1 

FINAL REPORT 

FATHOM Enhancements and Implementation 

to Support Development of 

Minimum Flows and Levels 

 for Florida Bay 

Contract C-C-15975-WO05-05 

Submitted to: 

Melody Hunt, Project Manager 

South Florida Water Management District 

Project Team: 

Bernard Cosby, Principal Investigator 

William Nuttle, Principal Investigator 

Frank Marshall, Project Manager 

 

Environmental Consulting & Technology, Inc. 

 809 State Road 44 

New Smyrna Beach, FL 32168-7271 

(386) 427-0694 

September 2005
 2 

CONTENTS

EXECUTIVE SUMMARY..................................................................................................................... 7 

1 INTRODUCTION ........................................................................................................................ 9 

1.1 Objectives and Approach.............................................................................................. 10 

1.1.1 Organization of Final Report and Supporting Materials....................................... 11 

1.1.2 Project Complexities............................................................................................. 11 

1.2 Description of Florida Bay and Contributing Watershed ............................................. 12 

1.2.1 Geographic Setting................................................................................................ 12 

1.2.2 Florida Bay Regions ............................................................................................. 15 

1.2.3 SFWMD Areas of Interest .................................................................................... 16 

1.3 Description of Models................................................................................................... 19 

1.3.1 FATHOM – Florida Bay Salinity ......................................................................... 19 

1.3.2 PHAST – Wetland Hydrology.............................................................................. 22 

1.4 Model Enhancements and Implementation................................................................... 24 

2 ENHANCEMENTS TO THE SALINITY MODEL – FATHOM....................................................... 26 

2.1 MFL Bathymetry .......................................................................................................... 26 

2.2 Boundary Salinity ......................................................................................................... 30 

2.3 Calculation of Residence Time..................................................................................... 37 

2.4 Long Term Input Data for Salinity Calculations .......................................................... 38 

2.4.1 Rainfall.................................................................................................................. 38 

2.4.2 Evaporation........................................................................................................... 38 

2.4.3 Boundary Salinity ................................................................................................. 39 

2.4.4 Fresh Water Inflow from Wetlands ...................................................................... 39 

2.4.5 Sea Level............................................................................................................... 39 

3 ESTIMATES OF FRESH WATER INFLOW FROM WETLANDS...................................................... 50 

3.1 Wetland Water Budget - 1996 through 2000................................................................ 50 

3.2 Enhancements to the Wetland Hydrology Model - PHAST......................................... 57 

3.2.1 Long Pine Basin.................................................................................................... 57 

3.2.2 Calibration............................................................................................................. 61 

3.2.3 Evaluation of PHAST Model................................................................................ 64 

3.3 Estimates of Fresh Water Inflow from Wetlands - 1970 through 2002........................ 64 

4 MFL BASE CASE CALCULATED SALINITY RECONSTRUCTION - 1970 THROUGH 2002........... 70 

4.1 Estimated Input Data..................................................................................................... 71 

4.1.1 Rainfall.................................................................................................................. 71 

4.1.2 Evaporation........................................................................................................... 74 

4.1.3 Boundary salinity.................................................................................................. 77 

4.1.4 Fresh Water Inflow from Wetlands ...................................................................... 80 

4.1.5 Sea Level............................................................................................................... 82 

4.2 Estimated Parameter Values ......................................................................................... 84 
 3 

4.2.1 Tides...................................................................................................................... 84 

4.2.2 Bathymetry............................................................................................................ 87 

4.2.3 Bottom Friction Parameter.................................................................................... 87 

4.3 Results of Salinity Calculations.................................................................................... 88 

4.4 Results of Residence Time Calculations....................................................................... 92 

5 ERROR, SENSITIVITY, AND UNCERTAINTY ........................................................................... 100 

5.1 Errors in the Base Case Simulation – 1991 through 2002.......................................... 101 

5.1.1 Error statistics ..................................................................................................... 101 

5.1.2 Results................................................................................................................. 102 

5.2 Sensitivity Analysis of Alternative Inputs – 1992 through 2002................................ 105 

5.2.1 Alternative Inputs and Parameter Values ........................................................... 105 

5.2.1.1 Rainfall............................................................................................................ 105 

5.2.1.2 Evaporation..................................................................................................... 106 

5.2.1.3 Boundary Salinity ........................................................................................... 108 

5.2.1.4 Fresh Water Inflow from Wetlands ................................................................ 108 

5.2.1.5 Bottom Friction Parameter.............................................................................. 108 

5.2.1.6 Bathymetry...................................................................................................... 109 

5.2.2 Results................................................................................................................. 109 

5.3 Comparison of Base Case and Measured Inflow – 1996 through 2000 ..................... 117 

6 DEVELOPMENT AND DESCRIPTION OF A WATER BUDGET - 1970-2000 ............................... 119 

6.1 Changes to Water Management Operations 1960-2000 ............................................. 119 

6.2 Summary of Water Budget for Florida Bay................................................................ 122 

6.3 Locations Where Salinity is Sensitive to Inflow from Wetlands................................ 129 

7 APPLICATION: PROJECTED EFFECTS OF WATER MANAGEMENT ALTERNATIVES ................. 132 

7.1 Coupling SFWMM Output to FATHOM ................................................................... 132 

7.2 SFWMM Scenarios..................................................................................................... 136 

7.3 Salinity Calculations ................................................................................................... 136 

7.4 Comparison of Results................................................................................................ 150 

8 SUMMARY AND RECOMMENDATIONS .................................................................................. 161 

8.1 Summary..................................................................................................................... 161 

8.2 Recommendations....................................................................................................... 162 

8.2.1 Application of models to MFL ........................................................................... 162 

8.2.2 Possible further refinements ............................................................................... 162 

9 REFERENCES ........................................................................................................................ 164 
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APPENDICES

Appendices Note: The appendices are an integral part of this final report. They provide the 

output from FATHOM upon which the summary results tables in Chapters 4 and 5 are based. 

They are voluminous so they have been provided under separate cover for any reader to review. 

A sample of the Table of Contents that is presented at the beginning of each appendix follows 

the list of appendices below. 

Appendix A: Analysis of Simulated Salinity Distributions for the MFL Base and Alternate 

Input Simulations in Selected SFWMD Special Interest Basins and Feasibility 

Study Regions. 

Appendix B: Analysis of Simulated Residence Time Distributions for the MFL Base and 

Alternate Input Simulations in Selected SFWMD Special Interest Basins and 

Feasibility Study Regions. 

Appendix C: Analysis of Model Performance for the MFL Base and Alternate Input 

Simulations: Comparison of Simulated and Observed Salinity Data for 1991-2002 

in Selected SFWMD Special Interest Basins and Regions. 

Appendix D Analysis of Model Performance for the MFL Base and Alternate Input 

Simulations: Comparison of Simulated and Observed Salinity Data for 1996-2000 

in Selected SFWMD Special Interest Basins and Regions. 

Appendix E: Analysis of Simulated Salinity Distributions for the MFL Base and Alternate 

Input Simulations in All FATHOM Basins and Regional Groups. 

Appendix F: Analysis of Simulated Residence Time Distributions for the MFL Base and 

Alternate Input Simulations in All FATHOM Basins and Regional Groups. 

Appendix G: Analysis of Model Performance for the MFL Base and Alternate Input 

Simulations: Comparison of Simulated and Observed Salinity Data for 1991-2002 

in All FATHOM Basins and Regional Groups. 

Appendix H: Analysis of Model Performance for the MFL Base and Alternate Input 

Simulations: Comparison of Simulated and Observed Salinity Data for 1996-2000 

in All FATHOM Basins and Regional Groups. 
 5 

Appendix XXX: Analysis of Simulated Salinity Distributions for the MFL Base and 

Alternate Input Simulations in Selected SFWMD Special Interest Basins and Feasibility 

Study Regions. 

 Page 

1. Explanation of Appendix XXX 

1.1 Overview .............................................................................. A - 1 

1.2 Evaluation of distributions of simulated salinity .................................. A - 1 

1.3 Basins and regions of interest ...................................................... A - 2 

1.4 Simulations: MFL base and alternate inputs ................................. A - 4 

1.5 Organization of Appendix A ....................................................... A - 8 

2. Results for all sites and regions presented each for alternate input 

2.1 MFL - base case ...................................................................... A - 9 

2.2 RF-1 – alternative rainfall input 1 ................................................ A - 13 

2.3 RF-2 – alternative rainfall input 2 ............................................... A - 17 

2.4 EV-1 – alternative evaporation input 1 .......................................... A - 21 

2.5 EV-2 – alternative evaporation input 2 .......................................... A - 25 

2.6 EV-3 – alternative evaporation input 3 .......................................... A - 29 

2.7 RN-1 – alternative inflow input 1 ................................................ A - 33 

2.8 RN-2 – alternative inflow input 2 ................................................ A - 37 

2.9 RN-3 – alternative inflow input 3 ................................................ A - 41 

2.10 RN-4 – alternative inflow input 4 ................................................ A - 45 

2.11 RN-5 – alternative inflow input 5 ................................................ A - 49 

2.12 BS-1 – alternative boundary salinity input 1 ..................................... A - 53 

2.13 BS-2 – alternative boundary salinity input 2 ...................................... A - 57 

2.14 FR-1 – alternative friction coefficient input 1 .................................... A - 61 

2.15 FR-2 – alternative friction coefficient input 2 .................................... A - 65 

2.16 BT-1 – alternative bathymetry input 1 .......................................... A - 69 

2.17 BT-2 – alternative bathymetry input 2 .......................................... A - 73 
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 Page 

3. Results for all alternate inputs for each site or region 

3.1 Florida Bay ....................................................................... A - 76 

3.2 SFWMD Feasibility Study Region 1 ......................................... A - 78 

3.3 SFWMD Feasibility Study Region 1a ......................................... A - 80 

3.4 SFWMD Feasibility Study Region 2 ......................................... A - 82 

3.5 SFWMD Feasibility Study Region 3 ......................................... A - 84 

3.6 SFWMD Feasibility Study Region 4 ......................................... A - 86 

3.7 SFWMD Feasibility Study Region 5 ......................................... A - 88 

3.8 SFWMD Feasibility Study Region 6 ......................................... A - 90 

3.9 SFWMD Feasibility Study Region 13 ......................................... A - 92 

3.10 SFWMD Feasibility Study Region 13a ......................................... A - 94 

3.11 SFWMD Feasibility Study Region 14 ......................................... A - 96 

3.12 SFWMD Feasibility Study Region 14a ......................................... A - 98 

3.13 SFWMD Feasibility Study Region 16 ................................. A -100 

3.14 FATHOM Basin 7, Long Sound ....................................... A - 102 

3.15 FATHOM Basin 13, Joe Bay .......................................... A - 104 

3.16 FATHOM Basin 14/15, Little Madeira (mouth) ..................... A - 106 

3.17 FATHOM Basin 15, Park Key Basin ................................. A - 108 

3.18 FATHOM Basin 34, Whipray Basin ....................................A - 110 

3.19 FATHOM Basin 37, Garfield Bight / Rankin Lake ............... A - 112 

3.20 FATHOM Basin 38, Rabbit Key Basin .............................. A - 114 

3.21 FATHOM Basin 46, Butternut Key Basin ........................... A - 116 

3.22 FATHOM Basin 47, Duck Key Basin ................................. A – 118 
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EXECUTIVE SUMMARY

This project updated and enhanced existing models of salinity in Florida Bay (FATHOM) and 

hydrology in the Taylor Slough C111 wetland basin (PHAST) and implemented FATHOM with 

input from the South Florida Water Management Model (SFWMM) to evaluate the effects of 

water management alternatives. General information on the hydrogeomorphic setting of Florida 

Bay and the upstream wetlands was compiled and the FATHOM and PHAST models were 

described as used in previous work for Everglades National Park (ENP). 

The FATHOM and PHAST models were adapted for the needs of the South Florida Water 

Management District (SFWMD) related to setting minimum flows and levels (MFL) criteria for 

Florida Bay. The model enhancements incorporate up-to-date bathymetric information, refine 

the representation of salinity variation along the western boundary of Florida Bay, implement 

calculations of residence time, improve estimates of fresh water inflow from the Taylor Slough 

C111 wetland basin, and assemble input data to support long-term calculation of salinity. 

Although direct measurements of inflows to Florida Bay are only available beginning in 1996, 

observed climate and hydrology data are sufficient to indirectly construct a 31-year water budget 

for Florida Bay (1970 through 2000) and calculate the variation in salinity over this period. This 

is used as the MFL base case. Data to estimate inflow to Florida Bay from the wetlands are not 

available prior to 1970. The input data assembled for this MFL base case were described. The 

results of calculations of salinity and residence time for this period were reported. 

A sensitivity analysis validates the selection of the input data and model parameters for the MFL 

base case and documents the errors associated with the salinity calculations. Because some of 

the input data assembled for the MFL base case (1970 – 2000) must be estimated indirectly from 

long term regional indices of rainfall, wetland hydrology, and meteorological conditions an 

additional source of uncertainty is introduce to the salinity calculations. The sensitivity analysis 

evaluates the error in the salinity calculations using the MFL base case and comparing to 

Salinity simulations using alternative input data and parameter values. . Overall the FATHOM 

model with the MFL base case input data and parameter values explains about 81% of the 

observed variation in salinity variability in Florida Bay for the period 1991 through 2000. 

The reconstructed water budget based on the MFL base case input data spans a period of 

significant change in inflow from the wetlands and variation in climate. Rainfall and 

evaporation dominate the fresh water budget in both the whole Bay and in the central and 

northeast regions. On an annual basis, inflow from the Taylor Slough C111 wetland basin 

contributes only about one tenth as much fresh water to the Bay as rainfall. However, during the 

wet season it accounts for a large portion of the net supply of fresh water to Florida Bay. In the 

northeast region of Florida Bay, year-to-year differences in peak annual salinity values vary in 

response to changes in inflow from the wetlands but in the central region of the Bay the response 

is not as strong. This may simply reflect the fact that very little or no inflow reaches the central 

region during dry years; therefore it cannot moderate high salinity values there. Even so, the 

response of model efficiency in the central region to inflow alternatives examined in the 

sensitivity analysis provides evidence that salinity does respond in a limited manner to changes 

in inflow to the central region as it does in the northeast region. 

 
 8 

Enhancements to the FATHOM salinity model provide water managers the ability to evaluate 

changes that will occur in Florida Bay as the result of operations. Output from the SFWMM 

defines hypothetical scenarios of inflow from the Taylor Slough C111 wetland basin that 

correspond to different regional water management alternatives. FATHOM extends the analysis 

of these management alternatives to include changes to salinity in Florida Bay. This is 

accomplished by using the output from the SFWMM as input for wetland inflow and western 

boundary salinity in FATHOM. Salinity simulations were generated using the MFL base case, 

FATHOM model for four water management alternatives; B2000, B20501, CERP1 and NSM. 

Compared to the other three alternatives, increased inflow to the central region of the Bay 

provided by the NSM alternative depresses salinity values there during periods of lower salinity, 

but higher salinity values, which occur when conditions are dry throughout the region, appear to 

be unaffected. 

In summary the FATHOM model has been upgraded and prepared for use in setting MFLs. 

Overall model efficiency Bay-wide is a respectable 81%, though there are certain basins that 

may show improved simulation performance with some site-specific parameter modifications 

that are beyond the scope of this project. PHAST was also upgraded to include the Long Pine 

basin, but it was found that the direct application of SFWMM flows in the same proportion as the 

U.S. Geological Survey (USGS) flow data performed just as well and was less cumbersome. 

Taking Florida Bay as a whole, as was expressed in the approved work plan, the MFL base case 

defines the set of model input data and parameters that provided the best performance in 

calculated salinity. Specific locations where improvements to model fidelity may be possible 

include Manatee Bay, Joe Bay, Terrapin Bay, and Whipray Basin. 
 9 

1 INTRODUCTION

The South Florida Water Management District (District) is working to establish minimum flows 

and levels criteria (MFL) for Florida Bay. In support of this work, the District contracted with 

Environmental Consulting & Technology, Inc. (ECT) to adapt two existing hydrologic models 

for this use, an estuarine salinity model (FATHOM) and a wetland hydrology model (PHAST). 

Everglades National Park previously supported the authors in the development of these models 

(Cosby et al. 1999, Nuttle et al. 2000, Nuttle and Teed 2002, Nuttle 2004, Cosby et al 2004). 

This report documents the work by ECT to refine the FATHOM and PHAST models so that they 

meet the District’s present MFL needs. 

Enhancements to the FATHOM model provide water managers with the ability to evaluate the 

effect on the salinity of Florida Bay from changes in management operations. Salinity serves as 

an important indicator for the effect of water management activities on the Florida Bay 

ecosystem. The amount, timing and distribution of fresh water flowing into an estuary influence 

its ecology through the effect that fresh water has on salinity. Operations of the District’s 

regional water management system influence the inflow of fresh water into Florida Bay. These 

operations have the potential to alter salinity and through this also affect the Bay’s valued 

ecological components. 

Work on this project provides the following information of use to water managers: 

• a reconstruction of the hydrology of Florida Bay and fluctuations in salinity for the period 

1970 through 2002; 

• an analysis and compilation of a water budget for Florida Bay identifying areas where 

changes in the inflow of fresh water has influenced salinity; and 

• a comparison of the projected effects of four alternative water management scenarios 

described by output from the South Florida Water Management Model. 

This project estimates rainfall and evaporation in Florida Bay and inflow from the adjacent 

wetlands for the period 1970 through 2002, and it applies this information to reconstruct salinity 

changes in the Bay over this period. By the early 1970s, there was sufficient concern over the 

consequences of water management activities in South Florida to motivate actions intended to 

mitigate the effect in Everglades National Park and Florida Bay. Comprehensive monitoring of 

rainfall and salinity in Florida Bay began only in the early 1990s, with measurement of creek 

flows into Florida Bay beginning in the mid-1990’s. Because of this, regional hydrologic data 

provide the basis for estimating fresh water fluxes over longer periods. 

This report analyzes Florida Bay’s water budget and salinity simulations for the period 1970 

through 2000. South Florida experienced several periods of high rainfall as well as drought in 

this period. Salinity fluctuations track changes in regional rainfall. Rainfall is the largest direct 

source of fresh water to Florida Bay, and rainfall also supplies fresh water that is stored in the 

upstream wetlands. In addition, the completion of a major portion of the South Dade 

Conveyance System significantly increased the amount of water delivered to the wetland areas 

that discharge into the northeast part of Florida Bay in the early 1980s. Analysis of the compiled 

hydrology data and simulated salinity allowed the identification of areas in Florida Bay where 

wetland inflow has a distinct influence on salinity, relative to other areas of the Bay. 
 10 

This report uses output from the South Florida Water Management Model (SFWMM or 2X2 

Model) as input to FATHOM and estimates salinity that would result from each of four water 

management alternatives. The SFWMM simulates water levels and flows in the Everglades 

based on actual climate conditions in Calendar Years 1965-2000 and scenarios of assumed water 

management operations. Included in this task was the development of protocols for applying this 

output as input to FATHOM. This project assembled input data sets for FATHOM based on the 

following SFWMM runs: base 2000 (B2000), base 2050 (B2050), CERP1, and the natural 

system model (NSM). 

1.1 Objectives and Approach 

The overall objectives for this work are to: a) enhance and extend the FATHOM and PHAST 

models so that they better represent wetland hydrology and estuarine salinity within Florida Bay, 

b) apply the enhanced models to various water management scenarios to examine their effect on 

Florida Bay salinity conditions, and c) use this information to establish scientifically defensible 

relationships between fresh water inflows and estuarine salinity response that can be used to 

establish minimum flows and levels criteria for Florida Bay. 

Work on this project was organized into the following tasks: 

Task 1 Project Communication and Coordination - communication between the ECT 

project team and the rest of the study team and overall coordination of the work by the 

ECT project team that is described in detail in the following sections. 

Task 2 Develop the Work Plan - draft the Final Work Plan for the project, including 

descriptions of the approach to be taken, information required and a detailed schedule 

for each of the tasks. 

Task 3 Model Improvements/Enhancements - make the improvements and enhancements 

to the existing versions of the PHAST and FATHOM models. 

Task 4 Model Calibration and Verification - establish the values of model parameters, 

select the data that will describe the boundary conditions for the application of the 

models, and estimate the error in model predictions of salinity. 

Task 5 Model Applications - apply the enhanced, calibrated models to examine the salinity 

response in Florida Bay over the period from 1970 through 2002 and simulate salinity 

conditions in Florida Bay that correspond to alternative water management scenarios 

defined by output from the SFWMM. 

Task 6 Water Budget Development – develop summary descriptions for the main elements 

of the fresh water budgets for Florida Bay and for the PHAST wetland basins in the 

Long Pine, Taylor Slough, and C111 basins. 

Task 7 Final Report & Technical Presentation of Results - document the technical aspects 

of the model(s) and the results obtained with these models over the entire project. 
 11 

1.1.1 Organization of Final Report and Supporting Materials 

This report describes the overall results obtained and serves as the final deliverable from ECT for 

this project. Sections 2 and 3 describe the models. Section 4 describes the input data and 

parameter values selected in the model calibration. Section 5 presents the results of a sensitivity 

analysis conducted to verify the selected input data and parameter values. Sections 6 and 7 

present the results of water budget development and model applications. 

In addition to this report, three progress reports document the progression and intermediate 

results of work performed. These reports contain details of parameter selection and the initial 

sensitivity analyses. 

Progress Report 1 Documents the enhancements to the PHAST wetland hydrology model, 

implementation of the PHAST and FATHOM models for the period 1996 

through 2000 with existing bathymetry data, and results of the initial 

sensitivity analysis for this period. 

Progress Report 2 Documents the methods used to construct long-term input data sets for the 

period 1965 through 2002 using the existing bathymetry and the sensitivity 

analysis for this period. 

Progress Report 3 Documents the selection of the parameters for the MFL base case (input 

data sets and parameter values for the MFL model), detailed model results 

for the sensitivity analysis around the base case, analysis of the water 

budget, residence time calculations, and salinity estimates for four water 

management alternatives defined by the output from runs of the SFWMM. 

Also as part of this work, ECT has provided the District with a number of working versions of 

the FATHOM salinity model, instruction on the application of this model, and copies of the input 

files and summary output for the model runs performed. 

1.1.2 Project Complexities 

The availability and completeness of data needed to construct the input data sets for the period 

1965 through 2002 presented the major challenges in this project. Some examples include the 

following: 

• Coverage by the most recent bathymetry data, intended to update the previous FATHOM 

bathymetry, proved to be incomplete. From the beginning of the project, the intent was 

to utilize the most up-to-date data from the most recent survey by the U.S. Geological 

Survey (USGS). However, shallow areas excluded from this bathymetric survey cover a 

significant fraction of the Bay. By virtue of their spatial arrangement, these areas exert 

critical control on circulation and tidal exchange. Therefore techniques had to be 

developed to estimate the bathymetry in the shallow areas not covered by the USGS 

survey. 

• Direct measurements of rainfall in the Bay are available only since the early 1990s, and 

measurements of inflow from the wetlands are available only since 1996. Multi-year 

estimates of evaporation do not exist. Components of the Bay’s water budget must be 
 12 

indirectly estimated from other information on regional hydrology and climate available 

to extend the period of analysis before the 1990’s. Though the SFWMM can produce 

freshwater flow estimates back to 1965, the period of record for the regional information 

related to inflow only extends to 1970. 

• The last ten years, for which the data on conditions in Florida Bay are most complete, 

may not be representative of the full range of hydrologic and climate variation that was 

experienced for the previous or the next twenty years. Regionally, the 1990s have seen 

wetter conditions in the Everglades and more moderate salinity conditions in Florida Bay 

compared to the preceding period, 1970-1990. 

• The records of rainfall in Florida Bay contain significant gaps. Rain gauges normally 

under-report rainfall depths by ten percent even in the best conditions (Sieck et al. 2003). 

• Available data on fresh water inflow underestimate the total amount of fresh water that 

flows into the Bay. Direct measurements of fresh water inflow by the USGS occur in 

only five estuarine creeks. Ungauged flow estimated by the USGS (Hittle et al. 2001) in 

four other creeks amounts to additional flows of about 23 percent of the gauged inflow. 

Large amounts of ungauged flow likely occur under conditions of high water levels when 

over bank flooding and overflow supplements creek flow through the mangrove swamps. 

To overcome these challenges the project team adopted an approach to populate and verify the 

models that relied on selection of the best available estimates for the input data and model 

parameters to the extent that these could be independently identified, and to confirm these 

selections with a sensitivity analysis. The progress reports contain the detailed results from 

several iterations of this approach. This report documents the final selection of input data and 

model parameters for the MFL model, and it summarizes the results of the final sensitivity 

analysis. The alternative input data sets and parameter values examined in the final sensitivity 

analysis are chosen based on consideration of the uncertainties inherent in the construction of the 

input data sets and selection of model parameters. 

1.2 Description of Florida Bay and Contributing Watershed 

Florida Bay lies between the southern tip of the Florida mainland and the island chain known as 

the Florida Keys. Over 85 percent of the Bay’s 2200 km2

 area lies within Everglades National 

Park, and the Florida Keys National Marine Sanctuary contains much of the rest. The Bay 

includes over 200 small islands, many of which are rimmed with mangroves. Florida Bay 

supports numerous protected species including the roseate spoonbill, the bottle-nosed dolphin, 

the American crocodile, the West Indian manatee, and several species of sea turtles. Moreover, 

Florida Bay provides critical habitat for commercially important species, such as spiny lobsters, 

stone crabs, and many important finfish species, and it serves as the principal nursery for the 

offshore Tortugas pink shrimp fishery. 

1.2.1 Geographic Setting 

Florida Bay, as a receiving water body, is an important component of the much larger South 

Florida drainage basin that is the focus of the Comprehensive Everglades Restoration Plan 

(CERP). The Bay receives freshwater inflow from the Everglades, a large portion of which is 

managed discharge from canals in the region. Decisions guiding the restoration of the 

Everglades carry implications for future conditions in Florida Bay, just as the development of the 
 13 

regional water management system over the past fifty years or so influenced present conditions. 

Although a specific restoration target has not yet been defined for Florida Bay per se, many 

expect that restoration of more natural hydrologic conditions in the Everglades will move the 

Bay toward an ecological state more typical of the period prior to the time of engineered changes 

imposed on the regional South Florida system. 

Rapid ecological changes are thought to have occurred in Florida Bay between 1987 and 1991. 

These came at the end of a multiyear drought that had elevated salinity values in the central 

portion of the Bay to nearly 70 PSU, double the typical salinity of seawater. Large areas of 

seagrasses began to die late in 1987. Concurrently, the shrimp harvest on the Tortugas Grounds, 

which depends on Florida Bay as a nursery area, declined to record lows. In 1991, turbidity and 

plankton concentrations increased dramatically, reducing the supply of light to the remaining 

seagrass beds through the previously “gin-clear” Bay waters. Mass mortality of sponges, which 

help to filter the Bay’s waters and provide habitat for juvenile lobster, followed in the path of the 

plankton blooms. By the end of 1991, there was widespread concern for the health of the Florida 

Bay ecosystem. 

The climate of South Florida is subtropical with a comparatively small annual temperature range 

but distinct wet (summer/fall) and dry (winter/spring) seasons. During the wet season, showers 

occur virtually daily with the afternoon southeastern sea breeze, and tropical storms are transient 

occurrences. During the dry season, cold fronts pass through the region on an approximately 

weekly basis with accompanying increased wind speeds and clockwise rotating wind directions 

from westerly to northerly with the passing of the front. 

Oceanographically, the entire coastal system of south Florida is one integrated system (Fig. 1.1). 

Florida Bay is connected to the southwest Florida shelf, and on occasion to more remote regions 

of the Gulf of Mexico. As a result, western Florida Bay can be influenced by the delivery of 

fresh water from rivers discharging in the Ten Thousand Islands region and along the west coast 

of Florida (the Shark, Broad, Harney, and Lostmans rivers). These river waters can be 

transported southward along the southwest Florida coastline and around Cape Sable, in a general 

pattern of outflow through the Keys to the reef tract (Lee et al., 2001a; 2001b). The influence of 

fresh water inflow from remote Gulf regions is more likely during summer and fall, and has been 

shown to include the influence of Mississippi River floods (Ortner et al., 1995). Subsequent 

transport of this water into Florida Bay and to the Keys is aided by oceanic flows, the Gulf Loop 

Current, and the Florida Current. 

Circulation of water in western Florida Bay and adjacent coastal regions on subtidal time scales 

is also strongly influenced by local wind forcing resulting in seasonal flow patterns within the 

Bay: 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 deliver warm, 

salty water to the reef tract from Florida Bay in the spring and early summer. Cold, turbid 

intrusions can occur in the winter. 

The wetlands in the Taylor Slough C111 wetland basin, north of Florida Bay, occupy a broad, 

flat, fresh water-contributing area with ill-defined drainage patterns in the southeast portion of 

Everglades National Park. This project divides this area into three wetland sub-basins, Long 
 14 

Pine, Taylor Slough and C111 (Figure 1.2). Long Pine Key and the main Park road to Flamingo 

form a surface water divide that isolates the Long Pine sub-basin from surface water in Shark 

Slough. Surface water flow within the Taylor Slough C111 wetlands is divided between flow 

following the natural course of Taylor Slough, south of the Park road gauging station (TSB), and 

sheet flow in the C111 basin fed by overflow from the C111 canal. The source of water in 

Taylor Slough is overflow from Shark Slough, rainfall on the Rocky Glades area of the Park, 

direct rainfall on the Slough, and discharge of the S332 and S332D pump stations. The source of 

sheet flow in the C111 basin is overflow from the C111 canal between the S18C and S197 

structures (not shown on Figure 1.2). In general, groundwater flows are thought to be small 

relative to other components of the wetland water budget (Price 2001, Sutula et al. 2001), and 

these are not accounted for directly in this work. 

Figure 1.1: Schematic representation of the average flow patterns in the interconnected 

South Florida coastal circulation system. The dark arrows indicate locations and relative 

magnitude of fresh water inflow, i.e. Shark River and Taylor Slough that influence salinity 

in Florida Bay (from Florida Bay Science Program 2003). 
 15 

Figure 1.2: Wetland basins used to describe fresh water inflow from the wetlands north of 

Florida Bay. The locations of the MFLx flow transects are show superimposed on the grid 

of the SFWMM model. Also shown are locations for flow (TSB, S175, S18C, and S197) 

data used in this study. 

1.2.2 Florida Bay Regions 

Salinity varies markedly in time and space in Florida Bay. Hypersaline conditions (>40 psu) in 

one part of the Bay frequently coexist with more usual estuarine conditions (<30 psu) in another 

(NOAA 1996, Boyer et al. 1997, Everglades National Park 2001). At some interior 

embayments, salinity regularly fluctuates between hypersaline and nearly freshwater conditions 

(Fourqurean and Robblee 1999, Frankovich and Fourqurean 1997). This variation occurs in 

response to the direct effects of fresh water inflow, rainfall, and evaporation and to the indirect 

influence of inflow from oceanographic processes outside of the bay on the southwest Florida 

Shelf. 

Florida Bay can be divided into four regions subject to different geophysical forcing, topographic 

constraints, and fresh water inputs (Figure 1.3). The northeast region of Florida Bay is not 

significantly affected by tides and is mostly isolated from influence by the marine waters of the 

Atlantic Ocean and Gulf of Mexico. Salinity in the embayments along the northern boundary of 

the northeast region responds very rapidly to rainfall and inflow from the estuarine creeks 

(Figure 1.4). High flow causes dramatic freshening in the small bays along the northern 

boundary. Subsequently, fresh water from these embayments slowly mixes with more saline 

Florida Bay waters to the south and southwest over a period of weeks to months (Johns et al., 

2001). 

15 20 25 30

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 16 

The central part of Florida Bay receives what little direct fresh water inflow that occurs through 

McCormick Creek into Terrapin Bay or Alligator Creek into Garfield Bight (Figure 1.4). During 

times of low rainfall and high evaporation the central region can become hypersaline with values 

often in excess of 40 PSU and historically as high as 70 PSU (Boyer, 2004; Robblee et al., 2001). 

High salinity can persist in this central region over periods of weeks to months to years (as it did 

in the late 1980’s), indicating that, like the northeastern region, waters of the central region have 

a relatively long residence time. 

 

The western region of Florida Bay is the least isolated, sharing an open boundary with the Gulf 

of Mexico and experiencing relatively robust tidal influence. Residence times in the western 

region are shorter than in the central and northeastern regions, and average salinity is higher. 

Salinity in the western region can exhibit a relatively rapid response to meteorological events 

such as tropical storms and cold fronts, but the range of variation is reduced relative to the 

northeast region. 

 

The south region of Florida Bay is similar to the west region except that it receives influence 

from the Atlantic Ocean through the middle Keys passages. The south region of Florida Bay is a 

source of water to the coral reef areas of the Florida Keys National Marine Sanctuary (FKNMS). 

1.2.3 SFWMD Areas of Interest 

Early in the project, the study team identified several basins of interest for setting MFL criteria. 

The selected basins include Long Sound (8), Joe Bay (10), Little Madeira Bay (11/23), Duck 

Key/Trout Cove (9), Whipray Basin (13), Garfield Bight / Rankin Lake (14/15), and Rabbit Key 

Basin (19) (Figure 1.5). The numbers in parentheses refer to the SERC / FIU monitoring station 

of salinity observations. These basins of interest were selected based on knowledge of where 

valued ecological components likely are thought to be sensitive to the influence of fresh water 

inflow. In addition, the zones of interest identified for the District’s Florida Keys Feasibility 

Study are used to evaluate model performance throughout the Bay; these zones include Butternut 

Key Basin (24) and Park Key Basin (23) in addition to the basins presented above. Results of 

the FATHOM salinity calculations and evaluation of the model performance by comparison to 

salinity data reference these basins and zones. 
 17 

Figure 1.3: LANDSAT-7 extended thematic map image of Florida Bay, showing its shallow 

bank bathymetry and four principal regions (from Florida Bay Science Program 2003). 

Figure 1.4: Location of principal points of fresh water inflow measured by the USGS (from 

Hittle et al. 2001) 
 18 

Figure 1.5: Map of Florida Bay basins showing the FATHOM basins, the Florida Bay and 

Florida Keys Feasibility Study Zones (colored zones and red numbers), and the locations 

(black) where monthly SERC salinity measurements are taken. 

 

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 19 

1.3 Description of Models 

1.3.1 FATHOM – Florida Bay Salinity 

FATHOM is a dynamic, spatially explicit, mass-balance model designed to investigate the 

response of salinity in Florida Bay to runoff, climate and variation in salinity on the Florida Shelf 

(Cosby et al. 1999, Nuttle et al. 2000, Cosby et al 2004). The model maintains a running account 

of the water and salt budgets in each well-mixed basin within the Bay No Comment (Figure 1.6). 

Circulation within Florida Bay and exchange with the Florida Shelf are controlled by the Bay’s 

network of shallow banks (Figure 1.3). The basins defined by these banks offer a natural 

framework for mass-balance accounting. 

FATHOM represents Florida Bay as a collection of well-mixed basins. Circulation and 

exchange are driven primarily by tides imposed along the western boundary. At each time step, 

the model solves for uniform hydraulic flow across each bank based on the depth, width, and 

frictional roughness of the bank, and water levels in the upstream and downstream basins. By 

this mechanism, tidal forcing at the boundary propagates into the Bay and drives the exchange of 

water and solutes among the basins. Solute fluxes are then calculated from water fluxes and the 

salinity of water on each bank. Details of the representation of flow over the banks and the 

hydraulic equations are given in Cosby et al. (1999). 

Despite the model’s computational simplicity, FATHOM requires highly detailed information 

about the bathymetry in Florida Bay. Bathymetric data are entered into a GIS database that 

classifies the depth for every 20 by 20 meter rectangle in the Bay (the pixel resolution of the 

data) into one of 11 classes: 1 land surface class and 10 depth classes. The depth classes covered 

the range from 0 to 10 feet in one-foot increments. Areas deeper than 10 feet occur locally in the 

Bay, but (based on these data) such areas are not extensive and occur infrequently. These depthclass data provide the basis for describing the hypsometry for each basin and the depth and 

widths of the shoals for the calculation of exchange fluxes between basins. 

The total length of the line segments that describe the shallow banks is 626 km (Figure 1.6). 

Along the boundaries, the line segments follow the mainland coastline and the keys, and in the 

interior of the Bay the lines traverse or connect islands. About 276 km of the "shoals" defined for 

FATHOM are dry land (no-flow boundaries). Greater than 70% (252 km) of the wetted length of 

the shoals is shallower than 1 foot. A small proportion of the 21% of shoal length with depth 

greater than 3 feet represents cuts and channels through the shoals. Most of the deeper shoals are 

located in the western and southwestern part of the Bay. These were defined as shoals to 

establish a basin boundary in the model. 
 20 

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Figure 1.6: The numbered polygons identify the basins used in FATHOM calculations. 

The color-coded regions and the alphabetic destinations identify the FATHOM groups 

used to summarize the results of salinity calculations. 
 21 

The solution scheme depends on the calculation of water velocity independently for each depth 

increment of each shoal. Conceptually, water flow from one basin to another over a bank in the 

Bay can be treated as flow over a broad crested weir with friction. Flow velocity across the weir 

depends on the difference in water levels on each side of the weir and (perhaps) the occurrence 

of critical flow. If critical flow occurs, then velocity does not depend on the water level on the 

outflow side. The influence of bottom friction may or may not have an important effect, 

depending on the velocity and the depth of flow. The difference in water levels across the weir 

provides the specific energy for the flow. 

There is no direct simulation of wind shear on the water surface in FATHOM. A key aspect of 

the conceptual basis of FATHOM is the assumption that the major effects of wind shear on 

circulation in Florida Bay can be accounted for by the structural assumptions and the inputs to 

the model, without having to be modeled explicitly. Effects of wind have been incorporated in 

FATHOM in two ways: 1) by the assumption that each basin is well mixed (i.e., the "local" 

effect of the wind is to stir the basins, but not to move much water among them); and 2) by the 

incorporation of water level changes in addition to tides and sea-level patterns at the Gulf and 

Atlantic ocean boundaries (i.e., the "remote" effect of the wind is to cause a sea level setup of 

varying magnitude and duration along the different parts of the Bay boundaries). 

As a consequence of the assumptions described above, salinity calculated by FATHOM 

represents a time-averaged value with a period of about one month. Even though circulation and 

exchange in the model are driven by tides, data on other processes such as rainfall and freshwater 

inflow are provided as monthly values. As well, the assumption of basins as well mixed imposes 

constraints on the time scale on which salinity calculations can be taken as comparable to 

observations at any particular location. 

Bay-wide inputs required by FATHOM include time series of rainfall and evaporation for each 

basin in the Bay. The model structure allows these inputs to be specified individually for each 

basin to reproduce spatial gradients in these forcing functions. In practice, however, observed 

data are not sufficient to support more than a regional approach to the spatial distribution of 

climate inputs. That is, the Bay must be divided into a few regions for which climate inputs are 

applied uniformly to the model. Groundwater inputs to the basins can also be specified, but 

these have not been employed in the simulations performed for this project. 

Time series of freshwater inflow volumes are required at the terrestrial boundaries of the Bay. 

Inflow (where it occurs) is specified as an input separately into each of the boundary basins 

along the Everglades coastline, though not all of the boundary embayments receive inflow. To 

compare the effects on the Bay of different runoff regimes, the distribution of inflow among the 

small embayments at the northern edge of the Bay was varied and analyzed. Along the Keys, 

inflows of fresh water are small, and these are not included in the FATHOM inputs. 

In addition to the runoff data at the terrestrial boundaries, FATHOM requires tide, sea level and 

salinity time series to set the open water boundary conditions for the Bay. The model allows 

these boundary conditions to vary spatially along the boundaries. 
 22 

1.3.2 PHAST – Wetland Hydrology 

The PHAST wetland hydrology model (Nuttle and Teed 2002, Nuttle 2004) calculates inflow to 

Florida Bay from the wetland sub-basins in the Taylor Slough C111 wetland basin, (Figure 1.2). 

The influence of water management operations on the Bay occurs primarily through changes in 

the inflow of fresh water from these wetlands. Within the context of this project, the PHAST 

wetland hydrology model is investigated as one approach to estimating fresh water inflow. One 

objective of this project was to extend the PHAST model to include the water balance of the 

Long Pine Basin in the water budget for the calculation of inflow; the prior implementation of 

PHAST (Nuttle 2004) excluded the Long Pine basin. 

The PHAST wetland model calculates inflow to Florida Bay by simulating water levels in each 

wetland sub-basin based on the hydraulics of overland flow. In effect, the model treats the 

wetland basins as shallow reservoirs, (Figure 1.7). Calculated water levels in the wetlands 

fluctuate depending on the balance between inflow from rainfall r and surface water sources Qin

and outflow from evapotranspiration e and discharge to Florida Bay Qout. Any imbalance 

between inflows and outflows results in a loss or gain in water storage, which is reflected as a 

change in water level, and consequent changes to the outflow, Equation 1.1. 

1.1 

The model represents instantaneous discharge Qout as a generalized power function of water 

level, measured above a zero-discharge threshold hsill, Equation 1.2. Calculations are carried out 

with a weekly time step. The parameter β is assigned the value 1.67, which is consistent with 

representing surface flow as occurring in a broad, shallow channel (Wong 2002). (Note: The 

flow units and time step used for calculation of the wetland water budget in PHAST differ from 

the flow units used in FATHOM as these reflect the prior implementation of the PHAST model 

as a separate model.) 

1.2 

The input data required for the PHAST wetland hydrology model include time series of weekly 

rainfall and surface inflow into each wetland basin. Long-term data on evapotranspiration are 

not available for this area, so this flux is estimated within the PHAST model by an empirical 

relationship based on time of year and rainfall (Nuttle 2004). Observations of wetland water 

levels are used for calibrating the unknown parameters, i.e. α and hsill in Equation 1.2. 

Parameters that describe how surface flows into the Taylor Slough C111 basin are allocated 

among the wetland sub-basins. Calculated inflow to Florida Bay is verified by comparison with 

the USGS measured estuarine creek discharge, (Figure 1.4). These flow data are not used in the 

calibration of PHAST. 

( ) in e Qout Q A r

dt

dh A = + − −

( )β

Qout = α h − hsill
 23 

Figure 1.7: Elements of water budget for a wetland basin 

 Q

 r e

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out
 24 

1.4 Model Enhancements and Implementation 

The work plan for this project identifies the following specific model enhancement tasks: 

• incorporate the latest bathymetric data into FATHOM; 

• integrate the PHAST wetland basin hydrology models into FATHOM as one option for 

generating fresh water discharge into the northeast region of Florida Bay; 

• link the time series of salinity values on the western boundary to hydrologic conditions 

and/or flows in Shark River; 

• incorporate an algorithm for estimating fresh water discharge into Florida Bay from the 

Long Pine wetland basin; 

• provide the capability of calculating residence time in each FATHOM basin; 

• gather the available long-term hydrologic data and construct input data that are 

compatible with the long-term data used to drive the SFWMM for regional hydrology 

simulations over the time period 1965 through 2000; and 

• use output from the SFWMM to estimate fresh water inflow into the northeast region of 

Florida Bay and for computation of salinity values on the western boundary of the Bay 

using regression equations. 

The general nature of these enhancements is to refine the representation of the boundary 

conditions required by the FATHOM model, to account for the effects of water management 

operations and to estimate Florida Bay salinity over the period 1965 through 2000. In the end, 

the availability of data for estimating inflow limited the period over which historical salinity 

calculations could be performed to the period 1970 through 2002. Sufficient data are available 

so that salinity calculations can be performed with FATHOM over the period 1965 through 2000 

when output from the SFWMM is used to specify fresh water inflow. 

Constructing the FATHOM input data sets beginning in 1970 entails making choices among 

alternative methods for assembling each component of the input data. For example, three 

methods for estimating the time series of rainfall over the Bay were considered. Model 

performance with different choices of inputs is evaluated by comparing calculated salinity with 

salinity measurements that are available for the period 1991 through 2002. A systematic 

sensitivity analysis verifies the choice of the “best” combination of inputs that will ultimately 

comprise the MFL base case, which will then be used for MFLs. The sensitivity analysis also 

quantifies the uncertainty in calculated salinity related to the uncertainty in the input data sets. 

The sensitivity analysis provides three types of information. First, it tests whether the selected 

input data and parameters are optimum. An input data set is considered optimum if making 

alternative choices does not improve the performance of the model. Second, the sensitivity 

analysis provides information about how different assumptions made in assembling the input 

data affect the calculated salinity. This information was important in deciding how to represent 

the contribution of ungauged flow in estimating the fresh water inflow into the northeast and 

central regions of the Bay. Third, the sensitivity analysis provides information about the degree 

to which uncertainty in the input data and model parameters affects the error in calculated 

salinity that is apparent in the comparison between model results and salinity measurements. 
 25 

The following sections describe the results obtained by this project: 

Section 2.0 describes the enhancements to the FATHOM model; specifically the updated 

bathymetry, the method used to assemble a time series of western boundary 

salinity, and the residence time calculations. 

Section 3.0 describes how fresh water inflow was estimated; specifically the enhancements 

made to the PHAST model, results of calibrating the enhance PHAST model, but 

also the alternative methods used in estimating inflow. 

Section 4.0 provides a complete description of the base case, specifically the selected input 

data and parameter values, and presents results of the salinity and residence time 

calculations for 1970 through 2002. 

 

Section 5.0 presents the approach used in the sensitivity analysis and the results. 

Section 6.0 provides an analysis of the water budget for Florida Bay and areas of the Bay 

where high salinity values are sensitive to changes in inflow based on the MFL 

base case data and salinity calculations. 

 

Section 7.0 describes the coupling of the SFWMM output to FATHOM and presents results of 

salinity calculations based on four water management scenarios. 
 26 

2 ENHANCEMENTS TO THE SALINITY MODEL – FATHOM 

Enhancements to the FATHOM salinity model for MFL development purposes incorporate the 

most recent bathymetry data, link variation of salinity along the western boundary to discharge 

from Shark Slough, calculate residence time, and assemble input data sets to support calculation 

of salinity simulations for CERP water management alternatives over the period 1965 through 

2002. This section describes these enhancements. 

2.1 MFL Bathymetry 

This project utilizes a Florida Bay bathymetric survey completed in 1990 (Hansen and Dewitt, 

2000) and other recent survey data into FATHOM. The product is referred to as the MFL 

bathymetry. The MFL bathymetry still relies on the previous survey data to describe the 

bathymetry of the shallowest areas in the Bay. This is because the equipment used for the new 

bathymetric survey was restricted to areas where water depths are greater than about 20 inches 

(51 cm). These areas are relatively extensive in Florida Bay, which is one of the hurdles that 

have to be crossed in modeling the Bay. The previous versions of the FATHOM model relied on 

bathymetric data that had been compiled from a number of sources (Cosby et al. 2004, Nuttle et 

al. 2000). Some of this information dated back to the original survey of the Bay conducted in the 

late 1880s. Other information quantified the local knowledge of boaters of the extensive shallow 

banks and the channels used for boat access across the banks. The new survey data replaces 

much of the out-of-date data from previous surveys. 

The new bathymetric data and the data on the shallow areas were compiled by the District into a 

GIS database for the entire Bay. This database was queried at each 20m by 20m area within in 

the Bay to produce the depth class information needed to describe the volume of the basins and 

conformation of the banks in FATHOM. These data are the MFL base case bathymetry 

parameters for FATHOM. 

District staff used a variety of elevation datasets for Florida Bay and surrounding water bodies, 

mainland, and island areas to compile the basis for the new bathymetry database. These datasets 

included: 

• USGS High Resolution Bathymetric Survey of Florida Bay 

(http://sofia.usgs.gov/projects/bathymetry/).

• NOAA GEODAS Survey Database for Barnes Sound (Survey 4H05542 

HYD9303F11484, entered into GEODAS 12/31/1979, referenced to MLW). 

• ACOE LIDAR of Eastern Dade County (processed in 2003, referenced to NAVD 88, 

feet). 

• USGS high accuracy elevation survey of the Everglades 

(http://sofia.usgs.gov/projects/elev_data/).

In addition, the District digitized areas with missing elevation data, including bank and land 

areas, and channel cuts not surveyed by any of the above. The elevations for these areas that 

were not surveyed were estimated from surrounding data and from photo interpretation of recent 

USGS-DOQ and DOT images. A buffer was applied to the banks polygon dataset to remove 

“stair steps” in the final surface. 
 27 

The process to combine these datasets included the following steps by the District in ArcGIS: 

(1) Convert all point data to common horizontal (FL East NAD83 Harn Feet) and vertical 

(NAVD88) datum, using referenced benchmarks where available 

(http://140.90.78.170/benchmarks/8723534.html). 

(2) Merge points into 1 dataset and create a triangulated irregular network (TIN) surface 

from these points. 

(3) Add estimated data for banks and land areas (polygons) and channels (lines) to TIN 

surface. 

(4) Convert the TIN surface to a raster grid surface with 50-foot cells. 

The process to convert the grid data into a format usable by FATHOM included the following 

steps in ArcView 3.2: 

(1) Change the vertical reference point of the grid from NAVD88 to MSL, using elevations 

for the Key West benchmark station (http://coops.nos.noaa.gov/benchmarks/8724580.html); do this by adding 0.869 ft (0.265 meters) 

to the NAVD88 grid with the Map Calculator function. 

(2) Symbolize the MSL converted grid to show 1 foot elevation classes. 

(3) Add themes for FATHOM basins (polygon shape file) and shoals (line shape file) to the 

view. 

(4) Perform Histogram by Zone analysis of MSL grid (represented in 1 foot elevation 

classes) for Shoals and Basins themes (respectively); this analysis calculates the number 

of grid cells within each elevation class for each Shoal and Basin, and outputs a 

temporary .dbf file with these data. 

(5) Convert .dbf file in MS Excel into format usable by FATHOM. 

Inspection of these output led to some concern about the accuracy of the estimated elevations of 

the areas that had not been surveyed. Therefore, a technique was used that took advantage of the 

USGS data in Florida Bay where available and used the previous bathymetry data for the Florida 

Bay basins with little USGS survey data. This technique also evaluated the shoals within each 

basin and a criterion was developed for assigning elevations on the shoals. Then, the additional 

survey data described above was added to fill in the needed gaps. This process created the MFL 

bathymetry. 

In a basin where there are survey points for > 50% of the basin area, the USGS survey data are 

used for the entire basin. There were 8 basins where the coverage was < 50%. There are also 2 

basins that are east of U.S. Highway No. 1 that are not included in the USGS survey. This 

means that there are 10 basins that will use the previous Everglades National Park (ENP) 

bathymetry (18% of the wetted area) and 33 basins that will use the USGS data (82% of the 

wetted area). 

For the shoal (banks) areas, the prior ENP bathymetry is used in the 10 basins that are using the 

prior ENP bathymetry for the open water areas. For the other 33 basins, if greater than half of 

the wetted shoal length was greater than one foot in depth, the USGS data were used. If less than 

half of the wetted length was greater than one foot in depth, the prior bathymetry data were used. 

Using these selection criteria, 202 of the shoals (55% of the total length) used the prior ENP 

bathymetry, and 176 shoals (45% of the total length) used the recent, USGS bathymetry data. 
 28 

The resulting depth distributions for the shoals and in the basins reinforce the importance of the 

network of shallow banks in controlling circulation and exchange in Florida Bay, (Figure 2.1). 

An overwhelming majority of the shoal pixels fall in the one to two foot depth class. As 

discharge calculated with Manning’s equation increases non-linearly with depth, the most 

significant exchange between basins will be concentrated in the relatively few deep areas. By 

contrast, the open-water basins are about four or five feet deep on average. Even so there is a 

significant representation in the one to two foot depth class that reflects the generally shallow 

conditions in the basins in the central and west regions of the Bay. 
 29 

Figure 2.1: Depth distribution on shoals and in basins for the MFL bathymetry (as totals 

across all shoals and all basins, excluding land areas) 

Depth Distribution on Shoals

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 30 

2.2 Boundary Salinity 

Along the southwest Gulf coast, fresh water from Shark Slough discharging through the Shark 

River alters the salinity of the shallow coastal waters that form the western boundary of the 

FATHOM model domain. For the FATHOM MFL model, this relationship is described through 

empirically derived (regression) models that relate salinity at the boundary salinity locations 

(Figure 2.2) to the flow and stage in Shark Slough. The water level data are taken from the longterm data record at the P33 gage in Shark Slough, and the inflow into Shark Slough is the 

discharge from the four S12 structures (total flow = S12T), (Figures 2.3 and 2.4). 

The SERC monthly salinity data are the primary observed salinity data used in this project. 

Beginning in the early 1990s, the Southeast Environmental Research Program (SERC) at Florida 

International University (FIU) has conducted a long-term program to monitor water quality in 

the coastal waters of South Florida. This program visits 24 stations in Florida Bay and 21 

stations along the southwest coast on a monthly basis, (Figure 1.5). Water samples are analyzed 

for salinity among a suite of nutrient and other water quality parameters. The report by Jones 

and Boyer (2001) summarizes the data and discusses long-term trends in water quality on a 

regional basis. 

For the purpose of estimating boundary salinity, regression equations were developed to estimate 

the salinity values measured at SERC stations 25, 26, 27, and 28 (Figure 2.5), based on the 

monthly values of P33 stage and S12T flow as regional indices of hydrologic variation. Linear 

regression models were formulated using the observed SERC salinity data collected in the period 

1991 through 2000. Table 2.1 reports the results of this analysis. The selected models 

incorporate a lagged response of salinity to variations in Shark Slough hydrology; lags up to 3 

months were investigated. Multiple variable regression equations that combine information 

contained in both P33 and S12T are better predictors of salinity than equations that use either 

data set alone. Marshall (2004) and Marshall, et al (2004) used multiple variable regression 

techniques to simulate salinity within Florida Bay from stage, sea surface elevation, and wind 

data using a similar regression method. 

The same approach was used to describe the variation of salinity on the boundary in the extreme 

east end of Florida Bay, SERC station 1 on Card Sound. Because the hydrologic conditions vary 

coherently throughout the area south of Tamiami Trail, there is strong statistical relationship 

between salinity in Barnes and Card Sound and the indices of hydrologic variation in Shark 

Slough used for the western boundary salinity simulations. 
 31 

Figure 2.2: Basin numbers and regional groups used in the FATHOM model. Dots 

identify locations of SERC salinity measurements used to define variable salinity boundary 

conditions. 

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

D

C B

A

boundary 

conditions conditions

(and card sound)

Aggregated FATHOM Groups Aggregated FATHOM Groups

D

C B

A

boundary 

conditions conditions

(and card sound)

boundary 

conditions conditions

(and card sound)

FATHOM basin numbers

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11

10

9

8

7

6

5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

D

C B

A

boundary 

conditions conditions

(and card sound)

boundary 

conditions conditions

(and card sound)

Aggregated FATHOM Groups Aggregated FATHOM Groups Aggregated FATHOM Groups Aggregated FATHOM Aggregated FATHOM Groups

D

C B

A

boundary 

conditions conditions

(and card sound)

boundary 

conditions conditions

(and card sound)

FATHOM basin numbers

25

26

27

28

1
 32 

Figure 2.3: Locations of the sources of long-term data on regional hydrologic conditions 

that affect Florida Bay 

S12T

TSB

P33

T21 Transect 

S196a

Joe Bay 
 33 

Figure 2.4: Regional indices for boundary salinity along the western and far eastern 

boundary of the Bay 

P33 Monthly Stage, cm

100

150

200

250

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

P33 Monthly Mean Stage, cm

150

160

170

180

190

200

mon 1 2 3 4 5 6 7 8 9 10 11 12

P33 Annual Mean Stage, cm

100

150

200

250

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Monthly Discharge (10**6 m3)/mo, S12T

0

100

200

300

400

500

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Mean Discharge (10**6 m3)/mo, 70-02 S12T

0

50

100

150

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Total Discharge, (10**6 m3)/yr, S12T

0

500

1000

1500

2000

2500

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 34 

Figure 2.5: Time series of monthly salinity on boundary data 1991 through 2002 

Monthly Salinity (psu), SERC Station 1

15

20

25

30

35

40

45

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Monthly Mean Salinity (psu), SERC Station 1

15

20

25

30

35

40

45

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Mean Salinity (psu), SERC Station 1

15

20

25

30

35

40

45

year 91 92 93 94 95 96 97 98 00 01 02

Monthly Salinity (psu), SERC Station 25

15

20

25

30

35

40

45

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Monthly Mean Salinity (psu), SERC Station 25

15

20

25

30

35

40

45

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Mean Salinity (psu), SERC Station 25

15

20

25

30

35

40

45

year 91 92 93 94 95 96 97 98 00 01 02
 35 

Figure 2.5: Time series of monthly salinity data on boundary1991 through 2002 (cont.) 

Monthly Salinity (psu), SERC Station 26

15

20

25

30

35

40

45

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Monthly Mean Salinity (psu), SERC Station 26

15

20

25

30

35

40

45

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Mean Salinity (psu), SERC Station 26

15

20

25

30

35

40

45

year 91 92 93 94 95 96 97 98 00 01 02

Monthly Salinity (psu), SERC Station 27

15

20

25

30

35

40

45

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Monthly Mean Salinity (psu), SERC Station 27

15

20

25

30

35

40

45

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Mean Salinity (psu), SERC Station 27

15

20

25

30

35

40

45

year 91 92 93 94 95 96 97 98 00 01 02
 36 

Figure 2.5: Time series of monthly salinity data on boundary1991 through 2002 (cont.) 

Table 2.1: Summary of regression models used to estimate salinity on western boundary 

and at Card Sound (SERC station 1) based on S12T flow and P33 level for the MFL base 

case (1970 through 2002) 

SERC 

Station 

Lag 

(months) 

S12T Flow 

Coefficient 

P33 Level 

Coefficient 

Intercept Multiple R2 

25 2 -0.014 -0.079 51.03 0.66 

26 2 -0.013 -0.065 48.54 0.64 

27 2 -0.012 -0.046 44.58 0.57 

28 2 -0.009 -0.052 46.19 0.53 

1 0 -0.009 -0.016 61.60 0.63 

Monthly Salinity (psu), SERC Station 28

15

20

25

30

35

40

45

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Monthly Mean Salinity (psu), SERC Station 28

15

20

25

30

35

40

45

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Mean Salinity (psu), SERC Station 28

15

20

25

30

35

40

45

year 91 92 93 94 95 96 97 98 00 01 02
 37 

2.3 Calculation of Residence Time 

FATHOM calculates residence time based on diagnostic statistics compiled for each basin and 

each month of simulation time. Two definitions of residence time are used: turnover time and 

decay half-life.

Turnover Time – Turnover time is calculated on a monthly basis for each basin and is defined as 

the monthly average volume of water in a basin divided by the monthly total influx of water into 

the basin (including flood tides, rainfall and runoff), with the results expressed in days. Turnover 

time (TT) is mathematically equivalent to the classically defined hydraulic retention time of a 

basin defined as 

TT = V / Q, 2.1 

where V is the volume of the basin and Q is the water flux. 

Decay Half-life – The decay half-life is operationally defined on a monthly basis for each basin 

by simulating the addition of a tracer at the beginning of each month and measuring the amount 

of tracer remaining in the basin at the end of the month. Each basin gets its own unique tracer so 

that decay half-lives can be calculated simultaneously for all basins during a simulation. The 

Decay Half-life (DH) for a given basin and month is calculated by solving for DH (in days) in the 

following equation: 

Ct = Co * exp (- t / DH ) 2.2 

where Co is the concentration of the tracer at the beginning of the month, Ct is the concentration 

at the end of the month and t is the number of days in the month. 
 38 

2.4 Long Term Input Data for Salinity Calculations 

The approach taken in estimating boundary salinity from Shark Slough hydrology, in section 2.2, 

also serves as the general approach for estimating other input data for the historical 

reconstruction period 1970 through 2002. Data that measure components of the Florida Bay 

water budget most directly, such as rainfall and inflow, are not available prior to 1996. Recent 

monitoring efforts have been in place for about the past ten years only. They include monthly 

measurements of water quality (SERC), continuous measurements of rainfall, salinity and water 

temperature at fixed stations by Everglades National Park (MMN), and continuous measurement 

of flow and salinity in estuarine creeks in the central and northeast region of the Bay (USGS), 

(Table 2.2). 

The available direct data are used to establish relationships between water budget components 

and longer term indirect data that represent the regional indices of climate and hydrology. The 

indirect data are long-term data sets from various agencies that monitor sea level and tides, 

wetland water levels, rainfall, and water flow through water management structures (weirs, gated 

structures, and pumps). The indirect data represent variations in regional climate that drive 

changes in the hydrology of South Florida and in salinity in Florida Bay. 

This section describes the indirect data that are used to estimate the long-term input data sets 

required by FATHOM, (Table 2.2)for the period 1970 through 2002. The methods used to 

construct the FATHOM input data sets from these indirect data are described in Section 2.1 

(bathymetry), Section 3 (inflow), and Sections 4.1 and 4.2 (rainfall and evaporation). 

2.4.1 Rainfall 

Long-term input data for rainfall are available from the records for Flamingo, Royal Palm and 

Tavernier monitoring stations, (Figures 2.6 and 2.7), and the Division 7 rainfall data product by 

the National Climatic Data Center (NCDC), (Table 2.2 and Figure 2.7). The Division 7 rainfall 

data are collected by primary and cooperating monitor stations throughout Florida Bay and the 

Keys, and includes the Tavernier station. The rainfall at Flamingo, Royal Palm, Tavernier, and 

the NCDC Division 7 rainfall provide the basis for estimating long-term rainfall in Florida Bay 

for the MFL base case. Royal Palm rainfall is also used to estimate the contribution of rainfall to 

fresh water inflow from the wetlands in the Taylor Slough C111 wetland basin. 

2.4.2 Evaporation 

Long-term input data for evaporation patterns can be developed using the records of mean air 

temperature, (Figure 2.8), and range of air temperature (monthly maximum minus monthly 

minimum), (Figure 2.9) for Flamingo, Royal Palm and Tavernier. Relative humidity and wind 

speed data are from Joe Bay, (Figures 2.1, 2.10 and 2.11). Only the seasonal pattern of humidity 

and wind speed are used, because the period of record for these data at Joe Bay covers only the 

period 1990 through 2002. 

These data are used in three approaches for estimating long-term evaporation. Air temperature, 

humidity and wind speed are used in a Dalton Law calculation of evaporation. The temperature 

range is used to estimate atmospheric transmissivity in a radiation-based approach to estimating 
 39 

evaporation, and temperature alone is used to calculate potential evaporation based on the 

empirical Thornthwaite method. 

2.4.3 Boundary Salinity 

The indirect data used to estimate boundary salinity are the S12T flow and P33 water level data 

compiled by the South Florida Water Management District (DBHYDRO). Section 2.2 describes 

these data and their application to estimate boundary salinity values. For CERP alternative 

simulations these data were provided by the SFWMM. 

2.4.4 Fresh Water Inflow from Wetlands 

Because fresh water inflow is a primary component of the MFLs, the estimation of inflow is 

described in its own section of this report. Section 3 describes the methods used to estimate 

fresh water inflow from the Taylor Slough and C111 wetland basin. 

2.4.5 Sea Level 

Long-term input data for the water level in Florida Bay over the 1970 – 2000 period is taken 

from the record of monthly mean sea level at Key West, (Figures 2.12 and 2.13). At supratidal 

and longer time scales, changes in water level are coherent over the whole Bay and with water 

level measured at the Key West gage (Wang et al. 1994; Smith 1997). It is assumed that over the 

long term biogenic accretion maintains the depth of the carbonate banks relative to mean sea 

level. Therefore, the (small) trend of increasing mean sea level over the period 1970 through 

2002 has been removed from the sea level index data. Seasonal and year-to-year changes in 

mean sea level remain in the de-trended data. 
 40 

Table 2.2: Information sources used for developing FATHOM input data to support 

simulation of salinity in Florida Bay for the period 1970 through 2002 

FATHOM Input Direct Data Indirect Data 

Rainfall ENP platform data (POR: 

1996-2002, for this study) 

Flamingo, Royal Palm, 

Tavernier, NCDC Division 7 

Evaporation N/A Air temperature (mean and 

range) from Flamingo, Royal 

Palm and Tavernier; relative 

humidity and wind speed 

(seasonal pattern) from Joe 

Bay 

Boundary 

salinity 

SERC monthly data for 

stations 25, 26, 27, 28 and 

1. (POR: 1991-2002) 

S12T flow, P33 level, season 

(month) of the year 

Inflow USGS measured creek 

discharge (POR:1996-

2000) 

TSB flow, S18c flow, S197 

flow, Royal Palm rainfall, 

USGS creek discharge (spatial 

distribution) 

Sea level ENP platform data 

(summarized by Smith 

1997) 

Key West sea level 
 41 

Figure 2.6: Locations of indirect data sources for rainfall (Royal Palm, Flamingo, 

Tavernier) and the regions where each set of data were applied as FATHOM input 
 42 

Figure 2.7: Indirect data used for regional rainfall indices 

Monthly Rainfall, Flamingo (cm/mo)

0

10

20

30

40

50

60

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Ave Monthly Rainfall, Flamingo (cm/mo)

0

5

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Rainfall, Flamingo (cm/yr)

0

50

100

150

200

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Monthly Rainfall, Royal Palm (cm/mo)

0

10

20

30

40

50

60

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Ave Monthly Rainfall, Royal Palm 

(cm/mo)

0

5

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Rainfall, Royal Palm (cm/yr)

0

50

100

150

200

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 43 

Figure 2.7: Indirect data used for regional rainfall indices (cont.) 

Monthly Rainfall, Tavernier (cm/mo)

0

10

20

30

40

50

60

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Ave Monthly Rainfall, Tavernier (cm/mo)

0

5

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Rainfall, Tavernier (cm/yr)

0

50

100

150

200

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Monthly Rainfall, NCDC Div 7 (cm/mo)

0

10

20

30

40

50

60

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Ave Monthly Rainfall, NCDC Div 7 

(cm/mo)

0

5

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Rainfall, NCDC Div 7 (cm/yr)

0

50

100

150

200

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 44 

Figure 2.8: Indirect data used for regional indices of air temperature 

Monthly Ave Air Temp, Flamingo (deg C)

15

20

25

30

35

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Ave Air Temp, Flamingo (deg C)

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Ave Air Temp, Flamingo (deg C)

22

24

26

28

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Monthly Ave Air Temp, Royal Palm (deg C)

15

20

25

30

35

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Ave Air Temp, Royal Palm (deg 

C)

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Ave Air Temp, Royal Palm (deg C)

22

24

26

28

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 45 

Figure 2.8: Indirect data used for regional indices of air temperature (cont.) 

Monthly Ave Air Temp, Tavernier (deg C)

15

20

25

30

35

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Ave Air Temp, Tavernier (deg C)

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Ave Air Temp, Tavernier (deg C)

22

24

26

28

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Monthly Ave air temp NCDC Div 7 deg C

15

20

25

30

35

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Ave Air Temp, NCDC Div 7 (deg 

C)

10

15

20

25

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Ave Air Temp, NCDC Div 7 (deg C)

22

24

26

28

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 46 

Figure 2.9: Indirect data used for regional indices of air temperature range 

Flamingo AirTmp Range, deg C

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Flamingo Air Temp Range, deg C

0

5

10

15

mon 1 2 3 4 5 6 7 8 9 10 11 12

Flamingo Air Temp Range, deg C

0

5

10

15

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Royal Palm AirTmp Range, deg C

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Royal Palm Air Temp Range, deg C

0

5

10

15

mon 1 2 3 4 5 6 7 8 9 10 11 12

Royal Palm Air Temp Range, deg C

0

5

10

15

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 47 

Figure 2.9: Indirect data used for regional indices of air temperature range (cont.) 

Tavernier AirTmp Range, deg C

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Tavernier Air Temp Range, deg C

0

5

10

15

mon 1 2 3 4 5 6 7 8 9 10 11 12

Tavernier Air Temp Range, deg C

0

5

10

15

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 48 

Figure 2.10: Indirect data used for seasonal pattern of relative humidity 

Figure 2.11: Indirect data used for the seasonal pattern of wind speed 

Joe Bay Monthly Ave Wind Speed, m/s

2

3

4

5

6

7

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Joe Bay Ave Monthly Wind Speed, m/s

3

4

5

6

mon 1 2 3 4 5 6 7 8 9 10 11 12

Joe Bay Ave Annual Wind Speed, m/s

3

4

5

6

year91 92 93 94 95 96 97 98 99 00 01 02

Joe Bay Monthly Ave Relative Humidity, %

60

65

70

75

80

85

90

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Joe Bay Ave Monthly Relative Humidity, %

70

75

80

85

mon 1 2 3 4 5 6 7 8 9 10 11 12

Joe Bay Ave Annual Relative Humidity, %

65

70

75

80

85

year 91 92 93 94 95 96 97 98 99 00 01 02
 49 

Figure 2.12: Locations of data for indirect sea level data 

Figure 2.13: Indirect data for sea level used as a regional index 

Mean Sea Level, cm (above MLLW), Key West

0

10

20

30

40

50

60

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Mean Sea Level, cm, 70-02, Key 

West

10

20

30

40

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Mean Sea Level, cm, Key West

10

20

30

40

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 50 

3 ESTIMATES OF FRESH WATER INFLOW FROM WETLANDS

Three characteristics define the inflow of fresh water from the adjacent wetlands into Florida 

Bay: the magnitude of flow, its timing, and its distribution along the north shore of the Bay. As 

with boundary salinity, estimates of inflow for the historical salinity reconstruction over the 

period 1970 through 2002 must be derived from indirect data rather than on direct 

measurements. Direct measurements of inflow have been made by the USGS since 1996 on five 

estuarine creeks, (Figure 1.4). These data provide a basis for estimating inflow over the longer 

period. However, the approach to estimating long-term inflow into Florida Bay must also 

account for an unknown amount of ungauged inflow that is not measured by the USGS 

monitoring stations. 

The estimation of long-term inflow utilizes a water budget approach. As originally conceived 

for this project, the PHAST wetland hydrology model was intended to serve this function. 

Enhancements to the PHAST model attempted to improve estimates of the contribution by the 

Long Pine wetland basin to inflow. This is of particular interest in estimating the inflow of fresh 

water into the central region of the Bay where hypersaline conditions are prone to develop. 

However, after enhancements and recalibration the PHAST model is unable to satisfactorily 

account for the measured inflow plus ungauged inflow estimated by the USGS for the period 

1996 through 2000. As an alternative, estimates of long-term inflow were made using a simple 

mass accounting approach that makes explicit assumptions about the amount of ungauged inflow 

and how this is allocated geographically as input to the FATHOM model. 

This section describes the MFL base case inflow input data and the alternative inflow data sets 

used in the sensitivity study (Section 5), and it documents the data and analysis on which these 

estimates of inflow are based. The wetland water budget for the period covered by the available 

USGS inflow data, February 1996 through September 2000, serves as the benchmark for 

compiling the long-term estimates of inflow. The compilation of the water budget is described 

first for this benchmark period. Then a discussion of the PHAST model enhancements follows, 

including the results of model calibration and an evaluation of the enhanced model. Based on 

this evaluation, it was decided not to base the estimation of wetland inflow only on the enhanced 

PHAST model. The section closes with a description of how fresh water inflow from the 

wetlands is estimated for the MFL base case and alternative inflow data sets used in the 

sensitivity analysis. 

3.1 Wetland Water Budget - 1996 through 2000 

The wetland sub-basins and fluxes across the related transects defined in Figure 3.1 define the 

framework for compiling the wetland water budget in the Taylor Slough C111 wetland basin. 

The fluxes designated MFLx are surface water fluxes that link the three wetland basins of the 

PHAST model to the surrounding wetland and to Florida Bay. This same framework is used to 

examine the output from the SFWMM (section 7), so for convenience the boundaries of the subbasins follow the cell boundaries in the SFWMM. In addition to the MFL fluxes, each wetland 

sub-basin gains water as the net of rainfall minus evaporation [R-E]. The term del S accounts for 

changes in storage in each basin as the effective net flux over a period of time. The del S flux 

can be large over short periods, especially between the wet season and dry season within a year. 
 51 

Over longer periods, such as that considered here, changes in storage do not contribute 

significantly to the water budgets. 

Flow in Taylor Slough (TSB), Figure 3.2, and discharges from the S175 structure and the S18C 

structure on the C111 Canal are the major sources of data on the surface water inflow into the 

Taylor Slough C111 wetland basin. Table 3.1 identifies the long-term data used to estimate 

components of the wetland water budget. Discharge through the S197 structure into Manatee 

Bay accounts for the large flux of surface water out of the basin, (Figure 3.3). Several of the 

surface water fluxes either cannot be estimated from the available data at all or the temporal 

coverage by available data is poor. This is the case for virtually all of the surface water fluxes in 

the water budget of the Long Pine basin. 

Based on the USGS studies of creek flow, the Central Region of Florida Bay (via McCormick 

Creek) receives very little fresh water inflow from the mangrove wetlands. The greatest rate and 

annual volume of inflow occurs through Trout Creek into Joe Bay, (Figure 3.4). Large flows can 

also be discharged into Manatee Bay when the S197 structure is opened during extreme (but 

recurring) wet conditions to alleviate upstream flooding. 

Estimates of inflow for the long-term input data set are made on the basis of the USGS gauged 

inflow for the period 1996 through 2000. This amounted to 311 million cubic meters per year, or 

252 thousand acre-feet per year. The period of record actually begins in March 1996 and ends 

with October 2000, but it will be referred to in this report as 1996 through 2000. Figure 3.5 

compiles estimates of the surface water fluxes, as annual averages, from the data described 

above. This compilation accounts for the major surface water fluxes in the basin, even though 

there are insufficient data to estimate some of the fluxes. The excess of rainfall over 

evapotranspiration in the basin accounts for most of the difference between total flows in (TSB 

plus S175 plus S18c) and total flows out (the gauged USGS flows plus the discharge of S197 

into Manatee Bay). Hittle et al. (2001) estimate flows in four ungauged creeks to amount to an 

additional 23 percent above the gauged flows, and this total (386 million cubic meters per year, 

or 313 thousand acre-feet per year) should be taken as the lower limit on actual inflow into 

Florida Bay during the period 1996 through 2000. 
 52 

Figure 3.1: Wetland sub-basins used to estimate fresh water inflow from the wetlands in 

the Taylor Slough C111 wetland basin. The locations of the MFLx flow transects are 

shown superimposed on the SFWMM grid. Also shown are locations for flow (TSB, S175, 

S18C, and S197) and rainfall (RPL) data used to estimate the inflow to Florida Bay for the 

period 1970 through 2002. The wetland water level data (CP and EPSW) are used to 

calibrate the PHAST model. 

Table 3.1: Sources of information for estimating the water budget and calculating salinity 

in Florida Bay for the period 1970 through 2002 

Wetland Water 

Budget 

Direct Data 

(1996-2000) 

Physically-based Model Indirect Data 

(1970 – 2002) 

Rainfall Craighead Pond (CP), 

Joe Bay (JBTS), P37, 

Royal Palm (RPL), 

S18C, Terrapin Bay 

(TB), Trout Cove (TC), 

Taylor River (TR) 

N/A Royal Palm rainfall, “excess 

rainfall” (see text) 

Evaporation German (2000) SFWMM potential 

evapotranspiration 

(SFWMD 2000) 

Estimated Florida Bay 

evaporation (Nuttle et al. 2003) 

Surface Water 

Inflow into 

Wetlands 

TSB flow, S18c flow, 

S197 flow, S175 flow 

N/A N/A 

Fresh water to 

Florida Bay 

USGS creek discharge 

(1996 – 2000) 

PHAST, SFWMM (for 

water management 

alternatives) 

Alternative Inflow Scenarios 

N/A – no information available 

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

RPL

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

RPL
 53 

Monthly Discharge (10**6 m3)/mo, Taylor Slough Bridge (TSB)

0

10

20

30

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Mean Discharge (10**6 m3)/mo, 

70-02, Taylor Slough Bridge

0

2

4

6

8

10

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Total Discharge (10**6 m3)/yr, Taylor Slough Bridge

0

20

40

60

80

100

120

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Figure 3.2: Data used for regional indices of fresh water discharge into the Taylor Slough 

C111 wetland basin 

Monthly Discharge (10**6 m3)/mo, S18C

0

20

40

60

80

100

120

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Mean Discharge (10**6 m3)/mo, 

70-02, s18c

0

10

20

30

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Total Discharge (10**6 m3)/yr, s18c

0

100

200

300

400

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 54 

Figure 3.2: Data used for the regional indices of fresh water discharge into the Taylor 

Slough C111 wetland basin (cont.) 

Monthly Discharge (10^6 m3/mo); S175

0

10

20

30

40

50

60

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Mean Discharge (10^6 m3/mo)

70-02; S175

0

2

4

6

8

10

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Total Discharge 10^6 m3/yr S175

0

50

100

150

200

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Monthly Discharge (10**6 m3)/mo, s197

0

10

20

30

40

50

60

70

80

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Monthly Mean Discharge (10**6 m3)/mo, 

70-02, s197c

0

2

4

6

8

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Total Discharge (10**6 m3)/yr, s197c

0

40

80

120

160

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 55 

0

20

40

60

80

100

120

140

160

180

200

MC TR MUD TC WHC

Gauged Flow (10**6 m3/yr)

Total USGS Gauged Flows (10**6 m3/mo)

0

20

40

60

80

100

120

140

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000

USGS Gauged Flows (10**6 m3/mo)

0

10

20

30

40

50

60

70

80

mon 1 2 3 4 5 6 7 8 9 10 11 12

Total USGS Gauged Flows (10**6 m3/yr)

0

50

100

150

200

250

300

350

400

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00

Figure 3.3: Monthly values of total inflow measured at the USGS estuarine creek 

monitoring stations (Figure 1.4) 

Figure 3.4: Distribution of annual average inflow measured at the USGS estuarine creek 

monitoring stations; McCormick Creek (MC), Taylor River (TR), Mud Creek (MUD), 

Trout Cove (TC), and West Highway Creek (WHC) 
 56 

Figure 3.5: Wetland water budget components for the period March 1996 through 

October 2000 estimated directly from data. Fluxes are in units of A) millions of cubic 

meters per year and B) thousands of acre-feet per year. 

 

A) in million cubic meters per year

B) in thousand acre-feet per year

 Long Pine Basin Taylor Slough Basin C111 Basin 

MFL5 n/a MFL6 130 TSB+S175 MFL7 205 S18C 

 

 MFL1 n.d. MFL2 n.d. MFL3 n.d. MFL4 36 S197 

Area (m2) 

Area (m2) 231 gauged Area (m2) 55 gauged 

5 gauged Total Inflow – USGS creeks

(excludes Ma natee Bay)

291 

1.7E+08 

2.1E+08 

2.5E+08 

361 

gauged + ungauged 

gauged 

 Long Pine Basin Taylor Slough Basin C111 Basin 

MFL5 n/a MFL6 105 TSB+S175 MFL7 166 S18C 

 

 MFL1 n.d. MFL2 n.d. MFL3 n.d. MFL4 29 S197 

187 gauged Area (acre) 45 gauged 

4 gauged Total Inflow – USGS creeks

(excludes Manatee Bay)

236 

6.1E+04 

293 gauged + ungauged 

gauged 

Area (acre) 

5.1E+04

Area (acre) 

4.1E+04
 57 

Enhancements to the Wetland Hydrology Model - PHAST 

3.2.1 Long Pine Basin 

For this project, the wetland basin hydrology model (PHAST) was enhanced by extending water 

budget and discharge calculations to include the Long Pine sub-basin. In contrast to the Taylor 

Slough and C111 wetland sub-basins, discharge from the Long Pine sub-basin is primarily the 

result of rainfall in excess of evapotranspiration in the sub-basin; no large tributary surface flows 

occur into or out of the sub-basin. The Everglades Park Road controls flow across the north and 

west sides of this sub-basin, and the flow that occurs through the culverts in the road is minor. 

Incorporating this sub-basin into the wetland basin models required adopting a rational scheme 

for allocating the total discharge estimated from excess rainfall among possible flow paths. Flow 

can occur in both directions across the boundary with the Taylor Slough basin. Flow in 

McCormick Creek, the major identified surface water discharge directly out of Long Pine subbasin, occurs only intermittently. Additionally, the nature of the hydrologic connection between 

the sub-basin and areas north and west of the Park Road is poorly understood. 

A number of culverts allow the exchange of surface water across the Park Road that bounds the 

Long Pine sub-basin on the north and the west. Flow in these culverts is not monitored 

continuously, but various measurements have been made over a number of years. Tillis (2001) 

and Stewart et al. (2002) reviewed these measurements. In general, the average direction of 

surface flow across the Park Road is directed out of the sub-basin. Based on this information, it 

is assumed that excess rainfall from one third of the Long Pine sub-basin discharges north and 

west through the culverts under the Park Road. 

The Buttonwood Embankment (Figure 3.6) impedes the discharge of surface water directly out 

of the Long Pine sub-basin south into the central region of Florida Bay. Lorenz (2000) and 

Holmes et al. (no date) describe this geomorphic feature and trace its influence on the hydrology 

of Florida Bay and the coastal mangroves in this area. The embankment extends east as far as 

Joe Bay, and restricts the southward discharge of surface water out of the Taylor Slough subbasin. Based on the USGS creek flow data, it appears that most of the surface water discharged 

from the Taylor Slough basin occurs as an eastward flow into the extreme southwest portion of 

the C111 sub-basin and eventually to Joe Bay. 
 58 

Figure 3.6: Wetland hydrology basins used in PHAST showing surface inflows included in 

water balance calculations (black), locations of USGS measured creek flow (light-colored 

arrows), and surface fluxes calculated internally (hatched). 

 
 59 

The influence of the Buttonwood Embankment on discharge from the Long Pine and Taylor 

Slough sub-basin is evident when the USGS creek flow data (aggregated weekly) for the creeks 

that breach the embankment, i.e. McCormick Creek, Mud Creek and Taylor River, are plotted 

relative to wetland water levels measured at CP, (Figure 3.7). The plots demonstrate the 

existence of a threshold in wetland water level between 1.0 and 2.0 feet that water levels must 

exceed before discharge occurs. The negative (upstream) flows and the scatter around the trend 

lines reveal the influence of additional forcing by wind, tides and variations in sea level on flows 

in the estuarine creeks. The threshold for wetland discharge into McCormick Creek across the 

Buttonwood Embankment is higher than for discharge through Mud Creek and Taylor River. 

Based on this information, the area of the remaining two thirds of the Long Pine sub-basin that 

is not assumed to discharge across the Park road is combined with the area of the Taylor Slough 

sub-basin for purposes of estimating rainfall in excess of evapotranspiration. Discharge from 

the combined sub-basins across the Buttonwood Embankment is assumed to follow the form of 

the discharge relationships that are evident in Figure 3.7, Table 3.2. This means that the zero 

discharge thresholds are held at the values shown in Table 3.2, and the values of α , the slopes of 

the discharge curves, enter the calibration of the models as minimum values. The additional 

discharge that occurs from the combined basins east into the C111 sub-basin is assumed to 

follow the general discharge relation described by equation 1.2. 

Table 3.2: Parameters for discharge rating curves for flow measured at selected USGS 

creeks as a function of water level at CP. The parameters are as defined in Equation 1.2, 

and units for the parameters are consistent with the implementation within the PHAST 

model. 

Parameter MC Mud TR 

α (1036ft3/week) 186 97.8 89.1 

hsill (ft) 1.6 1.3 1.3 

β 1 1 1 
 60 

Figure 3.7: Discharge rating curves for flow measured at selected USGS creeks as a 

function of water level at CP (MC = McCormick Creek, Mud = Mud Creek, and TR = 

Taylor River). 

-300

-200

-100

0

100

200

300

400

-1.00 0.00 1.00 2.00 3.00

CP level (ft)

MC flow (cfs)

-300

-200

-100

0

100

200

300

400

-1.00 0.00 1.00 2.00 3.00

CP level (ft)

Mud flow (cfs)

-300

-200

-100

0

100

200

300

400

-1.00 0.00 1.00 2.00 3.00

CP level (ft)

TR flow (cfs)
 61 

3.2.2 Calibration 

Calibration of the revised wetland models follows the approach described by Nuttle (2004) with 

the resulting parameter estimates reported in Table 3.3. The method of calibration minimizes the 

sum of squared deviations between modeled and observed water levels at CP for the Long 

Pine/Taylor Slough combined sub-basin, and at EPSW for the C111 sub-basin model. 

Optimization was performed using the solver routine in Microsoft Excel. In general, the basin 

hydrology models succeed in fitting the fluctuations in water levels measured at CP and EPSW, 

(Figure 3.8). Parameters of the discharge relation reported for the Taylor Slough sub-basin are 

for discharge east into the C111 sub-basin and ultimately Joe Bay. Calibrated values for 

discharge south through the Buttonwood Embankment match the minimum values reported in 

Table 3.2. 

Table 3.3: Calibrated parameter values for the wetland basin hydrology models 

Parameter Taylor Slough C111 

α (106 ft3/week) 911 688 

hsill (ft) 1.6 1.27 

A1 (million ft2) 4900 1400 

wet fraction 0.82 1.00 

S175 fraction 1.0 0.0 

Evap const. -0.65 -0.75 

1

 Set to measured basin area 

The calibration of the PHAST model to match the observed fluctuation in Everglades water level 

also determines the amount and timing of fresh water inflow from the wetland basins into Florida 

Bay. The measured USGS creek flows are not used in the calibration. Therefore the USGS 

inflow measurements are independent of the inflows calculated by the PHAST model, (Figure 

3.9). The volume of inflow to Florida Bay calculated by the PHAST model is sensitive to 

assumptions made in the representation of the water budget in the Long Pine sub-basin. In 

particular, the assumed proportion of surface flow out of the Long Pine sub-basin that flows west 

and north across the Park Road is not well characterized. The few measurements that have been 

made of this flow (Stewart et al. 2002) are inadequate to test the assumption that was used. The 

inflow calculated by PHAST is also sensitive to errors in the calculation of wetland 

evapotranspiration within the PHAST model. 
 62 

Figure 3.8: Results of calibration of the wetland hydrology PHAST model to water levels 

sampled weekly from time series of daily average values for Craighead Pond and EPSW 

locations. 

EPSW Water Level

R2 = 0.8117

0

0.5

1

1.5

2

2.5

3

0 0.5 1 1.5 2 2.5 3

Adjusted Level (ft)

Calculated Level (ft)

Craighead Pond Water Level

R2 = 0.8498

0

0.5

1

1.5

2

2.5

3

0 0.5 1 1.5 2 2.5 3

Adjusted Level (ft)

Calculated Level (ft)

EPSW Water Level

R2 = 0.8117

0

0.5

1

1.5

2

2.5

3

0 0.5 1 1.5 2 2.5 3

Adjusted Level (ft)

Calculated Level (ft)

Craighead Pond Water Level

R2 = 0.8498

0

0.5

1

1.5

2

2.5

3

0 0.5 1 1.5 2 2.5 3

Adjusted Level (ft)

Calculated Level (ft)
 63 

Figure 3.9: Summary of water budget supporting inflow to Florida Bay calculated from 

the PHAST wetland hydrology model for the period 1996 through 2000. All fluxes are in 

units of millions of cubic meters per year. See Figure 3.1 for reference map. 

Long Pine Taylor Slough C111 

MFL5 0 MFL6 131 MFL7 206

[R-E] [R-E] [R-E]

12 9 15

MFL1 0 MFL2 -4 MFL3 54 MFL4 39

del S del S del S

-2 -2 Area (m2) 0

Area (m2) 

236

Area (m2) 

77

18

Total Inflow

331

1.3E+08

2.0E+08

2.5E+08
 64 

3.2.3 Evaluation of PHAST Model 

The inflow to Florida Bay calculated by the PHAST suffers from large uncertainties related to 

the estimation of evapotranspiration. Both rainfall and evapotranspiration are large components 

of the wetland water budget, and individually their magnitudes exceed those of the surface water 

fluxes measured in the wetland basin, (Figure 3.5). Inflow to Florida Bay depends on the 

difference between rainfall and evapotranspiration, and this calculation amplifies the relative 

error in the result. The volume of inflow estimated by the PHAST wetland hydrology model for 

1996 through 2000 (330 million cubic meters per year) underestimates by 15 percent the 

minimum inflow estimated from the USGS monitoring of creek flows (386 million cubic meters 

per year). This discrepancy indicates the magnitude of the errors associated with the estimation 

of inflow based on an exact reconstruction of the water budget in the Taylor Slough C111 

wetland sub-basin. These errors cannot be reduced without a better estimate of 

evapotranspiration. 

3.3 Estimates of Fresh Water Inflow from Wetlands - 1970 through 2002 

In light of the errors apparent in the inflow estimate based on PHAST, an alternative approach 

was taken to constructing the inflow data for FATHOM. For this use of the model inflow is 

calculated indirectly by estimating the various components of the wetland water budget from the 

available regional hydrological and climatic data. This alternative approach maintains the 

framework of the wetland water budget for combining information from long-term data sets. 

The approach deals explicitly with the uncertainty related to the amount of ungauged fresh water 

inflow that occurs in addition to what is currently measured. The amount and location of the 

ungauged portion of inflow varies between the MFL base case and alternative inflow data sets, 

and a sensitivity analysis examines the effect on the FATHOM salinity calculations of the 

uncertainty related to ungauged inflow. 

The timing of changes in inflow is controlled entirely by the variation in the long-term data sets 

used to construct the inflow estimate for the historical reconstruction of salinity, 1970 through 

2002. These are the measured surface water flows in Taylor Slough (TSB) and in the C111 canal 

(S18C and S197, Figure 3.1), and excess rainfall (rainfall minus evapotranspiration) at Royal 

Palm, (Figure 3.11). Temporary storage and release of water in the wetland sub-basins also 

influences the timing of changes in inflow. Results from the initial implementation of the 

PHAST model (Nuttle and Teed 2002) indicate that this dynamic introduces about a one-month 

delay, on average, in the timing of the annual peak inflow to Florida Bay relative to the timing of 

peak surface water flows into the wetlands. 

Spatial distribution of inflow is defined by grouping FATHOM input basins into three inflow 

groups (Figure 3.10); the central inflow group, the northeastern inflow group, and the eastern 

inflow group. The eastern inflow group consists of Manatee Bay, where the C111 canal 

discharges fresh water to the coast through the S197 control structure. The northeastern inflow 

group consists of inflow regions in FATHOM that receive flow from creeks monitored by the 

USGS, (Figure 1.4). The central inflow group consists of the inflow regions in FATHOM, that 

do not receive flow from creeks monitored by the USGS, except for Manatee Bay. The 

distribution of flows to each of the FATHOM surface water basins within each inflow group is 

also presented on Figure 3.10. 
 65 

Figure 3.10: FATHOM inflow groups showing the distribution of flow among the basins in 

each group; percentages give distribution of total inflow within each group 

Figure 3.11: Excess rainfall for Taylor Slough C111 wetland basin 

12

11

10

9

8

7

6 5

18

15

14

13

26

25 24

23

40

37

36

35

41

47

46

12

11

10

9

8

7

6 5

18

15

14

13

26

25 24

23

40

37

36

35

41

47

46

12

11

10

9

8

7

6 5

18

15

14

13

26

25 24

23

40

37

36

35

41

47

46

Terrapin Bay 

3% (northeastern)

Santini Bight 

30% (central)

Rankin Bight 

10% (central)

Snake Bight 

0% (central)

Garfield Bight 

40% (central)

Madeira Bay 

20% (central)

Little Madeira Bay 

10% (northeastern)

Alligator Bay 

8% (northeastern) Joe Bay 

16% (northeastern)

Long Sound 

16% (northeastern)

Manatee Bay 

100% (eastern)

Trout Cove 

47% (northeastern)

12

11

10

9

8

7

6 5

18

15

14

13

26

25 24

23

40

37

36

35

41

47

46

12

11

10

9

8

7

6 5

18

15

14

13

26

25 24

23

40

37

36

35

41

47

46

12

11

10

9

8

7

6 5

18

15

14

13

26

25 24

23

40

37

36

35

41

47

46

Terrapin Bay 

3% (northeastern)

Santini Bight 

30% (central)

Rankin Bight 

10% (central)

Snake Bight 

0% (central)

Garfield Bight 

40% (central)

Madeira Bay 

20% (central)

Little Madeira Bay 

10% (northeastern)

Alligator Bay 

8% (northeastern) Joe Bay 

16% (northeastern)

Long Sound 

16% (northeastern)

Manatee Bay 

100% (eastern)

Trout Cove 

47% (northeastern)

Terrapin Bay 

3% (northeastern)

Santini Bight 

30% (central)

Rankin Bight 

10% (central)

Snake Bight 

0% (central)

Garfield Bight 

40% (central)

Madeira Bay 

20% (central)

Little Madeira Bay 

10% (northeastern)

Alligator Bay 

8% (northeastern) Joe Bay 

16% (northeastern)

Long Sound 

16% (northeastern)

Manatee Bay 

100% (eastern)

Trout Cove 

47% (northeastern)

Monthly Excess Rainfall - Taylor Slough C111 Basin (cm/mon)

0

5

10

15

20

25

30

35

40

45

50

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000

Ave Monthly Excess Rainfall (cm)

0

2

4

6

8

10

12

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Excess Rainfall (cm)

0

10

20

30

40

50

60

70

80

year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 66 

The distribution of inflow into the FATHOM basins always remains the same within each 

inflow group. However, the distribution of inflow among the inflow groups changes between 

MFL base case and the inflow alternatives examined in the sensitivity analysis. The eastern 

inflow group provides inflow only to Manatee Bay. The distribution of inflow from the 

northeastern inflow group into the FATHOM basins matches the distribution of inflow measured 

at the USGS monitoring sites, (Figure 3.4). The distribution of inflow from the central inflow 

group into the FATHOM basins is determined so that each basin receives the same depth of 

inflow, distributed over the surface of the basin With the exception of FATHOM basin 41. Basin 

41 (Snake Bight) receives no inflow in any of the inflow alternatives examined. 

The magnitude of inflow assigned to the inflow groups varies depending on what assumptions 

are made about how much the total inflow exceeds the amount measured at the USGS 

monitoring stations and how this additional inflow is distributed between the central and 

northeastern inflow groups, (Table 3.4). The inflow measured at the USGS monitoring stations 

from February 1996 through September 2000 provides the basis for calibrating estimates of 

inflow for the long-term period 1970 through 2002. It also serves as the basis for characterizing 

the magnitude of additional, “ungauged” flow included in the estimated inflow. The detailed 

description (below) of how the MFL base case inflow is constructed will illustrate the approach 

used to construct four alternative inflow data sets, (Table 3.5). A fifth alternative inflow data set 

is based on inflow calculated by the enhanced PHAST wetland hydrology model. 

The inflow data for the MFL base case is compiled from remote data on surface flows, rainfall 

and evaporation in the Taylor Slough C111 wetland sub-basin by the following detailed 

procedure: 

• Monthly volumes of flow assigned to the eastern inflow group (Manatee Bay) are equal 

to the monthly flows measured at the S197 control structure. 

• Monthly volumes of flow assigned to the northeastern inflow group are the sum of two 

components. The first component consists of the monthly volumes of the surface water 

discharge into the Taylor Slough C111 wetland sub-basin after accounting for the 

discharge into the eastern inflow group through S197. This first component is the sum of 

measured flows in Taylor Slough (TSB) and the C111 canal (S18C) minus the flow 

measured at the S197 control structure. The second component accounts for the 

additional inflow to Florida Bay generated by rainfall over the Taylor Slough C111 

wetland sub-basin in excess of evapotranspiration. For the MFL base case, the inflow 

assigned to the northeastern inflow group is calculated as the sum of all of the surface 

flow (TSB + S18C – S197) and 12 percent of the calculated excess rainfall. Adding 12 

percent of the excess rainfall calibrates the total inflow assigned to the northeast inflow 

group so that it equals the total inflow measured at the USGS monitoring stations for the 

period February 1996 through September 2000. 

In the calculation of excess rainfall, evapotranspiration is calculated as a fraction (53 

percent) of estimated total solar radiation by the method described by Abtew (1996) for 

South Florida. Total solar radiation is estimated from radiation incident at the top of the 

atmosphere, for given time of year, reduced by an amount to account for attenuation by 
 67 

moisture in the air. The attenuation factor is estimated from the daily range of 

temperatures measured at Royal Palm using the method developed by the SFWMD 

(2003). Monthly values of excess rainfall volume are calculated from the difference of 

Royal Palm rainfall minus estimated evapotranspiration and multiplied by the area of the 

Taylor Slough C111 wetland sub-basin (620 million square meters). Values of excess 

rainfall are set equal to zero in months when evapotranspiration exceeds rainfall. 

• The magnitude of inflow assigned to the central inflow group in the MFL base case is 

equal to 20 percent of the gauged flow measured by the USGS at their estuarine creek 

monitoring stations, (Figure 1.4), for the period February 1996 through September 2000. 

The USGS data are the only direct estimates of inflow to Florida Bay, and the total 

volume of measured inflow provides a logical reference in reporting the volume of 

“ungauged” flow included in the estimated inflow data. The 20 percent of additional 

inflow included in the MFL base case as ungauged-flow is comparable to the magnitude 

of inflow estimated by the USGS in four ungauged creeks (Hittle et al. 2001) for the 

same period. For the historical reconstruction, creek flows are not available prior to 

1996. Therefore, the monthly values for inflow assigned to the central inflow group are 

calculated as the measured monthly flow into Taylor Slough (TSB) multiplied by 0.67, 

which is approximately equal to 20% of the USGS creek flows. Of the two major 

sources of surface discharge into the Taylor Slough C111 wetland sub-basin, the flow 

measured at TSB is closer to the central region of Florida Bay, and thus it is considered to 

characterize better the temporal variation in the availability of surface water for inflow to 

Florida Bay from the western portion of the wetland basin. (Note that the addition of 

ungauged flow to the estimated inflow occurs only in the reconstruction of the historical 

inflow; no additional ungauged flow is included when inflow data are taken from output 

of the SFWMM) 
 68 

Table 3.4: Comparison of the amount and distribution of fresh water discharge for each 

inflow alternative. Estimated inflow is reported for the period 1996 through 2000 for 

comparison with the inflow measured by the USGS creek monitoring. For all cases, 

additional discharge of 39 units is routed to Manatee Bay (Eastern Group) through the 

S197 structure. 

Annual Average Runoff (106 m3/yr) 

Central NE Fl Bay Eastern 

Group Group Total Group 

 

MFL base 60 293 354 39 

RN-1 60 352 412 39 

RN-2 60 235 295 39 

RN-3 120 293 414 39 

RN-4 0 293 293 39 

RN-5 0 347 347 39 

Annual Average Runoff (103 Ac-ft/yr) 

Central NE Fl Bay Eastern 

Group Group Total Group 

 

MFL base 49 238 287 32 

RN-1 49 286 334 32 

RN-2 49 190 239 32 

RN-3 97 238 335 32 

RN-4 0 238 238 32 

RN-5 0 281 281 32 
 69 

Table 3.5: Summary of inflow alternatives 

Data Set Description

MFL Base 

Case 

Eastern Inflow Group - Monthly inflow was measured discharge at the S197 structure. 

All inflow was applied to Manatee Bay. 

Northeastern Inflow Group - Monthly inflow was calculated from measured discharge in 

Taylor Slough (TSB) and in the C-111 canal (difference in measured discharge between 

the S18C and S197 structures). Excess rainfall from the wetland basin was added in the 

amount needed for the total amount of inflow for the period 1996-2000 (surface flow plus 

excess rainfall) to equal the total discharge measured by the USGS from 1996-2000 in 

five creeks (McCormick C., Taylor R., Mud C., Trout C., West Highway C.) The monthly 

simulated inflow was applied to the FATHOM basins in this group based on the 

observed USGS discharge proportions in the five creeks for 1996-2000. (USGS 

estimates of un-gauged discharges into this group are not included). 

Central Inflow Group - Monthly inflow added to the central inflow group was proportional 

to the monthly measured discharge in Taylor Slough (TSB). The total amount added in 

the period 1996 through 2000 is equal to 20% of the flow in the Northeastern group. 

Central group inflow was added to Madeira Bay, Santini Bight, Garfield Bight and Rankin 

Lake. There is no inflow to Snake Bight 

(The MFL base case inflow data set is the same as the RN-a alternative in Progress 

Report II and Progress Report III.) 

Alternate 1 

(RN-1) 

 Eastern Inflow Group – same as base simulation 

Northeastern Inflow Group – all monthly values increased by 20% from the base case 

 Central Inflow Group – same as base simulation 

(The RN-1 inflow data set is the same as the RN-b alternative in Progress Report II and 

Progress Report III.) 

Alternate 2 

(RN-2) 

 Eastern Inflow Group – same as base simulation 

Northeastern Inflow Group – all monthly values decreased by 20% from the base case 

 Central Inflow Group – same as base simulation 

(The RN-2 inflow data set is the same as the RN-c alternative in Progress Report II and 

Progress Report III.) 

Alternate 3 

(RN-3) 

 Eastern Inflow Group – same as base simulation 

Northeastern Inflow Group – same as base simulation 

 Central Inflow Group – all monthly values increased to double the base case 

(The RN-3 inflow data set is the same as the RN-d alternative in Progress Report II and 

Progress Report III.) 

Alternate 4 

(RN-4) 

 Eastern Inflow Group – same as base simulation 

Northeastern Inflow Group – same as base simulation 

 Central Inflow Group – all monthly values set to zero 

(The RN-4 inflow data set is the same as the RN-e alternative in Progress Report II.) 

 

Alternate 5 

(RN-5) 

 Eastern Inflow Group – same as base simulation 

Northeastern Inflow Group – Inflow estimated from PHAST wetland hydrology model 

 Central Inflow Group – all monthly values set to zero 

(The RN-5 inflow data set is the same as the RN-f alternative in Progress Report II and 

Progress Report III.) 
 70 

4 MFL BASE CASE CALCULATED SALINITY 

RECONSTRUCTION - 1970 THROUGH 2002 

The MFL base case input data represent the “best available” information on the fresh water 

budget for Florida Bay in the period 1970 through 2002. Salinity calculations based on the MFL 

base case input data and parameter values are the best estimate of salinity conditions that 

occurred historically in Florida Bay. This section describes the input data and parameter values 

that comprise the MFL base case, and it summarizes the simulated salinity and calculated 

residence times based on these inputs. The fresh water input from the upstream wetland basins is 

described in detail in the previous section. 

The input data consist of the following time series of monthly data: 

• Rainfall, 

• Evaporation, 

• Inflow, 

• Boundary Salinity, and 

• Sea level. 

The model parameters include: 

• Tides (semi-diurnal, diurnal, and the spring-neap cycle), 

• Bathymetry, and 

• Bottom Friction (in flow over banks). 

Table 4.1: Sources of input data to FATHOM for the MFL base case. Input data cover the 

period 1970 through 2002. Sources of the data are indicated in parentheses. 

FATHOM 

Input 

Indirect Data 

(Regional Index) 

Rainfall Flamingo, Royal Palm, 

Tavernier (NCDC) 

Evaporation Air temperature (mean and 

range) from Flamingo, Royal 

Palm and Tavernier (NCDC), 

relative humidity and wind 

speed (seasonal pattern) from 

Joe Bay (DBHYDRO) 

Boundary 

salinity 

S12T flow, P33 level 

(DBHYDRO) 

Inflow TSB flow, S18c flow, S197 

flow, S175 flow (DBHYDRO) 

Sea level Key West sea level (NOAA) 
 71 

In absence of data available to provide direct information needed by the model, various 

techniques must be applied to construct the needed information from indirect data, (Table 4.1). 

As an example, direct precipitation to Florida Bay has only been measured since 1996. In order 

to construct a 31-year time series of direct rainfall, estimates must be constructed from long-term 

rain data measured at onshore locations. In the case of evaporation, neither direct data nor 

indirect measurements of evaporation are available, so a variety of physically based models were 

evaluated for use. Similarly, the PHAST wetland hydrology model was evaluated, along with 

other simpler techniques, as a method of estimating fresh water inflow into the central and 

northeast regions of the Bay based on data on related components of the water budget in the 

wetlands upstream. The input data that consistently provide the best fit to the existing salinity 

data using FATHOM were chosen for the base case reconstruction. Progress Reports 1 and 2 

document the details of these investigations that are not included in this report. 

The MFL base case runs are constrained to begin in 1970 because regional hydrological data 

needed to construct the time series of inflow from the Taylor Slough C111 wetland basin are 

missing prior to 1970. This restriction is relaxed when FATHOM is used to simulate salinity for 

the analysis of the water management alternatives described later in this report because the 

SFWMM is the source of the inflow data for this application, and the time series data for the 

alternatives covers the period from 1965 to 2000, a 36-year period. 

4.1 Estimated Input Data 

4.1.1 Rainfall 

The time series of estimated monthly rainfall for the MFL base case is compiled from the records 

of rainfall at Tavernier, Flamingo, and Royal Palm, (Figure 2.6). The spatial variation of rainfall 

across the Bay is represented in FATHOM by specifying uniform amounts for each of five 

regions, (Figure 4.1). These same regions are also used to describe evaporation inputs to the 

model. Monthly rainfall amounts for each of these regions were calculated from the three longterm data records using weights based on Thiessen polygons. Mean annual rainfall varies little 

across the Bay, (Table 4.2). Average rainfall for the entire Bay is plotted in Figure 4.2. 

Table 4.2: Mean annual estimated rainfall (in cm) for each of the FATHOM input regions 

Region 1 Region 2 Region 3 Region 4 Region 5 

125 118 118 120 114 
 72 

Figure 4.1: Regions used to define rainfall input to FATHOM 

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Region 5

Region 4

Region 3

Region 2

Region 1
 73 

Figure 4.2: Estimated monthly rainfall input to MFL base case, averaged across the five 

input regions 

Monthly Rainfall - MFL Base Case bay-wide average (cm/mon)

0

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50

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000

Ave Monthly Rainfall (cm)

0

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25

mon 1 2 3 4 5 6 7 8 9 10 11 12

Annual Rainfall - MFL Base Case (cm)

0

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year 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02
 74 

4.1.2 Evaporation 

Relative to rainfall, there are few data available from which one can estimate evaporation for 

Florida Bay. However, from the observed data from Florida Bay (Nuttle et al. 2003) and in the 

Everglades (German 2000), it appears that evaporation is less variable than rainfall viewed at 

comparable scales, both temporally and spatially. A variety of sources provide information 

about the likely long-term average annual rate of evaporation, (Table 4.3). Neglecting estimates 

at the high and low ends puts the likely value in the range of between 130 and 170 cm/yr. 

 

Evaporation for the MFL base case is estimated using a Dalton’s Law (mass transfer) approach. 

The Dalton’s Law approach assumes that evaporation is proportional to the difference between 

saturation vapor pressure at the water surface (corresponding to the surface water temperature) 

and the unsaturated water content of the air (corresponding to air temperature and relative 

humidity), and to a function of the mean wind speed: 

Evap = F * f(u) * (esat – eair), 4.1 

where esat is the saturation vapor pressure at the water surface, eair is the vapor pressure of the 

air, f(u) is the function of the mean wind speed and F is a factor used to scale the annual average 

evaporation to a fixed value. 

Monthly air temperature for NCDC Division 7, (Figure 2.8), was used with the relative humidity 

to calculate air vapor pressure eair. Monthly patterns of relative humidity and wind speed were 

derived from the Joe Bay weather tower, (Figures 2.10 and 2.11). The average monthly pattern 

of these variables over the period 1991 to 2002 was used for every year of evaporation inputs. 

Saturation vapor pressure esat is calculated from the temperature of the water. Surface water 

temperature data are estimated for the Everglades National Park Marine Monitoring Network 

stations by extrapolation based on correlation between water temperature at each station and air 

temperature measured at Tavernier, Flamingo, and Royal Palm, Figure 2.6. 

The estimated monthly evaporation inputs are shown in Figure 4.4 for the MFL base case. Based 

on best professional judgement, the wind function was scaled so that the long-term (1991-2002) 

annual average evaporation from the Bay is 135 cm/year. 
 75 

Table 4.3: Estimates of mean annual evaporation from Florida Bay 

Source Estimate 

(cm/year)

Flamingo evaporation pan 

(NCDC/NOAA data) 

210 

Lake Okeechobee water budget 

Morton (1986) 

160 

Everglades “wet” evaporation – Bowen ratio 

German (2000) 

160 

Florida Bay – Dalton Law, USACOE platforms 

Pratt and Smith (1999) 

75 

Florida Bay – steady state salinity box model 

Nuttle et al. (2000) 

110 

Florida Bay – Dalton Law, Long Key data 

Smith (2000) 

160 

Florida Bay – Dalton Law, Univ. Miami platforms 

Nuttle et al. (2003) 

150 

Florida Bay – Priestly-Taylor (radiation) method 

Nuttle et al. (2003) 

170 

Florida Bay – dynamic salinity box model 

Nuttle et al. (2003) 

140 (+/-10) 
 76 

Figure 4.4: Time series of evaporation for the MFL base case 

Monthl y Evaporation, cm 

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Region 1 Region 2 Region 3

Monthl y Evaporation, cm 

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Region 4 Region 5

Baywide Ave Mon Evap, cm, 70-02 

0

5

10

15

20

1 2 3 4 5 6 7 8 9 10 11 12

Monthl y Evaporation, cm 

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Region 1 Region 2 Region 3

Monthl y Evaporation, cm 

0

5

10

15

20

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Region 4 Region 5

Baywide Ave Mon Evap, cm, 70-02 

0

5

10

15

20

1 2 3 4 5 6 7 8 9 10 11 12

Baywide Ave Mon Evap, cm, 70-02 

0

5

10

15

20

1 2 3 4 5 6 7 8 9 10 11 12
 77 

4.1.3 Boundary salinity 

Boundary salinity for the MFL base case in each of ten input regions is specified based on 

monthly values at SERC monitoring stations on the model boundary (Figure 4.5) calculated with 

the regression models, (Table 2.1). The regression models relate salinity at SERC stations 25, 

26, 27, 28, and 1 from the monthly flow through the S12 structures (S12T) along Tamiami Trail 

and monthly average water levels at P33 in Shark Slough. Section 2.2 describes the 

development of these regression models. Figure 4.6 shows the boundary salinity time series 

provided as input to FATHOM. 

Figure 4.5: Location of boundary salinity regions for FATHOM input. Boundary salinity 

values for the MFL base case are derived from data collected by the SERC estuarine 

monitoring program and by the Florida Keys National Marine Sanctuary (NMS). 

42

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Region 6

Region 3

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Region 7

Region 10

Region 9

Region 1

SERC 25

average of 

SERC 25 & 26

average of 

SERC 26 & 27

SERC 28 SERC 28

average of 

NMS 237/240 

& SERC 28

average of 

NMS 231 & 234

NMS 228

average of 

NMS 225, 

222 & 216

SERC 1

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Region 1

Region 2

Region 5

Region 6

Region 3

Region 4

Region 8

Region 7

Region 10

Region 9

Region 1

SERC 25

average of 

SERC 25 & 26

average of 

SERC 26 & 27

SERC 28 SERC 28

average of 

NMS 237/240 

& SERC 28

average of 

NMS 231 & 234

NMS 228

average of 

NMS 225, 

222 & 219

SERC 1

SERC 25

average of 

SERC 25 & 26

average of 

SERC 26 & 27

SERC 28 SERC 28

average of 

NMS 237/240 

& SERC 28

average of 

NMS 231 & 234

NMS 228

average of 

NMS 225, 

SERC 1
 78 

Figure 4.6: Time series of boundary salinity for MFL base case 

Boundary Salinity, psu 

18

23

28

33

38

43

48

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

region1 region2

Boundary Salinity, psu 

18

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48

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

region3 region4

Boundary Salinity, psu 

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region5 region6

Boundary Salinity, psu 

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1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

region7 region8
 79 

Figure 4.6: Time series of boundary salinity for MFL base run (cont.) 

Boundary Salinity, psu 

18

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48

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

region9 region10

Yearly Ave Boundary Salinity, psu 

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Gulf Atlantic Card Sd

 Mon Ave Boundary Salinity, psu, 70-02 

20

25

30

35

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1 2 3 4 5 6 7 8 9 10 11 12

Gulf

Atlantic

Card Sd
 80 

4.1.4 Fresh Water Inflow from Wetlands 

MFL base case monthly inflow into the Bay is estimated from flow measured at Taylor Slough 

Bridge (TSB) and in the C111 Canal (S18C and S197), and from rainfall at Royal Palm in excess 

of potential evapotranspiration. Section 3.3 describes these calculations in detail. The total 

inflow estimated from these sources is assigned to FATHOM basins through inflow groups, 

(Figure 3.10). Figure 4.7 plots the monthly inflow volumes estimated for the MFL base case. A 

more detailed description of the quantity, timing, and spatial distribution of fresh water inflows 

can be found in the previous section of this report. It is summarized here. 

The estimated total inflow is based on a simple accounting of the water budget for the wetlands 

in the Taylor Slough and C111 sub-basin. This simple accounting includes an explicit estimate 

of the ungauged volume of inflow that is presumed to occur above what is measured at the 

USGS estuarine creek monitoring stations. For the MFL base case, the total ungauged inflow is 

estimated as 67% of the Taylor Slough flow, which is roughly equivalent to twenty percent of 

the flow at the USGS monitoring locations, and this inflow is assigned to the central inflow 

group only, with no ungauged flow augmenting estimated creek flows to the northeastern region. 
 81 

Figure 4.7: Time series of fresh water inflow for MFL base case, by FATHOM inflow 

group 

Annual Total Runoff (10**6 m3)/yr (MFL base case)

0

100

200

300

400

500

600

700

70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Total Runoff NE Group

Central Group Eastern Group

Monthly Runoff (10**6 m3)/mo (MFL base case)

0

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100

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Central Group Eastern Group

Monthly Runoff (10**6 m3)/mo (MFL base case)

0

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100

120

140

160

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Total Runoff NE Group
 82 

4.1.5 Sea Level 

The input data for sea level specifies monthly values for two input regions, (Figure 4.8). The 

Key West measured sea level data are applied directly to sea level input region 1. The sea level 

applied to the boundary region 2, adjacent to southern Biscayne Bay, is increased by 3 cm above 

the Key West data. This offset accounts for water level set up in the interior of Florida Bay as a 

result of non-linear interactions of the Gulf of Mexico tides with the shallow mud banks (Wang 

1994). Figure 4.9 plots the monthly average sea level in the MFL base case. 

Figure 4.8: Location of region for input of sea level into FATHOM 

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 83 

Figure 4.9: Time series of sea level input into FATHOM 

Annual average normalized sea level (cm) 1970-2002

-6

-4

-2

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10

70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02

Region 1 Region 2

Sea Level - cm deviation from mean (de-trended)

-25

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-5

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1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002

Region 1 Region 2

Monthly average normalized sea level (cm) 1970-

2002

-10

-5

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20

1 2 3 4 5 6 7 8 9 10 11 12

Region 1

Region 2
 84 

4.2 Estimated Parameter Values 

4.2.1 Tides 

Tides drive exchange and mixing within the Bay and across its boundaries. The complex pattern 

of water level forcing over the course of a simulation is represented by adding the repeated 

sequence of hourly tides to monthly values of sea level. The sequence of hourly tide levels 

describes water level fluctuations within a month; different sequences are specified for each of 

ten input regions, (Figures 4.10 and 4.11). These reproduce the general characteristics of tide 

predictions for each input region based on tides measurements at three primary NOAA tide 

stations Key West, Naples and the Miami Harbor Entrance. 

Figure 4.10: Ten boundary tide regions used for FATHOM. 

42

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Region 1
 85 

Figure 4.11: Semi-diurnal tidal patterns for boundary tide regions used for FATHOM. 

Data referenced by day of the month, and the same pattern is repeated each month of the 

simulation. 

28 day tidal cycle - cm relative mean

-80

-60

-40

-20

0

20

40

60

80

0 4 8 12 16 20 24 28

region1

28 day tidal cycle - cm relative mean

-80

-60

-40

-20

0

20

40

60

80

0 4 8 12 16 20 24 28

region3

28 day tidal cycle - cm relative mean

-80

-60

-40

-20

0

20

40

60

80

0 4 8 12 16 20 24 28

region5

28 day tidal cycle - cm relative mean

-80

-60

-40

-20

0

20

40

60

80

0 4 8 12 16 20 24 28

region2

28 day tidal cycle - cm relative mean

-80

-60

-40

-20

0

20

40

60

80

0 4 8 12 16 20 24 28

region4
 86 

Figure 4.11 (continued): Semi-diurnal tidal patterns for boundary tide regions used for 

FATHOM. Data referenced by day of the month, and the same pattern is repeated each 

month of the simulation. 

28 day tidal cycle - cm relative mean

-60

-40

-20

0

20

40

60

0 4 8 12 16 20 24 28

region6 28 day tidal cycle - cm relative mean

-60

-40

-20

0

20

40

60

0 4 8 12 16 20 24 28

region7

28 day tidal cycle - cm relative mean

-60

-40

-20

0

20

40

60

0 4 8 12 16 20 24 28

region9 28 day tidal cycle - cm relative mean

-60

-40

-20

0

20

40

60

0 4 8 12 16 20 24 28

region8

28 day tidal cycle - cm relative mean

-60

-40

-20

0

20

40

60

0 4 8 12 16 20 24 28

region10
 87 

4.2.2 Bathymetry 

The bathymetry of Florida Bay is represented in FATHOM by two sets of parameters. The first 

is the proportion of area by FATHOM basin in each depth class; this defines the hypsometry of 

each basin. The second is the proportion of length by FATHOM bank segment in each depth 

class that provides information on hydraulic radius used in the calculation of flow across the 

banks between basins. Section 2.1 provides a detailed description of how these parameter values 

are determined for the MFL bathymetry produced by this project. 

4.2.3 Bottom Friction Parameter 

The MFL base case specifies a uniform value for Manning’s n of 0.1 for the calculation of 

exchange flows between basins and at the tidal boundaries. The use of this value for hydraulic 

calculations over the shallow banks is supported by results of hydraulic modeling of measured 

estuarine creek flow at the USGS gauging stations (Swain et al. 2004) and of direct experimental 

measurement of flow over banks in Florida Bay (Fourqurean and Childers, pers. comm.). The 

sensitivity analysis investigates model performance with alternative values of the bottom friction 

parameter selected within the range measured by Swain et al. (2004). 
 88 

4.3 Results of Salinity Calculations 

This section reports summary results of salinity calculations based on the MFL base case input 

data and model parameters. Results are reported here for the SFWMD areas of interest with 

complete results contained in the appendices. Results are summarized as time series plots, 

(Figure 4.12); box and whisker summaries of salinity distributions calculated for each location, 

(Figure 4.13); and frequency of occurrence within salinity ranges, (Figure 4.14). Detailed output 

for the base case salinity simulations are presented in Appendix A and E. 

The frequency of occurrence of extreme values of salinity is closely linked to ecological 

response. This statistic was examined for the base case by calculating the frequency (% of 

months) for which the monthly average salinity falls into one of six different salinity ranges. The 

ranges chosen presented below have ecological significance: 

extreme hyper-haline > 50 psu, 

hyper-haline 41-50 psu, 

eu-haline 31-40 psu, 

poly-haline 19-30 psu, 

meso-haline 6-18 psu, and 

oligo-haline 0-5 psu. 

 
 89 

Figure 4.12: Time series plots of simulated salinity in practical salinity units (PSU) for 

MFL base case 

MFL Study - SFWMD Special Interest FATHOM Basins

Simulation = MFL base

42

12

11 10

9

8

7

6 5

19

18

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14

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25 24

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27

40

39

38

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36

35

44

43

41

47

46

45

1414

13 13a

1a

14a

22

3

1616

5

6

4

1 Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones

42

12

11 10

9

8

7

6 5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

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33

32

31

30

29

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27

40

39

38

37

36

35

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43

41

47

46

45

1414

13 13a

1a

14a

22

3

1616

5

6

4

1

42

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9

8

7

6 5

19

18

17

16

15

14

13

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25 24

23

22

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20

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33

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31

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9

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11 10

9

8

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6 5

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14

13

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25 24

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21

20

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33

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31

30

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27

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39

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36

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43

41

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46

45

1414

13 13a

1a

14a

22

3

1616

5

6

4

1

1414

13 13a

1a

14a

22

3

1616

5

6

4

1 Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones

Rabbit Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-38

Duck Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-47 Whipray Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-34

Park Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-15

Butternut Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-46

Long Sound

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-7

Joe Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-13 Little Madeira Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-14

Garfield/Rankin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-37
 90 

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 70-00 - Simulation: MFL base

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 70-00 - Simulation: MFL base

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 70-00 - Simulation: MFL base

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Figure 4.13: Overall summary of salinity distributions obtained for MFL base case 
 91 

Figure 4.14: Frequency of occurrence within salinity classes for the MFL base case 

Freq (%) of monthly mean salinity > 50 psu, Jan 1970 - Dec 2000 Simulation = MFL base

0

10

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 40-50 psu, Jan 1970 - Dec 2000 Simulation = MFL base

0

10

20

30

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 31-40 psu, Jan 1970 - Dec 2000 Simulation = MFL base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 19-30 psu, Jan 1970 - Dec 2000 Simulation = MFL base

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 6-18 psu, Jan 1970 - Dec 2000 Simulation = MFL base

0

20

40

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 0-5 psu, Jan 1970 - Dec 2000 Simulation = MFL base

0

20

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region
 92 

4.4 Results of Residence Time Calculations 

Residence time calculations were performed using two accepted estimates – turnover time and 

decay half-life. Calculated residence time in Florida Bay sub-basins ranges from a few days up to 

almost six months (Table 4.4). Basins in the central and northeast regions have longer residence 

times than basins in the west and south regions of the Bay, (Figure 4.15). Detailed output for 

residence time calculations can be found in Appendices B and F. 

The turnover time (Figures 4.16-4.18) and decay half-life (Figures 4.19-4.21) calculations yield 

almost identical results. Turnover time for a single input single output CSTR (continuously 

stirred reactor) is conceptually the same thing as the decay half-life. That is, a pulse of dye 

added to a CSTR would produce a concentration curve that has an exponential decline, and the 

characteristic time constant (defined as V/Q, i.e. the Turnover Time) would be the same as that 

determined by the numerical procedure for finding the decay half-life. 

Casual inspection of the residence time results and the results of the salinity calculations in the 

previous section suggests that periods of rapid increase in salinity coincide with periods of high 

residence times in the Bay. Basins with long residence times are more susceptible to the effect 

of evaporation in excess of rainfall leading to the development of hypersaline conditions. 

Residence time is also more variable in these basins. 

Table 4.4: Residence time values for the SFWMD areas of interest calculated from the 

FATHOM MFL base simulation for the period 1970 – 2002. 

Decay Half-life (days) Turnover Time (days) SFWMD Basin median max min median max min 

Long Sound 19 30 10 19 34 11 

Joe Bay 63 305 16 63 171 21 

Little Madeira Bay 34 88 14 39 82 18 

Duck Key 57 130 31 63 128 36 

Butternut Key 17 28 11 16 32 10 

Park Key 55 124 29 58 129 31 

Whipray Basin 19 38 10 19 42 9 

Rankin Lake 7 14 5 9 17 4 

Rabbit Key 6 8 5 6 10 4 
 93 

Figure 4.15: Distribution of FATHOM basis with median residence time (decay half-life) 

longer than ten days (show as darker shade) 

FATHOM Basins with median FATHOM Basins with median 

Decay Half-life greater than or life greater than or 

less than 10 days less than 10 days

42

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45

FATHOM Basins with median FATHOM Basins with median 

Decay Half-life greater than or life greater than or 

less than 10 days less than 10 days

42

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 94 

Figure 4.16: Time series of monthly values of simulated Turnover Time (days) for nine 

selected FATHOM basins. The map at upper left shows the location of the FATHOM 

basins and the Feasibility Study regions. 

Duck Key Basin

0

30

60

90

120

150

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-47 Whipray Basin

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-34

Rabbit Key Basin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Park Key Basin Basin-38

0

30

60

90

120

150

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-15

Long Sound

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-7

Joe Bay

0

30

60

90

120

150

180

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-13 Little Madeira Bay

0

30

60

90

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-14

Butternut Key Basin

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-46 Garfield/Rankin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-37

42

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14 13 13a

1a

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2

3

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5

6

4

1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones

42

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1a

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3

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1

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6 5

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14 13 13a

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1

14 13 13a

1a

14a

2

3

16

5

6

4

1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones

Duck Key Basin

0

30

60

90

120

150

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-47 Whipray Basin

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-34

Rabbit Key Basin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Park Key Basin Basin-38

0

30

60

90

120

150

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-15

Long Sound

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-7

Joe Bay

0

30

60

90

120

150

180

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-13 Little Madeira Bay

0

30

60

90

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-14

Butternut Key Basin

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-46 Garfield/Rankin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-37

42

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4

1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones

42

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1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones
 95 

Figure 4.17: Bar and whisker diagrams showing the percentiles (5% 25%, 50%, 75%, 

95%) of simulated Turnover Time (days). The percentiles are displayed for all seasons 

(upper panel), wet seasons (middle panel) and dry seasons (lower panel). 

Percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 70-02 - Simulation: MFL Base

0

30

60

90

120

150

180

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

Turnover Time (days)

SFWMD Region FATHOM Basin

Florida 

Bay

Percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 70-02 - Simulation: MFL Base

0

30

60

90

120

150

180

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

Turnover Time (days)

SFWMD Region FATHOM Basin

Florida 

Bay

Percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 70-02 - Simulation: MFL Base

0

30

60

90

120

150

180

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

TurnoverTime (days)

SFWMD Region FATHOM Basin

Florida 

Bay
 96 

Freq (%) of monthly mean Turnover Time > 120 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

10

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Turnover Time 61-120 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Turnover Time 31-60 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Turnover Time 15-30 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Turnover Time 8-14 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Turnover Time 0-7 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Figure 4.18: Frequency (% of months) with which Turnover Time (days) is simulated in 

different ranges. From top to bottom panels: > 120 days; 61-120 days; 31-60 days; 15-30 

days; 8-14 days; and 0-7 days. Frequencies are calculated for all seasons and for the wet 

and dry seasons separately. 
 97 

Figure 4.19: Time series of monthly values of simulated Decay Half-life (days) for nine 

selected FATHOM basins. The map at upper left shows the location of the FATHOM 

basins and the Feasibility Study regions. 

Duck Key Basin

0

30

60

90

120

150

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-47 Whipray Basin

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-34

Rabbit Key Basin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Park Key Basin Basin-38

0

30

60

90

120

150

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-15

Long Sound

0

30

60

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-7

Joe Bay

0

30

60

90

120

150

180

210

240

270

300

330

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-13 Little Madeira Bay

0

30

60

90

120

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-14

Butternut Key Basin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

Basin-46 Garfield/Rankin

0

30

1970 1973 1976 1979 1982 1985 1988 1991 1994 1997 2000 2003

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Basin-47 Whipray Basin

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Basin-46 Garfield/Rankin

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Basin-37

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1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones Feasibility Study Zones
 98 

Figure 4.20: Bar and whisker diagrams showing the percentiles (5% 25%, 50%, 75%, 

95%) of simulated Decay Half-life (days). The percentiles are displayed for all seasons 

(upper panel), wet seasons (middle panel) and dry seasons (lower panel). 

Percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 70-02 - Simulation: MFL Base

0

30

60

90

120

150

180

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

Decay Half-life (days)

SFWMD Region FATHOM Basin

Florida 

Bay

Percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 70-02 - Simulation: MFL Base

0

30

60

90

120

150

180

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

Decay Half-life (days)

SFWMD Region FATHOM Basin

Florida 

Bay

Percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 70-02 - Simulation: MFL Base

0

30

60

90

120

150

180

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

Decay Half-life (days)

SFWMD Region FATHOM Basin

Florida 

Bay
 99 

Figure 4.21: Frequency (% of months) with which Decay Half-life (days) is simulated in 

different ranges. From top to bottom panels: > 120 days; 61-120 days; 31-60 days; 15-30 

days; 8-14 days; and 0-7 days. Frequencies are calculated for all seasons and for the wet 

and dry seasons separately. 

Freq (%) of monthly mean Decay Half-life > 120 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

10

20

30

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Decay Half-life 61-120 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Decay Half-life 31-60 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Decay Half-life 15-30 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

120

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Decay Half-life 8-14 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

40

60

80

100

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FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean Decay Half-life 0-7 days, Jan 1970 - Dec 2002 Simulation = MFL Base

0

20

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FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region
 100 

5 ERROR, SENSITIVITY, AND UNCERTAINTY

This section evaluates the errors in salinity calculations by the FATHOM model with input data 

defined by the MFL base case and examines the sensitivity of these errors to alternative choices 

of input data and model parameters. The errors indicate the level of uncertainty inherent in 

applying the MFL base case inputs and FATHOM to predict salinity in Florida Bay under 

scenarios where Everglades hydrology differs from historical conditions. This uncertainty 

derives from a number of sources, including model error, errors in the estimated input data and 

boundary conditions, and variability in salinity not completely measured by the available data. 

The sensitivity analysis provides a test and validation of the selection of the input data and 

parameter values that comprise the MFL base case. 

This analysis combines information from calculations and data compiled over three periods of 

time, Table 5.1. The MFL base case input data supports calculation of salinity fluctuations over 

the period 1970 through 2002. Estimates of error in the MFL base case simulation are based on 

differences between calculated values and monthly salinity measurements. With one exception, 

the sensitivity analysis is based on comparing errors calculated over the period for which salinity 

measurements were available, 1991 through 2002. The exception compares errors for the MFL 

base case with those for salinity calculations based on directly measured inflow from the 

Everglades wetlands into Florida Bay. These inflow data were available for this study only for 

the period 1996 through 2000. 

In these comparisons, errors in the salinity calculations are defined by comparing the 30-day 

averaged salinity values calculated by FATHOM with salinity measurements collected by the 

SERC monitoring program. The SERC monitoring program has measured salinity once a month 

at 25 locations within Florida Bay since 1991 (Jones and Boyer 2001), Figure 1.5. These data 

provide the most comprehensive and consistent picture of salinity variation in the bay over this 

time period that can be obtained from a single source. 

Table 5.1: Time periods relevant to the calculation of salinity, error and sensitivity to 

alternative input data 

1970-2002 Florida Bay salinity calculated based on MFL Base Case and 

alternative input data sets – wetland inflow estimated from regional 

hydrology data. 

1991-2002 Florida Bay salinity measurements available for comparison with 

calculated salinity values. 

 

1996-2000 Wetland inflow measurements available as input into salinity 

calculations. 
 101 

5.1 Errors in the Base Case Simulation – 1991 through 2002 

Error and uncertainty are evaluated based on the set of residual errors, R. The residual errors are 

calculated as the differences between measured and calculated salinity values that correspond to 

the same location in time and space. In this analysis, the residual errors are calculated as the 

difference between the basin-wide average salinity calculated by FATHOM, based on monthlyaveraged input data, and salinity measured on one day each month at one location within the 

basin. Residual error represents that combined effects of model error, i.e. salinity variations 

due to processes not accounted for in the model calculations, and noise in the data, i.e. variations 

not adequately characterized by the available data. 

5.1.1 Error statistics 

This analysis characterizes the error in calculated salinity at three scales: for Florida Bay overall, 

for the sub-regions within the bay identified for the Florida Bay and Florida Keys Feasibility 

study, and for the areas of interest to the District for MFL criteria, Figure 1.5. 

Five error statistics are reported: 

• average error (avg e), 

• root mean squared error (rmse), 

• average absolute error (abs e), 

• coefficient of determination (r-sq), and 

• model efficiency (eff). 

The average error, the average of R, measures bias between simulated and observed values; a 

mean error of zero means no bias. Even if the average error is zero there can still be significant 

differences between simulated and observed values; these differences may simply cancel out in 

the calculation of the average error. 

The root mean squared error rmse and the average absolute error are measures of residual 

deviation between simulated and observed values, reported in the units of the simulated variable. 

The root mean squared error is calculated as the square root of the mean of the squared residuals 

MSE. The average absolute error is calculated as the mean of the absolute values of the R

values. These measures better reflect the expected magnitude of the difference between 

calculated and measured salinity at a particular location and time. 

Model efficiency is similar to the coefficient of determination, R-squared, i.e. R2

. The 

coefficient of determination measures the fraction of the variance in the observations that can be 

explained by a linear transformation of the simulated salinity values. Therefore, the definition of 

the coefficient of determination is based on the correlation between the simulated and observed 

values. In contrast, model efficiency is calculated from the mean square error normalized by the 

variance of the observed salinity; 

 

eff = 100* (1 - MSE / Var(obs)) 5.1 
 102 

where MSE is the mean of the squared residual errors and Var(obs) is the variance of the 

observed salinity data. This statistical measure of model fidelity is also known as the NashSutcliffe efficiency, c.f. Nash and Sutcliffe (1970) and Weglarczyk (1998). 

In this analysis, model efficiency proves to be the most sensitive and versatile measure of the 

fidelity of calculated to measured salinity. Model efficiency can be interpreted broadly as the 

percentage of the variance in the data that is accounted for directly by the model. A model 

efficiency of zero indicates that the model accounts for no more of the variation than does the 

mean of the data. An efficiency of 100 indicates that the model accounts for all of the variation 

in the data. However, model efficiency can take on negative values if, for example, the model 

produces a biased estimate of the data. 

5.1.2 Results 

The salinity calculations based on the MFL base case inputs scores a model efficiency of 81 

percent throughout Florida Bay, Table 5.2. Values of model efficiency in the feasibility study 

regions and in areas of interest range between 42 percent and 78 percent. Model efficiency 

evaluated for specific regions within the bay are expected to be lower than efficiency values 

obtained for the bay as a whole. This is because the variance of the salinity data for the whole 

bay, which appears in the denominator of Equation 5.1, is higher than the variance of salinity for 

any sub-region within the bay. 

Values for the coefficient of determination (R2

) are high, greater than 0.68 at all locations and 

equal to 0.9 overall. Largely, this reflects the ability of the MFL base case calculations to 

capture the seasonal cycles that dominate salinity variations, Figure 5.1. 

The overall average error of –0.1 indicates that calculations based on the MFL base case inputs 

match the overall the mean salinity in Florida Bay; however bias in the calculated salinity values 

evident at the scale of sub-regions and basins contributes to the errors measured by the root mean 

square error and average absolute error. Values of the root mean squared error and the average 

absolute error are generally consistent with each other throughout Florida Bay. 

Joe Bay and Garfield/Rankin (Feasibility Study Region 5) stand out as locations of interest 

where the performance of the model is lower than elsewhere. These are locations were fresh 

water enters the bay from the adjacent wetlands. The poorer performance of the model here 

might reflect errors in the amount, timing and spatial distribution of inflow as described by the 

MFL base case input data. These are also location where the limitations in the model 

calculations, such as lack of wind-driven circulation and the assumption that each basin is well 

mixed, likely have their largest influence. 

The model efficiency is low also for Feasibility Study Region 13. This region is isolated from 

Florida Bay by the Route 1 causeway, and the poor performance of the model here is likely due 

to poorly described boundary conditions in southern Biscayne Bay. 

The error values reported in Tables 5.2 are not true measures of the error in calculated salinity, 

but these are a conservative estimate of the model error. This distinction arises from a 

fundamental difference between the salinity that is being calculated and the salinity that is being 
 103 

eff rmse avg e abs e r-sq

All Florida Bay 81 4.1 -0.1 3.1 0.9

SFWMD Regions

Feasibility Study Region 1 65 6.3 0.0 4.5 0.8

Feasibility Study Region 1a 76 4.2 1.3 3.3 0.9

Feasibility Study Region 5 43 5.9 1.5 4.5 0.7

Feasibility Study Region 2 78 3.5 -0.2 2.9 0.9

Feasibility Study Region 3 58 5.1 1.0 4.1 0.8

Feasibility Study Region 4 51 2.8 -0.2 2.1 0.7

Feasibility Study Region 16 47 3.0 0.4 2.1 0.7

Feasibility Study Region 6 59 2.9 -0.5 2.3 0.9

Feasibility Study Region 13 42 4.7 -1.3 3.3 0.8

Feasibility Study Region 13a 74 2.8 -0.1 2.2 0.9

Feasibility Study Region 14 67 3.6 -1.9 2.8 0.9

Feasibility Study Region 14a 76 4.1 -1.1 3.2 0.9

FATHOM basins

Long Sound 7 77 4.3 1.9 3.4 0.9

Joe Bay 13 56 7.7 -1.9 5.6 0.8

Little Madeira (Mouth) 14 76 4.2 1.3 3.3 0.9

Park Key 15 77 3.7 2.0 3.1 0.9

Duck Key 47 76 3.7 -1.6 3.0 0.9

Butternut Key 46 76 3.5 -0.2 2.8 0.9

Garfield/Rankin 37 43 5.9 1.5 4.5 0.7

Whipray Basin 34 58 4.5 0.2 3.6 0.8

Rabbit Key Basin 38 51 2.6 0.0 1.9 0.7

Location

measured. Because of the temporal averaging that is inherent in the FATHOM calculations and 

in the input data provided to drive the model, calculated salinity values should be interpreted as 

estimates of time-averaged salinity values. The averaging period is about one month. 

By contrast, the salinity observations are collected as grab samples on one day in each month, 

and the variation in these data include the influence of short-term and day-to-day variability in 

salinity that is not present in the FATHOM calculations. This short-term variability accounts for 

some portion of the residuals R and the measures of model performance based on these. In 

consequence, the bay-wide value of model efficiency of 81 percent indicates a deficiency of 19 

percent in the ability of the model to explain the variation in the grab sample data. Removing the 

influence of short-term variation from the data, e.g. by comparison of model predictions to time 

averaged salinity measurements, would result in a somewhat higher value for model efficiency 

and better assessment of model performance. 

Table 5.2: Errors estimated by comparing salinity calculations for the MFL base case with 

monthly measurements over the period 1991 through 2002. The statistics used to 

characterize the errors are model efficiency (eff), root mean squared error (rmse), average 

error (avg e), average absolute error (abs e), and the coefficient of determination (r-sq). 
 104 

MFL Study - SFWMD Special Interest FATHOM Basins

Simulation = MFL Base

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0

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 38 SERC 18

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 47 SERC 9 Whipray Basin

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Fathom 34 SERC 13

Park Key

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 15 SERC 23

Butternut Key

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 46 SERC 24

Long Sound

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 7 SERC 8

Joe Bay

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 13 SERC 10 Little Madeira (Mouth)

0

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 14-15 SERC 11

Garfield/Rankin

0

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1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Fathom 37 SERC 14-15

Figure 5.2: Results for the MFL Base simulation (Jan 1991 - Dec 2002). Time series 

showing monthly average values of both simulated (FATHOM, blue) and observed (SERC, 

red) salinity values (psu). The time series are presented for nine selected FATHOM basins. 
 105 

5.2 Sensitivity Analysis of Alternative Inputs – 1992 through 2002 

Sensitivity analysis compares the performance of the salinity simulations for the MFL base case 

with the performance obtained with alternative choices of input data and model parameters. The 

sensitivity analysis addresses the question of whether the MFL base case is the best choice of 

input data sets and model parameter values among the alternatives considered. The sensitivity 

analysis also provides information about how different assumptions made in assembling the 

input data influence the calculated salinity values. 

5.2.1 Alternative Inputs and Parameter Values 

This section describes the alternative input data and parameter values used in the sensitivity 

analysis. Differences among the alternative input data and model parameter values span the 

range of uncertainty inherent in selecting the corresponding component for the MFL base case. 

Alternatives are examined for each input and parameter except sea level and tides. 

Sea level is excluded from the sensitivity analysis because fluctuations in sea level occur 

regionally and the Key West data adequately characterize these fluctuations within Florida Bay. 

The alternatives considered for bathymetry also account for uncertainty in the position of the 

mean sea level datum. Tides are excluded because, the idealized representation of tides within 

FATHOM is regarded as a feature of the representation of mixing and exchange within the 

model rather than an input into the calculations. Tidal fluctuations in water levels occur on a 

time scale smaller than the time scales resolved by the input data and on which predictions of the 

model are considered valid (monthly). 

5.2.1.1 Rainfall 

The MFL base rainfall input data are estimated regional values based on data from the three 

NCDC rainfall stations at Flamingo, Royal Palm and Tavernier, Table 5.3. Rainfall Alternative 

1 is based on data from the same three stations but attempts greater spatial resolution of the 

distribution of rainfall. Rainfall Alternative 2 applies rainfall estimated by the NCDC Florida 

Division 7 dataset, which includes data from Tavernier and other adjacent monitoring stations, 

uniformly over the bay. The Division 7 region includes Florida Bay and the Keys but not the 

Everglades or the southeast mainland coast. 
 106 

Table 5.3: MFL base case and alternative rainfall input data 

Data Set Description

MFL Base 

Rainfall 

Monthly rainfall amount was derived for five FATHOM regions within the bay from longterm observations of precipitation at three locations: Flamingo, Royal Palm and Tavernier. 

The monthly precipitation measured at the three locations around the bay was applied to 

the five FATHOM regions within the bay using Thiessen polygons. The bay-wide average 

annual rainfall is 120 cm/yr. 

Alternate 1 

(RF-1) 

Monthly rainfall amount was estimated for five FATHOM regions within the bay using 

regressions of monthly rainfall observed within the bay (at the fourteen ENP marine 

monitoring stations) on monthly rainfall observed around the bay (at Flamingo, Royal 

Palm, and Tavernier) for the period 1993-2002. The monthly rainfall estimates derived 

from the regressions for the fourteen stations within the bay were applied to the five 

FATHOM regions within the bay using Thiessen polygons. The bay-wide average annual 

rainfall is 109 cm/yr. 

Alternate 2 

(RF-2) 

Monthly rainfall amount was derived for five FATHOM regions within the bay from the 

observed NCDC Division 7 precipitation data. The monthly Division 7 rainfall amounts 

were applied uniformly over the bay by assigning the same monthly values to all five 

FATHOM regions within the bay. The bay-wide annual rainfall is 107 cm/yr. 

 

5.2.1.2 Evaporation 

The MFL base evaporation input data are estimated based on a Dalton Law (wind speed) 

formula; this approach results in an average rate of 135 cm/year, Table 5.4. 

Evaporation Alternative 1 takes a radiation-based approach to estimating evaporation; this 

approach results in an average rate of 137 cm/year. In the radiation approach, evaporation is 

calculated as a fraction (53 percent) of estimated total solar radiation by the method described by 

Abtew (1996) for South Florida. Total solar radiation is estimated from radiation incident at the 

top of the atmosphere, for given time of year, reduced by an amount to account for attenuation 

by moisture in the air. The attenuation factor is estimated using the method employed by the 

SFWMD (2003) based on daily temperature range interpolated over the bay from temperatures 

measured at Flamingo, Royal Palm, and Tavernier. 

Evaporation Alternative 2 applies the Thornthwaite formula (Thornthwaite and Holzman 1939), 

based on temperature indices; this approach results in an average rate of 147 cm/year. 

Evaporation Alternative 3 applies the same approach as the MFL base evaporation rescaled so 

that the average rate is 147 cm/year. 
 107 

Table 5.4: MFL base case and alternative evaporation input data 

Data Set Description 

MFL Base 

Evaporation 

Monthly evaporation amount was calculated for five FATHOM regions within the bay from 

Dalton’s Law using air temperature, surface water temperature, wind speed and relative 

humidity. Monthly mean air temperature was derived from long-term observations at three 

locations: Flamingo, Royal Palm and Tavernier. Monthly mean surface water temperature 

was estimated for fourteen locations within the bay using regressions of monthly average 

water temperature (observed at the 14 ENP marine monitoring stations) on monthly 

average air temperature (observed at 3 sites - Flamingo, Royal Palm, and Tavernier) for 

the period 1995-2002. Monthly mean wind speed and relative humidity were estimated 

using seasonal patterns based on average monthly observations at Joe Bay tower for 

1991-2002. The wind function was adjusted to set bay-wide average annual evaporation 

to 135 cm/yr. The monthly evaporation estimates at the fourteen stations within the bay 

were applied to the five FATHOM regions within the bay using Thiessen polygons. 

Alternate 1 

(EV-1) 

Monthly evaporation amount was calculated for five FATHOM regions within the bay from 

the SFWMD Simple Method using solar radiation at the water surface, the latent heat of 

evaporation, and a coefficient characteristic of the surface. The coefficient value selected 

was the SFWMD recommended value for mixed marsh, shallow lakes and open water. 

Radiation at the water surface was estimated from the solar constant, the latitude of the 

bay, and atmospheric transmissivity over the bay. Estimates of atmospheric transmissivity 

were obtained for three sites around the bay based on long-term observations of average 

daily max/min air temperatures at Flamingo, Royal Palm and Tavernier. Estimated 

average annual bay-wide evaporation given the selected surface characteristic coefficient 

was 137 cm/yr. The monthly evaporation estimates derived from the three transmissivity 

estimates were applied to the five FATHOM regions within the bay using Thiessen 

polygons. 

Alternate 2 

(EV-2) 

Monthly evaporation amount was calculated for five FATHOM regions within the bay using 

the Thornthwaite method based on observed mean monthly air temperatures from the 

NCDC Division 7 data set. The Thornthwaite method does not involve the selection of a 

scalar or coefficient value. Calculated average annual bay-wide evaporation given the 

Division 7 air temperature data was 147 cm/yr. The calculated evaporation amounts were 

applied uniformly over the bay by assigning the same monthly values to all five FATHOM 

regions within the bay. 

Alternate 3 

(EV-3) 

Same as base simulation except the wind function was adjusted to give a bay-wide 

average annual evaporation of 147 cm/yr. 
 108 

5.2.1.3 Boundary Salinity 

The boundary salinity for the MFL base case and the two alternatives, Table 5.5, differ in their 

representation of the temporal variability around the same long-term mean value. The MFL base 

boundary salinity input data are estimated from the regression with the S12T structure flows and 

the P33 water level data, Table 2.1. Boundary Salinity Alternative 1 estimates the boundary 

salinity as the pattern of averages by month of the observed boundary salinity values for the 

period 1992 through 2002. Boundary Salinity Alternative 2 estimates the boundary salinity as 

the average on each boundary for the period 1992 through 2002. 

Table 5.5: MFL base case and alternative boundary salinity input data 

Data Set Description 

MFL Base 

Boundary 

Salinity 

Monthly values of boundary salinity were estimated for three FATHOM boundary regions. 

Monthly salinity along the Gulf of Mexico and Card Sound boundaries were estimated from 

multivariate regressions of observed monthly salinity values (SERC monitoring data) on 

monthly discharges at the S12T structures and monthly water levels in the P33 well, for the 

period 1992-2002 (lag 2 for the Gulf boundary, lag 0 for the Card Sound boundary). 

Monthly salinity values for the Atlantic boundaries were set to the long-term average of 

observed data from monitoring in the Florida Keys National Marine Sanctuary for the 

period 1995-2002. 

Alternate 1 

(BS-1) 

Monthly values of boundary salinity along the Gulf and Card Sound boundaries were 

estimated as the seasonal pattern of observed mean monthly salinity values (SERC 

monitoring data) for the period 1992-2002. (The average seasonal pattern was repeated 

every year). 

Salinity at the Atlantic boundary was the same as in the base simulation. 

Alternate 2 

(BS-2) 

Monthly values of boundary salinity along the Gulf and Card Sound boundaries were 

estimated as the long-term annual mean value of all sites along each boundary (SERC 

monitoring data) for the period 1992-2002. (There was no variation with time or location the 

along boundaries). 

Salinity at the Atlantic boundary is the same as in the base simulation. 

5.2.1.4 Fresh Water Inflow from Wetlands 

The base case and alternative input data for fresh water inflow from wetlands are described in 

section 3.3. 

5.2.1.5 Bottom Friction Parameter 

The value of Manning’s n chosen for the MFL base case is an estimate derived from 

measurements of flow over shallow, grass-covered shoals at two locations in the West region of 

Florida Bay (Fourqurean and Childers, unpub. data). The values of Manning’s n chosen for the 

Friction Parameter Alternate 1 and Friction Parameter Alternate 2, Table 5.6, span the range of 

estimates of Manning’s n at the USGS estuarine creek monitoring stations (Swain et al. 2004). 
 109 

Table 5.6: MFL base case and alternative bottom friction parameter 

Data Set Description 

MFL Base 

Friction 

Coefficient 

Manning’s n (the friction coefficient), used in the hydraulic calculation of flows over the 

banks, was assumed to be constant over time and space. A value of 0.1 (mks systems) 

was used everywhere. The value, 0.1, was based on calculations from flume studies on a 

western bank and also agrees well with calculations based on observed USGS discharges 

in creeks flowing into the northeast of the bay. 

Alternate 1 

(FR-1) 

Manning’s n set equal to 0.2 for hydraulic calculation of flow over the banks, assumed to 

be constant over time and space. 

Alternate 2 

(FR-2) 

Manning’s n set equal to 0.05 for hydraulic calculation of flow over the banks, assumed to 

be constant over time and space. 

5.2.1.6 Bathymetry 

The parameters that describe the bathymetry of Florida Bay in FATHOM consist of the 

information on percent coverage by 1-foot depth class for each basin and for each line segment 

that mark the banks between the basins. Section 2.1 describes how bathymetric information was 

assembled from several sources and applied to estimate the parameter values that comprise the 

MFL bathymetry in FATHOM. The alternative bathymetry parameter sets, Table 5.7, increase 

the depth by 60 percent, first only in the mean depth of the basins, Bathymetry Alternate 1, and 

second in the mean depth of both the basins and the banks, Bathymetry Alternate 2. 

Table 5.7: MFL base and alternative bathymetry parameterization 

Data Set Description 

MFL Base 

Bathymetry 

(see description of the MFL bathymetry in section 2.1)

Alternate 1 

(BT-1) 

Basins – All depths in all basins increased by 60% (depths multiplied by 1.6) 

 Banks – same as in base simulation 

Alternate 2 

(BT-2) 

Basins – All depths in all basins increased by 60% (depths multiplied by 1.6) 

 Banks – All depths along all banks increased by 60% (depths multiplied by 1.6) 

5.2.2 Results 

Measures of model performance are reported for the MFL base case in Tables 5.8 through 5.13. 

Results are reported for Florida Bay as a whole, for each of the feasibility study regions, and for 

the areas of interest to the District for MFL criteria. Each of the columns to the right of the 

results for the base case reports the results of an alternative salinity simulation. In the alternative 
 110 

simulations, the indicated input data or model parameter substitutes for the corresponding input 

data or model parameter in the MFL base case. Substitutions are made one at a time. 

None of the alternatives examined performs generally better than the MFL base case. Values in 

Table 5.8 are highlighted where the model efficiency of an alternative exceeds the model 

efficiency for the MFL base case. Where model efficiencies are higher for an alternative, the 

difference is generally less that five percent higher, and these are balanced by much larger 

decreases in model efficiency for the same alternative at other locations, Table 5.13. The other 

measures of model performance, Tables 5.9 through 5.12, show results that are consistence with 

those for model efficiency. 

The results provide some insight into how uncertainty in the input data and model parameters 

affects the salinity calculations. Overall, the largest effect is seen for boundary salinity, bottom 

friction parameter, and bathymetry, Table 5.14. Model performance is much less sensitive to the 

other alternatives investigated, and response is less coherent spatially. Areas affected by choice 

of boundary salinity are in the West Region, adjacent to the Florida Shelf, and in the far eastern 

portion of the model domain where Florida Bay joins Biscayne Bay. (The eastern-most regions 

are effectively isolated from the rest of Florida Bay by a shallow bank and the Route 1 

causeway.) The same areas affected by choice of the bottom friction parameter are generally 

also affected by bathymetry alternatives, but these do not include the West Region. 

The areas affected by the bottom friction parameter and bathymetry are in the Northeast and 

Central Regions. In these areas, bottom friction and basin volume affect the degree of flushing 

by exchange with the other parts of the bay and the Florida Shelf. Generally, a higher degree of 

flushing, lower residence time, suppresses the ability of water loss by evaporation to generate 

high salinity peaks and the ability of rainfall events and seasonal inflow of fresh water to 

generate low salinity minima. Lower flushing, higher residence time, has the opposite effect. 

Feasibility regions 13, 14, and 14a are also sensitive to the application of the PHAST model to 

describe inflow (RN5). These regions are in the far eastern portion of the model domain where 

simulations are also affected by uncertainty in the boundary conditions with lower Biscayne Bay. 
 111 

Table 5.8: Values of MODEL EFFICIENCY computed for the period 1991 through 2002 from the differesimulated monthly average salinity and salinity measured in water samples taken once every month (n=14indicated. 

Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR

All Florida Bay 81 79 79 80 79 80 80 80 81 79 78 78 73 6

SFWMD Regions

Feasibility Study Region 1 1 65 67 66 68 63 65 62 62 65 65 60 65 56 1

Feasibility Study Region 1a 1a 76 61 59 72 59 67 77 64 77 74 82 75 75 -9 

Feasibility Study Region 5 5 43 37 39 38 43 40 43 43 45 30 31 38 26 3

Feasibility Study Region 2 2 78 70 68 73 68 75 74 75 77 77 82 75 76 4Feasibility Study Region 3 3 58 50 52 55 55 54 59 57 61 45 50 52 47 4Feasibility Study Region 4 4 51 51 51 50 53 52 51 51 51 51 51 30 7 4

Feasibility Study Region 16 16 47 47 47 47 47 47 47 47 47 47 47 30 0 4

Feasibility Study Region 6 6 59 60 58 57 61 61 59 59 59 58 60 46 31 5

Feasibility Study Region 13 13 42 46 48 40 47 43 36 46 42 42 21 39 10 5

Feasibility Study Region 13a 13a 74 74 75 72 75 75 74 74 74 74 75 54 -27 6

Feasibility Study Region 14 14 67 73 72 69 71 75 61 71 67 67 41 56 67 7

Feasibility Study Region 14a 14a 76 77 76 79 74 78 72 77 76 76 45 73 76 5

FATHOM basins

Long Sound 7 77 73 74 76 71 75 81 68 77 77 82 74 50 1

Joe Bay 13 56 61 59 62 56 58 48 56 55 56 44 57 58 6 

Little Madeira (Mouth) 14 76 61 59 72 59 67 77 64 77 74 82 75 75 -9 

Park Key 15 77 52 49 70 50 62 83 65 80 74 84 77 76 1

Duck Key 47 76 79 79 72 75 80 63 80 75 77 76 74 77 5

Butternut Key 46 76 70 68 69 69 75 72 73 75 76 83 72 72 3

Garfield/Rankin 37 43 37 39 38 43 40 43 43 45 30 31 38 26 3

Whipray Basin 34 58 53 53 56 59 57 58 57 57 51 53 51 44 4

Rabbit Key Basin 38 51 51 51 51 52 52 52 51 52 51 51 28 6 5

Notes:

62 efficiency is higher than MFL base case

62 efficency is higher than MFL base case by > 5% 

62 efficency is higher than MFL base case by > 10% 

Location Rainfall Evaporation Wetland Inflow Bnd Salinity M
 112 

Table 5.9: Values of RMSE (root mean squared error) computed for the period 1991 through 2002 from tbetween simulated monthly average salinity and salinity measured in water samples taken once every mon

Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR

All Florida Bay 4.1 4.3 4.3 4.2 4.3 4.2 4.2 4.2 4.1 4.3 4.4 4.4 4.9 5.

SFWMD Regions

Feasibility Study Region 1 1 6.3 6.1 6.2 6.0 6.4 6.2 6.5 6.5 6.3 6.2 6.7 6.3 7.0 10

Feasibility Study Region 1a 1a 4.2 5.3 5.4 4.5 5.4 4.8 4.0 5.0 4.1 4.3 3.6 4.2 4.2 8.

Feasibility Study Region 5 5 5.9 6.2 6.1 6.1 5.9 6.0 5.9 5.9 5.8 6.5 6.5 6.2 6.7 6.Feasibility Study Region 2 2 3.5 4.1 4.2 3.9 4.2 3.7 3.8 3.7 3.6 3.6 3.2 3.7 3.7 5.Feasibility Study Region 3 3 5.1 5.6 5.5 5.3 5.2 5.3 5.0 5.1 4.9 5.8 5.5 5.5 5.7 6.Feasibility Study Region 4 4 2.8 2.8 2.8 2.8 2.7 2.8 2.8 2.8 2.8 2.8 2.8 3.3 3.8 2.

Feasibility Study Region 16 16 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.5 4.2 3.

Feasibility Study Region 6 6 2.9 2.9 3.0 3.0 2.9 2.8 2.9 2.9 2.9 3.0 2.9 3.4 3.8 3.

Feasibility Study Region 13 13 4.7 4.5 4.5 4.8 4.5 4.6 4.9 4.5 4.7 4.7 5.5 4.8 5.8 4.

Feasibility Study Region 13a 13a 2.8 2.8 2.8 2.9 2.8 2.8 2.8 2.8 2.8 2.8 2.8 3.8 6.2 3.

Feasibility Study Region 14 14 3.6 3.2 3.3 3.5 3.3 3.1 3.9 3.3 3.6 3.6 4.7 4.1 3.5 3.

Feasibility Study Region 14a 14a 4.1 4.0 4.1 3.9 4.2 3.9 4.4 4.0 4.1 4.1 6.2 4.3 4.1 5.

FATHOM basins

Long Sound 7 4.3 4.7 4.6 4.5 4.9 4.6 3.9 5.1 4.3 4.4 3.8 4.7 6.4 8.

Joe Bay 13 7.7 7.2 7.4 7.1 7.7 7.5 8.3 7.7 7.8 7.7 8.6 7.6 7.5 11

Little Madeira (Mouth) 14 4.2 5.3 5.4 4.5 5.4 4.8 4.0 5.0 4.1 4.3 3.6 4.2 4.2 8.

Park Key 15 3.7 5.4 5.5 4.3 5.5 4.8 3.2 4.6 3.5 3.9 3.1 3.8 3.8 7.

Duck Key 47 3.7 3.5 3.5 4.0 3.8 3.3 4.6 3.3 3.8 3.6 3.7 3.9 3.6 5.

Butternut Key 46 3.5 3.9 4.0 3.9 3.9 3.5 3.8 3.6 3.5 3.5 2.9 3.7 3.7 5.

Garfield/Rankin 37 5.9 6.2 6.1 6.1 5.9 6.0 5.9 5.9 5.8 6.5 6.5 6.2 6.7 6.

Whipray Basin 34 4.5 4.7 4.7 4.5 4.4 4.5 4.4 4.5 4.5 4.8 4.7 4.8 5.1 5.

Rabbit Key Basin 38 2.6 2.6 2.6 2.6 2.5 2.5 2.6 2.6 2.5 2.6 2.6 3.1 3.6 2.

Location Rainfall Evaporation Wetland Inflow Bnd Salinity M
 113 

Table 5.10: Values of MEAN ERROR computed for the period 1991 through 2002 from the difference betmonthly average salinity and salinity measured in water samples taken once every month (n=144). High v

Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR

All Florida Bay -0.1 0.8 0.9 0.2 0.8 0.7 -0.7 0.6 -0.4 0.2 -0.5 -0.3 0.8 2.

SFWMD Regions

Feasibility Study Region 1 1 0.0 1.0 1.0 0.3 0.9 0.9 -1.6 1.9 0.0 0.0 -1.0 -0.2 1.5 8.

Feasibility Study Region 1a 1a 1.3 3.2 3.5 1.7 3.4 2.9 -0.4 3.1 0.9 1.6 -0.4 1.0 1.2 7.

Feasibility Study Region 5 5 1.5 2.0 1.9 1.8 1.9 2.1 1.5 1.5 0.2 2.9 2.9 1.2 1.6 1.Feasibility Study Region 2 2 -0.2 1.7 2.0 0.2 1.8 1.4 -1.4 1.0 -0.5 0.1 -0.4 -0.4 -0.1 3.Feasibility Study Region 3 3 1.0 1.8 1.8 1.4 1.8 2.1 0.9 1.2 -0.3 2.5 2.2 0.7 1.0 1.Feasibility Study Region 4 4 -0.2 -0.1 -0.1 -0.2 -0.1 -0.1 -0.2 -0.2 -0.3 -0.2 -0.2 -0.5 -0.5 -0

Feasibility Study Region 16 16 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.1 0.4 0.

Feasibility Study Region 6 6 -0.5 -0.1 -0.1 -0.4 -0.1 -0.1 -0.7 -0.4 -0.7 -0.3 -0.4 -0.7 -0.9 -0

Feasibility Study Region 13 13 -1.3 -0.6 -0.8 -1.0 -0.8 -0.8 -1.9 -0.8 -1.4 -1.3 -3.0 -1.5 2.5 1.

Feasibility Study Region 13a 13a -0.1 0.4 0.3 0.1 0.3 0.2 -0.2 0.1 -0.1 -0.1 -0.5 0.0 4.6 0.

Feasibility Study Region 14 14 -1.9 -0.5 -0.9 -1.7 -0.8 -1.0 -2.5 -1.3 -1.9 -1.9 -3.7 -2.1 1.3 0.

Feasibility Study Region 14a 14a -1.1 -0.1 -0.4 -0.7 -0.4 -0.4 -2.2 0.0 -1.1 -1.2 -4.7 -1.4 2.1 4.

FATHOM basins

Long Sound 7 1.9 2.6 2.4 2.3 2.4 2.5 0.7 3.2 1.9 1.9 -1.5 1.7 4.9 7.

Joe Bay 13 -1.9 -0.7 -0.5 -1.6 -0.6 -0.7 -3.8 0.7 -2.0 -1.8 -0.6 -2.1 -1.9 9.

Little Madeira (Mouth) 14 1.3 3.2 3.5 1.7 3.4 2.9 -0.4 3.1 0.9 1.6 -0.4 1.0 1.2 7.

Park Key 15 2.0 4.1 4.4 2.3 4.2 3.8 0.7 3.3 1.5 2.4 1.4 1.7 1.9 5.

Duck Key 47 -1.6 0.7 1.0 -1.2 0.8 0.3 -3.1 0.0 -1.8 -1.4 -1.6 -1.9 -1.2 2.

Butternut Key 46 -0.2 1.6 1.8 0.2 1.6 1.2 -1.4 1.0 -0.4 0.0 -0.3 -0.4 0.0 3.

Garfield/Rankin 37 1.5 2.0 1.9 1.8 1.9 2.1 1.5 1.5 0.2 2.9 2.9 1.2 1.6 1.

Whipray Basin 34 0.2 0.9 0.9 0.5 0.8 1.1 0.1 0.3 -0.9 1.3 1.1 -0.1 0.1 0.

Rabbit Key Basin 38 0.0 0.0 0.0 0.0 0.1 0.0 -0.1 0.0 -0.1 0.0 0.0 -0.4 -0.4 -0

Location Rainfall Evaporation Wetland Inflow Bnd Salinity M
 114 

Table 5.11: Values of AVERAGE ABSOLUTE ERROR computed for the period 1991 through 2002 from between simulated monthly average salinity and salinity measured in water samples taken once every monvalues are indicated. 

Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR

All Florida Bay 3.1 3.2 3.3 3.2 3.2 3.1 3.1 3.2 3.0 3.2 3.3 3.3 3.8 4.

SFWMD Regions

Feasibility Study Region 1 1 4.5 4.6 4.6 4.4 4.8 4.6 4.5 5.0 4.5 4.5 4.7 4.6 5.6 8.

Feasibility Study Region 1a 1a 3.3 4.4 4.5 3.7 4.4 3.9 3.2 4.1 3.2 3.4 2.7 3.3 3.4 7.

Feasibility Study Region 5 5 4.5 4.7 4.7 4.9 4.4 4.7 4.5 4.5 4.5 5.1 5.0 4.7 5.4 4.Feasibility Study Region 2 2 2.9 3.4 3.5 3.1 3.5 3.1 3.0 3.1 2.9 2.9 2.6 3.0 3.0 4.Feasibility Study Region 3 3 4.1 4.5 4.4 4.3 4.2 4.3 4.1 4.2 3.9 4.8 4.5 4.4 4.7 4.Feasibility Study Region 4 4 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.5 3.0 2.

Feasibility Study Region 16 16 2.1 2.2 2.1 2.2 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.6 3.1 2.

Feasibility Study Region 6 6 2.3 2.3 2.4 2.4 2.3 2.3 2.3 2.3 2.3 2.4 2.3 2.7 3.1 2.

Feasibility Study Region 13 13 3.3 3.2 3.1 3.5 3.1 3.3 3.5 3.2 3.3 3.2 4.1 3.3 5.0 3.

Feasibility Study Region 13a 13a 2.2 2.2 2.2 2.3 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.8 5.5 2.

Feasibility Study Region 14 14 2.8 2.5 2.6 2.7 2.6 2.4 3.1 2.6 2.8 2.8 4.1 3.2 2.8 2.

Feasibility Study Region 14a 14a 3.2 3.1 3.2 3.0 3.4 3.0 3.6 3.1 3.2 3.2 5.5 3.4 3.2 4.

FATHOM basins

Long Sound 7 3.4 3.8 3.7 3.6 3.9 3.7 3.0 4.2 3.4 3.4 2.9 3.6 5.7 7.

Joe Bay 13 5.6 5.4 5.5 5.2 5.7 5.5 6.0 5.8 5.6 5.6 6.4 5.6 5.5 10

Little Madeira (Mouth) 14 3.3 4.4 4.5 3.7 4.4 3.9 3.2 4.1 3.2 3.4 2.7 3.3 3.4 7.

Park Key 15 3.1 4.7 4.9 3.6 4.7 4.2 2.6 4.0 2.9 3.4 2.5 3.2 3.2 6.

Duck Key 47 3.0 2.7 2.8 3.1 2.9 2.7 3.8 2.7 3.1 3.0 3.0 3.2 2.9 4.

Butternut Key 46 2.8 3.3 3.4 3.2 3.3 2.9 2.9 3.0 2.8 2.8 2.3 2.9 2.9 5.

Garfield/Rankin 37 4.5 4.7 4.7 4.9 4.4 4.7 4.5 4.5 4.5 5.1 5.0 4.7 5.4 4.

Whipray Basin 34 3.6 3.8 3.8 3.7 3.5 3.6 3.6 3.6 3.6 3.9 3.8 3.8 4.2 4.

Rabbit Key Basin 38 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 2.2 2.7 1.

Location Rainfall Evaporation Wetland Inflow Bnd Salinity M
 115 

Table 5.12: Values of R-SQUARED computed for the period 1991 through 2002 from the difference betwmonthly average salinity and salinity measured in water samples taken once every month (n=144). Low va

Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR

All Florida Bay 0.90 0.89 0.89 0.89 0.89 0.90 0.90 0.90 0.90 0.89 0.89 0.88 0.86 0.8

SFWMD Regions

Feasibility Study Region 1 1 0.81 0.82 0.82 0.83 0.80 0.81 0.80 0.81 0.81 0.81 0.78 0.80 0.77 0.8

Feasibility Study Region 1a 1a 0.89 0.88 0.88 0.88 0.87 0.89 0.89 0.89 0.89 0.89 0.91 0.89 0.89 0.8

Feasibility Study Region 5 5 0.69 0.67 0.68 0.66 0.72 0.69 0.69 0.69 0.67 0.69 0.69 0.65 0.55 0.6Feasibility Study Region 2 2 0.89 0.89 0.88 0.87 0.87 0.89 0.89 0.89 0.89 0.89 0.91 0.89 0.90 0.8Feasibility Study Region 3 3 0.80 0.76 0.78 0.77 0.82 0.80 0.80 0.80 0.79 0.78 0.79 0.77 0.72 0.7Feasibility Study Region 4 4 0.75 0.74 0.75 0.74 0.76 0.75 0.75 0.75 0.75 0.75 0.75 0.60 0.35 0.7

Feasibility Study Region 16 16 0.70 0.70 0.70 0.70 0.70 0.70 0.70 0.70 0.70 0.70 0.70 0.55 0.19 0.7

Feasibility Study Region 6 6 0.87 0.87 0.87 0.85 0.89 0.87 0.87 0.87 0.87 0.87 0.88 0.85 0.73 0.8

Feasibility Study Region 13 13 0.79 0.79 0.80 0.79 0.80 0.79 0.79 0.79 0.79 0.79 0.81 0.73 0.70 0.7

Feasibility Study Region 13a 13a 0.87 0.87 0.87 0.85 0.88 0.87 0.87 0.87 0.87 0.87 0.87 0.77 0.73 0.8

Feasibility Study Region 14 14 0.88 0.87 0.87 0.89 0.86 0.88 0.88 0.88 0.88 0.88 0.89 0.91 0.92 0.9

Feasibility Study Region 14a 14a 0.89 0.88 0.87 0.89 0.87 0.89 0.89 0.88 0.89 0.89 0.88 0.90 0.91 0.9

FATHOM basins

Long Sound 7 0.90 0.90 0.90 0.91 0.89 0.90 0.91 0.90 0.90 0.90 0.92 0.89 0.89 0.8

Joe Bay 13 0.77 0.79 0.77 0.81 0.75 0.76 0.78 0.75 0.76 0.77 0.67 0.78 0.78 0.8

Little Madeira (Mouth) 14 0.89 0.88 0.88 0.88 0.87 0.89 0.89 0.89 0.89 0.89 0.91 0.89 0.89 0.8

Park Key 15 0.93 0.91 0.92 0.92 0.90 0.93 0.93 0.93 0.93 0.93 0.94 0.94 0.94 0.9

Duck Key 47 0.90 0.90 0.90 0.87 0.87 0.90 0.90 0.90 0.90 0.90 0.90 0.90 0.90 0.8

Butternut Key 46 0.89 0.90 0.89 0.85 0.88 0.89 0.88 0.89 0.89 0.89 0.92 0.89 0.89 0.8

Garfield/Rankin 37 0.69 0.67 0.68 0.66 0.72 0.69 0.69 0.69 0.67 0.69 0.69 0.65 0.55 0.6

Whipray Basin 34 0.78 0.75 0.76 0.76 0.81 0.78 0.78 0.78 0.77 0.77 0.78 0.76 0.68 0.7

Rabbit Key Basin 38 0.73 0.73 0.73 0.73 0.74 0.74 0.74 0.73 0.74 0.73 0.73 0.56 0.32 0.7

Location Rainfall Evaporation Wetland Inflow Bnd Salinity M
 116 

Table 5.13: Values of MODEL EFFICIENCY computed for the period 1991 through 2002 from the differsimulated monthly average salinity and salinity measured in water samples taken once every month (n=14indicated; otherwise contents are identical to Table 5.7. 

Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR

All Florida Bay 81 79 79 80 79 80 80 80 81 79 78 78 73 64 

SFWMD Regions

Feasibility Study Region 1 1 65 67 66 68 63 65 62 62 65 65 60 65 56 12 

Feasibility Study Region 1a 1a 76 61 59 72 59 67 77 64 77 74 82 75 75 -9 

Feasibility Study Region 5 5 43 37 39 38 43 40 43 43 45 30 31 38 26 34 Feasibility Study Region 2 2 78 70 68 73 68 75 74 75 77 77 82 75 76 43 

Feasibility Study Region 3 3 58 50 52 55 55 54 59 57 61 45 50 52 47 41 

Feasibility Study Region 4 4 51 51 51 50 53 52 51 51 51 51 51 30 7 49 

Feasibility Study Region 16 16 47 47 47 47 47 47 47 47 47 47 47 30 0 47 

Feasibility Study Region 6 6 59 60 58 57 61 61 59 59 59 58 60 46 31 50 

Feasibility Study Region 13 13 42 46 48 40 47 43 36 46 42 42 21 39 10 53 

Feasibility Study Region 13a 13a 74 74 75 72 75 75 74 74 74 74 75 54 -27 66 

Feasibility Study Region 14 14 67 73 72 69 71 75 61 71 67 67 41 56 67 74 

Feasibility Study Region 14a 14a 76 77 76 79 74 78 72 77 76 76 45 73 76 52 

FATHOM basins

Long Sound 7 77 73 74 76 71 75 81 68 77 77 82 74 50 14 

Joe Bay 13 56 61 59 62 56 58 48 56 55 56 44 57 58 6 

Little Madeira (Mouth) 14 76 61 59 72 59 67 77 64 77 74 82 75 75 -9 

Park Key 15 77 52 49 70 50 62 83 65 80 74 84 77 76 16 

Duck Key 47 76 79 79 72 75 80 63 80 75 77 76 74 77 54 

Butternut Key 46 76 70 68 69 69 75 72 73 75 76 83 72 72 33 

Garfield/Rankin 37 43 37 39 38 43 40 43 43 45 30 31 38 26 34 

Whipray Basin 34 58 53 53 56 59 57 58 57 57 51 53 51 44 44 

Rabbit Key Basin 38 51 51 51 51 52 52 52 51 52 51 51 28 6 50 

Notes:

30 efficency is lower than MFL base case

30 efficency is lower than MFL base case 

Location Rainfall Evaporation Wetland Inflow Bnd Salinity Ma

by > 20% 

 by > 40% 
 117 

5.3 Comparison of Base Case and Measured Inflow – 1996 through 2000 

In addition to the analysis using the input alternatives described above, salinity calculations were 

made using the data that directly measure the inputs required by FATHOM. These data include 

rainfall measured at the Everglades Park marine monitoring stations, boundary salinity based on 

the SERC monitoring data, and the USGS measured inflows from the Taylor Slough C111 

wetland basin. Salinity calculations based on the direct data span the period February 1996 

through October 2000, which is the period of record for the USGS flow data available to this 

project. Details of the compilation of these data are presented in Progress Report 1 (Mark I run). 

A comparison of model performance over this period using the MFL base case inputs with the 

FATHOM simulation using inputs based on direct local measurements provides information on 

the error in the calculated salinity that arises from using input data estimated from regional 

indices instead of direct measurements of the inputs. The results of this comparison, Table 5.14, 

show that there is no overall degradation in model performance related to using the estimated 

input data; bay-wide efficiency is 80 percent for the MFL base case compared to 78 percent for 

input data based on locally observed data. 

The reason for this can be seen from the detailed results by region within the Bay (Appendices D 

and H). The local observed data provide a better description of the boundary salinity, and this is 

reflected in higher model efficiencies in the West Region of the Bay using observed data . 

However, the local observed inflow, based on the measured USGS creek flow is a biased 

estimate of the actual inflow because ungauged flows are not included. By including an estimate 

of ungauged inflow to the Central Region, the MFL base case improves model performance in 

the Central Region of the Bay. 

The use of this comparison of model performance must remain in context. The model 

efficiencies in Table 5.12 and in Appendices D and H using the observed data were based on 

model input data and observed salinities in the sub-basins for the period 1996-2000. The model 

efficiencies for the use of the indirect regional data for the MFL base case model were computed 

using observed salinity values for the period 1991-2000, even though the base case model 

produced salinity estimates for 1970-2000. Even so, it appears that the use of indirect regional 

data to estimate FATHOM input data when observed values are not available produces a 

reasonable estimate of salinity over the longer time periods. 
 118 

Table 5.14: Values of MODEL EFFICIENCY computed for the period February 1996 

through October 2000 from the difference between simulated monthly average salinity and 

salinity measured in water samples taken once every month (n=56). 

Location base observed

case inputs

All Florida Bay 80 78

SFWMD Regions

Feasibility Study Region 1 1 57 53

Feasibility Study Region 1a 1a 64 52

Feasibility Study Region 5 5 45 20

Feasibility Study Region 2 2 68 71

Feasibility Study Region 3 3 57 26

Feasibility Study Region 4 4 53 77

Feasibility Study Region 16 16 47 74

Feasibility Study Region 6 6 62 66

Feasibility Study Region 13 13 36 41

Feasibility Study Region 13a 13a 76 86

Feasibility Study Region 14 14 21 21

Feasibility Study Region 14a 14a 67 54

FATHOM basins

Long Sound 7 81 65

Joe Bay 13 44 46

Little Madeira (Mouth) 14 64 52

Park Key 15 65 39

Duck Key 47 51 74

Butternut Key 46 66 74

Garfield/Rankin 37 45 20

Whipray Basin 34 60 46

Rabbit Key Basin 38 52 77

Notes:

62 efficiency is lower than MFL base case by > 10% 

62 efficency is higher than MFL base case by > 10%
 119 

6 DEVELOPMENT AND DESCRIPTION OF A WATER BUDGET - 

1970-2000 

Input data assembled for the MFL base case provide the best estimates for components of the 

fresh water budget in Florida Bay as estimated from FATHOM salinity estimates. This section 

summarizes key aspects of the water budget for the period 1970 through 2000, including the 

influence of water management activities and it presents results of an analysis to identify where 

in the Bay salinity is sensitive to changes in inflow from the Taylor Slough C111 wetland basin. 

Water management activities since 1970 have altered surface flows in the Taylor Slough C111 

wetland sub-basin. In particular, the completion around 1980 of the first phase of the South 

Dade Conveyance System markedly increased surface water discharge into the wetlands directly 

upstream from Florida Bay. Comparing the inflow component of the annual average fresh water 

budget for the Bay pre-1980 and post-1980 reveals the effect of this change. 

The summary of the water budget is presented in two parts. In the first part, average values of 

component fluxes by month illustrate their relative magnitude and seasonal variation. The 

second part compares components of the water budget for dry, wet, and average years to 

characterize the range of year-to-year variations. In this analysis, the water year provides the 

basis for compiling the water budget. The water year synchronizes with the seasonal variation in 

rainfall – the 1990 water year begins 1 November 1989 and ends on 31 October 1990. 

The analysis to identify areas where inflow from the wetlands affects salinity is based on the 

maximum salinity in a calendar year. The calendar year synchronizes with the seasonal variation 

of salinity in Florida Bay. The sensitivity of maximum annual salinity is of interest because the 

purpose for setting MFL criteria is to protect Florida Bay from ecological harm during extended 

periods of water shortage. Over the Bay as a whole, inflow from the wetlands makes a small 

contribution to the water budget compared to the amount of fresh water contributed by rainfall. 

However in near-shore areas, close to the estuarine creeks where inflow enters the Bay, inflow 

from wetlands and rainfall are comparable in magnitude. Analysis of the MFL base case 

simulation identifies locations where year-to-year changes in the volume of inflow from 

wetlands explain a significant portion of the year-to-year variation in maximum salinity that is 

separate from the effect of rainfall. 

6.1 Changes to Water Management Operations 1960-2000 

Water management activities that currently have the most direct effect on the supply of fresh 

water to Florida Bay began with the completion of the Central and Southern Florida Project in 

the early 1960’s. The completion of the Tamiami Trail levee and the S12 flow control structures 

in 1962 and the C111 Canal in 1968 allowed water managers for the first time to fully regulate 

the flow of surface water into Everglades Park and adjacent estuarine areas, including Florida 

Bay. Prior efforts since the late 1800s to drain the main body of the original Everglades had 

already irreversibly altered hydrological conditions throughout South Florida. These efforts 

interrupted the flow of water southward out of Lake Okeechobee into the Everglades and 

increased the volume of water draining east into the Atlantic Ocean. 
 120 

By the early 1970s, there was sufficient concern over the consequences of water management on 

Everglades National Park and in Florida Bay to motivate a series of actions intended to mitigate 

the effects of the structures and practices recently put in place. Modifications to the water 

management system and the operations continued over the next 30 years, (Table 6.1). Beginning 

in the late 1970s, a program of minimum prescribed water deliveries set monthly targets for the 

quantity of water to be supplied to Shark Slough, across Tamiami Trail, to Florida Bay through 

the C111 Canal, and for discharge into the headwaters of Taylor Slough. The Experimental 

Water Deliveries program replaced the minimum monthly delivery targets, but it continued to 

pursue the objective of increasing water deliveries to Florida Bay. 

Changes to water management activities that occurred around 1981 stand out as significant for 

the water budget of Florida Bay. Beginning in the early 1970s and continuing until about the 

mid-1980s, the implementation of the South Dade Conveyance System (SDCS) project enhanced 

flood protection in southern Miami-Dade County and further altered the hydrology in the region 

east of the headwaters of Taylor Slough, near the main entrance to Everglades National Park. 

The records of surface water discharge at Taylor Slough bridge (TSB) and at the S175 and S18C 

structures, document that a large increase in surface flow into the Taylor Slough - C111 Canal 

sub-basin occurred around 1980 and has continued, (Figure 3.2). 

The net effect of these more recent changes has not been as large as the increase in flow that 

occurred around 1981.In the early 1980’s, flooding concerns in Miami-Dade County prompted 

additional operational changes to the SDCS in an attempt to alleviate flooding and also provide 

additional fresh water to Everglades National Park. Additional operational modifications were 

made in the 1990’s in an attempt to restore flows and water levels in Taylor Slough. Structural 

changes were also planned and made to implement a more even distribution of flows from the C111 Canal across the mangroves. 
 121 

 Table 6.1: Water management activities affecting Florida Bay, 1960 through 2000 

Period Water Management Activities 

1960 - 

1969 

• Construction of the levee and S12 control structures completed in 1962. This blocks free 

flow of surface water into Everglades Park from wetland areas north of Tamiami Trail. 

Initially, there are no outlets through this dike to supply water into northeast Shark Slough 

and the headwaters of Taylor Slough. 

• Construction begins on C111 and associated canals that will alter the hydrology in south 

Miami-Dade County, adjacent to the headwaters for Taylor Slough and north of the 

freshwater wetlands and mangrove transition in the southwest portion of the Park. 

Initially the S173 structure limits the amount of flow that can occur from the wetlands 

north of Tamiami Trail into southern Miami-Dade county and Florida Bay. 

• Drainage of south Miami-Dade agricultural lands decreases water flow to the mangrove 

transition zone through the finger glades. 

• C111 canal and its control structures are completed in 1968. The C111 canal 

establishes a hydrologically significant new breach for flow through the coastal ridge, 

parallel to Taylor Slough. An earthen plug is installed at present location of S197 

structure to prevent salt-water intrusion by maintaining water levels above sea level in 

the lower reaches of the C111 canal. 

1970 - 

1979 

• Congressionally mandated Minimum Schedule Water Deliveries (MSWD) into 

Everglades Park begins in 1970 in response to concerns that not enough water is 

reaching Taylor Slough and other areas of the Park. 

• Work begins on the South Dade Conveyance System (SDCS) that is needed to 

implement the MSWD to Taylor Slough. The first phase of work is completed in 1980 

with installation of the S332 pump to deliver water to Taylor Slough. 

1980 - 

1989 

• High water levels and flooding in Miami-Dade County during 1981-1983 prompt changes 

in the SDCS. The plug at S197 is removed several times to allow free discharge of flood 

waters through the C111 canal; this eventually leads to construction (in 1992) of the 

present, gated control structure. The S133 pump is installed to increase the capacity to 

move water from wetlands north of Tamiami Trail into southern Miami-Dade County 

through the C111 and L31N canals. 

• Increased flows in C111 canal initially discharge into wetlands and Florida Bay through 

Long Sound, flowing along the eastern boundary of the Park formed by US Route 1. In 

1987, discharge from the C111 canal accounts for 90% of surface water delivered to the 

wetlands north of Florida Bay. Changes in water management operations supply more 

water to Taylor Slough over the next five years. 

• Beginning in 1983, the Experimental Water Deliveries program establishes operational 

goals for water deliveries to Everglades Park; this effectively replaces the MSWD goals. 

This program will institute a succession of changes in water management operations 

over the next 15 years. 

1990 - 

2000 

• Marked changes in the ecology of Florida Bay motivate actions to further increase water 

deliveries to Florida Bay through Taylor Slough and redistribute discharge from the C111 

canal west, into Joe Bay and away from Long Sound. 

• Capacity of the S332 pumps feeding water into Taylor Slough is increased in 1993 and 

again in 1994. Impediments to surface flow within Taylor Slough are decreased by 

removing a portion of the Old Ingram Highway and by widening the bridge where the 

main Park road crosses the slough (completed in 2000). 

• In 1992, the Modified Water Deliveries General Design Memorandum establishes a 

strategy for restoring flow and water levels in the portion of Everglades Park that feeds 

the headwater of Taylor Slough: implementation of this plan has been delayed. 

• In 1997, removal of the spoil mound along the C111 canal, south of S18C, allows a more 

even east-west distribution of discharge into the wetlands north of Florida Bay. 
 122 

6.2 Summary of Water Budget for Florida Bay 

For analysis of seasonal variation the water budget components by month are summarized four 

ways – for two reporting periods, 1970 through 2000 and 1996 through 2000, and for two 

regions, the entire Bay and the Central and Northeast Regions combined. The period 1996 

through 2000 corresponds to the period in which inflow from the wetlands is best known, 

because data are available from the USGS estuarine creek monitoring stations (Figure 1.4). 

Rainfall during this period has been more moderate compared to the longer historical period. All 

of the freshwater inflow from wetlands enters the Bay through the central and northeast regions 

of Florida Bay. Therefore, inflow from wetlands is a more important source of fresh water for 

these regions than for Florida Bay as a whole. The compilation of the water budget separately 

for the Central and Northeast Regions and for the whole Bay reflects this difference. 

Rainfall and evaporation dominate the fresh water budget, (Figures 6.1 and 6.2); the fluxes 

plotted in these figures are calculated from the MFL base case input data. The results obtained 

here are similar to results obtained previously by Nuttle et al. (2000). The magnitude of inflow 

is typically about ten percent of magnitude of rainfall over the whole Bay. The relative 

importance of inflow doubles in the water budget for just the central and northeast regions. 

Changes in salinity are driven by the net supply of fresh water, i.e. rainfall plus inflow minus 

evaporation. Changing the amount and timing of fresh water inflow from wetlands can affect the 

net supply of fresh water, and thus salinity, but this would require large changes in inflow from 

the wetlands. 

For analysis of year-to-year variation, components of the water budget are compared for 

“typical” wet, dry and normal years. Variation in regional rainfall determines the overall pattern 

of wet, dry and normal hydrologic conditions. However, for a given year, rainfall in Florida Bay 

may reflect normal or wet conditions at the same time that conditions in the upstream Everglades 

generally are dry, c.f. 1976 in Table 6.2 and Figure 6.3. For this analysis, water year rainfall 

amounts typical for the Everglades (Shark Slough and the Water Conservation Areas) were taken 

from the Florida Climate Division 5 rainfall. Florida Climate Division 5 rainfall is a data 

product compiled by the National Climatic Data Center - NOAA. Rainfall in Florida Bay has the 

more immediate effect on salinity as the largest source of fresh water, but water management 

decisions for inflow from the wetlands are made based on regional rainfall conditions over the 

Everglades. 

 

For consistency with respect to both conditions affecting Florida Bay and rainfall conditions 

most relevant to water management operations, the years 1970 – 2000 were ranked based on 

rainfall for the Bay (MFL base case) and for the Everglades (NCDC Division 5) separately, 

(Table 6.2). The NCDC Division 5 rainfall data are the long-term data for the region that 

includes most of south and southwest Florida including the Everglades, but does not include the 

east coast of south Florida or the Florida Keys. Wet, normal, and dry years were selected as years 

ranking near the 10%, 50%, and 90% exceedance level on both ranked lists. Years in which 

rainfall in Florida Bay and over the Everglades differ markedly were excluded from the selection 

of wet, normal and dry years. 

 

As discussed in Section 6.1, water management activities increased surface water discharge into 

the Taylor Slough - C111 wetland sub-basin around 1980. Surface flows increased by about a 
 123 

factor of four relative to rainfall at this time. This is perhaps the most significant change that 

occurred in Florida Bay’s fresh water budget during the period 1970 through 2000. To account 

for this change, normal and dry years were defined in both the pre-1980 and post-1980 periods 

for comparison. It is judged that the pre-1980 period does not contain a 90% exceedance wet 

year for the available data. 

The summary water budget fluxes for Florida Bay and the adjacent wetland basin are reported in 

Table 6.3 for the wet, normal, and dry years; pre-1980 and post-1980. The wetland water budget 

fluxes follow the naming conventions as defined in Figure 6.4. These can be compared to the 

flux estimates compiled for the upstream wetland basins from local direct measurements in 1996 

through 2000 in Figure 3.5. Significantly, the additional inflow to the wetland basins in the post1980 period is comparable to the difference between wet year and normal year rainfall and 

between normal year and dry year rainfall, (Table 6.3). 
 124 

Figure 6.1: Monthly average fluxes in the fresh water budget of Florida Bay for the period 

1970 through 2000; A) budget for entire Bay, B) budget for Central and Northeast regions 

only. 

 A 

 B 

Avg Water Budget 1970-2000

(all regions, by water year)

-300

-200

-100

0

100

200

300

400

N D J FM AM J J AS O

Acre-Feet/Month

Rainfall

Evaporation

Net

Inflow

Avg Water Budget 1970-2000

(all regions, by water year)

-300

-200

-100

0

100

200

300

400

N D J FM AM J J AS O

Acre-Feet/Month

Rainfall

Evaporation

Net

Inflow
 125 

Figure 6.2: Monthly average fluxes in the fresh water budget of Florida Bay for the period 

1996 through 2000; A) budget for entire Bay, B) budget for Central and Northeast regions 

only. 

 A 

 

B 
 126 

Table 6.2: Selection of Wet, Dry and Normal water years in the pre-1980 and post-1980 

periods. Annual rainfall is reported in inches both for Florida Bay (MFL base case) and 

for Everglades (NCDC region 5) regional rainfall. Regional differences result in individual 

years ranking differently based on total annual rainfall. The selection of specific Wet, Dry 

and Normal years preserves continuity between the two regions. 

Dry

Norma

Wet

1989 31.7 1976 41.4

1971 34.7 1971 42.72

1986 35.7 1985 44.02

1974 36.2 2000 44.45

1985 40.9 1990 44.71

1990 41.4 1981 44.81

2000 43.4 1977 45.55

1980 43.5 1972 46.53

1984 43.6 1989 46.55

1977 45.4 1988 46.91

1970 45.9 1980 47.03

1994 46.3 1996 47.38

1979 49.2 1974 47.85

1992 49.5 1975 48.62

1987 49.6 1997 48.97

1996 50.4 1987 49.78

1975 51.4 1986 50.5

1991 52.4 1984 50.91

1976 54.0 1973 51.09

1993 54.9 1992 52.31

1998 55.0 1994 53.6

1978 55.6 1979 53.69

1972 55.7 1993 55.15

1997 57.5 1978 55.67

1973 60.8 1970 57.46

1982 61.3 1991 57.53

1988 63.6 1998 57.56

1981 63.8 1983 59.8

1999 67.3 1982 60.41

1983 71.7 1999 63.22

1995 72.4 1995 78.2

Water 

Year

Fl. Bay 

Rainfall

Water 

Year

Div. 5 

Rainfall

Dry

Normal

Wet

1989 31.7 1976 41.4

1971 34.7 1971 42.72

1986 35.7 1985 44.02

1974 36.2 2000 44.45

1985 40.9 1990 44.71

1990 41.4 1981 44.81

2000 43.4 1977 45.55

1980 43.5 1972 46.53

1984 43.6 1989 46.55

1977 45.4 1988 46.91

1970 45.9 1980 47.03

1994 46.3 1996 47.38

1979 49.2 1974 47.85

1992 49.5 1975 48.62

1987 49.6 1997 48.97

1996 50.4 1987 49.78

1975 51.4 1986 50.5

1991 52.4 1984 50.91

1976 54.0 1973 51.09

1993 54.9 1992 52.31

1998 55.0 1994 53.6

1978 55.6 1979 53.69

1972 55.7 1993 55.15

1997 57.5 1978 55.67

1973 60.8 1970 57.46

1982 61.3 1991 57.53

1988 63.6 1998 57.56

1981 63.8 1983 59.8

1999 67.3 1982 60.41

1983 71.7 1999 63.22

1995 72.4 1995 78.2

Water 

Year

Fl. Bay 

Rainfall

Water 

Year

Div. 5 

Rainfall
 127 

Figure 6.3: Annual rainfall (water year basis) for period 1970 through 2000 showing 

selected Wet, Dry and Normal years. 

Figure 6.4: Wetland sub basins used to estimate fresh water inflow from the wetlands in 

the Taylor Slough C111 wetland basin. The locations of the MFLx flow transects are show 

superimposed on the SFWMM grid (see Table 6.3). 

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

RPL

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

15 20 25 30

10

5

MFL5

MFL9

MFL1

MFL2MFL3

MFL6 MFL7

MFL8

MFL10

S175

S18C

S197

TSB

MFL4

EPSW

CP

Long Pine Basin Taylor Slough Basin C111 Basin

RPL
 128 

Table 6.3: Summary of water budget components for Florida Bay and the Taylor Slough C111 wetland bafor reference map). 

(flows in 10^3 ac-ft/yr reported for water year; water year 1995 = Nov 1994 thru Oct 1995)

1. Rainfall

2. Evaporation

Net from Atmosphere

3. MFL6 - Taylor Slough bridge and S-1754. MFL2 - flow from Long Pine basin5. MFL9 - inflow to Madeira, Little Madeira6. MFL7 - S18c flow7. MFL3 - flow from Taylor Slough basin8. MFL4 - outflow via S197 to Manatee Bay9. MFL10 - inflow to Joe Bay and Long 

Sound

10. MFL5 - flow across Park road11. MFL1 - flow across Park road12. MFL2 - flow to Taylor Slough13. MFL8 - inflow to McCormick Creek and 

central region

14.15.

nd - no data available

Source of Freshwater InputsDirect Freshwater InputsFreshwater Inputs from Mangrove Transition Zone (5+9+13)Inflow from wetlandsBudget for Taylor Slough subbasin:Budget for C-111 subbasin:Budget for Long Pine subbasin:Freshwater Inputs from All Sources (1+5+9+13)

Wet 

Season

Dry 

Season

Total Wet 

Season

Dry 

Season

Total Wet 

Season

Dry 

Season

Total Wet 

Season

Dry 

Season

To

452 78 530 472 306 778 395 245 640 576 218 7

-428 -445 -873 -420 -477 -896 -503 -536 -1039 -377 -380 -7

23 -367 -344 52 -171 -119 -108 -291 -399 199 -162 3

1 0 1 7 0 7 18 0 18 56 31 8

nd nd nd nd nd nd nd nd nd nd nd n

2 0 2 7 1 8 9 2 11 19 7 2

2 1 3 23 0 23 57 10 67 115 32 1

nd nd nd nd nd nd nd nd nd nd nd n

0 0 0 0 0 0 0 0 0 27 0 2

14 1 15 48 7 54 66 11 77 133 51 1

nd nd nd nd nd nd nd nd nd nd nd nnd nd nd nd nd nd nd nd nd nd nd nnd nd nd nd nd nd nd nd nd nd nd n

2 0 2 7 1 8 10 2 12 21 8 2

470 79 549 534 315 848 480 260 740 749 284 10

18 1 19 62 9 71 85 15 100 173 66 2

Post-1980

Dry Year - 1971

472 306 778 395 245 640 576 218 7

-428 -445 -873 -420 -477 -896 -503 -536 -1039 -377 -380 -7

23 -367 -344 52 -171 -119 -108 -291 -399 199 -162 3

1 0 1 7 0 7 18 0 18 56 31 8

nd nd nd nd nd nd nd nd nd nd nd n

2 0 2 7 1 8 9 2 11 19 7 2

2 1 3 23 0 23 57 10 67 115 32 1

nd nd nd nd nd nd nd nd nd nd nd n

0 0 0 0 0 0 0 0 0 27 0 2

14 1 15 48 7 54 66 11 77 133 51 1

nd nd nd nd nd nd nd nd nd nd nd nnd nd nd nd nd nd nd nd nd nd nd nnd nd nd nd nd nd nd nd nd nd nd n

2 0 2 7 1 8 10 2 12 21 8 2

470 79 549 534 315 848 480 260 740 749 284 10

18 1 19 62 9 71 85 15 100 173 66 2

Post-1980

Dry Year - 1971

Pre-1980

Normal Year - 1975 Dry Year - 1990 Normal Year - 199

Simplified Water Budget for NE and Central 

-
 129 

6.3 Locations Where Salinity is Sensitive to Inflow from Wetlands 

As this work was progressing, it became apparent that two questions are relevant to the use of 

salinity in setting minimum flows and levels targets for water management. First - where in 

Florida Bay is salinity sensitive to changes in the inflow of fresh water from the Everglades at 

the monthly level? Second - do water management activities exert sufficient influence on this 

inflow to be detected against a background of the salinity variation driven by climate? The 

following analysis of the 31-year water budget, wetland water levels, and estimated salinity 

begins to answer the first question. The results of salinity projections for different water 

management scenarios, presented in the following section, address the second question. 

The approach to evaluating the sensitivity to inflow assumes that a linear relationship exists 

between rainfall and inflow, as independent variables, and rainfall and inflow are definitive 

characteristics of salinity as the dependent variable. The coefficients in the linear relationship 

provide a measure of the sensitivity of salinity to each of the independent variables. Standard 

statistical tests for the strength of the relationship between the dependent and independent 

variables and for the significance of the coefficients serve as objective measures of whether a 

significant relationship exists between any one of the independent variables and salinity. A map 

of areas of significant effect for each independent variable is constructed by fitting the model to 

salinity at a number of locations in the Bay, treated independently (Figure 6.4). 

The maximum salinity value in each year, calculated with FATHOM for the MFL base case, 

serves as the summary statistic in this application. This analysis is conducted on the basis of a 

calendar year. Evaluating sensitivity to inflow based on maximum salinity is consistent with the 

application of these results to setting minimum flows and levels in order to mitigate the effects of 

hypersalinity in Florida Bay. The difference between annual maximum salinity Smax and the 

average salinity at the boundary with the Gulf of Mexico Sb is assumed to be a linear function of 

the depth of rainfall R and the volume of inflow from the mangrove transition zone Q both in the 

current year and in the preceding year, Equation 6.1. 

6.1 

Taking the difference with the average boundary salinity removes the influences of year-to-year 

fluctuations in boundary salinity that are affected by either rainfall or inflow from the wetlands. 

The dependence of salinity in Equation 6.1 on rainfall and inflow in the preceding year helps to 

account for the effect of antecedent salinity conditions, recognizing that residence times are high 

in some parts of Florida Bay. 

For purposes of establishing operating rules for water management, it may be more desirable to 

establish goals with reference to water levels that are easily monitored in wetlands adjacent to 

the mangrove transition zone rather than using the volume of inflow into Florida Bay. This 

raises the question of where in the Bay are salinity values sensitive to changes in wetland water 

levels. The approach to addressing this question parallels that described for inflow, based on an 

b i Ri Ri Qi Qi i S − S = f + ε − − [ ] ( , , , ) max 1 1
 130 

assumed linear relationship between annual maximum salinity Smax and rainfall and water levels, 

Equation 6.2: 

6.2 

Here HCP and HEPSW refer to annual average water levels at the Craighead Pond (CP) and EPSW 

monitoring locations used in the calibration of the PHAST wetland hydrology model, (Figure 

3.1). 

Models based on Equations 6.1 and 6.2 were constructed for calculated salinity values in each 

basin containing a salinity-monitoring site, as shown in Figure 6.4. Maximum annual salinity is 

judged to be sensitive to rainfall, inflow or water level if the corresponding coefficient in the 

linear model tests significantly different from zero at the p = 0.05 level. The 31 years of salinity 

data produced by the FATHOM model using the “best” model input parameters, i.e. the MFL 

base case, were used at each location. 

Results of this analysis are shown as maps indicating locations where each rainfall, inflow, and 

water level variable are significant, (Figure 6.4). Generally, basins in which annual maximum 

salinity has been sensitive to year-to-year changes in inflow or wetland water level are clustered 

in the Northeast and the South Regions of the Bay. Models for locations in the west and western 

portion of the south region explained little of the variation in maximum annual salinity. 

Presumably this is because maximum annual salinity values here follow the variation in salinity 

on the open western boundary of the Bay. Part of this is due to changes in fresh water discharge 

from Shark Slough, but oceanographic processes in the Gulf of Mexico also contribute to this 

variability. 

The apparent lack of influence of inflow and water level on annual maximum salinity in the 

Central Region, according to this analysis, may simply reflect the fact that very little or no inflow 

reaches the Central Region during dry years. Therefore, annual maximum salinity values here 

are not affected by changes in inflow when inflow is essentially zero. Even so, the response of 

model efficiency in the Central Region to inflow alternatives provides evidence of the general 

sensitivity of salinity to inflow in the Central Region, (Table 5.11). 

b i Ri Ri HCP i HEPSW i i S − S = f + ε − [ ] ( , ,( ) ,( ) ) max 1
 131 

Figure 6.4: Areas of Florida Bay where annual maximum salinity (calendar year basis) is 

sensitive to annual rainfall in addition to A) annual inflow and B) annual average wetland 

water levels at either Craighead Pond (CP) or EPSW monitoring location. 

 A 

 

B 
 132 

7 APPLICATION: PROJECTED EFFECTS OF WATER 

MANAGEMENT ALTERNATIVES

This section presents results of applying the FATHOM salinity model (MFL base case) to 

compare salinity conditions in Florida Bay that would occur under four regional water 

management scenarios: the base 2000 scenario (B2000), the base 2050 scenario (B2050), the 

current preferred CERP restoration alternative (CERP1), and the current version of the natural 

system model (NSM 4.6.2). Output from the SFWMM provides a description of regional 

hydrological conditions projected for each water management alternative as if these alternatives 

had been in operation during the period 1965 through 2000. These alternative realizations of 

regional hydrology allow one to evaluate the benefits and impacts to water supply, flood control 

and wetland ecosystems of each water management alternative. FATHOM extends these 

projected conditions to include salinity conditions in Florida Bay, making it possible to also 

evaluate benefits and impacts on Florida Bay. 

7.1 Coupling SFWMM Output to FATHOM 

Regional hydrologic conditions calculated with the SFWMM provide the data necessary to 

estimate inflow from the wetlands and boundary salinity values along the western boundary of 

Florida Bay, (Table 7.1). Other base case input data and model parameters remain the same as 

described for the MFL base case, with the exception that the rainfall and evaporation time series 

are extended to cover the period 1965 through 2000. 

Coupling the SFWMM to FATHOM employs calculated wetland flows across the wetland basin 

boundaries, MFL8, MFL9 and MFL10 (Figure 3.1) and the total discharge across the T21 

transect in Shark Slough, (Figure 2.3). Small negative (northward) flows occur occasionally in 

the SFWMM output, and these are set to zero flow in preparing the input into FATHOM. The 

total monthly discharge across each transect is allocated into adjacent FATHOM basins in the 

proportions described for the inflow regions, (Figure 3.10). Output from the SFWMM 

completely specifies the inflow from wetlands; no ungauged flow is added to the output from the 

SFWMM. 

This approach for coupling the SFWMM and FATHOM was developed after an analysis of 

output for the calibration and verification run of the SFWMM. Output from the calibration and 

verification run simulates regional hydrologic conditions that occurred historically in the period 

1981 through 2000. The components of the wetland water budget calculated by the SFWMM for 

the period February 1996 through September 2000 compare well with estimates compiled from 

that data, (Figure 7.1). This is taken as verification of the wetland inflow calculations by the 

SFWMM and leads to the direct application of the SFWMM flows as the mangrove inflows into 

FATHOM. The apparent discrepancy in the sub-basin water budgets based on SFWMM output 

can be explained by the contribution of groundwater, which is not accounted in the MFLx fluxes. 
 133 

Table 7.1: Sources of input data to FATHOM applied to examine water management 

scenarios. Data are assembled for the calendar period 1965 through 2000. 

FATHOM 

Input 

Data Source 

Rainfall Flamingo, Royal Palm, 

Tavernier (same as MFL base 

case) 

Evaporation Air temperature (mean and 

range) from Flamingo, Royal 

Palm and Tavernier, relative 

humidity and wind speed 

(seasonal pattern) from Joe 

Bay (same as MFL base case) 

Boundary 

salinity 

SFWMM output for flow across 

T21 transect for corresponding 

SFWMM scenario (B2000, 

B2050, CERP1, NSM) 

Inflow SFWMM output for flow across 

MFL4, MFL8, MFL9 and 

MFL10 transects for 

corresponding SFWMM 

scenario (B2000, B2050, 

CERP1, NSM) 

Sea level Key West sea level 

 
 134 

 Long Pine Basin Taylor Slough Basin C111 Basin

MFL5 11 MFL6 58 MFL7 203

MFL1 -3 MFL2 7 MFL3 6 MFL4 109

142

Area (acre) 

75

5

39

Total Inflow 

(excluding Manatee Bay)

256 

6.1E+04

 

 

Area (acre) 

5.1E+04

Area (acre) 

4.1E+04

MFL8

MFL9

MFL10

33

[R-E]

23

[R-E]

24

[R-E]

 Long Pine Basin Taylor Slough Basin C111 Basin 

MFL5 n/a MFL6 105 TSB+S175 MFL7 166 S18C 

 

 MFL1 n.d. MFL2 n.d. MFL3 n.d. MFL4 29 S197 

187 gauged Area (acre) 45 gauged 

4 gauged Total Inflow – USGS creeks

(excludes Manatee Bay)

236 

6.1E+04 

293 gauged + ungauged 

gauged 

Area (acre) 

5.1E+04

Area (acre) 

4.1E+04

Figure 7.1: Comparison of wetland water budget components for the period February 

1996 through September 2000 A) calculated by the SFWMM (calibration and verification 

run) and B) directly from data. Fluxes are in units of thousands of acre-feet per year. [RE] is volume of rainfall in excess of evaporation. (Refer to Figure 6.4 for the location of the 

wetland basins shown) 

 

A) Output from SFWMM calibration/verification run (in thousand acre-feet per year)

B) Water budget components estimated from data (in thousand acre-feet per year), see Figure 6.4.
 135 

The wetland surface flow calculated by the SFWMM for the T21 transect serves as the basis for 

estimating the variation in western boundary salinity. The T21 simulated flows serve the same 

role as the total flow through the S12 structures and levels at P33 that are used to estimate 

boundary salinity values in the MFL base case, c.f. section 2.2. Regression models were 

calibrated using the T21 transect flows from the calibration and verification runs and data from 

the SERC boundary salinity stations (SERC stations 25, 26, 27 and 28) for the period 1991 

through 2000. The selected models incorporate a lagged response of salinity to variations in 

Shark Slough hydrology; lags up to 3 months were investigated. The models achieve adjusted rsquare values of between 0.41 and 0.65, with the highest r-squared associated with the model for 

the station closest to the mouth of Shark River, station 25, (Table 7.2). These are similar to the rsquare values obtained in the regression based on the S12T flows and P33 levels. 

Table 7.2: Summary of regression models used to estimate salinity on western boundary 

and at Card Sound (SERC station 1) for the application with the SFWMM scenarios 

SERC 

Station 

Lag 

(months) 

T21 Flow 

Transect 

Intercept R2

25 2 -3.59E-05 36.60 0.66 

26 2 -3.08E-05 36.70 0.64 

27 2 -2.65E-05 36.71 0.55 

28 2 -2.1E-05 36.52 0.42 

1 0 -4.31E-05 32.60 0.56 
 136 

7.2 SFWMM Scenarios 

The SFWMM scenarios differ mainly in the wetland inflow input data. Average annual inflow 

to the northeast portion of Florida Bay for the NSM scenario, which is the lowest inflow, is 42 

percent less than average annual inflow for the B2000 scenario to the Northeast Bay, the highest 

inflow, (Table 7.3). However, the NSM scenario has significantly higher inflow directed into the 

Central Region than the other three scenarios. Average annual inflow for the B2000 scenario is 

comparable to the average annual inflow for the MFL base case. 

The overall mean value for salinity imposed along the western boundary for the B2000 scenario 

is also comparable to that for the MFL base case, (Table 7.4). Variation among the SFWMM 

scenarios in mean boundary salinity is small and occurs in direct proportion to the amount of 

flow in Shark Slough for each scenario. The NSM scenario supports the highest flows, and 

water levels, in Shark Slough. This has the effect of lowering salinity along the western 

boundary, (Table 7.4). But it also supports greater inflow from the wetlands directly into the 

center region of Florida Bay. This latter effect might have the greater influence on salinity in the 

center region of the Bay. 

7.3 Salinity Calculations 

Results of salinity calculations are presented for each SFWMM scenario in the format used 

previously for the MFL base case, (Figures 7.2 through 7.13). There are three figures for each 

scenario. The first figure presents time series plots of simulated salinity at the FATHOM basins 

of interest. The second figure compares the distribution of salinity values across sites for the 

entire record, during the wet season (June through October), and during the dry season 

(November through May). The third figure summarizes the frequency (% of months) with which 

the monthly average salinity falls into one of the six different salinity ranges presented 

previously. 

 
 137 

Table 7.3: Summary of fresh water inflow defined by each of the SFWMM scenarios. 

Units are 1000 acre-feet per year, averaged over the period 1965 through 2000. Summary 

of the MFL base case inflow for the period 1970 through 2000 provided for reference. 

Table 7.4: Summary statistics for boundary salinity calculated from the SFWMM T21 

transect flows for each of the water management scenarios compared to the MFL base case 

Scenario Central Northeast Total

B2000 30 200 230

B2050 31 179 210

CERP1 34 152 186

NSM 61 117 178

MFL Base 28 204 232

(1970 - 2000)

Florida Bay Region 

Scenario Average St. Dev.

B2000 35.2 1.86

B2050 34.8 2.01

CERP1 34.2 2.28

NSM 33.4 2.87

MFL base 35.8 2.12
 138 

Figure 7.2: Time series plots of simulated salinity forB2000 scenario 

MFL Study - SFWMD Special Interest FATHOM Basins

Simulation = B2000

42

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Feasibility Study Zones Feasibility Study Zones

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Feasibility Study Zones Feasibility Study Zones

Rabbit Key Basin

0

10

20

30

40

50

60

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80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-38

Duck Key Basin

0

10

20

30

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50

60

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80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-47 Whipray Basin

0

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20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-34

Park Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-15

Butternut Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-46

Long Sound

0

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20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-7

Joe Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-13 Little Madeira Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-14

Garfield/Rankin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-37
 139 

Figure 7.3: Overall summary of salinity distributions obtained for B2000 scenario 

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 65-00 - Simulation: B2000

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 65-00 - Simulation: B2000

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 65-00 - Simulation: B2000

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay
 140 

Figure 7.4: Frequency of occurrence within salinity classes for the B2000 scenario 

Freq (%) of monthly mean salinity > 50 psu, Jan 1965 - Dec 2000 Simulation = B2000

0

10

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 40-50 psu, Jan 1965 - Dec 2000 Simulation = B2000

0

10

20

30

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 31-40 psu, Jan 1965 - Dec 2000 Simulation = B2000

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 19-30 psu, Jan 1965 - Dec 2000 Simulation = B2000

0

20

40

60

80

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 6-18 psu, Jan 1965 - Dec 2000 Simulation = B2000

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 0-5 psu, Jan 1965 - Dec 2000 Simulation = B2000

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region
 141 

Figure 7.5: Time series plots of simulated salinity for B2050 scenario 

MFL Study - SFWMD Special Interest FATHOM Basins

Simulation = B2050

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Feasibility Study Zones Feasibility Study Zones

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1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

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Duck Key Basin

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Basin-47 Whipray Basin

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Basin-34

Park Key Basin

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Basin-15

Butternut Key Basin

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Basin-46

Long Sound

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1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-7

Joe Bay

0

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1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-13 Little Madeira Bay

0

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1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-14

Garfield/Rankin

0

10

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50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-37
 142 

Figure 7.6: Overall summary of salinity distributions obtained for B2050 scenario 

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 65-00 - Simulation: B2050

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 65-00 - Simulation: B2050

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 65-00 - Simulation: B2050

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay
 143 

Figure 7.7: Frequency of occurrence within salinity classes for the B2050 scenario 

Freq (%) of monthly mean salinity > 50 psu, Jan 1965 - Dec 2000 Simulation = B2050

0

10

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 40-50 psu, Jan 1965 - Dec 2000 Simulation = B2050

0

10

20

30

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 31-40 psu, Jan 1965 - Dec 2000 Simulation = B2050

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 19-30 psu, Jan 1965 - Dec 2000 Simulation = B2050

0

20

40

60

80

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 6-18 psu, Jan 1965 - Dec 2000 Simulation = B2050

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 0-5 psu, Jan 1965 - Dec 2000 Simulation = B2050

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region
 144 

Figure 7.8: Time series plots of simulated salinity for CERP1 scenario 

MFL Study - SFWMD Special Interest FATHOM Basins

Simulation = Cerp1

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Feasibility Study Zones

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13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

1414 13 13a

1a

14a

2

3

1616

5

6

4

1

1414 13 13a

1a

14a

2

3

1616

5

6

4

1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones

Rabbit Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-38

Duck Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-47 Whipray Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-34

Park Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-15

Butternut Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-46

Long Sound

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-7

Joe Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-13 Little Madeira Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-14

Garfield/Rankin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-37
 145 

Figure 7.9: Overall summary of salinity distributions obtained for CERP1 scenario 

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 65-00 - Simulation: Cerp1

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 65-00 - Simulation: Cerp1

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 65-00 - Simulation: Cerp1

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay
 146 

Figure 7.10: Frequency of occurrence within salinity classes for the CERP1 scenario 

Freq (%) of monthly mean salinity > 50 psu, Jan 1965 - Dec 2000 Simulation = Cerp1

0

10

20

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 40-50 psu, Jan 1965 - Dec 2000 Simulation = Cerp1

0

10

20

30

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 31-40 psu, Jan 1965 - Dec 2000 Simulation = Cerp1

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 19-30 psu, Jan 1965 - Dec 2000 Simulation = Cerp1

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 6-18 psu, Jan 1965 - Dec 2000 Simulation = Cerp1

0

20

40

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 0-5 psu, Jan 1965 - Dec 2000 Simulation = Cerp1

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region
 147 

Figure 7.11: Time series plots of simulated salinity for NSM scenario 

MFL Study - SFWMD Special Interest FATHOM Basins

Simulation = NSM

42

12

11 10

9

8

7

6 5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

1414 13 13a

1a

14a

2

3

1616

5

6

4

1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones

42

12

11 10

9

8

7

6 5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

1414 13 13a

1a

14a

2

3

1616

5

6

4

1

42

12

11 10

9

8

7

6 5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11 10

9

8

7

6 5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

42

12

11 10

9

8

7

6 5

19

18

17

16

15

14

13

26

25 24

23

22

21

20

34

33

32

31

30

29

28

27

40

39

38

37

36

35

44

43

41

47

46

45

1414 13 13a

1a

14a

2

3

1616

5

6

4

1

1414 13 13a

1a

14a

2

3

1616

5

6

4

1 Florida Bay and Florida Keys Florida Bay and Florida Keys 

Feasibility Study Zones

Rabbit Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-38

Duck Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-47 Whipray Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-34

Park Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-15

Butternut Key Basin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-46

Long Sound

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-7

Joe Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-13 Little Madeira Bay

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-14

Garfield/Rankin

0

10

20

30

40

50

60

70

80

1965 1968 1971 1974 1977 1980 1983 1986 1989 1992 1995 1998 2001

Basin-37
 148 

Figure 7.12: Overall summary of salinity distributions obtained for NSM scenario 

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Dry seasons 65-00 - Simulation: NSM

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - All seasons 65-00 - Simulation: NSM

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay

Salinity percentiles (5%, 25%, 50%, 75%, 95%) - Wet seasons 65-00 - Simulation: NSM

0

10

20

30

40

50

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

sali

nity 

(psu

)

SFWMD Region FATHOM Basin

Florida 

Bay
 149 

Figure 7.13: Frequency of occurrence within salinity classes for the NSM scenario 

Freq (%) of monthly mean salinity > 50 psu, Jan 1965 - Dec 2000 Simulation = NSM

0

10

20

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 40-50 psu, Jan 1965 - Dec 2000 Simulation = NSM

0

10

20

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 31-40 psu, Jan 1965 - Dec 2000 Simulation = NSM

0

20

40

60

80

100

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 19-30 psu, Jan 1965 - Dec 2000 Simulation = NSM

0

20

40

60

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 6-18 psu, Jan 1965 - Dec 2000 Simulation = NSM

0

20

40

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region

Freq (%) of monthly mean salinity 0-5 psu, Jan 1965 - Dec 2000 Simulation = NSM

0

20

40

60

80

FB 1 1a 5 2 3 4 6 16 13 13a 14 14a 7 13 14 15 47 46 37 38 34

All seasons Wet seasons Dry seasons

FATHOM basin 

Florida 

Bay SFWMD Region
 150 

7.4 Comparison of Results 

Overall, all of the SFWMM scenarios would produce similar frequency distributions of salinity 

when compared by FATHOM group, (Table 7.5). In part this result may be an artifact of 

grouping basins in which salinity is sensitive to changes in wetland inflow together in FATHOM 

group C with basins in which the salinity is less sensitive to changes in wetland inflow. 

Differences are seen between scenarios when comparisons are made at the basin level, (Figures 

7.14 through 7.22), and when attention is paid to the extreme values that are not well represented 

in the regional summaries. Basins where evident differences occur among SFWMM scenarios 

correspond to the basins identified as sensitive to wetland inflow in the analysis reported in the 

preceding section, (Figure 6.4). The higher inflow into the Central Basin provided by the NSM 

scenario results in a depression of low values of salinity in Whipray Basin and Park Key basin 

(Figures 7.17 and 7.18); however, this does not occur during periods of high salinity, i.e. the dry 

years when minimum flows and levels management targets would come into play. 
 151 

Table 7.5: Distribution of monthly salinity values relative to the ecologically defined 

salinity ranges for each SFWMM scenario. Values are percent of months in each range for 

each FATHOM grouping of basins, Figure 1.6. The distribution obtained for the MFL 

base case is shown for reference. 

Fathom Group A

salinity 1965 - 2000

category (36 years)

(psu range)

1970-2000

(31 years)

MFL base B2000 B2050 CERP NSM

> 50 0 0 0 0 0

40-50 6 4 4 7 7

31-40 43 22 28 37 39

19-30 44 48 54 44 41

6-18 7 22 14 10 11

0-5 0 5 0 1 1

Fathom Group B

salinity 1965 - 2000

category (36 years)

(psu range) B2000 B2050 CERP NSM

> 50 4 6 6 6 7

40-50 16 14 13 13 12

31-40 38 35 35 37 37

19-30 25 17 19 22 23

6-18 15 15 17 12 11

0-5 2 12 11 11 10

Fathom Group C

salinity 1965 - 2000

category (36 years)

(psu range) B2000 B2050 CERP NSM

> 50 1 2 2 2 2

40-50 17 14 14 14 12

31-40 62 55 55 57 54

19-30 20 24 24 23 27

6-18 1 5 5 4 5

0-5 0 0 1 0 0

Fathom Group D

salinity 1965 - 2000

category (36 years)

(psu range) B2000 B2050 CERP NSM

> 50 0 0 0 0 0

40-50 3 1 1 1 1

31-40 94 95 94 92 85

19-30 3 4 5 7 14

6-18 0 0 0 0 0

0-5 0 0 0 0 0

1970-2000

(31 years)

MFL base

1970-2000

(31 years)

MFL base

1970-2000

(31 years)

MFL base
 152 

Figure 7.14: Comparison of salinity time series for the four SFWMM scenarios at Long 

Sound (Basin 7). The salinity time series obtained for the MFL base case is shown on all 

plots for reference (red). 

Monthly Salinity (psu), Long Sound (Basin-7)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Long Sound (Basin-7)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Long Sound (Basin-7)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Long Sound (Basin-7)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 153 

Figure 7.15: Comparison of salinity time series for the four SFWMM scenarios at Joe Bay 

(Basin 13). The salinity time series obtained for the MFL base case is shown on all plots for 

reference (red). 

Monthly Salinity (psu), Joe Bay (Basin-13)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Joe Bay (Basin-13)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Joe Bay (Basin-13)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Joe Bay (Basin-13)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 154 

Figure 7.16: Comparison of salinity time series for the four SFWMM scenarios at Little 

Madeira Bay (Basin 14). The salinity time series obtained for the MFL base case is shown 

on all plots for reference (red). 

Monthly Salinity (psu), Little Madeira Bay (Basin-14)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Little Madeira Bay (Basin-14)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Little Madeira Bay (Basin-14)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Little Madeira Bay (Basin-14)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 155 

Figure 7.17: Comparison of salinity time series for the four SFWMM scenarios at Park 

Key (Basin 15). The salinity time series obtained for the MFL base case is shown on all 

plots for reference (red). 

Monthly Salinity (psu), Park Key Basin (Basin-15)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Park Key Basin (Basin-15)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Park Key Basin (Basin-15)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Park Key Basin (Basin-15)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 156 

Figure 7.18: Comparison of salinity time series for the four SFWMM scenarios at 

Whipray Basin (Basin 34). The salinity time series obtained for the MFL base case is 

shown on all plots for reference (red). 

Monthly Salinity (psu), Whipray Basin (Basin-34)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Whipray Basin (Basin-34)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Whipray Basin (Basin-34)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Whipray Basin (Basin-34)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 157 

Figure 7.19: Comparison of salinity time series for the four SFWMM scenarios at 

Garfield/Rankin (Basin 37). The salinity time series obtained for the MFL base case is 

shown on all plots for reference (red). 

Monthly Salinity (psu), Garfield/Rankin (Basin-37)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Garfield/Rankin (Basin-37)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Garfield/Rankin (Basin-37)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Garfield/Rankin (Basin-37)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 158 

Figure 7.20: Comparison of salinity time series for the four SFWMM scenarios at Rabbit 

Key (Basin 38). The salinity time series obtained for the MFL base case is shown on all 

plots for reference (red). 

Monthly Salinity (psu), Rabbit Key Basin (Basin-38)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Rabbit Key Basin (Basin-38)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Rabbit Key Basin (Basin-38)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Rabbit Key Basin (Basin-38)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 159 

Figure 7.21: Comparison of salinity time series for the four SFWMM scenarios at 

Butternut Key (Basin 46). The salinity time series obtained for the MFL base case is shown 

on all plots for reference (red). 

Monthly Salinity (psu), Butternut Key Basin (Basin-46)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Butternut Key Basin (Basin-46)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Butternut Key Basin (Basin-46)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Butternut Key Basin (Basin-46)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 160 

Figure 7.22: Comparison of salinity time series for the four SFWMM scenarios at Duck 

Key (Basin 47). The salinity time series obtained for the MFL base case is shown on all 

plots for reference (red). 

Monthly Salinity (psu), Duck Key Basin (Basin-47)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2000 base

Monthly Salinity (psu), Duck Key Basin (Basin-47)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

b2050 base

Monthly Salinity (psu), Duck Key Basin (Basin-47)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

cerp1 base

Monthly Salinity (psu), Duck Key Basin (Basin-47)

0

10

20

30

40

50

60

70

80

1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001

nsm base
 161 

8 SUMMARY AND RECOMMENDATIONS

8.1 Summary 

This significant effort has produced the basic salinity modeling tool needed to establish 

minimum fresh water flows and levels based on Florida Bay salinity. As described in the 

approved Final Work Plan, an existing mass-balance model of Florida Bay (FATHOM) has been 

adapted for MFL use, and the wetland hydrology model (PHAST) has been updated by adding 

the Long Pine Basin and re-calibrated. Along the way, a better understanding has been gained of 

the role that fresh water inflow plays in the complex salinity regime of Florida Bay. This 

knowledge is important for meaningful goals to be established as MFLs. 

The project began by examining the original FATHOM input data, model parameters, and 

boundary conditions using the available data. However, the period for which existing model 

input data are directly available is short (1996 – present) and represents a moderately wet period. 

Initial alternative runs (Mark I) indicate that FATHOM is sensitive to inflow and rainfall inputs, 

and also to the bathymetry. The Progress Report 1 presents those activities in detail. 

At the onset of the project it was thought that the updated bathymetry would be available for use 

at the start of the project, but it was not. The upgrading of the bathymetry as part of this project 

is one of the most important accomplishments. 

Other input data were assembled for the extended period of analysis, (1970 through 2000), using 

a variety of indirect data that are regional indicators of important climatologic and hydrologic 

conditions. Regional data that are available for the extended period were used to create 

regression relationships with the existing data so that the period of analysis could be extended 

and salinity variation over a broader range of conditions could be examined. The primary results 

from the Mark II model run activities, as reported in Progress Report 2 are the assembled 31-year 

input data sets, an updated assessment of which combination of alternative input data provide the 

best reconstruction of the water budget, and an evaluation of alternative model input parameters 

using the 31-year period. 

At the onset of the project it was thought by all that an updated bathymetry data set would be 

available for all of the tasks after the Mark I runs, but it was not completed until later in the 

project, after the Mark II runs were completed. Therefore, the upgrading of the bathymetry is 

one of the most important accomplishments on this project, through cooperation between the 

District and ECT. The updated bathymetry was incorporated into the Mark III runs (Progress 

Report 3). 

The “best” input parameters from the Mark II and III analyses (Progress Reports 2 and 3) were 

chosen to be the MFL base case. When the uncertainty statistics were computed, over the entire 

Bay the FATHOM MFL base case model is capable of explaining about 81% of the monthly 

salinity variability. However, for some of the basins, particularly in the Northeast and Central 

Regions, model fidelity showed improvement through the use of rainfall and inflow alternatives 

other than the base case parameters. This suggests that FATHOM may be able to be improved 

further through the use of area specific model parameters in some basins. 
 162 

The 31-year MFL simulations were used to develop the water budget for the 31-year period. A 

statistical modeling technique was also used to determine that high salinity values in the 

northeast and south parts of Florida Bay were sensitive to inflows and water levels in addition to 

direct precipitation. It was also noted that the central area also reacts in a limited manner to fresh 

water inflows as hypersalinity conditions are known to form when fresh water inputs are very 

low or non-existing, sometimes for several years. 

The 31-year input data set was modified for use with SFWMM produced flow data and the runs 

were extended to 36 years. Four salinity simulations were then produced for the B2000, B2050, 

CERP1, and NSM 4.6.2 water management scenarios. 

8.2 Recommendations 

8.2.1 Application of models to MFL 

Based on the findings presented in the summary, above, the following findings are made relative 

to the use of FATHOM for MFL purposes: 

• The updated FATHOM model is recommended for use as the basic modeling tool for 

setting MFLs for Florida Bay with the input data and parameter values specified by the 

MFL base case, described in Section 4. 

• The enhanced PHAST model can provide an estimate of inflow from the Taylor Slough 

C111 wetland basin, though it is biased towards lower salinity estimates. Instead. the 

wetland inflow data derived by the mass accounting method using regional data and 

regression equations described in Section 3.3 are the preferred estimate of wetland 

inflow. 

• The method of applying results of regional hydrologic simulations with the SFWMM as 

input to FATHOM described in Section 7, appears to be satisfactory for extending the 

analysis of water management alternatives to include an evaluation of the expected effect 

of the CERP water management alternatives on Florida Bay salinity. 

• A relationship needs to be developed between fresh water inflows and water levels in the 

Everglades can be developed that can be used to assist in operational management once 

the minimum flow regime had been determined that protects against significant harm in 

Florida Bay. 

• An analysis of the timing of flows into Florida Bay indicates that minimum flows and 

levels may need to be invoked at the end of a normal wet season some years (in addition 

to dry periods) to protect the Florida Bay ecology against significant harm. 

8.2.2 Possible further refinements 

Specific locations where improvements to model fidelity may be possible include the following: 

• Manatee Bay 

• Joe Bay 

• Terrapin Bay 

• Whipray Basin 

• Group D (all). 

The Joe Bay and Manatee Bay situations may be influenced by the changes in flow direction that 

are thought to occur when S197 is open and discharging into Manatee Bay. Although the model 

takes into account the opening and closing of S197, Manatee Bay salinity is also influenced 
 163 

heavily by the boundary salinity condition nearby at the Card Sound Road bridge. Joe Bay may 

also be influenced by a change the hydraulic gradient pattern in the Everglades panhandle that 

nay be caused by the opening of S197. Recent observations by the USGS indicate that Joe Bay 

salinity can vary spatially, and the spatial variation may be relatively large (Hittle and Zucker, 

2004, personal communication). Wind effects appear to be responsible for trapping salt water in 

Joe Bay at times and density differences can keep adequate mixing from taking place. It is 

difficult for a grab sample or for a stationary platform measurement to characterize these spatial 

differences, and model performance in this basin may have been compromised by these 

conditions. 

Terrapin Bay and Whipray Basin model fidelity may be affected by the assignment of fresh 

water flows into the central area of Florida Bay as defined in the base case. There are several 

site-specific ways to address this should it be necessary. In addition, the FATHOM Group D 

salinities may be affected by the proximity of these basins to the western boundary salinity 

conditions. Model fidelity may also be compromised by inadequate fresh water flows to the 

central basin that in turn may affect the Group D salinities. 

Based on the findings presented above, the following recommendations are made: 

• Use the MFL base case FATHOM model to establish MFLs for Florida Bay. 

• Evaluate further the use of site-specific model parameters in the basins that showed the 

potential for additional improvement when alternative inputs were used in the MFL runs, 

for example Whipray Basin and the Group D basins. 

• Investigate the effect of the opening of the S197 structure on the hydraulic gradient in the 

northeastern portion of the Bay and the areas upstream of Joe Bay, Little Madeira Bay, 

Terrapin Bay, and Manatee Bay. 

• Evaluate the data available on the spatial variability of salinity in Joe Bay and 

communicate with the USGS on their findings in this regard. 

• Investigate the effect of the boundary salinity conditions in the proximity of Manatee Bay 

on the salinity in that basin. 
 164 

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