### 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

**K enneth D. Haddad** 

**E xecutive Director** 

**T he 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 perti**  **nent 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.** 

**T he FWRI publishes three series:**  **Memoirs of the Hourglass Cruises, Florida Marine Research Pub lications,**  **and FWRI Technical Reports. FWRI Technical Reports**  **contain information relevant to immediate resource-management needs.** 

**Gil McRae, FWRI Director** 

**J ames F. Quinn, Jr.,**  **Science Editor**

**J udith 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



# W illiam 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: T** **he 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); W**  **hite 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

**T**

**his document was composed in Microsoft Word ®**  **and produced using QuarkXPress ®**  **on Apple Macintosh ®**  **computers.The headline font is Adobe ®**  **Av ant Garde, the text font is Adobe**  **® P**  **alatino, and the cover headline is Adobe**  **® Gill Sans.** 

**T he 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.**

# Ta ble 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 W** 

**est 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 F** 

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19**  **NUTRIENT PATTERNS AND TRENDS . . . . . . . . . . . . . . . . . . . . . . . . . . . 21**  **Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21**  **F**

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22**  **OCCURRENCE AND PATTERN OF ALGAL BLOOMS . . . . . . . . . . . . . . . . . . . . 23**  **Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23**  **F**

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23**  **Status of Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23**  **SEAGRASS TRENDS AND PATTERNS . . . . . . . . . . . . . . . . . . . . . . . . . . . 24**  **Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24**  **F**

**indings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 W** 

**inds and Storms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35**  **Precipitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36**  **Evaporation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36**  **Surface-Water Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36**  **Groundwater Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37**  **Sea Level and Tides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38**  **Boundary Currents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38** 

iii **INFLUENCE OF DRIVING PROCESSES . . . . . . . . . . . . . . . . . . . . . . . . . . 38**  **Salinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38**  **Circulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40**  **Exchanges with Adjacent Waters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42**  **PREDICTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43**  **F**

**resh 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 PA**  **TTERNS AND TRENDS IN WATER QUALITY . . . . . . . . . . . . . . . . . . . . . . . 57**  **P**

**eriod 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**  **WA TER–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 Temp**  **erature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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**  **F**

**ield 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 V** 

**ARIATION 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

**T his 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. T** 

**opical 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.**



### T eam Leaders
Ecosystem History **G. L**  **ynn Wingard (USGS, Reston)** Physical Processes **T homas Lee (University of Miami), Elizabeth Johns (NOAA/AOML), Peter Ortner and Dawn Boyer**  **(NOAA/AOML, PMC)** Nutrient Dynamics **J oseph 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 **J oan Browder (NOAA/NMFS), John Lamkin (NOAA/NMFS, PMC)** 



### Editors

**W illiam 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 evaporation**  **precipitation patterns influence circulation and salinity patterns within Florida Bay and exchanges between the**  **bay and adjacent waters?**

**Th e research conducted addressing Question 1 was in** **tended to produce quantitative predictions of circu lation and salinity responses within Florida Bay.** **Exchange between the bay and the Gulf of Mexico, ex**

**c hange between the bay and the coastal zone of the** **Florida Keys, and oceanographic, climatic, and hy drological driving processes were also areas that were** **to be addressed.Table 4.1 includes relevant represen tative references to research addressing driving forces,** **system characteristics, and their intersection.The Re search Summary highlights major findings to date.** 



### Background

**T he south Florida coastal system surrounding and in**  **teracting 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 larger**  **scale 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. T** **he climate of south Florida is subtropical, with a comparatively small annual temperature range but** **distinct wet (summer-fall) and dry (winter-spring) sea sons. During the wet season, showers associated with** **the afternoon sea breeze occur almost daily, and trop ical storms are transient occurrences. During the dry** **season, cold fronts pass through the region on an ap proximately 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, topo graphic constraints, and freshwater inputs.The north**  **eastern region of Florida Bay is not significantly affected by**  **tides or directly influenced by the surrounding ma rine waters of the Atlantic and Gulf of Mexico.This re**  **gion is the direct recipient of freshwater flows from Ta** **ylor Slough and the C-111 canal system. Upstream**

**w ater-management practices influence the quantity,** **timing, and distribution of fresh water entering this re gion. Runoff varies spatially across the northern bound**  **ary, with the greatest flow through Trout Creek. Wind**

**ev ents often determine the timing of freshwater dis** 

**c harges on hourly to daily time scales, and regional**  **rainfall cycles ( e.g.,**  **seasonal and El Niño/La Niña driven) influence discharges on annual to multiyear**  **time scales. Salinity along the northern boundary of the bay responds very rapidly to rainfall and/or discharge** 

**ev ents. 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).**  **T he central region of Florida Bay receives less di**  **rect freshwater inflow, but fresh water can move into central Florida Bay through McCormick Creek into**  **T**

**errapin 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 sig nificant throughout the southern Everglades. During**  **times of reduced precipitation and high evaporation, this central area can become hypersaline, with salin** 

30 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 WillisHunt 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 peri ods of weeks to months, indicating that like waters of**  **the northeastern region, those of the central region have a relatively long residence time.**  **T he western region of Florida Bay is the least topo**  **graphically 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 cen tral 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 inte grated system (Figure 4.2). Florida Bay is connected to**  **the southwestern Florida shelf and, on occasion, to** T able 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)** 

W

inds and Storms **J ohns**  **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**  **W**

**illis (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**  **V**

**osburg 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**  **P**

**atino (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,**

**w estern Florida Bay can be influenced by the delivery**  **of fresh water from rivers discharging into the Ten T** **housand Islands region and along the west coast of Florida (the Shark, Broad, Harney, and Lostmans rivers).**  **T hese 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 sum**  **mer 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 con**  **nection 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 Ma**  **rine Sanctuary (FKNMS). Circulation of water in western Florida Bay and ad**  **jacent 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 intru**  **sions from Florida Bay can occur.**


### Research Summary

**To date, researchers have documented regional oceano** **graphic and hydrological driving processes. Circula tion 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 po**  **tential 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** 

**w ater properties, meteorology, and flow.**  **By comparison, major uncertainties remain about circulation within the interior basins, interbasin ex**  **ch ange, flow across the bank tops, the effect of evap**  **orative 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 ex** **tensive and complex western boundary. The hydro logical 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 south**

**w estern shelf including the Shark River slough. How** 

**ev er, we still do not have an adequate hydrodynamic**  **model of the interior of Florida Bay. As a result, our ability to rigorously forecast** 

**c hanges in salinity within the bay resulting from** **planned modifications in upstream water manage ment 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 cli** **matic cycle of surface runoff, evaporation, and pre cipitation over the 31-year period is shown in Figure** **4.3. Across the whole bay, discharge from the estuar ine 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 north eastern part of the bay and has a major influence on** **salinity variations therein, effectively inhibiting hy persalinity. 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 mod**  **els incorporating the most recent observational data and process-study results linked to appropriate re** **gional/boundary hydrodynamic and atmospheric mod els are required to rigorously address the most central**  **management concern: what salinity distributions will result from various upstream water-management al**  **ternatives.This has become a principal objective of the Florida Bay and Florida Keys Feasibility Study (FBFKFS).**  **Th e 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 ProcessesSALINITY

**• Historical salinity data and salinity proxy data show** 

**that large salinity changes are not yet understood. T** 

**hose 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.**  **• H istorical data from the salinity synthesis database** 

**(Robblee et al.,**  **2001) show that Florida Bay has be haved 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 ex**  **ceeded 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 an**  **other 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. • V**  **ariability of Florida Bay average salinity is directly related to the net flux of fresh water from the com**  **bined 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 evapo** 

**ration 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, re ceives 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 west**  **ern 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 re** 

**gression) of surface inflows to the bay from the Ever glades 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. • T**  **rout Creek contributes the largest volume of fresh**

**w ater to northeastern Florida Bay, varying from –6**  **to 32 m 3**  **/s. By contrast, the flow from each of the other eight creeks ranges from –1.4 to 6 m**  **3 /s. Negative**  **flows can occur during the dry season and storm**

**ev ents.**  **• F or the Ten Thousand Island region of the western** 

**Everglades, the mean annual river discharge is es timated at 13.3 m**  **3 /s for Harney River, 11.0 m**  **3 /s for**  **Broad River, and 12.4 m 3**  **/s for Shark River.**

**• Shark River’s low-salinity plume waters are com** 

**monly advected southward around Cape Sable to**

**w estern Florida Bay and the Keys reef tract by wind**  **driven coastal flows.**

**• Groundwater inflows are believed to be most influ** 

**ential along the northern boundary of the bay; how**

**ev er, estimates of the volume of this flow range over**  **four orders of magnitude. New measurements and h** 

**ydraulic modeling should help to put bounds on the inflow estimates.** 

CIRCULATION AND EXCHANGE **• T he entire south Florida coastal system, consisting** 

**of the southwestern Florida shelf, the Florida Keys reef tract, and western Florida Bay, is highly con** **nected by local and oceanic circulation patterns re sponding to wind and boundary-current forcing.**  **• L arge-volume, wind-forced flows through the Keys** 

**passages provide linkage for gulf-to-Atlantic exchange through the open western region of Florida Bay.**  **• M easurement of sea level slopes across the Florida** 

**Ke ys provides a tool for monitoring gulf-to-Atlantic** **transports of heat, salt, nutrients, and toxic algae to ward** **the reef tract.** Florida Bay Synthesis Hunt and Nuttle

34 FWRI Technical Report TR-11 Figure 4.3 **A verage seasonal rainfall, runoff, evaporation, and net** **freshwater gain/loss in Florida Bay (Nuttle, personal communi cation).**  Physical Processes**• Seasonal cycles in local wind forcing produce sea**  **sonal patterns in circulation pathways, connecting south Florida coastal waters through western Florida**  **Bay and transporting Everglades freshwater discharges. Southward flows through the Keys pas** **sages predominate in winter and spring, north northwestward flows in summer, and southwestward**  **flows toward the Tortugas in the fall.**

**• Seasonal cycles in south Florida coastal current sys** 

**tems provide seasonal pathways for local larval re cruitment and opportunities for recruitment from** 
**remote sources. • T**  **he south Florida coastal region is surrounded by an intense, large-scale oceanic boundary current (the** **Loop Current–Florida Current system) and its evolv ing eddies that link local coastal waters to remote up**  **stream 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. • Tw** **o-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 be cause the model outputs of salinity fields are simi**  **lar to observed salinity patterns.**

**• Better estimates of surface and groundwater inflows** 

**are available from recent measurements and hy draulic-model results of the United States Geolog**  **ical 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.**  **• I mproved estimates of precipitation patterns and** 

**quantities are available from calibrated Next Gen eration Radar (NEXRAD) measurements (P. Willis).**  **• M easurements of interior-basin circulation and ex** 

**c hange processes are available to improve under**  **standing of bay dynamics, quantify residence times, and help to validate and improve hydrodynamic**  **models (T. Lee, E. Johns,V. Kourafalou, and N. Smith). • M**  **odeling Terms of Reference (MTR) were estab**

**lished by the Physical Science Team (PST) and ap proved 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 hy drological models to provide boundary conditions**  **for the Florida Bay model (SFWMD, USGS, and the National Oceanic and Atmospheric Administration**  **[NOAA]).**


## Driving Processes

Wi nds and Storms

**W inds in south Florida, including Florida Bay, follow**  **a regular seasonal pattern: weak southeasterly winds and daily sea breezes in summer, persistent north**  **easterly 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 win ter. 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 di** **rectly into the central basin. Due to the absence of sig nificant 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 vari ability is significant.** **Recent measurements indicate that there is a sig nificant response of the salinity patterns, sea level,**  **currents, and turbidity of Florida Bay and adjacent coastal waters to wind forcing associated with the pas**  **sage 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** 

**c haracterized (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 re configured to match South Florida Water Management** **District (SFWMD) models at a 3.2-km resolution and in cluded land use and soil types. His model shows** **mesoscale structures in wind, evaporation, and precip itation fields that are associated with land use and land**  **sea interactions, including the sea breeze. Strong, divergent downdraft outflows that occur beneath thun**  **derstorms 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 pat** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 35 Physical Processes**terns in the wind fields, determine spatial patterns in the**

**ev aporation and precipitation fields over south Florida**  **and the surrounding waters, including Florida Bay. Indications are that we are entering a period of en**  **hanced 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 as sumption is made that the probability of a tropical storm** **affecting south Florida is directly related to overall ac tivity, 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 pro nounced 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 evap oration. The distribution of rainfall is highly hetero**  **geneous due to the dominance of local convective**

**ev ents, sea-breeze convergence, and to variations** **caused by urban development effects known as “de sertification”(Pielke**  **et al., 1999). However, significant** **climatic variability is possible and has been docu mented within the period of record of the ongoing**  **monitoring. T** 

**rimble et al.**  **(2001) indicated that low-frequency meteorological modes associated with ENSO and the**  **P**

**acific Decadal Oscillation can also have significant ef fects on south Florida rainfall and freshwater supply** 

**v ariability. 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** 

**w et season and a summer-fall dry season.**  **T**

**here 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 precip itation 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 wa**  **ter temperature differences, specific humidity, and wind speed. Although winds are highly coherent across** **the bay, ongoing studies suggest that there are signif icant spatial differences in evaporation minus precip**  **itation (E – P) (Price et al.,**  **2001). Recent estimates of**

**ev aporation in Florida Bay were derived using a vari**  **ety of independent methods and the comparison of those results is encouraging.**  **Nuttle et al.**  **(2000, 2001) estimated that bay-wide an nual 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**
**y ears 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 an nual water loss, with a maximum in late summer and**  **a minimum in mid winter. Calculations using the Long Ke** **y C-MAN data in bulk aerodynamic formulas indi cate average evaporative water losses of approximately** **0.7 cm/day in September and October and approxi mately 0.3 cm/day in December and January. Unpub**  **lished data from this 15-month study (N. Smith, personal communication) indicate a mean daily evap**  **orative water loss of 0.5 cm and a total annual water loss of approximately 180 cm.Therefore, reliable evapora**  **tion estimates appear to be converging upon the 75–180 cm/year range, but more research is required to con**  **firm 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 en**  **ters 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 Button**

**w ood Embankment (Johns**  **et al., 2001a).**  **F reshwater runoff enters principally through nat** **ural channels cut through the mangrove and button**

**w ood-confining berms (Hittle, 2001; Hittle**  **et al., 2001).** **USGS measurements indicate that Trout Creek con tributes 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 m**  **3 /s to 7.4 m**  **3 /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** 

**m 3**  **/s to 1.8 m 3**  **/s). Negative flows over the mangrove em bankments can be caused by storm events, and net neg**  **ative 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 be** **tween precipitation and inflow into Florida Bay, find ing that fall and winter storms cause pulses of** **freshwater inflow, with the flow in Taylor Creek show ing 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** 

**w eeks. During the winter, northeasterly winds drive** 

**w ater out of Taylor Creek into Florida Bay.** **Stable isotopic markers have identified the prin cipal sources of fresh water in various regions of the** **bay (Swart and Price, 2001). Freshwater inputs to north eastern Florida Bay are dominated by contributions**  **from Everglades runoff. Rainfall has a strong signal in the west, and both rainfall and runoff provide fresh** 

**w ater 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**

**v ery little vertical gradient except near the coastal**  **front.The only evidence of stratified, bidirectional flow is around the time of slack tide. Instantaneous dis** 

**c harges ranged from –2,400 to +3,500 cfs (–68 to +99** 

**m 3**  **/s) in the Broad River, –15,600 to +12,900 cfs (–442 to +365 m**  **3 /s) in the Harney River, and –10,100 to +10,500**  **(–286 to +247 m 3**  **/s) in the Shark River. When tidal ef fects have been filtered from the data, the residual**  **flows ranged from –900 to +2,500 cfs (–25 to +71 m 3**  **/s), –3,600 to +5,700 cfs (–102 to 161 m**  **3 /s), and –2,300 to**  **+4,400 cfs (–65 to +124 m 3**  **/s) for the Broad, Harney, and Shark rivers, respectively. Mean annual residual**  **discharge values have been reported to be 400 cfs (11**

**m 3**  **/s or 284,000 acre ft/year) for Broad River, 440 cfs (12.4**

**m 3**  **/s or 320,000 acre ft/year) for Shark River, and 470 cfs (13.3 m**  **3 /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**

**w ere 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, ground**

**w ater may be passing from the Floridan aquifer into**  **the surficial aquifer and then into Florida Bay. Because the Floridan aquifer is saline, the discharging ground** 

**w ater would be saline, not fresh. This hypothesis is** **supported by geophysical measurements in the south ern portions of Everglades National Park (ENP) be**  **tween 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 Deszcz P** 

**an, 2000, 2002). Results from the integrated surface groundwater 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 sur**  **face water can be impounded on the north side of the embankment, creating a hydraulic drive for ground** 

**wa ter discharge into Florida Bay. However, data are**  **lacking to support these model results. V** 

**osburg 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** 

**w ater 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 differ ences in sediment type.** **Price and Swart (2001) provided recent additional in formation about the role of groundwater in the hydro**  **logic 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**

**v alues of about 0.04–0.175 cm**  **3 /day.**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 37 Physical Processes**T op and Brand (2001) also recently studied ground** 

**w ater in Florida Bay. They used anomalies in the dis**  **solved helium concentrations in groundwater to estimate groundwater inputs to Florida Bay.These au**  **thors 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 ris**  **ing 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 ex plains the difference between the helium and radon**  **flux estimates. Note that the radio-isotope values convert to hy**  **pothesized groundwater inflows of 575 to 3,680 m 3**  **/s. Based on these results, if true, groundwater would ap**  **pear 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-bud get estimates and the observed large seasonal salinity** 

**va riations.** 



### Sea Level and Tides

**Sea level variability in Florida Bay is controlled by wind and tidal forcing, strongly modified by topogra**  **phy 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 Na** **tional Climatic Data Center [NCDC]), but the impli cations 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-to basin 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

**T he Loop Current in the Gulf of Mexico and its exten**  **sion, 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 cur** **rents are complex and can generate eddies and mean ders that can affect how the currents interact with Florida** **Bay.Together these oceanic currents cause sea level dif ferences across the Keys that can drive flows through** 

**w estern 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 Cur rent 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 en** **hance the exchanges of bay waters with the surround ing regions. The boundary currents and their induced** **flows along western Florida Bay can transport river wa ters and/or algal blooms from remote regions to inter**  **act 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** 

**v ariability 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 salin ity 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 re** **ported on a few occasions in central Florida Bay. Dur ing drought years, salinity typically exceeds 40 psu** 

**ov er most of the bay. Estuarine (**  **i.e., mesohaline) con**  **ditions 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 rel**  **atively 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 Interna tional University’s (FIU) Southeast Environmental Re**  **search 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 vari**  **ability 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 Uni** 

**v ersity of Miami’s [UM] Rosenstiel School of Marine**  **and Atmospheric Science [RSMAS]).**

WINDS AND STORMS**In combination with upstream water-management re leases (that are due to flood-control restrictions), storms** **can affect salinity by causing pulsed freshwater in flows 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 north**  **eastern Florida Bay. Northeasterly winds drive fresh**

**w ater out of the Everglades into Florida Bay. Biogeo** 

**c hemical materials in these freshwater flows follow**  **similar input patterns (Cable et al.,**  **2001). Higher-salin ity 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-forc**  **ing effects can be masked by storm events (Levesque and Patino, 2001).Wind-driven flows can redirect low** **salinity plumes from discharges in the western Ever glades into western Florida Bay and the Keys.**  **Wi nd-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 tropi cal 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 sig nificant and long-lasting (~months) changes in salin**  **ity 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. Evap oration and precipitation are the two largest compo**  **nents of the Florida Bay water budget, but we lack good spatial resolution for them.Their respective pos**  **itive and negative effects upon salinity are addressed under Driving Processes, above. Interannual varia**  **tions 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 simula**  **tion using a calibrated box model in which runoff was doubled decreased salinity in the eastern bay, in** **creased variability in the southern bay, but had no ef fect 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 an**  **nual evaporation slightly exceeded annual rainfall. On a seasonal basis, rainfall, evaporation, and runoff** 

**we re 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 oc curs 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** 

**w ater table is sufficiently high (see Hurricane Georges**  **W orkshop report available at http://www.aoml.** **noaa.gov/flbay/hurgeocoverpage.html). Enhanced ex**

**c hange 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 trans**  **ported by coastal and boundary currents to different parts of the south Florida ecosystem for mixing and ex**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 39 Physical Processes**c hange. 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 exam ples are the transport of the Shark River plume to** 

**w estern Florida Bay to help buffer salinity in that re**  **gion (Lee et al.,**  **2001, 2002) and the transport of Mis sissippi River waters to the Florida Keys (Ortner**  **et al., 1995). Exchange of surface water discharged into the** 

**w estern bay with adjacent interior basins is not well** **understood at present, and new observations are un derway 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 di** **rectly into the central basin, thereby reducing hyper salinity (see above). On the other hand, low sea level** **can restrict exchange between adjacent basins by min imizing 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 bound** **ary may also hinder freshwater flow to the bay by re ducing 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 pat**  **terns in south Florida coastal waters, including the**

**w esternmost regions of Florida Bay. Boundary cur**  **rents 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

**T he 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 con**  **nected to the southwestern Florida shelf along its wide**

**w estern 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 fresh**

**w ater 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 dra**  **matic increases in salinities observed in the interior basins indicate poor water exchange between the** **northeastern and central portions of the bay with ad jacent subregions.**  **T he entire south Florida coastal ecosystem, except**  **for the interior of Florida Bay, is highly connected by a regional recirculation system.This regional circula** **tion is driven by the combined forcing of winds, sea level 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 sea sonal shifts in the regional circulation system and pre**  **ferred pathways of exchange between waters of the southwestern Florida shelf (including the nearshore** 

**w aters 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**  **Ke ys to the reef tract in the winter and spring. They** **move toward the Dry Tortugas in the fall and north**

**w estward to the west Florida shelf in the summer, fol**  **lowed 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 ei ther 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-cur**  **rent 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 sea**  **sonal circulation patterns that link the south Florida coastal waters along the western boundary of interior**  **Florida Bay (Lee et al.,**  **2002): southward gulf-to-At** Florida 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 demon strated in the trajectory pathways of Lagrangian drifters**  **that have been regularly released over the past few**
**y ears (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. Estuarine like 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 Ever glades.**  **T he 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 pas**  **sage 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 di rect effects upon circulation. However, some anti-es**  **tuarine flow (flow toward areas with high rates of**

**ev aporation) presumably results from net evapora**  **tion 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**w estern Everglades tend to form a low-salinity band in** **the nearshore waters that is entrained by coastal cur rents and transported to western Florida Bay and the**  **Ke ys (Johns**  **et al., 2001a). This is a passive response to**  **existing circulation. The amount of buoyancy-forcing from these small rivers (5–30 m**  **3 /s) appears to be in**  **sufficient to produce a dynamic coastal current within the low-salinity plume. Salinity observations do indi**  **cate 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. Ground** 

**w ater-forcing is not included in present bay hydro**  **d**

**ynamic 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 ob servations.** 

SEA LEVEL AND TIDES **W ater movements occur on time scales ranging from** **minutes to seasons to years. Tidal currents often ac count 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 mech anisms 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 adja** **cent as well as remote regions to south Florida ecosys tems. Cross-Key sea-level slopes drive flows through** **the Keys tidal passages at tidal and subtidal frequen cies that couple the gulf and Atlantic coastal regions**  **of south Florida (Lee and Smith, 2002).**

BOUNDARY CURRENTS**Although boundary currents are the dominant fea ture of the regional circulation, their effect is indirect** **within Florida Bay. Long-term moored current obser**

**v ations indicate a mean southward flow on the south** 

**w estern Florida shelf that can transport eastern gulf** 

**w aters, 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 influ**  **ence 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 satel**  **lite 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 conti nental shelves: the wide, north-south-oriented south** 

**w estern 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 re**  **gions exchange waters with each other through the tidal**

**c hannels 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 At**  **lantic side of the Keys.There is strong interaction with the Florida Current by way of eddy processes through**  **out 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 am plitude of river discharge.** **Current measurements by N. Smith (2002) in sev eral 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 southeast ern 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 in terior 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 m 3**  **/s in the northern portion and an outflow (westward) of about 300 m**  **3 /s in the southern region,**  **giving a net inflow across the section of about 1,000 m 3**  **/s (Smith and Pitts, 2002; N. Smith, 2002). Because 400–500** 

**m 3**  **/s of this inflow exits southward through the mid dle Keys passages, approximately 500–600 m**  **3 /s are**  Florida Bay Synthesis Hunt and Nuttle

42 FWRI Technical Report TR-11 Physical Processes**av ailable 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 de gree, mixing during tidal exchanges must import gulf**  **and Atlantic water into Florida Bay and export bay**

**w ater to the gulf and to Hawk Channel. Further ob**  **servations and calibrated model simulations are needed before the net exchange resulting from this**  **process can be quantified.**

WINDS AND STORMS **W ind 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 m**  **3 /s over the duration of the event (typi** **cally 1–10 days) for Long Key Channel alone and pos sibly two to four times this amount of net flow for all**  **of the middle Keys channels. Recent current measurements in the main shipping** 

**c hannel at Key West indicate a net northward flow** **into the gulf that appears to be related to the prevail ing 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 Ke** **ys are much weaker than the middle Keys and ap pear 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 depen dent 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 m**  **3 /s during winter cold-front pas**  **sages, and inflows to western Florida Bay can reach 2,800 m**  **3 /s during fall northeast-wind events.The mag**  **nitude 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 m**  **3 /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**  **Ke ys 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 dif**  **ferences and along the seaward edges of the gulf and Atlantic shelves through eddy and wind-driven ex** 

**c hanges (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**  **d**

**ynamic mesoscale features can enhance exchange between the currents and adjacent shelf regions. Con** **tinued monitoring and modeling of boundary cur rents 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 ex**  **ch anges with adjacent waters under different restora**  **tion and climatic scenarios. Because of the physical complexities of the bay, these data need to be com**  **plemented by calibrated models, a number of which are listed below.** 



### Fresh Water Inflow

**To predict salinity, hydrological models that can pro**  **vide estimated runoff at the hydrodynamic model’s terrestrial boundary are essential.The freshwater-dis** 

**c harge model must also be able to estimate runoff** **under various Comprehensive Everglades Restora tion 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 devel oped that synchronizes surface-water tidal-compati**  Hunt 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 land surface boundary in the coupled model (Swain and**  **Langevin, 2001; Swain et al.,**  **2002). Hydraulic expres sions derived from studies of hydrologic processes in** **the Everglades have been formulated to link flow re sistance, 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 encom passes 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** 

**w estern sloughs, and subtidal embayments and tidal**  **creeks along the southwestern gulf coast. Measured surface-water discharges, water levels, and salt con**  **centrations in tidal creeks; wetland water levels and flow velocities; groundwater heads and salinities sup** **plemented by subsurface salinity maps; and soil prop erties are used for model calibration and verification.**  **T**

**ide levels and salt concentrations along the coast and discharges and water levels at hydraulic control struc**  **tures, bridges, and culverts are used to drive the SICS and TIME simulations. The models simulate flow ex** 

**c hanges and saltwater fluxes between the surface and**  **groundwater systems in response to these multiple driving forces, which could be altered based on pro** **posed changes to the system. Insight into flow pat terns and salt fluxes, which can be obtained only**  **through hydrodynamic transport models, is needed to fully evaluate the potential effect of restoration deci** **sions for the greater Everglades on ecologically sensi tive, 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 **A verage sub-tidal flow through the middle Keys passages (Lee and Smith, 2002).**  Physical Processes

### Exchanges with Adjacent Waters

**T**

**he predictions needed from Florida Bay numerical cir culation models can be carried out only with suitable** **inputs along their boundaries. These inputs are nec essary to introduce the complex interactions that dom**  **inate 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 simu**  **lations planned by the inner Florida Bay modeling teams (interannual, seasonal, and event-oriented sim**  **ulations). Existing global models are not suitable for this task because of their coarse resolution and the lack of** **flexibility in performing simulations that match cur rently planned and future Florida Bay modeling ac**  **tivities. Therefore, it is necessary to develop a regional-scale model that will perform simulations** **that are closely linked to interior Florida Bay model ing needs.The regional model must be dedicated to the** **computation of the required hydrodynamic fields sur rounding the Florida Bay model domain and to the cal**  **ibration of these fields with observational data. Such a model, currently under development, applies the** **three-dimensional, finite-difference community hy drodynamic 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/ h** 

**ycom/) to the coastal waters adjacent to Florida Bay and the Florida Keys, including the Florida Straits, the** 

**w estern 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 en**  **sures 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 evalu ation 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 suit able modeling approach to properly evaluate possible**  **future water delivery schemes to the bay. Expertise and modeling resources are available that can be ap** **plied to this problem in a reasonable time frame. How**

**ev er, two particular problems need to be addressed**  **urgently: (1) the bathymetry, which is not currently**

**av ailable at the detail needed by the models; and (2)**  **the appropriate inputs at the boundaries of Florida Bay models need to incorporate the complex interac**  **tions 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 man**  **agement in a timely manner.**


### Salinity Models

**To understand and predict salinity variability in Florida** **Bay, three types of models have been applied: statis tical (regression analyses), mass-balance, and mecha**  **nistic, the last of which will be discussed below under Unresolved Questions and Ongoing Research, Hy**  **drodynamic Models.**

STATISTICAL MODELS **T he 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 regres sion model that uses lagged terms should be con**  **structed. 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 follow**  **up meeting of the group recommended that the use of Seasonal, Autoregressive, Integrated Moving Average** **(SARIMA) models be explored. A preliminary evalu ation of current salinity performance measures relat**  **ing water levels in the Everglades to the salinity in northeastern Florida Bay has been reported on (Mar**  **shall, 2001). Problems with the use of linear regression models for this data set were identified, particularly sea** **sonality, cross correlation, and autocorrelation of hy drologic 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**

**ev aluated the use of SARIMA models to simulate salin**  **ity 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 W**  **ater Management Model, also known as the 2x2 (“2 by**  **2”) model. It was found that multivariable linear re gression models were much easier than SARIMA mod**  **els for coupling with the 2x2 model output. Statistical models have been developed that were capable of rea**  **sonably simulating salinity in the nearshore areas. Simulated salinities were functions of water levels in**  **the Everglades and other areas upstream of Florida Bay, Ta** **ylor 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) ap plied mass-balance calculations to the analyses of wet**  **land hydrology, Florida Bay salinity, and the salinity of Shark River. In each case, these models incorporated** **simplified representations of water flow that are pa rameterized by matching model prediction to observed**  **h**

**ydrology and salinity. W** 

**alker (1998) implemented a set of watershed hy drology models in Everglades National Park. These** 

**w ere 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. T** **he 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 cor rect 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** 

**w ater exchange between each of four regions in the bay,** **and water exchange with the Gulf of Mexico. The re gions used in this model correspond to the regions de**  **fined 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 esti mates 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 con**  **trol nutrient concentrations and plankton blooms. Nuttle**  **et al. (2000) employed two different box mod**  **els. 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. T** 

**he other, FATHOM (Cosby et al.,**  **1999), divided the bay into approximately 40 basins, based on morphology,** **and estimated exchanges between basins based on tide driven 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 val idated by comparison with observation.**  **T**

**willey (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 cal** **ibration.This is one of a set of models under develop ment 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 co**  **herent 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 convec**  **tive systems and sea breeze development. A number of questions remain: What are the long-term effects of**  **the daily development of convergent wind patterns ove**  **r 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**

**wa ters of the bay? It is not clear what changes may**  **occur from intense cyclones, nor how long these**

**c hanges 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 hydrolog** **ical (2x2) grid and are now archived at the SFWMD. Lo cally generated statistical functions relating radar**  **reflectance to tropical convective rainfall are now being used (Willis, 1999). As a result, we are now ready to ad**  **dress a number of unresolved questions in regard to precipitation such as: Do the spatial patterns of bay sur**  **face 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 de signed to provide mean rates of evaporation and its** 

**v ariation both spatially and temporally in Florida Bay.**  **T his investigation will be the first systematic attempt**  **at determining evaporation in Florida Bay and tying mean estimates of evaporation to longer-term moni** **toring efforts ongoing in the bay. Questions to be an swered 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 ad ditional precision can be gained by refinement of sta**  **ble isotope methods? Other questions regarding evaporation include**  **• T o what degree does the seasonality of evaporation**  **need to be considered in evaluating the effect that different salinity patterns have upon water-man**  **agement scenarios? • W** **hat is the effect of the bay’s bank-and-basin topog raphy upon evaporation?** 

**T he rate of evaporation over the extensive, shallow**  **banks may be different from the average estimates used to date. Neither instrumented-platform meteo**  **rological data nor synoptic radiation surveys have** Florida Bay Synthesis Hunt and Nuttle

48 FWRI Technical Report TR-11 Physical Processes**c haracterized conditions over shallow, seasonally ex**  **posed banks. Although the radiation-forcing over the banks will be the same as elsewhere, the different** 

**c haracteristics of the water column (shallow) and bot** **tom (dense sea grass) are expected to affect how out going 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 measure**  **ment 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 con** 

**ve ying nutrients and contaminants to Florida Bay and**  **southwest coastal estuaries. Langevin et al.**  **(2002) of USGS have developed a coupled surface-groundwa**  **ter model of the southern Everglades that is capable of simulating flow and salinity patterns in coastal em** **bayments of northern Florida Bay in response to nat urally occurring hydrologic events in the wetlands and** **the effects of upland-management practices on fresh**

**wa ter releases.The model provides the ability to eval**  **uate 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 on**  **going, and its computational domain is being extended to include Shark River, Lostmans River, and other** 

**w estern sloughs within Everglades National Park south**  **of Tamiami Trail (Schaffranek et al.,**  **2002). Both mod els are being developed at temporal and spatial reso**  **lutions that are facilitating the formulation of new estuarine species models (Cline and Swain, 2002) in the**  **Across Trophic Level Simulation System (ATLSS). T** **hese 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 **T he 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 ob servations and isotope estimates. Clearly, many unre**  **solved 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 ground w** **ater 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 Ke** **ys 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 con**  **cerning bay restoration targets. A SFWMD study has concluded, however, that the currently projected sea**  **level rise does not substantially affect CERP project**

**w ater deliveries.While not precisely a “research issue,”**  **additional tide gauge benchmarks are needed near each water-level recorder in Florida Bay and all the gulf** **coast stations to obtain absolute sea level measure ments. Multiple stations are in place, but many others**  **remain to be installed.The USGS mapping division and the USGS St. Petersburg laboratory are currently work** **ing to establish elevations at many gulf-coast plat forms.** 

BOUNDARY CURRENTS**Questions concerning the effects of boundary cur rents are given below under System Characteristics.**  **Modeling and observational studies are continuing to address how boundary currents are influencing the** 

**v ariability of flow through Florida Bay and the ex** 

**c hanges that take place between boundary currents and**  **adjacent shelf waters.**


### System Characteristics

SALINITY**Although the spatial and temporal variability of salin ity in Florida Bay is well documented and continues to** **be monitored both with field surveys and fixed in struments, a number of unresolved questions remain,**  **including the following: • H**  **ow is the salinity of Florida Bay influenced by** 

**atmospheric forcing on time scales from daily to in terdecadal, including significant transient meteoro**  **logical events such as hurricanes and tropical storms? • H**  **ow do the spatial patterns of evaporation, precip**  Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 49 Physical ProcessesFlorida Bay Synthesis Hunt and Nuttle

50 FWRI Technical Report TR-11 **itation, and basin residence time affect bay salinity distributions?**  **• F or example, does hypersalinity occur where it does** 

**because evaporation is greater over broad shallow banks than in the rest of the bay or because ex** 

**c hange with lower-salinity water is restricted?**  **• H ow**  **do the salinity records inferred from paleoe**

**cological data compare with salinity values mea sured over the past 45 years?** 

**• Is there a statistical transfer function sufficient to ad** 

**equately 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 ongo**  **ing 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**

**w ater-level recorders within basins and channels dur** **ing wet and dry seasons. Additional observations in clude 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 ques**  **tions 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 suc**  **cessful hydrodynamic and ecological modeling of the bay’s interior.The bathymetry of Florida Bay, particu**  **larly 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 den**  **sity of seagrass. The depth over many of the banks is approximately equal to or less than the range of sea** **sonal fluctuations in mean sea level. What conse quences 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**

**w estern, 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 east ern gulf and Atlantic coastal region of the Keys and its**  **long-period variations.This flow transports low-salin ity discharges from rivers emptying into the south**  **eastern 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 Ke** **ys. 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** 

**ov er 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 west ern Florida Bay and the gulf transition region are trans**  **ported southward toward the Florida Keys National Marine Sanctuary. There is evidence from the large** **scale hydrographic surveys that at times these high salinity 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 m**  **3 /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 un derstanding 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 be lieved 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 under stand the physical processes involved. Is it related to**  **the position and configuration of the Loop Current as gulf models and satellite observations suggest? Cou**  **pling 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 ProcessesHunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 51**models have pursued two radically different ap proaches: the aggregated representation of hydrology**  **and salinity in mass-balance models, described above, and the detailed representation of tide and wind-dri** 

**v en water movements in wetland hydraulic and estu**  **arine hydrodynamic models, for example, the RMA-10 model (Kim**  **et al., 1999). The PST reviewed the RMA**  **10 some time ago, but little work has proceeded on it since that time. The review raised fundamental con**  **cerns both in regard to the degree to which the model**

**w as 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. Multi**
**y ear simulations have been made and show patterns**  **similar to observations (http://anole.rsmas.miami.edu/ people/jwang/Florida_Bay_Model.html).**  **T he FBFKFS of CERP convened a Hydrodynamic**  **Model Review Workshop in June 2002, and a Review P** 

**anel was assigned to assess prospects for the suc cessful modeling of Florida Bay hydrodynamics to be**  **used as a management tool.This panel provided strong support for the development of a numerical hydrody** **namic model because of the need to support water quality and seagrass modeling of the bay.The panel also** **firmly recommended not combining different nu merical modeling frameworks (specifically, hybrid mix**  **ing of finite-element and finite-difference numerical grid solutions for hydrodynamic and water-quality** **modeling). The panel’s recommendations were gen erally 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 com**  **pleted in 2002 and was intended to help provide a basis for further development and application of a hy**  **drodynamic model for the FBFKFS and other projects. Phase I was done under contract by J. Hammrick, of**  **T**

**etra Tech, Inc. Numerical-model grids were generated, a five-year calibration data set was synthesized (and in**  **corporated into the Physical Sciences Team’s Standard Data Set), and the performance of the model was eval** **uated. Simulations of water-surface elevation, cur rents, 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 overpredic tion seemed likely to be due to uncertainties in esti**  **mates of freshwater discharge, evaporation, or other boundary exchanges.**  **Th e 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 work shop 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 cir**  **culation model for the interior bay that will enable the SFWMD, the United States Army Corps of Engi** **neers (USACE), and other partner agencies to evalu ate 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 hy drodynamic model for the Gulf of Mexico and Atlantic**  **boundaries and a regional hydrologic model at the Everglades boundary.** 



## Literature Cited

**ALBRECHT, B. A., S. S. CHEN, P. KOLLIAS, J. E. TENERELLI, and B. ETHERTON. 2003. High resolution**  **rainfall and evapo-transpiration over south Florida— Radar rainfall estimates and atmospheric mesoscale**  **model simulations. Report prepared for the South Florida Water Management District, Contract No.**  **C11808, Jan. 2003. 35 p.**
**BOYER, J. N., J. W. FOURQUREAN, and R. D. JONES. 1997. Spatial characterization of water quality in Florida**  **Bay and Whitewater Bay by multivariate analyses: zones of similar influence. Estuaries 20: 743–758.**  **BOYER, J. N., and R. D. JONES. 2001. Long-term trends in water quality of Florida Bay (June 1989–June 1999).**  **Pp. 64–66 in**  **2001 Florida Bay Science Conference. (Ab stract)** 

**CA BLE, J. E., E. REYES, S. E. DAVIS, C. HITTLE, and F.** **SKLAR. 2001. Hydrologic and biogeochemical puls ing events in Taylor Creek System, southeastern Ever**  **glades, Florida (USA). Pp. 5–6 in**  **2001 Florida Bay Science Conference. (Abstract)** **CLINE, J. C., and E. D. SWAIN. 2002. Coupling hydro logic and ecological modeling: SICS and ATLSS. Sec**  **ond Federal Interagency Hydrologic Modeling Conference, July 28–August 1, 2002. 12 p.** 
**COSBY, B. J.,W. K. NUTTLE, and J.W. FOURQUREAN. 1999. FATHOM: Model description and initial appli**  Physical ProcessesFlorida Bay Synthesis Hunt and Nuttle

52 FWRI Technical Report TR-11 **cation to Florida Bay. Progress report submitted to Everglades National Park.** 
**DeANGELIS, D. L., S. BELLMUND, W. M. MOOIJ, M. P.**  **NOTT, E. J. COMISKEY, L. J. GROSS, M. A. HUSTON, and W. F.WOLFF. 2002. Modeling ecosystem and pop**  **ulation dynamics on the South Florida hydroscape. Pp. 239–258**  **in J. W. Porter and K. G. Porter, eds. The**  **Everglades, Florida Bay, and Coral Reefs of the Florida Ke**  **ys: An Ecosystem Sourcebook. CRC Press, Boca Raton, Florida.** 
**FITTERMAN, D.V., and M. DESZCZ–PAN. 2000. Sum mary of ground-water related geophysical investiga**  **tions in Everglades National Park. Pp. 327–329 in**  **Proceedings of the Greater Everglades Ecosystem Restoration Science Conference, Naples, Florida.**  **FITTERMAN, D.V., and M. DESZCZ–PAN. 2001. Using airborne and ground electromagnetic data to map hy**  **drologic features in Everglades National Park. In**  **Pro ceedings of the Symposium on the Application of** **Geophysics to Engineering and Environmental Prob lems SAGEEP 2001, Denver, Colorado, Environmental**  **and Engineering Geophysical Society. 17 p. (CD–ROM)**
**FITTERMAN, D. V., and M. DESZCZ–PAN. 2002. He licopter electromagnetic data from Everglades Na**  **tional Park and surrounding areas: Collected 9–14 December 1994. U.S. Geological Survey Open-File Re**  **port 02-101. 38 p. (CD–ROM)**
**FITTERMAN, D.V., M. DESZCZ–PAN, and C. E. STOD D** 

**ARD. 1999. Results of time-domain electromagnetic soundings in Everglades National Park, Florida. U.S.**  **Geological Survey Open-File Report. 152 p. (CD–ROM)**
**FREDERICK, B. C., S. GELSANLITER, J. A. RISI, and H. R.WANLESS. 1994. Historical evolution of the south** 

**w est Florida coastline and its effect on adjacent marine**  **environments. Bulletin of Marine Science 54(3): 1074–1075.** 
**GOLDENBERG, S. B., C. W. LANDSEA, A. M. MES T** 

**AS–NUNEZ, and W. M. GRAY. 2001. The recent in crease in Atlantic hurricane activity: Causes and**  **complications. Science 293: 474–479. HITTLE, C. 2001. Quantity, timing, and distribution of**  **freshwater flows into northeastern Florida Bay. Pp. 11–13**  **in Florida Bay Science Conference. (Abstract)** 
**HITTLE, C., E. PATINO, and M. ZUCKER. 2001. Fresh**

**w ater flow from estuarine creeks into northeastern**  **Florida Bay.Water-Resources Investigations Reports 01- 4164, U.S. Geological Survey,Tallahassee, Florida.** 
**JOHNS, E., P. ORTNER, R. SMITH, D. WILSON, T. N. LEE, and E. WILLIAMS. 2001a. Salinity variability in**  **Florida Bay from monthly rapid high resolution sur**

**ve ys. Pp. 16–17**  **in 2001 Florida Bay Science Confer**  **ence. (Abstract)**
**JOHNS, E., R. SMITH, D. WILSON, T. N. LEE, and E. WILLIAMS. 2001b. Influence of hurricanes, tropical** **storms, and cold fronts on South Florida coastal wa ters. Pp. 14–15**  **in 2001 Florida Bay Science Conference.**  **(Abstract)**
**KIM, K.W., R. McADORY, and G. BROWN. 1999. A two dimensional physics based numerical hydrodynamic**  **and salinity model of Florida Bay. P. 149 in**  **1999 Florida Bay and Adjacent Marine Systems Science Confer**  **ence. (Abstract)**
**LANGEVIN, C. D., E. D. SWAIN, and M. A.WOLFERT. 2002. Numerical simulation of integrated surface** 

**w ater/groundwater flow and solute transport in the** **southern Everglades, Florida, Second Federal Intera gency Hydrologic Modeling Conference, July 28–Au**  **gust 1, 2002. 12 p. LEE,T. N., E. JOHNS, D.WILSON, and E. WILLIAMS.** **1999. Site characterization for the Tortugas region: Phys ical oceanography and recruitment.Tortugas 2000: Re**  **port by the Florida Keys National Marine Sanctuary.**
**LEE,T. N., E. WILLIAMS, E. JOHNS, D. WILSON, and N. P. SMITH. 2002. Transport processes linking south**  **Florida coastal ecosystems. Pp. 309–342 in**  **J. W. Porter and K. G. Porter, eds.The Everglades, Florida Bay, and** **Coral Reefs of the Florida Keys: An Ecosystem Source book. CRC Press, Boca Raton, Florida.** **LEE,T. N., and N. P. SMITH. 2002.Volume transport vari ability through the Florida Keys tidal channels. Con**  **tinental Shelf Research 22(9): 1361–1377.**
**LEE,T. N., and E. WILLIAMS. 1999. Mean distribution and seasonal variability of coastal currents and tem** **perature in the Florida Keys with implications for lar**

**v al recruitment. Bulletin of Marine Science 64: 35–56.** **LEVESQUE, V. A., and E. PATINO. 2001. Hydrody namic characteristics of estuarine rivers along the**  **southwestern coast of Everglades National Park. Pp. 23–25**  **in 2001 Florida Bay Science Conference. (Ab**  **stract) MARSHALL, F. E., III. 2001. Florida Bay salinity trans**  **fer function analysis. Pp. 20–22 in**  **2001 Florida Bay Sci ence Conference. (Abstract)** 
**MARSHALL, F. E., D. SMITH, and D. NICKERSON. 2003. Salinity simulation models for north Florida Bay**  **Everglades National Park. Final Report, Cooperative Agreement 1443CA528001020. Cetacean Logic Foun**  **dation, Inc., New Smyrna Beach, Florida.** Physical Processes**MAUL, G. A., and D. M. MARTIN. 1993. Sea level rise at Key West, Florida, 1846–1992: America’s longest in**  **strument record? Geophysical Research Letters 20(18): 1955–1958.** 
**NUTTLE, W. K., J. W. FOURQUREAN, B. J. COSBY, J. C. ZIEMAN, and M. B. ROBBLEE. 2000. Influence of net** **fresh water supply on salinity in Florida Bay.Water Re sources Research 36: 1805–1822.** 
**NUTTLE, W. K., R. PRICE, and P. K. SWART. 2001. Es timating evaporation from Florida Bay. P. 102**  **in initial**  **Conference Abstracts, 16th Biennial Conference of the Estuarine Research Federation, November 2001, St.**  **P**

**ete Beach, Florida.**
**ORTNER, P. B., T. N. LEE, P. J. MILNE, R. G. ZIKA, E. CLARKE, G. PODESTA, P. K. SWART, P. A.TESTER, L.**  **P. A TKINSON, and W. R. JOHNSON. 1995. Mississippi** **River flood waters that reached the Gulf Stream. Jour nal of Geophysical Research 100: 13595–13601.** 
**PIELKE, R. A., R. L. WALKO, L. STEYART, P. L.VIDAL, G.**  **E. LISTON, W. A. LYONS, and T. N. CHASE. 1999. T** 

**he influence of landscape change on weather in South Florida. Monthly Weather Review 127: 1663–1673.**  **PRATT,T. C., and N. P. SMITH. 1999. Florida Bay Field Data Report.Technical Report CHL-99-11, Waterways**  **Experiment Station, U.S. Army Corps of Engineers, Vic**  **ksburg, Mississippi.**
**PRICE, R. M., and P. K. SWART. 2001. Seawater intru sion: A mechanism for groundwater flow into Florida**  **Bay. Pp. 31–33 in**  **2001 Florida Bay Science Conference. (Abstract)** 
**PRICE, R. M., P. SWART, and W. NUTTLE. 2001. Esti mating evaporation rates in Florida Bay. Pp. 29–30**  **in 2001 Florida Bay Science Conference. (Abstract)** 
**ROBBLEE, M. B., G. CLEMENT, D. SMITH, and R. HALLEY. 2001. Salinity pattern in Florida Bay: A syn**  **thesis (1900–2000). Pp. 34–36 in**  **2001 Florida Bay Science Conference. (Abstract).** 
**SCHAFFRANEK, R. W., H. L. JENTER, and A. L. RISCASSI. 2002. Overview of the “Tides and Inflows in**  **the Mangroves of the Everglades”(TIME) project of the U**  **.S. Geological Survey’s South Florida Ecosystem Pro gram, Second Federal Interagency Hydrologic Mod**  **eling Conference, July 28–August 1, 2002. SMITH, D. 2001. Marine physical conditions: Ever**  **glades National Park October 1998 through December 1999. South Florida Natural Resources Center, Ever**  **glades National Park, Homestead, Florida.**
**SMITH, N. P. 1997. An introduction to the tides of Florida Bay. Florida Scientist 60: 53–67.**  **SMITH, N. P. 1998. Tidal and long-term exchanges through channels in the middle and upper Florida**  **Ke ys. Bulletin of Marine Science 62: 199–211.** **SMITH, N. P. 2000. Evaporation and the precipitation**

**ev aporation balance in Florida Bay. Florida Scientist 63:**  **72–83. SMITH, N. P. 2001. Wind-forced interbasin exchanges**  **in Florida Bay. Pp. 40–41 in**  **2001 Florida Bay Science Conference. (Abstract)**  **SMITH, N. P. 2002.Tidal, low-frequency and long-term mean transport through two channels in the Florida**  **Ke ys. Continental Shelf Research 22: 1643–1650.**  **SMITH, N. P., and T. N. LEE. 2003. Volume transport through tidal channels in the middle Florida Keys.**  **J ournal of Coastal Research 19(2): 254–260.**  **SMITH, N. P., and P. A. PITTS. 2002. Regional-scale and long-term transport patterns in the Florida Keys.**  **Pp. 343–360 in**  **J. W. Porter and K. G. Porter, eds. The Everglades, Florida Bay, and Coral Reefs of the Florida**  **Ke ys: An Ecosystem Sourcebook. CRC Press, Boca**  **Raton, Florida.**
**SMITH, R. H., E. JOHNS, D. WILSON, T. N. LEE, and E. WILLIAMS. 2001. Moored observations of salinity** 

**v ariability in Florida Bay and South Florida coastal** 

**w aters on daily to interannual time scales. Pp. 42–43**  **in 2001 Florida Bay Science Conference. (Abstract)** **SWAIN, E. D., and C. LANGEVIN. 2001. Developing in sight into coastal wetland hydrology through numer**  **ical modeling. Pp. 44–46 in**  **2001 Florida Bay Science Conference. (Abstract)** 
**SWAIN, E. D., C. D. LANGEVIN, and M. A.WOLFERT. 2002. Cooperative linkage of numerical models for**  **coastal wetlands planning. Pp. 375–380 in**  **A WRA Spring**  **Specialty Conference, 13–15 May 2002. SWART, P. K., and R. M. PRICE. 2001. Insights into the**  **origin of salinity variations in Florida Bay over short and long time periods. Pp. 47–48**  **in 2001 Florida Bay Science**  **Conference. (Abstract)**

**TO P,**  **Z., and L. E. BRAND. 2001. Helium as tracer of groundwater input into Florida Bay. Pp. 49–50**  **in 2001**  **Florida Bay Science Conference. (Abstract)**
**TRIMBLE, P. J., E. R. SANTEE, III, R.VAN ZEE, L. G. CA DA** **VID, J. T. B. OBEYSEKERA, and A. ALI. 2001. Sim ulation of the influence of climatic variability on fresh** 

**wa ter inflow to Florida Bay during the 20th Century.**  **Pp. 50–51 in**  **2001 Florida Bay Science Conference. (Ab stract)**  **TWILLEY, R. Evaluating the response of mangrove** Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 53 Physical Processes**w etlands to alterations of freshwater flow in Ever**  **glades National Park. http://www.ucs.louisiana.edu/ ~rrt4630/mangrove-restudy.htm.** 

**V**

**OSBURG, B. M., J. E. CABLE, J. P. BRADDY, E. REYES, D.**  **L. CHILDERS, and S. E. DAVIS. 2001. Wetland hy drogeologic responses along the Taylor Creek system,**  **southeastern Everglades, Florida (USA). Pp. 52–53 in**  **2001 Florida Bay Science Conference. (Abstract)**

**W**

**ALKER, W. W. 1998. Estimation of inputs to Florida Bay. Report prepared for U.S. Army Corps of Engi**  **neers & U.S. Department of the Interior. http:// wwwalker.net/flabay/.**  **W ANG, J., J.VAN DE KREEKE, N. KRISHNAN, and D.**  **SMITH. 1994. Wind and tide response in Florida Bay. Bulletin of Marine Science 54: 579–601.** 
**WILLIS, P. 1999. An evaluation of NEXRAD (WSR88D) data as a measure of fresh water flux into the Florida**  **Bay/Everglades System. P. 153 in**  **1999 Florida Bay Sci ence Conference. (Abstract)** 

**Y**

**ANG, H., R. H. WEISBER, G. P. P. NIILER, W. STURGES, and W. JOHNSON. 1999. Lagrangian cir**  **culation and forbidden zone on the West Florida shelf. Continental Shelf Research 19: 1221–1245.**  Florida Bay Synthesis Hunt and Nuttle

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