous skeletons

(cadmium [Cd], barium, and manganese [Mn]) may

be proxies for nutrient enrichment (see Swart et

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 23

al., 1999, for discussion of previous research on this

method).This method could be tested and used on

downcore specimens.

• The use of δ13C as a proxy for nutrient fluxes, in

combination with other analyses, should be explored.

• Additional analyses from critical areas within the bay

should be conducted in order to increase our understanding of past changes in nutrients.

Occurrence and Pattern of 

Algal Blooms

Only minimal ecosystem-history research has been

done to contribute information on past algal blooms,

and little of this work provides direct evidence. However, this is an area where there is the potential to obtain significant new information.

Methods

Huvane and Cooper (2001) have conducted assemblage analyses of diatoms, microscopic “algae”whose

siliceous shell, or frustule, is well preserved in the sediments (Table 3. 1, Figure 3.1). Diatoms can be planktonic or epiphytic and can be indicative of many

environmental factors. Edwards (Wingard et al., 1995;

Ishman et al., 1996; Brewster-Wingard et al., 1997, 1998b)

examined dinoflagellate cysts, a stage in the life cycle

of dinoflagellates, preserved in the sediments (Table 3.1,

Figure 3.1).

Orem et al. (1999a) inferred bloom conditions based

on analyses of organic carbon, total nitrogen, and total

phosphorus. Swart et al. (1999) inferred bloom conditions based on a shift in δ13C in small Siderastrea radians corals collected throughout Florida Bay.

Findings

• Surface sediments from eastern Florida Bay show indications of nutrient (C, N, and P) enrichment from

1980 to the present, which could be related to known

microalgal blooms within Florida Bay.

• The multidecadal-productivity event noted in sediment geochemistry from Whipray Basin cores may

represent a period of extensive algal blooms.

Orem et al. (1997) analyzed surface sediments from

eastern Florida Bay, including sites near Pass Key and

Russell Key banks.These analyses show indications of

nutrient (C, N, and P) enrichment over the past two

decades.This nutrient enrichment could be related to

recent microalgal blooms and/or seagrass die-off within

Florida Bay. The analyses of two cores from Whipray

basin (Orem et al., 1999a) may highlight a period of extensive, multidecadal bloom conditions during the

mid-1700s.

• Downcore changes in abundance and assemblages

of dinoflagellates and diatoms have been examined

at some sites in Florida Bay. Additional studies of the

ecology of dinoflagellates and diatoms are needed

to interpret the findings in terms of bloom conditions.

The findings on diatoms (Huvane and Cooper,

2001) and on dinoflagellate cysts (Wingard et al., 1995;

Ishman et al., 1996; Brewster-Wingard et al., 1997, 1998b)

have been inconclusive to date. Additionally, detailed

studies of the biology and ecology of diatoms and dinoflagellate cysts are needed to accurately interpret the

findings. In addition, because these phytoplankton

are found in the less than 63-μm fraction of the sediments, they are more susceptible than the benthic

microfauna (greater than 63 μm) to transport, redeposition, and reworking processes.

• Increases in heavy excursions of δ13C may indicate

the occurrence of algal blooms.

Swart et al. (1999) analyzed δ13C in small Siderastrea radians corals collected throughout Florida Bay

(Table 3.1, Figure 3.1).They separated the corals into two

groups—those with δ13C enrichment from approximately 1989 to 1993 and those with δ13C depletion over

the same time period. Corals showing the maximum

δ13C depletion, including the coral with the long record

from Lignumvitae Key, occurred around 1984.Two possible causes for δ13C increases seen in the first group

of corals: (1) either a relative decrease in the influence

of carbon derived from marine sources or (2) an increase in photosynthesis, which may indicate algal

blooms.They discussed the contradictory evidence of

the δ13C patterns seen in the two groups of corals.They

concluded that “the most probable cause is increased

oxidation of organic material in the northeastern portion of Florida Bay and an increase in algal blooms in

the western part of the bay.”

Status of Research

ONGOING RESEARCH

• No known research on downcore phytoplankton remains is currently being conducted.

• Continued analyses of δ13C in ostracodes,

foraminifera, mollusks, and corals are part of several

ongoing studies, but the primary intent of these

analyses is to address Question 1.

UNRESOLVED QUESTIONS AND NEEDED 

RESEARCH

The potential exists to extract information from sediment cores about phytoplankton blooms via analyses

of the remains in the core and through inferences

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

24 FWRI Technical Report TR-11

based on changes in sediment geochemistry, carbon

isotopes, and faunal assemblages. However, a great deal

of work needs to be done to understand the ecology of

the living phytoplankton and to understand the signature left in sediments following a bloom. In addition,

the relationship between δ13C and blooms needs to

be tested and calibrated in the modern environment

before information can be accurately applied to paleoanalyses. The questions that could be addressed include the following:

• Prior to human alteration of flow and circulation in

Florida Bay, did planktonic blooms occur? If yes,

what was their timing and duration? What natural

events may have triggered blooms?

• Did the frequency and duration of blooms change

after the construction of the Flagler Railroad or after

the alteration of freshwater flow into Florida Bay?

• Can algal blooms be recognized in the sedimentary

record? If so, can they be characterized and quantified? 

Seagrass Trends and Patterns

A significant amount of ecosystem history research

has addressed changes in seagrasses specifically and

subaquatic vegetation (SAV) in general over time and

the effects of changes in environmental components

(salinity, nutrients, water quality) on the vegetation.

These questions are critical to restoration.The massive

die-off in 1987–1988 focused public attention on the

plight of Florida Bay and the changes that were occurring in the ecosystem. It is important to place these

changes in historical context over decadal and even centennial time scales to determine if die-offs and fluctuations in seagrass abundance are natural, cyclical

events. In addition, ecosystem history data from sediment cores can provide insights into long-term sequences of change preceding die-offs.

Methods

Basic assemblage analyses and geochemical analyses

have been used to detect downcore trends and patterns

in subaquatic vegetation (SAV) from sediment cores

dated using 210Pb and other methods of dating (Table

3.1). Cronin (Cronin et al., 2001) and Wingard (Brewster-Wingard et al., 1998a, 2001; Brewster-Wingard and

Ishman, 1999) have used ostracodes and mollusks in

their downcore analyses of SAV trends by applying data

gathered in Florida Bay. Modern studies have established that some ostracode and mollusk species prefer living as epiphytes on Thalassia or Halodule (two

common true seagrasses in Florida Bay), some prefer

macrobenthic algae (such as Chondria or Laurencia),

and some are SAV generalists that do not have a preference for a particular species of grass or algae. The

modern data were gathered through field observations and samples collected from 1995 to the present

(field data available via http://sofia.usgs.gov/flaecohist/). (See Salinity Trends and Patterns methods section for a discussion of taphonomic and sediment

transport considerations in assemblage analyses.) 

Geochemical analyses of sediments can provide information on the presence and distribution of seagrasses (Orem et al., 1999b).The concentration of lignin

phenols in sediments is a potential marker for historical seagrass abundance in Florida Bay. Seagrasses in

Florida Bay, although angiosperms, have a lignin phenol distribution similar to that of gymnosperms (i.e.,

little or no syringyl phenols present). Apparently the

syringyl phenol content of the lignin in the seagrasses

has been lost evolutionarily in the transition of these

angiosperms back to the aquatic realm. This characteristic allows seagrass lignin (syringyl-phenol poor)

to be differentiated from the other dominant lignin

source in Florida Bay (mangroves; syringyl-phenol

rich). Analyses of organic carbon and total nitrogen

(Orem et al., 1999a) may also provide information about

seagrass die-offs, especially when combined with faunal assemblage and/or lignin phenol data.

Findings

• Frequent changes have occurred in the relative abundance of epiphytal species of ostracodes and mollusks over the past century.

• Prior to the mid-20th century, epiphytal ostracodes

were relatively rare at sites in central and eastern

Florida Bay, suggesting a greater abundance and/or

density of SAV over the past 50 years than in the first

half of the century. Epiphytal mollusks, although

not rare, increased significantly in relative abundance from approximately 1940 to the 1970s at most

sites.These data raise the possibility that dense and

abundant seagrass beds may not be natural; if this

finding is true, it will have great implications for

restoration.

• A decline in SAV-dwelling ostracodes and mollusks

occurred in cores from Whipray, Russell, Bob Allen,

and Pass keys during the 1970s and 1980s.

• Relative abundances of mollusks with a strong preference for Thalassia have declined since approximately

1970 in eastern Florida Bay and since 1910 at Whipray

Key, whereas SAV generalists have increased. These

findings may indicate that the amount of macrobenthic algae has increased more than Thalassia has.

Cronin et al. (2001) found that ostracode assemblages during 1900–1940 at Whipray Basin, Bob Allen

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 25

Key mudbank, Russell Key Bank, and Park Key were

characterized by moderate to large proportions of Peratocytheridea, which is typically found associated with

mud and Halodule substrates. Ostracode species associated with Thalassia and macroalgae were less common during this period. From approximately 1930 to

1950, Peratocytheridea declined significantly, whereas

Loxoconcha (a Thalassia indicator) and Xestoleberis (an

SAV generalist) increased (Figure 3.3).This pattern of

long-term decline in Peratocytheridea, coincident with

an increase in species associated with Thalassia and

macrobenthic algae, was seen in cores from central,

eastern, and northern Florida Bay. This shift suggests

greater abundance and/or density of SAV in central

Florida Bay during the past 50 years than in the first

half of the century. A second shift occurred in the

1970s and 1980s, when a decline in Thalassia- and algaldwelling species occurred in most cores. Cronin et al.

(2001: 176) stated that “although the strength of the decline varied by species and by site, the stark contrast

between the abundance of epiphytal species during the

1950s and 1960s and the very low abundance at times

during the following two decades suggests a broad

regional shift occurred at this time.” These shifts in

the 1970s and 1980s may be related to large-scale seagrass die-offs (principally Thalassia).

Brewster-Wingard et al. (1998a), Brewster-Wingard

and Ishman (1999), and Trappe and Brewster-Wingard

(2001) noted frequent and relatively dramatic shifts

in the populations of the epiphytal species of mollusks. Cores from Whipray Key, Russell Key Bank, and

Taylor Creek all show increases in epiphytal mollusks

beginning around 1940, so the molluscan data agree

with the ostracode data (Figure 3.3).There was a general increase in epiphytal organisms during the latter

half of the 20th century, indicating a greater SAV coverage during this period than in the first half of the century. The molluscan epiphytal species were split into

Figure 3.3 Percentage of abundance of select mollusk and ostracode species that are indicators of sub-aquatic vegetation, plotted against

estimated age for Russell Bank core 19B. Light gray are species indicative of any type of sub-aquatic vegetation (generalists). Black are

species primarily indicative of Thalassia (specialists). Note different percent abundance scales.

Ecosystem History
Florida Bay Synthesis Hunt and Nuttle

26 FWRI Technical Report TR-11

two groups based on modern field observations (Figure 3.3): (1) species that have a strong preference for

Thalassia and (2) nonspecific SAV dwellers that may be

found on either Thalassia or macrobenthic algae.These

data illustrate an interesting trend—the relative abundance of Thalassia dwellers has declined since approximately 1970 at Bob Allen and Russell keys and

since 1910 at Whipray Key, whereas the nonspecific SAV

dwellers have increased. The ostracode Xestoleberis is

a nonspecific SAV dweller, and its trends in abundance agree with the molluscan data.

• Downcore profiles of lignin phenols from a Pass Key

core show large variations in lignin-phenol distributions over short time intervals, therefore reflecting

the proximity of this site to the mangrove zone along

the coast and to the outlet of Taylor Creek and thus

to the influence of decaying mangrove and terrestrial

plant detritus.

• At Bob Allen Keys, the lignin-phenol distributions

show downcore variations in the abundance of seagrass over time. Seagrass abundance appears to

have been increasing since a recent minimum around

1960.

Downcore profiles of lignin phenols were analyzed from Pass Key and Bob Allen Keys (Orem et al.,

1999b). The Pass Key core shows large variations in

lignin phenol distributions over short time intervals.

These variations are consistent with the proximity of

this site to the mangrove zone along the coast and to

the outlet of Taylor Creek and the influence of decaying mangrove vegetation and influx of terrestrial plant

detritus. At Bob Allen Keys, the lignin distributions

show downcore variations in the abundance of seagrass

over time. At Bob Allen, seagrass abundance appears

to have been increasing since a recent minimum

around 1960.

• Surface sediments from eastern Florida Bay show indications of nutrient (C, N, and P) enrichment from

1980 to the present; which could be related to recent

seagrass die-off within Florida Bay.

The analyses conducted by Orem et al. (1999a) (discussed under Question 3 above) at sites near Pass Key

and Russell Key banks indicated that nutrient (C, N, and

P) enrichment from 1980 to the present could be related

to recent seagrass die-off within Florida Bay.

Status of Research

ACCOMPLISHMENTS AND QUESTIONS 

RESOLVED

• Common trends in mollusk and ostracode epiphytal species across basins and regions of Florida Bay

indicate that while substrate and seagrass coverage

may be patchy, it appears that there are bay-wide

forcing factors affecting the abundance and distribution of the beds.

• Frequent and relatively rapid changes occur in the

epiphytal indicator species, implying that the SAV

itself goes through frequent and significant changes.

• There is evidence of increasing macrobenthic algae

abundance in Florida Bay.

• Trends in SAV distribution throughout the 20th century imply that dense and abundant seagrass beds

occurred in an already altered system. This finding

has important implications for restoration.

ONGOING RESEARCH

• Current USGS work is focused on completing analyses of a core from Rankin Lake. This core was from

an area of documented seagrass die-off (P. Carlson,

personal communication) and was collected to examine the long-term (decadal-scale) sequences of

change in a number of variables prior to the die-off

event in 1987–1988. Ostracode and molluscan assemblages, ostracode geochemistry (Mg:Ca ratio),

sediment geochemistry, and lignin phenols are being

analyzed downcore.

• An additional core from the site of seagrass die-off

at Barnes Sound is currently being processed and will

be analyzed by the USGS group for faunal assemblage data and Mg:Ca ratios. A core from Whipray

Basin will be analyzed for lignin phenols.

• Samples have been collected and processed to begin

to quantify the relationships between molluscan

species and SAV species.

UNRESOLVED QUESTIONS AND NEEDED 

RESEARCH

• The causes of seagrass die-off are still poorly understood. Detailed studies of sediment cores from

sites of known die-off should help researchers examine the decadal-scale sequences of change that

have led to the recent die-off events. Multiple forcing factors are undoubtedly at play in massive dieoff events, and long-term data may allow researchers

to better understand the interaction of these factors

prior to die-offs.

• The potential influence of climate variability and its

role in factors that directly affect sea-grasses, such

as light attenuation, disease, and salinity fluctuations, need additional study.

• A quantitative analysis of modern vegetation and epiphytic species would allow more refined interpretations of the downcore assemblages.

Ecosystem History
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 27

Higher-Trophic-Level Species

Ecosystem history research and analyses of sediment

cores have contributed very little to Question 5, in

large part because Question 5 has been focused on the

higher-trophic-level species, which are generally absent or not well represented in the cores.The only exception is the molluscan fauna. As Brewster-Wingard

et al. (2001) pointed out, mollusks are well preserved

in the cores, and they represent a number of trophic

categories (filter feeding, grazing, scavenging, and carnivory). Simple measures of molluscan faunal diversity in cores from eastern and central Florida Bay have

illustrated patterns of change over time (BrewsterWingard et al., 2001; Trappe and Brewster-Wingard,

2001), but these measures have not been rigorously

tested. An apparent trend toward decreasing diversity

has been observed in the upper portions of most of the

cores beginning between 1960 and 1980.

If Question 5 were to expand and examine the

lower invertebrates, paleoecologic data could contribute more valuable data from the benthic microfauna. Some of these trends are discussed under

Question 1 and Question 4 above.

Status of Research

ONGOING RESEARCH

• No active research on higher trophic levels, other

than molluscan faunal assemblage analyses, is currently being done. The current focus of the molluscan studies is to address Question 1 and Question

4, but molluscan faunal changes in response to salinity and benthic habitat will provide secondary information to address Question 5.

• Benthic microfaunal assemblage analyses are also

contributing data about changes in the Florida Bay

benthic habitat over time.

UNRESOLVED QUESTIONS AND NEEDED 

RESEARCH

• There are significant questions about changes in

benthic habitat that could be addressed (and in part

are being addressed) by expanding Question 5 to

include lower invertebrates.These organisms form the

bottom of the food chain and are therefore essential

to the survival of the higher-trophic-level organisms.

Because the lower invertebrates are more readily

preserved in sediment cores, decadal- to centennialscale analyses of environmental change and its effect

on animals in Florida Bay would be possible.

• More rigorous analyses of the molluscan faunal diversity data should be conducted.

• The use of mollusks as proxies for higher-trophiclevel diversity should be explored.

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Ecosystem History
Introduction 

Question 1—How and at what rates do storms, changing

freshwater flows, sea level rise, and local evaporationprecipitation patterns influence circulation and salinity

patterns within Florida Bay and exchanges between the

bay and adjacent waters?

The research conducted addressing Question 1 was intended to produce quantitative predictions of circulation and salinity responses within Florida Bay.

Exchange between the bay and the Gulf of Mexico, exchange between the bay and the coastal zone of the

Florida Keys, and oceanographic, climatic, and hydrological driving processes were also areas that were

to be addressed.Table 4.1 includes relevant representative references to research addressing driving forces,

system characteristics, and their intersection.The Research Summary highlights major findings to date.

Background

The south Florida coastal system surrounding and interacting with the interior waters of Florida Bay (made

up of the gulf and Atlantic waters of the Florida Keys,

the Dry Tortugas, and the southwestern Florida shelf)

is highly coupled by the combined influence of coastal

and oceanic currents (Lee et al., 2002).The bay itself is

a lagoonal system; a complex network of shallow, often

intertidal, banks isolate the interior portions of Florida

Bay from the direct influence of regional or largerscale oceanographic processes (Figure 4.1). As a result,

local and direct climatic processes, such as the inflows

of surface and groundwater, rainfall, evaporation, and

wind-driven flow, greatly affect salinity, circulation,

and exchange processes.

The climate of south Florida is subtropical, with a

comparatively small annual temperature range but

distinct wet (summer-fall) and dry (winter-spring) seasons. During the wet season, showers associated with

the afternoon sea breeze occur almost daily, and tropical storms are transient occurrences. During the dry

season, cold fronts pass through the region on an approximately weekly basis, accompanied by increased

wind speeds and clockwise-rotating wind directions.

Spatially, the bay can be thought of as four distinct

regions subject to different geophysical forcings, topographic constraints, and freshwater inputs.The northeastern region of Florida Bay is not significantly affected

by tides or directly influenced by the surrounding marine waters of the Atlantic and Gulf of Mexico.This region is the direct recipient of freshwater flows from

Taylor Slough and the C-111 canal system. Upstream

water-management practices influence the quantity,

timing, and distribution of fresh water entering this region. Runoff varies spatially across the northern boundary, with the greatest flow through Trout Creek. Wind

events often determine the timing of freshwater discharges on hourly to daily time scales, and regional

rainfall cycles (e.g., seasonal and El Niño/La Niñadriven) influence discharges on annual to multiyear

time scales. Salinity along the northern boundary of the

bay responds very rapidly to rainfall and/or discharge

events. High flow causes dramatic freshening in the

small bays along the northern boundary. Subsequently,

fresh water slowly mixes with the more saline Florida

Bay waters to the south and southwest over a period

of weeks to months (Johns et al., 2001a).

The central region of Florida Bay receives less direct freshwater inflow, but fresh water can move into

central Florida Bay through McCormick Creek into

Terrapin Bay, through Alligator Creek into Garfield

Bight, as well as over the Buttonwood Embankment.

Groundwater inputs have also been hypothesized.

Under historically higher water levels, these surface

and groundwater inputs were presumably more significant throughout the southern Everglades. During

times of reduced precipitation and high evaporation,

this central area can become hypersaline, with salin30 FWRI Technical Report TR-11

Chapter 4

Physical Processes

Lead Authors Dr. Thomas Lee (University of Miami), 

Dr. Elizabeth Johns (NOAA/AOML), and Dr. Peter Ortner (NOAA/AOML)

Contributors Joseph Boyer, Jeff Chanton, Shuyi Chen, John Hammrick, Clinton Hittle, Villy Kourafalou ,

Chris Langevin, Victor Levesque, Frank Marshall , Zaki Moustafa, William Nuttle, Eduardo Patino, 

Joseph Pica, Rene Price, Michael Robblee, David Rudnick, Ray Schaffranek, DeWitt Smith, Ned Smith,

Eric Swain, Peter Swart, Zafer Top, Paul Trimble, Sandra Vargo, John Wang, Paul Willis
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 31

ity often exceeding 40 practical salinity units (psu) and

historically as high as 70 psu (Boyer and Jones, 2001;

Robblee et al., 2001). High salinity persists over periods of weeks to months, indicating that like waters of

the northeastern region, those of the central region have

a relatively long residence time.

The western region of Florida Bay is the least topographically isolated, sharing an open boundary with

the Gulf of Mexico and exchanging water with the

central region of Florida Bay through the main

Flamingo channel and with the Atlantic Ocean through

passages in the middle Keys.This western region is also

subject to robust tidal mixing. Therefore, residence

times in the western region are shorter than in the central and northeastern regions, and salinity can show a

relatively rapid response to meteorological events such

as tropical storms and cold fronts. Oceanographically,

the entire coastal region of south Florida is one integrated system (Figure 4.2). Florida Bay is connected to

the southwestern Florida shelf and, on occasion, to

Table 4.1 Research categories defined by Question 1 and representative references to relevant research.

System Characteristics

Driving Exchange with

Process Salinity Patterns Circulation Patterns Adjacent Waters

General Characteristics Robblee et al. (2001), Boyer et al. Lee and Williams (1999), Lee N. Smith (2002), Smith and Pitts

(1997), Boyer and Jones (2001), et al. (1999), Lee et al. (2002), Lee and Smith (2002),

Lee et al. (2002), Johns et al. (2002), D. Smith (2001) Yang (1999), Lee and Williams

(2001a), D. Smith (2001) (1999), Lee et al. (1999, 2002)

Winds and Storms Johns et al. (2001b), D. Smith Lee and Williams (1999), Lee Lee and Smith (2002), Smith and

Goldenberg et al. (2001), (2001), R. Smith et al. (2001) et al. (2002), Smith and Pitts Pitts (2002), N. Smith (2001), Johns et

Albrecht et al. (2003) (2002), Wang et al. (1994), al. (2001b)

N. Smith (2001)

Precipitation Swart and Price (2001), Nuttle et No observed effect of No observed effect of precipitation

Willis (1999),Trimble et al. al. (2000, 2001) Johns et al. precipitation on circulation on exchanges with adjacent waters

(2001), Mattocks (pers. com.), (2001a) has been reported. has been reported.

Pielke et al. (1999)

Evaporation Swart and Price (2001), Nuttle et No observed effect of No observed effect of

Pratt and Smith (1999), al. (2000, 2001) evaporation on circulation has evaporation on exchanges

N. Smith (2000), Price et al. been reported. with adjacent waters has been

(2001), Mattocks (pers. com.) reported.

Surface Water Lee et al. (2002) Ortner et al. Lee et al. (2002), Langevin et No observed effect of surface

Hittle et al. (2001), (1995), Nuttle et al. (2000, 2001), al. (2002a) water on exchanges with

Vosburg et al. (2001), Swart and Price (2001), Johns et adjacent waters has been

Cable et al. (2001) Swart and al. (2001a), Langevin et al. (2002a),

Price (2001), Levesque and Schaffranek et al. (2002), Hurricane

Patino (2001),Trimble et al.(2001) Georges Workshop

Groundwater Fitterman et al. (1999), Fitterman Langevin et al. (2002a) No observed effect of

Price and Swart (2001), and Deszcz-Pan (2001), groundwater on exchanges

Fitterman and Deszcz-Pan Langevin et al. (2002a) with adjacent waters has been

(2000, 2002),Vosburg et al. reported

(2001),Top and Brand (2001)

Sea Level and Tides Lee et al. (2001, 2002), Johns Lee and Smith (2002), Smith N. Smith (1998), Smith and

Maul and Martin (1993), et al. (2001a) (1998), Wang et al. (1994) Lee (2003), Lee and Smith

Smith (1997), Frederick et al. (2002), Smith and Pitts

(1994) (2002), N. Smith (2001) 

Boundary Currents Ortner et al. (1995), Lee et al. Lee et al. (2002),Yang et al. Lee et al. (2001, 2002),

Lee and Williams (1999), (2001, 2002) (1999) Yang et al. (1999)

Lee and Smith (2002)

Prediction Nuttle et al. (2000, 2001), Cosby Wang et al. (1994), Kim et al. HYCOM model group

et al. (1999), Wang et al. (1994), (1999)

Marshall (2001), Walker (1998),

Kim et al. (1999)

Physical Processes
more remote regions of the Gulf of Mexico. As a result,

western Florida Bay can be influenced by the delivery

of fresh water from rivers discharging into the Ten

Thousand Islands region and along the west coast of

Florida (the Shark, Broad, Harney, and Lostmans rivers).

These river waters are carried southward along the

southwestern Florida coastline and around Cape Sable

in a general pattern of outflow through the Keys to the

reef tract (Lee et al., 2001, 2002). Freshwater inflow

from remote gulf regions is more likely during summer and fall and has been shown to include that from

Mississippi River floods (Ortner et al., 1995). Subsequent

transport of this water to Florida Bay and the Keys is

aided by the Loop Current and the Florida Current.

Finally, the southern region of Florida Bay differs

from the central region because it has an open connection through the middle Keys passages and at times

can receive an influx of Atlantic Ocean water. The

southern region may also be a source of bay waters to

the coral reef areas of the Florida Keys National Marine Sanctuary (FKNMS).

Circulation of water in western Florida Bay and adjacent coastal regions on subtidal time scales is strongly

influenced by local wind forcing that results in seasonal

flow patterns: southward toward the Keys in winter and

spring, northwestward into the gulf in summer, and

southwestward toward the Tortugas in the fall. Episodic

transport processes can deliver warm, salty water to the

reef tract from Florida Bay in the spring and early

summer. During the winter, cold, turbid water intrusions from Florida Bay can occur.

Research Summary

To date, researchers have documented regional oceanographic and hydrological driving processes. Circulation in the outer portion of Florida Bay, the adjacent

southwestern Florida shelf, and Florida Keys; exchange

between Florida Bay and the Keys coastal zone; the potential pathway for exchange across the western

boundary; and the patterns of salinity variation

throughout the bay and adjacent marine systems are

among those processes. These results were derived

from several extensive observational programs that

have now collected almost 10 years of data on regional

water properties, meteorology, and flow.

By comparison, major uncertainties remain about

circulation within the interior basins, interbasin exchange, flow across the bank tops, the effect of evaporative processes upon bank-top waters, groundwater

Florida Bay Synthesis Hunt and Nuttle

32 FWRI Technical Report TR-11

Figure 4.1 LANDSAT–7 extended thematic mapper image of Florida Bay, showing its shallow bank bathymetry and four principal subregions.

Physical Processes
entering the bay across its northern boundary, and

the quantitative details of exchange across the bay’s extensive and complex western boundary. The hydrological model of surface waters entering northeastern

Florida Bay has been improved over the past few years,

and progress has been made on expanding the model

to the entire northern boundary and the lower southwestern shelf including the Shark River slough. However, we still do not have an adequate hydrodynamic

model of the interior of Florida Bay.

As a result, our ability to rigorously forecast

changes in salinity within the bay resulting from

planned modifications in upstream water management is inadequate. Nonetheless, a water budget has

been developed for Florida Bay based upon long-term

(31 years) salinity data.The budget takes into account

seasonal and interannual variations in the supply of

fresh water (Nuttle et al., 2000). A depiction of the climatic cycle of surface runoff, evaporation, and precipitation over the 31-year period is shown in Figure

4.3. Across the whole bay, discharge from the estuarine creeks amounts to about 2 cm/year, or about 20%

of the annual rainfall. In the northeast region, where

the majority (98%) of the creek discharge enters the bay,

creek discharges amount to about 67% of the annual

rainfall. Similar to the 31-year average, the majority of

the freshwater inflow is now concentrated in the northeastern part of the bay and has a major influence on

salinity variations therein, effectively inhibiting hypersalinity. Conversely, the lack of freshwater flow to

the central bay exacerbates hypersalinity.

Higher discharges through the Shark River slough

and higher water levels in the southern Everglades

could redistribute freshwater input to the bay and

could provide greater input to the central basins in

particular. Integrated hydrological/hydrodynamic models incorporating the most recent observational data and

process-study results linked to appropriate regional/boundary hydrodynamic and atmospheric models are required to rigorously address the most central

management concern: what salinity distributions will

result from various upstream water-management alternatives.This has become a principal objective of the

Florida Bay and Florida Keys Feasibility Study (FBFKFS).

The principal findings are summarized below and

relevant citations are enumerated in Table 4.1.

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 33

Figure 4.2 Schematic representation of the average flow patterns in the interconnected south Florida coastal circulation system.The single

arrows represent mean current directions, whereas the double arrows represent the Loop Current and the Florida Current.

Physical Processes
SALINITY

• Historical salinity data and salinity proxy data show

that large salinity changes are not yet understood.

Those changes have commonly taken place in Florida

Bay seasonally, interannually (the El Niño/Southern

Oscillation, ENSO), decadally (the North Atlantic

Oscillation, NAO), and for even longer periods.

• Historical data from the salinity synthesis database

(Robblee et al., 2001) show that Florida Bay has behaved as a marine lagoon for the past several

decades. Salinities have reached as high as 70 psu in

the central bay on a few occasions and typically exceeded 40 psu during drought years such as

1989–1990. For example, following the wet period of

1994–1995, salinity increased until tropical storms in

1999 induced a decrease, which was followed by another increase during the drought years of 2000 and

2001. Recent data from 2000–2002 indicate that Florida

Bay salinity may again be on the rise.

• Variability of Florida Bay average salinity is directly

related to the net flux of fresh water from the combined influence of evaporation, precipitation, and

runoff. For the bay as a whole on seasonal or annual

time scales, evaporation is approximately equal to

precipitation, while runoff is roughly 20% of either.

• Recent studies have narrowed the range of evaporation to around 75–180 cm/year.

• Shallow banks, which restrict water exchange, tend

to separate the bay’s interior into three regions with

distinct salinity variations. The northeastern basin

is the most isolated from oceanic influences, receives most of the surface runoff, and has the largest

seasonal cycle of salinity.The central basin receives

little runoff and has the highest salinity. The western basins have the greatest oceanic exchange and

the smallest seasonal change in salinity.

• Continuous surveys of the bay’s salinity patterns

show large spatial gradients coinciding with the

wide, shallow banks that tend to inhibit interbasin

exchanges.

FRESHWATER INPUT

• Stable isotopic markers indicate that the dominant

source of fresh water for northeastern Florida Bay is

Everglades runoff, whereas for the western region,

precipitation has a stronger influence. In the central

region, a mixture of runoff and precipitation provides

the fresh water.

• Measurements and modeling (both hydraulic and regression) of surface inflows to the bay from the Everglades continue to improve. These analyses show

that there have been increasing inflows to Taylor

Slough and the C-111 canal since 1985 as a result of

management activity.

• Trout Creek contributes the largest volume of fresh

water to northeastern Florida Bay, varying from –6

to 32 m3

/s. By contrast, the flow from each of the other

eight creeks ranges from –1.4 to 6 m3

/s. Negative

flows can occur during the dry season and storm

events.

• For the Ten Thousand Island region of the western

Everglades, the mean annual river discharge is estimated at 13.3 m3

/s for Harney River, 11.0 m3/s for

Broad River, and 12.4 m3

/s for Shark River.

• Shark River’s low-salinity plume waters are commonly advected southward around Cape Sable to

western Florida Bay and the Keys reef tract by winddriven coastal flows.

• Groundwater inflows are believed to be most influential along the northern boundary of the bay; however, estimates of the volume of this flow range over

four orders of magnitude. New measurements and

hydraulic modeling should help to put bounds on the

inflow estimates.

CIRCULATION AND EXCHANGE

• The entire south Florida coastal system, consisting

of the southwestern Florida shelf, the Florida Keys

reef tract, and western Florida Bay, is highly connected by local and oceanic circulation patterns responding to wind and boundary-current forcing.

• Large-volume, wind-forced flows through the Keys

passages provide linkage for gulf-to-Atlantic exchange

through the open western region of Florida Bay.

• Measurement of sea level slopes across the Florida

Keys provides a tool for monitoring gulf-to-Atlantic

transports of heat, salt, nutrients, and toxic algae toward the reef tract.

Florida Bay Synthesis Hunt and Nuttle

34 FWRI Technical Report TR-11

Figure 4.3 Average seasonal rainfall, runoff, evaporation, and net

freshwater gain/loss in Florida Bay (Nuttle, personal communication).

Physical Processes
• Seasonal cycles in local wind forcing produce seasonal patterns in circulation pathways, connecting

south Florida coastal waters through western Florida

Bay and transporting Everglades freshwater

discharges. Southward flows through the Keys passages predominate in winter and spring, northnorthwestward flows in summer, and southwestward

flows toward the Tortugas in the fall.

• Seasonal cycles in south Florida coastal current systems provide seasonal pathways for local larval recruitment and opportunities for recruitment from

remote sources.

• The south Florida coastal region is surrounded by an

intense, large-scale oceanic boundary current (the

Loop Current–Florida Current system) and its evolving eddies that link local coastal waters to remote upstream river sources in the Gulf of Mexico.

PREDICTION

Steady progress has been made toward developing a

predictive capability for salinity and circulation changes

in Florida Bay and connecting coastal waters.

• Two-dimensional hydrodynamic models with coarse

grids have been developed for Florida Bay as pilot

projects by J.Wang (finite element) and J. Hammerick

(finite difference). The results are encouraging because the model outputs of salinity fields are similar to observed salinity patterns.

• Better estimates of surface and groundwater inflows

are available from recent measurements and hydraulic-model results of the United States Geological Survey (USGS) and the South Florida Water

Management District (SFWMD).

• Improved estimates of evaporation are available

from recent studies by R. Price, P. Swart, W. Nuttle,

and N. Smith.

• Improved estimates of precipitation patterns and

quantities are available from calibrated Next Generation Radar (NEXRAD) measurements (P. Willis).

• Measurements of interior-basin circulation and exchange processes are available to improve understanding of bay dynamics, quantify residence times,

and help to validate and improve hydrodynamic

models (T. Lee, E. Johns,V. Kourafalou, and N. Smith).

• Modeling Terms of Reference (MTR) were established by the Physical Science Team (PST) and approved by the Program Management Committee

(PMC).

• A Standard Data Set has been established for model

use (J. Pica).

• An interagency, nested-model program has been

formulated using regional hydrodynamic and hydrological models to provide boundary conditions

for the Florida Bay model (SFWMD, USGS, and the

National Oceanic and Atmospheric Administration

[NOAA]).

Driving Processes

Winds and Storms

Winds in south Florida, including Florida Bay, follow

a regular seasonal pattern: weak southeasterly winds

and daily sea breezes in summer, persistent northeasterly winds in fall, and the regular passage of cold

fronts causing moderate increases in wind speed and

a clockwise rotation of wind direction during the winter. During hurricane season (summer–early fall), the

persistent southeasterly tradewind and sea breeze

pattern can be interrupted by the passage of tropical

storms, often resulting in substantial increases in wind

speed, precipitation, and runoff, which can flow directly into the central basin. Due to the absence of significant topography in south Florida, winds overall

are highly coherent across the bay, with the exception

of locally intense convective events. Low-frequency

wind stress varies seasonally (Smith, 2002). Because

low-frequency scatter about the monthly mean is an

important measure of wind forcing, this seasonal variability is significant.

Recent measurements indicate that there is a significant response of the salinity patterns, sea level,

currents, and turbidity of Florida Bay and adjacent

coastal waters to wind forcing associated with the passage of even relatively weak tropical cyclones (Johns et

al., 2001b; Hurricane Georges Workshop report,

http://www.aoml.noaa.gov/flbay/hurgeocoverpage.

html). Based on results from several research efforts

at different locations, the effect of storms on water

levels in the Everglades and in Florida Bay and the

freshwater flow response after storms pass has been

characterized (D. Smith, 2001; Johns et al., 2001b; Smith

et al., 2001).

Mattocks (personal communication) used a version

of the Advanced Regional Prediction System (ARPS)

mesoscale atmospheric weather prediction model reconfigured to match South Florida Water Management

District (SFWMD) models at a 3.2-km resolution and included land use and soil types. His model shows

mesoscale structures in wind, evaporation, and precipitation fields that are associated with land use and landsea interactions, including the sea breeze. Strong,

divergent downdraft outflows that occur beneath thunderstorms and over the Florida Keys appear to produce

their own sea-breeze convergence fronts.The different

soil types and land uses, together with the spatial patHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 35

Physical Processes
terns in the wind fields, determine spatial patterns in the

evaporation and precipitation fields over south Florida

and the surrounding waters, including Florida Bay.

Indications are that we are entering a period of enhanced Atlantic hurricane activity (Goldenberg et al.,

2001) and that the prior two or three decades represented

a period of diminished activity.The difference apparently

reflects a multidecadal climatic oscillation. If the assumption is made that the probability of a tropical storm

affecting south Florida is directly related to overall activity, then Florida Bay is more likely to be affected by

a storm than it has been for several previous decades.

Goldenberg et al. (2001) suggested that this pattern is

likely to continue for an additional 10 to 40 years.

Precipitation

South Florida in general, including Florida Bay, has pronounced dry (winter-spring) and wet (summer-fall)

seasons. Nuttle et al. (2000) used 31 years of historical

data to show that the seasonal rainfall pattern for the

bay as a whole is nearly balanced by bay-wide evaporation. The distribution of rainfall is highly heterogeneous due to the dominance of local convective

events, sea-breeze convergence, and to variations

caused by urban development effects known as “desertification”(Pielke et al., 1999). However, significant

climatic variability is possible and has been documented within the period of record of the ongoing

monitoring.

Trimble et al. (2001) indicated that low-frequency

meteorological modes associated with ENSO and the

Pacific Decadal Oscillation can also have significant effects on south Florida rainfall and freshwater supply

variability. For example, Johns et al. (2001a) have shown

that the El Niño of 1998 reversed the seasonal rainfall

pattern over south Florida, causing a winter-spring

wet season and a summer-fall dry season.

There is excellent agreement between independent

data set tests that used NEXRAD radar and rain gauges

(Willis, 1999). Cumulative rainfall distributions are

nearly identical except for the highest rainfall rates.

Radar-estimated rainfall distributions provide the high

resolution needed to resolve spatial patterns over

south Florida and Florida Bay. This NEXRAD precipitation product, done on a research basis for two years,

has now been mapped to the SFWMD grid and is

archived at SFWMD.These efforts have paved the way

for an operational rainfall-distribution product that

can be input to atmospheric models.

Evaporation 

Evaporation in marine systems is a function of air and

water temperature differences, specific humidity, and

wind speed. Although winds are highly coherent across

the bay, ongoing studies suggest that there are significant spatial differences in evaporation minus precipitation (E – P) (Price et al., 2001). Recent estimates of

evaporation in Florida Bay were derived using a variety of independent methods and the comparison of

those results is encouraging.

Nuttle et al. (2000, 2001) estimated that bay-wide annual evaporation, based on calibration of steady-state

box models that used historical salinity data for each

of four regions in the bay, was 110 cm. Pratt and Smith

(1999) estimated annual evaporation to be 73 cm by

using a Dalton Law formula. Subsequent to this study,

Smith (2000) refined the application of the Dalton Law

approach by including the effect of increasing estimated

annual evaporation. On the other hand, estimates

based on surrogate data differ by up to a factor of

three. Evaporation-pan data are available for several

years from Flamingo, a site located on the northern

shore of the bay. The average of these data is 210

cm/year (National Climatic Data Center, http://www.

ncdc.noaa.gov), which appears to be too high to accept

directly as an estimate of evaporation in the bay.

A distinct seasonal cycle underlies the mean annual water loss, with a maximum in late summer and

a minimum in mid winter. Calculations using the Long

Key C-MAN data in bulk aerodynamic formulas indicate average evaporative water losses of approximately

0.7 cm/day in September and October and approximately 0.3 cm/day in December and January. Unpublished data from this 15-month study (N. Smith,

personal communication) indicate a mean daily evaporative water loss of 0.5 cm and a total annual water loss

of approximately 180 cm.Therefore, reliable evaporation estimates appear to be converging upon the 75–180

cm/year range, but more research is required to confirm this amount.

Surface-Water Input

A significant amount of surface water enters Florida Bay

directly only along its northern boundary with the

southern Everglades and is concentrated at present in

the northeastern region. Fresh water occasionally enters the central bay directly if there is enough rain. For

example, during and after Hurricane Irene, fresh water

from the Everglades was able to flow over the Buttonwood Embankment (Johns et al., 2001a).

Freshwater runoff enters principally through natural channels cut through the mangrove and buttonwood-confining berms (Hittle, 2001; Hittle et al., 2001).

USGS measurements indicate that Trout Creek contributes the largest annual discharge of fresh water into

Florida Bay Synthesis Hunt and Nuttle

36 FWRI Technical Report TR-11

Physical Processes
northeastern Florida Bay, varying from about 110,000

to 190,000 acre-ft/yr (4.3 m3/s to 7.4 m3/s). By contrast,

the annual discharge from each of the other eight

creeks varies between 10,000 and 45,000 acre-ft/yr (0.4

m3/s to 1.8 m3/s). Negative flows over the mangrove embankments can be caused by storm events, and net negative monthly average flow, which usually lasts for

several months, occurs in all creeks during every dry

season represented by the data.

Cable et al. (2001) reported on the relationship between precipitation and inflow into Florida Bay, finding that fall and winter storms cause pulses of

freshwater inflow, with the flow in Taylor Creek showing a marked response to the storms. Typically, water

levels in the Everglades were found to be highest in

early fall and lowest in the winter. Tropical storms

cause the water levels in the Everglades and Taylor

Slough to rise relatively rapidly and then recede slowly

after the storms pass. The water level’s rise is on the

order of hours, whereas the fall is on the order of

weeks. During the winter, northeasterly winds drive

water out of Taylor Creek into Florida Bay.

Stable isotopic markers have identified the principal sources of fresh water in various regions of the

bay (Swart and Price, 2001). Freshwater inputs to northeastern Florida Bay are dominated by contributions

from Everglades runoff. Rainfall has a strong signal in

the west, and both rainfall and runoff provide fresh

water to the central portion of the bay.

Surface freshwater inputs from the rivers of the

southwestern coast of Florida (primarily the Broad,

Harney, and Shark rivers) may also be significant to

Florida Bay, particularly in its western region. Levesque

and Patino (2001) reported measurements of water

level, velocity, specific conductance, and temperature

in each of these three rivers during the calendar year

1999. Discharges from the three rivers are influenced

by the semidiurnal tides, wind, and freshwater flows

from the watershed. All three rivers are well mixed, with

very little vertical gradient except near the coastal

front.The only evidence of stratified, bidirectional flow

is around the time of slack tide. Instantaneous discharges ranged from –2,400 to +3,500 cfs (–68 to +99

m3

/s) in the Broad River, –15,600 to +12,900 cfs (–442 to

+365 m3/s) in the Harney River, and –10,100 to +10,500

(–286 to +247 m3/s) in the Shark River. When tidal effects have been filtered from the data, the residual

flows ranged from –900 to +2,500 cfs (–25 to +71 m3/s),

–3,600 to +5,700 cfs (–102 to 161 m3/s), and –2,300 to

+4,400 cfs (–65 to +124 m3

/s) for the Broad, Harney,

and Shark rivers, respectively. Mean annual residual

discharge values have been reported to be 400 cfs (11

m3/s or 284,000 acre ft/year) for Broad River, 440 cfs (12.4

m3/s or 320,000 acre ft/year) for Shark River, and 470

cfs (13.3 m3

/s or 343,000 acre ft/year) for Harney River

(Levesque and Patino, 2001).

Groundwater Input

Anecdotal or historical information suggests that prior

to water management, groundwater inputs to south

Florida estuaries like Biscayne Bay and Florida Bay

were significant. At present, because of lowered water

tables and the intrusion of seawater into the coastal

aquifer, fresh groundwater may be prevented from

discharging directly into Florida Bay. However, groundwater may be passing from the Floridan aquifer into

the surficial aquifer and then into Florida Bay. Because

the Floridan aquifer is saline, the discharging groundwater would be saline, not fresh. This hypothesis is

supported by geophysical measurements in the southern portions of Everglades National Park (ENP) between Flamingo and U.S. 1 that indicate that the aquifer

is saltwater-saturated from the surface to a depth of at

least 15 m (Fitterman et al., 1999; Fitterman and DeszczPan, 2000, 2002). Results from the integrated surfacegroundwater model of the southern Everglades suggest

that groundwater seepage beneath the Buttonwood

Embankment may be allowing brackish water from the

Everglades to discharge into northeastern Florida Bay

(Langevin et al., 2002). Model results suggest that surface water can be impounded on the north side of the

embankment, creating a hydraulic drive for groundwater discharge into Florida Bay. However, data are

lacking to support these model results.

Vosburg et al. (2001) reported on surface water and

groundwater measurements taken at two locations in

the dwarf mangrove wetlands along Taylor Creek near

its mouth at Florida Bay. The water level of surface

water and groundwater were measured at both sites.

Surface-water levels demonstrated a relatively rapid

response to rainfall, runoff, tide, and wind, whereas the

groundwater response was less rapid. However,

groundwater response times were different at each

site, which was attributed by the authors to the differences in sediment type.

Price and Swart (2001) provided recent additional information about the role of groundwater in the hydrologic regime of Florida Bay and the adjacent areas of the

Everglades. The extent of saltwater intrusion into the

surficial aquifer increases from east to west, extending

about 6 km inland along the C-111 canal basin to about

20–28 km inland at Shark River Slough (Fitterman and

Deszcz-Pan,2000,2001).Groundwater may be discharged

into the overlying surface waters of the Everglades within

this strip, which more or less parallels the coastline. An

empirical calculation of groundwater discharge yields

values of about 0.04–0.175 cm3

/day.

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 37

Physical Processes
Top and Brand (2001) also recently studied groundwater in Florida Bay. They used anomalies in the dissolved helium concentrations in groundwater to

estimate groundwater inputs to Florida Bay.These authors used a box model to estimate that the input of

groundwater to Florida Bay was 2.5–4.0 cm/day in the

summer and 10–16 cm/day in the winter. Radon-data

estimates yielded a groundwater flux of 0.8–1.7 cm/day.

According to Top and Brand (2001), saline water from

the Florida aquifer is under artesian pressure and is rising through breaks in the confining layer, where it

mixes with the shallow aquifer before entering Florida

Bay.This two-layer structure of the aquifer system explains the difference between the helium and radon

flux estimates.

Note that the radio-isotope values convert to hypothesized groundwater inflows of 575 to 3,680 m3

/s.

Based on these results, if true, groundwater would appear to be a significant source of saline water to Florida

Bay. However, these estimates have large differences

and appear to conflict with mass-balance water-budget estimates and the observed large seasonal salinity

variations.

Sea Level and Tides

Sea level variability in Florida Bay is controlled by

wind and tidal forcing, strongly modified by topography and coastline (Wang et al., 1994). Regional sea

level is thought to have risen rapidly in the last century

(Maul and Martin, 1993; see also the Key West sea

level record from 1913 to present, available from the National Climatic Data Center [NCDC]), but the implications of that observation are not addressed here.

Differences in sea level between basins and across

tidal passages can be a dominant factor controlling

flow and renewal of bay waters.The diurnal tide of the

Gulf of Mexico combined with the semidiurnal tide of

the Atlantic results in a mixed tide.This results in the

largest tidal ranges south of Savannah, Georgia, for the

region near the mouth of the Shark River (>2 m at

spring tide). Measurements at East Cape indicate a

mean tidal range of only 75 cm. The mean range is

half that at the southern end of the western boundary,

just north of Marathon. However, the tide entering

the interior part of the bay is strongly damped by the

shoals and mud flats, decreasing the range to just a few

cm in the northeast (Smith, 1997).

Smith (1997) also reported upon spatial patterns of

tidal water-level fluctuations in the interior portion of

Florida Bay and the seasonal pattern of water-level

fluctuations at subtidal frequencies. Wind set-ups of

10–30 cm are observed inside the bay, but the basin-tobasin variations in wind forcing are not well understood

at present. An annual change in sea level of about 30

cm is widespread over the western North Atlantic and

extends into the interior of the bay as well.

Boundary Currents

The Loop Current in the Gulf of Mexico and its extension, the Florida Current in the Atlantic, surround the

south Florida coastal waters and the Keys. Both are part

of the Gulf Stream system, which is one of the strongest

and best-studied western boundary currents. Both currents are complex and can generate eddies and meanders that can affect how the currents interact with Florida

Bay.Together these oceanic currents cause sea level differences across the Keys that can drive flows through

western Florida Bay. Lee and Smith (2002) recently

showed that changes in sea-level slopes across the Keys

are a direct response to tide and wind forcing. They

have suggested a longer period response to Loop Current extensions into the Gulf of Mexico. Wind forcing

affects sea level differently on the Atlantic and gulf

sides of the Keys, causing sea-level slopes that can enhance the exchanges of bay waters with the surrounding regions. The boundary currents and their induced

flows along western Florida Bay can transport river waters and/or algal blooms from remote regions to interact with the bay (Lee et al., 2001, 2002).

Influence of Driving Processes

Salinity

Florida Bay’s salinity varies with time on a wide range

of scales. Bay salinity normally reflects the annual wet

and dry seasons driven by regional precipitation and

temperature patterns but also responds to episodic

meteorological events such as tropical storms and cold

fronts. In addition, Florida Bay salinities are influenced

by interannual El Niño/La Niña cycles and by decadal

variability in precipitation driven by Atlantic Ocean

multidecadal forcing. Variability on all of these time

scales (and even longer scales, the causes of which are

completely unknown) can be seen in historical salinity and “salinity proxy”(i.e., paleoecological) data.

A preliminary analysis of historical data from the

Salinity Synthesis database (Robblee et al., 2001) shows

that for the past few decades, the bay has behaved as

a marine lagoon, with salinities as high as 70 psu reported on a few occasions in central Florida Bay. During drought years, salinity typically exceeds 40 psu

over most of the bay. Estuarine (i.e., mesohaline) conditions are rare in recent history and are associated with

episodic events such as hurricanes and tropical storms

or with other periods of above-average rainfall (e.g.,

Florida Bay Synthesis Hunt and Nuttle

38 FWRI Technical Report TR-11

Physical Processes
1994–1995). Increased water releases from the C-111

canal can also lower salinities across the bay during relatively dry years (e.g., 1983–1985).

Salinity variability is greatest in the northeast and

decreases to the west. Boyer et al. (1997) and Boyer

and Jones (2001) have described a decadal trend in

monthly salinity values collected by Florida International University’s (FIU) Southeast Environmental Research Center (SERC) in Florida Bay from 1989 to 1999.

During that decade, salinity in the eastern, central,

and western regions declined by 13.6, 11.6, and 5.6

psu, respectively.This “trend”was due largely to very

high salinities during the 1989–1990 drought and is

not descriptive of the substantial interannual variability of salinities in the bay. For example, following

the wet period of 1994–1995, salinity increased until

tropical storms in 1999 induced a decrease, and data

from the drought years of 2000 and 2001 indicated that

salinities increased again. More recent data from 2002

and early 2003 indicate another general freshening

trend (see South Florida Program (SFP) Web site at

www.aoml.noaa.gov/SFP for monthly survey maps of

salinity posted by NOAA’s Atlantic Oceanographic

and Meteorological Laboratory [AOML] and the University of Miami’s [UM] Rosenstiel School of Marine

and Atmospheric Science [RSMAS]).

WINDS AND STORMS 

In combination with upstream water-management releases (that are due to flood-control restrictions), storms

can affect salinity by causing pulsed freshwater inflows even in the “dry” season. Tropical storms can

cause Everglades water levels to rise rapidly and then

recede slowly as fresh water seeps down into northeastern Florida Bay. Northeasterly winds drive fresh

water out of the Everglades into Florida Bay. Biogeochemical materials in these freshwater flows follow

similar input patterns (Cable et al., 2001). Higher-salinity water moves from Florida Bay into the mangrove

fringe area for several months during the dry season

in typical years.

Along the southwestern coast of the Everglades,

river discharge is affected by tidal forces, but tidal-forcing effects can be masked by storm events (Levesque

and Patino, 2001).Wind-driven flows can redirect lowsalinity plumes from discharges in the western Everglades into western Florida Bay and the Keys.

Wind-driven currents tend to advect water masses

and realign salinity patterns in the direction of the

flow, causing low-salinity bands of river discharge and

subsequent transport to connecting regions (Johns et

al., 2001b). At present, the extent to which these plumes

exchange with the interior waters of Florida Bay is

unclear.

During the past several years, a number of tropical cyclones have influenced the south Florida region

through intense wind forcing, rainfall, or both. Johns

et al. (2001b), D. Smith (2001), and R. Smith et al. (2001)

recently showed that, although not as intense as in

past periods of cyclone activity, these events caused significant and long-lasting (~months) changes in salinity patterns and turbidity in Florida Bay.

PRECIPITATION AND EVAPORATION

Florida Bay salinity patterns are a function of spatial

and temporal patterns in precipitation, evaporation,

runoff, and exchange with the gulf and Atlantic. Evaporation and precipitation are the two largest components of the Florida Bay water budget, but we lack

good spatial resolution for them.Their respective positive and negative effects upon salinity are addressed

under Driving Processes, above. Interannual variations in salinity appeared to be affected primarily by

fluctuations in rainfall, which not only falls directly into

the bay but also results in variations in the volume of

surface water discharged into Florida Bay from the

southern Everglades.

An annual water budget for Florida Bay has been

constructed using 31 years of salinity, hydrological,

and climate data (Nuttle et al., 2000, 2001). A simulation using a calibrated box model in which runoff was

doubled decreased salinity in the eastern bay, increased variability in the southern bay, but had no effect in the central or western regions of the bay. During

1965–1995, annual runoff from the Everglades was one

fifth of the annual direct rainfall into the bay, and annual evaporation slightly exceeded annual rainfall.

On a seasonal basis, rainfall, evaporation, and runoff

were not in phase, leading to a strong seasonal pattern

of salinity in the bay.

SURFACE–WATER INPUTS 

Surface discharges from Trout Creek and Taylor Slough

significantly affect salinity patterns and variability in

northeastern Florida Bay, where minimum salinity occurs near river mouths and strong gradients occur in

the basin. In the fall, when sea level is relatively high,

interbasin exchange is enhanced, resulting in more

surface fresh water reaching the central basin. The

same can occur directly during tropical storms if the

water table is sufficiently high (see Hurricane Georges

Workshop report available at http://www.aoml.

noaa.gov/flbay/hurgeocoverpage.html). Enhanced exchange and tropical storms help reduce hypersalinity

in the bay’s interior. River discharges, from sources both

remote from and local to Florida Bay can be transported by coastal and boundary currents to different

parts of the south Florida ecosystem for mixing and exHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 39

Physical Processes
change. Under appropriate wind conditions, flow from

rivers along the southwestern Florida coastline can

reduce salinities along the perimeter of the interior bay

and perhaps into its westernmost basins. Clear examples are the transport of the Shark River plume to

western Florida Bay to help buffer salinity in that region (Lee et al., 2001, 2002) and the transport of Mississippi River waters to the Florida Keys (Ortner et al.,

1995). Exchange of surface water discharged into the

western bay with adjacent interior basins is not well

understood at present, and new observations are underway to better resolve these processes.

GROUNDWATER INPUTS

No large-scale effects of groundwater on salinity have

been observed. Observing this input is made more

difficult by the fact that the primary groundwater input

is thought to be saline. However, anecdotal evidence

indicates the existence of local springs, and scientists

in nearby Biscayne Bay have observed similar springs,

at least within a few hundred meters of the shoreline

(J. Proni, personal communication).

SEA LEVEL AND TIDES

At times of high sea level in the fall, especially during

and after tropical storms, overland flow can occur directly into the central basin, thereby reducing hypersalinity (see above). On the other hand, low sea level

can restrict exchange between adjacent basins by minimizing overbank exchange. Runoff to central Florida

Bay is probably more common in the fall tropical storm

season, when annual water levels are relatively high,

but could occur at any time of the year. Higher water

levels may facilitate movement of this fresh water

across banks to the south and west. However, seasonal

or wind-induced high water along the northern boundary may also hinder freshwater flow to the bay by reducing the head gradient.

BOUNDARY CURRENTS

Ortner et al. (1995) and Lee et al. (2001, 2002) have

clearly shown that fresh water from remote sources in

the eastern Gulf of Mexico, transported by boundary

currents, can have a significant effect on the salinity patterns in south Florida coastal waters, including the

westernmost regions of Florida Bay. Boundary currents surrounding south Florida coastal waters can

also change sea-level slopes and gulf-Atlantic flows

through western Florida Bay that enhance bay-water

exchange with adjacent waters.

Circulation

The interior portion of Florida Bay is made up of a

complex maze of shallow basins separated by mud

banks and mangrove islands. The bay is openly connected to the southwestern Florida shelf along its wide

western boundary, but exchange with the Atlantic

coastal zone of the Keys is restricted to a few narrow

tidal channels through the Keys island chain. The

northern boundary is mangrove fringed, with freshwater input in the northeastern region through Taylor

Slough and Trout River.The rapid fall-off of tidal range

with distance from the western boundary and the dramatic increases in salinities observed in the interior

basins indicate poor water exchange between the

northeastern and central portions of the bay with adjacent subregions.

The entire south Florida coastal ecosystem, except

for the interior of Florida Bay, is highly connected by

a regional recirculation system.This regional circulation is driven by the combined forcing of winds, sealevel slopes, oceanic currents such as the Florida

Current and Loop Current, and eddies at the offshore

boundaries (Lee and Williams, 1999; Lee et al., 1999,

2002). Seasonal patterns in wind forcing result in seasonal shifts in the regional circulation system and preferred pathways of exchange between waters of the

southwestern Florida shelf (including the nearshore

waters of the southwestern Everglades and western

Florida Bay) and the waters of the Keys Atlantic coastal

zone. Everglades discharges are typically advected

southeastward along the western boundary of Florida

Bay’s interior and through the channels of the middle

Keys to the reef tract in the winter and spring. They

move toward the Dry Tortugas in the fall and northwestward to the west Florida shelf in the summer, followed by entrainment by the Loop Current and return

to the Keys coastal zone (Lee et al., 2002). Advective time

scales to reach the Keys Atlantic coastal waters range

from one to two months in winter, spring, and fall to

as much as six months in the summer.

WINDS AND STORMS

Coherent mesoscale and synoptic-scale wind forcing

causes alongshore barotropic currents, which are

geostrophically balanced by coastal sea level on either side of the Keys, and cross-Key sea-level slopes that

drive exchange of Atlantic water with Florida Bay water

on daily to weekly time scales. A strong alongshore-current response to alongshore wind forcing was found

for the Keys Atlantic coastal zone (Lee and Williams,

1999) and for the southwestern Florida shelf (Lee et al.,

2002) for synoptic-scale and seasonal-scale winds.The

seasonal pattern of the wind forcing results in seasonal circulation patterns that link the south Florida

coastal waters along the western boundary of interior

Florida Bay (Lee et al., 2002): southward gulf-to-AtFlorida Bay Synthesis Hunt and Nuttle

40 FWRI Technical Report TR-11

Physical Processes
lantic flows in winter and spring, northwestward flows

to the gulf in summer, and southwestward flows toward

the Dry Tortugas in fall.This pattern is clearly demonstrated in the trajectory pathways of Lagrangian drifters

that have been regularly released over the past few

years (Figure 4.4).

Mean cross-shelf flows on the southwestern shelf

and along the western boundary of interior Florida

Bay indicate an estuarine-like circulation. Estuarinelike circulation has offshore flow in the upper layer and

onshore flow in the lower layer, suggesting a response

to prevailing eastward winds and buoyancy-forcing

from freshwater discharges through the western Everglades.

The transient effect that storms have on circulation

depends upon wind strength, direction, and duration.

Large increases in current speeds have been observed

in western Florida Bay and along the southwestern

Florida shelf and the Keys coastal zone with the passage of tropical storms (Johns et al., 2001b).

PRECIPITATION 

Precipitation has not been observed to have any direct

effects upon circulation.

EVAPORATION

Evaporation has also not been observed to have any direct effects upon circulation. However, some anti-estuarine flow (flow toward areas with high rates of

evaporation) presumably results from net evaporation during the dry season.

SURFACE–WATER INPUTS

Surface-water inputs through the small rivers of the

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 41

Figure 4.4 Representative seasonal trajectories of satellite-tracked surface drifters (Lee et al., 2002).

Physical Processes
western Everglades tend to form a low-salinity band in

the nearshore waters that is entrained by coastal currents and transported to western Florida Bay and the

Keys (Johns et al., 2001a). This is a passive response to

existing circulation. The amount of buoyancy-forcing

from these small rivers (5–30 m3/s) appears to be insufficient to produce a dynamic coastal current within

the low-salinity plume. Salinity observations do indicate that freshwater discharges to the northeastern bay

tend to move slowly to the south and west and can

serve as a passive tracer of the bay’s interior circulation.

GROUNDWATER INPUTS

Isotope-derived estimates of groundwater inputs to

Florida Bay vary by several orders of magnitude (see

above under Driving Processes). Efforts are underway

by USGS and SFWMD to resolve this discrepancy by

applying improved hydrological models. Groundwater-forcing is not included in present bay hydrodynamic or water-budget models. It does not appear

necessary for conservation of mass or for simulation

of large seasonal salinity cycles. The between-basin

flows that would result from the higher estimates are

also inconsistent with available intrabasin flow observations.

SEA LEVEL AND TIDES

Water movements occur on time scales ranging from

minutes to seasons to years. Tidal currents often account for a large part of the variation in coastal currents

and are important for local mixing and dispersion of

materials. However, because of the regular reversal

of tidal currents, they are not efficient transport mechanisms over distances larger than a few kilometers. In

the interior of the bay, cross-bank sea-level slopes are

believed to have an important influence on driving

flows between basins and ultimately on residence

times. Subtidal or low-frequency currents, driven by

sea-level slopes caused by wind or offshore boundary

currents, are principally responsible for linking adjacent as well as remote regions to south Florida ecosystems. Cross-Key sea-level slopes drive flows through

the Keys tidal passages at tidal and subtidal frequencies that couple the gulf and Atlantic coastal regions

of south Florida (Lee and Smith, 2002).

BOUNDARY CURRENTS

Although boundary currents are the dominant feature of the regional circulation, their effect is indirect

within Florida Bay. Long-term moored current observations indicate a mean southward flow on the southwestern Florida shelf that can transport eastern gulf

waters, including river discharges from the west Florida

shelf and Mississippi River to the Dry Tortugas and

through western Florida Bay to the Keys coastal zone

(Lee et al., 2002).The origin of the mean flow is not clear,

but the position of the Loop Current appears to influence mean flow magnitude and may be the driving

force.To more fully understand the relevant processes

will depend upon rigorous, calibrated regional model

simulations incorporating field observations and satellite data.

Exchanges with Adjacent Waters 

Exchanges with adjacent waters are related to three of

the driving forces that have been discussed above,

specifically winds and storms, sea level, and boundary

currents. Waters of the interior portion of Florida Bay

interact with waters from two very different continental shelves: the wide, north-south-oriented southwestern Florida shelf to the west and the narrow,

curving Keys coastal zone and its shallow, reef-tract

topography to the east and south.These two shelf regions exchange waters with each other through the tidal

channels between the Keys and with the strong oceanic

currents at their outer edges: the Loop Current in the

Gulf of Mexico and the Florida Current on the Atlantic side of the Keys.There is strong interaction with

the Florida Current by way of eddy processes throughout the Keys shelf domain. It is apparent by looking at

satellite imagery, water-property distributions, and

model results that a similar process occurs along the

outer edge of the southwestern Florida shelf. Recent

drifter trajectories (Yang, 1999) indicate that there is a

discontinuity between midshelf waters in the region

offshore of Tampa Bay that is possibly related to the amplitude of river discharge.

Current measurements by N. Smith (2002) in several channels connecting interior subbasins of Florida

Bay, suggest a generally southward motion of waters

from the north-central region of the bay that seem to

diverge toward the Atlantic and gulf in the southeastern region of the bay. Exchange between basins appears

to be strongly influenced by wind direction as well as

magnitude. Little is known about the physical processes

that regulate water renewal in the bay’s interior or

about the preferred pathways of circulation.

Mean flows through the western boundary of interior Florida Bay (between East Cape and Marathon)

have been roughly estimated from long-term current

observations to indicate an inflow (eastward) of about

1,300 m3

/s in the northern portion and an outflow

(westward) of about 300 m3

/s in the southern region,

giving a net inflow across the section of about 1,000 m3/s

(Smith and Pitts, 2002; N. Smith, 2002). Because 400–500

m3/s of this inflow exits southward through the middle Keys passages, approximately 500–600 m3

/s are

Florida Bay Synthesis Hunt and Nuttle

42 FWRI Technical Report TR-11

Physical Processes
available for transport into interior regions of Florida

Bay. Tidal, subtidal, and long-term transports into

Florida Bay are neither well resolved nor understood.

It is also unclear what portion of the net inflows to the

Florida Bay interior are used to balance mean sea level

rise, account for evaporative water losses, or drive

residual circulation. Observations have also quantified

tidal-period transports (N. Smith, 2002). To some degree, mixing during tidal exchanges must import gulf

and Atlantic water into Florida Bay and export bay

water to the gulf and to Hawk Channel. Further observations and calibrated model simulations are

needed before the net exchange resulting from this

process can be quantified.

WINDS AND STORMS

Wind forcing was found to set up cross-Key sea-level

slopes that can drive large flows into or out of western

Florida Bay (Lee and Smith, 2002). Strong easterly and

northeasterly winds during the fall cause a positive

cross-Key slope and consequently inflow to the bay

from the Atlantic. Gulf-to-Atlantic outflows from the

bay are associated with negative cross-Key sea-level

slopes from southeasterly (summer), westerly (winter),

and northerly (spring) winds.Wind-driven exchanges

through the middle Keys can produce net flows of

1,000–2,000 m3

/s over the duration of the event (typically 1–10 days) for Long Key Channel alone and possibly two to four times this amount of net flow for all

of the middle Keys channels.

Recent current measurements in the main shipping

channel at Key West indicate a net northward flow

into the gulf that appears to be related to the prevailing westward winds and suggests an Ekman response

in the Keys coastal zone (Smith and Pitts, 2002). The

magnitude of this flow has not yet been determined.

However, when combined with the gulf-to-Atlantic

flows in the middle Keys, this information provides an

indication of a possible clockwise recirculation around

the lower Keys.

Subtidal transports through passages in the upper

Keys are much weaker than the middle Keys and appear to be highly influenced by onshore or offshore

winds that may cause a set-down or set-up of water

level in northeastern Florida Bay (N. Smith, 2001).

SEA LEVEL AND TIDES

It is clear that the volume transports through the Keys

passages are produced by cross-Key sea-level slopes

and that low-frequency changes are strongly dependent on wind forcing over the dynamically different

shelf regimes on either side of the Keys.The strongest

flows occur in the middle Keys channels, where the

combined subtidal outflows toward the reef tract can

be as high as 7,000 m3

/s during winter cold-front passages, and inflows to western Florida Bay can reach

2,800 m3/s during fall northeast-wind events.The magnitude of these flows is 100–200 times larger than the

total freshwater inflows to Florida Bay.The mean flow

through the middle Keys passages is estimated to be

approximately 800 ± 100 m3/s toward the reef tract

(Figure 4.5).The cause of the mean flow is uncertain but

appears to be related to the mean sea level difference

between the gulf and Atlantic and may be influenced

by the Loop Current position. A series of investigations

by N. Smith (1998), Smith and Lee (2003), Lee and

Smith (2002), Smith and Pitts (2002), and N. Smith

(2001) have quantified the magnitudes and variability

of the inflows and outflows of Florida Bay through the

Keys tidal passes and across the western boundary in

the gulf transition region.

BOUNDARY CURRENTS

Boundary currents provide the coupling of the gulf and

Atlantic through western Florida Bay via sea level differences and along the seaward edges of the gulf and

Atlantic shelves through eddy and wind-driven exchanges (Lee et al., 2001, 2002). Boundary currents can

transport remote waters, including river discharges, to

near the bay. Eddies shed by these currents and related

dynamic mesoscale features can enhance exchange

between the currents and adjacent shelf regions. Continued monitoring and modeling of boundary currents and their relationship to local circulation and

exchange processes is essential.

Prediction

Observational data alone are not sufficient to predict

salinity patterns, circulation, freshwater input, and exchanges with adjacent waters under different restoration and climatic scenarios. Because of the physical

complexities of the bay, these data need to be complemented by calibrated models, a number of which

are listed below.

Fresh Water Inflow 

To predict salinity, hydrological models that can provide estimated runoff at the hydrodynamic model’s

terrestrial boundary are essential.The freshwater-discharge model must also be able to estimate runoff

under various Comprehensive Everglades Restoration Plan (CERP) alternatives.The USGS has developed

a hydrodynamic transport model to simulate water

flow and salt fluxes through connected surface and

groundwater systems. An algorithm has been developed that synchronizes surface-water tidal-compatiHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 43

Physical Processes
ble time steps with groundwater stress periods and that

assures mass conservation of simulated flux quantities

across the surface-groundwater interface and landsurface boundary in the coupled model (Swain and

Langevin, 2001; Swain et al., 2002). Hydraulic expressions derived from studies of hydrologic processes in

the Everglades have been formulated to link flow resistance, wind stress, and evapotranspiration processes

to the vegetation properties and shallow flows typical

of these low-gradient wetlands. Two applications of

the coupled model have been made that are largely

within the confines of ENP (Figure 4.6).The Southern

Inland and Coastal Systems (SICS) model encompasses the Taylor Slough wetlands, part of the C-111

drainage basin, and subtidal embayments along the

northern coastline of Florida Bay.The Tides and Inflows

in the Mangrove Ecotone (TIME) model encompasses

the SICS model domain, Shark River Slough, other

western sloughs, and subtidal embayments and tidal

creeks along the southwestern gulf coast. Measured

surface-water discharges, water levels, and salt concentrations in tidal creeks; wetland water levels and

flow velocities; groundwater heads and salinities supplemented by subsurface salinity maps; and soil properties are used for model calibration and verification.

Tide levels and salt concentrations along the coast and

discharges and water levels at hydraulic control structures, bridges, and culverts are used to drive the SICS

and TIME simulations. The models simulate flow exchanges and saltwater fluxes between the surface and

groundwater systems in response to these multiple

driving forces, which could be altered based on proposed changes to the system. Insight into flow patterns and salt fluxes, which can be obtained only

through hydrodynamic transport models, is needed to

fully evaluate the potential effect of restoration decisions for the greater Everglades on ecologically sensitive, land-margin ecosystems bordering the northern

coastline of Florida Bay and the southwestern gulf

coast of Everglades National Park.

Florida Bay Synthesis Hunt and Nuttle

44 FWRI Technical Report TR-11

Figure 4.5 Average sub-tidal flow through the middle Keys passages (Lee and Smith, 2002).

Physical Processes
Exchanges with Adjacent Waters

The predictions needed from Florida Bay numerical circulation models can be carried out only with suitable

inputs along their boundaries. These inputs are necessary to introduce the complex interactions that dominate circulation and water exchange between the

shallow bay interior and the adjacent shelf and oceanic

flows.The boundary conditions must cover a range of

time scales to accommodate different types of simulations planned by the inner Florida Bay modeling

teams (interannual, seasonal, and event-oriented simulations). Existing global models are not suitable for this

task because of their coarse resolution and the lack of

flexibility in performing simulations that match currently planned and future Florida Bay modeling activities. Therefore, it is necessary to develop a

regional-scale model that will perform simulations

that are closely linked to interior Florida Bay modeling needs.The regional model must be dedicated to the

computation of the required hydrodynamic fields surrounding the Florida Bay model domain and to the calibration of these fields with observational data. Such

a model, currently under development, applies the

three-dimensional, finite-difference community hydrodynamic model HYCOM (Hybrid Coordinate

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 45

Figure 4.6 South Florida satellite image showing SICS and TIME model domains (USGS).

Physical Processes
Ocean Model, http://oceanmodeling.rsmas.miami.edu/

hycom/) to the coastal waters adjacent to Florida Bay

and the Florida Keys, including the Florida Straits, the

western Gulf of Mexico and the southwestern Florida

Shelf (Figure 4.7).This model is being coupled with an

existing large-scale, coarse-resolution application of

HYCOM that includes the North Atlantic, the Gulf of

Mexico, and the Caribbean.This nested approach ensures the interaction of Florida Bay models with the

Loop Current, Florida Current and related eddies, and

remote sources of river-induced low salinity.

Circulation Models

To understand circulation and exchange within the

interior of Florida Bay, a fully calibrated and verified

circulation model is needed.The growing database of

salinity, currents, volume transports, surface and

groundwater inputs, and atmospheric forcing is rapidly

becoming sufficient to provide comprehensive evaluation and validation of circulation models.To this end,

a Standard Data Set has been agreed upon and is

under development (J. Pica, personal communication).

Florida Bay Synthesis Hunt and Nuttle

46 FWRI Technical Report TR-11

Figure 4.7 A nested-model approach. Planned regional south Florida model area (thick solid line). Thick dashed line marks the Florida

Bay and Florida Keys model area.The oceanic waters surrounding the regional model domain are included within the University of Miami’s

large-scale North Atlantic, Caribbean, and Gulf of Mexico model (HYCOM).

Physical Processes
Indeed, the complexities of Florida Bay demand a suitable modeling approach to properly evaluate possible

future water delivery schemes to the bay. Expertise

and modeling resources are available that can be applied to this problem in a reasonable time frame. However, two particular problems need to be addressed

urgently: (1) the bathymetry, which is not currently

available at the detail needed by the models; and (2)

the appropriate inputs at the boundaries of Florida

Bay models need to incorporate the complex interactions between the shallow coastal areas within Florida

Bay and the adjacent oceanic flows.

Both the bathymetry and the boundary conditions

must be part of an integrated modeling approach that

includes parallel, coupled numerical simulations in

Florida Bay and the adjacent seas.This comprehensive

modeling tool must get underway soon to correspond

with the observational programs and to advise management in a timely manner.

Salinity Models

To understand and predict salinity variability in Florida

Bay, three types of models have been applied: statistical (regression analyses), mass-balance, and mechanistic, the last of which will be discussed below under

Unresolved Questions and Ongoing Research, Hydrodynamic Models.

STATISTICAL MODELS

The PST subgroup evaluating salinity performance

measures recommended a two-phase plan to develop

updated salinity performance measures to predict

freshwater runoff. First, a multivariable linear regression model that uses lagged terms should be constructed. Second, a time-series model relating the

freshwater flows from the operation of the C-111 canal

to the salinity of the nearshore embayments should be

prepared for use in management decisions. A followup meeting of the group recommended that the use of

Seasonal, Autoregressive, Integrated Moving Average

(SARIMA) models be explored. A preliminary evaluation of current salinity performance measures relating water levels in the Everglades to the salinity in

northeastern Florida Bay has been reported on (Marshall, 2001). Problems with the use of linear regression

models for this data set were identified, particularly seasonality, cross correlation, and autocorrelation of hydrologic parameters. At that time, models and modeling

techniques were not capable of adequately simulating

the effect of changes in operations of the C-111 canal.

A subsequent project for Everglades National Park

evaluated the use of SARIMA models to simulate salinity in the nearshore embayments of Florida Bay using

the Park’s Physical Monitoring Network daily data set

(Marshall et al., 2003).The purpose of the evaluation was

to determine the appropriate statistical models that

could be coupled with the SFWMD South Florida

Water Management Model, also known as the 2x2 (“2

by 2”) model. It was found that multivariable linear regression models were much easier than SARIMA models for coupling with the 2x2 model output. Statistical

models have been developed that were capable of reasonably simulating salinity in the nearshore areas.

Simulated salinities were functions of water levels in

the Everglades and other areas upstream of Florida Bay,

Taylor Slough, and C-111 canal flows; wind; tide; and

rainfall. Improvements to the models are currently

being incorporated, including the potential inclusion

of a term in the model to simulate evaporation.

MASS–BALANCE MODELS

Box models by Walker (1998), Nuttle et al. (2000, 2001),

Cosby et al. (1999), and Twilley (http://www.ucs.

louisiana.edu/~rrt4630/mangrove-restudy.htm) applied mass-balance calculations to the analyses of wetland hydrology, Florida Bay salinity, and the salinity of

Shark River. In each case, these models incorporated

simplified representations of water flow that are parameterized by matching model prediction to observed

hydrology and salinity.

Walker (1998) implemented a set of watershed hydrology models in Everglades National Park. These

were used to estimate water and nutrient fluxes into

the coastal mangroves. The models constructed

monthly water budgets for several wetland basins

based on data provided by the 2x2 hydrology model.

The aggregated discharge from each basin was related

to mean water depth by a generalized power law.The

parameters of this power law were estimated by fitting

simulated water depths to observations. Over the long

term, the mean outflow from the basins must be correct if the data on other terms in the water balance are

accurate. The parameters of the flow model control

the variation of estimated flows around the long-term

mean value. Walker (1998) lacked the outflow data

necessary to validate his watershed models but did find

that predicted outflows were correlated with salinity

in the coastal bays in the Taylor Slough–C111 area.

Nuttle et al. (2001) implemented a mass-balance

model for estimating evaporation in Florida Bay.This

model calculates salinity, using monthly time steps,

from variation in the net supply of fresh water to and

water exchange between each of four regions in the bay,

and water exchange with the Gulf of Mexico. The regions used in this model correspond to the regions defined from similarities in water quality (Boyer et al.,

1997) and other attributes of the Florida Bay ecosystem.

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 47

Physical Processes
Rainfall and salinity data used to drive the model were

measured in the bay. Freshwater runoff was estimated

from measured flows in Taylor Slough and the C111

canal that discharge into the mangrove wetlands north

of Florida Bay. The four-box model by Nuttle et al.

(2001) has been calibrated against salinity data for the

period 1993 through 1995 and validated by comparison

with salinity data for the period 1996 through 1998.The

standard error of prediction is about 2 psu across all

four regions. Calibration of the model produces estimates for the unknown seasonal evaporation rates

and the exchange rates between basins and with the

Gulf of Mexico. These exchange rates can be used to

investigate residence times in the bay, information

that is needed to understand the processes that control nutrient concentrations and plankton blooms.

Nuttle et al. (2000) employed two different box models. One was essentially the annual averaged version of

the four-box model described above, which they used

to estimate mean annual evaporation from Florida Bay.

The other, FATHOM (Cosby et al., 1999), divided the bay

into approximately 40 basins, based on morphology,

and estimated exchanges between basins based on tidedriven hydraulic calculations. FATHOM has been used

to analyze the influence of changing runoff into Florida

Bay (Nuttle et al., 2000), but the calculated exchange

rates and resulting residence times have yet to be validated by comparison with observation.

Twilley (http://www.ucs.louisiana.edu/~rrt4630/

mangrove-restudy.htm) modeled salinity in the Shark

River by using boxes representing upper and lower

reaches along the channel. The model included the

effects of advection, estimated from long-term records

of freshwater flow and dispersion, determined by calibration.This is one of a set of models under development as part of a study of mangrove-forest dynamics.

Unresolved Questions and 

Ongoing Research

Driving Processes

WINDS AND STORMS

Although the synoptic-scale and seasonal winds over

south Florida coastal waters appear to be highly coherent over the whole region, there is now evidence

from high-resolution numerical atmospheric models

(Mattocks, personal communication; Albrecht et al.,

2003) that indicates considerable spatial variability as

a result of mesoscale activity associated with convective systems and sea breeze development. A number

of questions remain: What are the long-term effects of

the daily development of convergent wind patterns

over the bay? What are the magnitudes, spatial, and

temporal scales of this mesoscale wind forcing? How

does it influence the south Florida seascape in terms

of water levels, evaporation and precipitation patterns,

circulation and exchange between water bodies, and

surface and groundwater inflows to the bay? What is

the effect of winds on residence times of the interior

waters of the bay? It is not clear what changes may

occur from intense cyclones, nor how long these

changes may persist. Predictive modeling of different

classes of tropical cyclones is needed to anticipate

these impacts.

PRECIPITATION

Considerable progress has been made with regard to

the process of making precipitation observations into

an operational product. Applicable NEXRAD data

fields have been mapped onto the SFWMD hydrological (2x2) grid and are now archived at the SFWMD. Locally generated statistical functions relating radar

reflectance to tropical convective rainfall are now being

used (Willis, 1999). As a result, we are now ready to address a number of unresolved questions in regard to

precipitation such as: Do the spatial patterns of bay surface salinities measurably change as a result of the

heterogeneity of precipitation? To what degree has

precipitation over the bay been changing because of

land-use changes on the peninsula?

EVAPORATION

Price et al. (2001) described an investigation that is designed to provide mean rates of evaporation and its

variation both spatially and temporally in Florida Bay.

This investigation will be the first systematic attempt

at determining evaporation in Florida Bay and tying

mean estimates of evaporation to longer-term monitoring efforts ongoing in the bay. Questions to be answered by this project include these: What is the mean

rate of evaporation in Florida Bay? What is the spatial

and temporal variation of evaporation? How reliable

are long-term estimates of evaporation? How much additional precision can be gained by refinement of stable isotope methods?

Other questions regarding evaporation include 

• To what degree does the seasonality of evaporation

need to be considered in evaluating the effect that

different salinity patterns have upon water-management scenarios? 

• What is the effect of the bay’s bank-and-basin topography upon evaporation? 

The rate of evaporation over the extensive, shallow

banks may be different from the average estimates

used to date. Neither instrumented-platform meteorological data nor synoptic radiation surveys have

Florida Bay Synthesis Hunt and Nuttle

48 FWRI Technical Report TR-11

Physical Processes
characterized conditions over shallow, seasonally exposed banks. Although the radiation-forcing over the

banks will be the same as elsewhere, the different

characteristics of the water column (shallow) and bottom (dense sea grass) are expected to affect how outgoing heat flux is partitioned, which in turn could

significantly change local evaporation rates.

SURFACE-WATER INPUTS 

Simulation models under construction by USGS and

SFWMD in conjunction with their ongoing measurement programs are expected to resolve any remaining

uncertainty concerning surface-water discharges into

Florida Bay. Hydrodynamic transport models have

been developed that are capable of being linked to

upland-management models to address the effect of

freshwater inflows on tempering salinities and conveying nutrients and contaminants to Florida Bay and

southwest coastal estuaries. Langevin et al. (2002) of

USGS have developed a coupled surface-groundwater model of the southern Everglades that is capable

of simulating flow and salinity patterns in coastal embayments of northern Florida Bay in response to naturally occurring hydrologic events in the wetlands and

the effects of upland-management practices on freshwater releases.The model provides the ability to evaluate the complex exchange and interaction of water and

dissolved salt between the Everglades wetlands, the

Florida Bay estuaries, and the underlying Biscayne

Aquifer. Further enhancements of the model are ongoing, and its computational domain is being extended

to include Shark River, Lostmans River, and other

western sloughs within Everglades National Park south

of Tamiami Trail (Schaffranek et al., 2002). Both models are being developed at temporal and spatial resolutions that are facilitating the formulation of new

estuarine species models (Cline and Swain, 2002) in the

Across Trophic Level Simulation System (ATLSS).

These models will allow researchers and managers to

assess the ecological health of the total ecosystem and

to develop and evaluate performance measures within

CERP (DeAngelis et al., 2002).

GROUNDWATER INPUTS

The discrepancy between isotope-derived estimates

and the more traditional hydrological approaches (well

heads and models) has been discussed above, as has

the discrepancy between mass-balance and flow observations and isotope estimates. Clearly, many unresolved questions remain concerning not only the

absolute amount of groundwater input to Florida Bay

but also its temporal and spatial variability and the

resulting salt and nutrient fluxes. The consensus at

present is that the water-quality implications of groundwater input from either the southern Everglades or

Florida Keys may be more significant than its physical

consequences unless the larger estimates prove to be

correct.

SEA LEVEL AND TIDES

No major unresolved issues remain concerning tides.

Studies are underway concerning the effects of sea

level differences on interbasin exchange and upon

flow through the passages between the Florida Keys.

It is also not clear how long-term sea level differences

between the gulf and Atlantic affect the observed mean

southeastward flow that transports water to the Florida

Keys reef tract.

However, Frederick et al. (1994) and others have

noted an acceleration in local sea level rise over the past

century. The extent of this is not entirely clear nor is

there yet an adequate geophysical explanation. Such

a sea level rise would certainly have implications concerning bay restoration targets. A SFWMD study has

concluded, however, that the currently projected sea

level rise does not substantially affect CERP project

water deliveries.While not precisely a “research issue,”

additional tide gauge benchmarks are needed near

each water-level recorder in Florida Bay and all the gulfcoast stations to obtain absolute sea level measurements. Multiple stations are in place, but many others

remain to be installed.The USGS mapping division and

the USGS St. Petersburg laboratory are currently working to establish elevations at many gulf-coast platforms.

BOUNDARY CURRENTS

Questions concerning the effects of boundary currents are given below under System Characteristics.

Modeling and observational studies are continuing to

address how boundary currents are influencing the

variability of flow through Florida Bay and the exchanges that take place between boundary currents and

adjacent shelf waters.

System Characteristics

SALINITY 

Although the spatial and temporal variability of salinity in Florida Bay is well documented and continues to

be monitored both with field surveys and fixed instruments, a number of unresolved questions remain,

including the following: 

• How is the salinity of Florida Bay influenced by

atmospheric forcing on time scales from daily to interdecadal, including significant transient meteorological events such as hurricanes and tropical storms? 

• How do the spatial patterns of evaporation, precipHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 49

Physical Processes
Florida Bay Synthesis Hunt and Nuttle

50 FWRI Technical Report TR-11

itation, and basin residence time affect bay salinity

distributions? 

• For example, does hypersalinity occur where it does

because evaporation is greater over broad shallow

banks than in the rest of the bay or because exchange with lower-salinity water is restricted? 

• How do the salinity records inferred from paleoecological data compare with salinity values measured over the past 45 years? 

• Is there a statistical transfer function sufficient to adequately describe the effect of freshwater flows on

salinity for the purposes of predicting the effect of

restoration scenarios upon bay salinities? 

• If so, over what spatial domain does it apply? 

CIRCULATION

Circulation and exchange between isolated basins in

the interior of the bay is the subject of several ongoing field research projects and will be a focus of the

forthcoming interior Florida Bay model. Scientists

from RSMAS, AOML, Harbor Branch Oceanographic

Institute, ENP, and USGS have at various times been

maintaining arrays of current, temperature, salinity, and

water-level recorders within basins and channels during wet and dry seasons. Additional observations include shipboard Acoustic Doppler Current Profiler

(ADCP) observations, salinity surveys, and surface

drifter trajectories.These data will be used to directly

compute salt transports, water exchange, and interior

circulation. In contrast, the exchange between the Gulf

of Mexico and western areas of the bay has yet to be

quantified and is one of the principal unresolved questions concerning circulation.

A better understanding of flow across banks, and

bank characteristics in general (e.g., cover, elevation,

salinity, and temperature), will be necessary for successful hydrodynamic and ecological modeling of the

bay’s interior.The bathymetry of Florida Bay, particularly with respect to the shallow banks, needs to be

more adequately described for use by modelers. It is

not clear to what degree remote sensing (e.g., LIDAR)

can be used to address this deficiency, given the density of seagrass. The depth over many of the banks is

approximately equal to or less than the range of seasonal fluctuations in mean sea level. What consequences might this have for rates and patterns of

interbasin water exchange in the interior portion of the

bay? What are the rates and pathways of exchange

between the interior basins and across the banks in the

western, central, and eastern regions of Florida Bay and

with the southwestern Florida shelf?

On a regional scale, very little is known about the

cause of the net southward flow that couples the eastern gulf and Atlantic coastal region of the Keys and its

long-period variations.This flow transports low-salinity discharges from rivers emptying into the southeastern gulf around Cape Sable to western Florida

Bay, where they can interact with interior waters of the

bay as well as with the Atlantic coastal waters of the

Keys. It is essential to better describe and understand

this flow in order to aid future model development and

facilitate informed management decisions. What is

the influence of the Loop Current or synoptic winds

over the west Florida shelf on driving this flow? Are

topographic constraints on the southwestern Florida

shelf important? How is the flow related to observed

southward flows farther north on the west Florida

shelf that appear to diverge from the coast before

reaching the southwest shelf (Yang et al., 1999)?

EXCHANGES WITH ADJACENT WATERS

During the dry season, high-salinity waters from western Florida Bay and the gulf transition region are transported southward toward the Florida Keys National

Marine Sanctuary. There is evidence from the largescale hydrographic surveys that at times these highsalinity waters can form a near-bottom, salty layer in

the Hawk Channel region. However, very little is known

about this process. How are the salty bottom layers

formed? What are their spatial extent and transport

pathways? What are their durations?

Analysis of current records taken in different years

suggest that up to 500–600 m3

/s could be available for

exchange with the interior of Florida Bay. Transports

across the western boundary are very uncertain at this

time; however, field research is planned to improve understanding of transport processes and help quantify

this exchange. There are also unresolved questions

regarding the bank “overtopping”process and whether

this could explain the observed net outflow from the

central part of the bay.

Mean gulf-to-Atlantic flows through western

Florida Bay to the Keys coastal zone and reef tract

have been estimated from observations and are believed to be connected to the boundary currents (Loop

Current and Florida Current) surrounding south

Florida (Lee and Smith, 2002). More effort is needed to

quantify and monitor this mean flow to better understand the physical processes involved. Is it related to

the position and configuration of the Loop Current as

gulf models and satellite observations suggest? Coupling of a large-scale model that includes the gulf and

Straits of Florida to a finer-scale Florida Bay model is

needed to address this issue.

Hydrodynamic Models

Researchers developing and applying mechanistic

Physical Processes
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 51

models have pursued two radically different approaches: the aggregated representation of hydrology

and salinity in mass-balance models, described above,

and the detailed representation of tide and wind-driven water movements in wetland hydraulic and estuarine hydrodynamic models, for example, the RMA-10

model (Kim et al., 1999). The PST reviewed the RMA10 some time ago, but little work has proceeded on it

since that time. The review raised fundamental concerns both in regard to the degree to which the model

was calibrated and verified and also in regard to more

basic issues such as boundary conditions and transport

processes within the bay’s interior (http://www.aoml.

noaa.gov/flbay/pmcphysci.html). J. Wang (personal

communication) recently applied the finite-element

model CAFE3D in 2-D mode with realistic winds and

tides to estimate salinity fields in Florida Bay resulting

from a “climatological” run-off hydrography. Multiyear simulations have been made and show patterns

similar to observations (http://anole.rsmas.miami.edu/

people/jwang/Florida_Bay_Model.html).

The FBFKFS of CERP convened a Hydrodynamic

Model Review Workshop in June 2002, and a Review

Panel was assigned to assess prospects for the successful modeling of Florida Bay hydrodynamics to be

used as a management tool.This panel provided strong

support for the development of a numerical hydrodynamic model because of the need to support waterquality and seagrass modeling of the bay.The panel also

firmly recommended not combining different numerical modeling frameworks (specifically, hybrid mixing of finite-element and finite-difference numerical

grid solutions for hydrodynamic and water-quality

modeling). The panel’s recommendations were generally consistent with the Physical Sciences Team’s

previously issued Modeling Terms of Reference.

During this workshop, the SFWMD described their

exploratory analysis for determining the feasibility

and applicability of a finite-difference model based

on the Environmental Fluid Dynamic Code for Florida

Bay. SFWMD’s Phase I of model evaluation was completed in 2002 and was intended to help provide a

basis for further development and application of a hydrodynamic model for the FBFKFS and other projects.

Phase I was done under contract by J. Hammrick, of

Tetra Tech, Inc. Numerical-model grids were generated,

a five-year calibration data set was synthesized (and incorporated into the Physical Sciences Team’s Standard

Data Set), and the performance of the model was evaluated. Simulations of water-surface elevation, currents, and temperature were judged to be more than

adequate for confidence in long-term prediction of

these quantities. Using the observationally defined

inflows and their associated observed salinities, the

model tended to overpredict salinity, particularly in the

northeastern portion of Florida Bay. This overprediction seemed likely to be due to uncertainties in estimates of freshwater discharge, evaporation, or other

boundary exchanges.

The Phase I final report is currently under review

at the SFWMD. Based on past comments from the

Physical Science Team, the Florida Bay Science Program

Science Oversight Panel, the Feasibility Study’s workshop Review Panel, and information gained from Phase

I, a detailed work plan for Phase II is being written.This

phase will consist of the completion of a validated circulation model for the interior bay that will enable

the SFWMD, the United States Army Corps of Engineers (USACE), and other partner agencies to evaluate potential restoration alternatives as part of the

FBFKFS. The success of this model development and

application will be highly dependent upon inputs from

boundary models, including a regional, oceanic hydrodynamic model for the Gulf of Mexico and Atlantic

boundaries and a regional hydrologic model at the

Everglades boundary.

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Physical Processes
Introduction

Question 2—What is the relative importance of the influx

of external nutrients and of internal nutrient cycling in

determining the nutrient budget of Florida Bay? What mechanisms control the sources and sinks of the bay’s nutrients?

Ecological changes within Florida Bay, including Thalassia testudinum mass mortality and algal blooms,

which have been evident during the past two decades,

have commonly been attributed to many of the same

human activities that have changed the Everglades.The

diversion of freshwater to the Atlantic coast by canals

has increased the salinity of the bay. Freshwater discharges from canals to the Atlantic Ocean were roughly

four times larger than discharges to sloughs that flowed

toward Florida Bay during the 1980s. Additionally, anthropogenic nutrient inputs from the Florida Keys,

Gulf of Mexico, the atmosphere, and the Everglades

may have increased. Inputs from the gulf may include

phosphorus, which is transported by longshore currents

from the central Florida coast, and nitrogen (N), which

originates in the Everglades and flows into the gulf

through Shark River Slough.

The main informational needs relative to nutrient

cycles in Florida Bay is an understanding of the factors

that triggered and maintain the mass mortality of seagrasses and the episodic phytoplankton blooms. Also

critical is sufficient understanding to enable us to assess the effects of various environmental management

strategies being considered for bay restoration. In particular, we need to accurately predict the sensitivity of

the bay’s nutrient cycles to changing freshwater flow

into the bay and to the resultant change in the bay’s

salinity regime. For much of the bay, any factor that increases phosphorus (P) availability either by increasing input or decreasing removal is likely to exacerbate

the current problems of the bay. Recent evidence also

indicates that algal blooms in the central and western

bay are sometimes stimulated by nitrogen (N) enrichment.Thus we need a thorough understanding of the

bay’s nutrient cycles. Questions that the current monitoring and research program must address in order to

meet these needs follow.

The water column in Florida Bay is generally oligotrophic, and phytoplankton biomass has historically

been quite low throughout the system. Although phytoplankton in Florida Bay are generally phosphorous

limited (Fourqurean et al., 1993; Phlips and Badylak,

1996; Lavrentyev et al., 1998), other resources (e.g., light,

nitrogen, silicon) may also be important in controlling plankton biomass in some areas of the bay (Lavrentyev et al., 1998). Dissolved inorganic phosphorous

(DIP) concentrations are near detection limits (20

nmol), but concentrations of dissolved inorganic nitrogen (DIN) can be relatively high (median value 3.3

μmol, but concentrations >10 μmol are not uncommon) and dominated by ammonium (Fourqurean et al.,

1993; Boyer et al., 1997; as summarized in Fourqurean

and Robblee [1999]).

A spatial analysis of data from the monitoring program conducted by Boyer et al. (1997) resulted in the

delineation of three groups of stations (eastern, central, and western) that have robust similarities in water

quality (Figure 5.1). We deem these spatially contiguous groups of stations to be the result of similar hydrodynamic forcing and processing of materials; hence,

we call them “zones of similar influence.”The eastern

bay zone acts most like a ‘conventional’estuary in that

it has a quasi-longitudinal salinity gradient caused by

the mixing of freshwater runoff with seawater. In contrast, the central bay zone is a hydrographically isolated

area with low and infrequent terrestrial freshwater

input, a long water residence time, and high evaporaFWRI Technical Report TR-11 55

Chapter 5

Nutrient Dynamics

Team Leaders Joseph N. Boyer (Florida International University), 

Brian Keller (Florida Keys National Marine Sanctuary, PMC)

Contributors Joe Boyer, Larry Brand, Bill Burnett, Jaye Cable, Paul Carlson, Carl Cerco, Randy Chambers,

Jeff Chanton, Dan Childers, Reide Corbett, Jeff Cornwell, Susan Dailey, Cynthia Heil, Gary Hitchcock,

John Hunt, Ron Jones, Jennifer Jurado, Chris Kelble, Brian Keller, Steve Kelly, Mike Kemp, Gary Kleppel,

Margurite Koch-Rose, Bill Kruczynski, Brian Lapointe, Chris Madden, Bill Mcpherson, Frank Millero, 

Bill Nuttle, William Orem, Ed Phlips, Rene Price, Enrique Reyes, Dave Rudnick, Eugene Shinn, 

Fred Sklar, DeWitt Smith, Richard Stumpf, Peter Swart, Zafer Top, Gabe Vargo, 

Cecilia Weaver, Laura Yarbro, Jia-Zhong Zhang
tive potential.The western bay zone is the most influenced by the Gulf of Mexico tides and is also isolated

from direct overland freshwater sources.

Summary of Knowledge

Research on nutrient dynamics in Florida Bay focuses

on the exchange of nutrients with adjacent regions

(“external”dynamics), the cycling of nutrients within

Florida Bay (“internal”dynamics), and the influence of

these processes on ecosystem structure and function,

i.e., on spatial and temporal variation (Table 5.1). A

continuing program of monitoring and research, including computer modeling, addresses the question of

how human activity is affecting the nutrient dynamics of Florida Bay and how future restoration actions

will alter these dynamics.

• What do we know about status and trends in water

quality over space and time?

° Objective analysis shows that there are three zones

(eastern, central, and western) in the bay that exhibit significant differences in water-quality characteristics due to nutrient inputs, tidal advection,

and water residence time.

° In general, DIP concentrations increase and DIN

decreases from east to west, resulting in a shift from

P limitation to N limitation.

° Central bay waters have high ammonium concentrations, which may indicate a bottleneck in the

process of nitrification.

° Temporal trends over a 13-year period of record

show bay-wide declines in total phosphorus (TP),

total nitrogen (TN), and chlorophyll a and an overall increase in turbidity (cloudiness of the water).

• What do we know about sources and amounts of external nutrient loading to Florida Bay?

° Terrestrial nutrient loading fluctuates with freshwater flow, but flow-weighted concentrations decrease with increasing flow.

° Phosphorus loading from the Everglades is a small

proportion of the Florida Bay nutrient budget.

Most phosphorus (P) appears to be derived from

the Gulf of Mexico.

° Nitrogen output from the southern Everglades

(including Shark River Slough) is a significant

proportion of the Florida Bay nutrient budget

(similar in magnitude to atmospheric loading).

Most nitrogen flowing from the wetlands is in the

form of dissolved organic compounds. Studies on

the bioavailability of dissolved organic nitrogen

(DON) are currently underway.

° The atmospheric input of nutrients is large, and

most atmospheric nitrogen is inorganic.

° Knowledge of the bay’s nutrient budget is coarse

over time and space (annual averaging for entire

bay). Large uncertainty exists regarding the magnitude of nutrient exchange at the Gulf of Mexico

boundary and regarding saline groundwater

sources.

° There is a measurable effect of water management on the quantity and distribution of water

and nutrients through the length of the Taylor

Slough–C-111 basin system, influencing inputs to

Florida Bay.

° A serious disconnect exists between upland/canal

loading estimates and actual input to the bay because of unmeasured nutrient processing in the intervening wetland/mangrove areas.

• What do we know about internal nutrient-cycling

processes?

° Benthic denitrification is higher than expected

based on denitrification: N-loading relationships

in other estuaries.

° The balance of N2 fixation and denitrification in the

bay is highly variable, but there appears to be a net

loss of N in the overall system.

° Sediment regeneration of ammonium under dark

conditions is low relative to benthic dissolved oxygen demand.

° Sediment regeneration of ammonium decreases

with increases in sediment chlorophyll a concentration, indicating that the microphytobenthos is

important in regulating water column N concentrations.

° There is very little, if any, P flux out of the sediments, with the exception of the western bay-shelf

area.

° High rates of organic carbon (C) and N fluxes

occur, both into and out of sediments over diel cycles (particularly in the central and western bay).

° Phosphorus sorption-desorption varies strongly as

Florida Bay Synthesis Hunt and Nuttle

56 FWRI Technical Report TR-11

Figure 5.1 Zones of similar water quality in Florida Bay.

Nutrient Dynamics
a function of temperature and salinity.

° The decreasing bayward gradient in iron content

of sediments has implications in P availability,

sulfide toxicity, and primary production in the

benthos.

° The seagrass community is a major sink for nutrients from either the water column or sediment

pore waters in the bay.

Patterns and Trends in 

Water Quality

A network of water-quality monitoring stations was established in 1989 (and funded by SFWMD in 1991) to

investigate both spatial patterns and temporal trends

in water quality in an effort to elucidate mechanisms

behind the recent ecological change. One of the primary

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 57

Table 5.1 Research topics defined by Question 2 (cells in the matrix) and key references to the associated research.

Research Topics Spatial Variation Temporal Variation

Water-Quality Patterns and Trends Fourqurean et al., 1993; Boyer et al., 1999;

Boyer et al., 1997; Burd and Jackson, 2002

Burd and Jackson 2002

Overall Nutrient Budget Boyer and Jones, 1999; Boyer and Jones, 1999;

Rudnick et al., 1999; Rudnick et al., 1999;

Cerco et al., 2000 Cerco et al., 2000

External Nutrient Loading

Terrestrial Inputs

Everglades Walker, 1998; Rudnick Walker, 1998; Rudnick

et al., 1999 et al., 1999

Mangroves Childers et al., 1999a,b; Davis Childers et al., 1999a,b; Davis 

et al., 2001; Sutula et al., 2001, et al., 2001a,b; Cable et al.,

2003 2001; Sutula et al., 2001, 2003

Keys Kruczynski and McManus, 2002

Atmospheric Inputs Nuttle et al., 2000

Groundwater Inputs Shinn et al., 1994; Corbett et al.,

1999, 2000a,b; Price and Swart

2001

Gulf of Mexico Rudnick et al., 1999

Atlantic Ocean Szmant and Forrester, 1996

Internal Nutrient Cycling

N2 Fixation Cornwell, 2001; Owens and Cornwell, 2001

Benthic Flux Rudnick, 1999; Carlson and 

Yarbro, 1999; Yarbro and 

Carlson, 1999; Chambers et

al., 2001; Yarbro and Carlson,

unpublished

Nitrification/Denitrification Kemp and Cornwell, 2001 Kemp and Cornwell, 2001

Microbial Loop Cotner et al., 2000; Boyer et al., 2006

Boyer et al., 2006

DOM Remineralization Boyer et al., 2006 Boyer et al., 2006

Seagrass Effects on Water Quality Madden and McDonald, 2006; Madden and McDonald,2006;

Madden et al., 2003; Madden et al., 2003;

McDonald et al., 2003; McDonald et al., 2003;

Gras et al., 2003; Gras et al., 2003;

Nielson et al., 2006 Nielson et al., 2006

Higher-Trophic-Level Effects on 

Water Quality

Water Quality Modeling Cerco et al., 2000

Nutrient Dynamics
purposes for conducting long-term monitoring projects

is to be able to detect trends in the measured variables

over time.These programs are usually initiated as a response to public perception (and possibly some scientific data) that ‘the river-bay-prairie-forest-etc. is

dying.’ In the case of Florida Bay, during 1987, the impetus was the combination of a seagrass die-off, increased phytoplankton abundance, sponge mortality,

and a perceived decline in fisheries.

Period of Study

Climactic changes occurring over the data-collection

period of record had major effects on the health of the

bay. Precipitation rebounded from the drought during

the late 1980s and has been greater than the long-term

average (9.2 cm mo–1) for 9 of the past 12 years (Figure

5.2). Early in the record, salinity and total phosphorus

(TP) concentrations declined baywide, while turbidity

increased dramatically.The salinity decline in eastern

and central Florida Bay was dramatic early on but has

since stabilized into a regular seasonal cycle (Figure 5.3).

Some of the decrease in the eastern bay could be accounted for by increased freshwater flows from the

Everglades, but declines in other areas point to the climactic effect of increased rainfall during this period.

The central bay continues to experience hypersaline

conditions (greater than 35 practical salinity units

[psu]) during the summer, but the extent and duration

of the events are much smaller.

Chlorophyll a concentrations (CHLA), a proxy for

phytoplankton biomass, were particularly dynamic

and spatially heterogeneous (Figure 5.4). The eastern

bay generally has the lowest CHLA, and the central bay

has the highest. In the eastern bay, which makes up

roughly half of the surface area of Florida Bay, CHLA

have declined by 0.9 μg l–1 or 63%. Most of this decline

occurred over a few months in the spring-summer of

1994 and has remained relatively stable. The isolated

central bay zone underwent a fivefold increase in

CHLA from 1989 to 1994, and then rapidly declined to

previous levels by 1996. In western Florida Bay, there

was a significant increase in CHLA, but median concentrations remained modest (2 μg l–1) by most estuarine standards.There were significant blooms in the

central and western bay immediately following Hurricane Georges (November 1998), but it was Hurricane Irene’s large rainfall input (October 1999) that

induced a large bloom throughout the bay. It is important to note that these changes in CHLA (and turbidity) happened years after the poorly understood

seagrass die-off in 1987. It is possible that the death and

decomposition of large amounts of seagrass biomass

might partially explain some of the changes in water

quality of Florida Bay, but the connections are temporally disjunct and the processes are indirect and not

well understood.

As mentioned previously,TP concentrations have

declined baywide over the 12-year study period (Figure 5.5). As with salinity, most of these declines occurred

during the early part of the study. Unlike most other

estuaries, increased terrestrial runoff may have been

partially responsible for the decrease in TP concentrations in the eastern bay because the TP concentrations of the runoff were at or below ambient levels in

the bay.The elevated TP in the central bay was mostly

due to high evaporation. It is important to understand

that almost all the phosphorus measured as TP is in the

form of organic matter, which is less accessible to

plants and algae than inorganic phosphate.

The DIN pool is made up of three components: ammonium (NH4

+), nitrate (NO3–

), and nitrate (NO2

–

).The

western bay is lowest in DIN; phytoplankton in this region may be limited by N availability on a regular

basis (Figure 5.6). DIN in the eastern bay is a little

higher and is mostly in the form of NO3

–

, and highest

levels are found in the central bay as NH4

+.

Turbidities in the central and western bay have

increased tremendously since 1991 (Figure 5.7). Turbidity in the eastern bay increased twofold from 1991

to 1993, whereas those in the central and western bays

increased by factors of 20 and 4, respectively. Generally, the eastern bay has the clearest water, which is due

to a combination of factors such as high seagrass cover,

more protected basins, low tidal energy, and shallow

sediments. We are unsure what caused it, but the loss

of seagrass coverage may have destabilized the bottom

so that it is more easily disturbed by winds.

An extensive set of contour maps of water-quality

parameters for Florida Bay is available at http://serc.

fiu.edu/wqmnetwork/.

Recent Conditions

Most water-quality variables during 2001 generally

followed typical annual trends, with one prominent exception. All regions of the bay experienced a proFlorida Bay Synthesis Hunt and Nuttle

58 FWRI Technical Report TR-11

Figure 5.2 Monthly average rainfall in the Florida Bay area,

1991–2005.

Nutrient Dynamics
longed period of hypersalinity during the summer

months. Most of this was due to the previous dry year,

which set up the system for this occurrence.The annual

pattern in CHLA was unremarkable—no blooms reported. Total phosphorus values declined from very

high levels in the fall of 2000 to normal levels in 2001.

The western bay showed elevated DIN during the

early part of 2001 but was not excessive compared

with other years.Turbidity continued to fluctuate above

post-1993 levels. Note that the high turbidities observed in the western bay during the winter also correlated with elevated TP.

NOAA/AOML also has a water-quality monitoring program in Florida Bay. Its primary purpose is to

measure physical aspects of the system (see Question

1), but there is also a nutrient component to the

sampling. An example of this is the analysis of phosphorus (Figure 5.8) using long-path-length liquid waveguide technology from Zhang and Chi (2002).

Exogenous Sources of Nutrients

A budget of Florida Bay’s exogenous nutrient sources,

which was estimated for the 2001 Florida Bay ConferHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 59

Figure 5.3 Monthly median salinity in the three Florida Bay zones.

Nutrient Dynamics
ence, included inputs from the Everglades, wastewater

and storm water from the Florida Keys, saline groundwater, the Gulf of Mexico, the Atlantic Ocean, and the

atmosphere. Results from this exercise, with revision

of the estimated saline groundwater source, are presented in Figures 5.9–5.11.

Nutrient Inputs from the Everglades: 

Taylor Slough–C-111 and Shark River

Nutrient outputs from the Everglades in this budget

have been estimated from inputs to Everglades National Park wetlands from canals as reported by Rudnick et al. (1999).This approach can only be considered

a rough estimate because of nutrient-processing during transport through the southern Everglades. However, these estimates are more likely to be correct than

estimates of most other components of the bay’s nutrient budget.The accuracy of estimates for the southeastern Everglades nutrient outputs is indicated by

results of Sutula et al. (2003).This study found that TN

and TP inputs from the mouths of mangrove creeks into

Florida Bay in 1997 were similar to estimated inputs to

the wetland that year (TN loads differed by 7%, and TP

loads differed by one metric ton per year).

Florida Bay Synthesis Hunt and Nuttle

60 FWRI Technical Report TR-11

Figure 5.4 Monthly median chlorophyll a in the three Florida Bay zones.

Nutrient Dynamics
Studies of nutrient export from Taylor River,Trout

Creek, and McCormick Creek (Sutula et al., 2003; Davis

et al., 2003) have provided insights into the relationship

between patterns of freshwater discharge and those of

nutrient dynamics and output into Florida Bay. Nutrient outputs have been found to increase with increasing

water discharge. As observed for inflows to Everglades

National Park wetlands from canals, this increase is not

linear; flow-weighted mean nutrient concentrations

decrease with increasing discharge (Rudnick et al.,

1999; Figure 5.12). Output of phosphorus to Florida

Bay is mostly as dissolved organic phosphorus, but it

is very low in magnitude. During the dry season, both

suspended solids and phosphorus are imported into

the mangrove ecotone from the northeastern region of

the bay. Output of nitrogen is also largely as dissolved

organic nitrogen, but this quantity is high, resulting in

a very high TN:TP ratio in creek outputs (molar ratio

average near 200).

During the next year, RECOVER (the monitoring

and assessment program of the Comprehensive Everglades Restoration Plan [CERP]) will expand the network of creek discharge and nutrient-sampling stations

to include new sites along Florida Bay’s coastline and

the western Everglades rivers. A total of eight paired

(upstream-downstream) stations are planned, includHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 61

Figure 5.5 Monthly median total phosphorus in the three Florida Bay zones.

Nutrient Dynamics
ing four creeks entering Florida Bay and four rivers entering the Gulf of Mexico. It should also be noted that

the Florida Coastal Everglades Long Term Ecological

Research (LTER) is providing information on nutrient

processing in the southern Everglades and mangrove

zone, with particular emphasis on the formation, transport, and decomposition of dissolved organic matter.

Ground Water

The input of nutrients to Florida Bay via ground water

remains highly uncertain. No new estimates of groundwater flux have been made since the 2001 conference.

At that time, it was evident that subsurface freshwater inputs are negligible. Ground water beneath Florida

Bay and its mangrove ecotone along the Everglades

coast is saline (Reich et al., 2002; Price, 2001; C. Reich

and E. Shinn, personal communication). Thus, fresh

ground water beneath the Everglades that flows toward

Florida Bay appears to rise toward the surface, over

denser saline water, to the north of the bay boundary

(Price, 2001).

In contrast to fresh ground water, significant advection of saline ground water into the bay may occur

from beneath the bay itself. Based on groundwatertracer (radon, methane) concentrations, Corbett et al.

Florida Bay Synthesis Hunt and Nuttle

62 FWRI Technical Report TR-11

Figure 5.6 Monthly median dissolved inorganic nitrogen in the three Florida Bay zones.

Nutrient Dynamics
(1999, 2000a) have estimated a bay-wide vertical

groundwater flow of about 1 cm/d or higher (Top et al.,

2001).The nutrient budget presented at the 2001 Florida

Bay Conference used this value along with nutrient

concentrations of 0.1 μmol TP, 1 μmol DIN, and 10

μmol TN. These concentrations are typical of wells at

pristine sites in the Florida Keys (E. Shinn, personal

communication). However, C. Reich and E. Shinn (personal communication) now report that these concentrations are considerably lower than those found in

wells throughout Florida Bay. Over a four-year period,

concentrations averaged approximately 1.5 μmol TP, 80

μmol TN, and 44 μmol NH4. Still assuming a 1-cm/d

groundwater flow, these higher concentrations would

result in a groundwater nutrient input of 38 MT/y for

TP, 8,800 MT/y for TN, and 5,000 MT/y for DIN. Compared to nutrient inputs from the Everglades, these estimated groundwater inputs are about 10 times higher

for TP, about 6 times higher for TN, and more than 100

times higher for DIN. Some caution may be advised before applying these well-water concentrations because

they may be affected by biogeochemical processes

such as adsorption or denitrification prior to discharge,

thus lowering their input into surface waters.

However, if this groundwater-input estimate of

DIN is accurate, it would represent about 75% of all inHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 63

Figure 5.7 Monthly median turbidity in the three Florida Bay zones.

Nutrient Dynamics
organic nitrogen inputs to the bay. Furthermore, at

such a high concentration, this inorganic nitrogen

would be readily available for algal and submerged

aquatic vegetation (SAV) productivity (in contrast to the

low-concentration input from the Gulf of Mexico). It

should be noted that this estimated groundwater DIN

input is equivalent to 18 μmol m–2 h–1, or roughly half

of the median nocturnal nutrient flux across the sediment–water interface, as measured along the northern Florida Bay coast. It is also roughly equal to the

median nocturnal benthic input found in the interior

bay (P. Carlson, personal communication). The surprisingly high magnitude of the groundwater DIN

input estimate, combined with the fact that ground

water is usually hypersaline, is grounds for skepticism

regarding the estimated 1 cm/d groundwater input as

a rate that occurs commonly throughout the bay.This

does not, however, preclude the possibility that large

inputs of ground water occur at some locations in the

bay, particularly near the Keys (see below).

An additional source of uncertainty in groundwater input is the depth from which the ground water is

advected. For example, advective flow through surficial sediments can be caused by current-induced gradients over topographic expressions such as sand

ripples (Huettel and Gust, 1992). Presumably, flow over

Florida Bay Synthesis Hunt and Nuttle

64 FWRI Technical Report TR-11

Figure 5.8 Water column phosphate concentration in Florida

Bay.

Figure 5.9 Estimates of the annual exchange of total phosphorus

at Florida Bay’s boundaries. Everglades estimates are annual median inputs to wetlands from canals (since 1979 for Shark Slough

and since 1984 for Taylor Slough and the C-111 basin).

Figure 5.10 Estimates of the annual exchange of TN at Florida

Bay’s boundaries. Everglades estimates are annual median inputs

to wetlands from canals (since 1979 for Shark Slough and since

1984 for Taylor Slough and the C-111 basin). Note that flowweighted mean TN concentrations have been consistently decreasing since 1985 in both systems and that medians provided here

may be higher than those of recent years.

Figure 5.11 Estimates of the annual exchange of inorganic nitrogen

at Florida Bay’s boundaries. Everglades estimates are annual median inputs to wetlands from canals (since 1979 for Shark Slough

and since 1984 for Taylor Slough and the C-111 basin).

Nutrient Dynamics
banks, corals, or a host of other features could set up

such shallow, subsurface flows. Flow through the

seafloor caused by currents flowing over topography

or waves may be responsible for the elevated tracer concentrations in the water column.The nutrient concentrations of these advected waters are probably lower

than those sampled in wells and thus would lower the

estimates of nutrient flux from groundwater flow.

An additional mechanism that can drive groundwater flow is the difference in tidal elevations across

narrow reefs or barrier islands (Bokuniewicz and Pavlik,

1990; Reich et al., 2002; Chanton et al., 2003). Observations of seepage in the Upper Keys are consistent with

this hypothesized mechanism (Chanton et al., 2003). On

an annual average basis, the water level in Florida Bay

is several cm higher than the water level in the Atlantic

(Reich et al., 2002). However, the Atlantic has a daily tidal

range of roughly half a meter, whereas daily water

levels in Florida Bay are relatively constant.Therefore,

during a high Atlantic tide, the ocean level is higher

than the bay’s water surface, creating a pressure differential pushing water from the Atlantic toward

Florida Bay. In contrast, when the Atlantic tide is low,

the situation is reversed, and there is a pressure differential pushing ground water from Florida Bay toward

the Atlantic (Reich et al., 2002).

The porous nature of the Key Largo Limestone

that underlies the Upper Keys is consistent with this

delivery of ground water to Florida Bay by this tidalpumping mechanism. Studies employing viral and

chemical tracers have documented horizontal and vertical transport rates of meters per day for water flow

in the subsurface (Dillon et al., 1999, 2000, 2003; Paul et

al., 1995, 1997, 2000; Lapointe et al., 1990; Reich et al.,

2002). Hydraulic conductivity in the Key Largo Limestone ranges between 1,400 and 38,000 meters per day

(Dillon et al., 1999; Vacher et al., 1992). Dillon et al. (1999)

followed water-table height as a function of Atlantic tide

in an onshore well on Key Largo. In this well, the

groundwater table oscillated with Atlantic tide with

only a 1.4-hour lag between Atlantic high tide and the

highest water level in the well (Dillon et al., 1999).

There was only a 60% dampening of the tidal amplitude as the pressure wave moved through the carbonate rock.The extremely transmissive nature of the

Keys aquifer system, in conjunction with the varying

head differentials, promotes the interaction of subsurface waters with surface waters.

Ground waters in the shallow subsurface of the

Keys contain dissolved nutrients from organic materials disseminated within the matrix (Sansone et al.,

1990) and are further contaminated from on-site

sewage-disposal systems. Sewage in the Florida Keys

is discharged into more than 600 disposal wells that

penetrate the permeable Key Largo Limestone to

depths of 10–30 m. Additionally there are an estimated

24,000 septic tanks and 5,000 cesspits on the islands

(Kruczynski and McManus, 2002). Recent research has

demonstrated a direct interaction between waste water

delivered to the subsurface via injection wells and surface waters (Corbett et al., 2000b; Dillon et al., 1999,

2000, 2003). Natural tracers, including 15N of seagrass

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 65

Figure 5.12 Relationship between TN and TP concentrations (annual flow-weighted mean) in waters flowing into Shark River Slough

and annual water discharge into the slough.

Nutrient Dynamics
tissue, have indicated that the greatest impact of

groundwater discharge is along the shore of the Florida

Bay side of the Upper Keys (Corbett et al., 1999). Nutrient inputs from Keys ground water may be dominated by wastewater inputs and so are considered in

the next section.The associated nutrient load to coastal

waters would be substantial without significant subsurface biogeochemical alteration.This is particularly

true with respect to phosphate delivery, which has

been shown to be the limiting nutrient in eastern

Florida Bay. Studies of the fate of nutrients injected into

Class 5 wells in the Keys suggest phosphate removal

with moderate nitrate attenuation (Corbett et al., 2000b;

Dillon et al., 2003). Although it is understood that phosphate may be removed during transport, it is not clear

whether this removal will be sustained. One question

of particular importance is whether the phosphate

may be released at some point to the phosphorus-limited waters surrounding the Keys, thus creating a significant water-quality problem for the marine

environment. If phosphate uptake is ephemeral, then

long-term transport of phosphorus to coastal waters

may occur through the limestone aquifers. There is

some evidence that the limestone surrounding Class

5 injection wells may saturate with phosphorus (Dillon et al., 2003).

Atmospheric, Keys Waste Water, 

Keys Storm Water, and the 

Gulf of Mexico Nutrient Inputs

The remaining components of the Florida Bay nutrient budget (atmospheric, Keys wastewater and storm

water, and the Gulf of Mexico) have not been revised

since the 2001 conference. Atmospheric deposition is

certainly an important nutrient source, particularly

with regard to the relatively high input of inorganic nitrogen. The estimates in Figures 5.9–5.11 are derived

from a study by T. Meyers in 1999 and 2000 on Long Key

(T. Meyers, personal communication). Although bulk

deposition of nitrogen can be estimated from a longterm National Atmospheric Deposition Program

(NADP) site in Everglades National Park, few data are

available to estimate dry deposition of nitrogen or

phosphorus. Furthermore, phosphorus estimates in

south Florida are often suspect because of the contamination of low ambient concentrations (Redfield,

2000). Estimates of the Florida Keys and Gulf of Mexico contributions are based on methods and data described in Rudnick et al. (1999). The Keys estimate

entails far less uncertainty than the gulf estimate. It

should be noted that the gulf contribution provided

here (Figures 5.9–5.11) probably overestimates inputs

to interior Florida Bay because the flow meters that produced the data used in the calculation were west of

Florida Bay’s mud banks. A large proportion of water

flow measured by these flow meters never entered the

bay. It should also be noted that a large discrepancy between the estimates of Rudnick et al. (1999) and Cerco

et al. (2000) exists.The latter estimate was based on flow

fields derived from a hydrodynamic model (Table 5.2).

Summary

The major source of TP and TN was the Gulf of Mexico (Figures 5.9, 5.10) and the major source of DIN was

ground water (Figure 5.11). The smallest source of TP

was Taylor Slough–C-111 (Figure 5.9). The smallest

input of TN was from the Keys (Figure 5.10), whereas

the smallest inputs of DIN were from Shark River and

Taylor Sough–C-111 (Figure 5.11).

Internal Nutrient Cycling

Benthic Nutrient Fluxes

In situ benthic metabolism and nutrient regeneration

were measured seasonally for 3 years (1997 through

2000) at five sites near the northern Florida Bay coast

(Rudnick et al., 2001) and for 1.5 years (1997–1998) at six

bay sites away from the northern coast (Carlson and

Yarbro, 1999). Additional flux measurements have been

made more recently in sediment cores (Cornwell and

Owens, 2003).The most notable results of these studies have been that phosphorus fluxes are very low

(typically not significantly different from zero) and

that inorganic nitrogen fluxes from sediment to water

are surprisingly low. Sediments consistently removed

nitrates and nitrites from the water column under dark

and light conditions. Compared to rates of sedimentary oxygen uptake in the dark, rates of ammonium release have been found to be very low. Median O:N

(oxygen:nitrogen) molar ratios in dark chambers at

northern coastal sites greatly exceeded that expected

from the mineralization of algal or seagrass detritus,

ranging from 51 to 124 (O uptake:N release) (Rudnick

et al., 2001). Given the high organic matter concentrations of central Florida Bay, the finding of consistently

low (<50 μmol m–2 h–1) ammonium fluxes from Rankin

Lake sediments (Carlson and Yarbro, 1999; Kemp and

Cornwell, 2001) is surprising.

Studies by Cornwell et al. (2000) and Kemp and

Cornwell (2001) provide insights of mechanisms that

explain the observed low rates of ammonium regeneration. They found that ammonium fluxes were

negatively correlated with benthic chlorophyll a concentrations (Figure 5.13), perhaps because benthic

algae stimulate coupled nitrification-denitrification.

Florida Bay Synthesis Hunt and Nuttle

66 FWRI Technical Report TR-11

Nutrient Dynamics
These studies found that net N2 fluxes were typically

from sediment to water (dentrification exceeding nitrogen fixation). Denitrification rates (dark N2 fluxes)

at six sites averaged 127 ± 87 μmol m–2 h–1 in August and

65 ± 82 μmol m–2 h–1 in March.These fluxes greatly exceeded ammonium fluxes. Further support for the inference that low inorganic nitrogen regeneration is

attributable to coupled nitrification-denitrification was

provided by in situ hypoxia experiments (Rudnick et al.,

2001). Dissolved oxygen and nutrients were followed

in a time series over 28 hours in dark benthic chambers. When dissolved oxygen in the water column

dropped below 0.2 mg/L, ammonium fluxes increased

five fold.

Yarbro and Carlson (unpublished) measured benthic fluxes of filterable reactive phosphorus (FRP),

NH4

+, silicate, TP, TN, dissolved organic phosphorus

(DOP), and DON in seagrass beds in the eastern bay

(Sunset Cove and Swash keys), central bay (Rankin

Lake and Calusa Key), and western bay (Johnson and

Rabbit Key basins). FRP fluxes ranged from uptakes of

3 μmol m–2 h–1 in Johnson Key Basin in the western bay

to releases of 1–2 μmol m–2 h–1 in the eastern bay. Dissolved organic phosphorus (DOP) fluxes (2–4 μmol

m–2 h–1) were considerably higher than FRP fluxes and

were more often released from the benthos, especially

at central and western bay sites. These small fluxes

are in sharp contrast to the large phosphorus pool in

surficial sediments (1–12 μmol gDW–1).

Additionally, the sharp increase in sediment phosphorus from east to west in the bay was not reflected

in benthic fluxes. Keeping in mind that these fluxes represent net flux to or from the seagrass community, we

estimate that ammonium and the sum of FRP and

DOP fluxes can meet 20%–50% of the phytoplankton

demand in the eastern and western regions of Florida

Bay but only 5%–10% of the phytoplankton demand in

the highly productive, Synechococcus-dominated northcentral bay.

Internal Nutrient Cycling: 

Carbonate-Phosphorus-Iron Relations

A study by Chambers et al. (2001) documented the

spatial variation in sediment phosphorus, iron, and

sulfur.Total sediment phosphorus decreases on a westeast gradient across Florida Bay, similar to the pattern

in which surface-water quality decreases. Mineral sulfides and extractable iron in Florida Bay sediments

decrease on a north-south gradient. Most inorganic

phosphorus in the sediment is associated with abundant calcium carbonate minerals and not with reactive

iron oxides that occur in very low concentrations. Iron

availability limits mineral sulfide formation, but dissolved sulfide concentrations in Florida Bay sediments

are high. Experimental addition of reactive iron to seagrass plots in Florida Bay stimulated phosphorus retention in the sediment and buffered plants from toxic

sulfide accumulation. Phosphorus availability to seagrass still appears to limit production in carbonate

sediments more than sulfide toxicity. Generation of inorganic phosphorus in seagrass sediments may occur

directly via mineralization of organic matter and indirectly via concomitant carbonate mineral dissolution

(Ku et al., 1999).

Role of Sediment Resuspension in 

Phosphorus Cycling

Phosphorus is retained on the surface of calcium carbonate sediments (Zhang and Fischer, 2001). Within a

few minutes of sediment resuspension, phosphate that

is weakly bound to particle surfaces is released to the

water column, where it may be used by phytoplankton.

Coprecipitation of calcium phosphate with calcium

carbonate may scavenge dissolved phosphate out of the

water column.

Total sedimentary phosphorus (TSP) was fractionated into five chemically defined pools (Zhang and

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 67

Table 5.2 Comparing Florida Bay nutrient budgets (positive into system) (from Cerco et al., 2000).

Rudnick et al. Model Dry Season Model Wet Season

Total P Total N Total P Total N Total P Total N

System (kg/day) (kg/day) (kg/day) (kg/day) (kg/day) (kg/day)

Everglades 7.1 685 3.0 679 9.1 1,753

Atmosphere 104.1 1,945 127.0 2,393 127.0 2,393

Keys Loads 115.1 466 54.9 238 54.9 238

Western Boundary 1,112.3 21,918 192.7 3,105 -589.6 –6,217

Keys Passes –493.2 –32,877 101.8 2,068 158.4 4,154

Net 845.5 –7,863 479.4 8,483 –240.2 2,321

Nutrient Dynamics
Fischer, 2001): (1) adsorbed (readily exchangeable) inorganic and organic phosphorus, (2) Fe-bound inorganic phosphorus, (3) autogenic apatite calcium

carbonate-bound inorganic and organic phosphorus,

(4) detrital apatite phosphorus, and (5) refractory organic phosphorus. This study observed a strong gradient of decreasing TSP from the west (14.6 μmol g–1)

to the east (1.2 μmol g–1) across central Florida Bay

(Zhang et al., 2004).

Among the five pools, autogenic apatite calcium

carbonate-bound phosphorus accounted for the largest

fraction of phosphorus (45% of TSP; Zhang et al., 2004);

inorganic phosphorus dominated this pool (70%–90%).

The refractory organic phosphorus (24% of TSP) and

iron-bound inorganic phosphorus (19% of TSP) were

the second largest pools. Adsorbed phosphorus accounted for 8% of TSP (60% organic phosphorus), and

detrital apatite phosphorus composed the smallest

fraction (5% of TSP). Overall, organic phosphorus accounted for 38% of TSP.

Nutrient Flux at the Sediment–Water 

Interface

Yarbro and Carlson (1999) measured silicate fluxes

that ranged from –337 μmol m–2 h–1 at Rankin Lake,

(September 1997) to 766 μmol m–2 h–1 (August 1998).

Ammonium fluxes ranged from –8.3 μmol m–2 h–1 at

Rankin Lake (November 1998) to 156 μmol m–2 h–1 at

Sunset Cove in November 1998.Total dissolved nitrogen fluxes were highly variable between sites and

sampling dates, ranging from –340 μmol m–2 h–1 at

Rabbit Key Basin in August 1998 to 193 μmol m–2 h–1 at

Sunset Cove in November 1998. Dissolved organic nitrogen (DON) also varied between sites and sampling

dates, ranging from 5.7 μmol m–2 h–1 at Swash (May

1998) to 250 μmol m–2 h–1 at Rabbit Key Basin (August

1998). Net DON flux was always from the sediment to

the water column.

Because filterable reactive phosphorus (FRP) concentrations generally were very low, flux estimates

were highly variable (Yarbro and Carlson, 1999).Total

dissolved phosphorus and FRP fluxes ranged from

net uptakes of –6.23 to –0.02 μmol m–2 h–1 and sediment

releases of 0.02 to 11.57 μmol m–2 h–1. Most fluxes were

less than 1 μmol m–2 h–1.

Seagrass Modeling

An ecological model of the Florida Bay seagrass community, funded by USGS through the Critical Ecosystems Initiative, was conceived as a means of enhancing

the ability of managers to improve health of the Florida

Bay ecosystem, seagrass habitat in particular (Madden

Florida Bay Synthesis Hunt and Nuttle

68 FWRI Technical Report TR-11

Figure 5.13 Results from denitrification study conducted by

Cornwell (2001). This figure indicates the importance of benthic

microalgae in the nitrogen cycle. Ammonium uptake from the

water column is associated with high chlorophyll concentrations.

Nutrient Dynamics
et al., 2003, McDonald and Madden, 2003; Figures 5.14,

5.15). This model is a dynamic, mechanistic simulation of seagrasses, emphasizing nutrient cycling and

nutrient demand related to seagrasses. It is being used

as a tool for determining the causes of seagrass mortality due to environmental stress and to calculate nutrient-sink characteristics of the seagrass community.

In scenario analyses, this model was used to test

the effects of individual and simultaneous multiple

stressors, at levels measured to occur in situ on primary

productivity. Application of multiple stressors involving elevated nutrients, salinities, and elevated sulfide

concentrations produced dramatic results in the Thalassia growth profile. Biomass declined continuously

from the point of application of simultaneous stressors

in January throughout the growing season as Thalassia rapidly died off. Examination of processes underlying this model behavior revealed that photosynthesis,

though operational, was impaired and functioning at

such a low level that the net daily production was negative throughout the growing season.

Interaction of the above- and below-ground compartments played a strong role in the trajectory of the

seasonal biomass curve in the model. Exchanges of organic carbon and nutrients between leaf and root compartments are seasonally variable and critical for

survival of submerged plants.The modeled plants can

mobilize below-ground resources to supplement carbon input to the above-ground compartment should

autotrophic assimilation become deficient.The amount

of carbon in the root/rhizome material available for

growth supplementation can control the outcome of

plants subjected to stress conditions. Therefore, the

status of the below-ground compartment can determine the survival of the entire plant. Conversely, when

conditions are unfavorable to growth and belowground resources are depleted, the existence of aboveground plant material can mask a plant community in

fragile condition. We believe that this model’s conceptualization is realistic and is likely close to the physiological and community reactions that occur in the real

system, emphasizing the importance of thresholds

and nonlinear reactions, which can be tracked and revealed by model analysis.

A series of model runs were made to determine nutrient demand under a range of C:N ratios (15–36) and

C:P (400–1800) ratios typical of the bay. On an annual

basis, P supplied to sediment pore waters via organic

remineralization and rock dissolution each averaged

about 1–1.5 mg P m–2 d–1, whereas P exported from the

Everglades averaged 0.05 mg P d–1 to overlying waters

in Little Madeira Bay (Rudnick et al., 1999). Depending

on tissue ratios of nutrients applied to the model, these

rates supply from >1,000% to only 30% of P demand by

Thalassia. Significantly, the C:P ratio estimated by inverse modeling required to use 100% of the available

sediment P regenerated daily (2.3 mg–2 d–1) is 500:1,

which approaches the average C:P ratio of 800:1 that

has been measured empirically in Little Madeira Bay

and northeastern Florida Bay.

Influence of Florida Bay Water

Quality on the Reef Tract

Nutrient Export Through Keys Passes 

The rate of outflow was estimated by Lee and Smith

(2002) from measurements made in Channel 5 and

Channel 2 near Long Key in 1997 and 1998. The longterm mean was 370 m3

/s (11.7 × 109 m3/y).The estimated

exports (MT/y) were TP = 180; TN = 4,600; DIN = 200

(Figures 5.9–5.11). Nutrient concentrations were measured as part of FIU’s monitoring (Jones and Boyer,

2002), and the flux calculation assumed median concentrations.

Based on these estimates, Florida Bay is a sink for

approximately half of the inputs of TP and TN and

more than 80% of the inputs of DIN. Additional export

of N and P from Florida Bay may occur in the form of

drift seagrasses and algae but no quantitative estimates have been made of these exports.

Water-Quality Modeling

The water-quality model (Cerco et al., 2000) linked

modules including water-column eutrophication, seagrass dynamics, sediment diagenesis, solids and nutrient resuspensions, and benthic algal production.To

our knowledge, this is a first for Florida Bay. In fact, we

know of few systems that currently have a model application to rival the current effort in Florida Bay. However, the model requires substantial upgrading to fully

represent processes in the bay.

Nutrient loads from various sources to the bay

and surrounding waters were calculated for the model

study. Estimates indicated that the atmosphere is the

largest loading source to the bay. Runoff from the

mainland is the smallest source of phosphorus and second smallest source of nitrogen. Paradoxically, runoff

appears to be the most intensely studied loading

source.There are large degrees of uncertainty as to what

the greatest loads are. Attention should be devoted to

accurately quantifying atmospheric and phosphorus

loads from the Keys.

No in situ measures of nitrogen fixation were available to us. Rates associated with seagrass beds, measured in other systems, were adapted for the model.

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 69

Nutrient Dynamics
Estimated nitrogen fixation associated with seagrass

leaves equals the estimated atmospheric nitrogen load.

The sum of nitrogen fixed in the leaves and roots makes

nitrogen fixation the largest single source to the system.

Measures of nitrogen fixation are currently being conducted and these measures should be swiftly incorporated into the model and into system nutrient budgets.

Measures of denitrification within benthic sediments were also unavailable. Rates of denitrification

were calculated by the sediment diagenesis model,

with values adapted from Chesapeake Bay. Calculated

denitrification roughly equals total nitrogen fixation.

Denitrification rates should be measured and used to

verify the computations provided by the model.

The model underestimates the amount of nitrogen

in both the sediments and water column. Sensitivity

analysis indicates that the shortfall is unlikely to originate from the loading estimates. Either a source of

nitrogen has been omitted or the estimated loads are

greatly in error.Potential sources of omission or error include groundwater,nitrogen fixation,and denitrification.

The model does not indicate that material does not

concentrate in the central basins.This behavior may be

attributed to several factors. First, the underlying hydrodynamic calculations may not concentrate material. Second, the linkage method may introduce errors

in the computed hydrodynamic field.Third, the waterquality grid and numerics may introduce artificial

dispersion. Dye-tracer tests indicated that the waterquality model qualitatively tracks transport in the hydrodynamic model in Florida Bay. (Transport is not

equivalent on the western shelf because of artificial dispersion and boundary-condition specification.) The

tracer tests led us to the conclusion that the underlying hydrodynamics prevent computation of hypersalinity and concurrent concentration of nitrogen and

other materials.

Interpretation of results from the water-quality

Florida Bay Synthesis Hunt and Nuttle

70 FWRI Technical Report TR-11

Figure 5.14 Ecosystem process model of south Florida estuarine systems. Conceptual diagram of Florida Bay seagrass model emphasizing major nutrient cycles. (Madden et al., 2003).

Nutrient Dynamics
model was severely compromised by the lack of a verified hydrodynamic model operable on the same time

scale as the water-quality model.

Successful simulation of a ten-year sequence of

water quality was virtually impossible without corresponding hydrodynamics.The highest priority should

be given to applying a detailed, volume-conservative

hydrodynamic model to the bay and adjoining waters.The model should simulate at least a ten-year period and provide good agreement to salinities observed

within that period.

The major uncertainty in the system’s nutrient

budget is transport across the western boundary and

through the Keys passes.This transport cannot be observed on a long-term basis. Computation via a model

is the only alternative for long-term budget estimates.

High priority should be given to estimating flow across

system boundaries once a verified hydrodynamic

model is available.

Sensitivity analysis indicated that model computations are very sensitive to the biological activity at the

sediment–water interface. In the present model, this activity is represented by the benthic algal component,

and as formulated, the model cannot represent all observed fluxes, especially those of dissolved organic

matter. Attention should be devoted to quantifying

sediment–water fluxes, to investigating the nature of

the benthic community, and to process-based modeling of this community.

A great number of observations have been collected in the bay since this study commenced, and

considerably more is known about the bay than was

known a few years ago. Once suitable hydrodynamics

are available, the water-quality model should be reapplied on a ten-year time scale and validated with the

latest observations of conditions and processes in the

bay. Concurrent with the reapplication, first-order improvements (e.g., division of dissolved organic matter

into labile and refractory components) can be incorporated into the water-quality model.

As part of the Florida Bay and Florida Keys Feasibility Study of the CERP, a new attempt is currently

being made to develop, calibrate, validate, and apply

a Florida Bay water-quality model.

Current and Ongoing Research

Unresolved Questions

Past informational needs relative to nutrient cycling in

Florida Bay have been coupled to understanding the

factors that triggered the mass mortality of seagrass and

what initiated and maintained the phytoplankton

blooms. Current needs have become more focused

around assessing the effects of various environmental

management strategies being considered for bay

restoration. In particular, we need to accurately predict

the sensitivity of the bay’s nutrient cycles to changing

freshwater flow to the bay and the resultant change in

the bay’s salinity regime. For much of the bay, any factor that increases phosphorus availability, either by

increasing sources or decreasing removal, is likely to

exacerbate the current problems of the bay. Recent

evidence also indicates that algal blooms in the central and western bay are also stimulated by nitrogen

enrichment.Thus we need a thorough understanding

of the bay’s nutrient cycles, particularly with regard to

the fate and effects of dissolved organic nitrogen inputs from the Everglades. Understanding the mechanisms that have triggered and are sustaining algal

blooms in the bay is fundamental to restoration decision-making. This understanding entails quantifying

the nutrient demands of these algae and how these nutrients are supplied. Questions that the future program should address in order to meet these needs are

as follows:

• What are the sources of nutrients that sustain algal

blooms? 

Understanding the mechanisms that have triggered and are sustaining algal blooms in the bay is fundamental to restoration decision-making. This

understanding entails quantifying the nutrient demands of these algae and how these nutrients are

supplied.

• How will changing freshwater flow directly and indirectly alter the supply and availability of nutrients in the bay? What effect does changing salinity

have on nutrient availability in the bay? 

° How will the quality and quantity of nutrient outHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 71

Figure 5.15 Theoretical phosphorus demand by Thalassia in

mg per m2 per day as calculated by the seagrass model to satisfy

seagrass primary productivity rates in northeast Florida Bay.

Nutrient Dynamics
puts from the Everglades change with restoration?

° What is the fate and effect of dissolved organic

matter from the Everglades and how will this

change with restoration?

° What effect does changing salinity have on nutrient cycling and availability in the bay?

With increased freshwater flow expected from

restoration of the Everglades and Florida Bay, nutrient

loading from the Everglades watershed will also probably increase. For nitrogen, most of this loading will be

in the form of dissolved organic compounds. The

sources, fate, and effects of DON from the Everglades

watershed are unknown, and predictions of how changing freshwater flow will influence these DON dynamics are highly uncertain. Measurements of the

composition and bioavailability of Everglades DON to

Florida Bay’s microbial communities (pelagic, epiphytic, and benthic) are essential in order to assess the

functional relationship of Florida Bay and its watershed.

Although the magnitude of this expected increase is

unknown, this direct input may be less important than

the indirect effect of an altered salinity regime caused

by increased freshwater influx. Altered salinity can affect internal nutrient cycling by (1) altering community

structure (such as changing seagrass-species dominance, thus changing nutrient storage and cycling),

and (2) modifying specific processes, such as phosphorus surface reactions and sulfate reduction. A

change in freshwater flow and salinity could also alter

nutrient processing in the mangrove zone and thus alter

nutrient exchange along the bay’s northern boundary, the Gulf of Mexico boundary with the Everglades,

and near mangrove islands in the bay.

The factors that influence the loading of nutrients

into Florida Bay and the availability of nutrients within

the bay are not well understood. In particular, we need

to understand the effect that potential environmentalmanagement actions, such as increasing freshwater

flow and decreasing salinity, will have on the bay’s

nutrient transformations and fluxes. Information on

suspended sediment particles and on factors that may

influence the mobilization and immobilization of phosphorus in carbonate sediments is critical. Results of past

experiments (Zhang et al., 1999) need to be evaluated

in the context of the development of a water-quality

model to assess the sufficiency of current data for estimating salinity effects.

Given the unusually high ammonium concentrations of the bay and the potential for nitrogen limitation in the western bay, experiments on factors that may

influence key nitrogen transformations, such as nitrification and denitrification, are also needed. Experiments that explore how nutrient cycling is altered by

changes in seagrass community structure and physiological condition (particularly below-ground nutrient

changes) are also important but have yet to be done.

• What effect does a change in seagrass community

structure have on nutrient availability in the bay? Has

seagrass mortality only increased nutrient availability by releasing nutrients from this detrital source

or has seagrass mortality also caused other less direct changes, such as a decrease in the capacity of the

sediments to sequester nutrients? 

The lag of several years between the onset of seagrass mass mortality and the occurrence of algal blooms

in the bay argues against the hypothesis that only nutrients released from dead seagrass tissue fuel the

blooms. However, the increase in nutrients from this

detrital source, combined with a net decreased uptake capacity associated with seagrass mortality, may

explain the bloom’s temporal patterns.Thus, we need

estimates of net benthic nutrient uptake or release

rates over a range of seagrass growth rates, mortality

rates, and detrital decomposition rates for different

seagrass species. The accuracy of such estimates may

depend largely upon understanding sedimentary nutrient transformations, including how seagrass roots affect nutrient mobility and how such processes change

with seagrass mortality. Seagrass mortality may have

indirectly affected nutrient cycles in the bay. For example, sediment resuspension increases with decreasing seagrass density, and phosphorus associated

with this suspended sediment may be available to

phytoplankton. Finally, changing seagrass cover also influences the biomass and activity of benthic algal mats.

This change in microbial mats in turn affects nitrogen

availability by altering patterns of nitrification, denitrification, and nitrogen fixation. Measurements of the

quantitative relationships of these processes within

the algal and SAV community structures are needed.

Given the shallow depth and restricted circulation of Florida Bay, internal cycling and transformations

of nutrients probably have a strong influence on the

structure and productivity of bay communities.These

nutrient pathways and transformations have not been

well studied. Essential measurements include nutrient

uptake by primary producers (especially seagrass and

phytoplankton), the exchange of nutrients between

the sediments and the water column, the diagenesis of

nutrients within the sediments (especially phosphorus–carbonate reactions and nitrogen transformations),

and microbial and inorganic reactions within the water

column (such as nitrification and phosphorus sorption

to and removal from suspended sediment).

• How do we deal with the spatial heterogeneity of internal nutrient cycling in the bay? 

Florida Bay Synthesis Hunt and Nuttle

72 FWRI Technical Report TR-11

Nutrient Dynamics
There is no unified field theory for ecology—

process rates from one area may not be applicable to

another. What other factors are important in driving

these processes?

• What is the quantitative role of microphytobenthos

in nutrient cycling and how is this likely to change

with Everglades restoration?

The microphytobenthos has been shown to be influential in regulating benthic flux rates. Fluxes in the

form of drift seagrasses and algae have not been determined.

• To what extent is atmospheric deposition of nutrients

contributing to ecological changes in Florida Bay?

What is temporal variability (including long-term

trend) of this nutrient source?

Atmospheric inputs have been shown to be a significant component of external nutrient loading, especially of nitrogen.There are no estimates of long-term

trends in atmospheric nutrient-loading at present.

• Is ground water an important nutrient source in

Florida Bay? If so, what is the spatial and temporal

pattern of this input?

Given the high nutrient content of the groundwater beneath most of the bay, any groundwater flux approaching recently published rates (about 1 cm d–1)

would result in a very high nutrient flux.The accuracy

of these estimates should be checked—sites with significant upward groundwater advection should be

identified; if found, nutrient concentrations at these

sites should be measured.

Summary of Ongoing Research

• Continued monitoring of ambient water quality in

Florida Bay.

• Continued monitoring of freshwater inflows and

loads with expansion of network along Florida Bay

and southwest Florida gulf coast beginning.

• Continued monitoring of coastal circulation and biological and chemical parameters, with interpretation of transport and exchange of south Florida

coastal waters.

• Expanded research into nutrient cycling in wetland/mangrove areas and seagrasses/epiphytes.

• Study of carbonate system–phosphorus–iron relations.

• Characterization of chemical structure of organic

carbon and nitrogen from wetland/mangrove areas.

• Assessment of microbial bioavailability of organic

carbon and nitrogen from wetland/mangrove areas.

• Expanded measurements of benthic nitrogen fixation, nitrification, and denitrification rates.

• Measurements of phytoplankton nitrogen uptake

rates.

• Quantification of microbial loop parameters: heterotrophic bacterial numbers, bacterial production,

nanoflagellate/protist grazing rates, and phytoplankton primary production.

• Effects of variability in regional climate, freshwater

inputs, disturbance, and perturbations on the coastal

Everglades ecosystem.

• Development of nitrogen and phosphorus massbalance models and measurements of nutrient cycling rates in Florida Bay.

• Assessment and monitoring of dissolved nitrogen in

Florida Bay.

• Measurement of nutrient fluxes through Florida

Keys passes.

• Monitoring of salinity and estimates of fluxes of

water and total nitrogen and phosphorus across the

southern Everglades mangrove zone.

• Development of an integrated hydrodynamic and

water-quality model to evaluate relationships with

freshwater flow and oceanic/gulf hydrodynamics

and exchange is in a planning phase.

• Seagrass uptake kinetics of phosphorus.

• Influence of dissolved organic matter on seagrass,

epiphyte, and phytoplankton productivity.

• Seagrass survival and productivity under single and

multiple stresses.

• Dynamic simulation model analysis of spatial patterns of seagrass productivity, community structure,

and nutrient demand.

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Introduction

Question 3—What regulates the onset, persistence, and fate

of planktonic algal blooms in Florida Bay?

From the 1950s to the mid 1980s, Florida Bay was characterized by expansive seagrass beds, mangrove islands, and crystal-clear water. In the past 16 years,

there have been some dramatic changes in the ecology

of Florida Bay; examples are the die-off of large areas

of seagrass and the appearance of intense blooms of

planktonic algae. There is a general consensus in the

scientific community that these phenomena are indicative of changes in key environmental conditions

within the bay.The shift in primary producers and the

alteration of the photic environment in Florida Bay

have been hypothesized to have major effects on the

flora and fauna of the bay (e.g., Boesch et al., 1993).

Fourqurean and Robblee (1999) have recently reviewed

many of the changes. In this paper, we examine the current state of knowledge about the character and causes

of planktonic algal blooms in the bay.

In reviewing the scope of our knowledge on algal

blooms in Florida Bay, it is important to keep in mind

that detailed monitoring of water quality in the bay has

been underway for just over a decade.This is a somewhat surprising fact considering the importance of

this aquatic resource to Florida and the surrounding

waters of the Atlantic Ocean and Gulf of Mexico. One

of the factors that triggered the initiation of extensive

multidisciplinary research in the bay was the on set of

massive cyanobacterial blooms over large areas of the

bay in the early 1990s.

The first quantitative indications of major increases

in phytoplankton densities in the interior regions of

Florida Bay came from chlorophyll a data collected by

Florida International University (FIU) (Boyer et al.,

1997, 1999). Boyer et al.’s (1999) research, which began

in 1988, indicated a significant step increase in chlorophyll levels in 1991–1992. The increase in algal biomass within the bay was corroborated by incidental

observations by individuals frequenting the bay for

other research and recreation activities. In 1993, a separate research group from the University of Florida

joined FIU in monitoring efforts that revealed high

concentrations of cyanobacteria in the central portion

of Florida Bay (Figure 6.1; Phlips and Badylak, 1996;

Phlips et al., 1999). In 1994, the phytoplankton research

efforts were expanded further to include the Florida

Marine Research Institute [now the Fish and Wildlife

Research Institute]. All three research teams observed

large cyanobacterial blooms in the central regions of

the bay, particularly during the summer and fall (Phlips

et al., 1999; Steidinger et al., 2001).

During the same period, algal blooms were also

recorded in the western region of the bay (Figure 6.1).

However, these blooms were typically dominated by diatoms, not by cyanobacteria. (Phlips and Badylak, 1996;

Phlips et al., 1999; Steidinger et al., 2001) Recent efforts

by researchers from the University of Miami focusing

on the western bay have provided further support for

the importance of diatom blooms in the western region.

Analysis of sediment cores from the western side of

Florida Bay indicate that diatom blooms along the western margin were a well-established feature by 1970,

significantly prior to the increases in cyanobacteria

blooms within the bay’s interior (Jurado, 2003). Most recently, chemotaxonomic studies of phytoplankton in the

bay have been initiated using full-spectrum photodiode array detectors and high-performance liquid chromatography analysis (Louda, 2001).

Regional Differences

The observed disparity in the quantity and quality

(i.e., composition) of phytoplankton biomass in different parts of the bay manifests the need to view phytoplankton dynamics by ecological zones. In contrast

to the numerous phytoplankton blooms encountered

in the western and central regions of Florida Bay, almost no blooms are located in the eastern portion of

the bay (Figure 6.1).There have been several efforts to

divide Florida Bay into ecologically distinct zones.

These zonal breakdowns have been based on a variety of parameters, including geology (Prager et al.,

1996), distributions of benthic plants (Zieman et al.,

Chapter 6

Plankton Blooms

Team Leaders Gary Hitchcock (University of Miami), Ed Phlips (University of Florida), 

Larry Brand (University of Miami), Douglas Morrison (ENP, PMC)
Florida Bay Synthesis Hunt and Nuttle

78 FWRI Technical Report TR-11

1989), faunal distributions (Thayer and Chester, 1989;

Holmquist et al., 1989), and water-quality characteristics (Phlips et al., 1995, Boyer et al., 1997, 1999; Burd and

Jackson, 2001).These efforts have yielded from 3 to 20

zones with different boundary designations.The lack

of consensus on the specific boundaries and number

of zones is largely attributable to differences in the

choice of parameters used in the discrimination of the

regions.

If the focus is limited to the frequency of phytoplankton blooms and the general composition of the

blooms, it is possible to define three general regions

that roughly follow longitudinal lines of demarcation

(Figure 6.2): (1) The eastern region of the bay, east of

80°39 ́W and west of the Florida Keys, where major phytoplankton blooms are seldom observed; (2) the central region of the bay, between 80°39 ́W and 80°49 ́W,

where bloom concentrations of cyanobacteria (i.e.,

greater than 1 million cells per ml) are regularly encountered; and (3) the western region of the bay, west

of 80°49 ́W, which experiences periodic blooms of diatoms.These regions provide a useful context for discussing both the character of blooms in the bay and the

factors that control them.

In the most general terms, phytoplankton standing

crops are dictated by factors that control gains and

losses of algal biomass (Figure 6.3). From a gain perspective, the most obvious contributor to the increase

in phytoplankton biomass is cell growth. Net growth

rates are under the control of resource availability, such

as nutrient and light, and of factors that affect the rates

of photosynthetic and respiratory activity, such as temperature, salinity, and oxygen level. Algal biomass can

also increase as a consequence of inputs to the water

column from the benthos through resuspension or inflows of water from adjacent environments.

In terms of loss functions, one of the most important overriding considerations is water residence time.

In many coastal ecosystems, phytoplankton biomass is

limited by the flushing-rate of water that has lower phytoplankton content. Flushing rates are generally related

to a combination of rainfall inputs, tidal mixing, and

Figure 6.1 Biovolume of Synechococcus elongatus (Large Syn.), other cyanobacteria, dinoflagellates, diatoms and other phytoplankton at four sampling sites representative of different regions of Florida Bay (Phlips et al., 1999).

Plankton Blooms
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FWRI Technical Report TR-11 79

wind-driven circulation. Many environments with long

residence times tend to have higher phytoplankton

crops than do environments with short residence times,

assuming that nutrient and light availability are similar (Monbet, 1992).There are also biological processes

that contribute to the loss of biomass in many aquatic

ecosystems, such as grazing by benthic and planktonic filter-feeding organisms. The rates of loss are

closely tied to the structure and abundance of the

grazer community and to environmental factors that

affect the rate of activity, such as salinity, temperature, and phytoplankton composition (e.g., presence of

toxic species).

Summary of Research

Research to date indicates that there are three ecologically distinct regions within the bay from the standpoint of algal blooms: the northeastern, central, and

western regions.The nature and causes of blooms can

be most appropriately summarized within the context of these three regions (Table 6.1).

NORTHEASTERN REGION

• Algal blooms are largely absent from the northeastern region of Florida Bay. The phytoplankton

community of the northeastern region is a diverse

mixture of cyanobacteria, dinoflagellates, diatoms,

and microflagellates, none of which form blooms.

• The lack of algal blooms in the northeastern region

of Florida Bay is largely attributable to the severe

phosphorus limitation characteristic of the region.

Despite significant water inflows to the region from

the Everglades, the very low phosphorus levels in

these inputs combined with the calcium-carbonate

rich waters of the region, result in nutrient-limited

conditions.

CENTRAL REGION

• Large algal blooms have been a common feature of

the central region since 1992. The focal point for

blooms in the central region is in the north-central

region from Rankin Basin extending into Whipray

Basin.The greatest bloom activity is generally in the

summer and early fall, although blooms have been

Figure 6.2 Florida Bay basin configurations.

Plankton Blooms
Florida Bay Synthesis Hunt and Nuttle

80 FWRI Technical Report TR-11

observed in other seasons. In the fall and early summer, blooms originating in the northern central region are pushed southward by prevailing wind-driven

circulation into the southern central region, where

they can spread out into the Atlantic reef tract through

cuts in the Florida Keys.The dominant bloom-forming alga in the central region is the picoplanktonic

cyanobacterium Synechococcus cf. elongatus, though

several species of diatoms and dinoflagellates occasionally occur in bloom proportions.

• Nutrient limitation of phytoplankton growth in the

central region appears to switch back and forth from

phosphorus to nitrogen.The nature of the sources of

nutrients for blooms in the central region has been

a subject of considerable debate, yielding several

hypotheses: (1) a significant supply of nutrients for

algal production is available from the flocculent

muddy sediments within the region; (2) a groundwater source of phosphorus is present within the region that, in combination with nitrogen from the

northeastern region, feeds algal blooms; (3) nutrients

from the shelf region west of the bay are available

to blooms in the central region via tidal exchange;

and (4) atmospheric deposition is a significant source

of nutrients (particularly N) for algal primary production. These hypotheses are not mutually exclusive, and several mechanisms may be operational at

the same time.

• The domination of blooms in the central region by

Synechococcus cf. elongatusis attributable to the unique

ecophysiological characteristics of this species of

cyanobacterium. These characteristics include (1)

wide tolerance to salinity, (2) superior ability to compete for phosphorus at low concentrations, (3) ability to regulate buoyancy and thereby take advantage

of nutrients available in the sediments, and (4) lower

susceptibility to grazing losses.

WESTERN REGION

• Algal blooms are also a common feature of the western region of Florida Bay. In contrast to the cyanobacFigure 6.3 Gain versus loss-functions for phytoplankton standing crops.

Table 6.1 Summary of research on plankton blooms by region.

West Central East

General Phlips and Badylak, 1996 Phlips and Badylak, 1996 Phlips and Badylak, 1996

Characteristics Boyer et al., 1997, 1999 Boyer et al., 1997, 1999 Boyer et al., 1997, 1999

Phlips et al., 1999 Phlips et al., 1999, 2002 Phlips et al., 1999

Steidinger et al., 2001 Steidinger et al., 2001 Steidinger et al., 2001

Jurado, 2003

Nutrients Lapointe et al., 1990, 1994

Robblee et al., 1991

Carlson et al., 1994

Durako, 1994

Zieman et al., 1994

Paul et al., 1995a,b

Tomas et al., 1999

Lapointe et al., 2002

Composition and Tomas et al., 1999 Richardson et al., 2001

Growth Rates Jurado, 2003

Grazing and Lynch and Phlips, 2000

Flushing Brenner et al., 2001

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terial blooms in the north-central region, these

blooms are dominated by diatoms.The diatom-dominated blooms in the western region are mainly composed of Rhizosolenia spp., although Chaetoceros spp.

and pennates are major genera in terms of cellular

biomass. Diatom blooms in the western region begin

in late summer and are advected into the bay from

shallow coastal waters off Cape Sable.

• The diatom-dominated blooms in western Florida

Bay are mainly limited in their growth by nitrogen,

either singly or in combination with phosphorus

and/or silicon supply. Temperature, salinity, and

light do not appear to be important factors in the initiation or maintenance of diatom blooms. Maximum

growth rates of the diatom community during bloom

initiation in the western region range from 1 to 2 day–1

(first-order rate constant) based on increases in netplankton (greater than 5 μm size fraction), chlorophyll

a, or biogenic silica.The onset of diatom blooms on

the western Florida Shelf appears to be associated

with enhanced riverine outflow, predominantly from

the Shark River.The onset of increased diatom biomass occurs within the riverine, low-salinity plume

near Cape Sable.

Eastern Florida Bay

Phytoplankton abundance is lower in the eastern part

of the bay than it is in the other two zones within the

bay (Figure 6.1). Chlorophyll a concentrations in the

eastern bay are typically less than 2 mg m–3 throughout the year. Phlips et al. (1999) reported that the maximum chlorophyll a concentrations in this region were

less than 5 mg m–3 between August 1993 and October

1997, with most values less than 1 mg m–3 (Figure 6.4).

Similarly, Boyer et al. (1997, 1999) observed low chlorophyll a concentrations in eastern Florida Bay for the period between 1989 and 1997 (mean = 0.85 mg m–3).

The phytoplankton communities in the eastern

bay are principally composed of centric diatoms (e.g.,

Thalassiosira sp.), dinoflagellates (e.g., Protoperidium

spp., Ceratium sp., Prorocentrum micans), and small

cyanobacteria that constitute the major fraction of cellular biovolume (Phlips and Badylak, 1996). Steidinger

Figure 6.4 Chlorophyll a concentrations and salinities at sampling sites representative of different regions in Florida Bay (Phlips et al.,

1999).

Plankton Blooms
et al. (2001) reported that the dominant phytoplankton

taxa in the region from fall 1994 to early summer 1995

were dinoflagellates, whereas cyanobacteria were the

most abundant taxa from late 1996 to spring 1997. Cellular biovolume serves as a useful index to phytoplankton biomass that is independent of physiologically

induced changes in pigment concentrations such as

those that occur in chlorophyll a.In eastern Florida Bay,

total phytoplankton biovolume is less than 1 μm3 ml–1,

a value much less than that in the western and central

bay (Figure 6.1) (Phlips et al., 1999).

Two factors result in strong phosphorus limitation of primary production in the region, helping to explain the low phytoplankton concentrations that typify

this region of the bay.The eastern region of Florida Bay

receives significant freshwater inputs from Taylor

Slough and the C-111 canal system. Salinity values in

the eastern basins are on average lower than in the central and western bay, with typical values from 20 practical salinity units (psu) to 30 psu (Figure 6.4) (Phlips

et al., 1999).The external surface-water inputs to eastern Florida Bay are very low in phosphorus (Boyer et

al., 1999). In addition, the high concentrations of calcium in the region tend to bind free phosphate.

Central Florida Bay

Over the past twelve years, the central region of Florida

Bay has been the site of intense and prolonged algal

blooms. In the eastern region of the bay, biovolumes of

phytoplankton seldom exceeded 1 million μm–1/ml;

however, in the central bay phytoplankton biovolumes

have regularly exceeded 10 million μm–1/ml (Phlips et

al., 1999). The intensity of blooms in the central bay is

somewhat masked by the fact that the chlorophyll content of phytoplankton in the central region is relatively

low when compared to the chlorophyll content in the

western bay and some other coastal ecosystems in

Florida (Phlips et al., 1999, 2002). It has been hypothesized that this is partially attributable to the very shallow depth of the central region of the bay (generally less

than 2 m), resulting in high light availability and sunadaptation by algal cells (Phlips et al., 1999). It is also possible that the domination of the plankton community

by the cyanobacterium Synechococcus cf. elongatus and

the nutrient limitation contribute to the low ratio. Irrespective of the causes for the low ratios, it is important to consider the ratio when evaluating the intensity

of blooms in the bay. For example, peak chlorophyll concentrations in the St. Johns River in northeast Florida

are three to four times those in central Florida Bay, but

the peak biovolumes of phytoplankton are very similar (Phlips et al., 2000). These considerations manifest

the fact that the 20–40 mg m–3 chlorophyll levels commonly encountered in central Florida Bay are representative of serious bloom conditions, whereas similar

chlorophyll levels in other ecosystems might be viewed

as moderate bloom levels.

Over the twelve years since the initiation of major

phytoplankton blooms in central Florida Bay, the most

intense blooms have occurred during the summer and

early fall, except during 1993 and 1994, when high phytoplankton standing crops persisted throughout the

year.Three of the past ten years (1993, 1994, and 1998)

had particularly intense blooms. In central Florida

Bay, phytoplankton blooms originate in the northern

part of the region. For most of the peak bloom season

(May–September), phytoplankton populations in the

south-central region are relatively low. However, in

the fall and early winter, passing cold fronts, along

with the concomitant shift in wind direction to the

north, displace phytoplankton-rich water southward.

This recurring pattern is apparent in the appearance

of bloom concentrations of phytoplankton as far south

as the Florida Keys reefs.

Cause of Blooms in the Central Region

The apparent rise of planktonic algae blooms in the

central region of Florida Bay in the early 1990s raises

two fundamental questions: (1) What changes occurred

in the region that facilitated the onset of the blooms,

and (2) What are the nutrient sources that have sustained blooms since that time? In relation to the first

question, the onset of blooms indicates one of two

possibilities: (1) more nutrients were made available

for phytoplankton production either through redirection of internal reserves and/or increases in external

loading, and/or (2) biomass loss terms were dramatically reduced.The presence of a thick, organic sediment

layer in the north-central region of Florida Bay indicates

that this region of the bay has historically been productive. Prior to the 1990s, seagrasses were most likely

the dominant primary producers in the central bay.

Even after 1990, seagrasses were still present in the region, although were not as prominently as in previous

years.

One of the principal hypotheses about the cause

of phytoplankton blooms in the central bay focuses on

the role of seagrass die-off in making internal nutrient

reserves available for planktonic production (Robblee

et al., 1991; Carlson et al., 1994; Durako, 1994; Zieman

et al., 1994). There are a number of ways that the reduction of seagrass populations could enhance nutrient availability for planktonic production, including (1)

through the addition of recyclable nutrients from dead

seagrass, (2) by increasing access to sediment-bound

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nutrients via increased resuspension and diffusion,

and (3) by reducing competition for nutrients between

phytoplankton and epiphytic or benthic algae living in

seagrass communities. In addition to increasing nutrient availability, the reduction in seagrass communities can affect phytoplankton loss processes. The

populations of filter-feeding organisms associated with

seagrasses can influence phytoplankton densities, particularly in very shallow environments like Florida

Bay.The physical presence of dense seagrass beds also

increases the sedimentation of algae by reducing the

potential for resuspension of algae and sediments.

The importance of seagrass die-off in the stimulation of phytoplankton blooms is not a universally

accepted concept. Some researchers have suggested

that this line of reasoning is backwards and that increases in planktonic production have actually led to

the demise of seagrasses (Lapointe et al., 2002).The authors of this hypothesis cited observations by local

users of the bay of increases in turbidity prior to the

seagrass die-off in the late 1980s as evidence (DeMaria,

1996). However, these observations were principally restricted to the western region of the bay and therefore

do not provide substantial insight into what occurred

in the central bay during the 1980s.The north-central

region of the bay is very shallow (generally less than

2 m deep), and it remains to be demonstrated if blooms

could cause the demise of seagrass populations as a result of decreased light availability. It is possible that such

an argument might be more tenable in the western bay

and shelf environments, where average depths are

greater.

Irrespective of which came first, the seagrass dieoff or the algae bloom, the central questions remain the

same: what are the sources of nutrients for phytoplankton blooms and has the trophic state of the central bay increased over the past few decades. It is

important to consider the possibility that the overall

pool of nutrients may have remained stable but that the

distribution has changed, along with changes in loss

terms. This argument falls within the concept of “alternative stable states.”Under this scenario a major environmental disruption that resulted in seagrass die-off

could have ushered in environmental conditions conducive to the persistence of phytoplankton blooms.

Such disruptive events could include major storms, prolonged drought or flood periods, or a major shift in nutrient loading.

The first step in addressing these questions is to

identify what nutrients actually limit the production potential of phytoplankton in the central bay.There is little doubt that primary production in the eastern region

of the bay is strongly phosphorus-limited (Lavrentyev

et al., 1998; Tomas et al., 1999).There is also significant

evidence indicating that the western region of the bay

and adjacent shelf environment are commonly limited

by nitrogen or nitrogen-phosphorus co-limitation.This

information suggests that there is an excess supply of

phosphorus to this region.The nutrient limitation status of the central bay is more ambiguous. A number

of biogeochemical indicators, such as the ratios of total

nitrogen (TN): total phosphorus (TP) and inorganic

N:inorganic P, indicate that phosphorus should be the

most limiting nutrient (Fourqurean et al., 1993; Boyer

et al. 1997, 1999). However, it is well known that many

organic N molecules are not readily available to phytoplankton, whereas many organic P molecules are

bioavailable due to the activity of phosphatase enzymes (Vitousek and Howarth, 1991). The results of

nutrient-enrichment bioassays in the central region of

the bay suggest that the limiting status can alternate

between phosphorus and nitrogen (Tomas et al., 1999).

This observation implies that at different times, changes

in the loading rate of either nutrient could stimulate

increases in phytoplankton production. A number of

hypotheses have been forwarded regarding potential

sources of phosphorus and nitrogen for phytoplankton blooms in the central region of Florida Bay. Many

of these hypotheses deal specifically with the north-central region of the bay, where blooms appear to originate. It is important to recognize that these hypotheses

are not mutually exclusive. It is likely that various

pathways of nutrient supply operate simultaneously,

even though the relative importance of each varies

over time and space.

HYPOTHESIS 1—INTERNAL SUPPLY OF 

NUTRIENTS

There are a number of potential internal sources of nitrogen and phosphorus for phytoplankton production

(Rudnick et al., 1999). The thick layer of flocculent organic sediments found in the north-central region of

the bay represents a potential pool of bioavailable nitrogen and phosphorus. The recent die-off of seagrasses in the region has made this pool more

accessible via enhanced diffusion and resuspension

processes.There has been considerable debate within

the scientific community about whether the size of

this pool and the rate of supply from the sediments are

sufficient to sustain the blooms observed over the past

decade. The size and availability of the sediment nutrient pool is certainly an issue that warrants further

attention.The current information available is insufficient to either accept or reject this hypothesis.

There are a number of biological processes that

affect the internal supply rate of bioavailable nutrients. For example, nitrogen fixation by autotrophic and

heterotrophic bacteria and cyanobacteria is a potential

Plankton Blooms
source of nitrogen. In some aquatic ecosystems, nitrogen fixation can represent a major source of nitrogen

(Phlips et al., 1986). Conversely, denitrification processes

can result in a loss of bioavailable nitrogen. The relative roles of nitrogen fixation and denitrification are the

subject of ongoing research (Cornwell, 2001).

Other key elements of internal supply of nutrients for phytoplankton production are the rates of recycling of nutrients within the north-central region

and of export of nutrients from the region. Due to the

severe restriction of tidal exchange of water between

the north-central region and the waters of the Gulf of

Mexico and the Atlantic Ocean, water residence times

are long.The restriction should provide more time for

recycling and less opportunity for nutrient washout. Initial modeling efforts indicate that residence times in

the north-central region are on the order of months

(Jackson and Burd, 1999; Top et al. 2001) and could be

extended during drought periods.Very little is known

about the actual rate constants for recycling, sedimentation, or export of nutrients.

HYPOTHESIS 2—GROUNDWATER SOURCES

OF PHOSPHOROUS

Phosphorite deposits were created during the Miocene

in northeastern Florida and subsequently transported

into south Florida by Appalachian erosion, resulting in

high phosphorus levels observed in geological formations in certain areas of south Florida (Brand, 1996).

Groundwater outflows from these formations can contain high phosphorus levels (Brand, 2002). The distribution of water-column phosphorus correlates well

with the phosphorite deposits (Brand, 2002).There has

been an effort, though unsuccessful to date, to discover direct phosphorus-rich groundwater inputs

within the north-central region of Florida Bay. In a

less direct manner, phosphate mining in central Florida

may have increased the input of phosphorus into the

southwestern coast of Florida. It has been hypothesized

that the phosphorite deposits are a persistent source

of phosphorus that has not changed significantly over

the past few thousand years (Brand, 2002). Although

phosphate mining over the past century may have increased the input of phosphorus into coastal waters,

the extent to which P from this source was transported

to Florida Bay and how this has changed over the past

century is unknown. The timing of phytoplankton

blooms (in the 1990s) does not seem to support a hypothesis that this P source has been an important factor driving changes in Florida Bay phytoplankton.

There is little evidence that phosphorus input to Florida

Bay has increased substantially in the past two decades.

Overall, many questions remain about the importance

of groundwater inputs of nutrients to algal blooms in

Florida Bay, but there is an active research effort underway (Corbett et al., 2000).

HYPOTHESIS 3—EXTERNAL LOADING OF 

NUTRIENTS

Current information on geographical gradients of critical nutrient elements in and around Florida Bay suggests that two of the major external surface-water

sources of bioavailable nitrogen for the north-central

region are the eastern half of the bay and the Everglades boundary. Conversely, phosphorus gradients in

the region indicate that the most likely source of

bioavailable phosphorus is from the western portion

of the bay. These nutrient gradients suggest that the

blooms in the north-central part of the bay could be fed

by nitrogen inputs from the east and by phosphorus

inputs from the west.

It has been hypothesized that phytoplankton

blooms in north-central Florida Bay are a result of increases in nitrogen loading related to recent changes

(since 1980) in water-management practices in southeast Florida (Brand, 2002).The following scenario is envisioned for explaining the increase in N load to Florida

Bay. In the early 1980s, agricultural runoff from the

Everglades Agricultural Area (EAA) was diverted south

via the South Dade Conveyance System (Light and

Dineen, 1994; South Florida Water Management District, 1992).Walker (1991) observed significant increases

in nitrate in water flowing south through the C-111

canal toward Florida Bay and through the S12A station

where water flows into the Shark River system. Unfortunately, there is little nitrogen concentration data

for Florida Bay before the beginning of the large regional monitoring program in 1989.Therefore, it is difficult to determine the degree to which nitrogen levels

in the north-central region of Florida Bay were affected by the later alterations in flow. This scenario

also depends on several assumptions for which the evidence is currently lacking or insufficient.The primary

assumption is that there is sufficient water exchange

between the western shelf, the putative source of phosphorus, and the north-central bay to sustain blooms.

Current hydrodynamic data are insufficient to establish this rate of exchange.There is also a need to more

carefully examine the nutrient-limitation status of phytoplankton in the central bay. As mentioned above,

chemical data indicate that the north-central region

should be phosphorus-limited, but bioassay data indicate a mixed limitation status.

HYPOTHESIS 4—SEWAGE AS A SOURCE OF

NUTRIENTS

Another potential source of nutrients is sewage and

other nutrient-rich freshwater runoff from land in

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FWRI Technical Report TR-11 85

nearby areas of high human activity. In the case of

Florida Bay, this would primarily be the heavily populated Florida Keys. Human activities in the Florida Keys

generate considerable amounts of N and P (U.S. EPA,

1992), and a fraction of this is clearly entering the local

waters (Lapointe et al., 1990, 1994; Shinn et al., 1994;

Paul et al., 1995a,b). The problem with this hypothesis

is that the source of nutrients is downstream of the

algal blooms, not upstream. Sewage may be causing

local eutrophication and leading to algal overgrowth of

the coral reefs downstream but cannot be the source of

the nutrients generating the algal blooms upstream to

the northwest. Concentrations of nitrogen, phosphorus,

and chlorophyll all decrease, not increase, along transects from northern Florida Bay to the Florida Keys.The

algal blooms in Florida Bay are, in fact, the farthest

from the Florida Keys and the human population.

HYPOTHESIS 5—ATMOSPHERIC INPUTS

Until recently, the potential role of atmospheric deposition of bioavailable nutrients in supporting algal

blooms in Florida Bay was largely discounted. However,

recent information indicates that such inputs may indeed be an important element to the broader nutrient

budget of the bay (Rudnick et al., 1999).

Domination by Cyanobacteria

One outstanding feature of algal blooms in the central

region of Florida Bay is the domination of the cyanobacterium Synechococcus cf. elongatus. A study of algal

blooms in the region from 1993–1997 showed that S. cf.

elongatus represented over 90% of total phytoplankton

biovolume in most instances when total phytoplankton biovolume exceeded 5 million μm3

/ml (Phlips et al.,

1999). Although cyanobacteria are the most abundant

phytoplankton in central Florida Bay, other taxonomic

groups can play important roles (Phlips et al., 1999;

Steidinger et al., 2001). For example, between May 1994

and April 1995, the diatoms Cyclotella choctawatcheeana

and Chaetoceros cf.salsugineus were frequently important elements of phytoplankton biomass (Steidinger et

al., 2001). Again, in July 1995, March 1996, and January

1997, diatoms were numerous.

Based on empirical observations and experimental studies, a number of hypotheses have been forwarded to explain the domination of Synechococcus cf.

elongatus in the central region of Florida Bay. Several

of these hypotheses are based on some of the unique

ecophysiological characteristics of this cyanobacterium.

Several research groups have demonstrated the broad

range of salinities over which S. cf. elongatus can sustain high growth rates (5–50 psu; Phlips and Badylak,

1996; Richardson, 2001). Because of the isolation of

central Florida Bay from tidal mixing and the proximity of the north-central bay to the adjoining Everglades,

this region is subject to wide swings in salinity. For example, salinities exceeded 40 psu during the drought

period of 1992–1994 but dropped to as low as 11 psu

during subsequent flood periods, such as 1995 and

1997 (Figure 6.4) (Phlips et al., 1999; Boyer et al., 1999).

The euryhaline tolerances of S. cf. elongatus probably

provide the cyanobacterium with an advantage in

terms of long-term prominence. However, it does not

fully explain the fact that intense blooms of S. cf. elongatus have been observed during times when salinities

have remained in a moderate range (25–35 psu.)

Another factor that may contribute to the success

of S. cf. elongatus is its ability to compete for nutrients

at low concentrations (Richardson, 2001). As a picoplanktonic species, one might expect S. cf. elongatus

to have low half-saturation constants for nutrient uptake, strictly because of surface area to biovolume considerations. Experimental studies have provided

support for this hypothesis. A study of the kinetics of

phosphorus (PO4-P)-dependent growth compared four

important phytoplankton species found in the bay:

the cyanobacterium Synechococcus cf. elongatus, an

unidentified spherical picoplanktonic cyanobacterium,

and the diatoms Chaetoceros cf. salsugineus and Cyclotella choctawhatcheeana (Richardson et al., 2001).The

results of growth tests revealed maximal growth rates

for S. cf. elongatus, the spherical cyanobacterium,C. cf.

salsugineus, and C. choctawhatcheeana of 1.38, 1.37, 2.48,

and 3.37 divisions day–1, respectively.The half-saturation constant for growth, Ku, was determined to be

0.005–0.05 μmol liter–1 for the latter three species.The

Ku for S. elongatus could not be determined because the

growth rate was still maximal at the lowest test concentration of phosphate. A test of phytoplankton resource-based competition using Equilibrium Resource

Competition theory predicts that S. cf. elongatus is the

superior competitor under phosphorus-limitation over

the range of salinities examined (15–50 psu). The superior competitive ranking of S. cf. elongatus can be attributed to the exceptionally low Ku values.The model

ranked the spherical cyanobacterium second in terms

of phosphate competition, with the diatoms last. In

competition experiments under steady and varying

P-limitation, S. cf. elongatus also dominated in terms of

biovolume at the end of all experiments at all salinities.Thus, with sufficient time, S. elongatus should competitively displace all the other species under

phosphorus-limited conditions. Competition experiments further revealed that under nitrogen-limiting

conditions, the two species of cyanobacteria usually codominated in terms of biovolume under steady- and

non-steady-state conditions. In summary, under both

Plankton Blooms
steady-state and non-steady-state conditions, the

cyanobacterium S. cf. elongatus is the superior competitor for orthophosphate and can frequently outcompete diatoms under N-limiting conditions.

Related to the question of nutrient competition is

the ability of S. cf. elongatus to regulate its buoyancy by

altering the presence of gas vesicles (Phlips and Bledsoe, unpublished data). Under phosphorus-limited

conditions, the presence of gas vesicles diminishes

and S. cf. elongatus cells lose buoyancy. It has been

suggested that with the loss in buoyancy, nutrient-depleted cells sink to the sediment–water interface, where

they can take advantage of higher nutrient availability (Phlips et al., 1999).

Besides the characteristics that may enhance the

competitive advantage of S. cf. elongatus in acquiring

resources for growth, there may also be ways this

species is favored by lower magnitudes of certain loss

terms. Butler et al. (1995) proposed that S. cf. elongatus

was responsible for the observed demise of sponges in

Florida Bay because of its adverse effect on the filtration apparatus of sponges. Although there is evidence

that sponges can effectively filter out S. cf. elongatusfrom

the water column (Lynch and Phlips, 2000), the longterm effects of filtering the mucilage-producing

cyanobacterium are not known. Irrespective of the direct effects of S. cf. elongatus on sponge health, it is clear

that the diminishing sponge populations in the bay result in reduced grazing pressure on phytoplankton

and thereby increase the potential for blooms (Lynch

and Phlips, 2000).

As in the case of sponges, the relationship between S. cf. elongatus and other grazers, both benthic

(e.g., bivalves) and planktonic (e.g., zooplankton), are

not well defined. There is evidence that zooplankton

grazing rates are periodically high enough to affect phytoplankton population dynamics (Brenner et al., 2001).

In grazing experiments, daily metabolic carbon demand of the net zooplankton community ranged from

less than 2% to greater than 100% of the phytoplankton carbon stock. Microphytoplankton growth rates

ranged from 0.08 to 2.33 divisions d–1 at 50% available

light. Diatoms, dinoflagellates, and the cyanobacterium

Synechococcus typically dominated the microphytoplankton community, although chlorophytes and

prasinophytes were occasionally major constituents.

Microzooplankton grazing rates ranged from 0.00 to

5.28 d–1, and their average ingestion rates ranged from

0.67 to 3.42 mg C m–3 d–1. These ingestion rates correspond to a daily ingestion demand ranging from less

than 1% to greater than 300% of the initially available

carbon, indicating that microzooplankton are capable

of exerting a controlling influence on the phytoplankton community. Despite the observed grazing rates, the

frequency of cyanobacterial blooms in the north-central region of the bay demonstrates that grazing activity

is frequently not sufficient to prevent blooms, although

it may play a role in their ultimate demise.There is no

information on whether the domination of S. cf. elongatus in the north-central region is in any way related

to selective avoidance by grazers, either benthic or

planktonic.

Western Florida Bay

The highest phytoplankton biovolume in western

Florida Bay generally occurs in the late summer to

winter, when the annual diatom bloom reaches its seasonal peak. Phytoplankton composition in the western

bay is distinct from composition in the central bay because a higher proportion of total biovolume occurs in

diatoms. Phlips and Badylak (1996) were the first to

identify the species composition of bloom components

in western Florida Bay. They found that centric (predominantly Rhizosolenia) and pennate (Cocconeis, Navicula, Surirella) diatoms were dominant species in terms

of cell abundance in December 1993. Steidinger et al.

(2001) subsequently reported that other taxa, especially cyanobacteria, may also account for a large fraction of total biovolume in western Florida Bay and

could equal the biovolume attributed to diatoms. In

2000 and 2001, Jurado (2003) conducted a study of netphytoplankton (diatom) silica demand at Carl Ross

Key in western Florida Bay. She found that centric diatoms (predominantly Rhizosolenia spp., Chaetoceros

spp., and Thalassiosira nitzschiodes) and pennate diatoms (Nistchia, Navicula, Gyrosigma spp.) dominated

the netphytoplankton fractions (greater than 5 μm).

These observations are in general agreement with

Phlips and Badylak’s (1996) results. Peak concentrations

of chlorophyll a (2–9 mg m–3) were higher than values

observed in the eastern bay but less than concentrations in the north-central basins. Netplankton chlorophyll a accounted for more than 50% of total pigment

biomass.

Although relatively few, if any, observations of

phytoplankton-community species composition in

western Florida Bay exist prior to 1990, biogenic silica

in the sedimentary record from Carl Ross Key suggest

that an increase in the abundance of diatoms has occurred since 1960 (Figure 6.5). Biogenic silica is a distinct marker for the presence of diatoms. Although

only two values exist from the sedimentary record before 1960, the vertical profile suggests that biogenic silica concentrations increased from less than 1 mg silicon

(Si) to greater than 1 mg Si (g sediment)–1 sometime

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86 FWRI Technical Report TR-11

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FWRI Technical Report TR-11 87

after 1950, although values in the last decade have

been highly variable.This trend suggests that enhanced

diatom biomass in western Florida Bay has developed

within the past four or five decades.

Cellular division rates determine the success of a

species in the natural environment. Net growth rates

equal the difference between the cellular division rate

and the sum of all processes that represent losses, including grazing, sinking, advection, and death. Net

increases in phytoplankton communities of as little as

0.1 day–1 result in an increase of less than 1 to greater

than 20 mg m–3 chlorophyll a in less than a month. Although we have no direct measures of netphytoplankton growth rates in western Florida Bay,

community growth rates for netplankton have been estimated from increases in chlorophyll a and biogenic

silica in dilution gradient experiments. This method,

principally developed by Landry and Hassett (1982) and

their colleagues, provides a measure of maximum

growth. In March 2001, when phytoplankton abundance was low, netplankton chlorophyll a exhibited

growth rates of 1.5 day–1, increasing to 2.9 day–1 in May,

July, and September, as netplankton biomass increased.

By November 2001, netplankton biomass had reached

a stationary phase, and maximum growth rates were

again ca. 1 day–1. Grazing losses ranged from 0.6 to

1.75 day–1 in these experiments, yielding net growth

rates of 0.5 (November) to greater than 1.3 day–1 in

May and September. Although these experiments represent only the potential for diatom growth in situ,

they suggest that conditions in summer-fall provide diatoms with a setting for growth rates that exceed the

sum of losses.

Exchange of surface waters in western Florida Bay

with the West Florida Shelf is evident in the nature of

the phytoplankton community and property distributions. Salinity values in western Florida Bay show less

temporal variability than in the central or eastern

basins. On average, basins in the western bay have a

higher average salinity (mean = 35.2 psu) and lower average TN (30.5 μmol kg–1) and dissolved inorganic nitrogen (DIN) (<2 μmol kg–1) than do those in the eastern

or central bay (Boyer et al., 1999). Chlorophyll a concentrations from the long-term FIU monitoring program averaged 1.9 mg m–3, which, as suggested by

Phlips et al. (2000), is less than the average values in the

central bay but higher than in the eastern bay.

Ratios of TN:TP (x = 55.6) and DIN:SRP (soluble reactive phosphorus) (x = 51.8) in the western bay are

higher than Redfield values but lower than those in either the eastern or central basins.These characteristics

suggest that the western bay is strongly influenced by

the surface waters of the West Florida Shelf that exchange along the boundary of Everglades National

Park. The influence of coastal processes is evident in

tidal exchange, which is much greater in the western

bay than in the interior or eastern basins because the

amplitude of the tides is damped from west-to-east

across the bay (Wang et al., 1994).

Bioassays at two locations along the western margin of Florida Bay (Sprigger Bank and Sandy Key) indicate that nitrogen is a primary nutrient that limits

phytoplankton growth (Tomas et al., 1999). In more

than 70% of the bioassays between March 1994 and May

1997, Tomas found that nitrogen in combination with

silica stimulated growth more than did individual additions of phosphorus or silica. When individual nutrients were excluded from otherwise complete

enrichments (all nutrients – N, or all nutrients – P), the

lack of nitrogen yielded a final biomass that was similar to controls. Phosphorus limitation of phytoplankton growth rates was detected in about 20% of all

experiments, and iron was even less frequently identified as a nutrient potentially limiting growth.

The responses to N and Si enrichments are consistent with the marine waters that flow into the western margin of Florida Bay and the fact that diatoms

frequently dominate these waters.The observations of

Figure 6.5 Vertical profile of biogenic silica in a sediment core from

Carl Ross Key.The sediment samples with corresponding dates were

kindly provided by Dr. J. Trefrey, Florida Institute of Technology

(Jurado, 2003).

Plankton Blooms
Florida Bay Synthesis Hunt and Nuttle

88 FWRI Technical Report TR-11

Tomas et al. (1999) were confirmed by Jurado (2003), who

found that nitrogen was the principal nutrient limiting both total phytoplankton and netplankton (diatom) growth in western Florida Bay during the

2000–2001 diatom bloom (Figure 6.6). Bioassays were

made in September and November 2000, as diatom

abundance increased, and in January and March 2001,

when diatom biomass declined. The results consistently showed that enrichments with nitrogen, and

secondarily silica or phosphorus, stimulated growth of

natural populations incubated under simulated in situ

conditions. An assessment of temperature and irradiance during the course of the year suggests that these

two parameters did not effectively limit the growth of

diatoms in western Florida Bay. Thus nutrient supply

may be the main factor that accounts for the enhanced

growth of diatoms in summer and fall in western

Florida Bay.

Seasonal distributions of salinity, nutrients, chlorophyll a, and biogenic silica on the West Florida inner

shelf, south from the Ten Thousand Islands to the western boundary of Everglades National Park, indicate

that diatom blooms observed in western Florida Bay

originate in coastal waters off the southwestern Florida

Shelf.These features develop in the shallow coastal waters west of Cape Sable and are associated with the lowsalinity plume emanating from the Shark River and

other riverine sources along the southwestern Florida

coast. A chlorophyll a “plume” spreads south from

Cape Sable to the western margin of Florida Bay during the fall (Figure 6.7). Bimonthly cruises of the NOAA

SFERPM Program between 1998 and 2003 have mapped

surface-water properties (salinity, nutrients, chlorophyll a, and particulate matter) in this region. Spatial

distributions of these properties indicate that the Shark

River is a major source of nutrients, especially silicate,

supporting the diatom bloom. Concentrations of dissolved inorganic nutrients in the Shark River plume at

bimonthly intervals indicate that the average concentrations of silicon, inorganic nitrogen, and phosphorus

in the plume of the Shark River indicate excess silicate

relative to inorganic nitrogen and phosphorus. Little

seasonal variation exists in nutrient concentrations,

so the volume of freshwater flow appears to be the primary determinant of nutrient flux to the inner shelf.

On the southwestern Florida Shelf, exogenous nutrients that support diatom growth are derived from the

Shark River plume and along-shore flow. Increased

freshwater flow from rivers often occurs in June at the

onset of the rainy season and provides silicates to the

inner shelf that contribute to development of the diatom bloom. Between 1998 and 2000, the diatom-dominated bloom on the inner shelf began between August

and October. Estimates of the fluxes of nitrate, phosphate, and silicate from along-shore advection (based

on bimonthly nutrient measurements and alongshore

currents from ADCP currents made by T. Lee and colleagues) and that from the Shark River (derived from

river discharge and bimonthly nutrient measurements)

were for the period of bloom inception in 1999 (Jurado,

Figure 6.6 Bioassay results from September 2000 at Carl Ross Key

(Jurado, 2003). Values correspond to increases in chlorophyll a

biomass relative to a control in an incubation of 24 hours.The total

phytoplankton community was filtered on Whatman GF/F filter,

and the netplankton fraction on a 5-μm Nuclepore filter.The combination of nitrogen plus phosphorus or silicon typically results

in the greatest stimulation of phytoplankton growth.

Figure 6.7 Contours of total chlorophyll a concentrations (top)

and surface salinity (bottom) in October 2000 during the peak of

the annual diatom bloom. Maximum chlorophyll a concentration

was 17 mg l–1 off middle Cape Sable (Jurado, 2003).

Plankton Blooms
2003).This is the latest year in which Shark River flow

data were available at the time the estimates were

made.The resulting flux estimates suggest that during

bloom inception, exogenous nutrient sources that support diatom bloom development are largely met by the

southerly flow along the southwestern Florida Shelf

(Figure 6.8). When the bloom is at its maximum, after

the onset of the rainy season, Shark River is a major

source of nitrate, nitrite, and phosphate. Alongshore advection of silicate appears to be the primary source of

this essential nutrient for diatoms, at least in that year.

In summary, diatom blooms in the western basins

of Florida Bay are a seasonal extension of blooms that

initiate on the southwestern Florida Shelf. Various

species of Rhizosolenia and Chaetoceros are the dominant members of this assemblage, in combination with

pennates that are likely resuspended from the bottom. Diatoms begin net growth (i.e., growth rates exceed losses) with the onset of the rainy season.

Bioassays suggest that nitrogen, often in combination

with phosphorus and/or silica, potentially “limit”

growth. Nutrients that support diatom growth are derived from riverine sources, principally Shark River, and

along-shelf (southerly) advection.The relative contribution of inorganic nitrogen, phosphorus, and silicon

varies with the stage of the bloom, and likely varies

yearly with variations of river discharge and alongshore

flow.

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Introduction

Question 4—What are the causes and mechanisms for the

observed changes in the seagrass community of Florida

Bay? What is the effect of changing salinity, light, and nutrient regimes on these communities?

Seagrass beds are an important component in many

coastal marine environments; however, there are few

locations in the world where seagrasses are as dominant in the hydroscape as they are in south Florida

(Fourqurean et al., 2002). Seagrasses are the dominant

biological community in Florida Bay, historically covering more than 90% of the 180,000 ha of subtidal mudbanks and basins within the bay (Zieman et al., 1989).

By comparison, mangrove islands cover only about 7%

of Florida Bay. Because of the shallow nature of Florida

Bay (mean depth less than 2 m; Schomer and Drew,

1982), seagrasses are also the dominant physical feature

of the bay, and their presence greatly affects physical,

chemical, geological, and biological processes in this system (Zieman, 1982). Seagrass communities are also important to the economy of south Florida because they

provide food and shelter to numerous fish and invertebrate species, many of which are commercially important to the region (Powell et al., 1989; Thayer and

Chester, 1989; Tilmant, 1989; Chester and Thayer, 1990).

In addition, the waters of western Florida Bay form

a hydrodynamic link between the Everglades and the

coastal waters of the southwestern Florida peninsula

and eastern Gulf of Mexico to the north and the Florida

Keys reef tract and the Atlantic Ocean to the south

(Schomer and Drew, 1982).The seagrass communities

of this region form an important buffer by intercepting the flow of water and reducing nutrient and particulate loads in the waters reaching the reef tract

(Kenworthy et al., 1998). Continued loss of seagrasses

along this margin and proposed increases in water

flow from the Everglades could result in greater exports

of nutrients and particulates out of Florida Bay and onto

the reef tract (Kenworthy et al., 1998). Resource managers will need to consider actions that might aid in the

reestablishment of continuous seagrass cover in western Florida Bay.This would be an important step in reducing sediment-resuspension-induced turbidity along

this boundary that could reverse the cascading declines that characterize the present system.

Seagrasses act as integrators of net changes in

water-quality variables, which tend to show rapid and

wide fluctuations when measured directly.The shallow

distribution of seagrasses places them in close proximity to the land–sea interface, a region experiencing

a rapid growth of human populations.This coastal distribution also places seagrass communities at the end

of the watershed pipe, so the health of these communities reflects not only direct coastal influences but

larger-scale, landscape-to-regional influences as well.

Because most seagrasses are benthic-perennial plants,

they are continuously subjected to stresses and disturbances that are associated with changes in water

quality along the land–sea interface.To a large extent,

seagrass abundance determines public perception regarding the “health”of the coastal waters of Florida (Goerte, 1994; Boesch et al., 1993, 1995). Thus, the recent

changes in the distribution and abundance of seagrasses within Florida Bay have been perceived as a

change in the health of the bay. For these reasons, seagrasses may be the best indicators of changes in the

Florida Bay ecosystem (Fourqurean et al., 1992).

Although the initial die-off originated in the interior basins of the bay (Robblee et al., 1991), the greatest changes in seagrass abundance in the present

system are occurring far from the Everglades-Florida

Bay land–sea interface (Durako et al., 2002).The spatial

patterns of changes in abundance from 1995 to 2000

suggest that the most perturbed environment in Florida

Bay with respect to seagrasses is currently along the

western and southern margins of the bay. Much of the

focus of management and restoration efforts in south

Florida have been directed toward landscape-scale

modifications and an extensive flood-control system to

increase the quantity of freshwater delivered to northeastern Florida Bay and, more recently, to Shark River

slough.

Seagrass Communities in Florida Bay

Seagrasses continue to be the dominant biological

Chapter 7

Seagrass Ecology

Team Leaders Michael Durako (University of North Carolina at Wilmington), 

Joseph Zieman (University of Virginia), Michael Robblee (USGS, PMC)
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 93

community in Florida Bay. Of the more than 14,000

Braun-Blanquet samples (each 0.25 m2) taken in the bay

from 1995 to 2000 by the Fisheries Habitat Assessment

Program (FHAP; Durako et al., 2002), approximately

97% contained seagrass. In northeastern Florida Bay,

Thalassia was present at 75.9% and Halodule was present at 69.0% of the 762 randomly selected stations

sampled from May 1999 to May 2000 (Bacon et al.,

2001).The entire south Florida coastal zone, including

the areas west of Florida Bay and within the Florida

Keys National Marine Sanctuary (FKNMS), is dominated by seagrass habitats. Fourqurean et al., (2002) assessed seagrass species composition and density at

1,207 sites distributed across 19,402 km2 of nearshore

marine and estuarine environments in south Florida.

At these sites, a total of 8,434 quadrats (each 0.25 m2 total

area = 2,108.5 m2) were sampled from 1996 to 1998. At

least one species of seagrass was observed at 1,056 of

the 1,207 sites, or 87.5% of all sampling sites. Thalassia

testudinum (turtlegrass) was the most commonly encountered species, being found at 898 sites. Halodule

wrightii (shoalgrass) was the second most commonly

encountered species, occurring at 459 sites, followed

by Syringodium filiforme (manateegrass, 239 sites),

Halophila decipiens (paddlegrass, 96 sites),Ruppia maritima (widgeongrass, 41 sites) and Halophila engelmannii (stargrass, 28 sites).

Recent and Historical Changes

A widespread die-off of seagrasses within Florida Bay

began in 1987 (Robblee et al., 1991; Table 7.1; http://people.uncw.edu/durakom/seagrass/seagrass.htm). This

event was first observed by backcountry fishing guides

who reported the occurrence of “potholes”in the seagrass beds in the bights along the north-central part

of Florida Bay. Extensive areas of Thalassia began dying

rapidly in central and western basins, and by 1990,

4,000 ha were completely lost and 24,000 ha were affected by the die-off (Robblee et al., 1991).

The patterns of changes in seagrass abundance in

Florida Bay have recently undergone four phases: 1) primary die-off; 2) secondary mortality, with mortality

primarily due to light attenuation; 3) seagrass recovery associated with improving water clarity; and 4) renewed primary die-off in areas where die-off has not

been previously observed.The initial phase of primary

seagrass die-off occurred only in Florida Bay, which is

the most continentally influenced and least oceanically flushed of all of the extensive south Florida seagrass beds, and it occurred only in the most densely

developed beds within the bay. To this day, no occurrence of primary seagrass die-off has been found outside of the densest seagrass beds within Florida Bay,

and no primary seagrass die-off has occurred in sparseor medium-density beds within the bay.

PRIMARY SEAGRASS DIE–OFF

The first phase of primary seagrass die-off occurred

during the relatively dry and clear period of 1987 to

early 1991. During this period, density, standing crop,

and productivity of Thalassia were high but then declined as the die-off progressed (Durako, 1995; Zieman

et al., 1999). Some stations had shown large increases

in seagrass standing crop in the period prior to the dieoff (Zieman et al., 1999). In addition, Batophora oerstedi

and Halodule spread rapidly into die-off patches (Thayer

et al., 1994). At this time, Florida Bay waters as a whole

remained as clear as they had been in the years just

prior to the die-off, with limited turbidity from suspended sediments in the immediate vicinity of the

denuded die-off patches.

SECONDARY MORTALITY

Several years after the initiation of the seagrass die-off,

Florida Bay began exhibiting widespread and chronic

turbidity with a concomitant decline in Thalassia and

Halodule in Johnson Key Basin and Rankin Lake

(Stumpf et al., 1999). The increase in turbidity, which

began during the fall of 1991, was principally due to

cyanobacteria-dominated microalgal blooms and resuspended sediments, which were associated with the

loss of seagrasses on the western banks and was most

severe in the western and central bay (Phlips and

Badylak, 1996).These blooms may have been initiated

by the nutrients liberated by the die-off of seagrasses

(Butler et al., 1995). Loss of seagrass cover was the

major factor of the increases in sediment resuspension

in the bay (Prager, 1998). This resulted in a negative

feedback loop in which loss of seagrass cover from

die-off led to exposed, easily resuspended sediments

and more widespread losses of seagrasses due to turbidity. Sponge mortality, changes in juvenile lobster

population dynamics (Butler et al., 1995), and indications of cascading effects on plant and animal communities in adjacent systems (e.g., sea urchin

population explosions and unbalanced growth of Syringodium filiforme in the waters of the Florida Keys National Marine Sanctuary southwest of Florida Bay;

Kenworthy et al., 1998; Rose et al., 1999) were also observed. From 1992 to 1995, salinities showed a progressive decline throughout the bay (Boyer et al., 1999).

During this time, there was speculation regarding

how much seagrass had been lost, with as much as

100,000 acres (40,000 ha) estimated with no supporting

data. With the decline in water clarity, aerial photography became useless in determining seagrass distribution over much of Florida Bay. Because of the

Seagrass Ecology
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94 FWRI Technical Report TR-11

Table 7.1 Florida Bay seagrass die-off milestones.

Event or Observation Date Significant Publication/Research Initiated

SPOT image shows no die-off patch in Rabbit Feb 2,

Key Basin, Johnson Key Basin, or Rankin Lake. 1987

“Potholes”seen in Thalassia beds in Rankin Lake Summer FIU/SERP water-quality monitoring initiated.

and Cross Bank by back-country fishing guides. 1987

Heat stress kills tagged conch in Hawk Channel Jul 1987

(Berg); coral bleaching at Looe Key (Causey);

fish dying on Cross Bank (Holmquist, Robblee).

Robblee observes die-off patches Late Fall

along north shore of Johnson Key. 1987

Guides contact Susan Bell about dying seagrasses. Mar 1988

Guides meet Mike Robblee and Jim Tilmant at Apr 1988 Robblee and Zieman visit Rankin Lake and

Little Rabbit Key and observe extensive die-off. Johnson Key Basin.

ENP consults Jay Zieman.

May 1988 Zieman provides ENP a trip report on die-off,

indicating its uniqueness and stressing need to

monitor and conduct research. Carlson-Durako

survey Johnson Key Basin.

Zieman observes lesions were not apparent. Spring–

Robblee and Holmquist observe phytoplankton Summer

bloom NE of Long Key. 1988

SPOT imagery shows large die-off patch in Jun 1988

Rabbit Key Basin.

Sep 1988 Robblee provides memo on seagrass die-off to 

Superintendent Finley. Finley provides funds for 

researchers to evaluate die-off.

Nov 1988 ENP-sponsored field trip: Robblee, Carlson,

Durako,Fourqurean, Muehlstein, Porter, and

Zieman visit die-off areas. Labyrinthula detected.

Apr 1989 Durako initiates studies on morphometric changes,

Braun-Blanquet abundance, and demography.

Carlson begins studies on hypoxia/sulfide-ADH,

ethylene, H2S, conducts bucket experiments.

May 1989 Robblee initiates studies of seagrass associated

animal responses to die-off in Rankin Lake,

Johnson and Rabbit Key basins. Monitoring of 

plant community response to Thalassia die-off 

initiated.

Jun 1989 Zieman completes version 1 of his conceptual

model of seagrass die-off.

Zieman initiates long-term Thalassia productivity

measurements near four core die-off areas.

Jul 1990 Thayer et al. investigate plant community response

to die-off in Johnson and Rabbit Key basins.

Halodule begins to colonize die-off patches. 1990–1991

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FWRI Technical Report TR-11 95

Earliest observation of persistent turbidity Apr 1991 Robblee et al., 1991: Marine Ecology 

caused by tidally resuspended sediments Progress Series 71: 297–299. First published

observed in Johnson Key Basin. Kuss, observations of the die-off: clear, warm,

DiDomenico, Robblee observers. hypersaline conditions.

Early conceptual models of die-off Fall 1991 Durako-Kuss: Labyrinthula effects on Thalassia

developed: Zieman, Carlson-Durako. photosynthesis.

Cyanobacteria bloom begins in Rabbit Key basin. Nov 1991

Hurricane Andrew passes over south Florida; Aug 24,

has little direct impact on Florida Bay. 1992

High rainfall occurring the week after Andrew Approx.

washes mangrove “rot”into Florida Bay. Sep 1,

Zieman observes that this event began the 1992

severe turbidity events in the bay.

Major turbidity plume from western Dec 22,

Florida Bay reaches Big Pine Key. 1992

Apr 1993 Zieman et al. look at light-reduction effect on

Thalassia in Rabbit Key basin and Sunset Cove.

Oct 1993 Hefty et al.: DERM initiates seagrass monitoring

of northeastern basins.

Jun 1994 Hall-Durako: 107 stations previously sampled

in 1983–84 are resampled for decadal comparison

of seagrass abundance.

Oct 1994 Series of faunal studies conducted in mid-1980s

are repeated as a part of the decadal comparison

program: Thayer, Matheson and Camp, Robblee.

Nov Durako-Hall: Preliminary test of EMAP-based 

1994 Braun-Blanquet sampling.

Very wet spring and summer; true estuarine Spring Durako-Hall: Fish Habitat Assessment

conditions exist throughout Florida Bay. 1995 Program (FHAP) initiated.

Landsberg-Blakesley: Labyrinthula spatial and 

temporal dynamics.

Oct Montague initiates field studies in northern 

1995 Florida Bay; starts construction of a mesocosm 

system to look at effects of salinity fluctuations.

Halophila engelmannii first observed in Johnson Oct 1996

Key basin, suggests a shade-adapted community.

Aug 1997 Stumpf examines satellite imagery to detect

changes in seagrass abundance from 1986–1997.

Rudnick: Florida Bay ecosystem conceptual model. 1997

Oct 1997 Carlson-Blakesley initiate banktop die-off 

studies.

Nov 1997 Fourqurean et al. sample two areas in Rabbit Key

Basin to examine scale-based variability in 

potential Thalassia ecoindicators.

Flowering of Thalassia and Halodule widespread. May 1998

Table 7.1 Florida Bay seagrass die-off milestones. (continued)

Event or Observation Date Significant Publication/Research Initiated

Seagrass Ecology
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96 FWRI Technical Report TR-11

continuing concern regarding the extent of seagrass

changes within Florida Bay and the need to monitor the

effects on seagrass communities of proposed watermanagement alterations for the restoration of the Everglades-Florida Bay ecosystem, the FHAP was initiated

during spring 1995. The turbid conditions in western

Florida Bay from 1995 to 1997 made measuring and interpreting seagrass losses and changes in species distributions more complicated because of the primary

die-off versus secondary effects attributable to light limitation. Early FHAP data (1995–1997) indicated that

seagrass decline in the western basins was primarily

due to degraded water quality because mortality was

signified by a general thinning of shoots, rather than

the occurrence of distinct die-off patches surrounded

by dense beds. A comparison of seagrass distributions

in Florida Bay between 1984 and 1994 (Hall et al., 1999a)

and between 1995 and 1998 (Durako et al., 2002) also indicated that the chronically turbid regions had exhibited the most significant losses of T. testudinum.

STABILIZATION AND RECOVERY

Following the initial die-off and period of widespread

turbidity, seagrass abundance has shown three distinct

phases (Zieman et al., 1989, 1999): at stations associated

with primary seagrass die-off, standing crop declined

from 1989 to 1995; standing crop remained stable from

1995 through 1997; and standing crop has increased

during the past several years (1998–2001). Thalassia

has shown little net change in abundance (±8% of the

mean) at the bay scale from 1995 to 2001 (Figure 7.1),

although at the basin-scale, abundance has varied by

an average of ±30% (losses then gains in the west, contrasted with stability or gains in the middle and eastern basins). Most of the increase in seagrass abundance

has resulted from expanding coverage by Halodule

(Figure 7.2; + 200% baywide, + 450% in Johnson Key and

Rabbit Key Basins; Durako and Hall, 2000). Thus, the

dominance of Thalassia is declining, and mixed turtlegrass and shoalgrass beds are becoming more common.

In the past five years, relative Thalassia abundance has

dropped from being more than five times that of Halodule to being less than three times more abundant; in

spring 1997, Halodule replaced Thalassia as the most

abundant seagrass in Johnson Key Basin (Durako et al.,

2002). During fall 1996, the small-bodied, low-lightadapted seagrass Halophila engelmannii was observed

at one station in Johnson Key Basin. By spring 1998, this

species was present at 15 of the 32 stations in this

basin.

The passage of Hurricane Georges west of the bay

in the fall of 1998 uprooted much of the Halophila in

Johnson Key Basin (it was observed only at five stations

nine days after the storm); reduced the cover of Thalassia (especially in areas where it had been sparse); and

removed much of the litter layer on the bottom. However, by spring 1999, Halophila cover increased in Johnson Key Basin, and this species was observed in Rankin

Lake, Whipray Basin, and Twin Key Basin. This rapid

increase in spatial distribution suggests the hurricane

may have played a role in distributing Halophila

propagules (Durako et al., 2002). Longer internodes

and deep apical meristems on short shoots of Thalassia at Barnes Key were observed shortly after Hurricane

Hurricane Georges passes west of Florida Bay. Sep 1998

“Classic”die-off patches present on bank edge Oct 1998

east of Big Rabbit Key.

Barnes Key eastern bank and basin dense 

Thalassia, crystal-clear water.

Fall 1998 Koch: Sulfide phytotoxicity studies on Thalassia.

New “classic”die-off observed in Barnes Key Jan 1999 Hall-Blakesley monitor changes in Thalassia

area and in Sunset Cove. characteristics and Labyrinthula abundance.

Die-off patches present on bank to east of Apr 1999

Barnes Key and in basin north of key.

Flowering of Thalassia and Halodule again May 1999

observed in core samples from several stations.

Hurricane Irene passes west of Florida Bay. Oct 1999

Flowering of Thalassia observed in field, May 2000

recruiting seedlings observed in cores.

Table 7.1 Florida Bay seagrass die-off milestones. (continued)

Event or Observation Date Significant Publication/Research Initiated

Seagrass Ecology
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FWRI Technical Report TR-11 97

Georges, suggesting the hurricane resuspended sediments in Florida Bay. Hurricane Irene also reduced seagrass cover in areas of sparse Thalassia and reduced

Halophila distribution as determined by before-andafter sampling by FHAP.

Another recent dramatic change in the ecology of

seagrasses in Florida Bay is the widespread occurrence of flowering in both Thalassia and Halodule. In

spring 1999, reproductive short-shoots of Thalassia

were present at 19 sites in 7 basins across the bay; reproductive short-shoots of Halodule were present at 24

sites in 4 basins in the western part of the bay (Durako

et al., 2002). In spring 2000, flowering Thalassia was observed at 19 sites in 6 basins. The recent increases in

seagrass cover and the dramatic increase in flowering

may reflect improvements in water quality, although

shifts from turtlegrass to shoalgrass and the appearance and spread of Halophila engelmannii are often associated with declining light availability.

Since 1998, there has been an upturn in abundance,

Figure 7.2 Changes in relative abundance, as determined by Braun-Blanquet sampling, of Halodule from spring 1995 to spring 2001.

Seagrass Ecology

Figure 7.1 Changes in relative abundance, as determined by Braun-Blanquet sampling, of Thalassia from spring 1995 to spring 2001.
Florida Bay Synthesis Hunt and Nuttle

98 FWRI Technical Report TR-11

productivity, standing crop, and flowering of Thalassia

and Halodule that seems to be associated with improving water clarity (Zieman et al., 1999; Durako et al., 2002).

Some of this improvement in water clarity may be due

to a decrease in unvegetated bottom (Durako et al.,

2002). However, as recovery begins to occur at the original die-off sites, a new instance of primary seagrass dieoff that began in January 1999 has been observed north

of Barnes Key.This new primary die-off is occurring in

an area where die-off has not been previously observed,

but it has some characteristics very similar to those observed during the initial seagrass die-off in 1987.The area

has excessively dense beds of T.testudinum, with die-off

patches interspersed among the dense beds, and the

same unusual seagrass morphologies (“twinning”) have

been observed in surviving shoots (Zieman et al., 1999).

Seagrasses affected by the new die-off have symptoms

like those of the 1987 event; i.e., the short-shoot meristem tissue appeared to be the tissue most immediately

affected. Meristems seemed mushy and smelled like

“mustard,”whereas the rest of the blade looked green

and healthy (Carlson et al., 1990).

PALEOECOLOGICAL INVESTIGATIONS 

Although not part of the seagrass research program,

paleoecological investigations add relevant information

for understanding how recent seagrass changes fit

into the matrix of historical expansion and contractions

of seagrass cover. At present, it appears that seagrass

coverage, as estimated both by the abundance of seagrass-associated microfossils and by chemical signatures in the sediments, has shown repeated cycles of

presence and absence at the core sites.Thus, the recent

changes in seagrass cover are apparently not unprecedented. However, the paleoecological data come

from only a few selected locations, limiting the confidence that can be placed in their general applicability. Therefore, it would be extremely valuable to have

additional paleoecological information from more sites

throughout the bay.

Conceptual Models for Seagrass Die-Off

Early in the die-off studies, conceptual models were developed of hypothesized die-off mechanisms and the

conditions and processes leading up to the die-off.

Initially, the model developed by Zieman et al. was a

mostly process-oriented model and placed strong emphasis on the historic conditions leading up to the dieoff. The other model was developed by Carlson and

Durako and was a more mechanistic model with more

emphasis on the die-off process. These conceptual

models are shown in the accompanying figures.

The Zieman et al. (1999) model (Figure 7.3), has

three major phases: A Developmental Phase (A–C), in

which a combination of natural and anthropogenic

processes contributed to an extensively developed

(overdeveloped, actually) Thalassia ecosystem; an Initiation Phase (D–G), in which the heavily developed

system interacted with a suite of environmental stresses

to produce the initial die-off episodes; and a Maintenance Phase (G–L–G and repeat), in which the process

became self-sustaining. In this model, the interactions

of the dense Thalassia and the environmental stresses

formed the primary trigger to the initial die-off

episodes.

The Carlson and Durako model (Figure 7.4) included over-developed Thalassia as a component but

focused more on the role of physiological stress, especially hypoxia and sulfide toxicity, as major drivers.

In addition, this model gives a much larger role to the

effects of a slime mold, Labyrinthula, as a causative element. Although both of these models have matured

as research has progressed, the process has been one

of small refinements, and both have changed little in

the past decade.

As research progressed and the conceptual models matured, seagrass researchers found much common

Figure 7.3 Zieman et al. model for seagrass die-off.

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ground on which to agree. Among these points of

agreement are the following:

• Primary seagrass die-off is species-specific, restricted

to Thalassia testudinum.

• Primary die-off occurs only in very dense beds;

sparse and medium-density beds have never been

shown to have primary die-off.

• Primary die-off has occurred in Florida Bay only. It has

occurred in continentally influenced regions of the bay

with reduced circulation and reduced flushing.

• Primary die-off occurs principally during late summer–fall or fall–early winter. Both the Sunset Cove

and Barnes Key die-off events were first observed

during January–February. Most significantly, primary die-off does not occur in the hottest months of

summer.

• Researchers with experience in Florida Bay prior to

the initial primary die-off found the waters to be

clear and the seagrasses mostly free from epiphytes

during 1987–1989. Reduced water clarity and epiphytic growth followed seagrass die-off by several

years.

Factors such as high water temperature, prolonged

hypersalinity, and excessive seagrass biomass (due to

lack of recent disturbances, including hurricanes and

reduced salinities), which lead to increased respiratory

demands, hypoxia, and sulfide toxicity are some of the

physiological stressors thought to have contributed to

Thalassia die-off (Robblee et al., 1991; Carlson et al.,

1994). Observations indicated that the waters of Florida

Bay were generally clear, warm, and hypersaline in

most areas exhibiting die-off. High water-column light

attenuation from suspended sediments or eutrophic

phytoplankton growth was not present at the initiation

of the die-off or for the first several years (Boyer et al.,

1999).

Lesions were frequently observed on blades of

Thalassia in areas affected by die-off, but they were not

universally present during the earliest phases. An undescribed species of marine slime mold in the genus

Labyrinthula was the most common microorganism

isolated from short-shoots affected by die-off (Porter

and Muehlstein, 1989). Physiological stress and a negative carbon balance are associated with infection of

Thalassia by Labyrinthula (Durako and Kuss, 1994).

Based on these early observations and data, the two

conceptual models were formulated (the Zieman et al.

model and the Carlson and Durako model) incorporating distal and proximal elements thought to have

contributed to die-off.These models also included predictions of negative cascades following die-off.

Establishing the relative contribution of (primary)

die-off versus mortality induced by light stress to the

recent losses of Thalassia in western Florida Bay is

problematic. There is a high spatial coincidence between the distribution patterns of seagrass loss,

Labyrinthula abundance (Landsberg et al., 1996;

Blakesley et al., 1998), high sediment-sulfide levels

(Carlson et al., 1994), and turbidity (Phlips et al., 1995;

Stumpf et al., 1999). Increases in Halodule in the bay may

reflect its lower light requirements (Williams and

McRoy, 1982; Dunton and Tomasko, 1994), ability to

rapidly spread into areas where the Thalassia canopy

has been removed (Thayer et al., 1994), or resistance to

disease. There has been little change in Thalassia and

Halodule abundances in basins that are periodically subjected to low salinities. This may reflect the effects of

intermediate disturbance (sensu Connell’s Intermediate Disturbance Hypothesis) in maintaining a mixedspecies sub-climax (See fig. 13 in Zieman, 1982) as well

as offering a low-salinity refugium from disease—

Labyrinthula has never been found in Florida Bay at

salinities below 15 practical salinity units (psu)

(Blakesley et al., 1998).

Summary of Research

Research on seagrass dynamics has focused on the

Figure 7.4 Carlson and Durako model for seagrass die-off.

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100 FWRI Technical Report TR-11

influence of internal conditions in the ecosystem and

external driving factors on plant growth and metabolism. It has also emphasized documentation of the sequence and pattern of seagrass die-off and recovery in

Florida Bay (Table 7.2). The principal findings of this

work are as follows:

• Primary die-off is associated with high-density Thalassia beds. High-density beds result in conditions

that increase stress on Thalassia: high sedimentsulfide levels (greater than 2–4 mmol); self-shading

of shoots; nighttime/early morning anoxia/hypoxia

in meristems; and increased susceptibility to leafto-leaf transmission of Labyrinthula. Recent die-off

in the Barnes Key area occurred where Thalassia

densities and standing crop are among the highest

in Florida Bay.

• Geographic variation in patterns of seagrass loss

suggests multiple causes and a distinction between

primary die-off and secondary mortality.There is a

high spatial coincidence between the distribution of

Thalassia loss, Labyrinthula abundance, high sediment-sulfide levels, and turbidity, but determining

the relative contributions of these factors to die-off

versus secondary mortality has been difficult.

• Recent bay-scale changes in seagrass distribution and

abundance following the region-scale primary seagrass die-off (1987–1991) are largely due to secondary

mortality of Thalassia associated with areas of chronic

turbidity (since 1994) in western Florida Bay. These

changes are most likely due to light limitation as

indicated by stand-thinning in Thalassia beds with

concommitant increases in low-light-adapted species

such as Halodule wrightii and Halophila engelmanii.

There has also been a loss of Thalassia in northern

Little Madeira Bay, near the mouth of the Taylor

River, followed by colonization by Halodule and Ruppia.The cause of this loss is unknown. Primary acute

die-off (rapidly developing dead patches within

dense beds) is known to be currently occurring (initiated in 1999) only in the high-density Thalassia

beds of the Barnes Key area. A chronic die-off is occurring in dense beds in Sunset Cove. However, the

etiologies of these two sites are different.

• The boom-and-bust pattern of Halodule and Ruppia

characteristic of the Joe Bay and Highway Creek

areas of northeastern Florida Bay prior to 1991 has

Table 7.2 Research topics defined by Question 4 (cells in the matrix) and key references to the associated research.

Plant Growth and Seagrass Die-off and 

Research Topic Metabolism Recovery

General Characteristics Robblee et al., 1991; Fourqurean et al., 1992;

Thayer et al., 1994; Hall et al., 1999a,b;

Stumpf et al., 1999; Zieman et al., 1999;

Durako and Hall, 2000; Bacon et al., 2001;

Durako et al., 2002

Temperature and Salinity Chesnes et al., 1999 Blakesley et al., 1998; Boyer et al., 1999;

Fourqurean et al., 2003

Light Attenuation Williams and McRoy, 1982; Prager, 1998; Stumpf et al., 1999;

Dunton and Tomasko, 1994; Fourqurean et al., 2003

Thayer et al.,1994; Frankovich 

and Zieman, 2001; Holmquist

et al., 1989

Nutrients Fourqurean et al., 1992, 2003 Butler et al., 1995; Fourqurean et al., 2003

Anoxia and Sulfide Erskine and Koch, 2000 Barber and Carlson, 1993; 

Carlson et al., 1994; Erskine and Koch, 2000

Disease Durako and Kuss, 1994; Porter and Muehlstein, 1989;

Durako and Kunzelman, 2002 Muehlstein, 1992;

Blakesley et al., 1998, 1999a,b

Dense Grass Beds Durako, 1995; Hall et al., 1999a Durako, 1994, 1995; Durako et al., 2001

Sediment Characteristics Carlson et al., 1994

Climate

Freshwater Inflow Fourqurean et al., 2003

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stabilized with the occurrence of relatively constant

estuarine/marine salinities and the lack of periodic

intense hypersaline conditions.

• There has been little net change in seagrass distribution and abundance since 1995 in central basins

that are periodically subjected to low salinities or

have shallow sediments and lower overall densities

of Thalassia.These conditions may reduce density-related stresses and allow robust species communities to develop; low salinity may also provide refugia

from disease because Labyrinthula has never been observed in Florida Bay in salinities below 15 psu.

• The variable abundances of seagrass-associated microfossils in cores suggest repeated cycles of seagrass

presence and absence at core locations over the past

200 years.Thus, the recent changes in seagrass abundance may not be unprecedented.

• A statistical, discriminant-function model of seagrass species occurrence has been developed. The

model predicts that an increase in freshwater delivery

to Florida Bay will result in an expansion of Ruppia

maritima and Halodule wrightii distribution into the

northeastern bay with a concomitant loss of Thalassia in this region.

WHY DID SEAGRASS DIE–OFF OCCUR ONLY

IN FLORIDA BAY? 

Unique characteristics of the Florida Bay ecosystem

make it susceptible to conditions that contribute to

primary die-off. Other marine areas with high Thalassia densities and carbonate sediments, such as the

Lakes Region of the lower Keys, did not experience extensive die-off in the late 1980s. Relative to these other

areas, the central basins in Florida Bay are isolated

from tidal influences and are subject to relatively high

continental influence.

Effect of Ecosystem Characteristics

on Growth and Survival

“Physiological stressors such as elevated water temperature, prolonged hypersalinity, excessive seagrass

biomass leading to increased respiratory demands,

hypoxia and sulfide toxicity, and disease are some of the

factors thought to have contributed to Thalassia die-off.

However, the causative mechanisms responsible for initiating the die-off remain incompletely understood (Robblee et al., 1991; Carlson et al., 1994; Durako, 1994; Durako

and Kuss, 1994; Durako et al., 2002).”

—Durako et al., 2002

Changes in plant morphology and metabolism

measured in the field provide indicators of response

of seagrasses to environmental stressors in advance of

die-off. Zieman et al. (1999) reported results of longterm monitoring at sites of pre-existing die-off and at

sites not yet affected by die-off:

“Measurements were made of short-shoot density, standing crop, leaf morphology and productivity of Thalassia

testudinum. Seagrass beds in Florida Bay have continued

to decline in density and biomass since the die-off event

began in 1987. In contrast to the loss of seagrass density

and standing crop, we found that mass-specific productivity increased markedly from 1989 to 1995 at the dieoff sites. The increases in mass-specific productivity of

seagrasses in Florida Bay occurred at the same time

that transmission of light to the bottom was decreasing

dramatically. Despite increasing productivity on a massspecific basis over the period 1989–1995, area productivity

of Thalassia testudinum decreased at three of the five

die-off sites.This can be explained by a change in shoot

density and size.”

Seagrasses in Florida Bay are meristem-dependent and depend on rhizome growth and branching to

maintain or increase their populations. Excess carbon

from photosynthesis is needed for production and

growth of apical meristems to allow lateral growth

and spread of populations. Core samples (15-cm diameter) obtained during the springs of 1998 and 1999

FHAP sampling indicated that the mean branching

frequency was 0.24 during this period, or one rhizome

apical branch produced for every four short-shoots

(Paxson and Durako, 2001). This is very similar to the

branch frequency of 0.28 observed during the early dieoff from 1989 to 1990 (Durako, 1994). The relationship

between rhizome branching in 1998 and shoot density

changes from 1998 to 1999 was significant (P < 0.0001);

however, the r 2 value of 0.12 was low.

Carlson et al. (1994) have reported that alcohol dehydrogenase (ADH) increases in Thalassia exposed to

hypoxic conditions, exacerbating the carbon drain on

below-ground tissues. Apical meristem density and

branch frequency (rhizome apical density normalized

to short-shoot density) may act as “ecoindicators”of the

potential for increase or decrease of seagrass density.

Temperature

The large-scale distribution of marine plants is largely

controlled by temperature.The effects of temperature

on seagrasses have been extensively investigated and

are well known. The range of thermal tolerance in

tropical species is about half that of temperate species;

upper thermal limits are similar for both groups, but

tropical species are less tolerant of low temperatures

(Zieman et al., 1989). Because tropical species are growing near the upper temperature limits, thermal effects

of discharges from electrical power plants can result

in mortality during the warm summer months, although the productivity of these species may have

been enhanced during the winter (Barber and Behrens,

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1985). Thalassia may show defoliation or reductions in

leaf length when temperatures fall below 15°C or exceed 30°C (Phillips, 1960; Zimmerman and Livingstone, 1976; Durako and Moffler, 1985). Temperatures

below or above these extremes have been observed on

bank tops in Florida Bay. Syringodium seems to be more

tolerant of low temperatures than Thalassia (no defoliation at temperatures just below 15°C); Syringodium

has maximal growth between 23°C and 29°C, whereas

for Thalassia maximal growth occurs between 23°C

and 31°C (Zimmerman and Livingstone, 1976). In shallow bays with widely fluctuating temperatures, Thalassia, Syringodium, and Halodule have narrower leaf

widths, suggesting increased stress (McMillan, 1978).

Ruppia has a wide tolerance to temperatures (7°–35°C)

and has highest growth rates during the cooler spring

months (Phillips, 1960; Pulich, 1985). Water temperatures are not expected to be significantly affected by

altered water management.

Salinity

Salinity plays a very important role in controlling benthic plant communities in the upper estuaries of Florida

Bay. Areas of high variability in salinity have a low

biomass of submerged plants (Montague and Ley,

1993). Mesocosm studies (Chesnes et al., 1999) have produced data on how fluctuating salinities may affect

turtlegrass, shoalgrass, and widgeon grass. Unfortunately, operational difficulties plagued the mesocosm

facility, which slowed progress and resulted in problems with maintaining proper controls.

The role of hypersalinity in seagrass die-off still remains unclear. Salinities during the initial die-off

episodes in 1987–1989 were accompanied by hypersalinities ranging from 45 psu to 70 psu.The Barnes Key

die-off clearly did not correlate with this level of salinity but showed many of the other stresses that accompanied the primary die-off. Although the role of

hypersalinity may vary relative to other stresses, low

salinity provides refugia from Labyrinthula, because infection by that organism does not occur at <15 psu

(Blakesley et al., 1999b).

Light

Light penetration to the leaf blades, which sets the

limits for seagrass photosynthesis, varies as a function

of depth, turbidity, and epiphyte cover.

TURBIDITY

To assess the relationship between water clarity and

seagrass recovery in Florida Bay, Carlson et al. (2001)

have continuously measured subsurface and bottom

photosynthetically active radiation (PAR) at seven stations in Florida Bay since the fall of 1998. In addition

to continuous light data, discrete water samples for

analysis of turbidity, color, chlorophyll, and total suspended solids and plant samples for epiphyte light

attenuation measurements have been collected

monthly. Diffuse attenuation coefficients vary seasonally and between basins within Florida Bay: attenuation is higher in winter than in summer and is

generally higher in the basins that lost large amounts

of seagrass in die-off episodes between 1987 and 1991.

Persistent phytoplankton blooms in the north-central

region of the bay are associated with high (greater

than 3) Kd values, but water clarity at most sites was

higher in 2000 than in 1999.

EPIPHYTES

There are spatial and temporal gradients in species

composition of epiphytes, with coralline red algae

being more dominant in western high-flow areas of the

bay (Frankovich and Fourqurean, 1997). Fleshy epiphytes have restricted distributions, occurring only

near bird islands and near the Keys. The cyanobacterium Lyngbya is very common in the Syringodium filiforme beds in the west (Frankovich and Zieman, 2001).

Epiphyte attenuation is higher in winter and spring

(30%–50%) than in summer and fall (15%–30%), and

values are higher in the eastern region of the bay

(greater than 40%) than in the western region (ca.

20%). Calcium carbonate derived from calcareous algae

and resuspended sediment composes more than half

of the epiphyte load.

Epiphytic light attenuation has also been measured using Mylar strips and a light-attenuation measurement apparatus that has been successfully

employed by investigators in Australia and Chesapeake Bay (Frankovich and Zieman, 2001). The Mylar

strips have been set out within various seagrass meadows across the bay for a sufficient time period to allow

for the accumulation of epiphytic organisms. Distinct

epiphytic communities consisting of benthic diatoms,

coralline red algae (Melobesia membranacea, Hydrolithon

farinosum), and filamentous red and brown algae occur

seasonally in various regions across Florida Bay.These

various epiphyte functional forms, and combinations

thereof, result in differing levels of light attenuation at

the leaf surface relative to the amount of epiphyte

loading. Epiphyte loads at Barnes Key are at lower

than 5% of bay-wide averages (Frankovich and Zieman,

2001). Highest epiphyte loads are in areas of highest

seagrass productivity, so epiphytes are not reducing

production (Frankovich and Zieman, 2001).

Grazers may have an important role in controlling

epiphyte abundance. Snails (50/m2

) and hermit crabs are

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conspicuous at Rabbit Key Basin (Frankovich and

Fourqurean, 1997). In Florida Bay,Bittium occurs at densities of about 3/m2

,whereas in the Indian River Lagoon,

Bittium occurs at densities of 20/Halodule short-shoot or

at 1000s/m2 .

Macroalgae such as Laurencia are patchy in abundance. It is unknown at present whether its abundance has changed in response to the changes in

seagrass abundance (although these data are in the

FHAP dataset). Jeff Holmquist found that Laurencia

accumulation did not kill underlying Thalassia.

Nutrients

Worldwide, many estuaries have undergone loss of

seagrasses as a result of eutrophication.The mechanism

for nutrient-enrichment-induced seagrass losses is

that increased nutrients lead to increased epiphyte

loads and consequent shading and deterioration of

the seagrasses (Cambridge et al., 1986). Phytoplankton

blooms usually follow rather than cause seagrass dieoffs. As stated above, epiphyte loads on seagrasses are

relatively low in Florida Bay and do not seem to be reducing production.

Sulfide

Carlson et al. (1994) and Erskine and Koch (2000) have

explored the potential links between elevated sediment-sulfide concentrations and seagrass mortality

(a hypothesis long proposed to account for seagrass dieoff). Hydrogen sulfide is a known plant toxin. High sulfide levels in sediments have been observed during and

after die-off episodes (Carlson et al., 1994). Sulfide concentrations greater than 2–4 mmol have been measured in die-off sites, but it is not known if this is a cause

or an effect of die-off. If sulfide concentrations are less

than 2 mmol, no die-off has been observed. However,

photosynthetic rates in Thalassia increase as a function

of increasing sulfide up to 6 mmol, and sulfide levels

up to 10 mmol have failed to produce visual signs of

acute sulfide toxicity, although high sulfide levels have

been shown to result in reduced leaf-elongation rates

(Erskine and Koch, 2000).

A series of field experiments has been undertaken

to help us understand how sulfide concentrations may

influence seagrass growth and abundance and to clear

up uncertainties between the two conflicting sets of results. A submersible pulse-amplitude-modulated fluorometer (Diving-PAM) was used to investigate

photosynthetic yields of Thalassia testudinum leaf material in situ within bucket experiments established by

Carlson. Photosynthetic yields were significantly lower

in buckets with added glucose and acetate (Figure 7.5),

although both treatments should have increased sediment sulfide levels.

Labyrinthula Infection

A theoretical model for die-off as a disease (Blakesley

et al., 1999a) has suggested three different roles that

Labyrinthula might play in Florida Bay under different

environmental conditions. These roles include (1) a

nonpathogenic parasite, (2) an opportunistic secondary

pathogen, and (3) a primary pathogen. Five different

factors were discussed as critical elements in determining the role(s) of Labyrinthula in seagrass health at

a particular site in Florida Bay (Blakesley et al., 1999b).

Salinity controls infection (infection does not occur

at less than 15 psu). Seagrass density determines the

extent to which Labyrinthula infection spreads because

the slime mold transmission is thought to depend on

blade-to-blade contact (Muehlstein, 1992). Pathogenicity of a particular strain of Labyrinthula will determine severity of infection (Muehlstein et al., 1988).

Environmental stressors (abiotic factors), such as low

light or high temperatures, may weaken Thalassia and,

in combination with the infection by pathogenic

Labyrinthula, may cause seagrass die-off. Resistance to

disease due to genetic factors or production of phenolic

compounds may be important in determining the

health of Thalassia in Florida Bay.

Blakesley et al.’s (1999a) model predicted that in

areas with high seagrass density, high salinity, “suboptimal seagrass conditions (environmental stress),”

and presence of pathogenic Labyrinthula, the slime

mold could contribute to either chronic or acute dieoff by acting as an opportunistic secondary pathogen.

Figure 7.5 Photosynthetic quantum yields of Thalassia in Carlson buckets exposed to high glucose (HIG), low glucose (LOG),

molybdate (MO4), acetate (ACE), shaded (SHD), and shaded

with glucose (SHG) relative to controls inside (CON) and outside

(OC) plots.

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Under the same conditions but without environmental stress, Blakesley et al. (1999b) suggested that

Labyrinthula, acting as a primary pathogen, could still

cause “thinning”or patchy die-off. Labyrinthula occurrence was found to have significant adverse influences

on branching frequency (P = 0.03), shoot density (P =

0.004), and apical density (P = 0.033) (Paxson and Durako, 2001), suggesting that this microorganism may

have an adverse influence on seagrass growth and

carbon balance (sensu Durako and Kuss, 1994).

The occurrence of Labyrinthula has also been shown

to affect photosynthetic characteristics of Thalassia

(Durako and Kuss, 1994). Durako and Kuss (1994)

demonstrated that Labyrinthula infection reduces oxygen production and may increase susceptibility to sulfide.These results indicate that reduced photosynthetic

capacity may be caused by Labyrinthula-induced lesions

or elevated sulfide.This may make Thalassia more susceptible to sulfide toxicity, hypoxia, or disease by imposing a negative carbon drain on belowground tissues.

Photosynthetic yields of Thalassia testudinum leaf

material measured in situ at Sunset Cove and Cross

Bank by using a Diving-PAM were significantly lower

in regions of Thalassia leaves that had visible lesions.

These patterns agree with those previously reported

by Durako and Kuss (1994). However, close-interval

Diving-PAM-fluorescence measurements along an individual leaf with several visible lesions indicated the

reductions in photosynthesis were restricted to the immediate area of the lesion.Quantum yields of lesion-free

leaf regions of short-shoots also declined along transects

from dense, apparently healthy beds to recent die-off

patches at both Barnes Key and Cross Bank. The photosynthetic characteristics of solitary short-shoots within

the die-off patches were significantly lower than those

of shoots along the ecotones and shoots only 1 m inside

the bed. This indicates that photosynthesis may be

reduced even in the absence of visible lesions.The Diving-PAM data also revealed that the severity of stress

imposed by the leaf lesions will be a function of the proportion of total leaf surface that is necrotic,and it remains

to be determined what the lethal threshold is for lesion

coverage.

Sediment Characteristics

Carlson (unpublished data) has observed that highporosity sediments correlate with high hydrogen sulfide levels because of the sediments’low permeability.

Barnes Key surface sediments have very high porosity (lots of water and fine sediments) and high levels

of hydrogen sulfide.

Seagrass die-off has been observed only in biogenic

carbonate sediments, which are usually low in iron.

However, Florida Bay carbonate sediments have relatively high iron levels (Carlson et al., 1994). Spatially,

iron levels are high near the mainland and toward the

west. The role of atmospheric deposition of iron to

Florida Bay remains poorly understood. Addition of

iron to sediments decreases the flux of sulfide to Thalassia (Carlson bucket experiments) and results in a

small but significant increase in growth. Iron distribution may also have a role in controlling phytoplankton blooms in the bay.

Effect of Ecosystem Characteristics

on Community Structure and 

Distribution

“The present distribution and species composition of seagrasses in south Florida are a result of the interaction of

many factors, the most important being water depth,

water clarity, and nutrient availability. Changes in the

movement and quality of water in the region, whether

natural or anthropogenic, are likely to cause changes in

the large-scale patterns in abundance and composition

of these seagrass beds. It is also likely that the first

symptoms of a changing coastal environment will be a

change in species composition of seagrass beds, not a

wholesale loss of seagrass cover (e.g., Hall et al., 1999; Durako et al., 2001 [2002]). For this reason, accurate data on

the species composition of the seagrass communities

must be collected periodically as a measure of the status of the coastal environment.”

—Fourqurean et al., 2002

Correlation with Patterns of Water Quality

Fourqurean et al. (2003) developed a discriminant function model that uses seagrass species occurrence and

abundance data from 677 locations and water-quality

data from 28 monitoring stations in Florida Bay. This

model predicted that the distribution of benthic habitat types in Florida Bay would likely change if water

quality was affected by changes in water delivery to the

bay. Specifically, an increase in seasonal delivery of

fresh water should cause an expansion of the distribution and abundance of Ruppia maritima and Halodule

wrightii at the expense of Thalassia testudinum along the

northeast region of the bay.

Geographic Variation in Seagrass Die-Off

The production of distribution and abundance maps

of the seagrasses has proven valuable, and these maps

provide a quantitative record of distribution and abundance at both basin and bay scales. The changes between maps provide clear visualization of where and

how much the distribution and abundance changes and

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FWRI Technical Report TR-11 105

can thus point to “hot spots”that may be related to specific forcing events or conditions. The use of seagrass

cover has become an assessment standard in the region (FKNMS, DERM, FHAP). Cover may be a more

sensitive performance measure to short-term changes

than density because density changes require mortality

and recruitment of short-shoots, whereas cover can also

vary in response to changes in the leafiness of shortshoots. Short-shoot density may be a better longer-term

performance measure and is a quantitative measurement. Density is the net effect of mortality, recruitment, and life span (demographics).

The recurrence of an acute die-off in Barnes Key

presented an opportunity to test a portion of the theoretical model by comparing the symptoms and progression of an acute event in the Barnes Key mud bank

area with the symptoms and progression of what we

believed to be chronic die-off in Sunset Cove.The hypothesis was that in Sunset Cove, Labyrinthula acted as

a primary pathogen in an environmentally unstressed

site, whereas in Barnes Key, Labyrinthula more likely

played the role of a secondary pathogen in an environmentally stressed site.

Comparisons of results for the Sunset Cove and

Barnes Key sites revealed that although active die-off

was occurring in both places, the sites were very different. At both sites the pattern of die-off was patchy,

suggesting disease processes rather than a physical

process as the primary cause. Both sites had high salinities (greater than 15 psu) and dense Thalassia beds—

necessary elements for Labyrinthula infection and

transmission. However, the data from the two sites revealed important differences that are summarized in

Table 7.3.

These differences strongly suggest that the mechanisms for the die-offs in Barnes Key and Sunset Cove

are not the same. Blakesley et al. (1999b) proposed that

the acute die-off in Barnes Key resulted from a series

of events beginning with heat stress and an initial infection or disease (not Labyrinthula-induced) that

rapidly kills the infected seagrass.The resultant large

amount of decaying belowground biomass from the

rapidly dying Thalassia roots and rhizomes promotes

microbial activity that in turn elevates the sedimentsulfide levels selectively in those vegetative zones

where the die-off is occurring or has recently occurred.

The high sediment-sulfide levels do not kill seagrass

outright but instead further stress the other seagrass

in the immediate area. Finally, Labyrinthula, acting as

an opportunistic secondary pathogen, infects the already weakened remaining seagrass.

In contrast, the chronic die-off in Sunset Cove appears to be directly caused by Labyrinthula acting as a

primary pathogen. Sediment-sulfide levels may remain relatively low in all the vegetative zones tested

simply because the slow death of Thalassia roots and

rhizomes results in a smaller decaying belowground

biomass. As a result, the sediment-sulfide levels may

remain lower in the vegetative zones than in contrast

to the Barnes Key. Such chronic seagrass die-off is still

ongoing in many parts of Florida Bay, where the Thalassia beds are dense enough for transmission of the

disease and the salinity is high enough for infection to

occur.

Recent high-resolution in situ oxygen measurements show that the short-shoot meristems of Thalassia at the Barnes Key die-off site became anoxic during

the night in November and remained anoxic for up to

five hours (Borum et al., 2001). In contrast, leaf meristems at Rabbit Key Basin did not become hypoxic.The

Barnes Key samples showed a more rapid decline in

oxygen concentration after sunset and slower internal

oxygen concentration increases in the morning than did

samples from Rabbit Key Basin. Thalassia at Barnes

Key is very dense, with over 1,200–1,500 shortshoots/m2

, a very high biomass (SC 300 g/m2), low

turnover rate of grass blades (1.2%/day), and very thick

litter layer. In Rabbit Key Basin, densities are also high

(1,200–1,300 short-shoots/m2), but biomass (SC 109

g/m2

) and turnover rates (1.7%/day) are more moderate (Zieman et al., 1999).The long short-shoot stems at

Barnes Key lead to increases in diffusion distance for

oxygen. Long internodes may be a response to hypoxia or rapid sedimentation.

Table 7.3 Characteristics of seagrass die-off at two locations in Florida Bay.

Barnes Key Sunset Cove

Seagrass loss is rapid. Seagrass loss is slower.

Meristem “rots.” Meristem “healthy.”

Lesions occur after die-off. Lesions occur before die-off.

Water temps are high in summer. Water temps are “normal.”

“High”sediment-sulfide levels (up to “Low”sediment-sulfide levels

7,000 μmol). Levels vary in different zones, but (= 1,600 μmol) in bare, sparse, and 

highest values are found in active die-off zones. dense seagrass zones.

Seagrass Ecology
Florida Bay Synthesis Hunt and Nuttle

106 FWRI Technical Report TR-11

Seagrass loss has been recently observed in the

northern portion of Little Madeira Bay from the mouth

of the Taylor River to the south and west (Bacon et al.,

2001), and this area has been recolonized by Halodule

and Ruppia.This new seagrass die-off led to a plan for

a series of observations and experiments to test several

of the hypotheses that might explain seagrass die-off.

Modeling Change in 

Benthic Communities

Statistical modeling was commissioned by the Central

and Southern Florida Comprehensive Review Study

(Restudy) of the U.S. Corps of Engineers consistent with

recommendations from the 1998 Seagrass Modeling

Workshop (Fourqurean et al., 2003). The goal of this

work is to seek relationships between water-quality

variables and seagrass species composition and abundance, which if sufficiently strong, can be used to predict the effects of various alterations in Florida Bay

salinity regimes.The statistical models developed in this

project will be used in conjunction with output from

other models to predict the effects of Restudy scenarios on the benthic habitats of Florida Bay. This statistical model will not address mechanisms or degree of

change in water quality that result from Restudy scenarios; other models (such as the NSM, FATHOM,

and the Florida Bay salinity-transfer-function models

currently employed by the Restudy) must simulate

water-quality changes across Florida Bay that will provide the input to the new models developed in this project. As a consequence, it is anticipated that the benthichabitat-change predictions of the statistical models

will be the most reliable in the regions most closely coupled with water-management practices (i.e., the enclosed, mangrove-lined estuaries on the fringe of

Florida Bay). As the fidelity of the physical water-quality models to the behavior of the system declines, the

reliability of the benthic changes predicted by our

model will also decline. However, because the statistical relationships will be based on data from a larger

number of marine areas and upper estuaries, the basic

relationships between actual water quality (not modeled) and benthic habitats will be robust.

In addition, other seagrass-modeling efforts have

recently been initiated. These include the development of both seagrass unit models for Thalassia and

Halodule and a landscape model that will take output

from the unit models. Smith and colleagues are developing a hierarchical approach to modeling the interaction between plant and physical processes in

Florida Bay that involves two distinct spatial scales—

the demographic unit (ca. 10 m2

) and the landscape unit

(ca. km2). A preliminary landscape model of Thalassia

that explicitly relates patterns of photosynthesis, respiration, and carbon allocation to environmental conditions that include salinity, temperature, PAR, and

nutrient availability has been developed.

Physical processes such as sedimentation, decomposition, and nutrient cycling will be modeled on

a spatial scale of the landscape unit. This approach

provides a hierarchical framework in which the demographic units used to simulate plant processes exist

in the context of the landscape units, which will define

the underlying physical environment.The plant characteristics that are relevant to the feedbacks with the

physical environment (such as primary productivity

and inputs of dead organic matter) are described statistically for the demographic units and used to define

the biological environment for each landscape unit. In

this manner, the heirarchical framework functions as

a dynamic, interactive GIS in which each parameter and

process is described and simulated at the appropriate

temporal and spatial scales.

Current Research

Field Assessment

• FHAP is continuing spring and fall sampling and has

incorporated (since spring 2001) measurements of

photosynthetic characteristics of Thalassia using Diving-PAM-fluorometry at each station in addition to the

Braun-Blanquet and standing-crop measurements.

• FWRI (Carlson) is continuously monitoring benthic

light availability at fixed stations in several basins.

• Zieman is maintaining the long-term productivity

measurements.

Experimental

• SFWMD is funding a new study entitled “High salinity, nutrient and multiple stressor effects on seagrass communities of NE Florida Bay” being

conducted by Koch and Durako. The results of this

study are intended to help determine the parameters for the unit model with data from Florida Bay

seagrasses.

• FWRI (Carlson) bucket experiments have been conducted to examine effects of multiple stressors (sulfide, nitrogen, and light) on seagrasses in situ.

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Seagrass Ecology
110 FWRI Technical Report TR-11

Introduction

Question 5—What is the relationship between environmental and habitat change and the recruitment, growth,

and survivorship of animals in Florida Bay?

In the context of the Florida Bay Science Program,

higher-trophic-level species (HTLS) include zooplankton; benthic invertebrates such as sponges, mollusks, crustaceans (particularly decapods); fishes;

marine mammals; marine reptiles; and water birds. Scientific input about HTLS in the bay is critical to the successful restoration of Florida Bay and associated coastal

ecosystems because HTLS are both ecologically and

economically important and are viewed as important

by the public. Performance measures based on HTLS

are essential to protecting and restoring Florida Bay in

the Comprehensive Everglades Restoration Plan

(CERP) implementation process.

HTLS integrate the condition of the ecosystem

and reflect it in their responses to environmental

change. Question 5 investigates how HTLS respond to

changes in the characteristics of the ecosystem, such

as benthic communities, water quality, and circulation, and exchange with adjacent ecosystems and the

effect of human activities on these characteristics.

Question 5 also investigates how HTLS are affected by

fishing. Some HTLS play a critical role in regulating

ecosystem functions, so changes due to fishing or other

causes, anthropogenic or natural, can have repercussions on the entire Florida Bay ecosystem.

The higher-trophic-levels component of the Florida

Bay Science Program has approached Question 5 by addressing the following questions: 

• How do human activities (e.g., water management,

fishing) and major natural factors influence biological processes affecting growth, survival, and recruitment of fishery species, protected species, and

keystone species in Florida Bay?

• How do HTLS community composition and trophic

structure vary in time and space, what factors are responsible, and what processes are affected by the

variation?

• What major processes influence transport of presettlement stages of fish and invertebrates to and into

Florida Bay, what is their schedule, what parts of

the bay are most affected, and what is their importance to recruitment to fisheries inside and outside

of the bay?

• What animals affect major ecological processes in the

bay, such as primary productivity and nutrient cycling, and what is the magnitude of this role?

Substantial progress has been made on these topics but much remains to be done. This chapter synthesizes recent results, examines historical information

relevant to the central question, and identifies needed

future work.

Description of Higher-Trophic-Level

Species in Florida Bay

The HTLS component of the Florida Bay Science Program encompasses all the animals of the system. Recent work on higher trophic levels in Florida Bay builds

on prior research in coastal waters of Everglades National Park (ENP) before or in the 1950s and 1960s,

summarized by Tilmant (1989) and Tabb and Roessler

(1989); in the 1970s by Schmidt (1979); and in the 1980s

by Thayer and Chester (1989), Powell et al. (1989), Sogard et al. (1989), Holmquist et al. (1989), Robblee et al.

(1991), and Ley et al. (1994). More than 250 fish species

are known to occur in Everglades National Park coastal

waters (Loftus, 2000), although Schmidt (1979) found

only 128 fish species in Florida Bay. Tabb (1966) concluded that individuals of most species left ENP waters for unknown seaward spawning areas when they

reached sexual maturity.

A synthesis of past research for the March 1998

Chapter 8

Higher-Trophic-Level Species

Lead Author Joan A. Browder

Contributors Cynthia Yeung, Thomas Schmidt, Mark J. Butler, IV, Maria Criales, Allyn Powell, 

Don DeAngelis, David Evans, Larry Settle, Bill Sharp, Craig Faunce, Jerald Ault, Anne Marie Eklund, 

G. Lynn Wingard, Gordon Thayer, Darlene Johnson, David Rumbold, Jeffrey Chanton, C. Chasar, 

Jerome Lorenz, Ed Matheson, James Colvocoresses, Michael Robblee, Laura Engleby, 

Chris Koenig, Samantha Whitcraft
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 111

HTLS Group Report (Browder et al., 1998) organized the

animals of the bay into a generalized food web (Figure

8.1). The primary producers at the food-web base include phytoplankton, epiphytes, benthic algae, seagrass, and mangroves. The Florida Bay fauna is made

up of herbivores, detritivores, planktivores, and piscivores at three or four trophic levels.Within the bay, the

food web has two major branches: pelagic (water-column) and benthic (on or near the bottom), which may

converge at the highest trophic levels. Most of the following information is summarized from Browder et al.

(1998), but new information has been added as cited.

In the pelagic branch of the food web, filter-feeding planktonic stages of fishes, crustaceans, mollusks,

and other taxa feed on phytoplankton (e.g., diatoms,

dinoflagellates) in the water column and are preyed

upon by small, schooling pelagic fish such as bay anchovies and hardhead silversides.The benthic branch

includes filter feeders (e.g., sponges, bivalve mollusks,

ascidians, polychaetes) and demersal grazers or detritivores, such as amphipods, harpacticoid copepods,

polychaetes, striped mullet, and post-settlement stages

of mollusks and other invertebrates.The next level of

benthic consumers includes a host of small demersal

fish and macroinvertebrates that feed on small invertebrates. Dominant members of this group include

gulf toadfish, goldspotted killifish, rainwater killifish,

dwarf seahorse, dusky pipefish, gulf pipefish, spotfin

mojarra, silver jenny, white grunt, pigfish, pinfish, and

silver perch (Thayer et al., 1999). Pink shrimp and many

taxa of small caridean and penaeoidean shrimp also are

numerically abundant in the bay (Holmquist et al.,

1989; Robblee, personal communication). Juvenile spiny

lobsters are abundant in the southwestern portion of

Figure 8.1 Trophic levels in Florida Bay.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

112 FWRI Technical Report TR-11

the bay south of major mud bank barriers (Field and

Butler, 1994; Herrnkind et al., 1997). The limited research in the bay and nearby areas suggests that the

demersal fish in the bay are generalists that eat a variety of benthic invertebrates (Zieman, 1981; Schmidt,

1993a; Ley et al., 1994).

Florida Bay supports several highly sought-after

game fish, including red drum, spotted seatrout, gray

snapper, snook, tarpon, and bonefish (Schmidt et al.,

2001, 2002). Sharks are commonly seen during aerial

surveys (S. Bass, personal communication) and include nurse sharks, bonnethead sharks, and lemon

sharks. Rays (e.g., sting rays and manta rays) are commonly seen on aerial surveys. Small fish and macroinvertebrates are the prey of these larger fish.Within the

Florida Bay area, gray snapper and red drum principally eat shrimp and crabs, whereas barracuda,

seatrout, and snook eat more fish than crustaceans

(Marshall, 1954; Croker, 1960; Yokel, 1966; Fore and

Schmidt, 1973; Rutherford et al., 1983; Schmidt, 1986,

1989; Harrigan et al., 1989; Hettler, 1989). Of the abundant forage fish, those that appear to be important in

the diet of some piscivorous fishes are gulf toad fish

(lemon sharks, red drum, and bonefish), pinfish (lemon

sharks and snook), hardhead silversides (snook),

goldspotted killifish (barracuda), and rainwater killifish (barracuda and spotted seatrout) (Schmidt, 1986,

1989; Crabtree et al., 1998; Koenig et al., 2001). In southern Florida Bay, juvenile lobsters constitute a large

fraction of the diets of a variety of fish: nurse sharks,

bonnethead sharks, southern stingrays, bonefish, permit, and gulf toadfish (Smith and Herrnkind, 1992).

Small mollusks are abundant in Florida Bay and are

probably fed on by rays and fish such as sheepshead.

The pink shrimp, Farfantepenaeus duorarum, is a key

component of trophic webs.This species is an important prey of game fish (Croker, 1960; Stewart, 1961,

Yokel, 1966; Rutherford et al., 1983; Schmidt, 1986, 1989;

Hettler, 1989) and wading birds (Palmer, 1962), linking

them to small grazers and detritivores supported by

algae and seagrass and mangrove detritus (Fry et al.,

1999).The abundant small caridean shrimps in Florida

Bay are the principal prey of juvenile pink shrimp

(Schwamborn and Criales, 2000).

The many piscivorous water birds that live in the

bay seasonally or year-round eat small fish and

macroinvertebrates such as crabs and shrimps, although this is poorly documented. Piscivorous birds in

the bay include double-crested cormorants, brown

pelicans, red-breasted mergansers, laughing gulls,

ring-billed gulls, royal terns, many wading bird species,

and bald eagles and ospreys.The most abundant wading bird species in the bay seasonally are white ibis and

great egrets (Browder and Bass, unpublished data).

The bay is a major habitat for the great white heron,

roseate spoonbill, and reddish egret. All of these species

feed in Florida Bay proper or in shallow ponds on the

bay’s islands.

The bottlenose dolphin is another high-level predator in Florida Bay and, based on studies elsewhere in

south Florida, probably feeds on fish at several trophic

levels.The American crocodiles that occur in the northern bay and the American alligators that penetrate

the northern bay during wet years are also predators

on the bay’s small-fish populations.

Two large grazing animals, the West Indian manatee and the adult green sea turtle, may have once

been more abundant in Florida Bay than they are

today. They also may have influenced the structure

and productivity of seagrasses as a result of their grazing. A review by Thayer et al. (1984) described the dietary importance of seagrass to various herbivores

and the influence of herbivory on seagrass systems.

Green turtles once were the primary consumers of

seagrasses in the Caribbean, but they are now few in

number everywhere. In a major feeding area in

Nicaragua,Thalassia testudinum made up 87% of the diet

of green sea turtles, and other seagrasses (Syringodium

filiforme and Halodule wrightii) made up another 5%.

Grazing by green sea turtles may have profound influences on the seagrass community that are different

from the effects of grazing by other herbivores. Green

sea turtles may feed on Thalassia preferentially. They

are known to maintain discrete grazing plots in a Thalassia bed and feed repeatedly on the new growth in

these plots until food quality deteriorates. It is possible that the presence of grazing sea turtles might prevent the type of high-biomass Thalassia monoculture

that preceded the seagrass die-off in Florida Bay of the

late 1980s.The possible impact of loss of sea turtles on

Florida Bay was discussed by Jackson et al. (2001). Grazing by manatees may have a more disruptive effect than

that by turtles because the rhizophore is disturbed

and might jeopardize recovery (Thayer et al., 1984).

The density of large herbivores in Florida Bay today

may be too low for them to have much influence on the

present ecosystem.

Seagrass is the main diet of the caridean seagrass

shrimp (Schwamborn and Criales, 2000). Seagrass is

also important in the diet of sea urchins and has been

reported to be in the diets of some fishes (Thayer et al.,

1984). Even where grazing animals are more abundant, it is likely that more energy travels from seagrass to consumers through the detrital than the

grazing food web. In Florida Bay today, only the detrital food web is significant.

A conceptual model developed to help guide

Florida Bay HTLS research is shown in Figure 8.2.The

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 113

model incorporates the following major concepts:

• Critical ecosystem characteristics (i.e., salinity, water

quality, and biological benthic habitat) directly influence HTLS at the individual species level. Speciesand community-level response represents the

aggregate influence of these characteristics integrated over HTLS populations;

• Changes in HTLS at the species and community

level occur as the result of driving processes acting

on Florida Bay as a whole.These processes influence

HTLS by their effect on critical ecosystem characteristics and by controlling the movement of HTLS

into and out of Florida Bay;

• At the shelf scale, potentially influencing factors include temperatures on spawning grounds, larval

transport processes, and fishing;

• The scope of research on HTLS of Florida Bay must

include within-bay, cross-boundary, and greater

coastal ecosystem processes, and these processes

should be examined at time scales from seasons to

decades; 

• Higher-trophic-level processes and patterns potentially affected by water management occur at the

population, community/trophic, and ecosystem level; 

• HTLS responses to water management are expected

to occur through water management effects on salinity, the area of co-occurrence of biologically favorable

salinity and habitat, the condition of biological habitat (e.g., seagrass, sponge, coral), animal movements,

and loading of nutrients or toxicants; 

• Intrinsic factors potentially influencing responses

to water management include physiological salinity

requirements, dietary and energy requirements,

and trophic relationships, all of which may differ

by species, life stage, and spawning and migration

characteristics; 

• At the bay scale, other factors with the potential to

influence HTLS include salinity-temperature interactions, toxicant concentrations in freshwater inflow, and fishing.

Processes Driving Change in the 

Ecosystem 

Preceding chapters describe some major ecosystem

characteristics that influence higher-trophic-levelspecies in Florida Bay: salinity, water quality, and benthic habitat. All are subject to change, and an

understanding of how they might change is being developed in other parts of the Florida Bay program. Determining how their change might affect these species

is being determined by HTLS research. Relationships

between processes driving change, ecosystem characteristics, and characteristic species and communities of

Florida Bay are highly relevant to the CERP, which will

influence the change-driving processes. Defining and

quantifying these relationships is crucial to preparing

performance measures to restore or protect Florida Bay.

Augmenting the descriptions of ecosystem characteristics in the preceding chapters are studies on mercury.

These studies are defining previously unknown spatial

patterns of mercury and methylmercury concentrations

in Florida Bay waters, sediments, and biota.

The quest for answers to Question 5 must extend

beyond Florida Bay to include the greater ecosystem

that supports the movements of species into and out

of the bay and the processes that affect these movements. Animal movements, as well as the flow of water,

connect Florida Bay not only to the upstream Everglades and coastal mangrove areas but also to the

Florida Keys, the reef tract, the southwestern Florida

shelf, and the Dry Tortugas. Many higher-trophic-level

species range between the bay and the coastal reefs

during their life cycle.The processes driving change in

the Florida Bay ecosystem extend beyond the bay both

upstream and downstream.

The principal anthropogenic processes potentially

driving change in the Florida Bay ecosystem are water

management, contaminant and nutrient inputs, causeway and bridge construction in the Florida Keys, and

Figure 8.2 Conceptual model of factors affecting higher-trophiclevel species in Florida Bay.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

114 FWRI Technical Report TR-11

fishing. Climatic variation and oceanographic processes

are other instruments of change in the Florida Bay

ecosystem and may cause year-to-year and long-term

variation.

WATER MANAGEMENT

By affecting freshwater inflow to Florida Bay, water

management can affect Florida Bay’s HTLS through the

effects of freshwater inflow on salinity patterns, nutrients, organic detritus, and contaminant loads. Salinity directly affects physiological processes that

determine growth, survival, and reproductive rates of

many higher-trophic-level-species.The area in which

a favorable salinity range overlaps with other favorable

conditions (i.e., shoreline, depth, or bottom habitat) in

areas accessible to appropriate life stages determines

the productive capacity of the bay for a given species.

Salinity gradients may provide orientation cues that

promote the successful immigration into the bay of

postlarvae spawned offshore that use the bay as a

nursery ground. Nutrients and organic detritus may

have positive or negative effects depending on concentration. In excess, they degrade habitat (via reduced water clarity, low dissolved oxygen, etc.).

Effects of water management on salinity patterns,

nutrients, and contaminant loads are being studied in

other parts of the Florida Bay science program. A major

emphasis of the HTLS science plan is determining the

possible effect of changes in salinity on animal species

and communities. Water management may affect

higher-trophic-level organisms through effects on important living benthic habitat such as seagrass and

sponges (e.g., through salinity, nutrient, turbidity, or

other effects on the organisms that form living benthic

habitat), and these potential effects are also being evaluated through studies of relationships of HTLS to living benthic habitat.

FISHING

Many coastal fisheries in south Florida have ecological connections to Florida Bay. Especially notable of

these are the commercial fishery for pink shrimp and

the commercial and recreational fisheries for gray

snapper and spiny lobster. These species and others

(sparids, grunts, other snapper, and even groupers)

found on the Florida Keys reef tract and in the waters

near the Dry Tortugas spend part of their life cycle in

Florida Bay. Reef waters near Marathon in the middle

Keys are an important spawning ground for gray snapper (Rutherford, 1989). Shelf waters near the Dry Tortugas islands are the most important commercial

fishing grounds for pink shrimp in Florida, and Florida

Bay is the major pink shrimp nursery ground. Florida

Bay also contains important spiny lobster nursery

habitat, and Everglades National Park is a fishing-free

sanctuary for spiny lobster. Nearby areas and parts of

Florida Bay outside of ENP support recreational and

commercial fishing for Spanish mackerel, spiny lobster,

and other species.

Recreational fishing is an expanding sport in the

Florida Keys, the Tortugas waters, and Florida Bay, both

within and outside ENP boundaries.The number of fishing trips in ENP in 2001 was the highest ever reported

(Schmidt et al., 2002). ENP began phasing out commercial fishing in the bay in the early 1980s, when

analyses of recreational and commercial fishery data

suggested that overfishing might be occurring. Since

then, recreational fishing regulations have been

strengthened. Later analyses have suggested that environmental factors affect abundance (Tilmant et al.,

1989; Schmidt et al., 2002).The ratio of kept fish to total

fish caught changed dramatically from the 1980s to the

1990s. This may be an artifact of regulatory changes

(legal size limits, bag limits, seasonal closures); however,

it may be indicative of an increased catch of sizes that

were too small to keep (i.e., below legal size limits).

This issue will be addressed in current and future

analyses of size-frequency distributions in the creel

census data by ENP and the Fish and Wildlife Research

Institute.

The growing demand for fish and the popularity

of fishing have increased the pressure on fishery populations in south Florida. Fishing pressure is especially reflected in declining size and density of snappers

and groupers and changes in the trophic structure of

fish assemblages on reefs (Ault et al., 1998). These

changes are apparent even in the Tortugas area and are

consistent with similar changes previously detected in

the Florida Keys (Ault et al., 1998; Bohnsack et al., 1999;

Schmidt et al., 1999).The observed decline in fish abundance may be due to loss of coral habitat. For example,

the total area of Caribbean reef-building corals Acropora palmata and Acropora cervicornis has declined by

93% and 98% respectively since 1983 (Miller et al.,

2002).

OCEANOGRAPHIC PROCESSES

The Loop Current and Florida Current and their countercurrents, the Tortugas Gyre, and coastal eddies are

oceanographic features that may influence the migration of postlarvae to Florida Bay and to the Florida

Keys reef tract from offshore spawning areas. These

processes may affect the timing of abundance peaks

and year-class strength in fish and macroinvertebrate

populations in the bay and on the reef tract.

The Florida Keys reef tract extends almost without

interruption along the entirety of the Florida Keys and

is the core component of the Florida Keys National MaHigher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 115

rine Sanctuary. Florida Bay is connected to the reef tract

through interisland channels. Regional-scale and localscale oceanic processes that affect the reef tract likely

also affect Florida Bay. Reef tract populations are replenished not only by their spawning locally but also

by their spawning upstream of the reef tract. The upstream distance of sites contributing larvae is principally determined by current velocity and larval

development rate, which ranges from 2 weeks in some

invertebrates and fish to up to 12 months in spiny lobster. Recruitment of some species to the Florida Keys

reef tract from as far away as the western Caribbean

has been postulated. The argument for multiple upstream larval sources for the Florida spiny lobster population is especially strong, given the wide geographic

range of the species and its extraordinarily long planktonic larval life (Lyons, 1980; Yeung et al., 2000; Yeung

and Lee, 2002), and is supported by mtDNA analysis

(Silberman et al., 1994).

Having more local sources of larvae may be important to most populations. The lower southwest

Florida shelf in the vicinity of the Dry Tortugas is one

potential source of recruitment to the Florida Keys

reef tract and Florida Bay. The islands of the Dry Tortugas and their surrounding shallow waters lie roughly

150 km (70 miles) west of Key West and are known for

remoteness and relatively unspoiled marine richness

(Ault et al., 2002b; Franklin et al., 2003). The coastal

shelf in the vicinity of the Dry Tortugas is the major

spawning ground for pink shrimp in Florida. Recent

research is discovering luxuriant, previously unknown

and unmapped coral reefs near the Dry Tortugas and

near the Marquesas, which lie between the Dry Tortugas and Key West (Miller et al., 2001).

CAUSEWAY/BRIDGE CONSTRUCTION

The flow connecting Florida Bay to the Atlantic Ocean

through Lignum Vitae, Indian Key, and Teatable Key

channels was reduced by the construction of the Flagler railroad, which became the Overseas Highway.This

construction, which occurred in the early 1900s, partially blocked tidal passages and affected bay circulation and associated water quality (Healy, 1996). By

affecting transport between the bay and the Gulf of

Mexico and Atlantic Ocean, the construction areas

may also have affected the immigration of postlarvae

and early juveniles into Florida Bay.The U.S. Corps of

Engineers is leading a study to determine whether

Keys passes should be enlarged to restore the health

of Florida Bay. The Corps is planning a pilot study of

the effect of enlarging passes that have been restricted

by the highway. The pilot study will be performed in

passes located between Fat Deer (Marathon) and

Grassy keys.

Research Approaches

A major focus of Florida Bay HTLS research has been

to characterize the responses of species and species

groups to environmental and habitat conditions that

vary in space and time.The topic has been approached

via modeling, statistical analyses, experiments, and

field measurements. Modeling, supported by laboratory experiments, was used to characterize the response of individual organisms and was applied to

pink shrimp, spiny lobster, sponges, and spotted

seatrout to examine functional responses to salinity and

temperature and their consequences for populations.

Separately, statistical analyses of historical resource survey data were used to characterize the response of 11

forage species and 9 fishery species to environmental

variables at the population and community level. Field

studies were conducted to characterize the spatial and

temporal patterns of immigration of early life stages

into Florida Bay from offshore spawning grounds and

the density of juveniles on Florida Bay nursery grounds.

Most work has included an examination of the possible effects of salinity because salinity is likely to be affected by inland water management.

A more recent focus of Florida Bay HTLS research

has been to examine the effect of HTLS on critical

ecosystem characteristics, such as water quality and

benthic habitat, that determine habitat quality and

define distinct communities. In this regard, sponges are

a major interest because of the recent decline in sponge

biomass in the bay. Sponges are capable of regulating

water clarity through their filter feeding, and the volume of water filtered is largely determined by sponge

biomass density, which has declined substantially in

recent years.

Field sampling and comparative analysis of data

from fished and unfished areas provided information

on the effect of fishing on individual species and species

composition.

Comparative studies provided evidence that fishing in ENP affects size distribution within species (gray

snapper) and the species composition of communities.

Underwater visual resource surveys on the reef tract

and near the Dry Tortugas have found signs of overfishing of fish species that occur both on the reef tract

and in Florida Bay.

One approach to examining the effect of water

management on HTLS has been through statistical

analyses relating fishery catch or catch per unit effort

to indices of freshwater inflow to Florida Bay and

nearby southwestern Florida coastal waters. Another

approach, already mentioned above, has been to examine the effect of salinity on processes that affect

the abundance of these species.

Higher-Trophic-Level Species
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116 FWRI Technical Report TR-11

Summary of Recent Results

The following summary of recent results, presented as

bullets, is organized under specific research questions

(subsets of the four topic questions identified above)

to provide an overview of progress. Table 8.1 organizes research activities into specific topics, and these

topics provide a general framework for a series of sections synthesizing recent results and conclusions, by

specific research topic.

Does salinity affect survival and growth, do salinity patterns affect faunal abundance and distributions, and

will changes in salinity patterns affect the bay’s nursery function? 

• Five species of sponges found in Florida Bay expeTable 8.1 Research topics defined by Question 5 (cells in the matrix) and key references to the associated research.

Population Level— Individual Level—

Research Topic Species Abundance and Community Growth and Survival

General Read et al., 2001; Limouzy-Paris et al., 1997; Settle et al., 2001; Powell et al., 2004

Characteristics Costello et al., 1986; Robblee et al., 1991;

Thayer and Chester, 1989; Powell et al., 1989;

Chester and Thayer, 1990; Thayer et al., 1999;

Powell, 2002, 2003; Powell et al., 2004; 

Schwamborn and Criales, 2000;

Stevely and Sweat, 2001

Salinity Pattern Schmidt et al., 2001; Browder et al., 1999, 2002; Browder et al., 1999, 2001b, 2002; 

Brewster-Wingard et al., 2001; Camp et al., Butler et al., 2001a; Butler, 1999, 2003;

2001; Matheson et al., 2001; Field and Butler, Field and Butler, 1994; Wuenschel,

1994; Lorenz, 2001a 2001; Richards and DeAngelis, 2001

Water Quality Water quality effect on HTLS: Water quality effects on

(No results reported) contaminants and humans,

piscivorous birds, mammals, and

HTLS effect on water quality: reptiles: Evans and Crumley, 2000; 

Stevely and Sweat, 2001; Peterson and Sepulveda et al., 1998;

Fourqurean, 2001 Effects on invertebrates: Scott et al., 2002

Biological Habitat effect on HTLS: Habitat effect on HTLS: Butler et al.,

Benthic Habitat Dennis and Sulak, 2001; Robblee et al., 1995; Butler, 2003

2001; Matheson et al., 2001; Powell et al.,

2001a,b; Ortner et al., 2001; Robblee et al., 2001;

Chanton et al., 2001; Herrnkind and Butler,

1994; Field and Butler, 1994; Butler et al.,

1995; Butler, 2003; Koenig et al., 2001

HTLS effect on habitat:

Rose et al., 1999; Peterson and 

Fourqurean, 2001

Coastal Transport Field and Butler, 1994; Yeung et al., 2001; Settle et al., 2001; Yeung and Lee, 2002;

(Larval) Process Yeung and Lee, 2002; Jones et al., 2001; Acosta and Butler, 1997; Criales and 

Browder et al., 2001a, 2002; Lee, 1995; Criales and McGowan, 1993,

Butler et al., 2001b; Criales et al., 2003 1994; Jones et al., 2001; Jones et al., 1970;

Tabb et al., 1962; Roessler et al., 1969; 

Smith, 2000; Butler et al., 2001

Water Management Browder, 1985; Sheridan, 1996 Lorenz, 2001a, 2001b

and Hydrology Browder, 2000; Johnson et al., 2002a

Fishing Faunce et al., 2002; Bohnsack et al., 2001;

Schmidt et al., 2001

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 117

rience high mortality rates at low salinity. None survived at 15 practical salinity units (psu) (laboratory

experiments).

• Pink shrimp from Florida Bay are more sensitive to

low salinity than to high salinity.The salinity of maximum physiological survival varies with temperature.

Pink shrimp are more tolerant of high salinity at

high temperature and low salinity at low temperature. Acclimation improves survival at high salinity

(55 psu) but not at low salinity (5–10 psu). Growth of

pink shrimp is optimal at a salinity of 30 psu (laboratory).

• A salinity optimum of 35 psu has been reported for

postlarval Caribbean spiny lobster. The extreme

salinities that sometimes occur in portions of Florida

Bay are lethal to lobster postlarvae (laboratory).

• Larval and juvenile spottedseatrout survival and

growth are low at salinities over 45 psu (laboratory).

• Temperature and salinity have an interactive effect

on the metabolic rate of young spotted seatrout.Their

metabolic rate in relation to size is biphasic and

changes isometrically with body mass in early stages,

approximating an exponential relationship near unity,

but changes isometrically thereafter (laboratory).

• Spotted seatrout catch rates in the recreational fishery are negatively related to indices of freshwater inputs to Florida Bay (analyses of creel census data).

• Western Florida Bay is a major nursery ground for

spotted seatrout (field study). The high density of

planktonic postlarvae suggests that central Florida

Bay may also be a major nursery ground when conditions allow. Salinities greater than 45 psu have frequently occurred in central Florida Bay in the past,

which may limit this area’s nursery value.

• Pink shrimp recruitment from Florida Bay could

differ between years, seasons, and regions of the

bay due solely to observed salinity and temperature variation (simulation model).

• Observed salinities during a wet and a dry year

caused a predicted decline in lobster recruitment of

approximately 25% in the area of Florida Bay directly affected by salinity variation (individual-based

model).

• Habitat, tidal amplitude, freshwater inflow to Florida

Bay, and salinity were the most widely influential

variables explaining density in 11 forage species in

a meta-analysis of data from historical surveys. Seagrass density and tidal amplitude each were significant for 10 species, seagrass type and freshwater

inflow each were significant for 9 species, and salinity was significant for 7 species (statistical analyses

of combined data sets).

Does water management affect the productive

capacity of Florida Bay?

• When used in alternative testing to select the preferred plan for CERP, a statistical model relating an

abundance index of pink shrimp in the Tortugas

fishery to freshwater inflow to ENP at the Tamiami

Trail during certain months predicted that “natural

system”flows (as compared to the 1995-base case or

any alternative) consistently produced highest

shrimp abundance over a 31-yr period.The selected

alternative was predicted to lead to abundances intermediate between predictions for the natural system and 1995-base case.

• Remnants of molluscan faunas obtained in cores

suggest that molluscan faunal diversity and absolute

abundance in eastern and central Florida Bay began

a decline in the 1960s or earlier and reached a low

in the 1970s. The low species diversity and the increased abundance of Brachidontes exustus are evidence of a system under stress.

• Fish density in the wet season is positively related

to water depth in coastal marshes and the length of

time during which water depths are greater than

12.5 cm. Maximum concentration (to roughly twice

dry-down density) in low spots (e.g., creeks and shallow pans) occurs when water depths decline below

12.5 cm in adjacent marshes. Successful roseate

spoonbill nesting occurred in past years during dry

season when mean water depths in the coastal

marshes were less than 12.5 cm. Nesting failures in

recent years can be explained by out-of-season water

releases from the C-111 Canal.

What affects the balance between benthic and pelagic

trophic networks in Florida Bay? 

• The seagrass die-off was a suspected cause of a shift

from benthic to pelagic dominance in the fish community, because bay anchovy abundance was much

greater in 1995 than in 1984–1985. Recent findings discount this possible cause.The abundance of bay anchovy in the western bay has fluctuated since it

reached a maximum in 1995.The diversity and overall abundance of canopy-dwelling fauna have increased since 1995 without a return to the original

Thalassia-dominated seagrass canopy.

• Bay anchovy abundance may be related to the presence of salinity fronts. Bay anchovy abundance was

negatively correlated with salinity and positively

correlated with salinity standard deviation, chlorophyll, and an index of freshwater inflow in an analysis of historic data. A study in the Manatee River

associated low mean salinity and high salinity standard deviation with the presence of fronts and found

a relationship between anchovy egg abundance and

these indicators of fronts.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

118 FWRI Technical Report TR-11

• Seagrass diversity may determine faunal density. A

principal components analysis suggested that faunal

species have affinities to certain seagrass types—

Thalassia, Halodule, or Syringodium—or with macroalgae. Seagrass type was a significant explaining

variable in a meta-analysis of faunal density in

Florida Bay, and faunal density in relation to seagrass

type varied differently depending on faunal species.

No faunal species was identified that had pure

Thalassia as its sole affinity.

Do bottom and shoreline habitats affect abundance and

community composition?

• Mangrove prop-root habitat in northeastern Florida

Bay had significantly more fish larvae than did

nearby open-water sites or nearshore areas without

mangroves, but it had a lower density and diversity

of both forage fish and juvenile predator fishes than

found in similar habitat in the Bahamas and Puerto

Rico, leading to the hypothesis that the low densities were caused by isolation from offshore sources

of larvae or juveniles.

• Seagrass density was a significant explaining variable for density for 10 of 11 key forage species

examined, and seagrass type was a significant explaining variable for density of 9 of the 11 species.

Does fishing affect fish populations?

• According to a comparison of the length-frequency

distributions inside and outside of an area in the park

protected from fishing, recreational fishing in Everglades National Park affects the size structure of

gray snapper.

• Evidence of overfishing is seen in gray snapper and

other species on the reef tract.

Is spatial variation in influencing factors (e.g., freshwater inflow, tidal mixing) reflected in distinct regional

patterns in species distributions and community and

trophic composition in Florida Bay? 

• Peak concentrations of postlarval pink shrimp are

roughly an order of magnitude greater in passes

leading into western Florida Bay than in channels to

Florida Bay through the Florida Keys. Movement

into the bay occurs on the flood tide. The timing of

high immigration rates is more predictable when

shrimp immigrate from the west than from the east.

• Based on stable isotope analyses, the central bay

has a strongly seagrass-based trophic structure,

whereas the western bay has a more plankton-dominated trophic structure. The eastern bay offers a

non-seagrass-based diet (likely more water-column

based).The trophic structure of the southwestern bay

is based on macroalgae.

• Northern Florida Bay is probably not a significant

nursery area for red drum.

Is temporal variation in recruitment strength of spiny lobster, snapper, and pink shrimp related to oceanographic

processes, especially to the Tortugas gyres?

• Spiny lobster postlarvae that recruit throughout the

year had peaks of influx into the bay at the Middle

Keys coinciding with the presence of eddy and countercurrent conditions.

• Larval duration of gray snapper varied from one

year to the next and, within the first year, ranged from

35.50 to 41.45 days.

• Peak abundance of gray snapper larvae in Florida

Keys channels occurred in summer 1997 and was coincident with a well-developed Loop Current (high latitudinal extent) favoring gyre formation off the Dry

Tortugas, where gray snapper spawning aggregations occur.

• Temporal variability was observed in the influx of

pink shrimp postlarvae through two channels in the

Middle Keys and may be related to the position of

the leading edge of the cyclonic eddies relative to the

channels. Pink shrimp larvae at the spawning

grounds seem to be retained by the circulation of the

Tortugas gyre.

Are urban and agricultural sources, carried by the C111 canal, responsible for high methylmercury in

Florida Bay and its biota?

• Sources of elevated mercury concentrations in fish

from northeastern Florida Bay include (1) methylmercury in runoff from the Everglades and (2) in situ mercury methylation in sediments from both the

mangrove transition zone and the open bay itself.

• Mercury concentrations were higher along a Taylor

River–Little Madeira Bay sampling transect than

along a C-111 canal–Joe Bay transect, suggesting

that the urban and agricultural runoff that more

strongly influences the C-111 canal–Joe Bay transect is not the most important source of mercury to

the bay and its biota.

Did the former density of sponges in Florida Bay influence water quality to the extent that the sponge

die-off that followed seagrass die-off led to waterquality conditions that impeded the recovery of seagrass?

• At pre-die-off (before 1992) densities, sponges in

Florida Bay may have been capable of filtering the

entire water column in 24 hours. Recovery of the

largest and most abundant species has been extremely slow. At present densities, filtering takes an

estimated four days. Sponges are efficient filters of

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 119

small (<5 μm) planktonic particles. Loss of sponges

may have reduced water clarity and affected seagrass

recovery.

Do predators seek areas of higher prey abundance?

• Bottlenose dolphin were found in areas of highest

density of potential prey, supporting the working hypothesis that they search out feeding areas with

higher prey concentrations. Dolphin and prey densities are higher in the east-central and south-central bay than they are in the northeastern bay.

However, densities of both dolphin and prey are

lower in the east-central and south-central bay than

they are in other coastal areas.

Distribution of Species and 

Patterns of Abundance

Spatial variation in the influence of environmental

and physical factors shaping Florida Bay, especially

substrate, freshwater inflow, and degree of mixing

with waters of the Atlantic and the Gulf of Mexico, have

led to substantial regional differences in animal distributions within the bay. For example, the southern bay

is prime habitat for juvenile spiny lobster, which are

found in few other parts of the bay. On the other hand,

juvenile pink shrimp occur most densely in the western bay. Animal distributions have been used to define

distinct subregions of the bay, beginning with Turney

and Perkins’ (1972) delineations based on mollusks.

Subregional delineations based on animals roughly

correspond to those based on seagrasses (Zieman et al.,

1989) and water quality (Boyer, 1997). Short-term and

long-term temporal variations in environmental variables accentuate regional differences in bay habitat (for

example, the northeastern bay has the most seasonally

variable salinities). Temporal variation also undermines efforts to better describe and understand regional differences (for example, the northcentral bay

can be hypersaline one summer and mesohaline another, creating an entirely different environment for animals during the same time of year). Recent research

has expanded our understanding of how animal distributions vary spatially and temporally and the most

likely reasons for the variation. Results of studies that

address the spatial and temporal variations of a number of parameters follow.

Field studies have expanded the knowledge of

spawning areas and spawning periods. Powell (2003)

and Powell et al. (2002, 2004) determined that spotted

seatrout spawning occurs primarily in western Florida

Bay. Spawning at Bradley Key and Palm Key had been

observed historically, but spawning at Whipray Basin

and Little Madeira Bay was determined for the first time

in 1994–1995 sampling. Based on collections and hatchdate estimates from 1995 collections, they determined

that spawning occurred principally during the summer,

with spawning peaks in May and June. Larvae were collected over a wide range of bottom types with and

without seagrass, in waters with temperatures between 20°C and 35°C (majority 26°–34°C) and salinities between 12 psu and 41 psu (majority 25–40 psu).

Consistently high densities of larvae were collected at

Whipray Basin, which is located in the central portion

of the bay and is a valuable juvenile nursery area despite low seagrass above-ground standing crop and occasional (two occasions during sampling—40 psu and

41 psu) hypersaline conditions in 1998 and 1999.

Nursery grounds of several other gamefish species

that occur in Florida Bay as adults are not yet documented in Florida Bay. Recently Powell et al. (2002) attempted to locate Florida Bay nursery grounds of red

drum, which occur in Florida Bay and spawn in the

nearby Gulf of Mexico. Based on the work of Peters and

McMichael (1987) in Tampa Bay, Powell et al. (2002)

concluded that northern Florida Bay was the only suitable nursery habitat for red drum in the bay. Powell et

al. (2002) sampled intensively there, and concluded

that limitations on larval transport from offshore waters was preventing red drum from using this part of

the bay as nursery habitat. Colvocoresses (unpublished data) found young juvenile red drum in the

East River of Little Madeira Bay and near the mouth

of McCormick Creek, but the Powell et al. (2002) work

suggests that the occurrence of red drum juveniles in

northern Florida Bay is not a seasonally regular event.

Read et al. (2001) studied bottlenose dolphin in the

eastern half of Florida Bay and found that densities of

prey organisms in trawl samples were higher in areas

where bottlenose dolphin had been feeding than in

samples taken elsewhere. This supported their hypothesis that dolphin seek out feeding areas with higher

prey concentrations.These investigators found a greater

abundance of dolphins in the east-central and southcentral parts of the bay than they found in the northeastern bay. (Their study did not include the western

bay.) They suggested that the low abundance of dolphins

in the northeastern bay might be related to the lower

fish densities that have been reported there by other investigators. In 20 surveys conducted in all four seasons, they encountered 23 groups of bottlenose

dolphins, consisting of 133 individuals.They concluded

that the entire bay area they surveyed contained relatively few dolphins, corresponding to the low density

and diversity of potential prey items overall. In all seasons and areas, Read et al.’s (2001) trawl catches were

dominated by mojarras (family Gerreidae).

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

120 FWRI Technical Report TR-11

Effect of Ecosystem Characteristics

on Growth and Survival

Work on this topic addresses the principal question:

How do growth and survival of individuals in each

HTLS vary through the range of environmental conditions defined by salinity, water quality, and benthic

habitat found in Florida Bay? Major working hypotheses are as follows: 

• Salinity directly affects the growth and survival of

HTLS;

• The carrying capacity of Florida Bay nursery areas

is related to the overlap of favorable salinity and favorable bottom or shoreline habitat.

Effect of Salinity on Growth and Survival

Simulation models and associated experimental trials

suggest that several Florida Bay species, each with optimal habitat in a different part of the bay, can be affected by changes in freshwater inflow and the resultant

changes in salinity patterns. Both pink shrimp and

spiny lobster could be adversely affected by the extreme

high salinity that often occurs in the north-central part

of the bay and sometimes spreads westward into optimal shrimp nursery habitat and southward into optimal lobster habitat. Lobster and shrimp could both

be adversely affected by low salinities in otherwise

suitable habitat and locations.

The effects of salinity and temperature on the

growth, survival, and subsequent recruitment and harvest of pink shrimp (Farfantepenaeus duorarum) were examined via laboratory experiments and a simulation

model (Browder et al., 2002). The pink shrimp is an

ecologically and economically important species that

has major nursery grounds in Florida Bay. Experiments were conducted to determine the response of juvenile growth and survival to temperature (15°–33°C)

and salinity (2–55 psu), and the results were used to refine an existing model (Browder et al., 1999). Results of

these experiments (Figure 8.3a,b) (Browder et al., 2002)

indicated that juvenile pink shrimp can tolerate a wide

range of salinities in their optimal temperature range

(20°–25°C), but the salinity tolerance range narrows

with distance from that range. Acclimation improved

survival at extremely high salinity (55 psu) but not at

extremely low salinities (i.e., 5–10 psu). Analyses of

the laboratory data suggested that growth rate increases with temperature until tolerance is exceeded

beyond approximately 35°C. Growth is optimal in the

midrange of salinity (30 psu) and decreases as salinity increases or decreases. Potential recruitment and

harvests from regions of Florida Bay were simulated

Figure 8.3 Response curves of survival, growth, and potential offshore harvest of pink shrimp in relation to salinity and temperature (Browder et al., 2002).

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 121

based on locally observed daily temperatures and

salinities.The simulations predicted that potential harvests might differ between years, seasons, and regions

of the bay solely on the basis of temperature and salinity. Results indicated that harvests on the Tortugas

shrimp grounds could be affected by spatial extent, location relative to suitable bottom habitat, and duration

of unfavorable temperatures within a favorable salinity range.

Butler et al. (2001a) explored the effect of changing

salinity on lobster and hard-bottom habitat, especially

as it might relate to lobster microhabitat (i.e., various

species of sponges and octocorals). Salinity experiments at winter temperatures have recently been completed for several sponge species (Figure 8.4). The

results indicate that there is reduced survival for an increasing number of species as salinity decreases (Butler et al., 2001a). None of the five species tested survived

at 15 psu. Field and Butler’s (1994) results concerning

salinity and temperature effects on postlarval lobsters

suggested a salinity optimum of 35 psu. Survival rates

at salinities other than 35 psu were low below 18°C and

above 33°C.

Powell et al. (2004) examined temperature-related

spatial and temporal variation in growth and survival

of spotted seatrout between areas and months. They

found a strong parabolic relationship between temperature and the growth of juveniles (22–60 d) but no

significant relationship between temperature and the

growth of larvae. They did not have an appropriate

distribution of samples to look at spatial and temporal variation in relation to salinity.

In a laboratory experiment, Wuenschel et al.(2001,

2002) found a significant interactive effect of temperature and salinity on routine metabolic rates of spotted seatrout.They found a biphasic metabolic rate that

changed isometrically with body mass in early stages

of larval growth, approximating the exponential relationship near unity proposed in previous studies, and

changed allometrically thereafter. Response surfaces

describing the effects of temperature and salinity on

maximum consumption and growth rates were also developed from laboratory experiments.

The optimal salinity for spotted seatrout may differ for each life stage. Schmidt et al., 2001, 2002) found

a negative correlation between annual average spotted seatrout catch rates and indices of freshwater inputs to the bay. Johnson et al. (2002a) found a low but

significant negative correlation between spotted

seatrout catch rates and bay salinity but thought it

could be the spurious result of fish concentrating during hypersaline events in more limited favorable habitat with increased vulnerability to fishing. There is

indirect evidence that hypersaline conditions reduce

survival of spotted seatrout in the early-settlement

stage. Although larval concentrations suggest that central Florida Bay is a major spawning ground for spotted seatrout (Powell, 2003), juvenile spotted seatrout

appeared to extend their range into the central portion

of the bay when hypersaline conditions were absent

(Thayer et al., 1999; Powell, personal communication),

but this has to be tested more rigorously. Citing Alshuth

and Gilmore (1994), Powell (2003) noted that spotted

seatrout eggs do not float at salinities less than 15 psu,

so egg survival might be virtually zero percent at 0–15

psu. On the other hand, laboratory experiments of

spotted seatrout in Texas suggest that the species does

not spawn at salinities greater than 30 psu (Wakeman

and Wolschlag, 1977; Taniguchi, 1980).

Effect of Water Quality on 

Growth and Survival

The staff of Everglades National Park maintain a record

of fish kills in Florida Bay (Schmidt, 1993b; Schmidt and

Robblee, 1994).These deaths are believed to occur because of low dissolved oxygen in the water column.The

mass mortalities are usually reported in the Snake

Bight area, where episodic low dissolved oxygen may

be caused by a combination of extremely shallow water,

high summer temperatures, poor tidal and wind mixing, and high respiration rates. High ammonia levels

recently reported by Boyer (personal communication)

are another possible source of mortality.

Contaminants in Florida Bay biota have been investigated previously. Tissues of fish, macroinvertebrates, and birds were analyzed for concentrations of

heavy metals, pesticides, and polychlorinated biphenyls

(PCBs) in fish and macroinvertebrates (Ogden et al.,

1974). Concentrations of DDT, arsenic, and methylmercury in marine animals were high enough to warrant

Figure 8.4 Survival of five sponge species at four salinities at winter

water temperatures for four weeks (Butler, 2005).

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

122 FWRI Technical Report TR-11

further investigation and led to later air-quality studies in ENP. As part of a larger study of the possible effects of mosquito control in Monroe County, the

Environmental Protection Agency (Anonymous, 1980)

examined fish and shellfish tissues and water for concentrations of certain pesticides, including Naled and

Batex.They found negligible amounts of Naled in fish

and shellfish, although oysters accumulated an average of 0.007 ppb of Naled. Batex was not found in detectable amounts in either fish or shellfish. Results

may have been biased on the low side by the dry-season conditions that prevailed.

A multiyear study in the C-111 canal and associated sites in Florida Bay was undertaken in order to determine other contaminant risks that may exist in south

Florida (Scott et al., 2002). According to extensive surface-water data and results from analyses of sediment,

tissue, and semipermeable membrane devices, canal

contamination seems to be derived from the extensive

agricultural production that drains into the C-111

canal. The results of this study indicate that runoff

from agricultural fields led to quantifiable pesticide

residues found in both canal and bay surface water, at

levels that occasionally exceeded current water-quality criteria. The major pesticide of concern was endosulfan, which was detected at 100% of the sites sampled.

The decision to alter the C-111 canal flow and allow increased freshwater flow into the adjacent Everglades

may result in discharges of pesticides through Everglades National Park and into Florida Bay. Endosulfan

concentrations are highest in the northeastern part of

Florida Bay, where the special sensitivity of pink shrimp

could cause mortalities. Low pink shrimp densities in

northeastern Florida Bay have been documented since

at least the 1960s (Costello et al., 1986). Other factors (e.g.,

extreme and variable salinities, absence of broad banks,

sparse seagrass coverage) may limit the presence of

pink shrimp in the northeastern bay, but no investigation of the possible effect of endosulfan on pink

shrimp in the bay has been made.

Health advisories are now posted in eastern Florida

Bay warning of elevated levels of mercury in some

higher-trophic-level fish. Thirty percent of spotted

seatrout sampled from eastern Florida Bay exceed

Florida’s no-consumption advisory level of 1.5 μg/g–1

(Evans et al., 2001). Jack crevalles also contain comparably high mercury concentrations (Evans, personal

communication). Other species of gamefish and forage

fish, although not as high in mercury as these two

species, have concentrations several times those found

in the western bay or elsewhere in Florida.These high

concentrations may put humans, other mammals,

birds, and reptiles at risk. Reduction in body burdens

of mercury in top carnivores is one of the success criteria listed by the South Florida Ecosystem Restoration

Task Force. Work is underway by Marnie Billie at FIU

to assess the ecological risk of consumption of Florida

Bay fish by piscivorous ospreys in the bay. Planned

restoration activities in the Everglades will change

freshwater deliveries to Florida Bay. These deliveries

could alter the existing high levels of mercury in some

Florida Bay gamefish through enhanced mercury fluxes

as well as altered productivity and food web structure, which influence mercury bioaccumulation.

Effect of Benthic Habitat on 

Growth and Survival

This issue has generally been approached by relating

benthic habitat to animal densities, which implies survival and growth, rather than by measuring habitat

effects on growth and survival directly.The fact that faunal densities are correlated with certain benthic habitats suggests that growth and survival are highest in

the appropriate habitat. See section on effect of benthic habitat on abundance.

Immigration, Growth, and Survival of 

Offshore-Spawning Fishes that Use

Florida Bay as a Nursery

In an effort to understand spatial and temporal patterns

of variability in immigration, growth, and survivorship of upper-trophic-level fishes, Settle (unpublished

data) examined these life history attributes in several

important species in the bay. Juvenile great barracuda

using the bay as nursery habitat are the product of protracted spawning, which is centered during the summer but with nearly 15% occurring from late fall and

winter. Spawning during these later periods has not

been previously reported in south Florida and may

suggest that either some spawning does occur in the

region during those times or that some barracuda in

the bay originate from elsewhere in the species’ distribution.The youngest individuals are found in the Atlantic transition, gulf transition, and western subregions

of the bay, suggesting ingress from both the Atlantic

channels and the open Gulf of Mexico. Cohort-specific

growth rates of young fish (age 30–150 d) ranged from

1.44 to 2.65 mm d–1 during the 1990s. Over the same period, growth was significantly slower in two faunally

depauperate subregions, the eastern and the turbid

western bay. Relative condition (weight/length) of this

species over the period 1973 to 2000 declined during

the early to mid-1990s and appears to be returning to

values observed during the 1970s and mid-1980s.The

overall instantaneous natural mortality rate was 0.02656.

Average survival was 97.38% d–1.Cohort-specific growth

Higher-Trophic-Level Species
rates of juvenile lane snapper (age 30–242 d), which primarily inhabit the gulf transition and western subregions, showed significant intra- and interannual

variation and ranged from 0.59 to 0.93 mm d–1. Snappers spawned during the spring and summer grew

faster than those spawned during fall and winter, and

fish spawned during 1998 grew faster than those

spawned in 1997. Instantaneous natural mortality both

years was 0.03636, and average survival was 96.43% d–1.

Effect of Ecosystem Characteristics

on Species Distribution and 

Community and Trophic Structure

Work on this topic addresses the major questions: Do

HTLS’ community composition or trophic structure

in Florida Bay vary in time and space, what factors are

responsible for this variation, and what processes are

affected? Major working hypotheses are as follows: 

• The abundance of HTLS is low in the northeastern

portion of Florida Bay because of high-amplitude

variation in salinity, low density of seagrass, lack of

extensive banks, restrictions on the immigration of

postlarvae, or a combination of all of these factors; 

• Changes in community composition are related to

changes in salinity, which can be influenced by water

management, although the effect of benthic habitat,

tidal exposure, rainfall, and oceanographic events

may need to be filtered out to see these effects; 

• Changes have occurred in the species composition

of mollusks, foraminifera, and other sessile species

in Florida Bay, and these changes reflect changes in

salinity, water quality, and the cover and composition of benthic vegetation;

• Spatial and temporal patterns in trophic pathways

vary depending on salinity, water quality, and abundance and type of benthic vegetation; 

• Widespread sponge mortalities may affect both

hard-bottom and seagrass communities;

• Fishing reduces the number and size of some apex

predators, causing shifts in community structure;

and

• Changes in community composition are related directly to changes in benthic habitat.

Effect of Salinity on Species Abundance

and Community Structure

Several studies suggest that hypersalinity affects the

benthic fauna of Florida Bay. Schmidt (1977) reported

lower forage fish diversity, biomass, and numbers in

northcentral Florida Bay in salinities greater than 45

psu. Johnson et al. (2002a,b) noted that “evenness”(an

index of community structure) among 11 dominant

species, as estimated from statistical model predictions, was lower in 1990, a year of extreme high salinity in the bay, than in 1995, a wet year. Lyons (1999)

observed fewer species in the molluscan community

in the hypersaline part of Florida Bay. A simulation

model based on experimental data (Browder et al.,

2002) predicted lower juvenile pink shrimp densities

and fewer potential recruits to the Tortugas fisheries

from the hypersaline central part of Florida Bay. Based

on relative concentrations of smallest-stage seatrout

postlarvae, Powell (2003) determined that central

Florida Bay is a major spawning ground for spotted

seatrout; however, there is evidence that at salinities

greater than 45 psu, survival and growth of larval and

juvenile spotted seatrout could be diminished (Wuenschel, 2002). The frequency and duration of hypersaline events in the central bay might, therefore, affect

survival and growth of young seatrout and, consequently, the abundance of this species. Powell (2002)

noted that densities of the postlarvae of many species

collected with an epibenthic sled were higher in the

central bay, indicating that many species may be disproportionately exposed to hypersaline conditions in

an otherwise favorable nursery area. Sogard et al. (1989)

found lower species richness of both epibenthic and

water-column fishes. Holmquist et al. (1989) found a

lower species richness of macroinvertebrates in the

central bay, which was characterized by low tidal range

and hypersaline conditions during their studies.They

concluded that water circulation and salinity patterns

were influential in structuring Florida Bay’s epibenthic

faunal communities.

HISTORICAL DISTRIBUTIONS OF MOLLUSKS

AS INDICATORS OF PAST SALINITY 

PATTERNS

Historical records of salinity and bottom vegetation

were reconstructed based on molluscan assemblages

in shallow sediment cores. An analysis by BrewsterWingard et al. (2001) suggested that molluscan assemblages in Florida Bay have undergone distinct

changes over the past 100–200 years. Brachidontes exustus, a euryhaline species tolerant of diminished water

quality and a wide range of salinities, accounts for

more than 80% of the molluscan fauna in the upper

portions of six cores. Four cores from central and eastern Florida Bay and one from Featherbed Bank in Biscayne Bay suggest decreases in molluscan faunal

diversity and absolute abundance that began perhaps

in the 1960s or earlier and reached a low in the early

1970s (Figure 8.5).

The dominance of Brachidontes and the decreases

in faunal richness and abundance are indicative of a

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 123

Higher-Trophic-Level Species
system under stress. Interestingly, the transition-zone

cores from the mouth of Taylor Creek and in Manatee

Bay do not show the decline in faunal diversity and absolute abundance exhibited in the other cores. Based

on their analysis of molluscan epiphytic species within

the cores, Brewster-Wingard et al. (2001) concluded

that common factors are affecting the faunas and their

associated bottom vegetation across eastern and central Florida Bay, despite the isolation of some of the

basins.

Effect of Water Quality on Species 

Abundance and Community Structure

Ortner et al. (2001), who examined possible relationships between chlorophyll, zooplankton, and anchovy

from January 1994 through January 1999, found no evidence that phytoplankton blooms were causing a fundamental shift in community structure and trophic

dynamics in Florida Bay. Copepod concentrations were

not related to chlorophyll concentrations, and anchovy

density was not related to copepod concentrations.

On the other hand, Johnson et al. (2002a) found a significant relationship between bay anchovy density and

chlorophyll a concentrations. Intermittent high anchovy densities might be due to the attraction of anchovies to unvegetated bottoms and high turbidity

(Patillo et al., 1997). Peebles’ (2002) study of bay anchovy egg densities in the Manatee River suggests

that structured, spatially and temporally intensive

sampling of bay anchovy eggs may reveal relationships with prey abundance, salinity fronts, and freshwater inflow not obvious from previous sampling in

Florida Bay.

Effect of Benthic Habitat on Species

Abundance and Community Structure

FISH DISTRIBUTIONS IN MANGROVE 

PROP–ROOT HABITAT

Dennis and Sulak (2001) found that prop-root sites in

northeastern Florida Bay had significantly more fish larvae than did nearby open-water sites or nearshore

areas without mangroves. However, the densities of

both forage fish and juvenile predator fishes were

lower among mangrove prop-root habitats in Little

Madeira Bay, Trout Cove, and Manatee Bay than in

prop-root habitats in the Bahamas and Puerto Rico.

They proposed that isolation from offshore sources of

larvae or juveniles was the reason for the low densities. In support of this conclusion, they found that the

concentration of larval fish was much greater on the leeward side of Key Largo than at their northeastern

Florida Bay mangrove prop-root sites. Fish density

and biomass were greater in mangrove prop-root habitats than in adjacent fringing seagrass areas. In a previous study by Thayer et al. (1987), they determined that

the mangrove prop-root habitat in Florida Bay and

nearby areas was occupied by a distinct faunal assemblage.

CANOPY–DWELLING FISH AND 

MACROINVERTEBRATE ASSEMBLAGES 

IN RELATION TO SEAGRASS

Densities of many macroinvertebrate and fish species

in Florida Bay are higher inside seagrass beds than outside them (Holmquist et al., 1989; Sogard et al., 1989;

Thayer and Chester, 1989; Thayer et al., 1999; Matheson

et al., 2001). Johnson et al. (2002a) analyzed the combined

data of 6 field studies (including those cited above) and

quantified the relationship between animal density

and seagrass density for 11 key forage species. They

found that of the 10 species whose densities were significantly related to seagrass, 5 were densest in dense

Florida Bay Synthesis Hunt and Nuttle

124 FWRI Technical Report TR-11

Figure 8.5 Historical view of the dominance of a molluscan

water-quality indicator in the molluscan fauna (Brewster-Wingard

et al., 2001) at three Florida Bay locations. Brachidontes tolerates conditions that other mollusks cannot. Experiments are underway to better define the conditions tolerated by Brachidontes.

Higher-Trophic-Level Species
seagrass, 4 were densest in moderately dense seagrass, and 1 was densest in sparse seagrass. Bottom or

seagrass type was a significant variable explaining the

densities of 10 forage species.Three species were densest in Syringodium, three were densest in Halodule, two

were densest in mixed grasses with Syringodium, and

one was densest in mixed grasses with Thalassia. One,

bay anchovy, was densest in areas without seagrass.

SHIFTS BETWEEN BENTHIC AND PELAGIC

ZOOPLANKTIVORES

A prevailing hypothesis has been that the seagrass

die-offs and phytoplankton blooms experienced beginning in the late 1980s provoked a trophic shift in

western Florida Bay from a system based principally

on benthic production to one based principally on

water-column production.This hypothesis grew out of

comparisons of the fish and macroinvertebrate community compositions in 1984–1985 to those in 1994–1995.

Thayer et al. (1999) compared the fish assemblages of

1984–1985 to those of 1994–1995 in three regions of the

bay and found that canopy-dwelling species had declined and that pelagic zooplanktivores dominated

the fauna. Robblee et al. (2001) compared benthic vegetation, fish, and macroinvertebrate assemblages found

in Johnson Key Basin in 1985 to those found there in

1995. They observed a decrease in Thalassia and Syringodium and an increase in Halodule and bare bottom.

They found a decrease in Farfantepenaeus duorarum

(pink shrimp), seagrass-associated caridean shrimps

(–65%), and seagrass-associated fishes (–81%) and concluded that the decline in seagrass-associated species

was a result of seagrass die-off.

The hypothesis that loss of seagrass would result

in a trophic shift of fish was discounted by sampling

data beyond 1995.The juvenile and small-resident fish

assemblage in collections of Powell et al. (2001b) made

during 1996–2000 (especially 1998) differed markedly

from that in 1994–1995 and resembled the assemblage

observed in 1984–1985. The change from canopydwelling to pelagic zooplanktivores from 1984–1985

to 1994–1995 was followed by a change back to canopy

dwellers in 1998–1999. The investigators concluded

that the recovery of an assemblage of fish species dominated by seagrass canopy dwellers cannot be wholly

explained by recovery of seagrasses because there is

no evidence of seagrass recovery on a subdivisionwide basis in 1999–2000 relative to 1994–1995. In fact,

seagrass densities in 1999–2000 were much lower than

in 1984–1985 (Powell et al., 2001b).

Ortner et al. (2001) also refuted the hypothesis of

a trophic shift related to loss of seagrass coverage and

an increase in phytoplankton blooms.They concluded

that the recent history (1994–2000) of phytoplankton,

zooplankton, and planktivorous fish abundances provides little or no support for the concept of a fundamental, persistent shift from a demersal benthic-based

food web to a pelagic water-column-based food web.

Furthermore, there seems to be no clear relationship

between plankton bloom incidence or intensity and the

abundance of zooplanktonic herbivores, nor is there a

relationship between the abundance of the bay anchovy and its preferred copepod prey.

An alternative hypothesis for the observed fluctuation in dominance between demersal and water-column species is that the density of the small-juvenile

and small-resident canopy-dwelling fish assemblage

is influenced by the sporadic dominance of pelagic

zooplanktivorous clupeiforms that might be related to

water column chlorophyll a concentrations (Powell et

al., 2001b).

Another alternative hypothesis is that the establishment of a more heterogeneous bottom habitat, occupied by Halodule and Syringodium as well as some

Thalassia, might be responsible for the recovery of

canopy-associated species after 1995 (Robblee, personal communication) An exploratory principal component analysis revealed four PCs, each of which could

be interpreted to relate to a vegetation component:

Thalassia (PC1), Halodule (PC2), Syringodium (PC3), and

macroalgae (PC4) (Robblee et al., 2001). Pink shrimp correlated with PC2 and PC3.The rainwater killifish was

correlated with PC1. Affinities of various species to

certain types of seagrass habitat might lead to greater

overall abundance if seagrass habitat diversity increases.This is supported by the work of Johnson et al.

(2002a), who found that densities of various species varied, depending upon the type of seagrass they were

found in and that no species was found at highest

density in pure Thalassia beds.This result is especially

valuable because Somerfield et al. (2002) concluded

that even large faunal effects of seagrass habitat heterogeneity might be difficult to detect. This hypothesis might explain the recovery of canopy-dwelling

species after 1995 but not the fluctuations in bay anchovy density.

Peebles’ (2002) study of bay anchovy egg abundance in the Manatee River provides insight on the bay

anchovy fluctuations in Florida Bay. Using a spatially

and temporally intense sampling strategy, Peebles

(2002) found that nighttime bay anchovy egg abundance in Manatee Bay was positively related to Acartia tonsa abundance the previous day. Bay anchovy

appeared to spawn immediately upstream from salinity fronts (which he defined as a change of 1 psu/km)

that concentrated their prey. The effect of freshwater

inflow on bay anchovy egg abundance was non-linear.

Peak abundance occurred when salinity fronts formed

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126 FWRI Technical Report TR-11

near the river mouth. Egg abundance declined when

these fronts advanced seaward of the river mouth but

was lowest when fronts were weak or absent during

low-flow periods.The presence of a salinity front was

associated with relatively low mean salinity and high

standard deviation in salinity. In their analysis of a

data set compiled from several studies, Johnson et al.

(2002a) found a significant relationship between bay anchovy density and salinity (negative relationship), standard deviation in salinity (positive relationship), and

freshwater inflow index (positive relationship) in

Florida Bay. Peebles’ (2002) study might explain the

mechanisms behind these relationships.

EFFECTS OF MACROALGAE ON 

ANIMAL ABUNDANCE

The pattern of settlement of spiny lobster postlarvae

in southwestern Florida Bay may be highly dependent on the location of red macroalgae (Laurencia),

crevice shelters and planktonic postlarval abundance

(Herrnkind and Butler, 1994). Mud banks that restrict

transport, unfavorable salinity, and scarcity of hard-bottom settlement habitat may severely restrict the presence of spiny lobster in the interior bay (Field and

Butler, 1994).

EFFECT OF SPONGES ON 

JUVENILE SPINY LOBSTER

Butler et al. (1995) documented widespread sponge

mortality coinciding with months-long, extensive

cyanobacterial blooms in the south-central part of

Florida Bay in the early 1990s (1991, 1992, 1994). They

showed with field experiments that the loss of sponges

affected the distribution of spiny lobster juveniles,

which use crevices beneath sponges as nursery habitat. Use of artificial shelters increased following the

sponge decline. Juvenile spiny lobster abundance declined 23% at sites without artificial substrates and increased 76% at sites with artificial substrates. The

long-term effect of sponge mortality on lobster abundance is not known, but shelter such as that provided

by sponges reduces the risk of predation (Herrnkind

and Butler, 1994). Based on their results, the authors

suggested that loss of shelter might lead to increased

predation on animals that remain in areas without

shelter or are in search of shelter. Loss of area with shelter may cause crowding and resource limitation in

areas of remaining shelter (Butler et al., 1995). Other animals that use sponges as habitat include stone crabs

(Menippe mercenaria), spider crabs (Mithrax spp.), toadfish (Opsanus beta), and octopus (Octopus spp.).

SPATIAL VARIABILITY IN 

TROPHIC RELATIONSHIPS 

The relative importance of seagrass and phytoplankton in food webs differs across the bay, and neither is

important in certain parts of the bay. Chanton et al.’s

(2001) evaluation of stable carbon (C), nitrogen (N), and

sulfur (S) (δ13C, δ15N, δ34S) data for producers and consumers in Florida Bay indicated that the interior of

the bay has a strongly seagrass-based trophic structure,

whereas the gulf (outer or western) sites in the bay shift

toward a more plankton-dominated trophic system

(Figure 8.6). It is not yet certain whether the shift in Figure 8.6 reflects natural spatial variation or a temporal

trend forced by changing environmental conditions in

the bay. Stable carbon, nitrogen, and sulfur data in

Figure 8.7 from Evans et al. (2001) confirm Chanton et

al.’s (2001) description of the trophic structure of the

interior and western bay. In addition, the data suggest

a nonseagrass-based diet (likely a more pelagic-, or

water-column-, based food web) in the eastern bay.

Predominant food webs in the hard-bottom communities of Florida Bay (mainly the southwestern bay)

and bayside hard-bottom communities in the Florida

Figure 8.6 Summary comparison of consumer tissue δ13C vs δ34S

from several Florida coastal ecosystems. Data illustrate the gradient

in stable isotope values as trophic dependence shifts from seagrass

beds “benthic”, δ13C-enriched, δ34S-depleted) to the water-column

(“planktonic”) (δ13C-depleted, δ34S-enriched) (Chanton and Lewis,

2002).

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 127

Keys are based on macroalgae rather than seagrass, according to stable-isotope analyses (C, N, and S) conducted by Behringer and Butler (1999).They sampled

macroalgae, seagrass, suspended particulate organic

matter (POM), sediment POM, sponges, gastropods,

holothurians, bivalves, and spiny lobsters. With the

exception of suspension feeders, the hard-bottom animals were trophically independent of seagrass.

Koenig et al. (2001) found spatial, temporal, and ontogenetic dietary shifts in the major prey of red drum.

They speculated that the differences were due to differences in prey availability. This is consistent with

observations about the abundance of various prey,

which differs by region. They were not able to detect

spatial or seasonal differences in the diet of snook,

possibly because of the lower resolution of the snook

diet data.

Variation in Ecosystem 

Characteristics

Effects of Animals on the Ecosystem

Specific questions being addressed by this research are

as follows: (1) how do animals affect their ecosystem,

and what are the consequences of change in animal

abundance or distribution for the rest of the system?

(2) What is the ecological role of sponges in the ecosystem, and what does the loss of sponges in southwestern Florida Bay and an increasing fishery for some

sponge species portend? 

EFFECTS OF ANIMALS ON BENTHIC HABITAT

Benthic grazing animals in exceptionally high densities can adversely affect benthic vegetation in Florida

Bay. A dense aggregation of the variegated sea urchin

(Lytechinus variegatus) caused severe, localized defoliation of a seagrass bed in outer Florida Bay during

1997–1998 (Rose et al., 1999). Macia and Lirman (1999)

described the population dynamics of this aggregation

and Rose et al. (1999) described the short-term effect

of this aggregation on the benthic community. Subsequent monitoring of the aggregation during 1998–1999

revealed that urchin densities progressively declined,

as did their effect on seagrass biomass. However, as of

2002, seagrass biomass in the area of the meadow that

underwent the most severe defoliation remained drastically reduced compared to areas that had not been

damaged by urchins (W. Sharp, personal communication).

ROLE OF SPONGES IN REGULATING 

WATER QUALITY

The working hypothesis is that the large-scale loss of

suspension-feeding sponges may have rendered the

Florida Bay ecosystem susceptible to recurring phytoplankton blooms (Peterson and Fourqurean, 2001).

Sponges are capable of filtering large volumes of water

when feeding.Widespread sponge mortalities occurred

in Florida Bay from 1992 to 1994. By 1995, total sponge

biomass was a fraction of its former level: there had

been a 70% decline in the Long Key area and an 84.6%

decline in the Marathon area (Stevely and Sweat, 2001).

Loss of sponge biomass in Florida Bay may be having

major ecological effects on water quality (Stevely and

Sweat, 2001; Peterson and Fourqurean, 2001) 

Sponges are a particularly dominant structural

feature of Florida Bay seagrass and hard-bottom habitats, functioning as efficient filters of small (less than

5 μm) planktonic particles. Previous studies have illustrated that the grazing pressure of filter-feeding

bivalves may control phytoplankton abundance. If the

presence of sponges increases light availability to the

benthic plant communities, then sponges may reduce

the shading effects of phytoplankton blooms, and the

loss of sponges in Florida Bay may have cascading effects on the associated seagrass community (Peterson

and Fourqurean, 2001).

Since the initial seagrass die-off in the late 1980s,

blooms have swept over extensive portions of the bay

Figure 8.7 Stable isotope analysis of Florida Bay gamefish to

support methylmercury studies in Florida Bay (Evans et al., 2001).

The analysis complements the view of the bay in the previous

figure by adding information on the bay’s eastern and northern transition zones.

Higher-Trophic-Level Species
north of the middle Keys and have persisted for

months.The proliferation of the cyanobacterium (Synechococcus) and diatom (Rhizosolenia) blooms has caused

widespread concern among scientists and water managers.These blooms have the potential for disrupting

the ecology of the bay and harming benthic plant communities by depleting oxygen, producing toxins, and

reducing the light levels in the bay. Some regions of

Florida Bay exhibit high levels of algal and/or nonalgal suspended solids, resulting in low light penetration.

Although phytoplankton blooms were not likely the

cause of the initial seagrass die-off, the reduction in

light caused by high phytoplankton standing crops

may have contributed to poor seagrass recovery and

more recent seagrass die-offs.

Prior to the widespread sponge mortalities that occurred from 1992 to 1994, Stevely and Sweat (2001)

collected data on the abundance of commercial sponges

(Spongia and Hippospongia) and the entire sponge community at 15 locations in the Middle and Upper Keys

(4 locations were within Everglades National Park).

They have been evaluating the recovery of the sponge

community annually since 1994 and have identified to

family, genus, or species level approximately 95% of the

sponges counted. In general, recovery of the largest and

most abundant sponge species (in the genera Spheciospongia and Ircinia) has been extremely slow.The first

significant indication of recovery of these species was

found at Marathon in 1999 and 2000, but recovery was

still not apparent at Long Key by April of 2001. These

large species represented 70% of the sponge community biomass prior to the mortalities.

Based on their data prior to the 1992–1994 mortalities, Stevely and Sweat (2001) estimated that the mean

sponge abundance was 0.725 sponges/m2 and mean

sponge biomass volume was 364 ml/m2. Based on a

sponge pumping rate of 10,000 times the sponge volume per day (Reiswig, 1974; Reiswig, personal communication), the sponge biomass could therefore pump

3,640 liters of seawater per square meter per day. Since

the water column in the study area was approximately

three meters deep, sponge biomass could be expected

to pump the equivalent of the entire water column in

24 hours (Stevely and Sweat, 2001).The loss of 75% of

sponge biomass might be expected to lengthen the

time required to pump the water column from one day

to four days.

Peterson and Fourqurean (2001) speculate that

system-wide trophic dysfunction caused by the sponge

die-off has potentially contributed to the magnitude of

the nuisance phytoplankton blooms, and that the loss

of these organisms can explain why this system remains

susceptible to recurrent blooms of phytoplankton and

cyanobacteria.

Oceanographic Effects on 

Larval Transport and Recruitment

Major questions related to this topic are (1) What

processes are involved in the transport of presettlement

stages of fish and invertebrates to the boundaries of

Florida Bay, and what are their schedules? and (2)

What pathways do early life stages of offshore-spawned

HTLS use to enter Florida Bay, what is the relative importance and extent of penetration into the bay’s interior by these pathways, and what factors influence

transport and settlement?

Many species associated with the reef tract and the

southwestern Florida shelf spend some part of their

life cycle in Florida Bay. For example, Florida Bay is a

major nursery ground for pink shrimp that are harvested in waters off the Dry Tortugas, the most economically important pink shrimp fishing ground in the

state. Florida Bay also contains important spiny lobster nursery habitat, and Everglades National Park is

a fishing-free sanctuary for spiny lobster. Water flows

and animal movements connect Florida Bay not only

to the upstream Everglades and coastal mangrove

areas but also to the Florida Keys, the reef tract, the

southwest Florida shelf, and the Dry Tortugas. Many

HTLS range between the bay and coastal reefs within

their life cycle. The development of scientific knowledge about HTLS of the bay, therefore, must extend

beyond Florida Bay to address the greater ecosystem

that supports these species and the processes that

affect their movements. For example, research should

include the Loop and Florida currents and countercurrents, the Tortugas Gyre, and coastal eddies.The effect of these processes on larval transport and the

distribution and abundance of HTLS in the bay must

be addressed to improve the ability to distinguish

effects of changes in freshwater inflow.

Florida Bay lies between the Atlantic Ocean and the

Gulf of Mexico and is connected to both of these bodies through regional-scale circulation and exchange

processes and the oceanic boundary currents that influence these processes. The southwest Florida Shelf

to the west and the Keys coastal zone to the east and

south of Florida Bay interact with each other and the

bay through the tidal channels between the Keys and

also by means of their boundary currents (Herrnkind

and Butler, 1994; Lee et al., 2001). A dominant process

potentially affecting water transport and the transport of eggs and larvae to Florida Bay is the strong, coherent response to alongshore wind-forcing coupled

with seasonal stratification in response to variations in

wind-mixing, air-sea exchange, and river runoff along

the nearshore western shelf. Boundary current dynamics and eddy processes are also critical larval transFlorida Bay Synthesis Hunt and Nuttle

128 FWRI Technical Report TR-11

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 129

port mechanisms that operate both on the regional

and local scales.Transport response to prevailing easterly winds may vary along the Florida Keys as a result

of the curvature of the coastline (Lee and Williams,

1999), but they are expected to favor onshore larval

transport between the Lower Keys and the Dry Tortugas, where the coastline is east-west oriented. Onshore convergence of the Florida Current can also

facilitate transport into the coastal zone of the Keys, and

this occurs mainly in the upper Keys where the shelf

narrows and curves northwards (Yeung and Lee, 2002).

The area of the Dry Tortugas is an important spawning site for penaeid shrimps, spiny lobsters, and some

species of snappers and groupers (Limouzy-Paris et al.,

1997). Pink shrimp larvae were retained by the Tortugas gyre circulation for a period of two weeks (Criales

and Lee, 1995). Coastal eddies originating from the

Dry Tortugas and propagating downstream may be a

mechanism to deliver presettlement stages from

spawning site to nursery sites on the reef tract and in

Florida Bay (Yeung et al., 2001; Criales et al., 2003).The

lower southwestern shelf in the vicinity of the Dry

Tortugas is a potential source of recruitment to the

Florida Keys reef tract and Florida Bay for both reef fish

and pink shrimp.

Frontal eddies of the Loop Current in the Gulf of

Mexico that propagate southward along the outer edge

of the western shelf may be trapped and develop into

persistent gyres off the Dry Tortugas (Fratantoni et al.,

1998; Yeung and Lee, 2002). The subsequent arrival of

another frontal eddy or the abrupt retreat of the Loop

Current may dislodge the gyre, which then moves

eastward along the southeastern shelf off the Florida

Keys in the form of a transient coastal eddy. The Tortugas gyre provides a mechanism for retaining larvae

for periods of weeks to up to three months (Lee et al.,

1994).

EDDIES AND GYRES

Working hypotheses about the transport of larvae to

the boundaries of the bay are as follows: (1) Presettlement stages are transported and detrained into the

coastal zone of the Florida Keys by coastal eddies. (2)

Spawning and nursery sites for pink shrimp, spiny

lobsters, and some snappers are linked through the

evolution of the coastal eddies from the Tortugas gyre.

(3) The formation of the Tortugas gyre is enhanced by

a well-developed Loop Current (high latitudinal intrusion) whose dynamics may be modulated by climatic

shift. (4) Snapper larvae entering Florida Bay originate from spawning stocks that form seasonal aggregations off the Dry Tortugas. (5) Year-class strength of

six snapper species is enhanced by increased larval retention and nutrient-enrichment of the pelagic larval

habitat via gyre-induced upwelling during spawning

season off the Dry Tortugas (Criales and McGowan,

1994; Criales and Lee, 1995; Jones et al., 2001; Yeung et

al., 2001; Yeung and Lee, 2002).

Supply of early-life-stage recruits is a major limiting factor of the year-class strength of aquatic species.

Presettlement stages of the spiny lobster, snapper, and

pink shrimp that inhabit Florida Bay as juveniles and/or

adults enter the bay from the ocean through interisland

channels.

The eddy hypothesis of regional recruitment has

important implications over larger temporal and spatial scales. Because coastal eddies originate from the

Dry Tortugas, they may constitute the essential transport link between the spawning and nursery grounds.

Moreover, eddy formation at the Dry Tortugas is associated with Loop Current frontal dynamics, which are

in turn modulated by long-term climatic variability

(Yeung et al., 2001; Yeung and Lee, 2002).

Observed larval distribution patterns of some crustaceans in the Florida Keys coastal zone corroborate

many of the predictions based on key coastal transport

processes. Early-stage phyllosomata (less than 2 months

old) were concentrated within or at the boundaries of

a gyre in the pattern hypothesized for passive drifters

(Yeung and Lee, 2002).The abundance of strong-swimming spiny lobster postlarvae was not highly correlated

with wind-driven currents that can affect the coastal

transport of more passive drifters (Acosta and Butler,

1997). High concentrations of pink shrimp larvae were

found in the Tortugas Gyre in late spring–early summer (Criales and Lee, 1995). High densities of larvae and

postlarvae of 10 different shrimp families were found

Figure 8.8 Monthly mean influx density of spiny lobster postlarvae

observed at Long Key and the predicted density (densityLK) using

an index of countercurrent magnitude in a simple regression model

(r2 = 0.50, F1,16 = 17.90, P < 0.0006) (Yeung et al., 2001).The index

is the average magnitude of the countercurrent component for the

periods two weeks prior to and three days during sampling taken

at a current meter moored at Tennessee Reef in the middle Keys.

Satellite imagery confirmed that in most cases, enhanced coastal

countercurrents coincided with the presence of a cyclonic mesoscale

eddy in the vicinity.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

130 FWRI Technical Report TR-11

off Looe Key during the presence of a gyre (Criales and

McGowan, 1993, 1994).

Variability in the supply of larvae may be related

to the development of mesoscale eddies and their associated countercurrents on the oceanside of the channels. Peak influx of spiny lobster postlarvae into the bay

through the middle Keys coincided with the presence

of eddy and countercurrent conditions (Figures 8.8,

8.9) (Yeung et al., 2001; Yeung and Lee, 2002).

Temporal and spatial variability in the supply of

spiny lobster postlarvae to Florida Bay nursery grounds

may interact with local nursery-habitat structure to

influence recruitment and year-class strength. Butler

et al. (2001b) used an individual-based model to address

this question. They tested eight scenarios of variability describing postlarval supply (Uniform, Volumetric, Gradient, Broken Stick–Static, Broken Stick–

Variable, Pulsed, Aggregated, and Random).Their results indicated that random variation in the arrival of

postlarvae among regions of the Florida Keys leads to

the highest recruitment, whereas persistently patchy

settlement (i.e., pulsed and aggregated scenarios) yields

the lowest. Analyses of field data suggested that the random supply was the most realistic scenario. Field data

were based on artificial collectors positioned at eight

sites in the Florida Keys.

Eddy transport processes may also affect supply

and nutritional condition of pink shrimp and snapper

presettlement stages entering Florida Bay through the

Florida Keys. Influx of early-life-stage recruits was

monitored monthly on the new moon for two years at

two tidal channels on opposite ends of the middle

Keys: Whale Harbor (east end) and Long Key Channel

(west end). Back-counted birth dates based on counts

Figure 8.9 Example of a sequence of satellite SST images used to infer gyre displacement and progression down the Straits of Florida

(Yeung et al., 2001). Warmer waters are red, cooler waters are blue. The centers of each of two gyres (1 and 2) present during this period

are indicated. On March 5, a gyre (1) was centered off the Dry Tortugas; by March 14, it had begun moving downstream; and by March

25, the upstream frontal eddy (2) responsible for its displacement is clearly evident.

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FWRI Technical Report TR-11 131

of otolith daily increments suggested that snapper larval duration during the first year varied across species

and ranged from 35.50 to 41.45 days (Jones et al., 2001).

Preliminary analyses of Year-2 samples suggested that

larval durations differed from those of Year 1. Peak

abundance of snapper larvae in the channels occurred

in the summer of 1997 and was coincident with a welldeveloped Loop Current (high latitudinal extent) favoring gyre formation off the Dry Tortugas, where

snapper spawning aggregations occur. Criales et al.

(2003) showed that the temporal pattern of immigration of postlarval pink shrimp differed substantially between Long Key Channel and Whale Harbor Channel

(Figure 8.10).The influx of postlarvae at Long Key channel was lower in magnitude but steadier than the influx at Whale Harbor. Long Key channel showed the

highest postlarval influx in late spring–summer,

whereas the postlarval influx through Whale Harbor

(downstream from Long Key in terms of the Gulf

Stream and associated shelf gyre processes) showed

both spring–summer and winter peaks. The winter

peak may be associated with the countercurrent generated by eddies (Figure 8.10). This high variability

over small spatial scales suggests the influence of

mesoscale processes.

MOVEMENT INTO AND WITHIN 

FLORIDA BAY

Other working hypotheses that relate principally to

movement of postlarvae into the bay are as follows: (1)

Pink shrimp postlarvae enter Florida Bay from two directions: west (across the southwestern shelf) and

southeast (through the Lower Keys).The western and

southeastern pathways vary in importance and are affected differently by physical oceanographic factors and

tides. (2) Sufficient numbers of pink shrimp larvae

enter the bay’s interior for the interior bay to be a significant nursery ground and source of recruits to the

fishery during years of favorable conditions. (3) Snappers settle outside Florida Bay but near the boundary

and enter Florida Bay as juveniles. (4) The abundance

of bay-dependent species that are spawned offshore

is lower in northeastern Florida Bay because of weak

transport across the bay.

Transport across the lower and middle Keys has

previously been the most recognized pathway of larval transport to Florida Bay because past studies (Criales and McGowan, 1994; Yeung, 2001) have shown

that local winds, Florida Current flow, and coastal eddies interact to influence the onshore transport and recirculation of larvae in the Florida Keys. New work,

based on synchronized sampling of postlarvae on both

sides of Florida Bay, indicates that the dominant pathway of influx of postlarval pink shrimp into Florida Bay

is from the west (Browder et al., 2002). Peak concentrations of pink shrimp postlarvae in water moving

into the bay from the west (through Sandy Key and

Middle Ground channels) were substantially larger

than in water moving into the bay from the southeast

(Whale Harbor Channel). The temporal pattern from

the west consisted of one large, sustained summer

peak (Figure 8.11). In contrast, peak concentrations at

Whale Harbor were observed in February, May, and

July and were smaller (Figure 8.11). Prior studies examined the influx of pink shrimp postlarvae from the

southeast (Allen et al., 1980) and west (Tabb et al., 1962;

Roessler et al., 1969; Robblee et al., 1991), but these

studies were not designed in a way that would allow

us to make comparisons now.

Pink shrimp nursery grounds are on the western

Figure 8.10 Mean monthly postlarval influx of pink shrimp has

different temporal patterns in channels of the middle Florida Keys

(Criales et al., 2003). At Long Key Channel (the two upper graphs),

larval concentrations are associated with surface temperature. At

Whale Harbor Channel, larval concentrations were associated

with the coastal countercurrent flow.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

132 FWRI Technical Report TR-11

side of the bay (Robblee et al., 1991), not in the east

(Costello et al., 1986).The larvae spawned north of the

Dry Tortugas on the relatively shallow shelf may escape

from the strong flow of the Florida Current and move

northeast toward the bay with the winds and tidal

currents.

Effect of Human Activities

This topic was approached by addressing three major

questions: 

• What are the potential effects of water management

and other human activities on recruitment, growth,

and survivorship of HTLS? 

• What is the potential effect of water management on

bioaccumulation of mercury?

• How does fishing, both within the bay and outside

the bay, affect fishery populations and our ability to

detect effects of water management on recruitment,

growth, and survival? 

Some critical working hypotheses relative to these

questions were as follows:

• The timing and amount of freshwater releases to

coastal wetlands adjacent to Florida Bay affect the

nesting success of wading birds in northeastern

Florida Bay.

• Changes in water management that affect the spatial coverage, intensity, and duration of hypersalinity affect shrimp, lobster, and other species.

• Abrupt and out-of-season releases of large volumes

of fresh water into Florida Bay and coastal waters adversley affect benthic fauna and fish, shrimp, and lobster recruitment.

• Increased freshwater inflow to northeastern Florida

Bay will increase the load of mercury entering the bay

and the body burden of mercury in bay HTLS.

• Fishing on the reef tract, in the Tortugas, and throughout the bay affects the population structure and

abundance of predator fish species in Florida Bay.

WATER MANAGEMENT AND 

WADING–BIRD NESTING SUCCESS

Linkages of water management, fish production, and

roseate spoonbill nesting success in wetlands adjacent to northern Florida Bay have been quantified in

studies by Lorenz (2001a,b). Other investigators have

proposed that fish availability to wading birds during

their nesting season in south Florida is influenced by

two main factors: the extent to which water covers

wetlands during the wet season and the consistency of

the decrease in water depth and water coverage during the following dry season. Lorenz (2001b) demonstrated the effectiveness of the process of expansion and

contraction of water area in enhancing prey availability to wading birds in the coastal marshes immediately

north of eastern Florida Bay. He determined that fish

density during the wet season is positively related to

water depth in the marsh and the length of time in

which depths in the marsh are greater than 12.5 cm. He

found that concentrations of fish in topographic lows

occur—and reach roughly twice dry-down density—

when water depths in the adjacent marsh decline

below 12.5 cm. Roseate spoonbills that nest on islands

in northeastern Florida Bay feed in these coastal

marshes during the nesting season, which coincides

with the usual dry season. Lorenz (2001b) examined

their nesting record in relation to water-level data and

determined that, in general, mean water levels at his

Figure 8.11 The temporal pattern of monthly pink shrimp postlarval influx on the western side of the bay (upper-graph) differs from

the Middle Florida Keys stations (lower-graph) but is similar to that at Long Key Channel the two previous years (Figure 10, upper graphs,

(Criales et al., 2003).

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 133

fish-sampling sites in the coastal marshes were lower

than 12.5 cm during successful roseate spoonbill nesting periods and higher than 12.5 cm during failed

nesting periods. Furthermore, prey availability at the

sites during successful nesting periods was twice that

during failed nesting periods. On the other hand, nesting failed to occur during several recent years that

might have been expected to support successful nesting. This failure may be explained by out-of-season

water releases from the nearby C-111 canal.These releases have been shown to raise water levels in the

coastal wetlands. Such releases during spoonbill nesting periods could cause prey to become dispersed and

result in nesting failure.

The coastal marshes north of Florida Bay were

principally oligohaline prior to the extensive drainage

and water diversion that occurred with water management (Egler, 1952). Since the time that hydrologic

modification was begun, mangroves have encroached

inland, and there are other indications that the coastal

marshes have become more saline (Ross et al., 2000).

Lorenz’s (2001a) study of coastal fish populations

demonstrated that fish densities were substantially

greater and that community composition in the coastal

wetlands immediately north of northeastern Florida

Bay resembled that of an oligohaline marsh in recent

years of exceptionally high rainfall, when conditions

approximated predrainage conditions. Fish densities

were substantially greater in the years of oligohaline

conditions.This study demonstrated that it is possible

to regain wetland productivity with restoration of more

natural hydrologic responses to rainfall.

Several time series are being developed for birds

in Florida Bay.The database on nesting activity in bald

eagles extends back to the late 1950s and continues.The

osprey database is also lengthy, albeit interrupted, and

continues. Monthly data on the abundance and activity of water birds in Florida Bay is five years in length

and still growing.These databases provide the opportunity to analyze bird activity in the bay in relation to

freshwater inflow and other conditions that might affect these birds’ food supply. This information also is

available for use in trophic network models. Information on the diet of water birds in Florida Bay is very limited and largely anecdotal.

EFFECTS OF WATER RELEASES ON 

RECRUITMENT AND BENTHIC FAUNA

Some statistical studies have directly connected abundance indices from fishery data to indices of freshwater flow to Florida Bay and the southwestern coast.

These freshwater flows are affected by water releases

to ENP at the Tamiami Trail and by the management

of water levels and releases in the South Dade Conveyance system on the eastern border of ENP. Changes

in catch rates in fisheries can provide a rough index of

change in relative abundance. In an analysis of ENP

catch and effort data, Schmidt et al. (2001) found that

an index of freshwater runoff to Florida Bay and adjacent coastal waters was positively related to snook

catch rates but negatively related to spotted seatrout

catch rates. Change in harvests can provide a rough

index of abundance when change in effort is taken

into account. Browder (1985) found a positive relationship between pink shrimp harvests in the Tortugas

fishery and a freshwater inflow index (water levels at

P35 in ENP). Analyses by Browder (2000) and Sheridan

(1996) suggested that freshwater inputs as either rainfall or runoff influence pink shrimp catch rates. Browder’s (1985, 2000) work suggested that the timing of

freshwater inputs affects harvests and catch rates.

Johnson et al. (2002a) found that water releases at the

Tamiami Trail were a significant variable explaining the

density of 9 of 11 dominant species in Florida Bay’s forage fish assemblage (Table 8.2).

SPATIAL PATTERNS OF MERCURY AND

METHYLMERCURY 

Widespread patterns of elevated mercury (Hg) concentrations in game fish and forage fish have been observed in eastern Florida Bay (Evans et al., 2001).Within

this region, highest concentrations of both methylmercury and total mercury have been observed in water

and sediments in the mangrove transition zone near

the inflows of Everglades freshwater through Joe Bay

and Little Madeira Bay (Rumbold et al., 2003). Incubation studies with stable mercury isotopes revealed

substantial in situ methylation in open-water bay sediments as well. Inputs of bioavailable Hg(II) may be a

critical-determining factor driving this methylation.

Concurrent seasonal variations in both methylmercury and total mercury concentrations were observed

in sediment, water, and forage fish, with peak concentrations occurring during the warm rainy season

near the coast, where Everglades runoff enters the

bay. No significant long-term temporal trends in mercury levels in gamefish can be observed as yet for the

period 1996–2001. From these results, it has been concluded that the sources of elevated mercury concentrations in fish from northeastern Florida Bay include

(1) methylmercury in runoff from the Everglades and

(2) in situ mercury methylation in sediments from both

the mangrove transition zone and the open bay itself

(Rumbold et al., 2003). Mercury concentrations seem to

be higher along a Taylor River–Little Madeira Bay sampling transect than along a C-111 canal–Joe Bay transect, suggesting that the urban and agricultural runoff

that most strongly influences the C-111 canal–Joe Bay

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

134 FWRI Technical Report TR-11

transect is not the most important source of mercury

to the bay and its biota. All of these processes could

change with restored Everglades freshwater flows and

might be further altered by changes in nutrient inputs and trophic processing.

EFFECT OF FISHING ON AGE STRUCTURE

AND ABUNDANCE OF PREDATORS

Faunce et al. (2002) provided evidence that fishing in

areas of northern Florida Bay open to recreational fishing affects target fish populations there. The modal

length of gray snapper (Lutjanus griseus) along mangrove shorelines is substantially larger in the Crocodile Sanctuary of Everglades National Park, where

fishing has been excluded since 1980, than in other parts

of Florida Bay in Everglades National Park and the

nearby Biscayne National Park, where fishing is allowed. Modal lengths were 25–30 cm TL in the Crocodile Sanctuary vs. 15–20 cm TL elsewhere. Future work

may be needed to clearly separate effects of fishing from

effects of differences in habitat. Ley et al. (1999) found

a similar pattern. Other studies (Bohnsack et al., 2001;

Ault et al., 2002a,b) suggest that fishing affects reef

fish populations, some of which spend part of their life

cycle in Florida Bay. On the other hand, Schmidt et

al.’s (2001, 2002) recent analyses of Everglades National Park creel census data shows that catch rates were

positively correlated with fishing rates for four target

species—spotted seatrout, red drum, snook, and gray

snapper—suggesting that fishing pressure was not affecting overall abundance.

Modeling Change in 

Higher-Trophic-Level Species

Two types of models have thus far been applied to

HTLS research in Florida Bay. Empirical, statistical

models have been used to explore data for patterns that

suggest the major processes driving variation in species

abundance and community structure. Complementing

these models are simulation models, often incorporating population dynamics, to examine the sensitivity of individual organisms to varying characteristics

of their habitat, such as bottom cover and salinity.

Statistical Models

EXPLORATORY GENERAL ADDITIVE MODELS

Johnson et al. (2001, 2002a,b) assembled a database for

Florida Bay that integrated six independent forage

fish/macroinvertebrate studies conducted between

1974 and 1997.The database was used to examine the

dynamics of 11 key forage species. General additive

models were used to determine which major forcing

functions and habitat factors control the abundance and

distribution of these key forage species. The most

widely influential variables explaining abundance and

Table 8.2 Summary of forage fish models and significant factors. S = the factor was significant for that species.

NS = factor was not significant. A number following an S means the significant effect was lagged by that many months.

The bottom row represents the number of species where that factor is statistically significant.

Seagrass Seagrass Tidal

Species Gear Month Temp. Depth Salinity Habitat Type Density Amplitude Sea Level Wind Rain Flow

Transitory species

F. duoraram S NS S NS NS S S* S S S-3 NS NS NS

L. rhomboides NS S S S NS NS S S S NS NS S-1 S-1

Mojarras S NS S NS NS S S* S S S-2 S-2 S-2 S-2

Pelagic species

A. mitchilli S S S S S S S S S NS S-2 NS S

Resident species

O. beta NS S S NS S S NS S S NS S-3 NS S-3

G. robustum S S NS S NS S S S S NS NS S-2 S-1

F. carpio S NS NS NS S S NS NS NS NS S NS S-2

S. scovelli S S S SS S S S S NS NS NS S-2

M. gulosus S NS NS NS S S S S S NS NS NS S-2

L. parva S NS NS NS S S S S S NS NS S-3 NS

H. zosterae NS S NS NS S S S S S NS NS NS S-2

Significance 8 6 6 4 7 10 9 10 10 2 4 4 9

* The significant effect occurred only between presence vs. absence of seagrass.

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 135

distribution were seagrass density, habitat, and tidal

amplitude, which were significant variables for 10

species, followed by seagrass type and freshwater inflow to the bay (9 species), salinity (7 species), and

temperature and month (6 species). Depth, wind, and

rainfall (4 species each) and sea level (2 species) were

less important variables in predicting the abundances

of forage species (Table 8.2).The U-shaped relationships

of three species (Gobiosoma robustum, Floridichthys carpio, and Lucania parva) to salinity suggested they might

be adapted to extreme conditions (high and low salinities).The majority of species were positively correlated

with seagrass density, with the exception of the pelagic

bay anchovy (Anchoa mitchilli), F. carpio, the toadfish (Opsanus beta), and the gobies Microgobius gulosus and G.

robustum, which were more abundant in sparse seagrass.The specific types of bottom cover were important for seven animal species, as follows: Syringodium

(M. gulosus, Lagodon rhomboides, Hippocampus zosterae,

and L. parva), Halodule (Farfantepenaeus duorarum, Syngnathus scovelli),Thalassia (G.robustum), and no seagrass

(A. mitchilli).Three taxa (F. duorarum, L. rhomboides, and

Eucinostomus spp.) that spawned outside of the bay

showed relationships with tidal amplitude, sea level,

and/or wind, which suggests that transport mechanisms may affect abundance.

FORECASTS OF THE TORTUGAS 

SHRIMP FISHERY

Several empirical statistical models have been used to

relate Tortugas catches or catch rates to indices of

freshwater inputs to Florida Bay. Browder (1985) found

a statistical relationship between quarterly Tortugas

catches and the average water level in ENP monitoring well P35. Later, Sheridan (1996) developed a statistical model that related annual Tortugas catches to

Everglades well data, rainfall data, and air temperature and sea level measured at Key West the previous

spring and summer. The Sheridan model, which was

updated every year with new data, successfully predicted Tortugas catches for the upcoming year for a

number of years.

More recently, Browder (2000) developed a statistical model relating annual average Tortugas catch

rates to the rainfall of several prior months.Two models were developed, one for recruits to the fishery (assumed to be shrimp in the 68-count per pound

category) and another for larger shrimp. These models were designed to make rainfall-based predictions

of catch rates that could be compared with observed

catch rates to separate effects of south Florida’s highly

variable rainfall from effects of change in water management. Modeling results suggested that timing as

well as quantity of rainfall influence catch rates.The two

rainfall-based models, which were based on data for

biological years (July–June) 1964–1965 through

1994–1995, had high r 2 (0.89 and 0.76, respectively), but

their predictions differed greatly from observations

in five subsequent years, when few if any water management changes had occurred (Browder, 2001, unpublished report).

A second empirical model was prepared (Browder, 2000) to test alternative configurations of the water

management system proposed in the “Restudy”that

developed the CERP.This model related Tortugas catch

rates of recently recruited shrimp to releases of fresh

water into Everglades National Park at its northern

boundary immediately downstream from the leveed

Everglades Water Conservation Areas. The model,

based on data for the period 1964–1965 through

1994–1995, explained 92% of the variation in average

annual catch rate. Total monthly water releases for

several months of the year explained more than 57%

of the variation in catch rate.The rest of the explained

variance was due to other variables. These included

large-shrimp catch rates the previous year and

monthly average Key West air temperature (as a proxy

for water temperature) for several months. The relationship between catch rate and water flow was positive for some months and negative for others,

suggesting that timing as well as volume is important.

When used in alternative testing, the model predicted

consistently higher annual catch rates for the “Natural

System”than for the “1995 base case”or any alternative, suggesting that south Florida’s predrainage hydrologic system provided the best conditions for pink

shrimp production. To make these predictions, the

output of hydrologic models served as input to the

shrimp model.

Another analysis examined pink shrimp recruitment to the Tortugas grounds in relation to observed

salinity in the western and central bay (Browder, 2000).

Because of limitations in available salinity data, the time

series analyzed was very short compared to that available for relating recruitment to rainfall and water releases to Everglades National Park. A weak, but

significant, relationship was found between monthly

recruitment and time-lagged monthly average salinity in both areas.

Simulation Models

A simulation model was developed to predict survival,

growth of juvenile pink shrimp cohorts, and potential

harvests from these cohorts as a function of temperature and salinity in Florida Bay (Browder et al., 1999).

The model was recently refined with data from new laboratory experiments (Browder et al., 2002).The model

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

136 FWRI Technical Report TR-11

structure consists of three algorithms, which govern (1)

physiological survival as a function of temperature

and salinity; (2) growth as a function of temperature,

salinity, and total length; and (3) survival from predation as a function of total length. The model is driven

by observed daily temperatures and salinities from

specific locations in Florida Bay.The model simulates

juvenile densities in that part of the bay and potential

recruitment (and related harvests) to the Tortugas fishery from that part of the bay.

A spatially explicit individual-based model for

Caribbean spiny lobster (Panulirus argus) was developed in 1993 (Butler, 1994). Reformulations of the

same model have been used to investigate a variety of

issues, including (1) the potential effect on lobster recruitment of a massive loss of nursery habitat structure that was due to a sponge die-off (Butler, 2003), (2)

the consequences of temporal and spatial variation in

postlarval supply on recruitment (Butler et al., 2001b),

(3) the effect of nursery habitat structure and geographic specificity on recruitment (Butler et al., 2001b),

and (4) the direct and indirect consequences of altered salinity on recruitment (M. Butler, personal communication). The ecological aspects of recruitment

included in this model start with the arrival of spiny

lobster postlarvae in the nearshore nursery and terminate when larger juveniles begin to enter fishermen’s traps. The recruitment process is explicitly

incorporated into this model by superimposing on

the model’s spatial landscape the daily ecological

processes faced by juvenile spiny lobsters: settlement,

growth, shelter, selection, mortality, and movement.

The model tracks each hypothetical lobster from settlement until recruitment to 50-mm carapace length.

Settlement occurs once every 28 days, corresponding

to the lunar cycle. Growth is a discontinuous process

involving molts. Daily mortality is a function of various aspects of habitat and lobster-habitat interactions. Simulations with the model were run for

observed extreme conditions: a wet year (1995) and a

dry year (1993).The direct effects of salinity were limited to approximately 20% of the lobster nursery area,

where salinity varies naturally. Simulation results suggested that lobster recruitment during a very wet or

dry year would be similar. In both cases, recruitment

declined by approximately 25% in the area directly affected by salinity changes, which resulted in an approximately 5% decline in recruitment over the entire

Florida Keys region, as compared to control simulations where salinity was stable at 35 psu. Other simulations predicted that the lobster population would

be surprisingly resilient to sponge die-off. Although

nearly the entire sponge community was decimated

over approximately 20% of the nursery area, this loss

of habitat was predicted to result in only a 16% decline

in lobster recruitment in the perturbed region and a

2% decline over the entire Florida Keys region. The

model allowed a follow-up analysis of “why this is

so.” Apparently the effect was not just because the

supply of postlarvae was three times higher in the

post-die-off year simulated, but mainly because juvenile lobster movement to nearby unaffected areas

and shifts in shelter use on sites affected by sponge dieoff, a response supported by field evidence (Butler et

al., 1995; Herrnkind et al., 1997).

Richards (2003) examined the relationships of temperature and salinity to growth rates in crocodiles

(Crocodylus acutus) by tracking 30 radio-tagged hatchlings in the vicinity of the Turkey Point Power Plant for

up to several weeks.Water temperatures in habitats in

which the hatchlings were tracked were within the

range 29°–35°C, a range in which temperature is not expected to have a detrimental effect on growth (Mazzotti

et al., 1986). Richards found that temperature had no

effect on most measures of growth. Although laboratory work has shown that salinity has a strong negative effect on mass in hatchling American crocodiles

(Dunson, 1982), field observations suggest that they can

survive and grow in highly saline areas (Lang, 1975;

Mazzotti, 1983). Richards also found that salinity did

not significantly affect growth rates, supporting these

field observations.Two of the individuals in very high

salinities (approximately 60 psu) grew at the same rate

as most individuals in low-salinity water. In the laboratory, Mazzotti and Dunson (1984) showed that hatchling C. acutus maintained in seawater (35 psu) grew well

if given periodic access to brackish water (4 psu).

Richards observed that hatchlings used hollows in the

banks of canals and ponds and also that four individuals on five occasions (sometimes accompanied by

other hatchlings) moved out of their low-salinity pond

and into the hypersaline canal areas at night and returned to their pond the following day. These observations support the hypothesis that crocodiles may

have behavioral adaptations for escaping adverse effects of salinity.

Substantial progress has been made in the development of a bioenergetically based individual larval

spotted seatrout model to simulate metabolic rate,

consumption, and growth as a function of temperature

and salinity (Wuenschel et al., 2004).The model follows

the basic energy budget equation in which consumption equals the sum of metabolism, excretion, and

growth, and each component is a function of fish size,

temperature, and salinity, where appropriate.The final

model will incorporate variability for each component,

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 137

which will enable researchers to model a population

of individuals, rather than just the average individual.

Laboratory experiments (n = 779, SL 4.5–39.5 mm) provided the basic information for the model.

A spatially explicit prey-predator model for spotted seatrout and pink shrimp coupled to physical

processes was developed for Biscayne Bay (Ault et al.,

1999, 2003; Wang et al., 2003).The spotted seatrout component of the model was individual-based.

Ongoing Research

Projects

At the time of the 2001 Florida Bay Conference, five new

(or continuing) HTLS projects funded for two years by

the NOAA Coastal Oceans Program had barely started.

Although these studies have made substantial progress

to now, their results were not presented at the Florida

Bay Conference, and only a portion of these results

were available for this synthesis. These projects are

briefly described below.

MODELING PINK SHRIMP RECRUITMENT

FROM FLORIDA BAY

In this project, we are continuing to develop a simulation model and the associated performance measures to evaluate the potential effect that upstream

water-management changes resulting from efforts to

restore the Greater Everglades ecosystem have had

upon Florida Bay.This work seeks to (1) clarify the effects of freshwater inflow and seagrass habitat on

Florida Bay’s pink shrimp nursery function, (2) determine the major influences of meteorological and

oceanographic processes on postlarval pink shrimp

and their recruitment to the fishery, and (3) improve

the ability to predict recruitment to the Tortugas fishery in response to changes in water management. As

part of this work, a spatially explicit recruitment model

will be developed from the existing unit model; postlarval immigration pathways, transport rates, and influencing factors will be described and quantified; and

historical data on pink shrimp density will be analyzed and used to further refine and verify the model.

REGIONAL ASSESSMENT OF SPONGE 

DYNAMICS AND SPONGE FISHERY IMPACTS

This project is part of a multiyear investigation of the

hard-bottom communities of Florida Bay and the Florida

Keys. It combines modeling, laboratory experiments,

and fieldwork to explore the relationship of spiny lobster population dynamics to spatiotemporal patterns in

the structure of bottom habitat and environmental variables.The current project focuses on sponges, but some

elements also pertain to spiny lobsters and octocorals.

The four principal objectives of the project are (1) to describe size-specific population dynamics information

(e.g., growth and reproductive status) needed to model

and manage commercial sponge species, (2) to determine the effects of commercial fishing on sponges and

the bycatch of the sponge fishery, (3) to experimentally test the tolerance (e.g., survival, susceptibility to

disease, changes in behavior) of selected hard-bottomdwelling species (e.g., five sponge species, two octocoral species, and three size-classes of spiny lobster) to

different salinities and periods of exposure at winter

(18°C) and summer (28°C) water temperatures, and (4)

to incorporate new and existing information into a spatially explicit simulation model to quantitatively compare the effects of potential management strategies on

the sustainability of the sponge fishery and its effects

on hard-bottom community structure in the Florida

Keys National Marine Sanctuary.

POPULATION STUDIES, ABUNDANCE,

HABITAT USE, TROPHIC DESCRIPTIONS,

AND REPRODUCTIVE STATUS OF MARINE

TURTLES INHABITING FLORIDA BAY

The purposes of this study are (1) to capture and tag

sea turtles in Florida Bay to continue long-term monitoring of individual growth rates, foraging-site fidelity, residency rates, health status, and trends in

abundance, (2) to elucidate the trophic role of loggerheads as apex predators in Florida Bay, (3) to provide detailed descriptions of loggerhead habitat use

and behavior, and (4) to examine the sexual maturity

and reproductive frequency of adult-sized loggerheads inhabiting Florida Bay.The principal study area

is the central-western region.

REEF–FISH COMMUNITY DYNAMICS AND

LINKAGES WITH FLORIDA BAY

This continuing project will apply a visual sampling

strategy to quantify coral-reef fish community changes.

The project has the following goals: (1) to provide intensive and precise spatial and habitat-specific fisheryindependent assessment of reef fish communities; (2)

to document trends in reef fish size and abundance

within and outside no-take zones in the Florida Keys

reef tract; (3) to test specific hypotheses predicting

continuing changes in reef fish communities as the

result of no-take protection; (4) to provide a precise and

spatially explicit database for assessing any future reef

fish population changes resulting from Everglades

restoration actions; (5) to provide managers with options for optimizing long-term survey design strategies

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

138 FWRI Technical Report TR-11

to identify reef-fish population changes; and (6) to correlate the linkages between reef fish communities and

fishing, habitat, oceanographic, and other physical

processes to guide appropriate experimental studies

on dynamic mechanisms and to develop predictive

models.

DEVELOPMENT OF SPATIALLY EXPLICIT

MODELS TO PREDICT GROWTH–POTENTIAL

OF AGE–0 GRAY SNAPPER, LUTJANUS

GRISEUS, IN FLORIDA BAY DURING

RESTORATION OF FRESHWATER FLOWS

The general goal is to examine patterns of growth in

juvenile gray snapper and develop a bioenergetic

model of growth that is a function of temperature,

salinity, and fish size.This model will be extended into

a spatially explicit calculation of potential fish growth

using historical environmental data as well as predicted changes in the environment of Florida Bay

under different water-management strategies. Specific objectives are (1) to quantify patterns in juvenile

gray snapper growth through a retrospective analysis

of previously collected samples, (2) to examine the relationships between juvenile gray snapper growth and

temperature and salinity using previously collected

samples and historical monitoring data, (3) to develop

an individual-based bioenergetic model for juvenile

gray snapper under a range of temperature and salinity conditions, (4) to recalibrate and validate the bioenergetic model by comparing predicted growth with

observed growth, and (5) to develop a spatially explicit model that predicts growth-potential of young

snapper throughout Florida Bay under various freshwater flow regimes.

UPSTREAM LARVAL SUPPLY TO FLORIDA

BAY—THE DRY TORTUGAS CONNECTION

This project explores the pathways and transport

processes for migration of larval fish, shrimp, and lobster from the Dry Tortugas to Florida Bay. Emphasis is

on the role of episodic, mesoscale events, such as those

involving eddies and the Tortugas gyre.The hypothesis to be tested is that the presence of a coastal eddy

enhances the influx of presettlement recruits into

Florida Bay. Densities of incoming recruits in the middle and lower Keys during the presence and absence

of an eddy are being compared.This is a continuation

of a previous south Florida program project for which

substantial progress has been made in relating spiny

lobster larval transport to eddies and gyres (Yeung et

al., 2001). Planned work seeks to determine what happens closer to the origin of eddies at the Dry Tortugas

and lower Keys and the importance of the western recruitment pathway in connecting the Dry Tortugas

with Florida Bay over the southwestern Florida shelf.

Coordinated sampling at Southwest Channel in the Dry

Tortugas and bayside at Northwest Channel will attempt to link the newly spawned snapper larvae to subsequent early-settlement stages.

ATLAS OF LIFE HISTORIES OF JUVENILE AND

SMALL RESIDENT SPECIES IN FLORIDA BAY

The atlas will include information on the range, reproduction, diet, spatial and temporal abundance and

distribution, and length-frequency distributions in the

bay. This work is being conducted with NMFS base

funding.

ATLSS MODEL OF 

COASTAL WETLAND FISHES

A spatially explicit model of the resident fishes of the

coastal wetlands is being developed by Cline et al.

(2001) to further explore the relationships determined

by Lorenz (2001a,b). The model uses the object-oriented modeling framework provided by the Across

Trophic Level System Simulation (ATLSS), which is now

being applied to the Everglades. Development of the

coastal fish model will extend ATLSS into the coastal

marshes and provide a basis for expanding the wading bird elements of ATLSS into the coastal zone.

Unresolved Issues and Questions: 

Research Needs 

Criteria used to propose future research topics were

as follows: (1) follow-up of promising recent research

expected to sharpen or broaden answers to Question

5; (2) addressing promising new hypotheses that replace failed hypotheses; (3) development of performance measures based on species and communities

most likely to be affected by CERP changes; and (4) addressing gaps in the current program when new information suggests higher priority should be assigned.

The following series of topic areas fit one or more of

these criteria.

LOCATION OF NURSERY AREAS OF 

MAJOR GAME FISH SPECIES 

Many sought-after game fish species are found in

Florida Bay as preadults and adults, but the current

nursery grounds of most their populations are not delineated.This includes red drum, snook, tarpon, bonefish, and gray snapper. Recently, Powell (2003)

delineated nursery grounds for spotted seatrout in

central and western Florida Bay. Colvocoresses (unpublished data) found red drum juveniles in the East

River of Little Madeira Bay at a salinity of 6 psu; however, efforts by Powell (2002) to find red drum nursery

Higher-Trophic-Level Species
grounds in northern Florida Bay were unsuccessful,

possibly because the appropriate salinity was not present during sampling. Efforts need to be directed at the

southwestern mangrove estuaries of Everglades National Park, the most likely place to find the type of red

drum habitat described by Peters and McMichael (1987)

(i.e., low-energy, low-salinity [range = 0–25 psu, mean

= 7 psu], turbid, backwater environments “...of a river

at the head of the bay”). Odum and Heald (1972) collected many red drum juveniles in the Whitewater

Bay system (North River), and this system could be a

nursery area for red drum found as adults and subadults in Florida Bay.Tabb et al. (1962) found early-settlement-stage bonefish and tarpon in the Buttonwood

Canal–Flamingo area.There has been no follow-up to

better define the nursery areas of these species. Earlysettlement-stage snook have not been found south of

Chokoloskee (T. Schmidt, personal communication), although similar habitat appears to occur between

Chokoloskee and Cape Sable.The settlement grounds

for gray snapper that enter the bay are not well defined,

although Rutherford et al. (1989) identified mixed seagrass beds of Syringodium-Thalassia-Halodule in western Florida Bay as best settling-out habitats for juvenile

gray snapper. The nursery areas of some of these

species are likely to be in the front lines of changes

caused by new water-management structure and operations.These nursery areas need to be delineated so

that the potential effect of water-management changes

on salinity patterns, nutrient inputs, and other conditions in these areas can be predicted.

INFLUENCE OF HABITAT AND 

ENVIRONMENTAL VARIABLES ON SPECIES

COMPOSITION AND TROPHIC DYNAMICS

The following nonmutually exclusive hypotheses about

factors influencing the abundance and relative abundance of water column and seagrass canopy species

should be explored:

Hypothesis 1—Density and abundance of bay anchovy is related to salinity fronts.

Hypothesis 2—Density and abundance of canopy

species is related to seagrass diversity.

Regional trophic-web models should be developed to integrate existing and future information on

food webs and trophic structure in Florida Bay. Information on water birds and large marine vertebrates

(sharks, rays, bottlenose dolphins, and sea turtles)

should be incorporated into the models.The trophicweb models should be viewed as precursors to an

ecosystem model to be developed in a subsequent

funding phase. The work should include the use of

stable isotope analyses, including use of museum specimens (assuming the work to develop methods for

processing museum material has been completed).

Statistical analyses of historical resource survey

data should be expanded and the results used to design and quantify trophic-web and ecosystem models.

The database assembled by Johnson et al. (2001) provides the opportunity to develop trophic network models for Florida Bay. As a result of major differences in

the food-web base, separate network models should be

prepared for each of the bay’s subregions (Butler et al.,

2001b; Chanton et al., 2001; Evans et al., 2001; ). Network

models previously prepared for the bay by R. Ulanowicz (University of Maryland) and A. Acosta (Florida’s

Fish and Wildlife Research Institute) would provide a

starting point for a new effort. Acosta (personal communication) observed that network modeling suffered

from a lack of biomass information on benthic organisms. This is still a serious deficiency, although some

data on sponge biomass have been gathered. Molluscan samples collected by W. Lyons and archived at the

Fish and Wildlife Research Institute could be used to

develop data on molluscan biomass. Analyses and

comparisons of trophic structure in the various regions of the bay could be used to organize information

about HTLS and assess effects of salinity changes resulting from changes in water management.

FACTORS AFFECTING 

POSTLARVAL IMMIGRATION

IMMIGRATION INTO THE BAY’S INTERIOR

HTLS researchers, building on the work of physical

oceanographers, have gained some knowledge about

the pathways, mechanisms, and oceanographic factors influencing immigration of offshore-spawned larvae and postlarvae to the eastern edge of Florida Bay.

However, little information exists on physical processes

that influence the immigration of postlarvae onto potential nursery grounds in the bay’s interior. This information is highly relevant because it would better

elucidate the ecological importance and potential economic importance of reducing the frequency, duration, and intensity of hypersaline conditions in the

interior of the bay.To what extent is and how much of

the interior of the bay is accessible to offshore-spawned

species? What factors cause the accessibility of the

inner bay to vary? This information would allow researchers to determine what benefits of improved conditions might bring to these species. Greater

coordination of biological and physical research on

the movement of water and early-life stages into the

bay’s interior is needed. Physical research in the interior of the bay was initiated last year, opening new

opportunities for collaboration.

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FWRI Technical Report TR-11 139

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Florida Bay Synthesis Hunt and Nuttle

140 FWRI Technical Report TR-11

IMMIGRATION TO FLORIDA BAY

Recent research suggests that the major pathway for

transport of pink shrimp postlarvae from the Tortugas

to Florida Bay may be across the southwestern Florida

shelf. Research on larval immigration to Florida Bay

nursery grounds from the west is hampered by a lack

of physical oceanographic work that addresses questions biological researchers need to answer. For example, what dynamic, physical structures might enable

early-life stages spawned near the Dry Tortugas to

reach the bay from the west? Net flows across a hypothetical boundary of the bay stretching from Cape

Sable to Marathon have been described (Smith, 2000),

but the flow characteristics along the bay boundary

(boundary of the bay proper) that stretches from Cape

Sable to Long Key are less known. Water movement

across this boundary from both the west and the south

needs to be studied by oceanographers in integrated

studies with biologists studying immigration of earlylife stages onto Florida Bay nursery grounds.

EFFECT OF LARVAL BEHAVIOR AND 

FRESHWATER INFLOW ON LARVAL 

IMMIGRATION RATES

Freshwater inflow may provide directional cues or otherwise influence the rate of larval immigration from offshore spawning grounds to nearshore nursery grounds.

This topic has not been explored with respect to Florida

Bay species since Hughes (1969a,b) conducted experiments suggesting that presettlement pink shrimp postlarvae move vertically in the water column in response

to salinity gradients. He proposed that this behavioral

response resulted in net shoreward transport of postlarvae on flood tides. Hughes’results raise questions that

have never been addressed regarding the possible role

of freshwater inflow in postlarval immigration of pink

shrimp and other species: Do the volume and timing

of freshwater inflow influence the magnitude of influx

of postlarvae to Florida Bay?

EFFECT OF SALINITY ON SURVIVAL 

AND GROWTH 

Integrated studies that might include models, supporting field studies, laboratory experiments, and statistical analyses should be conducted to determine

the relationships between salinity, survival, growth,

and other biological processes. For example, the shrimp

model should be applied to assessing potential nursery grounds in the mangrove estuaries of ENP and examining the possible effects of alternative management

strategies on the larger Florida Bay system that includes these areas. Another needed application is in

interpreting juvenile density data in relation to postlarval immigration and fisheries data. A spotted

seatrout individual-based model should be developed

to integrate all the recently acquired new information

about this species in the bay. Questions about the impact of hypersaline conditions in the central bay on

year-class strength of spotted seatrout need to be addressed.The lobster model should be expanded to integrate new information on salinity tolerance of lobster

and living components of lobster habitat. Following up

on modeling results, field experiments should attempt

to quantify the effect on growth and survival of movements away from undesirable conditions (i.e., hypersalinity or hyposalinity).

QUANTIFICATION OF SIZE–RELATED 

PREDATION MORTALITY

Better quantification of size-related predation mortality is needed to adequately address the effects of

salinity on survival through the effect of salinity on

growth.This issue is especially pertinent to pink shrimp,

spotted seatrout, gray snapper, and lobster. Results

are needed to refine and quantify simulation models.

EFFECTS OF WATER QUALITY ON SURVIVAL

AND GROWTH

This question has not been specifically addressed in

current research in Florida Bay. Effects of both nutrient enrichment and common chemical contaminants

on Florida Bay fish and macroinvertebrates may be

relevant to determining the effects of changes in water

management.

EFFECTS OF BENTHIC HABITAT ON 

SETTLEMENT, SURVIVAL, AND GROWTH

What characteristics of habitat lead to initial settlement?

How do characteristics of settlement habitat affect survival and growth? How faithful are animals to the location of first settlement? What causes movement and

where do animals go? Information on these questions

is needed to further refine simulation models.

IDENTIFICATION OF OTHER SOUTH

FLORIDA COASTAL AREAS WITH ENHANCED

MERCURY BIOACCUMULATION IN FISH

Previous work (Rumbold et al., 2003) identified the

transitional mangrove ecotone in northeastern Florida

Bay as a region of enhanced mercury and methylmercury concentrations in water, sediments, and fish. In unpublished data, Evans found concentrations of mercury

in red drum and crevalle jack from Whitewater Bay that

were comparable to those found in the same species

in northeastern Florida Bay.Whitewater Bay is a mangrove-dominated embayment just north of western

Florida Bay that receives some runoff from the Shark

River, an area of known mercury contamination in

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 141

fish. It seems likely that other estuarine recipients of

Shark River drainage could support fish with high

mercury concentrations.The sensitivity of fish from the

mangrove ecotone of the entire Ten Thousand Islands

complex of southwestern Florida suggests the need for

a monitoring program to establish mercury concentrations in susceptible fish species. A research effort to

determine the mercury sources and responses to future CERP changes in the volume and timing of freshwater flows should be made.

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