## 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 

# C ONTENTS

E XECUTIVE 

## S UMMARY



## ..................................................................................................................... 7

1 I NTRODUCTION



## ........................................................................................................................ 9 1.1 Objectives and Approach.............................................................................................. 10 1.1.1 Organization of Final Repor t 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 E NHANCEMENTS TO THE 

## S ALINITY 

## M ODEL 

## – 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 E STIMATES OF 

## F RESH 

## W ATER 

## I NFLOW FROM 

## W ETLANDS



## ...................................................... 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 B ASE 

## C ASE 

## C ALCULATED 

## S ALINITY 

## R ECONSTRUCTION 

## - 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 E RROR 

## , S ENSITIVITY 

## , 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 Altern ative 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 M easured Inflow – 1996 through 2000 ..................... 117

6 D EVELOPMENT AND 

## D ESCRIPTION OF A 

## W ATER 

## B UDGET 

## - 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 A PPLICATION 

## : P ROJECTED 

## E FFECTS OF 

## W ATER 

## M ANAGEMENT 

## A LTERNATIVES



## ................. 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 S UMMARY AND 

## R ECOMMENDATIONS



## .................................................................................. 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 R EFERENCES



## ........................................................................................................................ 164

## 4 

# A PPENDICES

Appendices Note: The appendices are an integral part of this final report. They provide the output from FATHOM upon which the summary result s 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 pr esented 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 Sp ecial Interest Basins and Feasibility Study Regions. Appendix B: Analysis of Simulated Reside nce Time Distributions for the MFL Base and Alternate Input Simulations in Selected SFWMD Special Inte rest Basins and Feasibility Study Regions. Appendix C: Analysis of Model Performa nce for the MFL Base and Alternate Input Simulations: Comparison of Simulated a nd Observed Salinity Data for 1991-2002 in Selected SFWMD Special In terest Basins and Regions. Appendix D Analysis of Model Performa nce for the MFL Base and Alternate Input Simulations: Comparison of Simulated a nd Observed Salinity Data for 1996-2000 in Selected SFWMD Special In terest Basins and Regions. Appendix E: Analysis of Simulated Salinity Di stributions for the MFL Base and Alternate Input Simulations in All FATH OM Basins and Regional Groups. Appendix F: Analysis of Simulated Residenc e Time Distributions for the MFL Base and Alternate Input Simulations in All FATHOM Basins and Regional Groups. Appendix G: Analysis of Model Performan ce for the MFL Base and Alternate Input Simulations: Comparison of Simulated a nd Observed Salinity Data for 1991-2002 in All FATHOM Basins and Regional Groups. Appendix H: Analysis of Model Performa nce for the MFL Base and Alternate Input Simulations: Comparison of Simulated a nd Observed Salinity Data for 1996-2000 in All FATHOM Basins and Regional Groups.

## 5 Appendix XXX: Analysis of Simulated Salin ity Distributions for the MFL Base and Alternate Input Simulations in Selected SF WMD 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

## 6 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, Litt le 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

## 7 

# E XECUTIVE 

# S UMMARY This project updated and enhanced existing mode ls of salinity in Florida Bay (FATHOM) and hydrology in the Taylor Slough C111 wetland basi n (PHAST) and implemented FATHOM with input from the South Florida Water Management Model (SFWMM) to evaluate the effects of water management alternatives. General info rmation on the hydrogeomorphi c setting of Florida Bay and the upstream wetlands was compiled an d 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 incorpor ate up-to-date bathymetric information, refine the representation of salinity variation along the we stern boundary of Florida Bay, implement calculations of residence time, improve estimate s of fresh water inflow from the Taylor Slough C111 wetland basin, and assemble input data to support long-term cal culation of salinity. Although direct measurements of inflows to Fl orida 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 assemble d for this MFL base case were described. The results of calculations of salinity and residence time fo r 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 wi th 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, wetla nd hydrology, and meteorological conditions an additional source of uncertainty is introduce to the salinity calcula tions. 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 i nput data spans a period of significant change in inflow from the wetlands and variation in climate. Rainfall and evaporation dominate the fres h water budget in both the whol e Bay and in the central and northeast regions. On an annual basis, infl ow 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 ne t supply of fresh water to Florida Bay. In the northeast region of Florida Bay, year-to-year differ ences in peak annual sa linity 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; therefor e it cannot moderate high salinity values there. Even so, the response of model efficiency in the central regi on to inflow alterna tives examined in the sensitivity analysis provides evidence that sali nity 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 provi de 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 a lternatives, increased inflow to the central region of the Bay provided by the NSM alternative de presses salinity values there during periods of lower salinity, but higher salinity values, which occur when cond itions 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 respec table 81%, though there ar e certain basins that may show improved simulation performance with some site-specific parameter modifications that are beyond the scope of this project. PHAS T was also upgraded to include the Long Pine basin, but it was found that the di rect application of SFWMM flow s in the same proportion as the U.S. Geological Survey (USGS) flow data perf ormed 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 parame ters that provided the best performance in calculated salinity. Specific locations where im provements to model fidelity may be possible include Manatee Bay, Joe Bay, Te rrapin Bay, and Whipray Basin.

## 9 

# 1 I NTRODUCTION The South Florida Water Management District (Dis trict) is working to establish minimum flows and levels criteria (MFL) for Flor ida Bay. In support of this wor k, the District contracted with Environmental Consulting & Technology, Inc. (E CT) to adapt two existing hydrologic models for this use, an estuarine salinity model (F ATHOM) and a wetland hydrology model (PHAST). Everglades National Park previ ously supported the authors in th e 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 wate r managers with the ability to evaluate the effect on the salinity of Florida Bay from change s in management operations. Salinity serves as an important indicator for the effect of wa ter 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 ha s on salinity. Operations of the District’s regional water management system influence the in flow of fresh water into Florida Bay. These operations have the potential to alter salinity and th rough 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 budge t for Florida Bay identifying areas where changes in the inflow of fresh wa ter has influenced salinity; and

• a comparison of the projected effects of f our alternative water management scenarios described by output from the South Florida Water Management Model.
This project estimates rainfall and evaporati on in Florida Bay and inflow from the adjacent wetlands for the period 1970 through 2002, and it applie s 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 Florid a Bay began only in the early 199 0s, 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 fres h water fluxes over longer periods.
This report analyzes Florida Bay’s water budget and salinity simulati ons for the period 1970 through 2000. South Florida experienced several pe riods 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 Ba y, and rainfall also supplies fres h water that is stored in the upstream wetlands. In addition, the completi on of a major portion of the South Dade Conveyance System significantly in creased the amount of water de livered to the wetland areas that discharge into the northeast part of Florida Bay in the earl y 1980s. Analysis of the compiled hydrology data and simulated salini ty allowed the identification of areas in Florida Bay where wetland inflow has a distinct influence on sa linity, relative to ot her areas of the Bay.

## 10 This report uses output from the South Flor ida Water Management Model (SFWMM or 2X2 Model) as input to FATHOM and estimates salin ity 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 scenar ios of assumed water management operations. Included in this task wa s the development of protocols for applying this output as input to FATHOM. This project asse mbled 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 repr esent 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 info rmation to establish scientifically defensible relationships between fresh water inflows and estu arine salinity response that can be used to establish minimum flows and leve ls 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 c oordination 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 b oundary 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 resu lts obtained with these mode ls over the entire project.

## 11 1.1.1 Organization of Final Report and Supporting Materials This report describes the overall re sults 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 th e selected input data and parameter values. Sections 6 and 7 present the results of water budget de velopment and model applications.
In addition to this report, three progress repor ts document the progression and intermediate results of work performed. These reports contai n 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 construc t long-term input data sets for the period 1965 through 2002 using the existi ng bathymetry and the sensitivity analysis for this period.
Progress Report 3 Documents the selection of the parame ters 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, a nd 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, instru ction 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 th e most recent survey by the U.S. Geological Survey (USGS). However, shallow areas excl uded 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 ex change. Therefore techniques had to be developed to estimate the bathymetry in th e shallow areas not covered by the USGS survey.

• Direct measurements of rainfall in the Ba y are available only si nce 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 informati on 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 pe riod of record for the regional information related to inflow only extends to 1970.

• The last ten years, for which the data on c onditions 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 twen ty 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 cont ain 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 underest imate 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 un der 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 a dopted an approach to populate and verify the models that relied on selection of the best av ailable estimates for the input data and model parameters to the extent that these could be independently identifie d, and to confirm these selections with a sensitivity analysis. The progress reports contain th e detailed results from several iterations of this appro ach. This report documents the fi nal 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 pa rameter values examined in the final sensitivity analysis are chosen based on consid eration of the uncertainties inhe rent in the construction of the input data sets and selecti on of model parameters. 

# 1.2 Description of Florida Bay and Contributing Watershed Florida Bay lies between the southern tip of th e Florida mainland and the island chain known as the Florida Keys. Over 85 percent of the Bay’s 2200 km 2 

## area lies within Everglades National Park, and the Florida Keys Nati onal 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 includi ng 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 im portant component of the much larger South Florida drainage basin that is the focus of the Comprehensiv e Everglades Restoration Plan (CERP). The Bay receives freshw ater inflow from the Everglad es, 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 fi fty years or so influenced present conditions. Although a specific restoration ta rget has not yet been define d 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 th e 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 typi cal salinity of seawat er. Large areas of seagrasses began to die late in 1987. Concurren tly, the shrimp harvest on the Tortugas Grounds, which depends on Florida Bay as a nursery area, d eclined to record lows. In 1991, turbidity and plankton concentrations increased dramatically, reducing the supply of lig ht 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 comparativel y small annual temperature range but distinct wet (summer/fall) and dry (winter/sp ring) seasons. During the wet season, showers occur virtually daily with the afte rnoon 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 Florid a shelf, and on occasion to more remote regions of the Gulf of Mexico. As a result, western Fl orida Bay can be influenced by the delivery of fresh water from rivers discharging in the Te n Thousand Islands region and along the west coast of Florida (the Shark, Broad, Harney, and Lost mans 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 Ke ys 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 (Ort ner et al., 1995). Subsequent transport of this water into Florida Bay and to th e Keys is aided by oceanic flows, the Gulf Loop Current, and the Florida Current.

Circulation of water in western Florida Bay and adjacent coastal re gions on subtidal time scales is also strongly influenced by local wind forci ng resulting in seasonal fl ow patterns within the Bay: southward toward the Keys in winter a nd spring, northwestward into the Gulf in summer, and southwestward toward the Tortugas in the fa ll. 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 patte rns in the southeast portion of Everglades National Park. This project divides this area in to three wetland sub-basins, Long

## 14 Pine, Taylor Slough and C111 (Figure 1.2). Long Pi ne 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, sout h of the Park road ga uging station (TSB), and sheet flow in the C111 basin fed by overflow fr om the C111 canal. The source of water in Taylor Slough is overflow from Shark Slough, rain fall on the Rocky Glades area of the Park, direct rainfall on the Slough, and discharge of th e S332 and S332D pump st ations. The source of sheet flow in the C111 basin is overflow fr om the C111 canal betw een 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 av erage 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 Ri ver and Taylor Slough that influence salinity in Florida Bay (from Florid a Bay Science Program 2003).

## 15 Figure 1.2: Wetland basins used to describe f resh 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 loca tions 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 Fl orida 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 Nati onal Park 2001). At some interior embayments, salinity regularly fl uctuates between hypers aline and nearly fr eshwater conditions (Fourqurean and Robblee 1999, Frankovich and Four qurean 1997). This variation occurs in response to the direct effects of fresh water infl ow, rainfall, and evaporation and to the indirect influence of inflow from oceanographic processe s outside of the bay on the southwest Florida Shelf.
Florida Bay can be divided into four regions subject to differe nt geophysical forcing, topographic constraints, and fresh water i nputs (Figure 1.3). The northeast region of Florida Bay is not significantly affected by tides and is mostly isolat ed 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 cause s 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 we eks to months (Johns et al., 2001). 20 25 15 30

10

5

1 20 25 15 30

10

5

1 

## MFL5

MFL9 M FL 3 M FL 2 M FL 1 MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSB

M FL 4 EPSW

CP Long Pine Taylor Slough C111

Central Region Northeast Region 20 25 15 30

10

5

1 20 25 15 30

10

5

1 

## MFL5

MFL9MFL3MFL2MFL1 

## MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4 

## Long Pine Taylor Slough C111

## 16 The central part of Florida Bay r eceives 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 cen tral 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 cen tral region over periods of week s to months to years (as it did in the late 1980’s), indicating th at, 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 relati vely robust tidal infl uence. Residence times in the western region are shorter than in the cen tral and northeastern regions, a nd average salinity is higher. Salinity in the western region can exhibit a relatively rapid res ponse to meteorological events such as tropical storms and cold fronts, but th e range of variation is reduced relative to the northeast region.
The south region of Florida Bay is similar to th e west region except that it receives influence from the Atlantic Ocean through the middle Keys pa ssages. The south region of Florida Bay is a source of water to the coral reef areas of the Florida Keys Na tional Marine Sanctuary (FKNMS).

1.2.3 SFWMD Areas of Interest Early in the project, the study team identified several basins of inte rest for setting MFL criteria. The selected basins include Long Sound (8), Jo e Bay (10), Little Made ira Bay (11/23), Duck Key/Trout Cove (9), Whipray Basin (13), Garfie ld Bight / Rankin Lake (14/15), and Rabbit Key Basin (19) (Figure 1.5). The num bers in parentheses refer to the SERC / FIU monitoring station of salinity observations. These basins of in terest were selected based on knowledge of where valued ecological components like ly are thought to be sensitive to the influence of fresh water inflow. In addition, the zones of interest identified for the Dist rict’s Florida Keys Feasibility Study are used to evaluate model performance th roughout the Bay; these zones include Butternut Key Basin (24) and Park Key Basin (23) in add ition to the basins presented above. Results of the FATHOM salinity calculations and evaluatio n of the model performance by comparison to salinity data reference thes e basins and zones.

## 17 Figure 1.3: LANDSAT-7 extended thematic map image of Florida Bay, showing its shallow bank bathymetry and four principal regio ns (from Florida Bay Science Program 2003).

Figure 1.4: Location of principal points of f resh water inflow measured by the USGS (from Hittle et al. 2001)

## 18 Figure 1.5: Map of Florida Bay basins show ing the FATHOM basins, the Florida Bay and Florida Keys Feasibility Study Zones (colored zones and red numbers), and the locations (black) where monthly SERC salinit y measurements are taken.

3

19 18 17 16

20 22

21 13 12 15 14

23 5 10

9

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21 13 12 15 14

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24 11 6 8 4 14 13a 13

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21 13 12 15 14

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9

24 11 6 8 4 14 13a 13

1a 2

3

16 5 6

4 1 14 13a 13 14a
2

## 19 

# 1.3 Description of Models 1.3.1 FATHOM – Florida Bay Salinity FATHOM is a dynamic, spatially explicit, ma ss-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 ba sins defined by these banks offer a natural framework for mass-balance accounting.
FATHOM represents Florida Bay as a collect ion 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 prop agates 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. Bathymet ric data are entered into a GIS database that classifies the depth for every 20 by 20 meter rect angle in the Bay (the pi xel resolution of the data) into one of 11 classes: 1 land surface cla ss and 10 depth classes. The depth classes covered the range from 0 to 10 feet in one -foot increments. Areas deeper th an 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 th e hypsometry for each basin and the depth and widths of the shoals for the calculat ion of exchange fluxes between basins.
The total length of the line segments that de scribe 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 pr oportion of the 21% of s hoal length with depth greater than 3 feet repres ents cuts and channels through the shoa ls. Most of the deeper shoals are located in the western and southw estern part of the Bay. These were defined as shoals to establish a basin boundary in the model.

## 20 42 12
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19 18

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45 

## D C B A Aggregated FATHOM Groups Aggregated FATHOM Groups

D C B A

FATHOM basin numbers 

## Figure 1.6: The numbered polygons identify th e basins used in FATHOM calculations. The color-coded regions and the alphabetic de stinations identify the FATHOM groups used to summarize the results of salinity calculations.

## 21 The solution scheme depends on th e calculation of water velocity independently for each depth increment of each shoal. Conceptu ally, water flow from one basin to another over a bank in the Bay can be treated as flow over a broad crested we ir with friction. Flow velocity across the weir depends on the difference in water levels on each side of the we ir 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 fricti on 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 assu mption that the major effects of wind shear on circulation in Florida Bay can be accounted fo r by the structural assump tions and the inputs to the model, without having to be modeled explicitl y. 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 cha nges 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 desc ribed above, salinity calculated by FATHOM represents a time-averaged valu e with a period of about one m onth. 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 va lues. 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 pa rticular location.
Bay-wide inputs required by FATH OM include time series of ra infall and evaporation for each basin in the Bay. The model struct ure allows these inputs to be specified individually for each basin to reproduce spatia l gradients in these forcing functi ons. 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 divide d into a few regions for which climate inputs are applied uniformly to the model. Groundwater in puts to the basins can also be specified, but these have not been employed in the simu lations performed for this project.

Time series of freshwater inflow volumes are re quired at the terrestrial boundaries of the Bay. Inflow (where it occurs) is sp ecified 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 runo ff regimes, the distribu tion of inflow among the small embayments at the northern edge of th e 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 requi res tide, sea level and salinity time series to set th e 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 th e 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 a pproach to estimating fresh water inflow. One objective of this project was to extend the P HAST model to include the water balance of the Long Pine Basin in the water budget for the calc ulation 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 overla nd flow. In effect, the model treats the wetland basins as shallow reservoi rs, (Figure 1.7). Calculated water levels in the wetlands fluctuate depending on the balance between inflow from rainfall r and surface water sources Q in 

## and outflow from evapotranspiration e and discharge to Florida Bay Q out 

## . Any imbalance between inflows and outflows results in a loss or ga in in water storage, which is reflected as a change in water level, and conseque nt changes to the outflow, Equation 1.1.

1.1

The model represents in stantaneous discharge Q out 

## as a generalized power function of water level, measured above a zero-discharge threshold h sill 

## , Equation 1.2. Calculat ions 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 refl ect the prior implementation of the PHAST model as a separate model.)

1.2

The input data required for the PHAST wetland hydrology model include tim e series of weekly rainfall and surface inflow into each wetland ba sin. 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 y ear and rainfall (Nuttle 2004). Observations of wetland water levels are used for calibrati ng the unknown parameters, i.e. 

# α and h sill 

## in Equation 1.2. Parameters that describe how surface flows in to 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. 

# ( )
out in 

# Q e r A Q dt dh A

− − + =



# ( ) β 

# α sill out 

# h h Q

− =

## 23 Figure 1.7: Elements of wat er budget for a wetland basin



# Q r e

h Q in

out

## 24 

# 1.4 Model Enhancements and Implementation The work plan for this project identifies the following specific model enhancement tasks:

• incorporate the latest bathym etric data into FATHOM;

• integrate the PHAST wetland ba sin 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 re sidence time in each FATHOM basin;

• gather the available long-term hydrologic da ta 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 computat ion 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 wh ich historical salinity calculations could be performed to the period 1970 through 2002. Sufficient data are available so that salinity calculations can be perf ormed 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 componen t of the input data. For example, three methods for estimating the time series of ra infall over the Bay were considered. Model performance with different choices of inputs is evaluated by comparing calc ulated 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 i nputs 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. Firs t, it tests whethe r the selected input data and parameters are optimum. An in put data set is consid ered optimum if making alternative choices does not im prove the performance of the model. Second, the sensitivity analysis provides information about how differe nt assumptions made in assembling the input data affect the calculated salinity. This inform ation was important in de ciding how to represent the contribution of ungauged flow in estimating th e fresh water inflow into the northeast and central regions of the Bay. Thir d, the sensitivity analysis provid es information about the degree to which uncertainty in the input data and mode l parameters affects th e error in calculated salinity that is apparent in the comparison be tween model results and salinity measurements.

## 25 The following sections describe th e 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 es timated; 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 ba se 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 budge t 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 sa linity 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 E NHANCEMENTS TO THE 

# S ALINITY 

# M ODEL 

# – FATHOM
Enhancements to the FATHOM salinity model for MFL development purposes incorporate the most recent bathymetry data, link variation of sa linity along the western boundary to discharge from Shark Slough, calculate residence time, and a ssemble input data sets to support calculation of salinity simulations for CERP water mana gement alternatives over the period 1965 through 2002. This section describe s these enhancements. 

# 2.1 MFL Bathymetry This project utilizes a Flor ida 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 pr evious versions of th e 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 loca l knowledge of boaters of the extensive shallow banks and the channels used for boat access acros s 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 shal low 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 need ed to describe the volume of the basins and conformation of the banks in FATHOM. Thes e data are the MFL base case bathymetry parameters for FATHOM.
District staff used a variety of elevation datasets for Flor ida Bay and surrounding water bodies, mainland, and island areas to compile the basis for the new bathymetry database. These datasets included:

• USGS High Resolution Bathymet ric Survey of Florida Bay ( http://sofia.usgs.gov/projects/bathymetry/ ).

• NOAA GEODAS Survey Da tabase for Barnes Sound (Survey 4H05542 HYD9303F11484, entered into GEODAS 12/31/1979, referenced to MLW).

• ACOE LIDAR of Eastern Dade County (p rocessed 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 digiti zed areas with missing elevatio n data, including bank and land areas, and channel cuts not surveyed by any of th e 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 app lied to the banks polyg on dataset to remove “stair steps” in the final surface.

## 27 The process to combine these datasets included the following steps by th e 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 rast er 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 refere nce point of the grid from NAVD8 8 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 shap e file) and shoals (lin e shape file) to the view. (4) Perform Histogram by Zone analysis of MS L grid (represented in 1 foot elevation classes) for Shoals and Basins themes (resp ectively); this analysis calculates the number of grid cells within each elevation class for each S hoal 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 es timated elevations of the areas that had not been surveyed. Therefore, a technique was used th at 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 develope d for assigning elevations on th e 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 basi ns that will use the USGS data (82% of the wetted area).
For the shoal (banks) areas, the pr ior ENP bathymetry is used in the 10 basins that are using the prior ENP bathymetry for the open water areas. Fo r 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 prio r bathymetry data were used. Using these selection criteria, 202 of the shoals (55% of the total lengt h) used the prior ENP bathymetry, and 176 shoals (45% of the total le ngth) used the recent, USGS bathymetry data.

## 28 The resulting depth distributions for the shoals a nd in the basins reinforce the importance of the network of shallow banks in controlling circulat ion 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 wi th depth, the most significant exchange between basins will be concen trated 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 ce ntral 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

0.0E+00 2.0E+03 4.0E+03 6.0E+03 8.0E+03 1.0E+04 1.2E+04 1.4E+04

-14 - -13 -13 - -12 -12 - -11 -11 - -10 -10 - -9 -9 - -8 -8 - -7 -7 - -6 -6 - -5 -5 - -4 -4 - -3 -3 - -2 -2 - -1 -1 - 0 Depth Interval (feet)Number of Pixels



### Depth Distribution in Basins

0.0E+00 2.0E+05 4.0E+05 6.0E+05 8.0E+05 1.0E+06 1.2E+06 1.4E+06

-14 - -13 -13 - -12 -12 - -11 -11 - -10 -10 - -9 -9 - -8 -8 - -7 -7 - -6 -6 - -5 -5 - -4 -4 - -3 -3 - -2 -2 - -1 -1 - 0 Depth Interval (feet)Number of Pixels

## 30 

# 2.2 Boundary Salinity Along the southwest Gulf coast, fresh water fr om Shark Slough discharging through the Shark River alters the salinity of th e shallow coastal waters that form the western boundary of the FATHOM model domain. For the FATHOM MFL mode l, this relationship is described through empirically derived (regression) models that relate salinity at the boundary salinity locations (Figure 2.2) to the flow and stag e in Shark Slough. The water leve l 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 (tot al flow = S12T), (Figures 2.3 and 2.4).
The SERC monthly salinity data are the primary obs erved 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 Flor ida. This program visits 24 stations in Florida Bay and 21 stations along the southwest coast on a monthly ba sis, (Figure 1.5). Water samples are analyzed for salinity among a suite of nutri ent and other water quality pa rameters. The report by Jones and Boyer (2001) summarizes the data and disc usses long-term trends in water quality on a regional basis.
For the purpose of estimating boundary salinity, re gression equations were developed to estimate the salinity values measured at SERC sta tions 25, 26, 27, and 28 (Figure 2.5), based on the monthly values of P33 stage and S12T flow as regional indices of hydrol ogic 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 analys is. 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 ar e better predictors of salinity than equations that use either data set alone. Marshall (2004) and Marshall, et al (2004) us ed multiple variable regression techniques to simulate salinity within Florida Bay from stage, sea su rface elevation, and wind data using a similar regression method.
The same approach was used to describe the va riation 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 Tr ail, there is strong st atistical relationship between salinity in Barnes a nd Card Sound and the indices of hydrologic variation in Shark Slough used for the western bounda ry salinity simulations.

## 31 Figure 2.2: Basin numbers and regional grou ps used in the FATHOM model. Dots identify locations of SERC salinity measuremen ts used to define var iable salinity boundary conditions.

42 12
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## 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
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46

45 42 12
11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12
11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

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 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 

## 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



## S12 T

TSB P33

S196 aT21 Transect



## Joe Bay

## 33 Figure 2.4: Regional indices for boundary sa linity 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

1 2 3 4 5 6 7 8 9 10 11 12 mon P33 Annual Mean Stage, cm

100 150 200 250

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 year

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

1 2 3 4 5 6 7 8 9 10 11 12 mon A nnual Total Discharge, (10**6 m3)/yr, S12T

0 500 1000 1500 2000 2500

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 year

## 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Mean Salinity (psu), SERC Station 1

15 20 25 30 35 40 45

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

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Mean Salinity (psu), SERC Station 25

15 20 25 30 35 40 45

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

## 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Mean Salinity (psu), SERC Station 26

15 20 25 30 35 40 45

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

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Mean Salinity (psu), SERC Station 27

15 20 25 30 35 40 45

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

## 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 R 2



### 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Mean Salinity (psu), SERC Station 28

15 20 25 30 35 40 45

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

## 37 

# 2.3 Calculation of Residence Time FATHOM calculates residence time based on dia gnostic 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 monthl y 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, ra infall and runoff), with the resu lts expressed in days. Turnover time ( T T



## ) is mathematically equivalent to the clas sically defined hydraulic retention time of a basin defined as

T

T 

## = 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 de fined on a monthly basis for each basin by simulating the addition of a tracer at the be ginning of each month and measuring the amount of tracer remaining in the basin at the end of th e 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 ( D H



## ) for a given basin and month is calculated by solving for D H



## (in days) in the following equation:

C

t 

## = C o



## * exp ( - t / D H



## ) 2.2

where C o



## is the concentration of the tr acer at the beginning of the month, C t 

## 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 sali nity from Shark Slough hydrology, in section 2.2, also serves as the general approach for es timating other input data for the historical reconstruction period 1970 through 2002. Data th at measure components of the Florida Bay water budget most directly, such as rainfall and in flow, are not available pr ior 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 Na tional Park (MMN), and continuous measurement of flow and salinity in estuarine creeks in th e central and northeast re gion of the Bay (USGS), (Table 2.2).

The available direct data are used to establish relationships be tween water budget components and longer term indirect data th at represent the regional indice s of climate and hydrology. The indirect data are long-term data sets from vari ous agencies that monitor sea level and tides, wetland water levels, rainfall, and water flow th rough water management structures (weirs, gated structures, and pumps). The indi rect 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 estimat e the long-term input data sets required by FATHOM, (Table 2.2)for the peri od 1970 through 2002. The methods used to construct the FATHOM input data sets from th ese indirect data are described in Section 2.1 (bathymetry), Section 3 (inflo w), and Sections 4.1 and 4.2 (rainfall and evaporation).

2.4.1 Rainfall Long-term input data for rainfall are availabl e 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), (Tab le 2.2 and Figure 2.7). The Division 7 rainfall data are collected by primary and cooperating m onitor stations throughout Florida Bay and the Keys, and includes the Tavernier station. The ra infall at Flamingo, Royal Palm, Tavernier, and the NCDC Division 7 rainfall provide the basis fo r estimating long-term rainfall in Florida Bay for the MFL base case. Royal Palm rainfall is al so used to estimate the c ontribution 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 ai r 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 reco rd for these data at Joe Bay covers only the period 1990 through 2002.
These data are used in three approaches for es timating long-term evaporation. Air temperature, humidity and wind speed are used in a Dalton La w calculation of evapora tion. The temperature range is used to estimate atmospheric transmissi vity in a radiation-based approach to estimating

## 39 evaporation, and temperature alone is used to calculate potential eva poration based on the empirical Thornthwaite method.
2.4.3 Boundary Salinity The indirect data used to estim ate 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 compone nt of the MFLs, the estimation of inflow is described in its own section of this report. Se ction 3 describes the methods used to estimate fresh water inflow from the Ta ylor 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 an d 2.13). At supratidal and longer time scales, changes in water level ar e 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 in creasing mean sea level over the period 1970 through 2002 has been removed from the sea level index da ta. Seasonal and year-to-year changes in mean sea level remain in the de-trended data.

## 40 Table 2.2: Information sources used for de veloping FATHOM input data to support simulation of salinity in Florid a 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 i ndirect data sources for ra infall (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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Rainfall, Flamingo (cm/yr)

0 50 100 150 200

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 year

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Rainfall, Royal Palm (cm/yr)

0 50 100 150 200

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 year

## 43 Figure 2.7: Indirect data used fo r 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Rainfall, Tavernier (cm/yr)

0 50 100 150 200

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 year

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Rainfall, NCDC Div 7 (cm/yr)

0 50 100 150 200

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 year

## 44 Figure 2.8: Indirect data used for reg ional 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Ave Air Temp, Flamingo (deg C)

22 24 26 28

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 year

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Ave Air Temp, Royal Palm (deg C)

22 24 26 28

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 year

## 45 Figure 2.8: Indirect data used for regio nal 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Ave Air Temp, Tavernier (deg C)

22 24 26 28

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 year

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Ave Air Temp, NCDC Div 7 (deg C)

22 24 26 28

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 year

## 46 Figure 2.9: Indirect data used for regio nal 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Flamingo Air Temp Range, deg C

0 5 10 15

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 year

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Royal Palm Air Temp Range, deg C

0 5 10 15

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 year

## 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Tavernier Air Temp Range, deg C

0 5 10 15

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 year

## 48 Figure 2.10: Indirect data used for se asonal pattern of relative humidity

Figure 2.11: Indirect data used for th e 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Joe Bay Ave Annual Wind Speed, m/s

3 4 5 6

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

1 2 3 4 5 6 7 8 9 10 11 12 mon Joe Bay Ave Annual Relative Humidity, %

65 70 75 80 85

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

## 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Mean Sea Level, cm, Key West

10 20 30 40

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 year

## 50 

# 3 E STIMATES OF 

# F RESH 

# W ATER 

# I NFLOW FROM 

# W ETLANDS Three characteristics define the inflow of fresh water from the adjacent wetlands into Florida Bay: the magnitude of flow, its timing, and its di stribution 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 prov ide 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 infl ow 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 mode l 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 part icular interest in estimat ing the inflow of fresh water into the central region of the Bay where hy persaline 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 as sumptions about the amount of ungauged inflow and how this is allocate d geographically as input to the FATHOM model.

This section describes the MFL ba se case inflow input data and th e 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 wa ter 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 discus sion of the PHAST model enhancements follows, including the results of model calibration and an eval uation of the enhanced model. Based on this evaluation, it was decided not to base the estimation of we tland inflow only on the enhanced PHAST model. The section closes with a desc ription 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 fluxe s across the related transects de fined in Figure 3.1 define the framework for compiling the wetland water budge t in the Taylor Slough C111 wetland basin. The fluxes designated MFLx are surface water fluxe s that link the three wetland basins of the PHAST model to the surrounding wetla nd 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 effectiv e net flux over a period of time. The del S flux can be large over short periods, es pecially 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 di scharges 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 id entifies the long-term da ta used to estimate components of the wetland water budget. Discha rge through the S197 st ructure 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 ca se 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 Ce ntral 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 th e S197 structure is opene d 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 am ounted to 311 million cubic meters per year, or 252 thousand acre-feet per year. The period of re cord 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 ta ken 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 estima te fresh water inflow from the wetlands in the Taylor Slough C111 wetland basin. Th e locations of the MFLx flow transects are shown superimposed on the SFWMM grid. Al so 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 estima ting 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 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 

### RPL 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### 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

1 2 3 4 5 6 7 8 9 10 11 12 mon A nnual Total Discharge (10**6 m3)/yr, Taylor Slough Bridge

0 20 40 60 80 100 120

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 year 

## Figure 3.2: Data used for regional indices of fr esh 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

1 2 3 4 5 6 7 8 9 10 11 12 mon A nnual Total Discharge (10**6 m3)/yr, s18c

0 100 200 300 400

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 year

## 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Total Discharge 10^6 m3/yr S175

0 50 100 150 200

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 year 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

1 2 3 4 5 6 7 8 9 10 11 12 mon A nnual Total Discharge (10**6 m3)/yr, s197c

0 40 80 120 160

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 year

## 55 0 20 40 60 80 100 120 140 160 180 200

MC TR MUD TC WHCGauged 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Total USGS Gauged Flows (10**6 m3/yr)

0 50 100 150 200 250 300 350 400

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 year 

## 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 in flow measured at the USGS estuarine creek monitoring stations; McCormick Creek (M C), Taylor River (TR), Mud Creek (MUD), Trout Cove (TC), and West Highway Creek (WHC)

## 56 Figure 3.5: Wetland water budget compon ents for the period March 1996 through October 2000 estimated directly from data. Flux es are in units of A) millions of cubic meters per year and B) thou sands 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

205 S18C MFL5 n/a MFL6 1 30 TSB+S175 MFL7

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

166 S18C MFL5 n/a MFL6 105 TSB+S175 MFL7

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 Wetl and Hydrology Model - PHAST 3.2.1 Long Pine Basin 

## For this project, the wetland basin hydrology mo del (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 evapotranspirati on in the sub-basin; no large tributary surface flows occur into or out of the sub-basin. The Everglad es Park Road controls flow across the north and west sides of this sub-basin, a nd the flow that occurs through the culverts in the road is minor. Incorporating this sub-basin into the wetland ba sin models required adop ting 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 Ta ylor Slough basin. Flow in McCormick Creek, the major identified surface wa ter 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 Pa rk 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 gene ral, 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 surf ace 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 geomor phic 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 ap pears that most of the surface water discharged from the Taylor Slough basin occu rs 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 calc ulated 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 Cr eek, 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 be tween 1.0 and 2.0 feet th at 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 we tland discharge into McCormick Creek across the Buttonwood Embankment is higher than for disc harge through Mud Creek and Taylor River.
Based on this information, the area of the remaini ng 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 evapotranspira tion. Discharge from the combined sub-basins across the Buttonwood Embank ment 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 th e 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 cu rves 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 (10 36 

### ft 3 

### /week) 186 97.8 89.1 h sill 

### (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 = McCor mick 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 Ta ble 3.3. The method of calibration minimizes the sum of squared deviations be tween modeled and observed wate r 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 routin e 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 re lation 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 Embankmen t 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 (10 6 

### ft 3 

### /week) 911 688 h sill 

### (ft) 1.6 1.27 A 1 

### (million ft 2 

### ) 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 wa ter 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 charac terized. The few measurements that have been made of this flow (Stewart et al. 2002) are inadeq uate to test the assumption that was used. The inflow calculated by PHAST is also sensitiv e to errors in the calculation of wetland evapotranspiration within the PHAST model.

## 62 Figure 3.8: Results of calibra tion 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

R 2 

### = 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

R 2 

### = 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

R 2 

### = 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

R 2 

### = 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 p eriod 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 A rea (m2) 0

A rea (m2) 236 A rea (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 PHAS T suffers from large uncertainties related to the estimation of evapotranspiration. Both ra infall and evapotranspira tion are large components of the wetland water budget, and individually th eir 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 ev apotranspiration, 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 mon itoring of creek flows (386 million cubic meters per year). This discrepancy indicates the magnit ude of the errors associ ated 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 infl ow data for FATHOM. For this use of the model inflow is calculated indirectly by estimati ng 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 combin ing information from long-term data sets. The approach deals explicitly with the uncertain ty related to the amount of ungauged fresh water inflow that occurs in addition to what is cu rrently measured. The amount and location of the ungauged portion of inflow varies between the MFL base case and alternativ e 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 cont rolled entirely by the variati on in the long-term data sets used to construct the inflow estimate for the historical rec onstruction of salinity, 1970 through 2002. These are the measured surface water flow s 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 rel ease 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 FATH OM 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 cons ists of Manatee Bay, where the C111 canal discharges fresh water to the coast through the S 197 control structure. The northeastern inflow group consists of inflow regions in FATHOM th at 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 su rface water basins within each inflow group is also presented on Figure 3.10.

## 65 Figure 3.10: FATHOM inflow groups showing th e distribution of flow among the basins in each group; percentages give distributio n of total inflow within each group

Figure 3.11: Excess rain fall 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

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Excess Rainfall (cm)

0 10 20 30 40 50 60 70 80

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 year

## 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 exam ined in the sensitivity analysis. The eastern inflow group provides inflow only to Manatee Ba y. The distribution of inflow from the northeastern inflow group into th e FATHOM basins matches the di stribution of inflow measured at the USGS monitoring sites, (Figure 3.4). The distribution of inflow fr om 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 gr oups 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 in flow is distributed be tween the central and northeastern inflow groups, (Table 3.4). The inflow measured at the USGS monitoring stations from February 1996 through September 2000 provid es 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 in cluded in the estimated inflow. The detailed description (below) of how the MF L base case inflow is constructe d 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) a nd the C111 canal (S18C) minus the flow measured at the S197 control structure. The second component accounts for the additional inflow to Florida Bay genera ted by rainfall over th e Taylor Slough C111 wetland sub-basin in excess of evapotranspira tion. For the MFL base case, the inflow assigned to the northeastern inflow group is ca lculated 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 to tal inflow assigned to the northeast inflow group so that it equals the tota l inflow measured at the USGS monitoring stations for the period February 1996 through September 2000.
In the calculation of excess rainfall, evapot ranspiration is calculat ed as a fraction (53 percent) of estimated total solar radiati on by the method described by Abtew (1996) for South Florida. Total solar radiation is estimat ed 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 fact or is estimated from the daily range of temperatures measured at Royal Palm using the method developed by the SFWMD (2003). Monthly values of ex cess 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 meas ured 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 in flow data. The 20 percent of additional inflow included in the MFL base case as unga uged-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 reconstruc tion, creek flows are not available prior to 1996. Therefore, the monthly values for infl ow 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 Tayl or 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 te mporal variation in the availabil ity 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 reconstructi on 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 di stribution 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 (10 6 

## m 3 

## /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 (10 3 

## 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 t he 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 sa me 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 t he 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 t he 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 t he 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 t he 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 t he RN-f alternative in Progress Report II and Progress Report III.)

## 70 

# 4 MFL B ASE 

# C ASE 

# C ALCULATED 

# S ALINITY 

# R ECONSTRUCTION 

# - 1970 THROUGH 

# 2002
The MFL base case input data represent the “b est 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 sec tion 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 fres h water input from the upstream wetland basins is described in detail in the previous section.
The input data consist of the followi ng 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 dire ct information needed by the model, various techniques must be applied to co nstruct 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 rain fall, estimates must be constructed from long-term rain data measured at onshore locations. In th e case of evaporation, neither direct data nor indirect measurements of evaporation are availabl e, so a variety of physically based models were evaluated for use. Similarly, the PHAST we tland hydrology model was evaluated, along with other simpler techniques, as a method of estima ting 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 consisten tly 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 be gin in 1970 because regional hydrological data needed to construct the time series of inflow from the Ta ylor 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 alternativ es 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 fo r the MFL base case is compiled from the records of rainfall at Tavernier, Flamingo, and Royal Palm , (Figure 2.6). The spa tial 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 desc ribe evaporation inputs to the model. Monthly rainfall amounts for each of thes e regions were calculated from the three longterm data records using weights based on Thiess en polygons. Mean annual rainfall varies little across the Bay, (Table 4.2). Average rainfall fo r 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 defi ne rainfall input to FATHOM

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



## Region 5 Region 4 Region 3 Region 2 Region 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



## 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 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 Rainfall (cm)

0 5 10 15 20 25

1 2 3 4 5 6 7 8 9 10 11 12 mon Annual Rainfall - MFL Base Case (cm)

0 20 40 60 80 100 120 140 160 180 200

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 year

## 74 4.1.2 Evaporation 

## Relative to rainfall, there are few data availa ble 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 appear s that evaporation is less variable than rainfall viewed at comparable scales, both temporally and spatia lly. A variety of sources provide information about the likely long-term average annual rate of evaporation, (Tab le 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 evapora tion is proportional to the difference between saturation vapor pressure at the water surface (c orresponding to the surface water temperature) and the unsaturated water content of the air (corresponding to air temperature and relative humidity), and to a functi on of the mean wind speed:
Evap = F * f(u) * (e sat 

## – e air 

## )


## , 4.1

where e sat 

## is the saturation vapor pressure at the water surface, e air 

## is the vapor pressure of the air, f(u) 

## is the function of th e 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 e air 

## . Monthly patterns of relative humidity and wind speed were derived from the Joe Bay weather tower, (Figur es 2.10 and 2.11). The average monthly pattern of these variables over the peri od 1991 to 2002 was used for every year of evaporation inputs.
Saturation vapor pressure e sat 

## is calculated from the temperature of the water. Surface water temperature data are estimated for the Evergl ades National Park Mari ne Monitoring Network stations by extrapolation based on correlation be tween water temperature at each station and air temperature measured at Tavernier, Flamingo, and Royal Palm, Figure 2.6.
The estimated monthly evaporation inputs are show n in Figure 4.4 for the MFL base case. Based on best professional judgement, the wind functio n 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 evap oration 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 monitori ng stations on the model boundary (Figure 4.5) calculated with the regression models, (Table 2.1). The regre ssion models relate salinity at SERC stations 25, 26, 27, 28, and 1 from the monthly flow thr ough 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. Fi gure 4.6 shows the boundary salinity time series provided as input to FATHOM.

Figure 4.5: Location of boundary salinity reg ions for FATHOM input. Boundary salinity values for the MFL base case are derived fr om data collected by the SERC estuarine monitoring program and by the Florida Ke ys National Marine Sanctuary (NMS).

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 2 7 40

39

38 37 36 35

44

43 41 4 7

46

45

28 26 25

27 1

240 237 234 231 228 225 222 219

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 & 216 SERC 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 2 7 40

39

38 37 36 35

44

43 41 4 7

46

45

28 26 25

27 1

240 237 234 231 228 225 222 219

Region 2

Region 5 Region 6 Region 3

Region 4 Region 8

Region 7 Region 10

Region 9
Region 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 2 7 40

39

38 37 36 35

44

43 41 4 7

46

45

28 26 25

27 1

240 237 234 231 228 225 222 219

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 2 7 40

39

38 37 36 35

44

43 41 4 7

46

45

28 26 25

27 1

240 23 7 234 231 228 225 222 219

28 26 25

27 1

28 26 25

27 1

240 23 7 234 231 228 225 222 219

240 23 7 234 231 228 225 222 219

Region 2

Region 5 Region 6 Region 3

Region 4 Region 8

Region 7 Region 10

Region 9
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 bounda ry 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 23 28 33 38 43 48

1970 1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 region3 region4

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 region5 region6

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 region7 region8

## 79 Figure 4.6: Time series of boundary salinity for MFL base run (cont.)

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 region9 region10

Yearly Ave Boundary Salinity, psu

20 25 30 35 40

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 Gulf A tlantic Card Sd

Mon Ave Boundary Salinity, psu, 70-02

20 25 30 35 40

1 2 3 4 5 6 7 8 9 10 11 12 Gulf A tlantic Card Sd

## 80 4.1.4 Fresh Water Inflow from Wetlands 

## MFL base case monthly inflow into the Bay is estimated from flow m easured at Taylor Slough Bridge (TSB) and in the C111 Canal (S18C and S 197), and from rainfall at Royal Palm in excess of potential evapotranspiration. Section 3.3 descri bes these calculations in detail. The total inflow estimated from these sources is assi gned to FATHOM basins through inflow groups, (Figure 3.10). Figure 4.7 plots th e monthly inflow volumes estimat ed 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 simp le 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 presum ed 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, whic h is roughly equivalent to twenty percent of the flow at the USGS monitoring locations, and th is inflow is assigned to the central inflow group only, with no ungauged flow augmenting estimat ed creek flows to the northeastern region.

## 81 Figure 4.7: Time series of fresh water infl ow for MFL base case, by FATHOM inflow group

A nnual 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 Runof f NE Group Central Group Eastern Group Monthly Runoff (10**6 m3)/mo (MFL base case)

0 50 100

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 20 40 60 80 100 120 140 160

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 spec ifies monthly values for two i nput regions, (Figure 4.8). The Key West measured sea level data are applied directly to sea le vel input region 1. The sea level applied to the boundary region 2, adjacent to southe rn Biscayne Bay, is increased by 3 cm above the Key West data. This offset accounts for water level set up in the interi or of Florida Bay as a result of non-linear interactions of the Gulf of Mexico tides w ith the shallow mud banks (Wang 1994). Figure 4.9 plots the monthly aver age sea level in the MFL base case.

Figure 4.8: Location of region for input of sea level into FATHOM

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 Region 1 Region 2

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 Region 1 Region 2

## 83 Figure 4.9: Time series of sea level input into FATHOM

Annual average normalized sea level (cm) 1970-2002

-6 -4 -2 0 2 4 6 8 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 -20 -15 -10

-5 0 5 10 15 20 25 30

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 0 5 10 15 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 Ba y and across its boundaries. The complex pattern of water level forcing over th e course of a simulation is re presented by adding the repeated sequence of hourly tides to monthly values of s ea level. The sequence of hourly tide levels describes water level fluctuations within a mont h; different sequences ar e specified for each of ten input regions, (Figures 4.10 and 4.11). These reproduce the general ch aracteristics 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 12
11 10 9 8 7 6 5

19 18

1 7 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 2 7 40

39

38 3 7 36 35

4 4

43 41 4 7

46

45 Region 2

Region 5 Region 6 Region 3

Region 4 Region 8

Region 7 Region 10

Region 9 Region 1 42 12
11 10 9 8 7 6 5

19 18

1 7 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 2 7 40

39

38 3 7 36 35

4 4

43 41 4 7

46

45 42 12
11 10 9 8 7 6 5

19 18

1 7 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 2 7 40

39

38 3 7 36 35

4 4

43 41 4 7

46

45 42 12
11 10 9 8 7 6 5

19 18

1 7 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 2 7 40

39

38 3 7 36 35

4 4

43 41 4 7

46

45 Region 2

Region 5 Region 6 Region 3

Region 4 Region 8

Region 7 Region 10

Region 9 Region 1

Region 2

Region 5 Region 6 Region 3

Region 4 Region 8

Region 7 Region 10

Region 9 Region 1

## 85 Figure 4.11: Semi-diurnal tida l 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 pa tterns for boundary tide regions used for FATHOM. Data referenced by day of the mont h, 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 deta iled 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 performan ce with alternative values of the bottom friction parameter selected within the rang e 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 reporte d 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 salin ity 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 sa linity in practical sali nity 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

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 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 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 5 6

4 1

42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 5 6

4 1 14 14 13a 13

1a 14a 2 2

3

16 16 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 A ll 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 A ll 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 A ll 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 A ll 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 A ll 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 A ll seasons Wet seasons Dry seasons

FATHOM basin Florida Bay SFWMD Region

## 92 

# 4.4 Results of Residence Time Calculations Residence time calculations were performed us ing two accepted estimates – turnover time and decay half-life. Calculated residence time in Fl orida Bay sub-basins ranges from a few days up to almost six months (Table 4.4). Basins in the central and northeast regi ons 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 ha lf-life (Figures 4.19-4.21) calculations yield almost identical results. Tu rnover time for a single input si ngle output CSTR (continuously stirred reactor) is conceptually th e 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 in crease in salinity coincide with periods of high residence times in the Bay. Basins with long re sidence 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 SFWM D 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 FAT HOM basis with median resid ence 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 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 

## 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 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

## 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 Basin-38 Park Key Basin

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 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 14 13a 13

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

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 14 13a 13

1a 14a 2

3

16 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 14 13a 13

1a 14a 2

3

16 5 6

4 1 14 13a 13

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 Basin-38 Park Key Basin

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 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 14 13a 13

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

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 14 13a 13

1a 14a 2

3

16 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 14 13a 13

1a 14a 2

3

16 5 6

4 1 14 13a 13

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

## 95 Figure 4.17: Bar and whisker diagrams show ing the percentiles (5 % 25%, 50%, 75%, 95%) of simulated Turnover Time (days). Th e 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 34Turnover Time (days)

SFWMD Re g ion 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 34Turnover 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 34TurnoverTime (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 pa nels: > 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 Hal f-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 Basin-38 Park Key Basin

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 Basin-37 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 14 13a 13

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

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 14 13a 13

1a 14a 2

3

16 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 14 13a 13

1a 14a 2

3

16 5 6

4 1 14 13a 13

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 Basin-38 Park Key Basin

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 Basin-37 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 14 13a 13

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

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 14 13a 13

1a 14a 2

3

16 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 14 13a 13

1a 14a 2

3

16 5 6

4 1 14 13a 13

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

## 98 Figure 4.20: Bar and whisker diagrams show ing 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 34Decay Half-life (days)

SFWMD Re g ion 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 34Decay 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 34Decay Half-life (days)

SFWMD Region FATHOM Basin Florida Bay

## 99 Figure 4.21: Frequency (% of months) with wh ich Decay Half-life (days) is simulated in different ranges. From top to bottom pa nels: > 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 80 100 120

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 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

## 100 

# 5 E RROR 

# , S ENSITIVITY 

# , AND UNCERTAINTY
This section evaluates th e errors in salinity calculations by the FATHOM model with input data defined by the MFL base case and examines the sens itivity 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 FAT HOM to predict salinity in Florida Bay under scenarios where Everglades hydrology differs fr om historical conditions. This uncertainty derives from a number of sources, including model e rror, errors in the estimated input data and boundary conditions, and variability in salinity no t completely measured by the available data. The sensitivity analysis provides a test and validation of the se lection 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 s upports calculation of salinity fluctuations over the period 1970 through 2002. Estim ates of error in the MFL ba se case simulation are based on differences between calculated values and monthl y salinity measurements. With one exception, the sensitivity analysis is base d 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 infl ow 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 (J ones and Boyer 2001), Figure 1.5. These data provide the most comprehensive and consistent pi cture 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 calcul ation of salinity, erro r 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 ba sed on the set of residual errors, R 

## . The residual errors are calculated as the differences betw een measured and calculated sali nity values that correspond to the same location in time and space. In this anal ysis, the residual errors are calculated as the difference between the basin-wide average sa linity calculated by FAT HOM, 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 cal culations, and noise in th e data, i.e. variations not adequately characteri zed 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 fo r the Florida Bay and Florida Keys Feasibility study, and for the areas of interest to th e 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 aver age error is zero there can still be significant differences between simulated and observed valu es; these differences may simply cancel out in the calculation of th e average error. The root mean squared error rmse and the aver age absolute error are measures of residual deviation between simulated and obs erved values, reported in the uni ts of the simulated variable. The root mean squared error is ca lculated 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 e xpected magnitude of the difference between calculated and measured salinity at a particular location and time.
Model efficiency is similar to the coeffici ent of determination, R-squared, i.e. R 2 

## . The coefficient of determination measures the fraction of the variance in the ob servations that can be explained by a linear transformation of the simulate d salinity values. Therefore, the definition of the coefficient of determination is based on th e correlation between the simulated and observed values. In contrast, model efficiency is calculat ed 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 measur e 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 accoun ts for no more of the variation than does the mean of the data. An efficiency of 100 indicate s that the model accounts for all of the variation in the data. However, model efficiency can ta ke 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 with in 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 (R 2 

## ) are high, greater than 0. 68 at all locations and equal to 0.9 overall. Largely, this reflects th e ability of the MFL base case calculations to capture the seasonal cycles that dominat e 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 cont ributes 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 thro ughout Florida Bay.
Joe Bay and Garfield/Rankin (Feas ibility 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 spa tial 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 circul ation 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 Tabl es 5.2 are not true measures of the error in calculated salinity, but these are a conservative estimate of the m odel error. This distinction arises from a fundamental difference between the sa linity that is being ca lculated and the sali nity that is being

## 103 ef f 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 th at is inherent in the FATHOM calculations and in the input data provided to dr ive 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 observati ons are collected as grab samples on one day in each month, and the variation in these data include the influe nce of short-term and day-to-day variability in salinity that is not pres ent 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 effici ency 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 salin ity 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

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 14 13a 13

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

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 14 13a 13

1a 14a 2

3

16 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 14 13a 13

1a 14a 2

3

16 5 6

4 1 14 13a 13

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

Rabbit Key Basin

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 38 SERC 18

Duck Key

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 47 SERC 9 Whipray Basin

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 34 SERC 13 Park Key

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 15 SERC 23

Butternut Key

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 46 SERC 24 Long Sound

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 7 SERC 8

Joe Bay

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 13 SERC 10 Little Madeira (Mouth)

0 10 20 30 40 50

1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 Fathom 14-15 SERC 11

Garfield/Rankin

0 10 20 30 40 50

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 simu lation (Jan 1991 - Dec 2002). Time series showing monthly average values of both simu lated (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 Alt ernative Inputs – 1992 through 2002 Sensitivity analysis compares the performance of the salinity simulations for the MFL base case with the performance obtained with alternative ch oices of input data and model parameters. The sensitivity analysis addresses th e question of whether the MFL base case is the best choice of input data sets and model parameter values am ong the alternatives considered. The sensitivity analysis also provides informa tion 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 inpu t data and model parame ter values span the range of uncertainty inherent in selecting the corresponding com ponent 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 anal ysis 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 repr esentation 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 Tave rnier and other adjacent monitoring stations, uniformly over the bay. The Division 7 regi on includes Florida Bay a nd 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 th ree locations around the bay was applied to the five FATHOM regions within the bay us ing 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 obs erved 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 Thiess en 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 prec ipitation 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 av erage rate of 135 cm/year, Table 5.4.
Evaporation Alternative 1 takes a radiation-base d approach to estimati ng evaporation; this approach results in an average rate of 137 cm/y ear. In the radiation a pproach, evaporation is calculated as a fraction (53 percen t) of estimated total solar ra diation by the method described by Abtew (1996) for South Florida. Total solar radia tion is estimated from ra diation 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 temp erature range interpolated ove r the bay from temperatures measured at Flamingo, Royal Palm, and Tavernier.
Evaporation Alternative 2 applies the Thornthw aite formula (Thornthwaite and Holzman 1939), based on temperature indices; th is approach results in an average rate of 147 cm/year.
Evaporation Alternative 3 applies the same appro ach 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 de rived from long-term observations at three locations: Flamingo, Royal Palm and Tavernie r. Monthly mean surface water temperature was estimated for fourteen locations within the bay using regressions of monthly average water temperature (observed at the 14 EN P marine monitoring stations) on monthly average air temperature (observed at 3 site s - 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 estimate s 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 radiatio n at the water surface, the latent heat of evaporation, and a coefficient char acteristic 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 se lected surface characteristic coefficient was 137 cm/yr. The monthly evaporation estimate s 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 me an 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/y r. The calculated evaporation amounts were applied uniformly over the bay by assigning t he 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 tem poral variability around the same long- term mean value. The MFL base boundary salinity input data are esti mated 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 aver ages by month of the observed bo undary salinity values for the period 1992 through 2002. Boundary Salinity Alte rnative 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 monthl y 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 bounda ries 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 MF L base case is an estimate derived from measurements of flow over shallow, grass-covere d 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 Paramete r 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 base d on calculations from flume studies on a western bank and also agrees well with calc ulations based on obse rved 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 calc ulation 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 calc ulation 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 dept h class for each basin and for each line segment that mark the banks between the basins. Sectio n 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 ba thymetry parameter sets, Table 5.7, increase the depth by 60 percent, first onl y in the mean depth of the basi ns, 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 MF L bathymetry in section 2.1)

Alternate 1 (BT-1) Basins – All depths in all basins increas ed by 60% (depths multiplied by 1.6) Banks – same as in base simulation

Alternate 2 (BT-2) Basins – All depths in all basins increas ed 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 crit eria. 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 cas e. 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 effi ciency of an alternative exceeds the model efficiency for the MFL base case. Where model e fficiencies 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 altern ative at other locations, Table 5.13. The other measures of model performance, Tables 5.9 throu gh 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 spa tially. Areas affected by choice of boundary salinity are in the West Region, adjacen t to the Florida Shelf, and in the far eastern portion of the model domain where Florida Bay jo ins 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 parame ter 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 th e Florida Shelf. Generally, a higher degree of flushing, lower residence time, suppresses the ab ility of water loss by ev aporation 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 app lication 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.111Table 5.8: Values of MODEL EFFICIENCY computed for the period 1991 through 2002 from the difference betweensimulated monthly average salinity and salinity measured in water samples takenonce every month (n=144). High values areindicated.BasecaseRF1RF2EV1EV2EV3RN1RN2RN3RN4RN5BS1BS2FR1FR2BT1BT2All Florida Bay8179798079808080817978787364497663SFWMD RegionsFeasibility Study Region 1165676668636562626565606556122536Feasibility Study Region 1a1a76615972596777647774827575-9-1068-12Feasibility Study Region 554337393843404343453031382634384637Feasibility Study Region 227870687368757475777782757643-256641Feasibility Study Region 335850525555545957614550524741695741Feasibility Study Region 44515151505352515151515130749555148Feasibility Study Region 1616474747474747474747474730047474747Feasibility Study Region 665960585761615959595860463150675648Feasibility Study Region 13134246484047433646424221391053-285458Feasibility Study Region 13a13a747475727575747474747554-2766787567Feasibility Study Region 14146773726971756171676741566774-115169Feasibility Study Region 14a14a7677767974787277767645737652-395456FATHOM basinsLong Sound77773747671758168777782745014607410Joe Bay13566159625658485655564457586-4038-1Little Madeira (Mouth)1476615972596777647774827575-9-1068-12Park Key15775249705062836580748477761646213Duck Key477679797275806380757776747754-1036452Butternut Key467670686969757273757683727233-276632Garfield/Rankin374337393843404343453031382634384637Whipray Basin345853535659575857575153514444655644Rabbit Key Basin38515151515252525152515128650545150Notes:62efficiency is higher than MFL base case62efficency is higher thanby >5%MFL base case62efficency is higherby >10%than MFL base caseBnd SalinityManning nBathymetryLocationRainfallEvaporationWetland Inflow112Table 5.9: Values of RMSE (root mean squared error) computed for the period 1991 through 2002 from the differencebetween simulated monthly average salinity and salinity measured in water samples taken once every month (n=144).Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR1 FR2 BT1 BT2All Florida Bay4.1 4.3 4.3 4.2 4.3 4.2 4.2 4.2 4.1 4.3 4.4 4.4 4.9 5.7 6.7 4.6 5.7SFWMD RegionsFeasibility 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 10.0 10.5 7.2 10.3Feasibility 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 8.8 8.9 4.8 8.9Feasibility 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 6.4 6.1 5.7 6.2Feasibility 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 5.7 8.4 4.4 5.8Feasibility 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 6.0 4.4 5.2 6.0Feasibility 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 2.8 2.7 2.8 2.9Feasibility 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 3.0 3.0 3.0 3.0Feasibility 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 3.2 2.6 3.0 3.3Feasibility 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 4.2 7.0 4.2 4.0Feasibility 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 3.3 2.6 2.8 3.2Feasibility 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 3.2 6.5 4.4 3.4Feasibility 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 5.8 9.9 5.7 5.5FATHOM basinsLong 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 8.5 5.8 4.7 8.6Joe 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 11.2 13.7 9.1 11.7Little 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 8.8 8.9 4.8 8.9Park 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 7.1 7.6 4.8 7.3Duck 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 5.1 10.8 4.5 5.2Butternut 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 5.8 7.9 4.1 5.8Garfield/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 6.4 6.1 5.7 6.2Whipray 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 5.1 4.1 4.5 5.1Rabbit 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 2.6 2.5 2.6 2.6Location Rainfall Evaporation Wetland Inflow Bnd Salinity Manning n Bathymetry113Table 5.10: Values of MEAN ERROR computed for the period 1991 through 2002 from the difference between simulatedmonthly average salinity and salinity measured in water samples taken once every month (n=144). High values are indicated.Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR1 FR2 BT1 BT2All 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 2.3 -3.1 -0.2 2.2SFWMD RegionsFeasibility 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 8.2 -7.0 -0.6 8.3Feasibility 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 7.1 -6.4 1.3 7.1Feasibility 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 1.6 1.6 1.4 1.4Feasibility 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 3.2 -5.5 -0.1 3.1Feasibility 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 1.3 0.1 0.8 1.1Feasibility 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 -0.2 -0.2 -0.2 -0.2Feasibility 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 0.4 0.4 0.4 0.4Feasibility 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 -0.3 -1.1 -0.5 -0.3Feasibility 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 1.3 -4.4 -1.7 1.5Feasibility 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 0.6 -1.0 -0.2 0.6Feasibility 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 0.7 -5.1 -1.8 0.2Feasibility 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 4.1 -8.1 -1.7 3.5FATHOM basinsLong 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 7.1 -4.2 1.3 7.2Joe 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 9.3 -9.8 -2.4 9.3Little 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 7.1 -6.4 1.3 7.1Park 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 5.4 -3.2 2.1 5.4Duck 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 2.8 -8.2 -1.4 2.6Butternut 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 3.5 -6.2 -0.1 3.4Garfield/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 1.6 1.6 1.4 1.4Whipray 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 0.3 -0.2 0.0 0.1Rabbit 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 -0.1 0.0 -0.1 0.0Location Rainfall Evaporation Wetland Inflow Bnd Salinity Manning n Bathymetry114Table 5.11: Values of AVERAGE ABSOLUTE ERROR computed for the period1991 through 2002 from the differencebetween simulated monthly average salinity and salinity measured in water samples taken once every month (n=144). Highvalues are indicated.Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR1 FR2 BT1 BT2All Florida Bay3.1 3.2 3.3 3.2 3.2 3.1 3.1 3.2 3.0 3.2 3.3 3.3 3.8 4.3 4.9 3.4 4.3SFWMD RegionsFeasibility 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 8.9 7.4 5.2 9.1Feasibility 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 7.9 7.6 3.9 8.0Feasibility 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 4.7 5.0 4.3 4.6Feasibility 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 4.8 7.3 3.6 4.8Feasibility 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 4.9 3.5 4.2 4.9Feasibility 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 2.2 2.0 2.1 2.2Feasibility 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 2.1 2.1 2.1 2.1Feasibility 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 2.5 2.1 2.4 2.6Feasibility 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 3.3 5.5 3.0 3.1Feasibility 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 2.6 2.1 2.2 2.5Feasibility 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 2.5 5.6 3.5 2.7Feasibility 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 4.8 8.7 4.7 4.4FATHOM basinsLong 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 7.7 4.7 3.6 7.8Joe 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 10.2 10.2 6.8 10.4Little 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 7.9 7.6 3.9 8.0Park 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 6.3 6.6 4.1 6.4Duck 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 4.2 9.7 3.8 4.2Butternut 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 5.0 7.0 3.4 5.0Garfield/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 4.7 5.0 4.3 4.6Whipray 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 4.1 3.3 3.8 4.1Rabbit 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 1.9 1.8 1.9 1.9Location Rainfall Evaporation Wetland Inflow Bnd Salinity Manning n Bathymetry115Table 5.12: Values of R-SQUARED computed for the period 1991 through 2002 from the difference between simulatedmonthly average salinity and salinity measured in water samples taken once every month (n=144). Low values are indicated.Basecase RF1 RF2 EV1 EV2 EV3 RN1 RN2 RN3 RN4 RN5 BS1 BS2 FR1 FR2 BT1 BT2All Florida Bay0.90 0.89 0.89 0.89 0.89 0.90 0.90 0.90 0.90 0.89 0.89 0.88 0.86 0.88 0.86 0.87 0.88SFWMD RegionsFeasibility 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 0.87 0.68 0.73 0.86Feasibility 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 0.83 0.77 0.84 0.87Feasibility 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 0.68 0.71 0.72 0.72Feasibility 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 0.87 0.77 0.82 0.90Feasibility 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 0.75 0.84 0.82 0.79Feasibility 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 0.73 0.77 0.75 0.73Feasibility 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 0.70 0.70 0.70 0.70Feasibility 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 0.84 0.87 0.87 0.85Feasibility 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 0.77 0.82 0.83 0.80Feasibility 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 0.83 0.90 0.89 0.85Feasibility 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 0.92 0.78 0.77 0.89Feasibility 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 0.91 0.75 0.76 0.89FATHOM basinsLong 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 0.87 0.90 0.88 0.88Joe 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 0.86 0.58 0.65 0.85Little 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 0.83 0.77 0.84 0.87Park 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 0.91 0.77 0.84 0.94Duck 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 0.88 0.77 0.82 0.92Butternut 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 0.85 0.80 0.83 0.90Garfield/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 0.68 0.71 0.72 0.72Whipray 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 0.74 0.81 0.80 0.78Rabbit 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 0.72 0.75 0.74 0.72Bnd Salinity Manning n BathymetryLocation Rainfall Evaporation Wetland Inflow116Table 5.13: Values of MODEL EFFICIENCY computed for the period 1991 through 2002 from the difference betweensimulated monthly average salinity and salinity measured in water samples takenonce every month (n=144). Low values areindicated; otherwise contentsare identical to Table 5.7.BasecaseRF1RF2EV1EV2EV3RN1RN2RN3RN4RN5BS1BS2FR1FR2BT1BT2All Florida Bay8179798079808080817978787364497663SFWMD RegionsFeasibility Study Region 1165676668636562626565606556122536Feasibility Study Region 1a1a76615972596777647774827575-9-1068-12Feasibility Study Region 554337393843404343453031382634384637Feasibility Study Region 227870687368757475777782757643-256641Feasibility Study Region 335850525555545957614550524741695741Feasibility Study Region 44515151505352515151515130749555148Feasibility Study Region 1616474747474747474747474730047474747Feasibility Study Region 665960585761615959595860463150675648Feasibility Study Region 13134246484047433646424221391053-285458Feasibility Study Region 13a13a747475727575747474747554-2766787567Feasibility Study Region 14146773726971756171676741566774-115169Feasibility Study Region 14a14a7677767974787277767645737652-395456FATHOM basinsLong Sound77773747671758168777782745014607410Joe Bay13566159625658485655564457586-4038-1Little Madeira (Mouth)1476615972596777647774827575-9-1068-12Park Key15775249705062836580748477761646213Duck Key477679797275806380757776747754-1036452Butternut Key467670686969757273757683727233-276632Garfield/Rankin374337393843404343453031382634384637Whipray Basin345853535659575857575153514444655644Rabbit Key Basin38515151515252525152515128650545150Notes:30efficency is lowerthan MFL base case30efficency is lowerthan MFL base caseRainfallEvaporationWetland InflowBnd SalinityManning nBathymetryLocationby >20%by >40%

## 117 

# 5.3 Comparison of Base Case and Measured Inflow – 1996 through 2000 In addition to the analysis using the input altern atives 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 mari ne 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 th e 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 Progres s Report 1 (Mark I run).
A comparison of model performance over this pe riod 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 measur ements of the inputs. The results of this comparison, Table 5.14, show that there is no overall de gradation 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 detail ed results by region within the Bay (Appendices D and H). The local observed data provide a better descri ption of the boundary sa linity, 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 th e measured USGS creek flow is a biased estimate of the actual inflow because ungauged flow s 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 rema in 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 sa linities in the sub-basins fo r 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 pe riod 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 by > 10% MFL base case 62 efficency is higher by > 10% than MFL base case

## 119 

# 6 D EVELOPMENT AND 

# D ESCRIPTION OF A 

# W ATER 

# B UDGET 

# - 1970-2000
Input data assembled for the MFL base case provi de the best estimates for components of the fresh water budget in Florida Bay as estimated fr om FATHOM salinity estim ates. This section summarizes key aspects of the water budget fo r the period 1970 through 2000, including the influence of water management activities and it pr esents 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 alte red surface flows in the Taylor Slough C111 wetland sub-basin. In particular, the comple tion around 1980 of the firs t phase of the South Dade Conveyance System markedly increased surf ace 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 reve als 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 rela tive 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-ye ar variations. In this anal ysis, the water year provides the basis for compiling the water budget. The water y ear synchronizes with th e 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 co ntributed by rainfall. However in near-shore areas, close to the estuar ine 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-y ear changes in the volume of inflow from wetlands explain a significant portio n of the year-to-year variati on in maximum salinity that is separate from the effect of rainfall. 

# 6.1 Changes to Water Manage ment 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 ma nagers 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 drai n the main body of the original Everglades had already irreversibly altered hydrological conditio ns throughout South Florida. These efforts interrupted the flow of water southward out of Lake Okeechobee into the Everglades and increased the volume of water draini ng 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 mo tivate a series of actions intended to mitigate the effects of the structures and practices recen tly 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 deliver ies 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 discharg e into the headwaters of Tayl or Slough. The Experimental Water Deliveries program replaced the minimum m onthly 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 cont inuing 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 ha s 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 Pa rk. Additional operational modifications were made in the 1990’s in an attempt to restore flows and water levels in Tayl or Slough. Structural changes were also planned and made to implemen t a more even distributi on of flows from the C111 Canal across the mangroves.

## 121 Table 6.1: Water management activiti es affecting Florida Bay, 1960 through 2000

Period Water Management Activities
1960 - 1969 • Construction of the levee and S12 control stru ctures 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 di ke 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 headw aters 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 ag ricultural 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 Convey ance 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 se veral times to allow free discharge of flood waters through the C111 canal; this eventua lly 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 Tamiam i Trail into southern Miami-Dade County through the C111 and L31N canals.

• Increased flows in C111 canal initially disc harge 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 c hanges in water ma nagement 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 Hi ghway 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: implement ation 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 in to the wetlands north of Florida Bay.

## 122 

# 6.2 Summary of Water Budget for Florida Bay For analysis of seasonal varia tion the water budget components by month are summarized four ways – for two reporting periods, 1970 th rough 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 estu arine 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 fo r the whole Bay reflects this difference.
Rainfall and evaporation dominate the fresh wa ter budget, (Figures 6.1 and 6.2); the fluxes plotted in these figures are calc ulated from the MFL base case i nput 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 budge t 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 fr esh 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 th e water budget are compared for “typical” wet, dry and normal y ears. Variation in regional rainfall determines the overall pattern of wet, dry and normal hydrologic conditions. Howeve r, 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 Figur e 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 Ce nter - NOAA. Rainfall in Florida Bay has the more immediate effect on salinity as the larges t 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 operati ons, the years 1970 – 2000 were ranked based on rainfall for the Bay (MFL base case) and for the Everglades (NCDC Di vision 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 sout hwest Florida including the Evergl ades, but does not include the east coast of south Florida or the Florida Keys. We t, normal, and dry years were selected as years ranking near the 10%, 50%, and 90% exceedance le vel on both ranked lists. Years in which rainfall in Florida Bay and over the Everglades di ffer markedly were excluded from the selection of wet, normal and dry years.
As discussed in Section 6.1, water management activities increased surfac e water discharge into the Taylor Slough - C111 wetland sub-basin arou nd 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 pr e-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 ba sins 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 be tween wet year and normal year rainfall and between normal year and dry y ear rainfall, (Table 6.3).

## 124 Figure 6.1: Monthly average flux es 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 OAcre-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 OAcre-Feet/Month 

### Rainfall

Evaporation Net Inflow

## 125 Figure 6.2: Monthly average flux es 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 ra infall. 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 ba sis) for period 1970 through 2000 showing selected Wet, Dry and Normal years.

Figure 6.4: Wetland sub basins used to estima te 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).

20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 

### RPL 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 20 25 15 30

10

5 

### MFL5

MFL9MFL3MFL2MFL1 

### MFL7 MFL6

MFL8 MFL10 S175

S18C

S197 TSBMFL4



### EPSW

CP Long Pine Basin Taylor Slough Basin C111 Basin 

### RPL128Table 6.3: Summary of water budget components for Florida Bay and the Taylor Slough C111 wetland basin (See Figure 6.4for reference map).(flows in 10^3 ac-ft/yr reported for water year; water year 1995 = Nov 1994 thru Oct 1995)1.Rainfall2.EvaporationNet from Atmosphere3.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 LongSound10.MFL5-flow across Park road11.MFL1-flow across Park road12.MFL2-flow to Taylor Slough13.MFL8-inflow to McCormick Creek andcentral region14.15.nd-no data availableSource of Freshwater InputsDirect Freshwater InputsFreshwater Inputs from MangroveTransition 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)WetSeasonDrySeasonTotalWetSeasonDrySeasonTotalWetSeasonDrySeasonTotalWetSeasonDrySeasonTotalWetSeasonDrySeasonTotal452785304723067783952456405762187946884471135-428-445-873-420-477-896-503-536-1039-377-380-757-400-463-86323-367-34452-171-119-108-291-399199-16237288-152731017071801856318712470195ndndndndndndndndndndndndndndnd2027189211197262522472132302357106711532147197154351ndndndndndndndndndndndndndndnd000000000270279320114141154875466117713351184174155329ndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndnd202718102122182927245147079549534315848480260740749284103391564815631811962971851510017366239226201428Post-1980Dry Year - 19714723067783952456405762187946884471135-428-445-873-420-477-896-503-536-1039-377-380-757-400-463-86323-367-34452-171-119-108-291-399199-16237288-152731017071801856318712470195ndndndndndndndndndndndndndndnd2027189211197262522472132302357106711532147197154351ndndndndndndndndndndndndndndnd000000000270279320114141154875466117713351184174155329ndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndndnd202718102122182927245147079549534315848480260740749284103391564815631811962971851510017366239226201428Post-1980Dry Year - 1971Pre-1980Normal Year - 1975Dry Year - 1990Wet Year - 1995Normal Year - 1996Simplified 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 re levant 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 th e 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 th e salinity variation driven by climate? The following analysis of the 31-y ear water budget, wetland water levels, and estimated salinity begins to answer the first quest ion. 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 in flow assumes that a line ar relationship exists between rainfall and inflow, as independent vari ables, and rainfall and inflow are definitive characteristics of salinity as the dependent variab le. 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 rela tionship between the dependent and independent variables and for the significance of the coeffici ents serve as objective measures of whether a significant relationship exists betw een 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, calcul ated with FATHOM for the MFL base case, serves as the summary statistic in this application. This analys is is conducted on the basis of a calendar year. Evaluating sensitiv ity to inflow based on maximum sa linity is consistent with the application of these results to setting minimum flow s and levels in order to mitigate the effects of hypersalinity in Florida Bay. The di fference between annual maximum salinity S max 

## and the average salinity at the boundary with the Gulf of Mexico S b 

## 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 salin ity removes the influences of year-to-year fluctuations in boundary salinity th at are affected by either rainfa ll or inflow from the wetlands. The dependence of salinity in Equation 6.1 on rain fall and inflow in the preceding year helps to account for the effect of antecedent salinity condi tions, recognizing that residence times are high in some parts of Florida Bay.
For purposes of establishing opera ting rules for water management, it may be more desirable to establish goals with reference to water levels th at are easily monitored in wetlands adjacent to the mangrove transition zone rather than using the volume of infl ow 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 addres sing this question parallels that described for inflow, based on an i i i i i i b 

# Q Q R R f S S ε + = −

− − 

# ) , , , ( ] [
max 1 1

## 130 assumed linear relationship be tween annual maximum salinity S max 

## and rainfall and water levels, Equation 6.2:

6.2

Here H CP 

## and H EPSW 

## refer to annual average water levels at the Craighead Pond (CP) and EPSW monitoring locations used in the calibration of the PHAST wetland hyd rology 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 sh own in Figure 6.4. Maximum annual salinity is judged to be sensitive to rainfall, inflow or wa ter level if the correspond ing 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 “b est” model input parameters, i.e. the MFL base case, were used at each location.
Results of this analysis are shown as maps i ndicating locations where each rainfall, inflow, and water level variable are significan t, (Figure 6.4). Generally, basins in which annual maximum salinity has been sensitive to ye ar-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 expl ained 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 Ba y. 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 a nd water level on annual maximum salinity in the Central Region, according to this analysis, may simply reflect the fact that ve ry little or no inflow reaches the Central Region during dry years. Th erefore, annual maximum salinity values here are not affected by changes in infl ow when inflow is essentially zer o. 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). i i EPSW i CP i i i b 

# H H R R f S S 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 A PPLICATION 

# : P ROJECTED 

# E FFECTS OF 

# W ATER 

# M ANAGEMENT 

# A LTERNATIVES This section presents results of applying th e 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 scenar io (B2000), the base 2050 scenario (B2050), the current preferred CERP restoration alternative (C ERP1), 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 fo r each water management alterna tive as if these alternatives had been in operation during the period 1965 thro ugh 2000. These alternat ive realizations of regional hydrology allow one to ev aluate the benefits and impact s to water supply, flood control and wetland ecosystems of each water manageme nt alternative. FATHOM extends these projected conditions to include salinity conditions in Florida Ba y, making it possible to also evaluate benefits and impacts on Florida Bay. 

# 7.1 Coupling SFWMM Output to FATHOM Regional hydrologic conditions cal culated with the SFWMM provide the data necessary to estimate inflow from the wetlands and boundary salinity values along th e western boundary of Florida Bay, (Table 7.1). Othe r base case input data and model parameters remain the same as described for the MFL base case, with the excepti on that the rainfall and evaporation time series are extended to cover the period 1965 through 2000.
Coupling the SFWMM to FATHOM employs calcula ted 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, (Figur e 2.3). Small negative (northwa rd) 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 FA THOM 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 occurr ed historically in the period 1981 through 2000. The components of the wetla nd 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 veri fication of the wetland in flow 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 FAT HOM applied to examine water management scenarios. Data are assembled fo r 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

203 MFL5 11 MFL6 58 MFL7

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

166 S18C MFL5 n/a MFL6 105 TSB+S175 MFL7

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 budg et 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 evaporatio n. (Refer to Figure 6.4 fo r 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 fo r the T21 transect serves as the basis for estimating the variation in western boundary salin ity. 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 MF L base case, c.f. section 2. 2. Regression models were calibrated using the T21 transect flows from the calibration and ve rification runs and data from the SERC boundary salinity stations (SERC stat ions 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 ofShark 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 th e application with the SFWMM scenarios



## SERC Station Lag (months) T21 Flow Transect Intercept R 2



## 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 Nort heast Bay, the highest inflow, (Table 7.3). However, the NSM scenario ha s significantly higher in flow directed into the Central Region than the other thr ee scenarios. Average annual in flow for the B2000 scenario is comparable to the average annual in flow for the MFL base case.
The overall mean value for salinity imposed al ong 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 NS M 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 infl uence 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 pl ots of simulated salinity at the FATHOM basins of interest. The second figure co mpares the distribution of salin ity values acro ss sites for the entire record, during the wet season (June through October), and during the dry season (November through May). The third figure summari zes the frequency (% of months) with which the monthly average salinity falls into one of the six different salin ity 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, average d 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 manageme nt 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 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 4 1 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 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 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 5 6

4 1

42 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 5 6

4 1 14 14 13a 13

1a 14a 2 2

3

16 16 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

## 139 Figure 7.3: Overall summary of salinity di stributions 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

42 12

11 10 9 8 7 6 5

19 18

17
16 15 14 13

26 25 2 4

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 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 2 4

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 5 6

4 1

42 12

11 10 9 8 7 6 5

19 18

17
16 15 14 13

26 25 2 4

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17
16 15 14 13

26 25 2 4

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17
16 15 14 13

26 25 2 4

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2 2

3

16 16 5 6

4 1 14 14 13a 13

1a 14a 2 2

3

16 16 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

## 142 Figure 7.6: Overall summary of salinity di stributions 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

42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 4 1 47

46

45 14 14 13a 13

1a 14a 2

3

16 16 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 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2

3

16 16 5 6

4 1

42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17
16 15 1 4 13

26 25 2 4

23

22

21

20 3 4

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2

3

16 16 5 6

4 1 14 14 13a 13

1a 14a 2

3

16 16 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 di stributions 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 1 4 13

26 25 24

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2

3

16 16 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 1 4 13

26 25 24

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2

3

16 16 5 6

4 1

42 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 24

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 24

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 42 12

11 10 9 8 7 6 5

19 18

17 16 15 1 4 13

26 25 24

23

22

21

20 34

33

32

31 30 29 28 27 40

39

38 37 36 35

4 4

43 41 47

46

45 14 14 13a 13

1a 14a 2

3

16 16 5 6

4 1 14 14 13a 13

1a 14a 2

3

16 16 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 di stributions 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 produ ce similar frequency distributions of salinity when compared by FATHOM group, (Table 7.5). In part this result ma y 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 comp arisons 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 Ce ntral 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 hi gh salinity, i.e. the dry years when minimum flows and levels mana gement targets would come into play.

## 151 Table 7.5: Distribution of monthly salinity va lues relative to the ecologically defined salinity ranges for each SFWMM scenario. Valu es 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 salinit y 1965 - 2000 categor y (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 salinit y 1965 - 2000 categor y ( 36 y ears ) (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 salinit y 1965 - 2000 categor y ( 36 y ears ) (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 salinit y 1965 - 2000 categor y (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 sa linity time series for the fo ur SFWMM scenarios at Long Sound (Basin 7). The salinity ti me series obtained for the MF L 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 salin ity time series for the four SFWMM scenarios at Joe Bay (Basin 13). The salinity time se ries 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 salin ity time series for the four SFWMM scenarios at Little Madeira Bay (Basin 14). The sa linity time series obtained fo r 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 sa linity time series for the fo ur SFWMM scenarios at Park Key (Basin 15). The salinity ti me 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). Th e 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 sa linity time series for the fo ur SFWMM scenarios at Rabbit Key (Basin 38). The salinity time series obta ined 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 sa linity time series obtained fo r 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 sa linity time series for the fo ur SFWMM scenarios at Duck Key (Basin 47). The salinity ti me 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 S UMMARY AND 

# R ECOMMENDATIONS
8.1 Summary This significant effort has produced the basi c 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-ba lance model of Florida Bay (FATHOM) has been adapted for MFL use, and the wetland hydrolog y model (PHAST) has been updated by adding the Long Pine Basin and re-calibrated. Along the way, a better understandi ng 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 av ailable is short (1996 – present) and re presents a moderately wet period. Initial alternative runs (Mark I) indicate that FA THOM is sensitive to inflow and rainfall inputs, and also to the bathymetry. The Progress Re port 1 presents those activities in detail.
At the onset of the project it was thought that th e updated bathymetry woul d be available for use at the start of the project, but it was not. The upg rading of the bathymetry as part of this project is one of the most important accomplishments.
Other input data were assembled for the extende d period of analysis, (1970 through 2000), using a variety of indirect data that are regional in dicators of important climatologic and hydrologic conditions. Regional data that are availabl e for the extended period were used to create regression relationships with the existing data so that the period of anal ysis could be extended and salinity variation over a broader range of co nditions 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 combinati on 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 wa s 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, th e 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 uncer tainty statistics were computed, over the entire Bay the FATHOM MFL base case model is capab le of explaining about 81% of the monthly salinity variability. However, for some of the ba sins, particularly in the Northeast and Central Regions, model fidelity showed improvement thr ough the use of rainfall and inflow alternatives other than the base case parame ters. 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 sens itive to inflows and water levels in addition to direct precipitation. It was also no ted that the central area also r eacts 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 us e with SFWMM produced flow data and the runs were extended to 36 years. Four salinity si mulations 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 esti mate 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 Secti on 3.3 are the preferred estimate of wetland inflow.

• 

## The method of applying results of regiona l hydrologic simulations with the SFWMM as input to FATHOM described in Section 7, ap pears 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 th at 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 Fl orida 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 infl uenced by the changes in flow direction that are thought to occur when S197 is open and disc harging into Manatee Bay. Although the model takes into account the opening and closing of S197, Manatee Ba y 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 gr adient pattern in the Everglades panhandle that nay be caused by the opening of S197. Recent ob servations by the USGS indicate that Joe Bay salinity can vary spatially, and the spatial varia tion may be relatively large (Hittle and Zucker, 2004, personal communication). Wind effects app ear 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 pl atform 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 compro mised 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 mode l parameters in the basins that showed the potential for additional improvement when alte rnative inputs were us ed 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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