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
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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