TECHNICAL REPORT 

MFL ESTABLISHMENT 

FOR THE 

LOWER SUWANNEE RIVER & ESTUARY, 

LITTLE FANNING, FANNING, 

& 

MANATEE SPRINGS

OCTOBER 2005 

In association with: 

SDII Global · Janicki Environmental

4260 West Linebaugh Ave, Tampa, FL 3362 

Fax: 813-265-6610 

Water Resource Associates, Inc. 

www.wraconsultants.com 

Engineering ~ Planning ~ Environmental Science

Phone: 813-265-3130 

Technical Report 

MFL Establishement for the 

Lower Suwannee River & Estuary, 

Little Fanning, Fanning & Manatee Springs 

SUWANNEE RIVER WATER MANAGEMENT DISTRICT 

Principal Authors: 

Mark D. Farrell, P.E., Water Resource Associates, Inc. 

John Good, P.E., Suwannee River Water Management District 

David Hornsby, Suwannee River Water Management District 

Anthony Janicki, Ph.D., Janicki Environmental, Inc. 

Rob Mattson, Suwannee River Water Management District 

Sam Upchurch, Ph.D., P.G., SDII Global Corp. 

Contributing Authors: 

Kyle Champion, P.G., SDII Global Corp.

Jian Chen, P.G., SDII Global Corp. 

Steve Grabe, Janicki Environmental, Inc. 

Kate Malloy, Janicki Environmental, Inc. 

Ravic Nijbroek, Janicki Environmental, Inc. 

Jim Schneider, Ph. D., SDII Global Corp. 

David Wade, Janicki Environmental, Inc. 

Michael Wessel, Janicki Environmental, Inc 

Pat Batchelder – Graphics – Suwannee River Water Management District 
i 

TABLE OF CONTENTS 

List of Figures ............................................................................................................................ vi 

List of Tables..............................................................................................................................xii 

1.0 Introduction...........................................................................................................1-1 

1.1 State of Florida Law Pertaining to the Establishment of MFLs.............................1-1 

1.2 Project Scope .......................................................................................................1-2 

1.3 Water Body Regulatory Designations ..................................................................1-2 

1.4 Relevent Water Resource Values ........................................................................1-4 

2.0 Introduction to the Suwannee River Basin and Study Area .................................2-1 

2.1 Suwannee River Basin .........................................................................................2-1 

2.1.1 Physical Setting of the Suwannee Basin..............................................................2-1 

2.1.2 Climate of the Suwannee River Basin..................................................................2-6 

2.1.3 Geology of the Suwannee Basin ........................................................................2-10 

2.1.4 Regional Systems ..............................................................................................2-15 

2.1.5 Land and Water Use in the Basin.......................................................................2-19 

2.1.5.1 Land Use and Population Characteristics ..........................................................2-19 

2.1.5.2 Water Use ..........................................................................................................2-20

2.2 Suwannee River .................................................................................................2-23 

2.2.1 Surfacewater Hydrology .....................................................................................2-23 

2.2.1.1 Annual Yield .......................................................................................................2-23

2.2.1.2 Spatial Flow Patterns .........................................................................................2.23 

2.2.1.3 Seasonal Flow Patterns .....................................................................................2-28 

2.2.1.4 Tidal River and Estuary ......................................................................................2-28 

2.2.1.5 Chemical Characteristics....................................................................................2-32 

2.2.2 Ecology...............................................................................................................2-35 

2.2.2.1 Aquatic and Wetland Communities ....................................................................2-35 

2.2.2.2 River Reach Ecology..........................................................................................2-35 

2.2.2.2.1 Suwannee River Mainstream .............................................................................2-35 

2.2.2.2.2 Santa Fe River ...................................................................................................2-39

2.2.2.2.3 Withlacoochee River ..........................................................................................2-39 

2.2.2.2.4 Alapaha River.....................................................................................................2-40 

2.2.2.2.5 Suwannee Estuary .............................................................................................2-40 

2.2.2.2.6 Species and Habitats of Interest ........................................................................2.40 

2.3 Lower Suwannee Drainage Basin and Springs..................................................2-47 

2.3.1 Introduction.........................................................................................................2-47

2.3.2 Population and Water Use .................................................................................2-49 

2.3.2.1 Population Distribution .......................................................................................2-49 

2.3.2.2 Land Use ............................................................................................................2-49 

2.3.2.3 Water Use ..........................................................................................................2-51

2.3.3 Topography, Physiography, and Drainage.........................................................2-51 

2.3.4 Geology and Hydrology......................................................................................2-55 

2.3.4.1 Local Stratigraphy and Geomorphology.............................................................2-55 

2.3.4.2 Surfacewater Hydrology .....................................................................................2-57 

2.3.4.3 Karst and Groundwater Hydrology .....................................................................2-57 

2.3.4.4 Ground Water Hydrology....................................................................................2-59 

2.3.4.4.1 Recharge............................................................................................................2-59 

2.3.4.4.2 Potentiometric Surface .......................................................................................2-59 

2.3.4.4.3 Groundwater Chemistry .....................................................................................2-63 
ii 

2.3.5 Fanning and Manatee Springs ...........................................................................2-63 

2.3.5.1 Function of Springs as Estavelles ......................................................................2-63 

2.3.5.2 Fanning Springs .................................................................................................2-65 

2.3.5.2.1 Introduction.........................................................................................................2-65 

2.3.5.2.2 Flow Characteristics ...........................................................................................2-66 

2.3.5.2.3 Ecological Characteristics ..................................................................................2-70 

2.3.5.3 Manatee Springs ................................................................................................2-73 

2.3.5.3.1 Introduction.........................................................................................................2-73 

2.3.5.2.2 Flow Characteristics ...........................................................................................2-76 

2.3.5.3.3 Ecological Characteristics ..................................................................................2-79 

2.3.5.4 Temporal Trends in Spring Discharge................................................................2-83 

2.3.5.5 Nitrate Issues .....................................................................................................2-84

3.0 Hydrologic Approach ............................................................................................3-1 

3.1 Surfacewater Systems (Lower Suwannee River).................................................3-1 

3.1.1 Overview ..............................................................................................................3-1

3.1.2 Stream-Flow Data ................................................................................................3.2 

3.1.2.1 Field Measurements.............................................................................................3-2 

3.1.2.1.1 Gage Locations ....................................................................................................3-2

3.1.2.1.2 Stage and Discharge Measurement Methods ......................................................3-4 

3.1.2.1.3 Data Quality and USGS Gage Rating of Data......................................................3-5 

3.1.2.1.4 Tidal Signal...........................................................................................................3-8 

3.1.2.1.5 Stream-Flow Data Trends ....................................................................................3-8 

3.1.3 Summary and Characterization of Stream-Flow Data........................................3-10 

3.1.4 Summary and Characterization of Wilcox Data..................................................3-11 

3.1.5 Antecedent Hydrologic Conditions During MFL Study .......................................3-13 

3.1.6 Reach Pickup .....................................................................................................3-15 

3.1.7 Tides and Salinity ...............................................................................................3-19 

3.1.8 Numerical and Statistical Models of the Lower Suwannee Study Area..............3-21 

3.1.8.1 HEC-RAS River Model .......................................................................................3-21 

3.1.8.2 Linked Groundwater/Surfacewater Model ..........................................................3-22 

3.1.9 Relationships between Flow and Salinity in the Lower Suwannee 

River and Estuary...............................................................................................3-25 

3.1.10 Hydrologic Issues ...............................................................................................3-27 

3.1.10.1 Long-term Climatic Cycles .................................................................................3-27 

3.1.10.2 Sea-Level Rise ...................................................................................................3-28 

3.1.10.3 Tidally-Forced Extreme Events ..........................................................................3-28 

3.2 Springs ...............................................................................................................3-28 

3.2.1 Overview ............................................................................................................3-28 

3.2.2 Data....................................................................................................................3-28 

3.2.2.1 Gage Locations and Periods of Record .............................................................3-29 

3.2.2.2 Spring Bathymetry Data .....................................................................................3-32 

3.2.2.2.1 Manatee Spring Bathymetric Survey..................................................................3-32 

3.2.2.2.2 Fanning Spring Bathymetric Profiles ..................................................................3-34 

3.2.2.3 Groundwater Data ..............................................................................................3-36 

3.2.2.3.1 Groundwater Levels ...........................................................................................3-36 

3.2.2.5 Precipitation Data ...............................................................................................3-42 

3.2.2.6 Summary ............................................................................................................3-44

3.2.3 Data Synthesis and Analyses.............................................................................3-44 

3.2.3.1 Introduction.........................................................................................................3-44 

3.2.3.2 Methods..............................................................................................................3-47 

3.2.3.2.1 Simulating Stage Data........................................................................................3-47 
iii 

3.2.3.2.2 Simulating Discharge Data.................................................................................3-47 

3.2.3.2.3 Uncertainty Associated with Data Simulation.....................................................3-47 

3.2.3.3 Fanning Spring ...................................................................................................3-47 

3.2.3.3.1 Simulating Spring Stage.....................................................................................3-48 

3.2.3.3.2 Simulation of Fanning Spring Discharge ............................................................3-51 

3.2.3.3.3 Data Characteristics ...........................................................................................3-55 

3.2.3.3.3.1 Population Descriptors .......................................................................................3-55 

3.2.3.3.3.2 Flow and Stage Duration Curves .......................................................................3-55 

3.2.3.3.3.3 Relationship to Wilcox Stage and Flow ..............................................................3-60 

3.2.3.3.3.4 Discharge Trends ...............................................................................................3-60

3.2.3.3.4 Hydrologic Conditions During MFL Study ..........................................................3-60 

3.2.3.4 Manatee Spring ..................................................................................................3-64 

3.2.3.4.1 Simulation of Manatee Spring Stage..................................................................3-68 

3.2.3.4.2 Simulation of Manatee Spring Discharge ...........................................................3-68 

3.2.3.4.3 Data Characteristics ...........................................................................................3-72 

3.2.3.4.3.1 Population Descriptors .......................................................................................3-72 

3.2.3.4.3.2 Flow and Stage Duration Curves .......................................................................3-77 

3.2.3.4.3.3 Relationship to Wilcox Stage and Flow ..............................................................3-77 

3.2.3.4.3.4 Discharge Trends ...............................................................................................3-77

3.2.3.4.4 Hydrologic Conditions During MFL Study ..........................................................3-77 

3.2.3.5 Contribution of Springs to River Flow.................................................................3-77 

3.2.3.6 Relationship of Spring Discharge and Stage to 

 Dishcarge at Wilcox Gage..................................................................................3-81 

4.0 Ecological Foundations ........................................................................................4-1 

4.1 Hydrology-Habitat Linkages .................................................................................4-1 

4.1.1 Manatee Thermal Refuge.....................................................................................4-1 

4.1.2 Upper Estuary Submerged Aquatic Vegetation....................................................4-2 

4.1.3 Tidal, Fresh-water Swamps..................................................................................4-3 

4.1.4 Tidal Creeks .........................................................................................................4-5 

4.1.5 Oyster Bars and Reefs .........................................................................................4-6 

4.1.6 Other Important Habitats ......................................................................................4-7 

4.2 Target Species ...................................................................................................4-10 

4.3 Habitat-Based Hydrologic Analyses ...................................................................4-13 

4.3.1 Riverine Studies and Data..................................................................................4-13 

4.3.2 Estuarine studies and data.................................................................................4-16 

5.0 Flow-Habitat Relationships : Establishment of Hydrologic Shifts .........................5-1 

5.1 Approach and Rationale.......................................................................................5-1 

5.2 Springs Target Habitat Analysis ...........................................................................5-2 

5.2.1 Introduction...........................................................................................................5-2 

5.2.2 Thermal Refuge Analyses for Manatee and Fanning Springs..............................5-3 

5.2.2.1 Data Sources........................................................................................................5-3

5.2.2.2 Water-Temperature Data .....................................................................................5-4 

5.2.2.3 Spring Bathymetry Data .......................................................................................5-4 

5.2.2.4 Manateee Sighting Data.......................................................................................5-4 

5.2.2.5 Thermal Model Description for Manatee Spring...................................................5-7 

5.2.5 Model Development .............................................................................................5-7 

5.2.2.5.2 Model Calibration .................................................................................................5-9

5.2.2.5.3 Model Scenarios.................................................................................................5-11 

5.2.2.6 Flow Analyses for Manatee Protection at Manatee Springs...............................5-12 

5.2.3 Stage (Level) Analysis for Manatee Protection at Fanning Spring.....................5-13 

5.3 Lower Suwannee River Target Habitat Analyses...............................................5-15 
iv 

5.3.1 Quantifying Relationships between Flow and Salinity for 

Downstream Habitats .........................................................................................5-15 

5.3.1.1 Data Sources......................................................................................................5-15 

5.3.1.2 Relating Flow and Isohaline Location.................................................................5-15 

5.3.1.3 Quantification of Habitat .....................................................................................5-17 

5.3.1.4 Estimating Habitat at Risk with Changes in Flow ...............................................5-19 

5.3.2 Upper Estuary Submerged Aquatic Vegetation..................................................5-20 

5.3.2.1 Data Sources......................................................................................................5-20 

5.3.2.2 Spatial Extent of SAV .........................................................................................5-21 

5.3.2.3 SAV Habitat Requirements ................................................................................5-23 

5.3.2.4 Estimating Location of 9 ppt Isohaline................................................................5-25 

5.3.2.5 Estimating SAV Habitat at Risk ..........................................................................5-26 

5.3.3 Tidal Freshwater Swamps..................................................................................5-27 

5.3.3.1 Data Sources......................................................................................................5-27 

5.3.3.2 Spatial Extent of Tidal Fresh-Water Swamps in the Upper Estuary...................5-31 

5.3.3.3 Tidal Swamp Habitat Requirements...................................................................5-31 

5.3.3.4 Esitmating Location of 2 ppt Isohaline................................................................5-35 

5.3.3.5 Estimating Tidal-Swamp Habitat at Risk ............................................................5-37 

5.3.4 Tidal Creeks .......................................................................................................5-38 

5.3.4.1 Data Sources......................................................................................................5-38 

5.3.4.2 Habitat Requirements.........................................................................................5-39 

5.3.4.3 Spatial Extent of Tidal Creeks ............................................................................5-41 

5.3.4.4 Estimating Location of 5 ppt Isohaline................................................................5-43 

5.3.4.5 Estimating Tidal Creek Habitat at Risk...............................................................5-43 

5.3.5 Oyster Bars and Reefs .......................................................................................5-45 

5.3.5.1 Data Sources......................................................................................................5-45 

5.3.5.2 Spatial Exent of Sampling ..................................................................................5-45 

5.3.5.3 Habitat Requirements.........................................................................................5-47 

5.3.5.4 Estimating Exceedance of 20 ppt Surface Salinity.............................................5-50 

5.3.6 Other Important Habitats ....................................................................................5-53 

5.3.6.1 Riverine Upper Tidal Bottomland Hardwood Swamps .......................................5-53 

5.3.6.1.1 Methodology and Analysis .................................................................................5-53 

5.3.6.2 Flood depths in Upper Tidal Forests ..................................................................5-56 

5.3.7 Riverine Snag (Wood) Habitat............................................................................5-56 

5.3.7.1 Methodolgy and Analysis ...................................................................................5-56 

5.3.7.2 River Stage and Wood Volume ..........................................................................5-57 

5.3.8 Tidal Marshes.....................................................................................................5-61 

5.3.8.1 Methodology and Analysis .................................................................................5-61 

5.3.8.2 Caldium/Juncus ratios ........................................................................................5-63 

5.3.9 Integrating Relationships between Habitat Avaliability and River Flow..............5-65 

5.3.9.1 Assumptions and Considerations.......................................................................5-65 

5.4 Critical Flows to Maintain Thermal Refuge and Passage and 

 Lower Manatee Suwannee River Habitats .........................................................5-67 

5.4.1 Manatee Spring ..................................................................................................5-67 

5.4.2 Fanning Spring ...................................................................................................5-67 

5.4.3 Lower Suwannee River ......................................................................................5-67 

5.4.4 Sustaining River Low Flow Conditions During the Dry Season..........................5-69 

6.0 Summary and MFL Recommendations................................................................6-1 

6.1 Summary ..............................................................................................................6-1 

6.1.1 Lower Suwannee River Study Area .....................................................................6-1 

6.1.2 Fanning Spring .....................................................................................................6-2 
v 

6.1.3 Little Fanning Spring ............................................................................................6-2 

6.1.4 Manatee Spring ....................................................................................................6-2 

6.2 MFL Evaluation Procedure...................................................................................6-2 

6.3 MFL Ecological Evaluation ...................................................................................6-3 

6.3.1 MFL Ecological Evaluation Conclusions ..............................................................6-3 

6.4 Recommended MFLs ...........................................................................................6-3 

6.4.1 Manatee Spring – Recommended MFL ...............................................................6-3 

6.4.2 Fanning Spring – Recommended MFL ................................................................6-5 

6.4.3 Lower Suwannee River – Recommended MFL....................................................6-6 

6.5 Recommendations ...............................................................................................6-8 

APPENDICES: 

Appendix A Stream Measurements 

Appendix B Manatee Spring Run Topographic Profiles 

Appendix C Fanning Spring Run Topographic Profiles 

Appendix D Ground Water Data 

Appendix E Rainfall Data 

Appendix F Manatee Spring Thermal Plume Modeling Results 

Appendix G Construction of the Lower Suwannee River Mile System 

Appendix H Submerged Aquatic Vegetation 

Appendix I Tidal Swamps 

Appendix J Tidal Creek 

Appendix K Oysters 

LITERATURE CITED 
vi 

LIST OF FIGURES 

1-1 Map showing the Lower Suwannee River MFL study area...........................................1-3 

2-1 Suwannee River Basin in Florida and Georgia.............................................................2-2 

2-2 Physiographic regions in the SRWMD and regional hydrography 

 in relation to the Suwannee River Basin in Florida .......................................................2-3 

2-3 Marine terraces in the SRWMD in relation to the Suwannee River Basin ....................2-5 

2-4 Average annual and monthly rainfall patterns in the Suwannee River Basin ...............2-7 

2-8 Twelve-month total rainfall for the North Florida climate division 

 for the period 1900 to 2003...........................................................................................2-8 

2-6 Mean monthly rainfall and reference evapotranspiration in the 

 north Florida region.......................................................................................................2-9

2-7 Extent of the limestone unit bearing the Floridan aquifer in the 

 southeastern U.S. .......................................................................................................2-11 

2-8 Elevation of the upper surface of the Tertiary limestone strata 

 that constitute the Floridan aquifer within the District .................................................2-12 

2-9 Generalized geologic cross section of the region .......................................................2-14 

2-10 Potentiometric surface of the Floridan aquifer in May 1976........................................2-16 

2-11 Confinement conditions of the Floridan aquifer in the region .....................................2-18 

2-12 Map showing permitted water use patterns in the SRWMD .......................................2-21 

2-13 Daily and annual discharge (1942-2003) for the Suwannee 

 River near Wilcox (USGS Station Number 02323500) ...............................................2-24 

2-14 Discharge flow duration curve (1942-2003) for the 

Suwannee River near Wilcox (USGS Station Number 02323500) .............................2-24 

2-15 Relationship between annual rainfall and discharge 

for the Suwannee River near Wilcox (USGS Station Number 02323500)..................2-25 

2-16 Relationship of drainage area and mean annual streamflow 

for the Suwannee Basin for gages with 10 or more years 

of systematic record....................................................................................................2-26 

2-17 Mean monthly streamflow at four USGS gaging sites 

 in the upper (A) and lower (B) Suwannee and Santa 

 Fe Rivers, reflecting stream hydrology in the upper and 

 lower portions of the drainage (after Mattson et al., 1995) .........................................2-27 

2-18 Climatic river-basin divide of Heath and Conover (1981) ...........................................2-29 

2-19 Gage locations and mean monthly discharge patterns at 

 selected long term surface water gages in the Suwannee River Basin......................2-30 

2-20 Major features if the Suwannee estuary .....................................................................2-31 

2-21 Map showing the “ecological reaches” of the Suwannee River in Florida ..................2-33 

2-22 Plot of mean alkalinity (mg/L as CaCO3) in the five 

 reaches of the Suwannee River in Florida..................................................................2-34 

2-23 Plot of mean color (platinum cobalt units; PCU) in the 

Five reaches of the Suwannee River in Florida..........................................................2-34 

2-24 Basic geomorphology of the river channel and floodplain 

 and typical plant communities in each of the five ecological 

 regions (Figure 2-20) of the Suwannee River.............................................................2-37 

2-25 Study area showing the springsbeds of Manatee and Fanning Springs.....................2-48 

2-26 Major land uses in the Lower Suwannee River Study Area........................................2-50 

2-27 Topography of the Lower Suwannee River Study Area..............................................2-52 

2-28 Physiographic regions in the Lower Suwannee River Study Area..............................2-53 

2-29 Closed depressions (sinkholes and other karst features) 
vii 

 In the Lower Suwannee River Study Area..................................................................2-54 

2-30 Geologic map of the Lower Suwannee River Study Area...........................................2-56 

2-31 Hydrolographic features in the Lower Suwannee River Study Area...........................2-58 

2-32 Relative groundwater recharge in the Lower Suwannee River Study Area................2-61 

2-33 September 1995 potentiometric surface of the upper 

 Floridan aquifer in the study area ...............................................................................2-62 

2-34 Comparison of continuous stage at Wilcox with 

 AVM discharge measurements at Fanning Spring .....................................................2-64 

2-35a View of Fanning Spring in June, 2005 ........................................................................2-65 

2-35b View of Fanning Spring in December, 2001 – a period of low flow.............................2-65 

2-36a View of the Fanning Spring run during low river stage in December, 2001................2-66 

2-36b View of the Fanning Spring run in December, 2001 – a period of low flow ................2-66 

2-37a View of Little Fanning Spring in June, 2005 ...............................................................2-67 

2-37b View of the Little Fanning Spring run in June, 2005 ...................................................2-67 

2-38a View of Manatee Spring in June, 2005 .......................................................................2-73 

2-38 View of the swimming area on the north side of the 

 spring run, just downstream from the vent..................................................................2-73 

2-39 iew of Catfish Hotel, a karst window utilized for 

 cave divers access to the Manatee Spring cavern system.........................................2-74 

2-40a View upstream of the Manatee Springs run in June, 2005 .........................................2-75 

2-40b View of water color in the Manatee Springs run in July, 2005 ....................................2-75 

2-41a View of the mouth of the Manatee Springs run 

 taken from the floating dock in the Suwannee River in June, 2005............................2-76 

2-41b View of the floating dock in the Suwannee River 

 looking downstream (south)........................................................................................2-76 

2-42 Taxa richness of benthic macroinvertebrates in Manatee Springs .............................2-80 

2-43 Mean number of manatee sightings /month from 

 1993 to 2004 at Manatee Springs...............................................................................2-82 

2-44 Linear estimations of discharge trends at Fanning and Manatee Springs..................2-83 

2-45 Increase in nitrate (NO3, as N) in Fanning and Manatee Springs...............................2-84 

2-46 Comparison of nitrate concentrations (NO3, as N) and spring discharge ...................2-85 

3-1 Location of primary stream flow gage sites used 

 in development of MFLs for the Lower Suwannee River ..............................................3-9 

3-2 Flow-Duration Curve for the Lower Suwannee River near Wilcox gage.....................3-11 

3-3 Pattern of discharge in cubic feet per second at 

 Wilcox gage for the period of record...........................................................................3-12 

3-4 Monthly mean discharge of the Suwannee River 

 near Wilcox for the period 1995-2003 compared 

 to the maximum, minimum, and monthly mean 

 discharge for the period of record (1941-2005) ..........................................................3-14 

3-5 Suwannee River near Wilcox flow duration curve 

 for the period 1996-2003 compared to the period of record 

 flow duration curve......................................................................................................3-15 

3-6 Relationship between mean monthly stream flow 

 at the Above Gopher River (AGR) and Wilcox gages.................................................3-17 

3-7 Comparison of raw and smoothed daily values at AGR and Wilcox gages................3-18 

3-8 Typical tidal patterns associated with extremely low freshwater flow .........................3-20 

3-9 Average location of (A) head of tide with discharge 

 at Wilcox and (B) flow reversal point with discharge at Wilcox...................................3-23 

3-10 HEC-RAS simulated and observed hydrographs 

 for discharge at (A) and stage (B) at Wilcox ...............................................................3-24 
viii 

3-11 MODBRANCH simulated and observed hydrographs 

 for stream flow at (A) Bell and stage (B) at Wilcox .....................................................3-26 

3-12 Location of stream gages within the Fanning and 

 Manatee Springs springshed ......................................................................................3-30 

3-13 Bathymetry surface of Manatee Spring and the 

 adjacent Suwannee River...........................................................................................3-33 

3-14 Locations of cross-sectional profiles across the Fanning Spring run..........................3-35 

3-15 Location of water-level monitoring wells within 

 the Fanning and Manatee Springs springshed ...........................................................3-37 

3-16 Location of rainfall gages within the Fanning and 

 Manatee Springs springshed ......................................................................................3-43 

3-17 Simulated average monthly discharge for Manatee and Fanning Springs .................3-46 

3-18 Cross-plot of stage data from the Suwannee River 

 near Wilcox and the Fanning Spring gages................................................................3-49 

3-19 Comparison of measured and simulated stage at Fanning Spring.............................3-50 

3-20 Comparison of Wilcox stage and water levels in nearby wells ...................................3-52 

3-21 Comparison of measured and simulated average 

 monthly discharge for Fanning Spring ........................................................................3-54 

3-22 Box-whisker plot of simulated daily stage for Fanning Spring, by month....................3-56 

3-23 Box-whisker plot of simulated monthly discharge 

 for Fanning Spring, by month .....................................................................................3-57 

3-24 Flow-duration curve for simulated average monthly 

 discharge at Fanning Spring.......................................................................................3-58 

3-25 Stage-duration curve for synthesized average daily 

 stage at Fanning Spring..............................................................................................3-59 

3-26 Box-whisker plot of measured stage at the Wilcox gage, by month ...........................3-61 

3-27 Comparison of Wilcox flow conditions during the 

 MFL study period for the springs and the period of record .........................................3-62 

3-28 Analysis of aquifer levels during the MFL study 

period for the springs and the period of record...........................................................3-63 

3-29 Average daily stage and discharge, Manatee Spring gage ........................................3-66 

3-29 31-day running average discharge for Manatee 

 and Fanning Spring ....................................................................................................3-67 

3-30 Cross-plot of Suwannee River near Wilcox stage and 

 Manatee Springs stage...............................................................................................3-69 

3-32 Comparison of measured and simulated Manatee Spring stage................................3-70 

3-33 Comparison of measured and simulated average 

 monthly discharge at Manatee Spring ........................................................................3-71 

3-34 Box-whisker plot of simulated daily stage data for 

 Manatee Spring, by month..........................................................................................3-73 

3-35 Box-whisker plot of simulated monthly average 

 discharge for Manatee Spring, by month....................................................................3-74 

3-35 Flow-duration curve for simulated average monthly 

 discharge at Manatee Spring......................................................................................3-75 

3-36 Stage-duration curve for synthesized average daily 

 stage at Manatee Spring.............................................................................................3-76 

3-38 Comparison of average monthly Wilcox discharge 

 and average monthly Fanning + Manatee discharge..................................................3-79 

3-39 omparison of Wilcox + Fanning + Manatee discharge 

 with the period of discharge from Fanning + Manatee................................................3-80 
ix 

3-40 Relationships of discharge and stage at Fanning Spring 

to discharge at the Wilcox gage on the Suwannee River ...........................................3-81 

3-41 Relationships of discharge and stage at Manatee Springs 

 to discharge at the Wilcox gage on the Suwannee River ...........................................3-82 

4-1 A bed of V. americana (center and foreground) in 

 upper West Pass in the Suwannee estuary..................................................................4-3 

4-2 Tidal, fresh-water swamp forest in the upper Suwannee estuary.................................4-4 

4-3 Portion of the Suwannee estuary delta.........................................................................4-5 

4-4 Lone Cabbage Reef; an oyster reef habitat in Suwannee Sound.................................4-7 

4-5 Map of the riverine portion of the Lower Suwannee 

 River MFL study area and reaches upstream to the 

 confluence with the Santa Fe .....................................................................................4-15 

4-6 Map of the upper Suwannee estuary, showing locations 

Of Clewell tidal marsh transects, USGS tidal freshwater 

Swamp transects, Mote SAV study sites, and SRWMD 

Long-term surfacewater/biology site...........................................................................4-18 

4-7 Satellite image of the Suwannee estuary showing locations 

Of UF oyster study sites and SEAS salinity sites .......................................................4-19 

4-8 Satellite image of the Suwannee estuary showing locations 

Of the FWCC Fisheries Independent Monitoring (FIM) sites 

used in analysis in this report .....................................................................................4-21 

5-1 Plots of monthly manatee sightings at Fanning Springs...............................................5-5 

5-2 Plots of monthly manatee sightings at Manatee Springs..............................................5-6 

5-3 Plot showing manatee sightings in Fanning Springs versus stage...............................5-6 

5-4 Temperature sampling sites and model grids for 

 Suwannee River near Manatee Spring.........................................................................5-8 

5-5 Manatee Spring flow .....................................................................................................5-9

5-6 Total river flow (Suwannee River near 

 Wilcox + Fanning Springs near Wilcox)......................................................................5-10 

5-7 Fraction of total river flow made up of Manatee Spring flow.......................................5-10 

5-8 Distribution of Fanning Spring Stage with cold-season 

 reference line at 2.71 feet NGVD................................................................................5-13 

5-9 Stage-discharge graph for the Wilcox gage at low stage/discharge...........................5-14 

5-10 Probability that the stage at Fanning Springs will greater 

 than 2.71 NGVD for a given discharge at the 

 Wilcox gage (cold season only) ..................................................................................5-15 

5-11 Salinity sampling stations used by the SRWMD and 

 USGS to characterize salinity in the Lower Suwannee River .....................................5-16 

5-12 Conceptual relationship between flow at Wilcox and 

 the location of an isohaline in the Lower Suwannee River .........................................5-17 

5-13 River mile system used to quantify habitat in the 

 Lower Suwannee River...............................................................................................5-18 

5-14 Conceptual relationship between river mile and 

 cumulative habitat distribution ....................................................................................5-19 

5-15 Conceptual relationship between flow and associated 

 risk of habitat loss .......................................................................................................5-20 

5-16 Map of the upper Suwannee estuary showing river 

 mile system and SAV/potential SAV polygons mapped 

 by Golder Associates in summer 2000 .......................................................................5-22 
x 

5-17 Braun-Blanquet abundance data of Vallisneria

americana from surveys conducted by Mote 

 Marine Laboratory in 1998-99; 2000; and 2002..........................................................5-24 

5-18 Plot of regression model relating flow at Wilcox 

 to the location of the 9 ppt surface isohaline in 

 Wadley Pass and West Pass......................................................................................5-25 

5-19 Relationship between flow at Wilcox and predicted 

 percentage of SAV at risk ...........................................................................................5-26 

5-20 Map showing effects of drought on SAV habitat 

 In the lower SuwanneeRiver as a result of drought of 2000 .......................................5-27 

5-21 Daily high and low stage at gages and tidal 

 transects in relation to flow in the lower Suwannee River, Florida..............................5-30 

5-22 Map showing the extent of tidal swamp in the 

 upper Suwannee estuary............................................................................................5-32 

5-23 Composition of the fish community in East Pass........................................................5-36 

5-24 Regression relating the location of the 2 ppt 

 isohaline to river flow at Wilcox in the upper Suwannee estuary................................5-37 

5-25 Estimates of flow associated risk for Tidal Swamp habitat ........................................5-38 

5-26 Biologically based salinity zone classifications 

 using Principal Components Analysis on tidal creek 

 fish data collected by the FIM program in the 

 Lower Suwannee River 2001-2003 ............................................................................5-41 

5-27 Map showing tidal creek coverage and related FWCC 

 and USGS salinity stations used for the analysis 

 of tidal creek habitat....................................................................................................5-42

5-28 Predicated location of the 5 ppt isohaline as a function 

 of flow at Wilcox..........................................................................................................5-43 

5-29 Flow associated risk for tidal creek access points in the 

 Lower Suwannee River...............................................................................................5-44 

5-30 Sampling stations of the SEAS program used to assess 

 Suwannee Sound salinities.........................................................................................5-46 

5-31 Grouping of SEAS stations used for estimating salinity 

 flow relationships in Suwannee Sound .......................................................................5-47 

5-32 Plots relating oyster reef community characteristics 

 to mean salinity one year prior to collection of the oyster data...................................5-49 

5-33 Exceedance frequency plots for each of the PCA 

 groups for the Suwannee estuary...............................................................................5-51 

5-34 Flow associated risk of an annual average salinity 

 of at least 20 ppt in the Inshore Reef group................................................................5-52 

5-35 Flow associated risk of an annual average salinity 

 of 20 ppt in the Offshore group ...................................................................................5-53 

5-36 Daily mean stage at gages and riverine transects 

 in relation to flow in the lower Suwannee River, Florida .............................................5-54 

5-37 Relationships between river stage and volume of 

 submerged wood habitat at locations on the Suwannee River...................................5-58 

5-38 Estimated streamflow with a .25 foot shift in stage 

 for submerged wood at Manatee study site................................................................5-60 
xi 

5-39 Relationship between river flow and proportion 

 of filtering collector invertebrates on 

 Hester-Dendy samplers at SRWMD 

 long term site SUW150C1 – Suwannee River at Rock Bluff.......................................5-61 

5-40 Relationship maximum salinity at sampling sites 

 in East and West Passes ant the ratio of occurrence of Cladium to Junucus.............5-64 

5-41 Distibution of U. minax with salinity in three rivers estuaries in Delaware ..................5-65 

5-42 Flow associated risk for SAV in 0.5 % increments from 0 to 5% ................................5-69 

6-1 Lower Suwannee System Flow Relationships..............................................................6-1 

6-2 Percent of time stage at Fanning spring is greater than 2.71 ft. for selected 

monthly median cold season Wilcox discharges ..........................................................6-6 
xii 

LIST OF TABLES 

1-1 MFL DECISION MATRIX: FANNING SPRINGS ..........................................................1-8 

1-2 MFL DECISION MATRIX: MANATEE SPRINGS .........................................................1-9 

1-3 MFL DECISION MATRIX: LOWER SUWANNEE RIVER...........................................1-10 

2-1 Descriptive data on the Suwannee River and its major sub-basins..............................2-1 

2-2 Generalized lithostratigraphic column and aquifer systems in the 

Suwannee Basin.........................................................................................................2-13 

2-3 Land use/land cover conditions in the Florida portion of the Suwannee River 

Basin, based on 1994 NAPP aerial photography .......................................................2-22 

2-4 Summary of current and projected water use in SRWM.............................................2.22 

2-4 Discharge Statistics of the Suwannee River at Wilcox (USGS Station 

Number 02323500), Levy County, Florida..................................................................2-23 

2-6 Summary of hydrologic characteristics at flow gaging sites along the 

 Suwannee River and its major tributaries ...................................................................2-27 

2-7 Aquatic and wetland-dependent species of interest in the lower 

Suwannee River Study area.......................................................................................2-42 

2-8 FWRI “Selected Taxa” and NOAA “Estuarine Living Marine Resources” 

(ELMR) taxa found in the Suwannee estuary.............................................................2-45 

2-9 Aquatic and wetland habitats of conservation interest in the lower Suwannee 

study area...................................................................................................................2-46 

2-10 Annual flow and stage distribution data, Fanning and Manatee Springs....................2-68 

2-11 Monthly discharge and stage data for Fanning Spring ...............................................2-69 

2-12 Aquatic and wetland-dependent species of conservation interest in the 

Fanning and Manatee Springs study areas (including the immediately adjacent 

Suwannee River) ........................................................................................................2-78 

2-13 Monthly reported discharge and stage data for Manatee Spring................................2-82 

3-1 Stream flow gage sites used in lower Suwannee MFL study .......................................3-3 

3-2 Summary of stage measurement information in Lower Suwannee River.....................3-6 

3-3 Descriptive discharge statistics for the Suwannee River at Wilcox gage 

For 10/01/1941 – 5/31/2005 .......................................................................................3-10 

3-4 Distribution statistics for discharge and stage at the Wilcox gage. Period of 

record is 10/1/1941 – 5/31/2005 for discharge data and 4/1/1942 – 5/31/2005 

for stage......................................................................................................................3-12 

3-5 Distribution statistics for monthly discharge in cubic feet per second at the 

Wilcox gage. Period of record is 10/1/1941 – 5/31/2005...........................................3-13 

3-6 Distribution statistics for stage in feet NGVD at the Wilcox gage. Period of 

record is 4/1/1942 – 5/31/2005...................................................................................3-13 

3-7 Comparison of results for base-flow estimation for the reach between the 

Wilcox and Above the Gopher River gages, Lower Suwannee River.........................3-18 

3-8 Continuous, MFL project-specific gaging sites in the Lower Suwannee 

River and Estuary .......................................................................................................3-19 

3-9 Summary of salinity monitoring programs in the Suwannee River Estuary 

that provided data used in the development of Minimum Flows and Levels. .............3-21 

3-10 Stage and discharge data available within the study area..........................................3-31 

3-11 Historical discharge measurements, in cubic feet per second, for Fanning, 

Little Fanning, and Manatee Springs..........................................................................3-32 

3-12 Wells located within the Fanning and Manatee springshed........................................3-38 

3-13 Available precipitation data in the Fanning and Manatee Spring basins ....................3-42 
xiii 

4-1 List of targeted taxonomic group/priority taxa and commensurate 

habitats for development of minimum flows and levels for the Suwannee River........4-11 

4-2 Estuarine fish and invertebrate taxa examined by McMichael and Tsou (2003) 

and/or Janicki Environmental (2005a) ........................................................................4-12 

4-3 Summary of ecological studies and data networks conducted on the 

Lower Suwannee which provided data used in MFL development.............................4-14 

5-1 Thermal Modeling Scenario Definitions ......................................................................5-11 

5-2 Suwannee River and Manatee Spring monthly flow rates ..........................................5-12 

5-3 Basic descriptive information on the six tidal freshwater swamp study 

transects in the upper Suwannee estuary ..................................................................5-28 

5-4 Summary of plant community and soil characteristics in the Lower Tidal 

forest types .................................................................................................................5-30 

5-5 Summary of literature reviewed to determine salinity tolerance of the 

dominant trees (or similar species) found in tidal swamps of the upper 

 Suwannee estuary ......................................................................................................5-33 

5-6 Common invertebrates found in Suwannee estuary tidal marshes and tidal 

creeks and their characteristic salinity ranges............................................................5-40 

5-7 Summary of PCA analysis of SEAS salinity data in the Suwannee estuary...............5-50 

5-8 Basic descriptive information on the two forested wetland study transects 

in the Upper Tidal Reach of the lower Suwannee Study area....................................5-54 

5-9 Summary of plant community and soil characteristics in the Upper Tidal 

forest types .................................................................................................................5-55 

5-10 Flow associated risk estimates for 0 to 15% of each habitat type ..............................5-68 

5-11 Warm season calculated stage and discharge conditions at Fanning and 

Manatee springs .........................................................................................................5-70 

6-1 MFL for Manatee Spring .............................................................................................6-36 

6-2 Manatee Spring Recommended MFL...........................................................................6-4 

6-3 MFL for Fanning Spring ................................................................................................6-5 

6-4 Fanning Spring Recommended MFL............................................................................6-5 

6-5 MFL for Lower Suwannee River at Wilcox Gage..........................................................6-6 

6-6 Warm season calculated stage and discharge conditions at Fanning and Manatee 

Springs..........................................................................................................................6-6 

6-7 Lower Suwannee River Recommended MFL ...............................................................6-7 
SECTION 1 
1-1 

1.0 Introduction 

This Minimum Flows and Levels for the Lower Suwannee River and Estuary – Technical Report 

(Report) presents the data and analyses which provide technical support for the establishment 

and adoption of Minimum Flows and Levels (MFLs) for the Suwannee River Estuary (“Lower 

Suwannee River”), Manatee Springs, and Fanning Springs. The goals for these MFLs are: 

• To implement the intent and policy of the Governing Board of the Suwannee River Water 

Management District; 

• To satisfy the requirement of state water law and policy. 

1.1 State of Florida Law Pertaining to the Establishment of MFLs 

Chapter 373.042, F.S: 

(1) Within each section or the water management district as a whole, the Department 

(Florida Department of Environmental Protection) or the district Governing Board 

shall establish the following: 

(a) Minimum flow for all surface watercourses in the area. The minimum flow for a 

given watercourse shall be the limit at which further withdrawals would be 

significantly harmful to the water resources or ecology of the area. 

(b) Minimum water level. The minimum water level shall be the level of groundwater 

in an aquifer and the level of surface water at which further withdrawals would 

be significantly harmful to the water resources of the area. 

Subsequent language in the statute (Chapter 373.042(1), F.S.) provides guidance that the 

Governing Board shall use the “best information available”, and that the Board may consider 

“seasonal variations” and the “protection of nonconsumptive uses” in establishing MFLs. 

Additional policy guidance is provided in the State Water Resources Implementation Rule 

regarding MFLs (Chapter 62-40.473, Florida Administrative Code [F.A.C.]), indicating that “. . . 

consideration shall be given to the protection of water resources, natural seasonal fluctuations 

in water flows or levels, and environmental values associated with coastal, estuarine, aquatic, 

and wetlands ecology. . . .” These environmental values may include: 

a) Recreation in and on the water; 

b) Fish and wildlife habitats and the passage of fish; 

c) Estuarine resources; 

d) Transfer of detrital material; 

e) Maintenance of freshwater storage and supply; 

f) Aesthetic and scenic attributes; 

g) Filtration and absorption of nutrients and other pollutants; 

h) Sediment loads; 

i) Water quality; and 

j) Navigation. 
1-2 

These requirements constitute the statutory framework and the outline for the scope of work 

required to develop the MFLs for the Lower Suwannee River including Manatee Spring and 

Fanning Springs. 

1.2 Project Scope 

In September 1994, the Governing Board of the Suwannee River Water Management District 

(District) initiated the effort to develop MFLs for the Lower Suwannee River. The study area 

(Fig. 1.1) included the Lower Suwannee River from Fanning Springs to the river mouth, and 

including the estuary of the river (the region including Suwannee Sound, Horseshoe Cove, 

Cedar Key, and the nearshore waters of the Gulf of Mexico influenced by freshwater discharge 

from the river). Note that the study area, which is termed the Lower Suwannee River in this 

report, is the tidal portion of the Lower Suwannee hydrologic unit as identified by the U.S. 

Geological Survey (USGS; Kenner, et al., 1967). 

As the Lower Suwannee River MFL was being developed, it became evident that the two major 

springs on the Lower Suwannee River (Fanning and Manatee Springs), which are also on the 

District’s list for MFL development, would play a significant role in MFLs for the river. This is 

due to the fact that the Suwannee River has an integral relationship to the MFLs for each spring 

as a contributing flow back into the springs and as a dilution factor for thermal effects of the 

spring discharges which impacts manatee refuge. Therefore, it was decided that the three sets 

of MFLs would be established simultaneously. 

1.3 Water Body Regulatory Designations 

The Suwannee River is widely regarded as a river system with high conservation value. In a 

study using data from the National Rivers Inventory (NRI), Benke (1990) identified the 

Suwannee as one of 42 “large, intact” river drainages remaining in the U.S. He defined these 

as rivers with more than 124.2 miles (200 km) of length that are unaffected by any major dams, 

flow diversions, or navigation projects. These 42 river systems cumulatively represented only 

2% of the total length of river reaches in the NRI database. Based largely on Benke’s work, 

Noss et al. (1995) designated large intact streams and rivers in the U.S. as “Endangered 

Ecosystems”, which they defined as those ecosystem types which have experienced an 85-98% 

decline in the existence of high-quality, intact examples. In similar fashion, a report on U.S. 

river ecosystems by The Nature Conservancy (Master et al., 1998) classified the 

Suwannee/Santa Fe drainages as “critical watersheds to protect freshwater biodiversity.” 

Moreover, the federal government has designated portions of the Suwannee River as Critical 

Habitat for Gulf sturgeon, a federally threatened species. Existing state designations recognize 

the Suwannee as a river system of both regional and statewide importance. The Suwannee is 

recognized as a system having high conservation and recreational value, through designations 

such as Outstanding Florida Water (OFW) and Aquatic Preserve. 

The Suwannee River, including the Lower Suwannee River MFL study area, is designated an 

Outstanding Florida Water (Chapter. 62-302.700[9][i][34], F.A.C.). This designation is conferred 

to waters of the state with “exceptional recreational or ecological significance” (Chapter 62-

302.700[3], F.A.C.). 
1-3 

Figure 1-1 Map showing the Lower Suwannee River MFL study area. 

A substantial portion of the MFL study area also lies within the Big Bend Seagrasses Aquatic 

Preserve. Aquatic Preserves are established by the State Legislature “...for the purpose of 

being preserved in an essentially natural or existing condition so that their aesthetic, biological 

and scientific values may endure for the enjoyment of future generations.” (Chapter 18-

20.001[2], F.A.C.). The Big Bend Seagrasses Aquatic Preserve was created in 1985 and 

includes the Lower Suwannee River from Fanning Springs to the mouth and all of the coastal 

waters of the Suwannee estuary. 

The Lower Suwannee River study area also includes a number of important conservation areas, 

including two National Wildlife Refuges (Lower Suwannee and Cedar Keys NWRs), two State 

Parks (Fanning Springs and Manatee Springs), a state Wildlife Management Area (Andrews 
1-4 

WMA) and numerous parcels of Water Management District lands. These lands provide 

important ecological services as well as public recreation benefits (hiking, swimming, fishing, 

hunting, kayaking, etc.). 

The springs play an integral role in the ecological and health and hydrology of the Lower 

Suwannee system. Manatees move freely from the river to the springs to find refuge if winter 

months and the river provides a carbon source to the spring biota for maintenance of the spring 

ecosystem. 

Fanning Springs is a State Park. The spring is classified as a 1st magnitude spring but the flow 

no longer meets 1st magnitude flow requirements of 100 cfs median flow. Based on review of 

available discharge data, Fanning Springs has not ever met the criteria for 1st magnitude 

classification (mean or median discharge of 100 cfs or greater). The spring does experience 

intermitting discharge greater than 100 cfs. The spring is currently being renovated and is a 

popular swimming and picnicking area. Attendance at the spring for fiscal year 2003/2004 was 

recorded at 249,565. 

Manatee Springs is a popular State Park that boasts a 1st magnitude scenic spring and spring 

run, swimming area, manatee viewing, and cave diving, among other activities. Attendance at 

the spring for fiscal year 2003/2004 was recorded at 129,661 (FDEP- 2004). 

1.4 Relevant Water Resource Values 

As noted in Section 1.1, Chapter 62-40.473, F.A.C. provides policy guidance regarding 

establishment of MFLs. In particular, this section of Florida’s Water Policy lists 10, specific 

environmental and water resource values that should be considered in setting MFLs. As part of 

the MFL establishment process, Chapter 62-40.473, F.A.C. environmental and water resource 

values evaluation matrices are prepared to allow the MFL evaluators the opportunity to identify 

potential target values that may be the limiting factors for the proposed MFLs (Tables 1-1 thru 1-

3). This process helps to focus the evaluation and shape the types of analyses needed to 

complete the MFL. This ranking process is initiated after compilation of all available data and 

review by the MFL evaluators. The rankings represent the professional opinion of the WRA 

team of experts based upon their collective experience in the development of MFLs after 

reviewing available data for each waterbody. Each ranking is based upon the collective 

experience of the evaluation team in establishing MFLs and review of the available data. Target 

values have the highest probability of limiting the amount of water available for the water body 

without causing significant harm. As an example, if the fish passage criterion requires the most 

water flow to avoid significant harm to the water body, then that value becomes the limiting 

factor for the proposed MFL since all other values would require less flow to avoid significant 

harm. This value ranking procedure is not inflexible and new target criteria can emerge in the 

evaluation process, but in most cases the initial determinations are accurate 

The relevance of each, and how they were incorporated into the establishment of MFLs for the 

Lower Suwannee River, Fanning Springs and Manatee Springs, is discussed below: 

a. Recreation in and on the water. This water resource value is considered relevant to the 

Lower Suwannee River and its springs. The Outstanding Florida Water designation of 

the river is in part based on the recreational significance of the Suwannee system. Uses 

include swimming, boating, water skiing, recreational fishing, kayaking and canoeing. 

The District and the Florida Department of Environmental Protection (FDEP) are 

currently engaged in creating the “Suwannee Wilderness Trail”; a 207-mile canoe trail on 

the Suwannee River, linked with a network of camping and cabin facilities located on 

State and District lands. In establishing MFLs for the Lower Suwannee River and 
1-5 

Estuary, general information was considered on the economic value of ecotourism, 

recreational fishing, and related activities. 

Similarly, recreation is a major use of Fanning and Manatee springs. Both are popular 

and heavily utilized. Maintaining an acceptable spring discharge for recreation was 

considered for each. 

b. Fish and wildlife habitats and the passage of fish. This water resource value is 

considered relevant for the Lower Suwannee River MFLs. Fish passage is not as much 

an issue in the river channel itself, due to the general lack of shallow shoal areas in the 

MFL study area, but it may be considered as a component of adequate water depths on 

the floodplain and tidal marshes. A major focus of the studies conducted to support the 

Lower Suwannee River MFLs was on the major wetland and aquatic habitats of the 

lower river and estuary (see Chapter 4 in this report), and how hydrologic conditions 

structure those habitats. 

The springs are both secondary refuges for the West Indian Manatee (Warm Water Task 

Force, 2004). Consideration was given to providing acceptable refuge for manatees 

during cold months as well as for fish passage and wildlife habitat in general. 

c. Estuarine resources. This water resource value is considered relevant for the Lower 

Suwannee River. The estuary of the river is the largest and most extensive river estuary 

in the Big Bend region of the Florida Gulf Coast (Mattson, 2002a); it is part of the Big 

Bend Seagrasses Aquatic Preserve, an OFW, and it supports extensive recreational and 

commercial fisheries. To support establishment of the Lower Suwannee River MFLs, 

relationships between stream flow and estuarine salinity dynamics were investigated, 

and studies of important estuarine habitats were conducted to evaluate the effects of 

freshwater inflow and salinity on those habitats. The results of these were incorporated 

into the Lower Suwannee River MFLs. 

The spring flows did not in themselves merit consideration as having impacts on the 

estuarine resources but consideration was given to the contribution of spring discharge 

to overall discharge of the river below Wilcox (Fanning Springs). 

d. Transfer of detrital material. It has been well-established that a principal food base in 

aquatic and wetland ecosystems is decaying plant material, collectively termed “plant 

detritus” or simply detritus. Transport of this material from the river floodplain wetlands 

to the river channel is an important source of food material for riverine invertebrates, and 

transport of material from the river to the estuary is similarly a vital component of 

maintenance of the food base for estuarine consumers. This water resource value is 

relevant to the Lower Suwannee River MFLs, and existing data in the scientific literature 

were used to assist in determination of MFLs for the Lower Suwannee River. 

Transport of detrital material is not a consideration with respect to spring discharge. 

During periods of high discharge in the river, the springs perform as estevelles. That is, 

they backflow and transport humic substances and minor detritus from the river into the 

cavern systems that feed the springs. No data exist as to the importance of this process 

or how it specifically impacts these springs. 

e. Maintenance of freshwater storage and supply. This water resource value is considered 

relevant to the Lower Suwannee River MFLs, and it is considered in more detail in 
1-6 

Chapters 3. Establishment of an MFL for a water body implicitly establishes potential 

availability of that water. This water resource value refers to the long-term maintenance 

(i.e., sustainability) of water storage and supply capability of the water body. The result 

of the protection of this value by MFL establishment is to ensure that, over time, the 

ability of the water body to serve as a supply source for existing and future legal 

permitted users is preserved without causing “significant harm” to the water resource or 

ecology of the area. 

f. Aesthetic and scenic attributes. This water resource value is closely linked with the first 

one pertaining to recreation, in that part of the recreational value of the Lower 

Suwannee River is the aesthetic experience. 

Aesthetic and scenic attributes are considered relevant to the establishment of MFLs for 

the Lower Suwannee River, and were incorporated as an important characteristic along 

with recreation. 

Both springs are in state parks and are considered to have high aesthetic and scenic 

value. MFL consideration included acceptable maintenance of these attributes through 

provisions for a full spring bowl, minimization of black water reversal from the river and 

maintenance of stage in the spring runs. 

g. Filtration and absorption of nutrients and other pollutants. This water resource value is 

considered relevant to the Lower Suwannee River MFL. The role of wetlands in 

maintenance of water quality is well-established (Mitsch and Gosselink, 1986). By 

allowing for settlement of suspended particulates, uptake of nutrients by plants, and 

sequestration of heavy metals and other contaminants in sediments, wetlands help 

protect water quality. Data from the scientific literature on nutrient cycling and other 

biochemical functions of wetland were taken into consideration in establishing MFLs, 

with the assumption that maintaining an acceptable level of ecological integrity for 

wetland ecosystems of the Lower Suwannee River would maintain this particular 

function. 

Both spring systems have records of increasing nitrate concentrations. The spring 

systems, however, have little nutrient sorption capability. Submerged aquatic vegetation 

(SAV) provides minor sorption because of the short residence time of water in the spring 

systems. 

h. Sediment loads. This water resource value is considered relevant to the Lower 

Suwannee River MFL. Available evidence indicates that the Suwannee River carries 

substantially lower sediment loads than similar-sized rivers along the northern Gulf 

Coast (USDA, 1977). This is primarily due to the physiography and soil types present in 

the basin. Despite this fact, the presence of alluvial features in the floodplain of the river 

and the existence of an estuarine delta indicates that the river does carry some 

sediment, which is important in the maintenance of these geomorphic features and their 

associated ecological communities. It is probable that most of the river’s sediment load 

is carried at higher flows. General information from the literature on riverine fluvial 

dynamics was considered in setting the MFLs. 

Transport of sediment loads is not considered to be an issue with respect to the springs. 

Both spring systems are sediment starved. 
1-7 

i. Water quality. This water resource value is considered relevant to setting MFLs on the 

Lower Suwannee River. The main water quality consideration was salinity variation in 

the estuary in relation to freshwater inflow and its effects on important estuarine habitats 

and fauna. 

While increasing nitrate concentrations in the springs is a concern, the increases are not 

related to levels or flows. They are related to land use within the springsheds. Water 

quality was not considered in MFL development for the springs. 

j. Navigation. This water resource value was considered not relevant to the Lower 

Suwannee River MFLs, in that the system is not a waterway which supports commercial 

shipping or barge traffic. Passage by recreational vessels, canoes, etc. was considered 

under the “Recreation in and on the water” value, above. 

Neither spring has a navigable run. Canoeing and swimming were considered as 

recreational and scenic/aesthetic criteria. 
Potential Criteria

Resource at 

Risk

Resource 

Value

Legal 

Factors Rank

Available 

Data

Preliminary 

Data Analysis

Related to 

Flow/Level?

Notes 12345 6 

Recreation in and on the water 33282 Y Fish and wildlife habitats and the passage of fish 33394 Y Estuarine resources 11134 Y Transfer of detrital material 11131 N Maintenance of freshwater storage and supply 23166 Y Aesthetic and scenic attributes 33391 Y nutrients and other pollutants 11131 N Sediment loads 11131 N Water quality 32163 N 

Navigation 11131 N 

Notes:

SUWANNEE RIVER WATER MANAGEMENT DISTRICT

Table 1-1 MFL DECISION MATRIX: FANNING SPRINGS

1. Evaluation of the level to which the resource is potentially at risk. 1 = low risk, 2 = medium risk, 3 = high risk6. Evaluation as to whether criterion is related to flow or level in resource. (Yes or No)7. Evaluation as to whether criterion is potentially limiting for MFL development. (Yes or No)2. Evaluation of importance of the criterion with respect to resource. 1 = low importance, 2 = medium importanceimportant3. Legal constraints on resource, such as endangered species, Outstanding Florida Water, etc. 1 = low, 2 = medium4. Sum of columns 1, 2, and 3. Indicates overall importance of criterion to MFL development.5. Evaluation of available data for use in development of MFL based on the criterion. 0 = no data available, 8 = abdata available

 1-8
Potential Criteria

Resource at 

Risk

Resource 

Value

Legal 

Factors Rank

Available 

Data

Preliminary 

Data Analysis: 

Related to 

Flow/Level?

Notes 12345 6 

Recreation in and on the water 33282 Y Fish and wildlife habitats and the passage of fish 33394 Y Estuarine resources 11134 Y Transfer of detrital material 11131 N Maintenance of freshwater storage and supply 23166 Y Aesthetic and scenic attributes 33391 Y nutrients and other pollutants 11131 N Sediment loads 11131 N Water quality 32164 N 

Navigation 11131 N 

Notes:

SUWANNEE RIVER WATER MANAGEMENT DISTRICT

Table 1-2 MFL DECISION MATRIX: MANATEE SPRINGS

1. Evaluation of the level to which the resource is potentially at risk. 1 = low risk, 2 = medium risk, 3 = high risk6. Evaluation as to whether criterion is related to flow or level in resource. (Yes or No)7. Evaluation as to whether criterion is potentially limiting for MFL development. (Yes or No)2. Evaluation of importance of the criterion with respect to resource. 1 = low importance, 2 = medium importanceimportant3. Legal constraints on resource, such as endangered species, Outstanding Florida Water, etc. 1 = low, 2 = medium4. Sum of columns 1, 2, and 3. Indicates overall importance of criterion to MFL development.5. Evaluation of available data for use in development of MFL based on the criterion. 0 = no data available, 8 = abrelevant data available

 1-9
Potential Criteria

Resource at 

Risk

Resource 

Value

Legal 

Factors Rank

Available 

Data

Preliminary 

Data Analysi

Related to 

Flow/Level?

Notes 12345 6 

Recreation in and on the water 33171 Y Fish and wildlife habitats and the passage of fish 33398 Y Estuarine resources 33398 Y Transfer of detrital material 22151 Y Maintenance of freshwater storage and supply 23274 Y Aesthetic and scenic attributes 22371 Y nutrients and other pollutants 32161 N Sediment loads 11131 N Water quality 33398 N 

Navigation 21141 N 

Notes:

SUWANNEE RIVER WATER MANAGEMENT DISTRICT

Table 1-3 MFL DECISION MATRIX: LOWER SUWANNEE RIV

1. Evaluation of the level to which the resource is potentially at risk. 1 = low risk, 2 = medium risk, 3 = high risk6. Evaluation as to whether criterion is related to flow or level in resource. (Yes or No)7. Evaluation as to whether criterion is potentially limiting for MFL development. (Yes or No)2. Evaluation of importance of the criterion with respect to resource. 1 = low importance, 2 = medium importanimportant3. Legal constraints on resource, such as endangered species, Outstanding Florida Water, etc. 1 = low, 2 = medi4. Sum of columns 1, 2, and 3. Indicates overall importance of criterion to MFL development.5. Evaluation of available data for use in development of MFL based on the criterion. 0 = no data available, 8 = relevant data available

 1-10
SECTION 2 
2-1 

2.0 Introduction to the Suwannee River Basin and Study Area 

2.1 Suwannee River Basin 

2.1.1 Physical Setting of the Suwannee Basin 

The Suwannee River Basin encompasses 9,950 mi2

 (25,770 km2) in Florida and Georgia 

(Figure 2-1; Franklin et al., 1995). It is the second largest river system in Florida by drainage 

area and mean annual flow (Table 2-1). Major tributaries of the river are the Withlacoochee and 

Alapaha Rivers, which are mostly located in Georgia, and the Santa Fe River in Florida. In total, 

approximately 57% of the basin is in Georgia. The Suwannee is a low-gradient stream, with an 

average gradient of 0.4 feet per mile. The following discusses general characteristics of this 

complex river system. 

Table 2-1. Descriptive data on the Suwannee River and its major sub-basins (Franklin et al., 1995, 

and Berndt et al., 1996). 

 Total Florida Average 

 Basin Area Length Length Gradient Flow 

 (mi2

) (miles) (miles) (ft/mile) (ft3/sec)

Suwannee River** 9,950 235 206.7 0.42 10,540** 

Withlacoochee River 2,360 120 30.0 2.32 1,714 

Alapaha River 1,840 130 22.6 1.80 1,674 

Santa Fe River 1,360 79.9 79.9 1.90 1,608 

** - includes contributions of the Withlacoochee, Alapaha and Santa Fe sub-basins 

The physiographic setting of the basin (Allan, 1995; Berndt et al, 1996), acting in conjunction 

with regional climatic characteristics controls the basic water chemistry and hydrologic 

characteristics of the river. The river basin lies entirely within the Southeastern Coastal Plain 

(Berndt et al., 1996). Major physiographic provinces in Florida include the Northern Highlands 

and Gulf Coastal Lowlands physiographic regions (White, 1970; Ceryak et al., 1983; Figure 2-

2). 

Characteristics of the Northern Highlands include gently rolling topography, generally from 100-

200 feet above mean sea level (msl). Soils typically range from sand to clayey sand. Clayey 

sediments in the subsurface serve as a base for a surficial aquifer and retard infiltration of 

rainwater into the underlying Floridan Aquifer System. The result is abundant surfacewater 

features (streams, lakes and ponds) throughout the Highlands. 
2-2

Figure 2-1. Suwannee River Basin in Florida and Georgia. Basins shown are USGS hydrologic 

units (Kenner et al., 1967). 
2-3

Figure 2-2. Physiographic regions in the SRWMD and regional hydrography in relation to the 

Suwannee River Basin in Florida. Data sources include White (1970); Ceryak et al. (1983); SRWMD 

data. 
2-4

The Gulf Coastal Lowlands are characterized by elevations from sea level to about 100 feet 

above msl. The Lowlands feature low relief, karstic topography, and shallow sandy soils with 

muck in many wetland areas. Karst landforms are widespread in the lowlands, with abundant 

features such as sinkholes, sinking streams and springs, and a high degree of interconnection 

between surfacewater and groundwater systems. Carbonate rock (limestone, dolostone) is at 

or near land surface throughout the Lowlands. Whereas the surfacewater features in the 

Highlands reflect the water table of the surficial aquifer, those in the Lowlands represent the 

water table in the upper Floridan aquifer. 

A significant geologic region separating the two major provinces is the Cody “Scarp,” or 

Escarpment (Figure 2-2; depicted as a line for illustrative purposes), the most persistent 

topographic break in Florida (Puri and Vernon, 1964). There can be as much as 80 feet of relief 

along the Scarp. It is a karst escarpment that has been highly modified by marine shoreline 

processes. The Scarp region is characterized by active sinkhole formation, large uvalas, poljes 

and lakes, springs, sinking streams, and river rises (Ceryak et al., 1983). During average and 

lower flows, the Santa Fe and Alapaha Rivers are completely captured by sinkholes as they 

cross the Scarp and re-emerge down-gradient as river rises. The Withlacoochee River is partly 

captured as it crosses the Scarp near Valdosta, Georgia. Due to its size, the Suwannee is the 

only stream that is not significantly captured by a sink feature. Upgradient of the Scarp, surficial 

drainage has developed, with numerous small creeks branching off the upper Suwannee and its 

tributaries (Figure 2-2). Below the Scarp, drainage is predominantly internal and streams that 

are tributary to the Suwannee are rare. 

Ridges, such as Bell Ridge and the Brooksville Ridge, are prominent features in the southern 

part of the District (Figure 2-2). These ridges were formed by a combination of karst scarp 

retreat and marine terrace development. 

Relict marine terraces are important features of the Suwannee basin in Florida. These terraces 

were established by different stands of sea level during the Pleistocene (and possibly Pliocene) 

Epoch. The terraces stair-step from the Gulf to the Highlands, and the marine and coastal 

processes that created the terraces were responsible for deposition of the surficial sands that 

mantle the region (Healy, 1975; Schmidt, 1997). The progression of these terraces from the 

coast inland and upward includes (Figure 2-3): 

Terrace Approximate Elevation

 Silver Bluff Terrace 1-10 feet above mean sea level (msl) 

 Pamlico Terrace 8-25 feet msl 

 Talbot Terrace 25-42 feet msl 

 Penholoway Terrace 42-72 feet msl 

 Wicomico Terrace 70-100 feet msl 

 Sunderland Terrace 100-170 feet msl 

 Coharie Terrace 170-215 feet msl 

 Hazlehurst Terrace 215-320 feet msl 

The terraces from Silver Bluff to Wicomico occur primarily in the Gulf Coastal Lowlands 

physiographic region, while the Sunderland, Coharie, and Hazlehurst terraces are found in the 

Northern Highlands. 
2-5

Figure 2-3. Marine terraces in the SRWMD in relation to the Suwannee River Basin. Data sources: 

USGS topographic GIS data and Healy, (1975). 
2-6

2.1.2 Climate of the Suwannee River Basin 

Climate is a description of aggregate weather conditions, including all statistical weather 

information for a region (Lutgens and Tarbuck, 1989). The climate of the Suwannee River basin 

can be described as a mixture of warm temperate and subtropical conditions. Mean annual 

temperature in the Florida portion of the basin is 68.6 °F (NOAA, 2002). The maximum and 

minimum average monthly temperatures are 81.3 °F (in July) and 54.2 °F (January), 

respectively. 

Precipitation and evapotranspiration (ET) are the climatic features most significant to long-term 

hydrologic conditions in the Suwannee Basin. Average annual rainfall in the Basin is 

approximately 53.4 inches (NOAA, 2002) but varies spatially from 46 inches in the upper basin 

to over 60 inches near the Gulf coast (Figure 2-4). This precipitation gradient is largely 

controlled by the range in latitude of the basin (equivalent to approximately 200 miles) and the 

proximity of the lower third of the basin to the Gulf of Mexico (NOAA, 1972). 

Year-to-year rainfall is rarely comparable to the average annual spatial differences. In the area 

covered by the NOAA North Florida Climatic Division, annual (calendar year) rainfall has varied 

from a low of 35.5 inches (1955) to a high of 77.9 inches (1964). Figure 2-5 shows the longterm (104 year) rainfall conditions for the north Florida region. The data were smoothed with a 

LOESS-type smoothing algorithm as implemented in TableCurve 2D (AISN Software, 2000). As 

shown, the smoothed curve suggests that a drier period existed in the first half of the 20th

Century, with wetter conditions subsequently prevailing through the 1990’s. 

The month-to-month variation in rainfall is as important to understanding the Suwannee’s 

hydrology as annual rainfall. Figure 2-4 shows the typical monthly rainfall pattern at three 

locations in the Suwannee Basin. As with annual rainfall, there is a gradient in seasonal climatic 

conditions from the northern to southern regions of the basin. The seasonal pattern is strongest 

in the south where a pronounced wet season occurs in the summer months (June through 

September). In this area, summer rainfall is associated with localized, convectional 

thunderstorms or periodic tropical weather systems (hurricanes, tropical storms). The pattern 

weakens in the middle and northern parts of the basin (compare Usher Tower to the Jasper and 

Tifton insets, Figure 2-4). More northerly portions of the basin are characterized by lower 

average annual rainfall, and a weakened seasonal pattern with precipitation that is more evenly 

distributed between the warmer and cooler months. Winter rainfall to the north is somewhat 

higher than to the south. Winter precipitation events are due to mid- latitude frontal weather 

systems with individual rainfall events that are usually more widespread. 
2-7

Figure 2-4. Average annual and monthly rainfall patterns in the Suwannee River Basin (Data: 

NOAA, 2002). 
2-8 

30405060708090

1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 

Year

Rainfall (Inches)

12 Month Running AvePeriod AverageLOWESS Smoothed (5

Twelve-month total rainfall for the North FL climate division for the period 1900 through 2003. Rainfall totals are running averages, and are plotted at the first month of the 12-month period. Number of stations varies over the Period of Record.

Missing Data*

*Missing data for 19

estimated from lon

monthly means for u

LOWESS smo

Figure 2-5. Twelve-month total rainfall for the North Florida climate division for the period 1900 to 2003. Rainfall taverages, and are plotted at the first month of the 12-month period Data: NOAA (2005). 
2-9 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Month

0

2

4

6

8

Depth (inches)

Rainfall

Reference ET

Rainfall Deficit

Rainfall Excess

Figure 2-6. Mean monthly rainfall and reference evapotranspiration in the north Florida region. 

Data: NOAA (2002); Jacobs and Dukes (2004); Jacobs and Satti (2001). 

Rates of evapotranspiration (ET) in the region have been estimated with a variety of direct 

measurements and/or computational methods. The average annual ET pattern shown in Figure 

2-6 is estimated from computed reference ET for Gainesville (Jacobs and Dukes, 2004) 

multiplied by monthly crop coefficients for pasture (Jacobs and Satti, 2001). Reference ET is 

the potential ET from a short, well-watered grass crop. The resulting mean annual ET is 40.8 

inches, with the largest mean monthly value of 5.20 inches in June and a minimum of 1.3 inches 

in December. The monthly rainfall values in Figure 2-6 are the North Florida Climatic Division 

means (NOAA, 2002). 

Figure 2-6 indicates potential months of net rainfall surplus and/or deficit. During the cooler 

winter months, a water surplus can exist that serves to recharge the groundwater system. 

During late spring, a rainfall deficit can occur. Utilization of soil moisture (Fernald and Purdum, 

1998) and late frontal systems can offset this effect. In the summer, the situation reverses, with 

rainfall typically exceeding ET. However, for climate-affected activities, such as agriculture, the 
2-10

scattered nature of summer convective rainfall events combined with excessive- to well-drained 

soils often result in site conditions that require supplemental irrigation. 

2.1.3 Geology of the Suwannee Basin 

The Suwannee River Basin lies in the Coastal Plain Physiographic Province of the United 

States (Hunt, 1974). The highly productive Floridan aquifer (Miller, 1997) underlies the region. 

It is capable of producing thousands of gallons of water per minute to wells. This section 

describes the geologic and groundwater systems of the Suwannee River Basin. Note that the 

lower Suwannee MFL study area is described in more detail in Section 2.3. 

Carbonate rock (limestone and/or dolostone) as much as 5,000 feet thickness exists in the 

subsurface of the basin. These strata, which are primarily Tertiary in age, make up the Florida 

Platform. The Floridan aquifer is found within these strata and in similar strata in Georgia, the 

Carolinas, and portions of Alabama. The permeable portion of this carbonate-rock platform 

ranges from about 600 feet to 1700 feet in thickness (Miller, 1982). 

The extent and elevation of the upper surface of the limestone are depicted in Figure 2-7. The 

upper surface of the Tertiary limestone ranges from sea level to 90 feet msl throughout most of 

the basin. The limestone begins dipping to the northeast in the northeastern corner of the 

District. This dip is about 20 feet per mile, and the top of the limestone reaches a depth of 

about 300 feet below sea level in the eastern corner of the District (Figures 2-7 and 2-8). Figure 

2-8 illustrates details of the elevation of the top of the Tertiary limestone within the District and 

the Suwannee Basin. 

Table 2-2 presents the lithostratigraphic (geologic formation) as well as the hydrostratigraphic 

(aquifer system) nomenclature used to characterize the shallow geologic and hydrogeologic 

units in the District. 

The uppermost geologic unit consists of the Pliocene- and Quaternary-aged 

(Pleistocene/Holocene) surficial sand deposits. These deposits are undifferentiated and may 

include shell and clay horizons. They were primarily formed by deposition associated with 

marine terraces and by erosion and chemical weathering of pre-existing strata. 
2-11

Figure 2-7. Extent of the limestone unit bearing the Floridan aquifer in the southeastern U.S. 

Fault line labels indicate: U = Uplift; D = Downlift. Adapted from Miller (1982). 
2-12

Figure 2-8. Elevation of the upper surface of the Tertiary limestone strata that constitute the 

Floridan aquifer within the District. Adapted from Allison et al. (1995). 
2-13

Table 2-2. Generalized lithostratigraphic column and aquifer systems in the Suwannee Basin. 

 

LITHOSTRATIGRAPHIC (ROCK) NOMENCLATURE 

SYSTEM SERIES FORMATION

AQUIFER 

SYSTEM 

Quaternary Holocene/Pleistocene Undifferentiated Sands Surficial 

Tertiary Pliocene Undifferentiated Sands Surficial 

Tertiary Miocene Hawthorn Group 

St. Mark’s Formation 

Intermediate 

Aquifer System 

and Confining 

Beds 

Tertiary Oligocene Suwannee Limestone Upper Floridan 

Tertiary Eocene 

Ocala Limestone 

Avon Park Limestone 

Oldsmar Limestone 

Upper Floridan 

Tertiary Paleocene Cedar Keys Formation Mid-Floridan 

Confining Unit 

The Miocene Hawthorn Group is present in the northern and northeastern portions of the 

District. It consists of interbedded clay, sand, and carbonate strata (Scott, 1988). 

While the Miocene and Plio-Pleistocene strata are predominantly composed of siliciclastic 

materials (sand, clay, silt) interbedded with carbonate-rich strata, the underlying strata are 

predominantly composed of limestone and/or dolostone. These formations include (from top, or 

youngest, to bottom, or oldest) the Oligocene Suwannee Limestone, Eocene Ocala, Avon Park, 

and Oldsmar formations, and the Paleocene Cedar Keys Formation (Giller, 1997). These strata 

comprise the upper Floridan aquifer and, where present, the mid-Floridan confining unit. The 

Ocala Limestone, the uppermost section of the Floridan in the majority of the Basin, is also the 

source of the majority of ground water pumpage. The Suwannee Limestone overlies the Ocala 

in places, and ranks second in water production. 

Figure 2-9 is a geologic east-west cross section that depicts the relationships of these 

formations. From the cross section, it is evident that, in the west, the Suwannee Limestone 

overlies the Ocala Limestone from the Gulf to the Suwannee River. The Suwannee Limestone 

is more dolomitic than the Ocala Limestone within the District. East of the Suwannee River, the 

Suwannee Limestone is generally missing. Note that the Hawthorn Group overlies the Ocala 

and thickens as the Ocala dips to the east. 
2-14

Figure 2-9. Generalized geologic cross section of the region. Adapted from Ceryak et al. (1983). 
2-15

2.1.4 Regional Aquifer Systems 

The uppermost aquifer within the District is the surficial aquifer (Table 2-2). The surficial aquifer 

occurs within the undifferentiated, Plio-Pleistocene, marine-terrace sands. This aquifer is only 

present in the northern and eastern parts of the District where the Hawthorn Group provides an 

effective aquitard under the surficial aquifer, which minimizes recharge to the underlying aquifer. 

The surficial aquifer is found locally in the Northern Highlands (Tallahassee Hills west of the 

Withlacoochee River) Province, and where water is perched over clays within the San 

Pedro/Mallory Swamp complex. The surficial aquifer is locally utilized for domestic well water. 

However, because of dissolved organics, color, odor, and iron problems, water quality is 

generally poor and undesirable. 

The Hawthorn Group (Table 2-2) includes the Intermediate Aquifer and Confining Beds System. 

The strata act primarily as aquitards within the District, but thin layers of gravel, sand, and 

carbonate rock form localized aquifers that are capable of producing water to small-yield wells. 

The upper Floridan aquifer extends throughout Florida, coastal plain Georgia and portions of the 

coastal plain in Alabama, North Carolina and South Carolina (Figure 2-7). The limestone unit 

begins along the Fall Line, where Coastal Plain sedimentary rocks lap against the metamorphic 

rocks of the Piedmont Province in central Georgia. The upper surface of the limestone dips 

easterly and southerly from the Fall Line. The rock surface elevation is about 300 feet above 

MSL along the Fall Line and dips to elevations lower than 600 feet below MSL in southeastern 

Georgia (Miller, 1982). Within the District, the top of the Upper Floridan aquifer ranges from 

approximately –100 to +100 feet MSL (Figure 2-8). 

Figure 2-10 depicts the regional potentiometric surface for the upper Floridan aquifer in the 

District in May 1976. The contour lines depict the elevation of the water table where the 

Floridan is unconfined and correspond to the elevation to which water would rise in wells where 

the aquifer is confined. The general direction of flow can be estimated by drawing flow lines that 

are perpendicular to the lines of equal potential from high to low potentials. The head pressure 

caused by elevation differences in the potentials drives movement of water in the aquifer. The 

average flow rate through the aquifer is estimated to be a few feet per day. 

The Floridan aquifer is primarily composed of limestone and dolostone, and the movement of 

water through the aquifer is via both “conduit flow” (flow through fractures, caverns, etc.) and 

“diffuse flow” (flow through intergranular pore spaces in the rock). As such, water quality is 

generally excellent because of extensive dilution, chemical interactions with the rock matrix, and 

mechanical filtration. 

The saltwater/freshwater transition zone is the wedge-shaped groundwater zone where fresh 

ground water flows seaward, up and over saline water related to the 
2-16

Figure 2-10. Potentiometric surface of the Floridan aquifer in May 1976. Adapted from Laughlin 

(1976); Rosenau and Meadows (1977); Fisk and Rosenau (1977). 
2-17

Gulf of Mexico. The transition zone is characterized by upward movement and mixing of fresh 

water with saline water. The position of the transition has been roughly delineated by sodium 

and chloride data (Upchurch, 1990) along the Gulf of Mexico, and it has been defined by 

geophysics within a 20-kilometer radius around the mouth of the Suwannee River (Countryman 

and Stewart, 1997). Shallow aquifer water within about 5 miles of the Gulf coast tends to have 

relatively higher concentrations of sodium, chloride and potassium; however, chloride 

concentration does not exceed the 250 mg/L drinking water standard, (Copeland, 1987). Well 

depths in the larger coastal communities range from 85 feet to 170 feet without a significant 

increase in sodium, chloride or sulfate concentrations. 

The degree of confinement of the upper Floridan aquifer is a critical factor in aquifer dynamics. 

Poorly confined areas tend to be rapidly recharged, while highly confined areas may receive 

minimal recharge on an annual basis. The District has compiled a hydrogeologic classification 

based on the degree of confinement of the Floridan aquifer (Figure 2-11) by combining and 

evaluating the physiography, geology, and hydrogeology (SRWMD, 1982). The classes of 

confinement are as follows. 

Class 1 – Unconfined. Class I conditions exist where the Floridan is unconfined, is the only 

aquifer present, and the carbonate rock is at or near land surface. Where it is not exposed, the 

Floridan is usually covered by porous sand. The limestone is porous and permeable, exhibiting 

a high degree of secondary porosity that has been enhanced by a fluctuating water table. Due 

to the porous nature of the rock and sand, rainwater recharges the aquifer directly. Recharge 

rates in this region range from 16 to 31 inches annually (Grubbs, 1998). Surface water features 

usually represent exposures of the water table in the Floridan aquifer. 

Class II - Semi-confined. Class II conditions exist where the Floridan aquifer is semi-confined 

on top by discontinuous, leaky, clay beds. The Class II area in Gilchrist, Alachua and Levy 

counties coincides with the Waccasassa Flats and the Class II area in Madison, Taylor, Dixie 

and Lafayette counties coincides with the San Pedro Bay/Mallory Swamp region. Because of 

reduced recharge, there are streams that drain the Waccasassa Flats and the San Pedro Bay, 

and there are lakes on the edges of these features. The Class II area that extends southeast 

from Suwannee County to Columbia County is the transition zone that parallels the Cody Scarp. 

This area is characterized by sinking streams, sinkhole lakes that periodically drain into the 

Floridan, and numerous steep-sided sinkholes. Recharge rates to the Floridan in this region are 

variable (Grubbs, 1998) and highly focused in location. 
2-18

Figure 2-11. Confinement conditions of the Floridan aquifer in the region. Adapted from SRWMD 

(1982). 
2-19

Class III – Confined. The Class III area is characterized by deeper and confined portions of the 

Floridan aquifer. Confinement is a result of at least 80 feet of Hawthorn Group clay overlying 

the Floridan. Recharge rates to the Floridan in this region average 12 inches or less annually 

(Grubbs, 1998). Confinement creates artesian conditions, and water levels in wells that 

penetrate these aquifers usually rise to within 15 feet of land surface. 

The surficial aquifer locally overlies the Floridan in the Class II and most of the Class III areas 

(Figure 2-11). The surficial aquifer consists of unconfined, saturated sand and ranges up to 55 

feet in thickness. The water table is a subdued replica of the topography and is at, or near, 

land surface. It coincides with surface water levels observed in the swamps, lakes, and ponds. 

Streams in these areas drain the surficial aquifer in addition to removing surface runoff. The 

surficial aquifer is recharged directly by rainfall and water level fluctuations are directly related to 

the amount of rainfall. 

As suggested by Figure 2-11, recharge to the Floridan is highly variable. In Class III areas 

recharge is limited. The Cody Scarp is an area of generally moderate to high recharge owing to 

the presence of sinking streams that flow off the confined, Class III areas (i.e., the Northern 

Highlands) of the District and the presence of large sinkholes. A similar pattern exists in the 

transition from Class II to Class I regions west of the Suwannee River and in eastern Levy 

County (Figure 2-11). Recharge is generally high in the Class I (Coastal Lowlands, etc.) 

because of the thin deposits that overlie the limestone of the Floridan and the presence of many 

sinkholes. 

Areas defined by their high potentiometric surface elevations (Figure 2-10) vary in origin. In 

general, they reflect locations within the District where the hydraulic conductivity (permeability) 

of the Floridan is relatively low, and groundwater flow is, therefore, slow. The reduction in ability 

to effectively drain water from the aquifer results in the potentiometric highs in spite of the low 

relative recharge. Because of focused recharge on the Cody Scarp and the margins of other 

areas where recharge is limited, the margins of the potentiometric highs are supported by high 

recharge. 

The lower Suwannee groundwater basin is characterized by flow toward the river (Figure 2-10) 

from the east and west. The groundwater basin boundary to the east is in central Levy and 

Gilchrist counties (Figure 2-10). There, a groundwater divide separates the Suwannee 

groundwater basin from the Waccasassa basin and the High Springs Gap groundwater flow 

system. The divide is located under the Waccasassa Flats and Bell and Brooksville Ridges. To 

the west, the groundwater basin is limited by the potentiometric surface high in Dixie and 

Lafayette counties (Figure 2-10). 

The total fluctuation of the Floridan aquifer potentiometric surface in the basin ranges up to 40 

feet in the Alapaha River Basin in the northern part of the Suwannee River Basin. There is less 

than 15 feet of total fluctuation in at least two-thirds of the District and there is less than 5 feet of 

total fluctuation along the coast. Average annual fluctuation is less than 4 feet for approximately 

two-thirds of the District. 

2.1.5 Land and Water Use in the Basin 

2.1.5.1 Land Use and Population Characteristics 

A summary of land cover/land use conditions (based on 1994 aerial photography) in the Florida 

portion of the Suwannee basin is shown in Table 2-3. Major human land uses in the basin in 

Florida include managed pine forests and agriculture. Available information indicates that these 

two uses also dominate land cover in the Georgia portion of the basin (Berndt et al., 1996). 

Residential, commercial and industrial land uses collectively comprise less than 6% of the total 
2-20

land use in Florida. The other dominant land cover types in Florida are upland and wetland 

forests in a largely natural or relatively less-disturbed condition. 

Population density in the basin averages 29.8 persons per square mile, which is well below the 

statewide average of 239 persons per square mile. The two largest private employment sectors 

are the forest products industry (pulp manufacturing, lumber milling, and related silvicultural 

activities) and phosphate mining and processing. The largest single source of employment in 

the region is government, with slightly over half of the total workforce in the region working for 

local, state, or federal governments. Major government employers include local school systems 

and county governments, the Florida Dept. of Corrections, the Florida Dept. of Transportation, 

and the federal Veterans Administration. 

Most of the point source discharges to the river are located in Georgia. These point-sources are 

mostly municipal wastewater discharges. The three major point-source discharges are 

phosphate processing facilities, which discharge indirectly via Hunter and Swift Creeks on the 

upper Suwannee; a pulp mill located in Clyattville, GA, which discharges to the Withlacoochee 

River in Florida via Jumping Gulley Creek; and a poultry processing plant, which discharges 

directly to the Suwannee River near the Withlacoochee confluence. 

Relative to other areas of Florida, urban non-point sources of water pollution are fairly low 

intensity and dispersed. The largest urban area in the drainage basin is Valdosta, GA, which 

lies adjacent to the Withlacoochee and Alapaha Rivers. In Florida, relatively urbanized areas 

along or adjacent to the river or its tributaries include the towns of White Springs, Dowling Park, 

Branford, Fanning Springs, Ft. White, and High Springs. 

2.1.5.2 Water Use 

Estimated water use in the District in 2000 (Table 2-4) was 314 million gallons/day (mgd; WRA, 

2005), which equates to about 486 cfs. Water use patterns in the District somewhat mirror land 

use. Agricultural irrigation accounts for a large fraction of the existing and projected water use, 

although commercial/ industrial is also a large overall use, principally due to phosphate mining 

and processing and once-through cooling water for power generation (Marella, 2004; WRA, 

2005). By 2020 and 2050, agriculture and industrial water uses are predicted to continue being 

the largest uses in the District (WRA, 2005). Total water use in the District is projected to be 

approximately 547 mgd in 2020 (which equates to about 846 cfs), and 895 mgd in 2050 (1385 

cfs). 

Spatial patterns in existing permitted water use are shown in Fig. 2-12. This indicates that a 

large proportion of the permitted water use in the District is within the Suwannee basin. Total 

2000 water use for counties entirely or partly within the Suwannee River Basin in Florida was 

259 mgd, which is 82% of the 314 mgd total District water use. 
2-21

Figure 2-12. Map showing permitted water use patterns in the SRWMD. Each symbol represents 

the sum of the Average Daily Rate of Withdrawal (ADR) within each 1 mi.2

 section. 
2-22

Table 2-3. Land use/land cover conditions in the Florida portion of the Suwannee River basin, 

based on 1994 NAPP aerial photography (Source: SRWMD data). 

 CATEGORY ACRES %

Residential (all types) 153,324 5.5 

Commercial (shopping, office parks, malls, 6,186 0.2 

motels, campgrounds, etc.) 

Industrial 3,296 0.1 

Mining 39,278 1.4 

Institutional (prisons, military facilities, 4,031 0.1 

schools, churches, hospitals, etc.) 

Recreational (golf courses, race tracks, 2,409 0.1 

marinas, parks, etc.) 

Other developed uses (land being 22,992 0.8 

developed, cleared land in urban areas) 

Agriculture (pasture and row crops) 584,754 20.9 

Agriculture (groves) 4,751 0.2 

Agriculture-other (dairy, poultry, hogs, 21,408 0.8 

nurseries, aquaculture, etc.) 

Non-forested uplands (shrubland, coastal 32,106 1.1 

scrub, etc.) 

Forested uplands 426,120 15.2 

Managed pine forests 1,001,541 35.8 

Streams and lakes 33,017 1.2 

Artificial waterbodies (dug ponds, flooded 5,822 0.2 

rock pits, etc.) 

Forested wetlands 420,265 15.0 

Herbaceous wetlands 16,870 0.6 

Disturbed lands 670 <0.1 

Infrastructure (airports, powerline corridors, 21,267 0.8 

sewer and water treatment facilities, roads) 

Table 2-4. Summary of current and projected water use in SRWMD (Sources: SRWMD data; WRA 

2005). 

Water Use Category Existing (2000) Projected (2020) Projected (2050) 

Public supply (utilities) 15.8 mgd 25.2 mgd 40.5 mgd 

Domestic (self-supplied) 15.4 25.4 41.2 

Commercial/Industrial** 190.1 311.7 505 

Agriculture 91.1 182.2 305 

Recreation 1.5 2.3 3.6 

TOTAL 314 mgd 546.8 mgd 895.2 mgd 

** - includes commercial, industrial, mining, and power generation