Exchanges of Water between the Upper 

Floridan Aquifer and the Lower Suwannee 

and Lower Santa Fe Rivers, Florida

By J.W. Grubbs and C.A. Crandall

Prepared in cooperation with the

Suwannee River Water Management District

Professional Paper 1656-C

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2007

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Suggested citation:

Grubbs, J.W., and Crandall, C.A., 2007, Exchanges of Water between the Upper Floridan Aquifer and the Lower 

Suwannee and Lower Santa Fe Rivers, Florida: U.S. Geological Survey Professional Paper 1656-C, 83 p.

Library of Congress Cataloging-in-Publication Data

Grubbs, J.W., Crandall, C.A. 

Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, 

Florida/ Grubbs, Crandall

p. cm. –(U.S. Geological Survey Professional Paper ; 1656-C)

Includes bibliographic references.

TN24.M9 M55 2002

553’.09786’6—dc21

2001051109

ISBN 0-607-97815-9 (Set)
Preface

Many areas of the United States have experienced water shortages as a consequence of 

increased water use due to population pressures, industrial growth, and changes in agricultural 

irrigation practices. As a result of these increasing demands on water resources, many states 

have established, or are considering, instream-flow protection programs to ensure that the 

water requirements for ecosystem maintenance will be met. The State of Florida in 1972 

adopted legislation directing the water-management districts to establish minimum flows and 

levels (MFLs) for all watercourses, and minimum levels for aquifers and surface water, in 

their respective regions. Section 373.042 of the Florida Statutes specifies that a minimum flow 

for a watercourse is the flow at which further withdrawals would be substantially harmful to 

the water resources or ecology of the area. Similarly, the Statute defines the minimum level 

as the level of water in an aquifer, or level of surface water, at which further withdrawals 

would be substantially harmful to the water resources of the area. The Statute also allows 

the development of minimum flows and levels using the “best information available” and the 

recognition of seasonal variation in setting the flows and levels.

The Suwannee River Water Management District (SRWMD) in the north-central part 

of the State is one of five regional water-management districts in Florida. The District’s first 

priority is to set MFLs for the lower Suwannee River, from its confluence with the Santa Fe 

River to the Gulf of Mexico. The SRWMD began the process for setting MFLs in 1994 with a 

series of long-term cooperative studies with the U.S. Geological Survey (USGS) that included 

data collection, analysis, and interpretation. The USGS program culminated in the completion 

of three major studies, which were conducted to understand the effects that reduced flow in 

the river could have on the forested floodplain and the mixing of freshwater and saltwater in 

the estuary, as well as the effects that ground-water withdrawals could have on flows in the 

river. These studies are reported in Chapters A, B, and C of this Professional Paper 1656 series. 

Additionally, a summary of the program is presented in Chapter D, which includes a discussion 

of how the results from these three studies can be used collectively by the SRWMD.

Chapter A of the series describes the hydrology, vegetation, and soils of the forested 

floodplain of the Lower Suwannee River. The chapter further describes the relation of forest 

types and other floodplain characteristics to long-term river flow, and estimates potential 

impacts on the floodplain if river flows were reduced. Chapter B focuses on flow and the 

mixing of freshwater and saltwater in the lower river and estuary. Salinity and other hydrologic 

data collected during a period of unusually low flow were used to calibrate a three-dimensional 

hydrodynamic and transport model that simulates time-varying water levels, currents (lateral, 

longitudinal, and vertical), and salinity conditions. This chapter includes important discussions 

of modeled scenarios and hydrologic changes that could result from a reduction of flow in the 

river. Reductions in streamflow could come from changes in climatic conditions or from direct 

withdrawal, but may also come from ground-water pumpage adjacent to or many miles from 

the river. Chapter C presents a discussion of hydrologic conditions governing the interaction 

between ground water and surface water, an evaluation of the magnitude and timing of water 

exchanges between the Lower Suwannee River and the Upper Floridan aquifer using historical 

data, and the models that were used to simulate the exchanges. Also presented in this chapter 

is a discussion of how a hydrologic model could be used to evaluate hypothetical water-use 

scenarios, and the ground-water and surface-water exchanges that could result from these 

hypothetical conditions. Chapter D summarizes the cooperative program and highlights the 

importance of this multidisciplinary program to our understanding of the hydrology in the 

Lower Suwannee Basin—an understanding borne out of an extensive data-collection program 

and complex interpretive studies. Chapter D provides a “roadmap” for water managers to make 

better use of the integrated results of these studies.

iii
iv
Contents

Preface ...........................................................................................................................................................iii

Abstract...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Purpose and Scope ..............................................................................................................................4

Description of Study Areas .................................................................................................................4

Previous Studies ...................................................................................................................................6

Acknowledgments................................................................................................................................8

Surface-Water Hydrology ............................................................................................................................8

Lower Suwannee and Lower Santa Fe Rivers.................................................................................9

Channel and Floodplain Characteristics..................................................................................9

Flow Characteristics .................................................................................................................10

Water-Level Characteristics....................................................................................................15

Smaller Rivers and Streams..............................................................................................................17

Ground-Water Hydrology ...........................................................................................................................17

Hydrogeologic Framework................................................................................................................17

Ground-Water Flow System Boundaries ........................................................................................19

Lateral Boundaries ....................................................................................................................19

Upper and Lower Flow-Sysem Boundaries...........................................................................27

Patterns of Ground-Water Levels and Flow...................................................................................28

Hydraulic Properties...........................................................................................................................33

Aquifer Tests...............................................................................................................................34

Results from Previous Modeling Studies...............................................................................36

Inferences from Geologic Characteristics and Potentiometric Surface Maps ..............37

Sources and Sinks of Water .............................................................................................................38

Natural Recharge and Discharge ...........................................................................................38

Well Pumpage ............................................................................................................................40

Evaluation of Ground-Water and Surface-Water Exchanges Using Hydrologic Data.....................42

Temporal Characteristics ..................................................................................................................42

Spatial Characteristics ......................................................................................................................46

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model ..............47

Model Construction............................................................................................................................47

Ground-Water Flow Model.......................................................................................................47

 Mathematical Basis and Approach.......................................................................49

 Discretization and Model Boundaries...................................................................49

 Representing Sources and Sinks of Water ..........................................................50

 Representation of Hydraulic Properties ...............................................................50

Surface-Water Flow Model......................................................................................................51

 Mathematical Basis and Approach.......................................................................51

 Schematic and Discretization.................................................................................51

 Hydraulic Characteristics of the River Channel and Floodplain .......................52

Coupled Ground-Water and Surface-Water Flow Model ...................................................52
Model Calibration................................................................................................................................53

Uncoupled Ground-Water Flow Model ..................................................................................53

Uncoupled Surface-Water Flow Model .................................................................................57

Coupled Ground-Water and Surface-Water Flow Model ...................................................61

Model Evaluation ................................................................................................................................69

Temporal and Spatial Characteristics of Ground- and Surface-Water Exchanges .......69

Simulated Effects of Water Withdrawals on Streamflow...................................................71

Model Limitations................................................................................................................................78

Summary........................................................................................................................................................78

Selected References...................................................................................................................................80

Figures

1-4. Maps showing:

1. Location of regional and subregional study areas and the Suwannee 

River Drainage Basin.........................................................................................................2

2. Location of rivers and springs in the subregional and regional study 

areas and the Suwannee River Water Management District.....................................3

3. Physiographic areas in and adjacent to the Suwannee River Water 

Management District.........................................................................................................5

4. Selected streamgaging stations and streamflow measurement sites 

on the Suwannee and Lower Santa Fe Rivers ..............................................................7

5. Thalweg profiles of the Lower Suwannee and Lower Santa Fe Rivers ............................10

6. Boxplots of monthly mean discharge in the Lower Suwannee and Lower 

Santa Fe Rivers ...........................................................................................................................11

7-10. Graphs showing:

7. Streamflows in the Lower Suwannee and Lower Santa Fe Rivers from 

October 1, 1997, to September 30, 1999 ........................................................................12

 8. Tidally affected water levels and flows in the Suwannee River during 

a spring tide.......................................................................................................................13

 9. Tidally affected water levels and flows in the Suwannee River during 

a neap tide.........................................................................................................................13

10. Flow in the Suwannee River near Wilcox, Florida, during water year 1998...........14

11. Map showing definition of river mileage system and selected river reaches 

in the subregional study area ...................................................................................................15

12. Boxplots of monthly water-surface elevation at selected locations on the 

Lower Suwannee and Lower Santa Fe Rivers.......................................................................16

13. Diagram showing geologic and hydrogeologic units present within 

and adjacent to the regional study area.................................................................................18

14-19. Maps showing:

 14. Extent and thickness of the Hawthorn Group sediments (intermediate 

confining unit) in the Suwannee River Water Management District.......................20

 15. Elevation of the top of the Upper Floridan aquifer......................................................21

 16. Elevation of the base of the Upper Floridan aquifer...................................................22

 17. Thickness of the Upper Floridan aquifer......................................................................23

vi
 18. Potentiometric surface of the Upper Floridan aquifer during May 1980, 

including key features of the ground-water flow system..........................................24

 19. Predevelopment potentiometric surface of the Upper Floridan aquifer, 

including key features of the ground-water flow system..........................................26

20-21. Graphs showing ground-water levels:

 20. In the Upper Floridan aquifer near Lake Butler, Florida, from 1957 to 1999............27

21. Of the collocated wells tapping the unconsolidated surficial sediments 

and Upper Floridan aquifer near Bell, Florida, 1991-93..............................................27

22-23. Maps showing:

22. Elevation of the base of freshwater in the Upper Floridan aquifer..........................28

23. Potentiometric surface of the Upper Floridan aquifer during March 1998 

and general spatial patterns of ground-water flow ...................................................29

24-26. Graphs showing:

24. Boxplots of monthly mean ground-water levels near Chiefland and 

Cross City, Florida.............................................................................................................30

25. Boxplots of monthly rainfall near Chiefland and Cross City, Florida........................31

26. Temporal variations in ground- and surface-water levels near 

river miles 25 and 56 of the Suwannee River...............................................................32

27-29. Maps showing:

27. Network of wells used to measure ground-water levels within the 

subregional study area....................................................................................................33

28. Location of selected sites and estimated transmissivity in the Upper 

Floridan aquifer based on aquifer tests........................................................................35

29. Recharge totals in the subregional study area based on results of the 

soil-moisture accounting method, water years 1998 and 1999 ................................39

30-31. Graphs showing:

30. Daily ground-water levels, rainfall, and estimated recharge for Cross City,

 Florida, during water years 1998-99 .............................................................................40

31. Estimated monthly ground-water withdrawals from wells in the 

subregional study area during waters 1998-99 ...........................................................41

32. Map showing geographic distribution of ground-water withdrawals from the 

Upper Floridan aquifer during water years 1998-99 .............................................................42

33-38. Graphs showing:

33. Cumulative distribution of the median annual change in streamflow 

(streamflow pickup) in reach 1 of the Lower Suwannee and Santa Fe Rivers .........43

34. Time-series plot of annual streamflow in the Suwannee River near Wilcox, 

Florida, and the streamflow pickup in reach 1 of the Lower Suwannee and 

Santa Fe Rivers during 1941-2000..................................................................................43

35. Relation between annual streamflow in the Suwannee River near Wilcox, 

Florida, and the streamflow pickup in the Lower Suwannee and 

Santa Fe Rivers.................................................................................................................43

36. Boxplots of monthly mean streamflow pickup in river reach 1 of the Lower 

Suwannee and Santa Fe Rivers.....................................................................................44

37. Relation between streamflow, streamflow pickup, surface storage, and 

river-aquifer water exchanges ......................................................................................45

38. Tidally induced changes in spring tool elevation and spring flow in 

Manatee Springs during May 1997................................................................................46

vii
39-40. Maps showing:

39. Model grid and lateral boundary conditions for the subregional 

ground-water flow model................................................................................................48

40. Calibrated transmissivity distribution from the uncoupled ground-water 

flow model .........................................................................................................................54

41. Time-series plots of measured ground-water levels and ground-water levels 

that were simulated with the ground-water flow model, October 1997 to 

September 1999...........................................................................................................................57

42-43. Maps showing:

42. Spatial distribution of ground-water level residuals from the ground-water 

flow model during a high water-level period...............................................................58

43. Spatial distribution of ground-water level residuals from the ground-water 

flow model during a low water-level period ................................................................58

44. Time-series plot of measured and simulated streamflows in the Suwannee River 

near Wilcox, Florida ...................................................................................................................59

45-48. Graphs showing comparison of simulated and measured:

45. Water-surface elevations in the Lower Suwannee River during 

September 1999 ................................................................................................................60

46. Water-surface elevations in the Lower Suwannee River during 

August 1997 .......................................................................................................................60

47. Flows in the Lower Suwannee River during September 1999 ..................................61

48. Flows in the Lower Suwannee River during August 1997 .........................................62

49-51. Time-series plots showing comparisons of measured and simulated (coupled model)

 ground-water levels for selected wells from October 1997 to September 1999:

49. Wells s364, s337, s245, and s333 ....................................................................................63

50. Wells s315, s330, s331, s346, and t059...........................................................................64

51. Wells s360, s385, and s319 ..............................................................................................65

52-53. Maps showing potentiometric surface of the Upper Floridan aquifer and 

differences between measured and simulated ground-water levels in:

52. March 1998........................................................................................................................66

53. September 1999 ................................................................................................................66

54-59. Graphs showing comparisons of measured and simulated (coupled model):

54. Flows in the Suwannee River near Wilcox, Florida, October 1997 to 

September 1999 ................................................................................................................67

55. Stage in the Suwannee River near Bell, Florida, October 1997 to 

September 1999 ................................................................................................................67

56. Stage in the Suwannee River near Wilcox, Florida, October 1997 to 

September 1999 ................................................................................................................67

57. Flows in the Suwannee River near Bell, Florida, September 28-29, 1999 ...............68

58. Flows in the Suwannee River near Wilcox, Florida, September 28, 1999 ...............68

59. Flows in the Suwannee River above Manatee Springs, Florida, near 

Chiefland, Florida, September 29-30, 1999....................................................................68

60. Graphs showing simulated daily ground-water inflow to reach 3 and measured 

daily streamflows in the Suwannee River at Branford, Suwannee River near 

Wilcox, and Santa Fe River near Fort White, Florida............................................................70

61. Map showing simulated average and standard deviation of ground-water 

leakage to selected river reaches ...........................................................................................72

viii
62-63. Graphs showing:

62. Mean daily flows during water years 1998-99, simulated for scenarios 1 and 4 

in the Suwannee River near Wilcox, Florida..........................................................................73

63. Relation between daily flows during water years 1998-99, simulated for 

scenarios 1 and 4........................................................................................................................74

Tables

1. Selected streamgaging stations and streamflow measurement sites on the 

Lower Suwannee and Santa Fe Rivers............................................................................................8

2. Identifiers for the network of wells used to measure ground-water levels within 

the subregional study area ..............................................................................................................34

3. Transmissivity estimates from aquifer tests and flow-net analyses of the 

Upper Floridan aquifer......................................................................................................................36

4. Estimated parameter values and 95-percent confidence limits from the 

uncoupled ground-water flow model.............................................................................................55

5. Specified parameter values from the uncoupled ground-water flow model ..........................55

6. Values of composite and composite-scaled parameter sensitivities for the 

uncoupled ground-water flow model.............................................................................................56

7. Simulated and measured water-surface elevations in the Lower Santa Fe River 

for selected time periods .................................................................................................................59

8. Description of baseline and hypothetical withdrawal scenarios that were simulated 

with the coupled model of ground-water and surface-water flow...........................................73

9. Estimates of streamflow characteristics of the Suwannee River near Bell, 

Florida, under baseline and hypothetical conditions ..................................................................75

10. Estimates of streamflow characteristics of the Suwannee River near Wilcox, 

Florida, under baseline and hypothetical conditions ..................................................................75

11. Estimates of the parameters necessary for estimating changes in streamflow

characteristics of the Suwannee River above the Gopher River under baseline 

and hypothetical conditions ............................................................................................................76

12. Estimates of the parameters necessary for estimating changes in streamflow

characteristics of the Suwannee River near Bell, Florida, under baseline and

hypothetical conditions ....................................................................................................................76

13. Estimates of the parameters necessary for estimating changes in streamflow

characteristics of the Suwannee River near Wilcox, Florida, under baseline

and hypothetical conditions ............................................................................................................76

14. Standard deviation and coefficient of variation of predicted values of selected

streamflow statistics for scenario 4 (500 cubic feet per second) for locations on 

the Suwannee River corresponding to the gaging stations near Bell and Wilcox, 

Florida, and above the Gopher River..............................................................................................77

ix
Conversion Factors, Abbreviations, and Datum

Multiply By To obtain

Length

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

square mile (mi2) 2.590 square kilometer (km2) 

Volume

gallon (gal) 3.785 liter (L) 

Flow rate

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

inch per day (in/d) 0.0254 meter per day (m/d)

inch per year (in/yr) 25.4 millimeter per year (mm/yr)

Hydraulic gradient

foot per mile (ft/mi) 0.1894 meter per kilometer (m/km)

Transmissivity*

foot squared per day (ft2/d) 0.09290 meter squared per day (m2/d) 

*Transmissivity: The standard unit for transmissivity is cubic foot per day per square foot times 

foot of aquifer thickness [(ft3/d)/ft2]ft. In this report, the mathematically reduced form, foot 

squared per day (ft2/d), is used for convenience.

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius 

(°C) as °C = (°F - 32)/1.8.

Vertical coordinate information is referenced to the National Geodetic Vertical Datum of 1929 

(NGVD 1929), and horizontal coordinate information is referenced to the North American Datum 

of 1983 (NAD 83). NGVD 1929 is approximately equal to sea level.

Acronyms

ADCP acoustic Doppler current profiler

PEST parameter estimation program

SMA soil-moisture deficit accounting algorithm

SRWMD Suwannee River Water Management District

USACE U.S. Army Corps of Engineers

USGS U.S. Geological Survey
Abstract

Exchanges of water between the Upper Floridan aquifer 

and the Lower Suwannee River were evaluated using historic 

and current hydrologic data from the Lower Suwannee River 

Basin and adjacent areas that contribute ground-water flow 

to the lowest 76 miles of the Suwannee River and the lowest 

28 miles of the Santa Fe River. These and other data were 

also used to develop a computer model that simulated the 

movement of water in the aquifer and river, and surface- and 

ground-water exchanges between these systems over a range 

of hydrologic conditions and a set of hypothetical water-use 

scenarios.

Long-term data indicate that at least 15 percent of the 

average annual flow in the Suwannee River near Wilcox 

(at river mile 36) is derived from ground-water discharge 

to the Lower Suwannee and Lower Santa Fe Rivers. Model 

simulations of ground-water flow to this reach during water 

years 1998 and 1999 were similar to these model-independent 

estimates and indicated that ground-water discharge accounted 

for about 12 percent of the flow in the Lower Suwannee River 

during this time period.

The simulated average ground-water discharge to the 

Lower Suwannee River downstream from the mouth of the 

Santa Fe River was about 2,000 cubic feet per second during 

water years 1998 and 1999. Simulated monthly average 

ground-water discharge rates to this reach ranged from about 

1,500 to 3,200 cubic feet per second. These temporal variations in ground-water discharge were associated with climatic 

phenomena, including periods of strong influence by El Niñoassociated flooding, and La Niña-associated drought. These 

variations showed a relatively consistent pattern in which the 

lowest rates of ground-water inflow occurred during periods of 

peak flood levels (when river levels rose faster than groundwater levels) and after periods of extended droughts (when 

ground-water storage was depleted). Conversely, the highest 

rates of ground-water inflow typically occurred during periods 

of receding levels that followed peak river levels.

Introduction

The Suwannee River drains an area of about 9,930 mi2

in southern Georgia and northern Florida (fig. 1). In much of 

the river, the flow is intimately linked to ground-water conditions. This is evident in the lower reaches of the river and its 

main tributary, the Santa Fe River, where some of the highest 

concentrations of springs in Florida are found (fig. 2). The 

ground-water inflow that sustains these springs accounts for 

most of the average annual flow of the Lower Suwannee River, 

and supplies nearly all of the flow in the river during periods 

of low flow in the dry seasons and during droughts.

The Lower Suwannee River and adjacent Upper Floridan 

aquifer are an important water resource in this region of 

Florida. Freshwater flow in the Lower Suwannee River helps 

maintain the proper balance of freshwater and saltwater that 

sustains estuarine life in the Gulf of Mexico near the mouth 

of the Lower Suwannee River. The river also provides numerous recreational opportunities and important aesthetic benefits 

to the region. Ground water from the Upper Floridan aquifer 

supplies all of the water for drinking, irrigation, and commercial 

uses in the Lower Suwannee River Basin.

Exchanges of Water between the Upper Floridan 

Aquifer and the Lower Suwannee and Lower 

Santa Fe Rivers, Florida

By J.W. Grubbs and C.A. Crandall
 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

The flow of water in the Lower Suwannee River and its 

springs depends on the ground-water level in the contiguous Upper Floridan aquifer. When ground-water levels are 

high relative to the river stage, ground-water inflow rates 

to the river are also high and flow in the river is sustained. 

As ground-water levels decline relative to river stages, 

ground-water inflow to the river declines and the flow in the 

river declines accordingly. Ground-water levels depend on 

several factors: rainfall that recharges the aquifer, the amount 

of ground water that is consumed for various uses, and river 

stage (for locations close enough to the river). Because of 

these linkages between the river and Upper Floridan aquifer, 

a good understanding of their hydraulic interaction and the 

corresponding hydraulic and hydrologic characteristics is 

essential for managing water in the Lower Suwannee River 

Basin and assessing the potential consequences of future water 

development on streamflows.

In 1996, the U.S. Geological Survey (USGS), in cooperation with the Suwannee River Water Management District 

(SRWMD), initiated a study to evaluate the ground-water 

and surface-water interactions between the Lower Suwannee 

River and the contiguous Upper Floridan aquifer. The specific 

objectives of the study were twofold. The first objective was to 

integrate historic and current ground- and surface-water data 

to better understand the hydrology of the river and aquifer and 

their interaction. Development of a hydrologic model of the 

river and aquifer systems was an essential element of this integration. The second objective was to use this model to assess 

the effects of future water-withdrawal scenarios on streamflow.

The primary (subregional) study area covers about 

2,300 mi2 in northern peninsular Florida (figs. 1 and 2), and 

includes the lowest (most downstream) 76 mi of the Suwannee 

River from the town of Branford to the Gulf of Mexico (defined 

here as the Lower Suwannee River) and the lowest 28 mi of the 

G E O R G I A

F L O R I D A

G u l f

o f

M e x i c o

A t l a n t i c O c e a

n

84°

32°

31°

30°

29°

83° 82°

Suwannee

Fe River Santa

Withlacoochee

River

Ala ha pa Rive

R

r

iver

Base from U.S. Geological Survey digital data, 1972

Albers Equal-Area Conic Projection,

Standard parallels 29°30’ and 45°30’, central meridian 83°00’

GA

FL

Location

map REGIONAL

STUDY AREA

BOUNDARY

SUBREGIONAL

STUDY AREA

BOUNDARY

0 15 30 KILOMETERS

0 15 30 MILES

441

27

441

27

Albany

Tallahassee

Jacksonville

Gainesville

Lake City

Valdosta

Cedar

Key

Fernandina

Beach

Keystone

Heights

SUWANNEE RIVER

DRAINAGE BASIN

Figure 1. Location of regional and subregional study areas and the Suwannee River 

Drainage Basin.
Gopher River

East Pass

West

Pass

Little

River

Spring

Ichetucknee

River and

Springs

Group

Rose

Creek

Clay Hole

Creek

Hart

Springs

Fanning Springs

Ginnie

Springs

Group

Manatee

Springs

Rock

Bluff

Springs

Little Fanning Springs

Cow

Creek

G E O R G I A

F L O R I D A

SUWANNEE

LAFAYETTE

DIXIE

LEVY

GILCHRIST ALACHUA

MARION

COLUMBIA

TAYLOR

MADISON

HAMILTON

JEFFERSON LEON

GRADY

THOMAS

BROOKS

LOWNDES

ECHOLS

CLINCH

WARE

CHARLTON

BAKER

UNION

BRADFORD

CITRUS

SUMTER

WAKULLA Suwannee River

Suwannee River

Stei e nhatch e Riv

re

California

Creek

Wacca e sassa Riv r

Rocky

Run

Cow Creek

Tenmile Creek

Wekiva River

30°

84° 83° 82°

29°

0 20 40 MILES

0 20 40 KILOMETERS

G u l f o f M e x i c o

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

SUWANNEE RIVER WATER MANAGEMENT

DISTRICT BOUNDARY

1st MAGNITUDE SPRING LOCATION

2nd MAGNITUDE SPRING LOCATION

3rd MAGNITUDE SPRING LOCATION

EXPLANATION

Hildreth

Ellaville

Keystone

Heights

Perry

Thomasville Valdosta

Ocala

Gainesville

Tallahassee

Fort

White

Lake

City

Live

Oak

Branford

Bell

Old Wilcox

Town

High

Springs

White

Springs

Suwannee

Springs

O’Leno

State Park

Fanning Springs

Chiefland

Cross

City Trenton

Newberry

Bronson

Worthington

Springs

Santa Fe

River

Rise

Luraville

Fowlers Bluff

Suwannee

27

441

27

441

Fe River

Santa

Santa

Fe River

Figure 2. Location of rivers and springs in the subregional and regional study areas and the Suwannee River Water Management 

District.

Introduction 
 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Santa Fe River from U.S. Highway 441 near High Springs to 

the mouth of the river at its confluence with the Suwannee River 

(defined here as the Lower Santa Fe River). The subregional 

study area also includes places where the Upper Floridan aquifer contributes ground water to these two river reaches, all of the 

Lower Suwannee River Basin, and adjacent areas in Lafayette, 

Dixie, Gilchrist, Alachua, and Levy Counties (fig. 2). Hydrologic and hydrogeologic characteristics of a larger regional 

study area, encompassing all of the SRWMD (fig. 2), are also 

examined to provide the regional hydrogeologic setting.

Purpose and Scope

The purposes of this report are to: (1) describe the 

surface- and ground-water hydrology of the subregional 

study area; (2) evaluate the magnitude and timing of water 

exchanges between the Lower Suwannee River and Upper 

Floridan aquifer using historical and current data and a 

hydrologic model; and (3) describe how a hydrologic model 

for simulating these exchanges could be used to evaluate 

changes in streamflow under hypothetical water-use scenarios. 

This report describes the analysis of ground-water and surfacewater data collected from August 1996 to September 1999, 

and available historic data. The report also describes the 

development and application of a model to simulate streamflow, ground-water flow, and river-aquifer exchanges.

Description of Study Areas

The regional study area and all of Florida lie within the 

Coastal Plain physiographic province (Fenneman, 1938). 

Puri and Vernon (1964) presented a detailed map of the 

physiographic divisions within Florida, and identified three 

major physiographic divisions within or adjacent to the study 

area: the Northern Highlands, Central Highlands, and Gulf 

Coastal Lowlands. The Northern Highlands and Gulf Coastal 

Lowlands make up most of the regional study area (fig. 3).

The Northern Highlands typically has broad, gently 

sloping, and generally continuous high elevation plateaus in its 

interior regions, and marginal slopes that are well drained by 

dendritic streams. The Central Highlands is also characterized 

by broad, generally coast-parallel high elevation areas, some 

of which have been divided into distinct areas of elongated 

ridges, separated by low elevation uplands and broad valleys 

(Puri and Vernon, 1964). The Brooksville Ridge is the most 

prominent example of the Central Highlands ridges in the 

regional study area.

Most of the subregional study area is within the Gulf 

Coastal Lowlands, a region of generally coast-parallel terraces 

and ancient shorelines that slope gently from the Northern 

Highlands and Central Highlands toward the coast. Relict 

barrier islands that form sand ridges, such as Bell Ridge, and 

that are commonly underlain by karst limestone are present 

in the Gulf Coastal Lowlands (Puri and others, 1967). Limestone is at or near land surface over much of this area, and 

karst topographic features are common. Other features of the 

Gulf Coastal Lowlands include: (1) extensive areas of poorly 

drained swamps and wet-pine flatwoods; (2) Lower Suwannee 

River and Lower Santa Fe River valleys which, apart from 

the two main rivers and the numerous springs that feed them 

(fig. 2), are nearly devoid of surface drainage; and (3) coastal 

areas that are drained by a network of sluggish streams, 

coastal swamps, and salt marshes.

The boundary between the Northern Highlands and Gulf 

Coastal Lowlands is defined by the Cody Scarp, which is the 

most persistent topographic break or escarpment in Florida 

(Puri and Vernon, 1964). This escarpment is also approximately coincident with the northeastern boundary of the 

subregional study area and the boundary between confined 

and unconfined areas of the Upper Floridan aquifer (Miller, 

1986). Many of the streams draining the Northern Highlands 

are captured by sinkholes near the margins of the Northern 

Highlands and reemerge below the Cody Scarp (Burnson and 

others, 1984). Two prominent examples of stream capture and 

reemergence occur in the vicinity of the subregional study 

area. The first is the Santa Fe River, which drains into a sinkhole at O’Leno State Park and reemerges about 3 mi southwest 

of the sinkhole at the Santa Fe River Rise (fig. 2). The second 

example is the springfed Ichetucknee River (fig. 2), which 

occurs at the downstream end of an abandoned drainage way 

(Ichetucknee Trace). Intermittent runoff from two ephemeral 

streams (Clay Hole Creek and Rose Creek) flows into two 

large sinkholes within this drainage way, about 7 to 9 mi 

northeast of the Ichetucknee River Springs Group (fig. 2).

The climate of the study areas is humid subtropical 

(Raulston and others, 1998). Monthly average temperatures 

typically range from 54 to 57 °F in the winter and from 79 

to 91 °F in the summer (National Oceanographic and Atmospheric Administration, 2002). Average annual precipitation ranges from about 51 to 59 in/yr, with about half of this 

amount typically occurring from June to September (National 

Oceanographic and Atmospheric Administration, 2002). 

Summer precipitation is generally associated with localized 

thunderstorm activity that can produce intense rainfall. Winter 

precipitation is generally associated with the passage of cold 

fronts and is more evenly distributed geographically. Averageannual evapotranspiration estimates in the SRWMD range 

from about 35 to 41 in/yr (Bush and Johnston, 1988, pl. 9; 

Knowles, 1996).

Most of the subregional study area is sparsely populated. 

The most densely populated areas are the towns of Cross City 

(1,800), Chiefland (2,000), Newberry (3,300), High Springs 

(3,900) Trenton (1,600), and Bronson (1,000) shown in figure 2. 

Primary economic activities in the study area are silviculture, 

the manufacture of forest products, and agriculture. Accordingly, forest and agricultural lands account for most of the 

land use in the study area, although wetlands also cover a 

large part of the study area. Agricultural land use is found in 

the better drained areas of eastern Lafayette, eastern Dixie, 

Gilchrist, northeastern and northwestern Levy County, southern 

Suwannee, southern Columbia, and western Alachua Counties.
0 20 40 MILES

0 20 40 KILOMETERS

G u l f o f M e x i c o

30°

84° 83° 82°

29°

Perry

Thomasville Valdosta

Ocala

Gainesville

Tallahassee

G E O R G I A

F L O R I D A

SUWANNEE

LAFAYETTE

DIXIE

LEVY

GILCHRIST

ALACHUA

MARION

COLUMBIA

TAYLOR

MADISON HAMILTON JEFFERSON

LEON

GRADY

THOMAS

BROOKS

LOWNDES ECHOLS

CLINCH

WARE

CHARLTON

BAKER

UNION

BRADFORD

CITRUS SUMTER

WAKULLA Suwannee River

Suwannee River

NORTHERN HIGHLANDS

CENTRAL HIGHLANDS

Undifferentiated Central

Highlands (in this report)

Brooksville Ridge

GULF COASTAL LOWLANDS

Ridges and Sand Hills

Undifferentiated Gulf Coastal Lowlands

Coastal Swamps

Other areas referenced in report

EXPLANATION

Lake City

Brooksville Ridge

Bell Ridge

Chiefland

Limestone

Plain

Mallory

Swamp

Waccasassa

Flats

CODY SCARP

CODY SCARP

Santa Fe River

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

SUWANNEE RIVER WATER MANAGEMENT

DISTRICT BOUNDARY

San

Pedro

Bay

Stei e nhatch e Riv

re

Keystone

Heights

Figure 3. Physiographic areas in and adjacent to the Suwannee River Water Management District.

Introduction 
 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Previous Studies

Clarke (1965) studied the relation between ground-water 

inflow, bank and channel storage, and change in streamflow 

along a 6.8-mi reach of the Lower Santa Fe River between 

gaging stations near High Springs (map index no. 13, fig. 4 

and table 1) and near Fort White (map index no. 14, fig. 4 and 

table 1). In this reach, streamflow typically increases from 

about 850 ft3/s at the upstream station near High Springs to 

about 1,600 ft3/s at the downstream station near Fort White, 

respectively. Clarke (1965) noted that the difference in streamflow (streamflow pickup) at the upstream and downstream 

ends of this river reach changes slowly over seasonal and 

longer time scales. Clarke (1965) observed that the streamflow pickup in this reach can decrease abruptly, and even 

reverse to a difference greater than 1,000 ft3/s, over shorter 

time scales when water levels in the Santa Fe River increase 

rapidly following periods of increased rainfall. After this 

abrupt decrease, the streamflow pickup subsequently increases 

to a rate greater than that occurring before the rise in river 

levels. Clarke (1965) did not determine how much of these 

short-term changes in streamflow pickup were due to changes 

in the surface storage (water temporarily stored in the river 

channel and overbank areas) and changes in the rates of water 

exchanges between the river and aquifer in this reach.

Pittman and others (1997) evaluated spring contributions to water quantity and nitrate loads in a 33-mi reach of 

the Suwannee River just upstream from the subregional study 

area between Ellaville and Branford (fig. 4) during a period of 

low flow in the river. They concluded that all of the 950-ft3/s 

increase in flow in the reach was derived from ground water. 

Of this total increase in flow, 41 percent was derived from 11 

springs that were measured. When unmeasured springs are 

considered (those known at the time of their study and those 

subsequently discovered), 75 to 85 percent of the flow increase 

that was measured in this reach was probably due to springflow contributions.

The chemical composition of surface and ground waters 

has also been used to evaluate interactions between ground 

and surface waters in the study areas. Crandall and others 

(1999) found evidence for the migration of water from the 

Suwannee River into the Upper Floridan aquifer by observing changes in the chemical composition of water obtained 

from wells, sinkholes, and springs during a period of rising 

water levels in the Suwannee River. Evidence for this mixing 

included decreased concentrations of calcium, silica, and 

radon-222 (222Rn, a naturally occurring isotope of radon) and 

increased concentrations of dissolved organic carbon, tannic 

acid, and chloride. The fraction of river water in ground water 

ranged from 13 to 65 percent at a sinkhole located about 

1 mi from the Suwannee River. Tannic-colored river water 

was also observed flowing into Little River Spring (fig. 2), 

which discharges into the Suwannee River at rates from 50 to 

230 ft3/s at lower river stages (Crandall and others, 1999).

Ellins and others (1991) and Kincaid (1998) used 222Rn 

and other tracers to evaluate mixing of water between the 

Lower Santa Fe River and the Upper Floridan aquifer. Kincaid 

(1998) found that appreciable quantities of river water can 

rapidly infiltrate into the aquifer. The degree of mixing of 

river and aquifer waters was also highly variable. An analysis 

of samples collected from the Devil’s Ear cave system (fig. 2, 

part of the Ginnie Springs Group), which discharges about 

300 ft3/s to the Lower Santa Fe River, indicates that river water 

represented from less than 10 percent to slightly greater than 

60 percent of the sample. Kincaid (1998) also described a 

relation between the degree of mixing and the distribution of 

rainfall within the Santa Fe River Basin. When large rainfall 

events occur primarily in the confined areas of the Northern Highlands (Upper Santa Fe River Basin), the resulting 

storm runoff from the Upper Santa Fe River Basin creates a 

downward (river-to-aquifer) head gradient and more mixing 

of river and aquifer water. Conversely, when rainfall occurs 

primarily in the Lower Santa Fe River Basin, an upward 

(aquifer-to-river) head gradient and less mixing of river and 

aquifer water results.

Crane (1986) studied the degree of ground-water/surfacewater interactions in the Suwannee River by evaluating the: 

(1) relation between streamflow and specific conductance 

in river water; and (2) activity ratios of uranium isotopes 

(

234U/238U) in river, spring, and aquifer waters. Crane (1986) 

found an inverse relation between streamflow and specific 

conductance in the Suwannee River at and downstream from 

White Springs, and further noted that the relation became 

“...progressively evident downstream as more ground water 

enters the river and runoff contributions to the river become 

negligible at Suwannee Springs, Branford, and Wilcox.” The 

“increasing downstream importance of ground-water contributions to the flow of the Suwannee River” was also evident in 

his analysis of 234U/238U ratios. Crane (1986) found that from 

White Springs southward, “...ground-water flow from areas of 

moderate to high recharge completely dominates the character of the river water.” Similar conclusions were made in an 

earlier study by Hull and others (1981), reporting downstream 

trends in pH, total organic carbon, specific conductance, and 

inorganic chemical constituents.

Grubbs (1997) used streamflow and specific conductance 

measurements of streamflow, direct (storm) runoff, and ground 

water to evaluate the ground-water/surface-water exchanges in 

a reach of the Lower Santa Fe River between gaging stations 

near Worthington Springs and Fort White. Grubbs concluded 

that ground-water discharge to the river accounts for all, or 

nearly all, of the increase in flow in this reach of the Santa Fe 

River on an average annual basis. Evaluations of the changes 

in streamflow, which occur along reaches of the Suwannee and 

Santa Fe Rivers, also indicated that most of the increase in the 

streamflow pickup, which occurs along the Suwannee River 

(below Ellaville) and the Lower Santa Fe River, is derived 

from ground water discharging to these river reaches.
27

441

27

441

Keystone

Heights

Perry

Thomasville Valdosta

Ocala

Gainesville

Tallahassee

Fort

White

Lake

City

Live

Oak

Branford

Bell

Wilcox

Old Town

High

Springs

White

Springs

Suwannee

Springs

O’Leno

State Park

Fanning Springs

Chiefland

Cross

City Trenton

Newberry

Bronson

Worthington

Springs

Santa Fe

River Rise

Hildreth

Ellaville

Luraville

Fowlers

Suwannee Bluff

Gopher River

East Pass

West Pass

Rocky

Run

Cow Creek

Tenmile Creek

Wekiva River

Rose

Creek

Clay Hole

Creek

G E O R G I A

F L O R I D A

SUWANNEE

LAFAYETTE

DIXIE

LEVY

GILCHRIST ALACHUA

MARION

COLUMBIA

TAYLOR

MADISON

HAMILTON

JEFFERSON LEON

GRADY

THOMAS

BROOKS

LOWNDES

ECHOLS

CLINCH

WARE

CHARLTON

BAKER

UNION

BRADFORD

CITRUS

SUMTER

WAKULLA Suwannee River

Suwannee River

Stei e nhatch e Riv

re

California

Creek

Wacca e sassa Riv r

9

SUWANNEE RIVER WATER

MANAGEMENT DISTRICT

BOUNDARY

REGIONAL STUDY AREA

BOUNDARY

SUBREGIONAL STUDY AREA

BOUNDARY

MAJOR SPRING

GAGING STATION AND NUMBER ndex

number given in table 1

STREAMFLOW MEASUREMENT SITE AND

NUMBER–Index number given in table 1

–I

EXPLANATION

19

0 20 40 MILES

0 20 40 KILOMETERS

30°

84° 83° 82°

29°

G u l f o f M e x i c o

Ginnie

Springs

Group

Rock

Bluff

Springs

Ichetucknee

River and

Springs

Group

Manatee

Springs

River

Santa

Fe

10

7

6

5

8

4

3

2

1

11

9

14

12 16

15

13

19

18

17

Usher Fire Tower

Weather Station

Figure 4. Selected streamgaging stations and streamflow measurement sites on the Suwannee and Lower Santa Fe Rivers.

Introduction 
 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Acknowledgments

The authors wish to thank the numerous volunteers 

from the SRWMD and the hydrologic technicians from the 

Orlando, Tampa, and Tallahassee USGS offices for their hard 

work during several field trips when streamflow was measured 

continuously (in some instances, for one or more days at a 

time) at several locations on the Lower Suwannee and Lower 

Santa Fe Rivers and associated springs. We also acknowledge the work performed by the SRMWD field staff and by 

Darlene Blum and Lavetra Sloan of the USGS, who measured 

ground-water levels during the study. Ron Ceryak provided 

essential information concerning the details and history of data 

collection by the SRWMD, as well as valuable insight into the 

hydrogeology of the SRWMD, particularly in the Waccasassa 

Flats area. Ron Ceryak and Donald Monroe also provided 

ground-water level and other data from the SRWMD database that was essential to the success of this project. Marvin 

Franklin gave important information about the history of the 

interpretation and collection of streamflow and water-level 

data in the Lower Suwannee and Lower Santa Fe Rivers. The 

Division of Forestry of the Florida Department of Agriculture 

was helpful, by granting data-collection access at fire tower 

and work center sites. The Natural Resources Conservation 

Service contributed timely information about the soils in Dixie 

County, as well as crop acreage estimates that were required to 

estimate irrigation withdrawals of ground water. Keith Halford 

provided valuable assistance by evaluating some of the historic 

aquifer test results. John Doherty of Watermark Numerical 

Computing conveyed timely and valuable suggestions, regarding use of parameter estimation software for calibrating the 

ground-water flow model. The authors appreciate the work 

of Richard Marella of the USGS, who compiled much of the 

water-use data used in the project. Finally, the authors are 

grateful for the contributions that the technical reviewers made 

in improving the project analyses and final report. The primary 

project reviewers, Bob Faye (USGS), John Good (SRWMD), 

Eve Kuniansky (USGS), Gary Mahon (USGS), Eric Swain 

(USGS), and Dann Yobbi (USGS), provided invaluable guidance on all aspects of the study, particularly in refining the 

data-collection plans, improving the way the boundary conditions were treated in the numerical model, and calibration of 

the simulation models.

Surface-Water Hydrology

Perhaps the most important aspect of the surface-water 

hydrology of the subregional study area is that much of the 

study area is devoid of channelized surface drainage and 

most of the drainage occurs instead through the subsurface. Subsurface drainage occurs because of the: (1) karst 

topography of the area, which is generally flat and contains 

numerous sinkholes and closed topographic depressions; and 

(2) highly permeable rocks of the Upper Floridan aquifer, 

Table 1. Selected streamgaging stations and streamflow measurement sites on the Lower Suwannee 

and Santa Fe Rivers.

Site No.

(this report only) Station number Station name

1 02315500 Suwannee River at White Springs 

2 02315550 Suwannee River at Suwannee Springs

3 02319500 Suwannee River at Ellaville

4 02320000 Suwannee River at Luraville

5 02320500 Suwannee River at Branford

6 02323000 Suwannee River near Bell

7 02323500 Suwannee River near Wilcox

8 02323570 Suwannee River near Old Town

9 02323590 Suwannee River at Fowlers Bluff

10 02323592 Suwannee River above the Gopher River

11 02321500 Santa Fe River at Worthington Springs

12 02321975 Santa Fe River at U.S. Highway 441 near High Springs

13 02322000 Santa Fe River near High Springs

14 02322500 Santa Fe River near Fort White

15 02322703 Santa Fe River at Three Rivers Estates

16 02322800 Santa Fe River near Hildreth

17 295309082523801 Suwannee River below the mouth of the Santa Fe River

18 294041082571701 Suwannee River upstream from Hart Springs Run near Wilcox

19 292940082590301 Suwannee River above Manatee Springs near Chiefland
which are generally either exposed at the surface or overlain 

by a relatively shallow layer of permeable surficial sediments. 

These two characteristics allow rainfall to easily move into 

and through the subsurface and discourage the formation of 

organized surface drainage networks.

Despite the dominance of subsurface drainage in the 

subregional study area, some surface drainage does occur. 

The most important surface drainage features are the Lower 

Suwannee and Lower Santa Fe Rivers. Smaller streams are 

also present in some areas, especially along the coast, and 

some can convey the discharge of springs. Much of the subregional study area lacks good surface or subsurface drainage; 

these areas are typically covered by broad wetlands and wetpine flatwoods that are commonly bordered by shallow lakes.

Lower Suwannee and Lower Santa Fe Rivers

The Lower Suwannee and Lower Santa Fe Rivers are 

the major rivers that drain the subregional study area. In this 

report, the Lower Suwannee River is defined as the 76-mi 

reach of the Suwannee River that begins upstream at Branford 

and extends downstream to the mouth of the river at the Gulf 

of Mexico (fig. 4). The Lower Santa Fe River is defined in 

this report as the 28-mi reach of the Santa Fe River, beginning 

just upstream from U.S. Highway 441 about 2 mi downstream 

from the Santa Fe River Rise (figs. 1 and 4) where it emerges 

from the Upper Floridan aquifer, extending downstream to 

its confluence with the Suwannee River, about 10 river miles 

downstream from Branford. The subsequent sections describe 

the geometry of the channels and floodplains of the Lower 

Suwannee and Lower Santa Fe Rivers and their flow and stage 

characteristics. Flow and water-level data were collected from 

gaging stations on the Suwannee and Lower Santa Fe Rivers 

and from additional streamflow-measurement sites that were 

established during this study (fig. 4 and table 1).

Channel and Floodplain Characteristics

Channel and floodplain geometry affect the relation 

between flow and stage in various reaches of the Lower 

Suwannee and Lower Santa Fe Rivers. This relation is important because both rivers represent an important boundary 

within the ground-water flow system in the subregional study 

area. Variations in streamflows and the resulting changes in 

river stages play a major role in the timing of ground-water/

surface-water exchanges along these two rivers. Temporal and 

spatial patterns of river stages are also an important influence 

on ground-water levels (for example, the configuration of the 

potentiometric surface) and directions of ground-water flow.

Most of the river channel and floodplain geometry data 

for the present study were obtained from previous research and 

data files (U.S. Army Corps of Engineers, 1989; John Good, 

U.S. Army Corps of Engineers, written commun., 1996). The 

U.S. Army Corps of Engineers (USACE) used these data to 

develop a HEC-2 water-surface profile model (Hydrologic 

Engineering Center, 1991) of the Lower Suwannee River and 

its largest tributaries. Other data were obtained from field 

measurements taken at a few sites during the present study and 

from discharge measurement notes, which contain depth and 

stage data. These data were used to estimate the elevation of 

the channel bottom, changes in the channel-bottom elevation 

along the axis of the channel thalweg (the deepest part of the 

river channel), channel top width at bankfull stage, and width 

of the floodplain at flood stages.

The elevation and slope of the channel bottom, as 

measured along the channel centerline, are important variables 

that influence the slope of the water surface. These variables 

also help determine whether the elevation of the water surface 

at a given location is affected by downstream water conditions, 

such as tides or flooding at a downstream confluence. When 

this condition occurs, the location is said to be affected by 

“backwater.” Data for the Lower Suwannee River indicate that 

the elevation of the deepest part of the channel (the thalweg 

elevation) near the Branford gaging station is close to sea 

level or NGVD 1929 (fig. 5). The thalweg elevation is highly 

variable. In some instances, elevations range from about 30 to 

5 ft below NGVD 1929 over short distances. Despite this variability, a trend of generally decreasing thalweg elevation in the 

downstream direction is evident in the data, and is on the order 

of 0.24 ft/mi (fig. 5). This thalweg elevation slope is mild, and 

as a result, the flow of the Santa Fe River can affect the stage 

in the Lower Suwannee River upstream from the mouth of the 

Santa Fe River. Additionally, the low elevation of the thalweg, 

relative to NGVD 1929, allows the tides in the Gulf of Mexico 

to affect the stage in much of the Lower Suwannee River 

downstream from the mouth of the Santa Fe River, especially 

during periods of low flow.

The thalweg profile of the Lower Santa Fe River is generally steeper than that of the Lower Suwannee River, with the 

reach upstream from the gaging station near Fort White having 

an average channel-bottom slope of about 1.4 ft/mi. The 

thalweg elevation at the upstream end of the Lower Santa Fe 

River at U.S. Highway 441 is about 26 ft above NGVD 1929, 

and the thalweg elevation near the mouth is about 10 ft below 

NGVD 1929 (fig. 5). Under average flow conditions, most of 

the Santa Fe River downstream from the gaging station near 

Fort White is affected by backwater from the mouth of the 

Suwannee River. Some of the reaches at and upstream from 

the Fort White gaging station have sections with shoals at 

low flows; however, all of the Lower Santa Fe River may be 

subject to backwater from the Suwannee River during periods 

of flooding.

The Lower Suwannee River has an average channel 

top width at bankfull stage (when all of the river channel is 

submerged) of about 600 ft. The bankfull channel top width 

is as narrow as 250 ft near the Branford gaging station and as 

wide as 1,000 ft just upstream from the bifurcation of the river 

into East Pass and West Pass. The bankfull channel top width 

of the Lower Santa Fe River averages about 200 ft and ranges 

between 125 and 750 ft. Analysis of the channel geometry 

data also indicates that the width of the 10-year floodplain of 

Surface-Water Hydrology 
10 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

the Lower Suwannee River ranges from about 3,000 ft in the 

narrower parts of the reach upstream from the mouth of the 

Santa Fe River to about 21,000 ft about 12 mi upstream from 

the mouth of the Suwannee River. The width of the 10-year 

floodplain of the Lower Santa Fe River ranges from about 

450 ft in the narrower reaches of the river upstream from the 

Fort White gaging station to about 5,800 ft near the mouth.

Flow Characteristics

Long-term records of river stages and flow are available 

at several gaging stations on the Lower Suwannee, Lower 

Santa Fe, and (to a lesser extent) Ichetucknee Rivers. The 

gaging stations on the Suwannee River at Branford (map index 

no. 5, fig. 4) and the Santa Fe River near High Springs (map 

index nos. 12 and 13, fig. 4) were used to estimate the amount 

of upstream streamflow entering the Lower Suwannee and 

Lower Santa Fe Rivers. These data indicate that the flow at the 

upstream boundary of the Lower Suwannee River ranged from 

1,400 to 84,000 ft3/s, with an average annual flow of about 

7,000 ft3/s during 1931-99. Flow at the upstream boundary 

of the Santa Fe River ranged from 30 to 20,000 ft3/s, with an 

average annual flow of about 850 ft3/s during the period of 

record (1931-71) for the High Springs gaging station (map 

index no. 13, fig. 4).

There is a noticeable relation between streamflow and 

time of year, and the nature of this relation varies within 

the subregional study area. In the Suwannee River at Branford, flows are typically higher from February to April than 

during the remaining months of the year (fig. 6). The highest monthly mean flows typically occur during March and 

April. The timing of these high flow periods is consistent with 

climatic data, which indicate that March is the last month 

in a period (beginning in June) when precipitation typically 

exceeds potential evapotranspiration in the northern peninsula. 

Although rainfall rates are high during the summer-early fall 

(June-September) period, streamflows are typically not as 

high as during the late winter-spring period (February-April) 

because of low net precipitation rates (precipitation minus 

evapotranspiration) from April to June.

A different seasonal pattern is evident in the streamflow 

data for the Lower Santa Fe River. For example, the monthly 

mean streamflows in the Santa Fe River near Fort White are 

highest from February to April and from August to October 

(fig. 6). The surface- and ground-water contributing areas to the 

Lower Santa Fe River are south of the contributing areas to the 

Suwannee River at Branford, and therefore, less influenced by 

rainfall from cold fronts, which weaken as they move southward 

into peninsular Florida. The higher mean flows in August and 

September coincide with the summer wet season. The Santa Fe 

River streamflows are most variable during the high-flow periods from February to April and from August to October.

The seasonal patterns in the streamflow data for the 

Suwannee River downstream from the mouth of the Santa Fe 

River are a mixture of the seasonal patterns of the Suwannee 

River at Branford and the Lower Santa Fe River. The seasonal 

distribution of monthly mean discharges in the Suwannee 

River near Wilcox (fig. 6) is most similar to the Suwannee 

River at Branford, with the highest flows generally occurring 

from February to April. This distribution is to be expected 

because average flow in the Suwannee River at Branford is 

about 70 percent of that in the Suwannee River near Wilcox, 

and average flow in the Santa Fe River near Fort White is 

about 15 percent of that in the Suwannee River near Wilcox. 

-30

-20

-10

0

10

20

30

DISTANCE FROM MOUTH OF RIVER, IN FEET

-40

0 50,000 100,000 150,000 200,000 250,000 300,000 350,000 400,000 450,000

THALWEG ELEVATION, IN FEET

ABOVE AND BELOW NGVD 1929

Suwannee

River

Santa Fe River

Ft. White gage

(site 14) Old Town gage

(site 8)

Wilcox gage

(site 7)

Bell gage

(site 6)

Branford gage

(site 5)

Confluence with

Santa Fe River (site 17)

Hildreth gage (site 16)

Ichetucknee

River mouth

High Springs gage

(site 13)

Figure 5. Thalweg profiles of the 

Lower Suwannee and Lower Santa Fe 

Rivers. Site locations are shown in 

fig. 4.
JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT NOV DEC

(67)

(67)

(67)

(67)

(67)

(67)

(67)

(67)

(67)

(67)

(67)

(67)

Santa Fe River near Fort White, Florida

(58) (58)

(58) (58)

(58)

(58)

(58)

(58)

(58)

(58)

(58)

(58)

Suwannee River near Wilcox, Florida

7,000

6,000

5,000

4,000

3,000

2,000

1,000

0

DISCHARGE, IN CUBIC FEET PER SECOND

60,000

50,000

40,000

30,000

20,000

10,000

0

60,000

50,000

40,000

30,000

20,000

10,000

0

-10,000

(68) (68)

(68) (68) (68)

(68)

(68)

(68)

(68)

(68)

(68) (68)

Suwannee River at Branford, Florida

(67)

EXPLANATION

SAMPLE SIZE–Years of

record

75th PERCENTILE+ –Or

largest value

1.5*IQR

75th PERCENTILE

MEAN

MEDIAN–50th percentile

25th PERCENTILE

25th PERCENTILE-1.5*IQR–Or

smallest value

OUTLIER

FAR OUTLIER

INTERQUARTILE RANGE (IQR)

Site 14

Site 7

Site 5

Figure 6. Monthly mean discharge in the Lower Suwannee and Lower Santa Fe Rivers. Site locations are shown in fig. 4.

Surface-Water Hydrology 11
12  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

The remaining 15 percent is derived from ground-water 

discharge to the Lower Suwannee and Lower Santa Fe Rivers.

Year-to-year variations in the streamflows that occur in 

a given month or season are even greater than the previously 

described seasonal variation in streamflows. This interannual 

variability occurs, in part, because streamflows in the Suwannee 

and Santa Fe River Basins are subject to wetter-than-normal and 

drier-than-normal periods associated with climatic phenomena, 

such as the El Niño-La Niña Southern Oscillation (National 

Oceanic and Atmospheric Administration, 2005) and possibly the Pacific Decadal Oscillation (Nigam and others, 1999). 

During the present study, for example, there was a transition 

from El Niño (from 1997 to mid-1998) to La Niña (from mid1998 continuing into the first part of 2000) conditions. These 

two disparate climatic conditions resulted in different flow 

conditions in the subregional study area during the “high-flow” 

months. The El Niño period from February to April 1998 was 

characterized by extreme flooding on the Suwannee and Santa Fe 

Rivers (fig. 7). The peak daily streamflow in the Suwannee 

River near Wilcox was close to 50, 000 ft3/s — a flow that 

typically occurs only once every 20 to 25 years. During La Niña 

conditions of the following year, however, flows during these 

“high-flow” months were as low or lower than the values that 

typically occur during the dryer months of the year. Tropical 

weather systems occur frequently in the study area; there is a 

24- to 36-percent chance of a tropical storm or hurricane passing over the study area in a given year. These weather systems 

also increase the variability of monthly streamflow during the 

hurricane season (June to November).

Short-term variations in streamflow in the lower reaches 

of the Lower Suwannee River are associated with the ebbing 

and flooding of tides in the Gulf of Mexico. At the mouth of 

the Suwannee River, the Gulf of Mexico typically has a mixed 

semidiurnal pattern in which two high tides of unequal height, 

and two low tides of unequal height typically occur each day. 

The mean tidal range (between the higher high tide and lower 

low tide) of water levels recorded at the nearby Cedar Key 

(fig. 1) tidal gage was 3.7 ft from October 1, 1997, to September 30, 1999 (data obtained from National Oceanographic and 

Atmospheric Administration, 2004). The tidal range is generally higher during the “spring tides” that occur twice each 

month, coinciding with the new and full phases of the moon. 

During some of these periods, the tidal range can be close to 

5 ft. The tidal range is lower (close to 2 ft) during the “neap 

tides” that occur twice each month, coinciding with the first 

and third quarter phases of the moon.

The effects of tides on streamflows are shown in figures 

8 and 9. The two examples occurred within 7 days of each 

other, during spring tide and neap tide conditions, and the 

mean daily flow in the river (averaged over a day) was nearly 

the same during both periods. During spring tide conditions, 

the tidal range was 3.8 ft near the mouth of the Suwannee 

MEAN DAILY STREAMFLOW, IN CUBIC FEET PER SECOND

J F M A M J J A S O N D

100

200

5,000

500

1,000

2,000

10,000

O N D J F M A M J J A S

1997 1998 1999

20,000

50,000

100,000

Santa Fe River

near Fort White, Florida

(site 14)

Suwannee River

near Branford, Florida (site 5)

Suwannee River

near Wilcox, Florida

(site 7)

Figure 7. Streamflows in the Lower Suwannee and Lower Santa Fe Rivers from October 1, 1997, to September 30, 1999. Site locations are 

shown in fig. 4.
0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

24-HOUR TIME, JUNE 13, 1999

0

STREAMFLOW, IN CUBIC FEET PER SECOND

0600 1200 1800 2400

-2

-1

0

1

2

3

4

5

WATER-SURFACE ELEVATION,

IN FEET ABOVE AND BELOW NGVD 1929

Discharge, in the

Suwannee River

near Wilcox, Florida

Water-surface elevation,

in the Suwannee River,

at Suwannee, Florida

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

24-HOUR TIME, JUNE 21, 1999

0

STREAMFLOW, IN CUBIC FEET PER SECOND

0600 1200 1800 2400

-2

-1

0

1

2

3

4

5

WATER-SURFACE ELEVATION,

IN FEET ABOVE AND BELOW NGVD 1929

Discharge, in the Suwannee River

near Wilcox, Florida

Water-surface elevation, in the

Suwannee River at Suwannee, Florida

Figure 8. Tidally affected water levels and flows in the Suwannee River during a spring tide.

Figure 9. Tidally affected water levels and flows in the Suwannee River during a neap tide.

Surface-Water Hydrology 13
14  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

River, and the observed flow range in the river upstream near 

Wilcox was 5,000 ft3/s (from about 1,200 to 6,200 ft3/s) over 

the tidal cycle. A week later during neap tide conditions, the 

tidal range was only 2.3 ft, and the observed flow range in the 

river upstream near Wilcox was 3,800 ft3/s (from about 1,800 

to 5,600 ft3/s) over the tidal cycle.

The effects of tides on flow in the Lower Suwannee River 

can also be enhanced or mitigated by the amount of water 

flowing in the Suwannee River. For example, the difference 

between the minimum and maximum flows in the Suwannee River near Wilcox is typically 2,000 to 3,000 ft3/s over 

the course of a tidal cycle during low-flow conditions. This 

range of fluctuation, however, decreases as the average daily 

discharge increases in the river (fig. 10). When the mean daily 

discharge is greater than 18,000 ft3/s in the Suwannee River 

near Wilcox, the difference between the minimum and maximum flows during a tidal cycle is generally small or negligible 

(fig. 10). Sustained winds, especially when blowing in an 

offshore or onshore direction, can also enhance or mitigate 

the effects of tides on short-term variations in the flow of the 

Lower Suwannee River.

The effects of these tidal variations also vary with 

distance to the Gulf of Mexico. For example, during the 

extreme low-flow period of late September 1999 (when 

mean daily discharge at the Wilcox gaging station was about 

3,800 ft3/s, measured flow in the Suwannee River above 

the Gopher River (map index no. 10, river mile 7.5, fig. 11) 

ranged from -5,000 ft3/s (where the negative value indicates 

net upstream flow) to 15,000 ft3/s over the course of the tidal 

cycle. The difference between the minimum and maximum 

flows, however, was substantially smaller upstream during 

this same period. For example, flows ranged from 1,600 to 

5,000 ft3/s in the Suwannee River at the gaging station near 

Wilcox (map index no. 7, river mile 33.5, fig. 11) and from 

3,700 to 4,100 ft3/s farther upstream at the gaging station near 

Bell (map index no. 6, river mile 56.5, fig. 11). The extent of 

this tidal influence is reduced at higher flows. For example, 

during mid-August 1997 when the mean daily discharge in the 

Suwannee River near Wilcox was about 10,000 ft3/s, a tidal 

signal was difficult to detect in the streamflows measured at 

a site just upstream from Hart Springs (near river mile 43, 

fig. 11).

50,000

40,000

30,000

20,000

10,000

0

OCT NOV DEC

1998

JAN FEB MAR APR MAY JUNE JULY AUG SEPT

1997

INSTANTANEOUS FLOW, IN CUBIC FEET PER SECOND

Suwannee River near Wilcox, Florida

Figure 10. Flow in the Suwannee River near Wilcox, Florida, during water year 1998. Tidally induced discharge fluctuations are greatest 

at low flows and dissipate as flow in the river increases.
Water-Level Characteristics

Water levels in the Lower Suwannee and Lower Santa Fe 

Rivers are associated with interannual, seasonal, and (for the 

lower reaches of the Lower Suwannee River) tidal variations 

in flow. Water-level characteristics are also affected by the 

geometry of the river channels and floodplains that convey the 

water flowing in the Lower Suwannee River.

The correlation between water levels and streamflow is 

evident in the seasonal distribution of water levels (fig. 12). 

The pattern of the monthly average water levels on the 

Lower Suwannee and Lower Santa Fe Rivers is similar to 

the pattern of the monthly average flows on these rivers. The 

Lower Suwannee River sites have the highest water levels 

from February to April, and the Lower Santa Fe River has a 

pattern of high water levels from February to April and from 

August to October. In addition to their association with higher 

flow in the Santa Fe River, high water levels in the Santa Fe 

River are also caused by high water levels on the Suwannee 

River because of the aforementioned backwater effects.

As previously described, flow in most of the Lower 

Suwannee River is affected by tides in the Gulf of Mexico. 

Water-level changes associated with these tides propagate 

upstream into the Lower Suwannee River, causing changes in 

the slope of the water surface, and thus, streamflow during a 

given tidal cycle. The magnitude of the water-level changes 

decreases as the distance from the Gulf of Mexico increases 

and as streamflow increases. For example, during spring tide 

27

441

27 441

Hart Springs

Santa Fe River

Suwannee River

East Pass

Ichetucknee

River

Gopher

River

COLUMBIA

SUWANNEE

DIXIE

MARION

UNION

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

Fanning

Springs

Bell

Branford

Fort White

Wilcox

Old

Town

High Springs

Trenton

Cross

City

Bronson

30°

83° 82°

29°

0 20 MILES

0 20 KILOMETERS

G u l f o f M e x i c o

EXPLANATION

SUBREGIONAL MODEL BOUNDARY

GAGING STATION AND

NUMBER–Index number given in

table 1

RIVER MILE INDICATOR–Shows

distance from mouth, in 5-mile

increments

10

10

50

10

20

30

40

60

70

80

10

20

30

RIVER REACH 1

RIVER REACH 2

RIVER REACH 3

7

6

14

5

9

8

12

13

10

Figure 11. Definition of river mileage system and selected river reaches in the subregional study area.

Surface-Water Hydrology 15
16  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

(53) (55)

(52) (51)

(53)

(55)

(55)

(55)

(51)

(52)

(54)

(56)

(56)

(57)

(56)

(56)

(56)

(56)

(56)

(56)

(56)

(56)

(56)

(56)

32

30

28

26

24

22

20

20

16

12

8

4

0

Suwannee River

near Wilcox, Florida

Santa Fe River

near Fort White, Florida

40

35

30

25

20

15

10

5

ELEVATION, IN FEET ABOVE NGVD 1929

JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT NOV DEC

(58) (58)

(58) (58)

(58)

(58)

(58)

(58)

(58)

(58)

(58)

(58)

Suwannee River

at Branford, Florida

(56)

EXPLANATION

SAMPLE SIZE–Years of

record

75th PERCENTILE+ –Or

largest value

1.5*IQR

75th PERCENTILE

MEAN

MEDIAN–50th percentile

25th PERCENTILE

25th PERCENTILE-1.5*IQR–Or

smallest value

OUTLIER

FAR OUTLIER

INTERQUARTILE RANGE (IQR)

Site 7

Site 14

Site 5

Figure 12. Monthly water-surface elevation at selected locations on the Lower Suwannee and Lower Santa Fe Rivers. 

Site locations are shown in figs. 4 and 11.
and low-flow conditions in June 1999, the tidal range near the 

divergence of the Suwannee River near the town of Suwannee at river mile 4.2 was about 3.8 ft, but decreased to 1.8 ft 

at the gaging station near Old Town (river mile 23.5, map 

index no. 8, figs. 4 and 11) and to 1.10 ft at the gaging station 

near Wilcox (river mile 33.5, map index no. 7, figs. 4 and 11). 

Tidally induced water-level changes occurred at and downstream from the Suwannee River at the mouth of the Gopher 

River for all streamflows. However, tidally induced water-level 

changes did not occur upstream at Fowlers Bluff (map index 

no. 9, figs. 4 and 11) when flow at the Wilcox gaging station 

exceeded about 23,000 ft3/s, nor at the gaging station near Old 

Town when Wilcox flows were greater than about 21,000 ft3/s.

Smaller Rivers and Streams

Although nearly all of the drainage to the Lower Suwannee and Lower Santa Fe Rivers occurs through the subsurface, 

smaller rivers and streams drain much of the remainder of the 

subregional study area that does not contribute runoff to the 

Lower Suwannee River. Most of this part of the study area has 

a flat to gently sloping topography and is covered by wet-pine 

flatwoods. These smaller rivers and streams that drain this 

area either discharge directly into the Gulf of Mexico or form 

drainage networks that discharge to the Gulf of Mexico. On 

the northwestern (Dixie County) side of the Suwannee River, 

most of the smaller streams are within several miles of the 

coast. Although the runoff characteristics of these streams are 

not well understood because of limited streamflow data, these 

small tidal streams convey tidal currents in and out of marshes 

as well as some local runoff. Runoff rates from smaller rivers 

and streams that drain toward the Gulf of Mexico and Lower 

Santa Fe River were computed from historic streamflow 

measurements stored in the USGS National Water Information 

System (U.S. Geological Survey, 1998).

The Waccasassa River (fig. 4) system of streams represents the largest coastal stream network in the subregional 

study area southeast of the Suwannee River, draining an area 

of about 617 mi2. Runoff rates from this system generally 

range from zero during dry conditions, 4 to 8 in/yr during 

average conditions, and 0.1 to 1 in/d during peak wet conditions (although some smaller subbasins have higher runoff 

rates). The California Creek (fig. 4) system of tributaries and 

distributaries, the largest coastal stream network on the northwestern (Dixie County) side of the Suwannee River, drains a 

77-mi2 area of wetlands south of Cross City. Streamflow data 

for the California Creek system are limited to measurements 

taken on September 14, 1964, which coincided with the period 

of record flood (with an approximate 400-year recurrence 

interval) on the nearby Steinhatchee River. Runoff rates from 

the California Creek system were about 0.6 in/d on this same 

date. During more typical conditions, runoff rates are probably 

slow or negligible because of the flat topography, high evapotranspiration rates due to the shallow water table, and wetland 

storage of potential runoff.

A few small rivers and streams drain directly into the 

Lower Santa Fe River Basin (fig. 1). The largest of these is the 

spring-fed Ichetucknee River (fig. 4), with a surface drainage 

area of 213 mi2 (only 55 mi2 of which has a defined drainage 

network). The Ichetucknee River contributes an average flow 

of about 350 ft3/s to the Lower Santa Fe River, as estimated 

from 405 discharge measurements taken at a site about 1.5 mi 

upstream from the mouth of the Ichetucknee River from 

1917 to 1999. Minimum and maximum measured flows were 

240 and 580 ft3/s, respectively, with about 50 percent of the 

measured flows ranging between 320 and 400 ft3/s. The Lower 

Santa Fe River also receives some channelized inflow from 

several streams draining the northern end of the Waccasassa 

Flats in Gilchrist County (fig. 3). Cow Creek is the largest 

of these streams (fig. 4), with runoff rates at about 0.1 in/yr 

during low-flow (7-day, 10-year) conditions and 5 in/yr during 

average conditions (data were not available for high-flow 

conditions).

Ground-Water Hydrology

The ground-water flow system plays a critical role in the 

overall hydrology of the subregional study area because of the 

dominance of subsurface drainage and because ground-water 

discharge sustains the flows of the Lower Suwannee River, 

Lower Santa Fe River, and numerous springs. To understand 

the hydrology of the ground-water system, several characteristics must be evaluated including the hydrogeologic framework, 

hydrologic boundaries, patterns of ground-water levels and 

flows, hydraulic properties, and the spatial and temporal distribution of sources and sinks of water to the ground-water flow 

system. Collectively, these characteristics define a conceptual 

model of the ground-water flow system.

Hydrogeologic Framework

The three principal hydrogeologic units that are present 

within and adjacent to the study areas are the surficial aquifer 

system, intermediate aquifer system and intermediate confining unit, and the Floridan aquifer system (fig. 13). The unconsolidated surficial sediments of the surficial aquifer system 

are present throughout the Northern Highlands area (fig. 3). 

In the Gulf Coastal Lowlands (fig. 3), the surficial sediments 

are more locally distributed, but may yield usable quantities 

of water where the sediments are of sufficient thickness. The 

surficial aquifer system, where present, is contiguous with the 

land surface and is composed principally of unconsolidated to 

poorly indurated siliciclastic deposits (Southeastern Geological Society Ad Hoc Committee on Florida Hydrostratigraphic 

Unit Definition, 1986). The surficial sediments consist of 

undifferentiated sands, silts, and clays that are Pliocene and 

younger age. These sediments are generally less than 40 ft 

thick, but may be as much as 80 ft thick or greater in areas of 

the high elevation sand ridges and depressions in the top of 

Ground-Water Hydrology 17
18  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

* Middle part of Avon Park Formation consists of low-permeability gypsum in the southern half of Levy County,

where it forms a middle confining unit within the Floridan aquifer system

References: Crane (1986), Florida Geological Survey (2004), Miller (1986)

Limestone and dolostone*

Dolomite,

moderately to highly porous

Dolomite with

interbedded anhydrite

Limestone and dolostone;

some evaporites and chert

Limestone,

poorly to well-indurated

Pleistocene

Fine to coarse,

clayey quartz sands

Quarternary

and sandy clays

System

Holocene

Pliocene

Stratigraphic

unit

Undifferentiated

sands and

sandy clays

Alachua Formation

Miocene

Hawthorn Group

Tampa Limestone

Poorly to well-indurated

limestone, with

10- to 35-percent very fine

to fine quartz sand

Tertiary

EraCenezoic

Upper

Middle

Lower

Paleocene

Poorly to well-indurated,

crystalline to

pelletal limestone

Oligocene Suwannee

Limestone

Eocene

Avon Park

Formation

Cedar Keys

Formation

Oldsmar Formation

Ocala Limestone

Phosphatic clay,

occasionally with

quartz sand and

phosphatic sand

Quartz sand, silt, and clay

commonly containing

accessory minerals of

dolomite, limestone,

phosphatic sand, and

phosphatic gravel. Interbeds

of dolostone and limestone

occasionally present

Notes General

lithology

Middle

confining

Floridan aquif

unit

er system

Upper Floridan aquifer

Lower confining unit

of the Floridan

aquifer system

Lower

Floridan

aquifer

Occurring only locally

in subregional study area

(may include part of the

Upper Floridan aquifer,

where sufficiently permeable)

Thick anhydrite beds of

Cedar Keys form the

lower confining unit of

the Floridan aquifer system

In subregional study area,

only present in

southern Levy County

Occurring only locally

in the subregional

study area

The surficial aquifer

system only occurs

locally, in areas where

these sediments are

of sufficient saturated

thickness and lateral

continuity

Hydrogeologic

unit

Surficial

aquifer

system

Hawthorn Group is generally

absent in the subregional

study area. It comprises the

intermediate aquifer system/

confining unit in the

Northern Highlands

Intermediate

aquifer

system/

confining unit

Figure 13. Geologic and hydrogeologic units present within and adjacent to the regional study area.
the Floridan aquifer system (Hunn and Slack, 1983; Rupert, 

1988a; Ron Ceryak, Suwannee River Water Management 

District, oral commun., 1996). The surficial aquifer system is 

unconfined and the water table is generally within 10 ft of land 

surface, but may be deeper in some areas. The water table of 

the surficial aquifer system is at or near the surface in areas of 

ground-water discharge (for example, along river and stream 

corridors) and in the broad wetland areas of Mallory Swamp, 

San Pedro Bay, and the Waccasassa Flats (fig. 3) where low 

permeability sediments in the surficial aquifer system (Col and 

others, 1997) and possibly the Floridan aquifer system impede 

the vertical flow of ground water. The presence of these sediments in the Waccasassa Flats is consistent with evidence 

indicating that a closed basin or settling environment existed 

during the formation of the surficial aquifer system (Col and 

others, 1997). The saturated thickness of the surficial aquifer 

system ranges from 10 to 80 ft.

The intermediate aquifer system and intermediate confining unit lie below the surficial aquifer system (where present), 

and generally consist of fine-grained, unconsolidated deposits 

of quartz sand, silt, and clay with interbedded limestone 

of Miocene age (Scott, 1992, p. 55). Regionally, the intermediate aquifer system and intermediate confining unit act as a 

confining unit that restricts the exchange of water between the 

overlying surficial aquifer system and the underlying Floridan 

aquifer system. Accordingly, the term, “intermediate confining 

unit,” is used in this report to refer to the intermediate aquifer system and intermediate confining unit. The intermediate 

confining unit is generally present in the Northern Highlands, 

coinciding with the Hawthorn Group sediments, and is generally absent in the Gulf Coastal Lowlands (figs. 3 and 14). The 

top of the intermediate confining unit ranges from about 50 to 

150 ft above NGVD 1929 (Scott, 1992, p. 44) in elevation, and 

coincides with the base of the surficial aquifer system. The 

base of the intermediate confining unit coincides with the top 

of the Floridan aquifer system and ranges from about 200 ft 

below to 100 ft above NGVD 1929 (Miller, 1986, pl. 26) in 

elevation. The thickness of the intermediate confining unit 

ranges from 0 ft, where the unit pinches out, to greater than 

400 ft thick in Baker and Bradford Counties (fig. 14).

The Floridan aquifer system is a thick sequence of 

carbonate (limestone and dolomite) rocks of mostly Paleocene 

to early Miocene age. It is subdivided into the Upper Floridan 

aquifer (Miller, 1986) and in some areas, a middle confining unit and the Lower Floridan aquifer (fig. 13). The Lower 

Floridan aquifer is present only where a middle confining unit 

separates the more permeable Upper and Lower Floridan aquifers. The Lower Floridan aquifer is not used for water supply 

in the study areas, and is only present in the northern part of 

the SRWMD from Jefferson County east to Columbia County, 

and in the southern half of Levy County. The Upper Floridan 

aquifer is present throughout the study area, is highly permeable, and thus typically capable of transmitting large volumes 

of water. This high permeability mostly is due to the widening of fractures and formation of conduits within the aquifer, 

caused by dissolution of the limestone from infiltrating water. 

This process has also produced numerous karst features such 

as springs, sinking streams, and sinkholes in the study area.

The Upper Floridan aquifer is generally at or near land 

surface and is unconfined in the Gulf Coastal Lowlands, but 

is confined or poorly confined in the Northern Highlands. The 

elevation of the top of the Upper Floridan aquifer (fig. 15) 

ranges from about 360 ft below to 100 ft above NGVD 1929 

(Miller, 1986, pl. 26) in the regional study area, and from 

NGVD 1929 to 40 ft above NGVD 1929 in the subregional 

study area. The elevation of the base of the Upper Floridan 

aquifer in the regional study area (fig. 16) ranges from about 

2,100 ft below NGVD 1929 in the coastal areas of Jefferson 

County to about 400 ft below NGVD 1929 in Lowndes 

County near Valdosta, Georgia (Miller, 1986, pl. 29). The 

elevation of the base of the Upper Floridan aquifer (fig. 16) in 

the subregional study area ranges from about 500 to 1,600 ft 

below NGVD 1929 (Miller, 1986, pl. 29). The thickness of 

the Upper Floridan aquifer in the regional study area (fig. 17) 

ranges from about 400 ft near Valdosta, Georgia, to 2,300 ft 

in the coastal areas of Jefferson County (Miller, 1986, pl. 28) 

and from about 500 to 1,600 ft in the subregional study area. 

Where present, the top of the middle confining unit is the base 

of the Upper Floridan aquifer, resulting in the apparent discontinuity in the base and thickness of the Upper Floridan aquifer 

(figs. 16, 17).

Ground-Water Flow System Boundaries

Defining the location and type of boundaries of the 

ground-water flow system is essential for developing a 

conceptual model of this system. The subsequent sections 

describe the location of the horizontal (lateral) and vertical 

(upper and lower) boundaries of the ground-water flow system 

in the subregional study area. These sections also describe the 

direction of ground-water flow along and across these boundaries, including spatial and temporal flow variability at some 

of the boundaries.

Lateral Boundaries

The lateral boundaries of the ground-water flow system 

in the subregional study area define horizontal limits of the 

system. These limits were defined, in part, by the geographic 

scope of the project and by key features of the regional 

ground-water flow system adjacent to the subregional study 

area. These features include areas of relatively high groundwater levels on the potentiometric surface (potentiometric 

“highs”), areas of relatively low ground-water levels near 

important areas of ground-water discharge (such as major 

rivers or the Gulf of Mexico), and points and lines (divergence 

points” and divides,” respectively) where ground-water flow 

paths diverge. These features collectively define the location 

of the following key lateral boundaries: the northeastern lateral 

no-flow boundary, the southeastern lateral no-flow boundary, 

the western lateral no-flow boundary, and the constant-head 

Ground-Water Hydrology 19
20 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

80

120

0

40

80

80

40 80

160

120

40

0

80

80

80

120

40 40

120

40

80

120

160

160

120

40

80

120

40

40

80

80

120

80 40

120

160

200

240

280

320

360

400

160

200

240

280

320

360

400

120

80

120

40

80 80

HAMILTON

SUWANNEE

DIXIE

GRADY

MARION

THOMAS

CITRUS

SUMTER

UNION

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

LEON

BROOKS

LOWNDES ECHOLS

CLINCH

WARE

CHARLTON

W BAKER AKULLA

COLUMBIA

MADISON

JEFFERSON

30°

84° 83° 82°

29°

Data Source: Florida Geological Survey, Tallahassee; and Suwannee River Water Management District, Live Oak, written communs., 1997

0 20 40 MILES

0 20 40 KILOMETERS

G E O R G I A

F L O R I D A

LINE OF EQUAL THICKNESS OF CONFINING

UNIT–In feet. Contour interval is 40 feet.

Dashed where approximately located.

SUWANNEE RIVER WATER MANAGEMENT

DISTRICT BOUNDARY

EXPLANATION

40

G u l f o f M e x i c o

Figure 14. Extent and thickness of the Hawthorn Group sediments (intermediate confining unit) in the Suwannee River Water 

Management District. 
Figure 15. Elevation of the top of the Upper Floridan aquifer.

TAYLOR

CHARLTON

DIXIE

MARION

CITRUS SUMTER

COLUMBIA

GILCHRIST

GRADY

MADISON

THOMAS

UNION

SUWANNEE

ALACHUA

BRADFORD

LAFAYETTE

LEVY

HAMILTON JEFFERSON

LEON

BROOKS

LOWNDES ECHOLS

CLINCH

WARE

BAKER

WAKULLA -160

-360

-320

-240

-280

-200

-120

-80

-40

0

0

40

40

80

40

40

0

80

80

0

40

0

0

0

0

40

40

40

80

40

40

0

0

0

0

0

0

40

40

0 20 40 MILES

0 20 40 KILOMETERS

G E O R G I A

F L O R I D A

Suwannee River

Suwannee

River

Santa Fe

EXPLANATION

STRUCTURE CONTOUR–Shows elevation of

the top of the Upper Floridan aquifer, in feet.

Datum is NGVD 1929. Contour interval is 40 feet

SUWANNEE RIVER WATER MANAGEMENT

DISTRICT BOUNDARY

40

River

Data Source: Florida Geological Survey, Tallahassee; and Suwannee River Water Management District, Live Oak, written communs., 1996

30°

84° 83° 82°

29°

G u l f o f M e x i c o

Ground-Water Hydrology  21
22  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

CLINCH

DIXIE

GRADY

MADISON

MARION

THOMAS

CITRUS

SUMTER

UNION

COLUMBIA

SUWANNEE

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

HAMILTON JEFFERSON

LEON

BROOKS

LOWNDES ECHOLS

WARE

CHARLTON

BAKER

WAKULLA

G E O R G I A

F L O R I D A

30°

84° 83° 82°

29°

Source: Miller, 1986.

0 20 40 MILES

0 20 40 KILOMETERS

EXPLANATION

AREA OF THE MIDDLE CONFINING UNIT

OF THE UPPER FLORIDAN AQUIFER–And

identifying number (from Miller, 1986)

ELEVATION OF THE BASE OF THE UPPER

FLORIDAN AQUIFER–In feet. Datum is

NGVD 1929. Contour interval is 100 feet

BOUNDARY OF SUWANNEE RIVER

WATER MANAGEMENT DISTRICT

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

-200

G u l f o f M e x i c o

I

I

I

II

III

-700

-600

-800

-400

-2,300

-300

-2,400

-2,100

-1,100

-500

-1,300

-1,800

-1,800

-2,000

-1,600

-2,000

-1,500

-1,600

-2,200

-1,500

-1,600

-1,400

-1,300

-2,500

-1,200

-500

-400

-800

-600

-700

-900

-1,000

-1,700

-1,800

-1,900

-800

-1,900

-800

-700

-500

-700

-2,000

-1,800

-1,700

-1,600

-500

-600

-400

-300

-800

-1,500

-1,600

-1,500

-1,400

-1,700

-500

-600

-700

-800

-800

-200

-200

-600

-500

Valdosta

Figure 16. Elevation of the base of the Upper Floridan aquifer.
Figure 17. Thickness of the Upper Floridan aquifer.

I

I

II

III

MARION

CITRUS SUMTER

CLINCH

SUWANNEE

HAMILTON

TAYLOR

LEON

DIXIE

GRADY

MADISON

THOMAS

UNION

COLUMBIA

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

JEFFERSON

BROOKS

LOWNDES ECHOLS

WARE

CHARLTON

BAKER

WAKULLA

Valdosta

G E O R G I A

F L O R I D A

30°

84° 83° 82°

29°

Source: Miller, 1986.

0 20 40 MILES

0 20 40 KILOMETERS

G u l f o f M e x i c o

EXPLANATION

AREA OF THE MIDDLE CONFINING UNIT OF

THE UPPER FLORIDAN AQUIFER–And

identifying number (from Miller, 1986)

THICKNESS OF THE UPPER FLORIDAN

AQUIFER–In feet. Contour interval is 100 feet

BOUNDARY OF SUWANNEE RIVER

WATER MANAGEMENT DISTRICT

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

500

I

600

300

400

500

600

500

2,200

400

500

600

700

800

700

800

900

900

2,400

2,300

1,800

2,100

2,000

1,300

1,600

1,400

1,200

2,000

1,800

1,700

1,600

1,600

1,400

1,500

1,500

700

600

700

700

500

800

800

200

200

1,500

1,700

1,800

1,900

1,500

1,500

300

900

1,500

600

500

400

400

400

1,600

1,500

1,700

1,700

1,600

400

Ground-Water Hydrology  23
24  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

boundary represented by the Gulf of Mexico coastline. These 

four boundaries define the lateral limits of the area that 

contribute water to the Lower Suwannee and Lower Santa Fe 

Rivers, and therefore, represent an important constraint on the 

amount of water that is available to sustain streamflows and 

ground-water withdrawals.

 The northeastern lateral flow boundary is largely defined 

by two prominent dome-shaped potentiometric highs that are 

centered near Valdosta, Georgia (fig. 18), and in the Keystone 

Heights area in Florida along the border between Clay, 

Putnam, Alachua, and Bradford Counties (fig. 18). Groundwater flow paths (flow lines) can be drawn that originate at the 

highest points of the Valdosta and Keystone Heights potentiometric highs and flow toward one or more points of divergence 

along the boundary. These flow lines change direction abruptly 

at the points of divergence, either flowing southward toward 

the Suwannee, Ichetucknee, and Lower Santa Fe Rivers or 

northward toward the Atlantic Ocean coastline and regional 

cones of depression centered near Jacksonville and Fernandina 

Beach. Thus, the flow path between the potentiometric highs 

and divergence points between Valdosta and Keystone Heights 

defines the northeastern limit of the area that contributes 

ground-water flow to the subregional study area.

Historic ground-water level data and the estimated 

predevelopment potentiometric surface of the Upper Floridan aquifer indicate that the location of the northeastern 

LEON

LAKE

CLAY

LEVY

DIXIE

UNION

BAKER DUVAL

SUMTER

CITRUS

MARION

PUTNAM

TAYLOR

NASSAU

VOLUSIA

WAKULLA

FLAGLER

ALACHUA

MADISON

BRADFORD

ST.

JOHNS

SUWANNEE COLUMBIA

HAMILTON

GILCHRIST

LAFAYETTE

JEFFERSON

WARE

GRADY

ECHOLS

CAMDEN CLINCH

BROOKS

THOMAS

LOWNDES CHARLTON

Perry

Thomasville

Valdosta

Ocala

Gainesville

Tallahassee

Branford

Fort

White

Keystone

Heights

Jacksonville

Rainbow Springs

Fernandina

Beach

Silver

Springs

Suwannee

5

10

20

30

50

40

60

70

80

80

70

90

80

90

30

40

50

10

20

30

40

50

60

50

50

50

60

70

80

50

70

60 50

5

80

20

40

50

50

40

30

20

10

0

-10 -10

-20

-30

20

20

30

20

40

30 20

10

5

5

10

60

10

20

10 5 20

20

30 70

20

Mallory

Swamp

Waccasassa

Flats

Suwannee

River

Suwan

i

n R ee

ver

Withlacooche i e R

ver

0 20 40 MILES

0 20 40 KILOMETERS

84° 83° 82°

30°

29°

10

EXPLANATION

GROUND-WATER

CONTRIBUTING

AREA–To the Suwannee

River Water Management District

under predevelopment conditions

FLOW

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

GROUND-WATER LEVEL–In the Upper Floridan

aquifer for May 1980, in feet above NGVD 1929. Contour

interval 5 and 10 feet (Bush and Johnston, 1988)

GROUND-WATER FLOW LINE

POINT WHERE GROUND-WATER

LINES DIVERGE

Atlantic Ocean

Sant

i

a Fe R ver

Cow

Creek

Withlacoo

e

chee Riv r

Tenmile Creek

Stein

e

hatche i R ver

Ich

r

et i ucknee R ve Cow Creek

Otter

Creek

San

Pedro

Bay

Waccasassa River

River

Aucilla

New

River

USGS Lake

Butler Well

G u l f o f M e x i c o

Wekiva

River

Figure 18. Potentiometric surface of the Upper Floridan aquifer during May 1980, including key features of the ground-water flow system. 

USGS is U.S. Geological Survey.
lateral flow boundary has migrated to the southeast over the 

last century (figs. 18 and 19). Before substantial withdrawals 

occurred from the Upper Floridan aquifer, the SRWMD was 

almost completely enclosed by the bounding flow lines that 

originate at the highest points of the Valdosta and Keystone 

Heights highs (fig. 19). Large ground-water withdrawals 

from the Upper Floridan aquifer began in the Jacksonville 

and Fernandina Beach areas of Florida during the late 1800s 

and have increased in these and other areas northeast of the 

regional study area. These withdrawals have caused large 

regional drawdowns in the Upper Floridan aquifer in the 

northeastern part of the regional study area and the concurrent 

westward migration of the northeastern part of the flow line 

boundary. This has resulted in the reduction of the area of the 

Upper Floridan aquifer that contributes water to the SRWMD 

and the diversion of water from the SRWMD to the pumping centers near Jacksonville and Fernandina Beach. Historic 

water-level data from long-term observation wells (fig. 20) 

along the northeastern lateral flow boundary indicate that: 

(1) the rate of drawdown has slowed, and perhaps stopped, in 

recent times; and (2) movement of this boundary has slowed 

or the boundary may have reached a new equilibrium location 

(fig. 18).

The southeastern lateral flow boundary is defined by five 

ground-water flow paths (fig. 18). The first of these flow paths 

originates on the potentiometric high near Keystone Heights, 

and is directed downgradient in a southwesterly direction 

toward eastern Levy County where it intersects a second flow line 

originating from the potentiometric high along the Waccasassa 

Flats to the west (described later). This part of the boundary 

delimits the contributing areas to the Lower Santa Fe River 

to the north and Rainbow Springs and Silver Springs to the 

south. The southeastern lateral flow boundary continues along 

two ground-water flow paths: (1) along the southern end of 

the ridge of the Waccasassa Flats potentiometric high; and 

(2) along a path directed northward from the potentiometric 

high west of Rainbow Springs. The location of this part of 

the southeastern lateral flow boundary determines whether 

recharge to the Upper Floridan aquifer flows east toward 

Rainbow Springs or west toward the Gulf of Mexico. The rest 

of the southeastern lateral flow boundary is defined by a short 

ground-water flow line directed westward toward the Gulf of 

Mexico from the potentiometric high west of Rainbow Springs.

The western lateral no-flow boundary defines the boundary between areas that contribute ground-water flow to the 

Withlacoochee River and Suwannee River to the east, and 

those that contribute ground-water flow to the Gulf of Mexico 

(and streams and rivers draining into the Gulf) to the west. 

This lateral boundary is defined by three ground-water flow 

paths. The northern part of the western boundary is defined 

by a southward-directed flow path originating on the Valdosta 

potentiometric high and terminating at a point where it intersects a northward-directed flow path originating on another 

potentiometric high centered in southern Madison County. 

The latter potentiometric high (the “San Pedro Bay potentiometric high”) coincides with an elevated area that has generally flat topography covered with poorly drained flatwoods 

and swamps, most notably San Pedro Bay and Mallory Swamp 

(fig. 18). The western lateral no-flow boundary continues 

along a flow path that originates on the San Pedro Bay potentiometric high and is directed southward toward the Gulf of 

Mexico.

The lateral boundary near the Gulf of Mexico coastline 

defines a final key external boundary for the subregional 

study area, and its location is defined by the line of intersection of two surfaces: (1) the interface between freshwater and 

saltwater in the Upper Floridan aquifer using the conceptualization of Cooper (1959, p. 464); and (2) the top of the Upper 

Floridan. In the study areas, this line of intersection represents 

the westward limit of freshwater discharge from the Upper 

Floridan aquifer. Only a few direct observations of saline 

ground water are available in the study areas and are insufficient to map the elevation of the freshwater-saltwater interface. 

Countryman and Stewart (1997) studied the subsurface electrical resistivity and conductivity of the coastal areas of Dixie 

and Levy Counties to locate the freshwater-saltwater interface 

near the mouth of the Suwannee River. Interpretations of 

harmonic electromagnetic, direct-current resistivity, and transient electromagnetic data placed the interface on the landward 

side and within several miles of the coastline; however, these 

results could not be confirmed due to insufficient water-quality and lithologic data (Countryman and Stewart, 1997, p. ix). 

The data are probably best used to interpret the configuration of 

the surface of the freshwater-saltwater interface, rather than its 

precise elevation near the Suwannee River (Tony Countryman, 

Northwest Florida Water Management District, oral comm., 1997).

Despite the absence of direct observations of the location of the freshwater-saltwater interface, several types of 

data can be used to infer the location of the western boundary. 

First, the elevation of the interface under static freshwater and 

saltwater conditions can be approximated using ground-water 

level data and the Ghyben-Herzberg principle (Fetter, 1988, 

p. 151), which place the interface at an elevation below NGVD 

1929 that is equal to 40 times the ground-water level above 

NGVD 1929. Ground-water level data from several wells less 

than 1 mi from the Gulf coast indicate that average groundwater levels near the coast are typically 1 to 2.5 ft higher than 

NGVD 1929, which indicates that the freshwater-saltwater 

interface is on the order of 40 to 100 ft below NGVD 1929 

near the coast. Second, recent data from two shallow well 

nests in the coastal marshes, several miles north and south of 

the mouth of the West and East Passes of the Suwannee River, 

indicate a consistent pattern of upward-seeping, brackish 

ground water (Ellen A. Raabe and others, U.S. Geological 

Survey, written commun., 2004). Thus, both well nests appear 

to be located in a zone of mixing that defines a diffuse boundary between fresh and salty ground water discharging on the 

landward and seaward sides of the boundary, respectively. 

Finally, the unconfined and highly permeable nature of the 

Upper Floridan aquifer in the subregional study area limits 

the seaward extent of the boundary because ground water can 

easily discharge through the top of the Upper Floridan aquifer. 

Ground-Water Hydrology  25
26  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Suwannee

River

Econfi

e

na Cr e

A

k

ucilla

River

Stei e

nh

h

atc

e

River

Ich

r

et i ucknee R ve

S

R

anta Fe

iver

W

o

ith c la

ochee

River

Suwannee River

New

River

Rainbow Springs

Tenmile Creek

Otter

Creek

Withlacoochee River

Waccas s as a

River

Wekiva River

Perry

Thomasville Valdosta

Ocala

Gainesville

Tallahassee

Fanning

Springs

Bell

Branford

Fort

White

Wilcox

Oldtown

Keystone

Heights

Chiefland

White

Springs

Suwannee

Springs

Suwannee

LEON

MADISON

THOMAS

CITRUS

SUMTER

MARION

CHARLTON

LOWNDES

DIXIE

GRADY

UNION

COLUMBIA

SUWANNEE

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

HAMILTON

JEFFERSON

BROOKS

ECHOLS

CLINCH

WARE

BAKER

WAKULLA

PUTNAM CLAY

30°

84° 83° 82°

29°

Gopher River

East Pass

West

Pass

0 20 40 MILES

0 20 40 KILOMETERS

G E O R G I A

F L O R I D A

EXPLANATION

SUWANNEE RIVER WATER MANAGEMENT

DISTRICT BOUNDARY

ELEVATION OF THE PREDEVELOPMENT

POTENTIOMETRIC SURFACE OF THE

UPPER FLORIDAN AQUIFER–Contour

interval is 10 feet. Datum is NGVD 1929

(from Bush and Johnston, 1988, pl. 4)

GROUND-WATER FLOW LINE

POINT WHERE GROUND-WATER FLOW

LINES DIVERGE

10

G u l f o f M e x i c o

90

80

80

70

70

60

50

40

30

90

20

10

70

80

100

70

50

60

40

30

40

50

10

80

90

50

50

60

20

50

70

Figure 19. Predevelopment potentiometric surface of the Upper Floridan aquifer, including key features of the ground-water flow system.
Collectively, the above observations indicate that the fresh­watersaltwater interface is probably close to the coastline. Thus, the 

western boundary is conceptualized as being a constant-head 

boundary with a head value equal to zero, which is the approximate elevation of the Gulf of Mexico in the subregional study 

area located within 1 mi offshore of the coastline.

Upper and Lower Flow-System Boundaries

For this study, the top of the ground-water flow system 

in the subregional area was conceptualized to be the top of the 

Upper Floridan aquifer or the top of the unconsolidated surficial sediments (where present). Therefore, the Upper Floridan 

aquifer and any overlying sediments are treated as a single 

flow system. This conceptualization is supported by data 

from collocated wells (not shown) near Bell, Florida (fig. 4), 

tapping both the Upper Floridan aquifer and surficial deposits, 

which indicate that water levels in these units are similar in 

magnitude and in their patterns of fluctuations (fig. 21).

The lower boundary of the ground-water flow system is 

coincident with the base of the Upper Floridan aquifer. This 

boundary is defined by one of three features, including the: 

(1) top of a middle confining unit within the aquifer where 

present; (2) base of the aquifer in areas where a middle confining unit is absent and where freshwater is present throughout the 

entire thickness of the aquifer; or (3) freshwater-saltwater interface when it occurs within the aquifer. As previously described, 

the elevation of the freshwater-saltwater interface was estimated using the Ghyben-Herzberg principle, and the resulting 

surface of the base of the flow system is shown in figure 22.

YEAR

1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

50

52

54

56

58

60

62

64

66

68

WELL NAME: USGS LAKE BUTLER

USGS WELL NUMBER: 300747082225885

SRWMD WELL ID: -041923001

GROUND-WATER LEVEL, IN FEET ABOVE NGVD 1929

Figure 20. Ground-water 

levels in the Upper 

Floridan aquifer near 

Lake Butler, Florida, 

from 1957 to 1999. 

USGS is U.S. Geological 

Survey, and SRWMD is 

Suwannee River Water 

Management District. 

Well location is shown 

in fig. 18.

1991

M J J A S O N D

1992

J F M A M J J A S O N D

1993

J F M A M J J A S O N D 75

76

77

78

79

80

81

82

83

Surficial sediments well

(Suwannee River Water Management District

ID number -081535001)

Upper Floridan aquifer well

(Suwannee River Water Management District

ID number -08135002)

GROUND-WATER LEVEL, IN FEET ABOVE NGVD 1929

Figure 21. Ground-water 

levels of the collocated 

wells tapping the unconsolidated surficial sediments and Upper Floridan 

aquifer near Bell, Florida, 

1991-93. The location of 

Bell is shown in fig. 4.

Ground-Water Hydrology  27
28  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Patterns of Ground-Water Levels and Flow

The ground-water flow system within and adjacent to the 

subregional study area can be characterized by a number of 

spatial and temporal patterns. Several of the spatial patterns 

were discussed in the previous description of the ground-water 

flow system boundaries. The general spatial pattern of groundwater flow is one in which flow is directed away from western 

and eastern external boundaries that pass through the San 

Pedro Bay-Mallory Swamp, Keystone Heights, Waccasassa 

Flats, and Rainbow Springs potentiometric highs toward 

three sets of features for ground-water discharge. These three 

sets of features, in order of decreasing size of contributing 

area, are the: (1) Lower Santa Fe River-Ichetucknee RiverLower Suwannee River drainage network; (2) Otter CreekWaccasassa River-Tenmile Creek drainage network; and 

(3) Gulf of Mexico coastal area. Ground-water flow lines that 

delineate the approximate location of the boundaries between 

the contributing areas to these features during March 1998 

are shown in figure 23. Analysis of potentiometric surface 

maps from different periods of time and under a range of 

hydrologic conditions indicate that the overall configuration of 

the potentiometric surface of the Upper Floridan aquifer has 

remained reasonably consistent over time (except where noted 

previously). Accordingly, the spatial patterns of flow and 

contributing areas described above and in the previous descriptions of key external boundary conditions have also remained 

reasonably consistent.

COLUMBIA SUWANNEE

DIXIE

MARION

UNION

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

400

30°00’

83°00’ 82°30’

29°00’

0 20 MILES

0 20 KILOMETERS

30’

83°30’

EXPLANATION

AREA WHERE

FRESHWATER EXTENDS

BELOW BASE OF THE

UPPER FLORIDAN AQUIFER

LIMIT OF THE MIDDLE

CONFINING UNIT OF THE

FLORIDAN AQUIFER SYSTEM

BASE OF FRESH GROUND

WATER–In feet below NGVD 1929.

Contour interval is 400 feet

G u l f

o f M e x i c

o

400

800

1,200

1,600

2,000

2,400

2,800

3,200

400

800

1,200

1,600

2,000

2,400

2,800

3,200

1,600

800

1,200

2,000

2,400

2,800 3,200

Figure 22. Elevation of the base of freshwater in the Upper Floridan aquifer.
BROOKS CLINCH

WARE

ALACHUA

LEVY

HAMILTON

DIXIE

GRADY

MADISON

MARION

THOMAS

CITRUS

SUMTER

UNION

COLUMBIA

SUWANNEE

BRADFORD

LAFAYETTE

GILCHRIST

TAYLOR

JEFFERSON

LEON

LOWNDES ECHOLS

CHARLTON

BAKER

WAKULLA

30°

84° 83° 82°

29°

G u l f o f M e x i c o

90

80

70

60

50

40

10

20

30

40

50

60

70

80

70

20

30

40

50

60

80

70

80

60

70

80

60

50

EXPLANATION

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

GROUND-WATER FLOW LINE–Defining key

external and internal flow-system boundary

GROUND-WATER FLOW LINE–Defining boundaries

of selected ground-water contributing areas

POTENTIOMETRIC SURFACE CONTOUR–For the

Upper Floridan aquifer during March 1998, in

feet above NGVD 1929. Contour interval is 10 feet

GROUND-WATER FLOW ARROW–Shows general

direction of ground-water flow

POINT WHERE GROUND-WATER FLOW LINES DIVERGE

20

0 20 40 MILES

0 20 40 KILOMETERS

G E O R G I A

F L O R I D A

Suwannee River

Suwannee

River

Rainbow Springs

Tenmile Creek

Cow

Creek

Otter

CreekCow

Creek

Ich

r

et i ucknee R ve

S

R

anta Fe

iver

Waccasassa River

Econfi

e

na Cr e

A

k

ucilla

River

Stei e

nh

h

atc

e

River

W

o

ith c la

ochee

River Withlacoochee River

Suwannee River

Wekiva

River

Figure 23. Potentiometric surface of the Upper Floridan aquifer during March 1998 and general spatial patterns of ground-water flow.

Ground-Water Hydrology  29
30 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Several temporal patterns are also evident in the groundwater system in the subregional study area. High ground-water 

levels typically occur during two periods: from late summer 

to mid-fall, and from early to mid-spring (fig. 24). Low 

ground-water levels typically occur in the intervening periods. The pattern of high water levels is similar to the pattern 

of monthly rainfall data (fig. 25), although the monthly mean 

ground-water levels generally lag the monthly mean rainfall 

totals by about 1 month during the summer.

During the study period, ground-water levels exhibited 

varying degrees of consistency with the previously discussed 

seasonal pattern. In water year 1998, ground-water levels 

exhibited a relatively typical seasonal pattern: peak groundwater levels occurred during March-April and October in 

most of the observation wells. The October 1998 period 

represented a particularly sharp peak in ground-water levels, 

coinciding with a tropical storm that produced heavy rainfall 

in the subregional study area, with several weather stations 

(19)

EXPLANATION

SAMPLE SIZE–Years

of record

75th PERCENTILE+ –Or

largest value

1.5*IQR

75th PERCENTILE

MEAN

MEDIAN–50th percentile

25th PERCENTILE

25th PERCENTILE-1.5*IQR–Or

smallest value

OUTLIER

INTERQUARTILE RANGE (IQR)

MONTHLY MEAN GROUND-WATER ELEVATION, IN FEET ABOVE NGVD 1929

JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT NOV DEC

28

30

32

34

36

38

40

42

20

22

30

24

26

28

32

34

36

38

SRWMD Well ID -121508002

(near Chiefland, Florida)

SRWMD Well ID -101210001

(Cross City, Florida)

(19)

(19)

(19)

(18)

(18)

(17) (18) (18)

(18) (19)

(19) (19)

(20)

(24) (21) (23)

(24) (23)

(23) (21)

(21) (21)

(25) (22)

Figure 24. Monthly mean ground-water levels near Chiefland and Cross City, Florida. Locations of Chiefland and Cross City are shown in 

fig. 4. SRWMD is Suwannee River Water Management District.
reporting rainfall totals that were two to three times (6-11 in.) 

higher than normal for the month. In water year 1999, 

ground-water levels were less consistent with typical seasonal 

weather patterns. The typical late winter-early spring peak 

was absent or minimal in all wells. Many of the wells showed 

little response to the rains that eventually came in August and 

September 1999, and ground-water levels were better characterized as being in a relatively steady recession since the 

October 1998 peak.

Because of the close linkage between the river and 

aquifer, ground-water levels along the river are sensitive to 

fluctuations in river levels (fig. 26). Data from wells in these 

areas confirm this association and also indicate the direction of flow between the Lower Suwannee River and Upper 

Floridan aquifer. For example, in the vicinity of the gaging 

station of the Suwannee River near Bell near river mile 56, 

ground-water levels in nearby well t059 (figs. 26, 27; table 2) 

indicate that the direction of ground-water flow probably 

MONTHLY MEAN RAINFALL, IN INCHES

JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT NOV DEC

-5

0

20

5

10

15

25

Usher Fire Tower Weather Station,

(near Chiefland, Florida,

National Weather Service

Coop ID 089120)

-5

0

20

5

10

15

25

Cross City, Florida

2008

(National Weather Service

Coop ID 08 )

(41)

(42) (42)

(41)

(41)

(41)

(41) (41)

(42)

(42)

(42)

(41)

(57)

(56)

(56)

(56)

(55)

(57)

(57)

(57)

(57)

(56)

(56)

(56)

(41)

EXPLANATION

SAMPLE SIZE–Years of

record

75th PERCENTILE+ –Or

largest value

1.5*IQR

75th PERCENTILE

MEAN

MEDIAN–50th percentile

25th PERCENTILE

25th PERCENTILE-1.5*IQR–Or

smallest value

OUTLIER

FAR OUTLIER

INTERQUARTILE RANGE (IQR)

Figure 25. Monthly rainfall near Chiefland and Cross City, Florida. Locations of Chiefland and Cross City are shown in fig. 4.

Ground-Water Hydrology  31
32  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

reversed during periods of peak river levels when well water 

levels were at or below river levels. Conversely, downstream 

near river mile 25 and the gaging station (map index no. 9, 

fig. 4) near Old Town and Manatee Springs, ground-water 

levels in well s346 (figs. 26, 27) near the river were consistently higher than river levels, indicating a consistent pattern 

of ground-water discharge to the river. In the lower reaches 

of the river, tidally induced changes in river levels produce 

tidally induced changes in aquifer levels. Because of the 

small lag in the response of the ground-water levels to the 

tidal fluctuations in the river levels, the difference between 

river and aquifer levels also fluctuates. As a result, this 

causes ground-water discharge to the lower river to fluctuate over the course of a tidal cycle. Observations of these 

short-term fluctuations in ground-water discharge were made 

during a series of continuous spring-flow measurements 

taken in Fanning Springs and Manatee Springs, and are 

briefly described later.

0

5

10

15

20

25

30

0

2

4

6

8

10

12

14

1998

O

ELEVATION, IN FEET ABOVE NGVD 1929

N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

Suwannee River

near Bell, Florida

at river mile 56

Well t059

(near river mile 56)

Well s346

(near river mile 25)

Suwannee River

near Old Town, Florida

at river mile 25

Figure 26. Temporal variations in ground- and surface-water levels near river miles 25 and 56 of the Suwannee River. Well locations 

are shown in fig. 27.
Hydraulic Properties

Two types of hydraulic properties influence ground-water 

flow in aquifers: conductive and storage properties. Conductive properties influence the rate of ground-water flow for a 

given hydraulic head gradient and are a function of the degree 

of intergranular connections and secondary dissolution of the 

subsurface rocks and sediments. Conductive properties are 

typically expressed as hydraulic conductivity or transmissivity (conductivity multiplied by aquifer thickness). Storage 

properties influence how much ground water is released from 

storage for a given change in hydraulic head and are a function 

of the compressibility of water and the elasticity and waterretentive characteristics of the subsurface rocks and sediments. 

Storage properties are typically expressed as: (1) specific 

yield (volume of water released from desaturation of the pore 

space of a unit volume of an unconfined aquifer by gravity), 

(2) specific storage (volume of water released per unit volume 

of aquifer per unit change in hydraulic head), or (3) storativity 

(specific storage multiplied by aquifer thickness). Estimates of 

hydraulic properties can be made from aquifer tests, calibration of numerical (simulation) models, and by making inferences from other hydrologic and hydrogeologic data.

Figure 27. Network of wells used to measure ground-water levels within the subregional study area.

Ground-Water Hydrology  33

COLUMBIA

SUWANNEE

DIXIE

MARION

UNION

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

Santa Fe River

Suwannee River

0 20 MILES

0 20 KILOMETERS

30°

83° 82°

29°

EXPLANATION

SUBREGIONAL MODEL BOUNDARY

GROUND-WATER LEVEL

MONITORING WELL LOCATION

AND IDENTIFIER

s389

G u l f o f M e x i c o

s389

s386

s385 s384

t024

s382

s381

s376 s373

s371

s370

s369

s366

s364

s360

s355

s354

o038

s353

s350

s349

s346

s342

s338

s336 s337

s335

s333

s331

s330

s328

s327

s321

s319 s316

s315

s314

s312

s296 s300

s295

t057

s292

s291

s289

s288

t059

s286

s271

s267

s265

s264

s261

s251

s245

s228

o028

o014

t075

t067

s262 t065

t039

t030 t029

s375

t025

t016
Aquifer Tests

Aquifer tests have been used to estimate hydraulic 

properties of the Upper Floridan aquifer at selected sites 

within and adjacent to the regional study area (fig. 28 and 

table 3). Results from these tests indicate that transmissivity in the Upper Floridan aquifer ranges from about 1,600 

to 1,000,000 ft2/d in the regional study area and from about 

9,100 to 2.7 million ft2/d in areas adjacent to the study area. 

Additionally, storage coefficient estimates from these tests 

range from about 4 × 10-4 to 0.5 (dimensionless). A review 

of some of the tests also indicates that some of the storage 

coefficient values may have wide confidence intervals, and 

therefore, limited significance.

Several limitations in the aquifer tests make it difficult to 

evaluate the accuracy of individual transmissivity estimates or 

to identify meaningful geographic patterns in Upper Floridan 

aquifer transmissivity within the regional study area. One 

limitation arises from various interpretations of the results of 

the aquifer tests, which can yield estimates of transmissivity that differ by orders of magnitude in some instances. For 

example, the transmissivity value derived from the Andrews 

Nursery aquifer test (site 8, fig. 28 and table 3) was based on 

a Theis curve analysis in which the curve was a poor fit to the 

measured drawdown data. A transmissivity estimate that is 

close to 10 times higher than the value shown in figure 28 can 

be obtained if the Jacob straight-line method is used to obtain 

a better fit of data from the later stages of the test period (Keith 

Halford, U.S. Geological Survey, written commun., 1997).

Another source of uncertainty arises because none of 

the tests conducted in the regional study area employed fully 

penetrating pumping or observation wells, and the effects of 

partial penetration were not considered in any of the analyses. 

Additionally, because most of the observation wells used in 

the tests penetrated less than 200 ft of the Upper Floridan 

aquifer, no data were available to evaluate whether vertical 

differences in hydraulic conductivity exist within the aquifer and whether such differences could have affected the 

hydraulic property estimates that were inferred from the tests 

(even if partial penetration effects were considered).

Another limitation is that the results of an aquifer test 

in a given area may not be representative of the larger area 

surrounding the test because of heterogeneity present at the 

site of the test or in the larger area. For example, data were 

collected at two observation wells for the Piedmont Farms test 

(site 23, fig. 28 and table 3). Analysis of the drawdown data 

from the first observation well yielded a transmissivity estimate 

of about 300,000 ft2/d, using results from the Neuman method 

of analysis. Analysis of data from the second observation well 

yielded a transmissivity estimate of 1 million ft2/d using the 

same method. A cursory reanalysis of this test indicated that the 

latter estimate may actually be greater than the reported value 

(about 2 million ft2/d ±1 million ft2/d), which indicates that the 

transmissivity at this site is even more spatially variable or at 

least that the mean value of transmissivity at this site has a wide 

confidence interval.

Table 2. Identifiers for the network of wells used to measure 

ground-water levels within the subregional study area.

[Well locations shown in fig. 27. Well numbers beginning with the letters ‘s’, ‘o’, 

or ‘t’ indicate that the well was measured by personnel from the Suwannee River 

Water Management District (SRWMD), U.S. Geological Survey (USGS) Orlando 

office, and USGS Tallahassee office, respectively. Also note that some of the 

wells were measured by personnel from more than one office. Therefore, a given 

well may have more than one well number (for example, USGS well identifier 

294743082543901 has two well numbers: s288 and t59). NA indicates that the 

well does not have the corresponding well number]

Well

No.

(this 

report

only)

 SRWMD 

well 

identifier

USGS well 

identifier

Well

No.

(this 

report

only)

 SRWMD 

well 

identifier

USGS well 

identifier

s228 -051521001 300205082484401 s350 -111436001 292843082514201

s245 -061401003 295950082514685 s353 -111809001 NA

s251 -061629001 295618082440985 s354 -111811001 293252082292385

s261 -071417001 295246082553885 s355 -111920001 NA

s262 -071515001 295214082482501 s360 -121330002 NA

s264 -071526001 295055082465201 s364 -121508002 292713082493685

s265 -071528001 295057082483485 s366 -121708005 NA

s267 -071532001 294931082501685 s369 -131203001 NA

s271 -071632001 NA s370 -131219001 291940083090101

s286 -081313005 294654082581085 s371 -131306001 NA

s288 -081416001 294743082543901 s373 -131526001 NA

s289 -081425001 294521082514901 s375 -131705001 NA

s291 -081515002 294709082473001 s376 -131736001 291910082341185

s292 -081518005 NA s378 -131821001 NA

s295 -081618001 294721082443001 s381 -141305001 NA

s296 -081624001 294701082402201 s382 -141429001 291414082560985

s300 -081724001 NA s384 -141620001 291508082432901

s312 -091212003 294311083041085 s385 -141707002 NA

s314 -091311001 NA s386 -141711001 NA

s315 -091420001 294135082553485 s389 -151624001 NA

s316 -091504001 294400082491385 o014 NA 290743082341501

s319 -091607001 294330082445085 t016 NA 291048083011801

s321 -091704001 294428082362901 t022 NA 291241082300101

s327 -101120001 NA t024 NA 291508082432901

s328 -101210001 293731083061885 t025 NA 291806082545601

s330 -101428001 NA o028 NA 291855082472601

s331 -101429011 NA t029 NA 292310082373701

s333 -101516017 293822082483285 t030 NA 292507082560201

s335 -101603001 NA o038 NA 293252082292385

s336 -101634001 293414082415285 t039 NA 293525082585301

s337 -101722001 293619082362385 t057 NA 294721082443001

s338 -101816001 NA t059 NA 294743082543901

s342 -111117007 293137083143085 t065 NA 295114082393801

s346 -111326004 292921082583285 t067 NA 295214082482501

s349 -111405001 NA t075 NA 295737082480801

34  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida
30°

84° 83° 82°

29°

G u l f o f M e x i c o

0 20 40 MILES

0 20 40 KILOMETERS

8

25,000 TRANSMISSIVITY–Values in feet squared per day

EXPLANATION

SUWANNEE RIVER WATER

MANAGEMENT DISTRICT BOUNDARY

REGIONAL STUDY AREA BOUNDARY

SUBREGIONAL STUDY AREA BOUNDARY

LOCATION OF AQUIFER TEST

MAP INDEX NUMBER–See table 3 for site name

16

2,100,000 15

20,000

Ocala

Perry

Thomasville Valdosta

Gainesville

Tallahassee

Fanning

Springs

Bell

Branford

Fort

White

Wilcox

Old Town

Keystone

Heights

G E O R G I A

F L O R I D A

SUWANNEE

LAFAYETTE

DIXIE

LEVY

GILCHRIST ALACHUA

MARION

COLUMBIA

TAYLOR

MADISON

HAMILTON

JEFFERSON

LEON

GRADY

THOMAS

BROOKS LOWNDES

ECHOLS

CLINCH

WARE

CHARLTON

BAKER

UNION

BRADFORD

CITRUS SUMTER

WAKULLA

Suwannee River

River

Chiefland

Santa Fe

Suwannee

9

28,000

3

33,000

22

9,100

21

2,700,000

18

230,000

20

201,000

19

67,000

17

62,000

8

25,000

13

25,000

23

300,000

to

1,000,000

7

30,000

4

36,000

2

190,000

14

1,600

5

300,000

6

450,000

10

37,000

11

125,000

1

214,000

12

1,300,000

Figure 28. Location of selected sites and estimated transmissivity in the Upper Floridan aquifer based on aquifer tests.

Ground-Water Hydrology  35
36  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Nearly all of the pumping and observation wells used 

in the aquifer tests (fig. 28) had open intervals (between the 

bottom of the well casing and the bottom of the well), which 

were constructed within the Ocala Limestone or Avon Park 

Formation. The remaining two tests, City of Tallahassee and 

Finlayson (sites 12 and 1, respectively, fig. 28 and table 3), 

used wells that were open to the Suwannee Limestone; the 

City of Tallahassee test also used observation wells open to 

the Ocala Limestone. No wells were completed in the Oldsmar 

Formation. Because of the limited number of tests available 

within and adjacent to the regional study area, the wide range 

in the reported transmissivity values, and the uncertainties 

in the individual estimated values, significant differences in 

the conductive properties of the Suwannee Limestone, Ocala 

Limestone, Avon Park Formation, and Oldsmar Formation 

were not apparent; nor were differences apparent within 

different depth intervals of the Upper Floridan aquifer.

Results from Previous Modeling Studies

Results from previous ground-water modeling studies 

represent another source of information about the hydraulic 

properties of the Upper Floridan aquifer. Several models have 

been developed for areas that include all or part of the regional 

or subregional study areas. The hydraulic properties used in 

these models represent the investigators’ interpretation of the 

most likely values of the conductive and storage properties of 

the aquifer given a limited amount of water-level, flow, boundary condition, and hydrogeologic data.

Bush and Johnston (1988) developed steady-state models 

of the entire Floridan aquifer system that simulated predevelopment and “modern conditions” as represented by 1980 

ground-water withdrawal rates. Calibrated transmissivity 

values from the models ranged from 10,000 to greater than 

1,000,000 ft2/d in the SRWMD and adjacent areas (with most 

values ranging from 250,000 to greater than 1,000,000 ft2/d). 

The calibrated transmissivity values from the models differed 

from aquifer-test values in the SRWMD, sometimes by 

one order of magnitude. Bush and Johnston (1988) largely 

attributed these discrepancies to scale effects; for example, the 

tendency to include highly conductive conduits and fractures 

as the area being considered increases in size.

The model by Bush and Johnston (1988) was based, in 

part, on several small-scale models. Ryder (1985) developed 

a ground-water flow model of the Floridan aquifer system 

in west-central Florida that overlapped part of the subregional study area in Levy County and adjacent areas to the 

south and east. The calibrated transmissivity values of the 

model by Ryder (1985) ranged from 17,000 ft2/d in western 

Levy County to 13,000,000 ft2/d near large springs. Ryder 

(1985) also attempted a transient simulation from May 1976 

to September 1976, using specific yield and specific storage values of 0.20 and 1.0x10-6

, respectively, and reported a 

good match between simulated and measured heads in most 

of the model area. Calibration was not completed, however, 

because of uncertainties in the amount of irrigation pumpage 

and the values of model parameters in the southern part of the 

Table 3. Transmissivity estimates from aquifer tests and flow-net analyses of the Upper Floridan aquifer.

[Well locations are shown in fig. 28. SRWMD, Suwannee River Water Management District; USGS, U.S. Geological 

Survey; SWFWMD, Southwest Florida Water Management District]

Site No.

(this report 

only)

Site name

Transmissivity, 

in feet squared 

per day

Source of information

1 Finlayson 214,000 SRWMD files in Live Oak

2 Oxy 190,000 SRWMD files in Live Oak

3 Osceola National Forest 33,000 Miller and others (1978)

4 Lake City 36,000 SRWMD files in Live Oak

5 Boatright 300,000 SRWMD files in Live Oak

6 Wet Farms 450,000 SRWMD files in Live Oak

7 City of Fort White 30,000 SRWMD files in Live Oak

8 Andrews Nursery 25,000 SRWMD files in Live Oak

9 City of Gainesville 28,000 SRWMD files in Live Oak

10 City of Valdosta #4 37,000 Vorhis (1961)

11 Proctor and Gamble Foley Plant 125,000 USGS files in Tallahassee

12 City of Tallahassee #2 1,300,000 Davis (1996)

13 R.D. Williams 25,000 SRWMD files in Live Oak

14 John Folks, Division of Forestry, Midway 1,600 SRWMD files in Live Oak

15 Tidewater 20,000 Bush and Johnston (1988)

16 Silver Springs 2,100,00 Faulkner (1973)

17 Circle Square 62,000 SWFWMD (2000)

18 Florida Power – Crystal River 230,000 SWFWMD (2000)

19 Marion Oaks 67,000 SWFWMD (2000)

20 Crystal River 201,000 SWFWMD (2000)

21 Hampton Hills 2,700,000 SWFWMD (2000)

22 Tompkin Park Romp111 9,100 SWFWMD (2000)

23 Piedmont Farms 300,000 to

 1,000,000

SRWMD files in Live Oak
model area. Tibbals (1990) calibrated steady-state and shortterm (60-day) transient models of the Floridan aquifer system 

in a large part of east-central Florida (adjacent to the Ryder 

(1985) model area). Tibbals (1990) used transmissivity values 

of 100,000 to 400,000 ft2/d and a storage coefficient value 

of 1x10-3 in the areas of his model that were adjacent to the 

subregional area of the present study. Tibbals (1990) further 

noted that the calibration could have been improved in some 

locations by adjusting the storage coefficient value, but that this 

was not done because most of the calibration error was caused 

by uncertainty in the rates and areal distribution of pumping. 

Krause and Randolph (1989) calibrated a steady-state model 

of the Floridan aquifer system in southeastern Georgia and 

adjacent parts of Florida and South Carolina. Calibrated values 

of transmissivity in this model generally ranged from 100,000 

to 250,000 ft2/d in parts of Baker and Bradford Counties.

Davis (1996) developed a steady-state model of the Upper 

Floridan aquifer for parts of northern Florida and southern 

Georgia along the western boundary of the SRWMD. The 

calibrated transmissivity values for the model were highly variable, ranging from 5,000 ft2

/d in the region of the Apalachicola 

Embayment-Gulf Trough to greater than 10,000,000 ft2/d in the 

area surrounding the large springs in parts of southern Leon, 

Wakulla, and Jefferson Counties (fig. 3).

A steady-state model was developed for a 340-mi2 area 

surrounding a paper mill in Taylor County to evaluate the 

extent to which unpotable water from the Fenholloway River 

could affect the water in the underlying aquifers (Lee and 

Passehl, 1995). The hydraulic conductivity values calibrated 

for the model generally ranged from 80 to 1,200 ft/d, although 

a small part of the study area had a high value of 6,000 ft/d. 

The corresponding transmissivity values generally ranged 

from 64,000 to 960,000 ft2/d, but was 4.8 million ft2/d in the 

area with high hydraulic conductivity.

Sepúlveda (2002) developed a steady-state model of the 

intermediate and Floridan aquifer systems in peninsular Florida. This model covered most of the regional study area and 

subregional study areas near the Suwannee River basin, where 

transmissivity values ranged from 3,000 to 12,000,000 ft2/d. 

The highest transmissivity values were located near springs, 

and the lowest transmissivity values were located in the 

poorly drained areas of San Pedro Bay in Lafayette County, 

the Waccasassa Flats in Gilchrist County, and the Keystone 

Heights area in eastern Bradford County (fig. 3).

Inferences from Geologic Characteristics and 

Potentiometric Surface Maps

Qualitative inferences about the transmissivity of one 

area relative to another can also be made from various other 

hydrologic and hydrogeologic data. These data include potentiometric surface maps, geological inferences about the depositional and post-depositional environments of different areas, 

estimates of recharge and runoff rates, geographic distributions 

of springs, and results of tracer tests. In this study, these data 

indicate several areas where the transmissivity of the Upper 

Floridan aquifer is relatively high and two areas where the 

transmissivity is relatively low.

Relatively high transmissivity values are indicated by the 

gradual slope of the potentiometric surface in the areas along 

the Lower Suwannee River corridor, especially east of the 

river in the Chiefland Limestone Plain physiographic region 

(fig. 3) where the slope of the potentiometric surface is 5 to 

8 ft/mi; in the middle and lower reaches of the Waccasassa 

River drainage network where the slope is 5 to 8 ft/mi; and 

in western Alachua County where the slope is 2 ft/mi or less. 

The slope of the potentiometric surface is also a function of 

recharge rates, and low recharge rates can result in gradual 

slopes. Recharge rates in these areas, however, are relatively 

high, as indicated by the high rates (16-22 in/yr on average) 

of ground-water discharge and net rainfall (Bush and Johnston, 1988, pls. 7 and 9; Grubbs, 1997, table 5). Thus, a large 

volume of ground-water moves through these areas and high 

transmissivities are necessary to convey this water, given the 

low hydraulic gradient. The high density of karst features, 

such as sinkholes and springs, and the highly permeable surficial sediments in these areas are consistent with active dissolution of the limestone and associated high transmissivity values. 

High transmissivities are also indicated for the areas along 

and upgradient from the Ichetucknee River. This area has one 

of the highest concentrations of ground-water discharge in 

Florida, and dye-tracing studies have indicated that the time of 

travel between the springs and sinkholes 7-mi upgradient may 

be as fast as 7 days (Butt and others, 2000).

In contrast, the potentiometric surface has a steeper 

slope and substantially higher levels in the Waccasassa Flats 

area of Gilchrist County and north-central Levy County. This 

north-south trending potentiometric “high” coincides with 

the Waccasassa Flats geomorphic subprovince of the Gulf 

Coastal Lowlands (Col and others, 1997). Recharge rates in 

the Waccasassa Flats are probably similar in magnitude to 

those described above for the Suwannee River corridor and 

Waccasassa River network because the patterns of rainfall and 

evapotranspiration are the same, and the potential for direct 

(storm) runoff is limited because of the flat topography and 

absent or poorly developed drainage network. Thus, recharge 

in the Waccasassa Flats should be close to the difference 

between precipitation and actual evapotranspiration and, 

therefore, similar to that found in the adjacent areas where 

transmissivity is probably substantially higher. Recharge rates 

may be slightly lower in the Waccasassa Flats area because 

the potential for direct (storm) runoff during wet periods and 

rates of evapotranspiration should be higher because of a shallower water table, less-permeable surficial deposits, presence 

of wetland and lake features, and limited surface drainage in 

these areas (although surface storage in the form of wetlands 

and lakes reduces the potential for direct runoff). Thus, high 

elevations and steep gradients in the potentiometric surface 

in the Waccasassa Flats area relative to the surrounding areas 

appear to be explained by relatively low transmissivities in 

these areas rather than relatively high recharge rates.

Ground-Water Hydrology  37
38  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

This inference is consistent with the conclusions from 

several hydrogeologic studies of the Waccasassa Flats (Yon and 

Puri, 1962; Puri and others, 1967; Col and others, 1997). These 

studies and one study by Vernon (1951) describe physiographic 

and geologic characteristics that are consistent with at least the 

shallow part of the Upper Floridan aquifer having low permeability under the Waccasassa Flats. Vernon (1951) presented 

several lines of evidence that the Waccasassa Flats represents 

a former stream course, including the presence of deltaic sediments at the southern end of the flats in central Levy County. 

Col and others (1997) note that “... clayey sediments deposited 

by such a stream would thus be responsible for shielding the 

underlying carbonates from dissolution and supporting the 

generally swampy standing water conditions in the flats.” Yon 

and Puri (1962) and Puri and others (1967) conducted detailed 

studies of the Waccasassa Flats and hypothesized that the 

silicilastic sediments above the Upper Floridan aquifer were 

deposited in a low-energy setting between barrier islands on the 

western boundary of the Waccasassa Flats and on a mainland 

paleo-shoreline along the eastern boundary of the flats (Col and 

others, 1997). They also concluded that a graben was present 

under the southern part of the flats, which was filled with low 

permeability miocene and Pliocene sediments that minimized 

karst dissolution because these sediments restricted recharge to 

the Upper Floridan aquifer (Col and others, 1997). The presence of the graben, however, could not be confirmed because 

of the limited number of available lithologic logs. Col land 

others (1997) did conclude that sediment size analyses of various intervals of borehole sediment cores indicated that “... the 

clastic sediments underlying the flats were deposited in quiet 

water conditions.”

Sources and Sinks of Water

Water is supplied to and removed from the ground-water 

flow system as ground-water recharge, ground-water discharge, 

and direct withdrawals from pumped wells. Ground-water 

recharge and discharge occur naturally as water moves across 

the upper boundary of the ground-water system, either as a 

downward flux from land surface to the water table (recharge) 

or as an upward flux of ground water (discharge) to coastal 

wetlands and near-shore areas. Ground-water recharge and 

discharge also occur naturally through the exchange of water 

between the ground-water system and rivers, streams, and 

springs. This important mechanism of ground-water recharge 

and discharge is discussed later. Pumping wells, especially 

those used for irrigating agricultural crops, represent another 

important mechanism for withdrawing water from the groundwater system in the subregional study area.

Natural Recharge and Discharge

The ground-water system is recharged by infiltrating 

rainfall and seepage from streams and wetlands when water 

levels in the streams and wetlands are higher than the watertable elevation. In areas that lack surface drainage, average 

annual recharge can be approximated as the difference 

between precipitation and evapotranspiration and ranges from 

18 to 23 in/yr (Bush and Johnston, 1988, pls. 7 and 9); interception and changes in soil moisture storage can also affect 

recharge, but these terms become negligible as the averaging time increases and the thickness of the unsaturated zone 

decreases. This range is similar to average annual recharge 

rates of 14 to 20 in. found using eddy correlation and waterbudget methods (Knowles, 1996), 15 in. using a chloride tracer 

approach (Lee, 1996), and 18 to 24 in. using a water-budget 

method (Grubbs, 1997). In other areas that have surface drainage, recharge is reduced somewhat by direct runoff. Streamflow data from basins with well developed drainage networks 

in the Northern Highlands and from Cow Creek (in Gilchrist 

County) and the Waccasassa River indicate that direct runoff is 

generally about 3 to 6 in/yr. This result indicates that in some 

of the wetland areas with limited drainage networks, such as 

the Waccasassa Flats, Mallory Swamp, and unnamed coastal 

swamps (fig. 3), recharge to the Upper Floridan aquifer may 

be as much as 3 to 6 in/yr lower than the difference between 

annual precipitation and evapotranspiration.

Daily rainfall was estimated over a set of Thiessen polygons, using data collected at 19 stations from October 1996 

to September 1999 (water years 1997-99). Daily potential 

evapotranspiration was estimated by multiplying the daily pan 

evaporation measured at the National Weather Service station, 

Gainesville 11 WNW (National Oceanic and Atmospheric 

Administration coop identifier, 083322) during water years 

1997-99 by pan coefficients of 0.62 (April-October) and 0.82 

(November-March). These values yield a weighted annual 

average pan coefficient of 0.70, which is a typical value for 

calculating potential evapotranspiration in Florida (Jones and 

others, 1984).

Daily estimates of actual evapotranspiration and recharge 

were computed for the subregional study area, using the above 

daily precipitation and potential evapotranspiration data for 

water years 1996-99 by means of the following daily soilmoisture deficit accounting (SMA) algorithm (E.P. Weeks, 

U.S. Geological Survey., written commun., 1993):

SMD(t) = SMD(t - 1) + ETA(t) – P(t), (1)

where

SMD(t) is the soil-moisture deficit on day t (the 

current day),

SMD(t - 1) is the soil-moisture deficit on the previous day,

ETA(t) is the actual evapotranspiration on day t, and 

P(t) is the precipitation (rainfall) on day t.

The actual evapotranspiration is calculated from a function of 

potential evapotranspiration and the soil-moisture deficit:
ETA(t) = ETP(t) if SMD(t) ≤ SMD1, (2)

 

ETA( )t ETP( )t 1

SMD t( ) SMD1 –

SMD2 SMD1 – = – ----------------------------------------- if SMD1 ≤ SMD(t) ≤ SMD2, and

ETA(t) = 0 if SMD(t) > SMD2 ,

where 

ETP(t) is the potential evapotranspiration rate on day t,

SMD1is the soil-moisture deficit value beyond which ETA = ETP, and

SMD2is the soil-moisture deficit value beyond which ETA(t) = 0.

Equations 1 and 2 were solved iteratively until changes 

in the values of SMD(t) and ETA(t) were negligible. On days 

when rainfall was greater than SMD(t-1) and ETA(t), SMD(t) 

was negative, indicating an excess amount of moisture in the 

soil zone on that day. Accordingly, recharge was set equal to 

the absolute value of SMD(t) on these days and SMD(t) was 

set to zero. This procedure is consistent with the complete 

drainage of the excess soil moisture from the soil zone during 

that day and the concomitant flux of this excess moisture to 

the water table as recharge.

Results obtained from the SMA algorithm were 

consistent with previous evapotranspiration measurements 

taken within and near the subregional study area, and with 

expected recharge rates. For example, the evapotranspiration rates computed with the SMA algorithm were 31.3 and 

31.9 in/yr for water years 1998 and 1999, respectively, in the 

vicinity of the National Weather Service station near Cross 

City (fig. 4). Actual evapotranspiration at the closest site 

(about 11 mi southeast of Gainesville) with measured data was 

32 in. for water year 1994 (Knowles, 1996). Sumner (2001) 

measured somewhat higher rates of 36 and 42 in. for calendar 

years 1998 and 1999, respectively, at a site farther south in 

central Volusia County, east-central Florida. At the weather 

station near Cross City, the annual recharge rates computed 

with the SMA algorithm were 46 and 23 in/yr for water years 

1998 and 1999, respectively. The recharge rate calculated 

at the Cross City weather station for water year 1998 was 

substantially higher than the difference between long-term 

average estimates of precipitation and actual evapotranspiration of 17 in/yr (Bush and Johnston, 1988, pls. 7 and 9) 

because of above average rainfall (78 in.) during water year 

1998. Conversely, the recharge rate was similar to the estimated long-term average recharge rate during water year 1999 

when rainfall was more typical (55 in.).

Similar patterns in the annual recharge rates for water 

years 1998 and 1999 were evident in the rest of the subregional study area (fig. 29). During water year 1998, recharge 

rates were substantially higher than typical values, ranging 

from 35 to 75 in. (fig. 29) or two to three times greater than 

the 14- to 24-in/yr range from the estimates of Knowles 

(1996), Lee (1996), and Grubbs (1997). The 

maximum value (75 in.) occurred in the Thiessen polygon corresponding to the Wekiva Fire 

Tower rain gage where rainfall measured 104 

in. This rainfall total was close to the record 

rainfall totals for Florida (107 in.), and for the 

nearby Usher Fire Tower weather station near 

Chiefland where 99 in. of rain fell in 1964. 

Rainfall totals at the other gages were also 

higher than normal, ranging from 65 to 96 in. 

During water year 1999, recharge rates were 

lower, ranging from 13 to 25 in. (fig. 29), and 

were consistent with the smaller rainfall totals 

(41 to 55 in.) recorded for the year.

Over shorter time periods, the SMA algorithm produced 

estimated recharge rates that were also consistent with 

ground-water level fluctuations. An example of this relation 

is presented in figure 30 for the Cross City area. The timing 

and magnitude of ground-water level rises generally coincided 

with the timing and magnitude of SMA-estimated recharge 

events. Additionally, rainfall occurred without a corresponding increase in water levels during several periods. Estimated 

recharge rates were generally equal to zero during these 

periods, indicating that the SMA algorithm was a reasonably 

Figure 29. Recharge totals in the subregional study area based on 

results of the soil-moisture accounting method, water years 1998 

and 1999.

65

25

56

18

46

23

39

21

43

22 39

21

35

17

41

15

37

15

48

14

44

13

75

24

51

21

55

15

49

13

47

16

39

21 42

21

42

17

83°30’ 83°00’ 82°30’

Gulf of Mexico

Chiefland

Wekiva Fire Tower and

rain gage

CITRUS

0 20 MILES

0 20 KILOMETERS 51

21

THIESSEN POLYGON WITH

RECHARGE VALUES–In inches.

Lower value represents water year 1999

SUBREGIONAL GROUND-WATER MODEL BOUNDARY

Upper value represents water year 1998

EXPLANATION

30°00’

29°00’

SUWANNEE

LAFAYETTE

DIXIE

LEVY

GILCHRIST

ALACHUA

MARION

COLUMBIA

TAYLOR

UNION

Suwannee River

30’

Ground-Water Hydrology  39
40 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

good predictor of the effects of soil-moisture depletion and 

replenishment on recharge. The algorithm, however, was not a 

perfect predictor of recharge. There were a few periods when 

water-level rises occurred but the SMA algorithm failed to 

predict recharge (for example, the small water-level rise during 

March 1999 in the Cross City well), or conversely, when the 

water levels declined despite SMA-algorithm predictions of 

recharge sufficient to raise ground-water levels.

Although natural discharge from the Upper Floridan aquifer takes place primarily as ground-water discharge to streams, 

natural discharge also occurs from the Upper Floridan aquifer 

to coastal wetlands, tidal creeks, and near-shore discharge to 

the Gulf of Mexico. Analysis of the potentiometric surface 

maps of the Upper Floridan aquifer indicates that the groundwater contributing area to these coastal areas is about 700 mi2. 

Assuming a long-term recharge rate of about 20 in/yr to this 

contributing area, the long-term average discharge from the 

Upper Floridan aquifer to the coastal areas is on the order 

of 1,000 ft3/s. During the study period, recharge was higher 

(about 38 in/yr) than the long-term rate, so discharge from 

the Upper Floridan aquifer to the coastal areas was probably 

closer to 2,000 ft3/s.

Well Pumpage

Data from monthly measurements of ground-water withdrawals for public, self-supplied commercial and industrial, 

and power-generation uses were obtained from the permit files 

at the Southwest Florida Water Management District and the 

SRWMD and from the water-use data bases of the St. Johns 

River Water Management District, and the Florida Department 

of Environmental Protection. Additional monthly data were 

obtained from several ground-water users. These data were 

then merged with data describing the location of the wells that 

were the source of the withdrawals. To simplify this process 

of merging the two types of information (withdrawal and location data), data were not merged if a user withdrew less than a 

monthly average of 200,000 gal or less than a daily average of 

10,000 gal.

Agricultural withdrawals in the subregional study area 

were estimated using data describing the type, amount, and 

irrigation requirements of each crop grown during the study 

period. The crop data were compiled for each county in the 

study area, using the following crop categories: fruit crops, 

field crops, vegetables, ornamentals, and grasses. The area 

32

34

36

38

40

0

1

2

3

4

5

6

1998

O

GROUND-WATER ELEVATION,

IN FEET ABOVE NGVD 1929

N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

RAINFALL AND RECHARGE,

IN INCHES

MEASURED RAINFALL

ESTIMATED RECHARGE

Cross City Well

(Suwannee River Water Management District

ID number -101210001)

Figure 30. Daily ground-water levels, rainfall, and estimated recharge for Cross City, Florida, during water years 1998-99. 

Well location is shown in fig. 27 (see map identifier s328).
O

1998 1999

50

100

150

200

N D J F M A M J J A S O N D J F M A M J J A S

1997

0

WELL WITHDRAWAL, IN

CUBIC FEET PER SECOND

Figure 31. Estimated monthly ground-water withdrawals from wells in the subregional study area during water 

years 1998-99.

of each crop grown in the study area was obtained from the 

county extension offices of the University of Florida Institute 

of Food and Agricultural Sciences. Monthly water-use values 

were estimated by interpolating between the normal (50-percent 

probability of occurrence) and dry-period (20-percent probability of occurrence) values of monthly net irrigation requirements (the irrigation required after accounting for rainfall) for 

each crop, using the following formula:

NIRi,j(p) = NIRi,j (0.2) – [NIRi,j (0.50) – NIRi,j (0.20)] (0.20 – p); (3) (0.50 – 0.20) 

where 

NIR is the interpolated net irrigation requirement 

(NIR);

 i is an index representing a particular crop 

category (for example, i = 1 might indicate the 

fruit crop category, i = 2 the field crop category, 

and so forth);

 j is an index representing the months of the year 

(j = 1 indicates January, j = 2 indicates February, 

and so forth until j = 12, which indicates 

December);

 p is probability of occurrence of the observed 

monthly precipitation total for a particular month 

during the study (for example, June 1999) in 

National Weather Service Climate Zone 2 for the 

State of Florida (p is calculated by comparing 

the value for that month with historical values 

from climate zone 2);

NIRi (0.20) is the dry-season NIR value for crop category 

i and month j; and

NIRj (0.50) is the normal-season NIR value for crop category 

i and month j.

The agricultural withdrawal for a given crop type during a 

given month of the study was then estimated by multiplying the 

area of a crop by the interpolated NIR value, then dividing this 

value by an estimated irrigation efficiency of 70 percent (Richard 

Marella, U.S. Geological Survey, written commun. 2000).

During water years 1998-99, the average withdrawal rate 

from the Upper Floridan aquifer in the subregional study area 

was estimated to be about 35 ft3/s. There was considerable 

variability about this mean value: (1) the minimum monthly 

withdrawal was about 5 ft3/s and occurred in January of both 

water years; (2) the maximum monthly withdrawal rates were 

about 190 ft3/s and 175 ft3/s and occurred in May 1998 and 

1999, respectively (fig. 31). Most of this variability was due 

to seasonal changes in irrigation rates. The crop data indicate 

that negligible irrigation occurs in December and January 

and that rates of irrigation withdrawals peak in May, reaching rates of 130 to 140 ft3/s. Agricultural withdrawals also 

accounted for most (80 percent) of the withdrawals occurring 

within the subregional study area during water years 1998-99. 

The remaining withdrawal categories (public supplies and 

self-supplied commercial and industrial withdrawals) showed 

a seasonal pattern of withdrawal rates similar to the agricultural withdrawals, but substantially less variable. The average 

monthly withdrawal for all of these less variable uses ranged 

from a minimum of 5 ft3/s in January 1998 to a maximum of 

15 ft3/s in May 1998.

The geographic distribution of ground-water withdrawals 

from the Upper Floridan aquifer in the subregional area is 

shown in figure 32. Most of the withdrawals occur in the 

Chiefland Limestone Plain of the Gulf Coastal Lowlands and 

the Central Highlands areas (fig. 3). These areas are typically 

underlain by well-drained soils that are favorable for agricultural uses and development of cities, towns, and homesteads. 

The largest withdrawals occur in the towns of Cross City, 

Trenton, Chiefland, and High Springs and in irrigated areas 

near Chiefland, Trenton, east of Manatee Springs, and southwest of Williston.

Ground-Water Hydrology  41
42  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Evaluation of Ground-Water and 

Surface-Water Exchanges Using 

Hydrologic Data

The interactions between the Upper Floridan aquifer and 

the Lower Suwannee and Lower Santa Fe Rivers represent an 

important process that affects the flow and water-level characteristics of these rivers. A key element in understanding these 

interactions is quantifying the magnitude of water exchanges 

across the river-aquifer interface and how they vary with time 

and location along these two rivers. A necessary first step for 

developing a more comprehensive understanding of processes 

that are affected by streamflows and water levels was to use 

hydrologic data to evaluate how ground- and surface-water 

exchanges along the Lower Suwannee and Lower Santa Fe 

Rivers vary in time and space along different river reaches.

Temporal Characteristics

Ground- and surface-water exchanges in the subregional 

study area vary across time scales that range from hours to 

decades and longer. Inferences about these temporal variations 

were made using data collected at long-term gaging stations 

and from miscellaneous measurements taken before and during 

the study. Streamflow data from the long-term gaging stations 

on the Suwannee River at Branford (map index no. 5, fig. 4), 

Santa Fe River near Fort White (map index no. 14, fig. 4), and 

Suwannee River near Wilcox (map index no. 7, fig. 4) indicate 

that the difference between the combined streamflow from the 

two upstream gaging stations (Branford and Fort White) and 

the downstream gaging station (Wilcox) was about 1,500 ft3/s 

for flows measured during climate years 1942-2000. (Climate 

years are defined by the year beginning on April 1 and ending 

on March 30 of the following year.) The difference (pickup) 

between the upstream and downstream flow in this reach 

(referred to as reach 1, fig. 11) represents about 15 percent 

of the long-term, average annual streamflow at the Wilcox 

gaging station (10,000 ft3/s). In about half of these years, the 

average annual pickup in this reach was between 1,200 and 

1,900 ft3/s, and the minimum and maximum annual pickup 

values were about 500 and 3,000 ft3/s, respectively (figs. 33 

and 34). Streamflow pickup can be used to estimate the amount 

of ground water discharged to this reach of the Lower Suwannee and Lower Santa Fe Rivers because: (1) direct runoff to this 

reach is minimal, and (2) changes in the amount of water stored 

within the river channels and floodplains (surface storage) are 

typically small or negligible over an annual averaging period, 

and therefore, should not substantially affect the annual pickup 

values. The accuracy of the pickup-derived estimates of groundwater discharge, however, is still affected by the uncertainties of 

the daily discharge data (from individual gaging stations) that 

are used to compute streamflow pickup rates.

Inspection of the time-series plots and scatter plots of 

annual pickup relative to streamflow at the Wilcox gaging 

station indicates that the magnitude of pickup in reach 1 has a 

significant (but weak) positive correlation with the streamflow 

measured at the Wilcox gaging station (fig. 35). Thus, small 

pickup values tend to occur in years with low flows, and large 

pickup values tend to occur in years with high flows. This 

relation is not surprising given that: (1) the annual flow of the 

Suwannee River near Wilcox is correlated with rainfall, and 

thus, recharge; and (2) year-to-year differences in the magnitude of this pickup are determined by year-to-year differences 

in recharge occurring within the contributing area to reach 1. 

The relation between streamflow and pickup, however, is 

subject to a fair amount of scatter because flow in the Suwannee River near Wilcox is more strongly related to upstream 

runoff entering the Suwannee and Santa Fe Rivers from 

outside of the subregional study area than to recharge occurring within the contributing area of this reach.

Analysis of the time series of the annual pickup values 

also indicates that there is a substantial amount of interannual 

correlation in streamflow pickup. Thus, even though annual 

streamflow pickup along reach 1 tends to increase as flow in 

the Suwannee and Santa Fe Rivers increases, there may be a 

lag in this response. For example, annual streamflows at the 

Wilcox gaging station increased sharply from climate years 

1963 to 1964, and then declined sharply from 1964 to 1968 

(fig. 34). The annual pickup values also began to increase 

(albeit less abruptly than the increase in streamflows) in 1963, 

but continued to increase in the two climate years following 

83°30’ 83°00’ 82°30’

GROUND-WATER

WITHDRAWAL, IN

CUBIC FEET

PER SECOND

EXPLANATION

Chiefland

High Springs

Trenton

Cross City

Williston

Manatee Springs

Suwannee

0 20 MILES

0 20 KILOMETERS

SUBREGIONAL MODEL

BOUNDARY

30°00’

29°00’

SUWANNEE

LAFAYETTE

DIXIE

LEVY

ALACHUA

MARION

COLUMBIA

TAYLOR

UNION

CITRUS

Suwannee River

River

Fe

Santa

30’

0 - 0.05

0.06 - 0.1

0.11 - 0.5

0.51 - 1

1.01 - 2.09

GILCHRIST

G u l f

o f

M e x i

c

o

Figure 32. Geographic distribution of ground-water withdrawals from 

the Upper Floridan aquifer during water years 1998-99.
Figure 33. Cumulative distribution of 

the median annual change in streamflow (streamflow pickup) in reach 1 

of the Lower Suwannee and Santa 

Fe Rivers. Location of river reach 1 is 

shown in fig. 11.

Figure 34. Time series of annual 

streamflow in the Suwannee River 

near Wilcox, Florida (map index no. 7 

in fig. 4), and the streamflow pickup 

in reach 1 of the Lower Suwannee 

and Santa Fe Rivers during 1941-2000. 

Location of river reach 1 is shown 

in fig. 11. USGS is U.S. Geological 

Survey.

Evaluation of Ground-Water and Surface-Water Exchanges Using Hydrologic Data  43

Figure 35. Relation between annual 

streamflow in the Suwannee River 

near Wilcox, Florida (map index no. 7 

in fig. 4), and the streamflow pickup 

in the Lower Suwannee and Santa 

Fe Rivers. Location of river reach 1 is 

shown in fig. 11.

500

1,000

1,500

2,000

2,500

3,000

3,500

MEDIAN ANNUAL STREAMFLOW IN THE SUWANNEE RIVER

NEAR WILCOX, FLORIDA, IN CUBIC FEET PER SECOND

MEDIAN ANNUAL STREAMFLOW PICKUP

0 2,000 4,000 6,000 8,000 10,000 12,000 14,000 16,000 18,000 20,000

IN REACH 1, IN CUBIC FEET PER SECOND

STREAMFLOW OR STREAMFLOW PICKUP,

IN CUBIC FEET PER SECOND

YEAR

1940 2000

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

1950 1960 1970 1980 1990

Median annual flow in the

Suwannee River near Wilcox, Florida

(USGS ID 02323500)

Median annual change in flow in Reach 1

500

1,000

1,500

2,000

2,500

3,000

3,500

PROBABILITY OF EXCEEDING A GIVEN LEVEL OF STREAMFLOW PICKUP

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

STREAMFLOW PICKUP, IN

CUBIC FEET PER SECOND
44  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

the peak annual streamflow in 1964. Additionally, the annual 

pickup increased by a factor of 2 from the trough (in 1963) to 

the peak (in 1966) in the annual pickup time series. This was 

substantially smaller than the change in the streamflows at 

Wilcox where the peak flow in 1964 was more than three times 

the flow in 1963. These interannual correlations arise because 

changes in the ground-water flow system occur more slowly 

than in the river system, and the effects of stresses on the 

ground-water system are smoothed over longer time periods.

Streamflow-pickup rates can also be used to evaluate 

variations in the magnitude of the ground- and surface-water 

exchanges over monthly and seasonal time scales. Although 

the median monthly pickup values for the 1942 to 2000 

period were similar for all calendar months, there was a 

general pattern of decreasing values from January to March, 

when the minimum monthly pickup of about 1,000 ft3/s 

occurred (fig. 36). This period of decreasing pickup values 

was followed by a period of increasing values from March to 

May, when the maximum monthly pickup of about 1,800 ft3/s 

occurred (fig. 36). This pattern appears to be associated with 

conditions that occur during the late winter to early spring 

flood period. The January to March period typically coincides 

with rising river levels associated with flooding. Ground-water 

discharge to reach 1 may be lower during this period because 

river levels are generally high relative to ground-water levels. 

From March to May, water levels in the rivers are typically 

receding from peak flood levels. Ground-water discharge to 

reach 1 may be higher during this period because river levels 

are low relative to ground-water levels.

 Rates of ground- and surface-water exchanges may not 

reflect the pattern of decreasing mean and median streamflow 

pickup rates from January to March followed by increasing 

rates from March to May (fig. 36) because changes in surface 

storage affect streamflow-pickup rates. Streamflow pickup is 

approximately equal to ground- and surface-water exchanges

minus the rate of change in surface storage. Therefore, groundwater discharge to reach 1 is typically greater than pickup 

during the January to March period because surface storage is 

increasing as river levels rise in the river channel and floodplains. Conversely, ground-water discharge to reach 1 is typically less than pickup during the March to May period because 

surface storage is decreasing as river levels decline in the river 

channel and floodplains. 

The effects of surface storage on streamflow pickup are 

even more pronounced over shorter time periods, such as 

within seasons or during shorter periods of rising or receding river levels preceding or following a peak river level. An 

attempt was made to account for surface storage effects at this 

time scale to evaluate the short-term changes in river-aquifer 

water exchanges before, during, and after flooding events. This 

was done by: (1) calculating the daily pickup occurring along 

the Suwannee River between the Branford and Wilcox gaging 

station (map index nos. 5 and 7, fig. 4) and Santa Fe River 

downstream from the Fort White gaging station (map index 

no. 4, fig. 4) during water years 1998-99; and (2) estimating 

daily ground- and surface-water exchanges in reach 1 by 

correcting the daily pickup calculations with estimates of the 

daily rate of change in the amount of water stored in the river 

channels and floodplains. This “corrected-pickup” estimate of 

river-ground-water exchange was computed as follows:

Qgw↔sw(t) = Qpickup(t) – Ssw(t) (4)

where

t is time in days;

Qgw↔sw is the average water exchange between the river 

reach and the aquifer on day t, in cubic feet per 

second;

Qpickup(t) is equal to the mean daily flow in the Suwannee 

river near Wilcox minus the sum of the mean daily 

flows of the Suwannee River at Branford and the 

Santa Fe River near Fort White on day t, in cubic 

feet per second; and

Ssw(t) is the rate of change in the amount of water stored 

in the river channels and floodplains on day t, in 

cubic feet per second.

(58) (58)

(58)

(58) (58)

(58)

(58) (58) (58)

(58) (58)

(58)

6,000

4,000

2,000

0

-2,000

-4,000

-6,000

MONTHLY MEAN STREAMFLOW PICKUP,

IN CUBIC FEET PER SECOND

JAN FEB MAR APR MAY JUNE JULY AUG SEPT OCT NOV DEC

(58)

EXPLANATION

SAMPLE SIZE–Years of

record

75th PERCENTILE+ –Or

largest value

1.5*IQR

75th PERCENTILE

MEAN

MEDIAN–50th percentile

25th PERCENTILE

25th PERCENTILE-1.5*IQR–Or

smallest value

OUTLIER

FAR OUTLIER

INTERQUARTILE RANGE (IQR)

Figure 36. Monthly 

mean streamflow 

pickup in reach 1 of 

the Lower Suwannee 

and Santa Fe Rivers. 

Location of river 

reach 1 is shown in 

fig. 11.
 The variable, Ssw(t), was estimated by computing the 

surface storage for each day, Ssw(t), then computing the difference between the surface storage on a given day from the 

surface storage on the previous day and dividing by 86,400 

seconds per day:

Ssw(t) = [Ssw(t) – Ssw(t–1)]/(86400) (5)

These corrected-pickup estimates of Qgw↔sw(t) should 

be interpreted with caution because they can be sensitive to 

errors in the daily flow estimates from the gaging stations 

and to errors in estimating the surface storage. This is especially true during periods of overbank flow, when errors in the 

streamflow or surface storage could be much larger than the 

estimated values of Qgw↔sw(t).

The estimates of the average rate of ground- and surfacewater exchanges along reach 1 (using eq. 4) during water years 

1998-99 were somewhat lower than the long-term average 

of 1,500 ft3/s during 1951-99. The net ground- and surfacewater exchanges averaged about 1,000 and 1,100 ft3/s during 

water years 1998 and 1999, respectively. The Qgw↔sw(t) data 

computed using equation 4 also indicated that aquifer-to-river 

leakage (ground-water outflow) rates into the study reach were 

as high as 7,600 ft3/s and followed the patterns in the surface 

storage, Ssw(t), hydrograph (fig. 37). The statistical significance of the above estimates of the calculated rates, however, 

are limited. For example, the 95-percent confidence interval for the average net ground- and surface-water exchange 

was from -1,500 to 3,600 ft3/s during water years 1998-99 

(where negative values indicate river-to-aquifer leakage). The 

uncertainty of the above-estimated value of the maximum rate 

was even greater (with a 95-percent confidence interval from 

1,300 to 13,900 ft3/s) because of uncertainty in estimating the 

Qgw↔sw(t) and Ssw(t) terms in equation 4.

More accurate estimates from equation 4 are possible 

if the analysis is limited to conditions when river levels 

are not changing rapidly. The longest period of relatively 

stable river levels along reach 1 occurred from November 

1998 to September 1999, when the corrected pickup estimate 

of average ground-water exchange was about 1,200 ft3/s, with 

a corresponding 95-percent confidence interval ranging from 

about 300 to 2,100 ft3/s.

The peak river-to-aquifer leakage (Qgw↔sw(t)< 0) rates 

were estimated to be about 3,100 and 1,900 ft3/s in water 

years 1998 and 1999, respectively (fig. 37). Again, these peak 

values are insignificant when compared with uncertainties in 

the underlying data that were used to compute them. The 95-

percent confidence intervals for peak river-to-aquifer leakage 

rates were about ±7,000 and ±3,400 ft3/s during water years 

1998 and 1999, respectively.

0

10,000

20,000

30,000

40,000

50,000

1998

O

FLOW, IN CUBIC FEET PER SECOND

N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

-10,000

0

5,000

10,000

15,000

-5,000

FLOW IN THE SUWANNEE RIVER–Near Wilcox, Florida

(map index number 7, figure 4)

CHANGE IN FLOW–Along reach 1 (pickup).

ESTIMATED GROUND-WATER INFLOW–To reach 1

(pickup minus river storage change).

FLOW INTO OR OUT OF CHANNEL OR

OVERBANK STORAGE–In reach 1.

Figure 37. Relation between streamflow, streamflow pickup, surface storage, and river-aquifer water exchanges. Location of river 

reach 1 is shown in fig. 11.

Evaluation of Ground-Water and Surface-Water Exchanges Using Hydrologic Data  45
46  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Temporal variations were evident over the course of tidal 

cycles. These variations were apparent in measurements taken 

at Manatee Springs during several spring-tide periods, when 

the difference between river levels at lower-low and higherhigh tides was greatest. Results from one set of measurements 

taken during May 1997 indicate that the median flow was 

about 160 ft3/s, and measured flow rates ranged from 152 to 

175 ft3/s (fig. 38). The flow of Manatee Springs (fig. 4) tended 

to increase during periods when the spring pool elevation was 

falling (in response to the ebbing stage in the Suwannee River) 

and to decrease when the pool elevation was rising. During 

this same period, the median flow from Fanning Springs 

(fig. 4) was about 80 ft3/s, and ranged from about 70 to 

90 ft3/s. The range in spring-flow variations at both sites was 

about ±10 ft3/s even though the range in spring pool elevation 

was about 0.25 ft higher at Manatee Springs, which indicates 

that smaller springs may have a wider range of flows during a 

tidal cycle, perhaps because there is less momentum to resist 

the variable stress imposed by the tidally induced fluctuations 

in spring-pool elevations. 

Spatial Characteristics

Hydrologic data collected before and during the study 

period can be used to make inferences about how ground- and 

surface-water exchanges might vary along different reaches 

of the Lower Suwannee and Lower Santa Fe Rivers. Two sets 

of hydrologic data were used for this purpose: (1) locations 

of springs and estimates of their median flow rates, and 

(2) measured streamflows at the upstream and downstream 

limits of selected river reaches. These data were also used to 

evaluate what fraction of the total ground- and surface-water 

exchange might be accounted for by known springs.

More than 50 springs in the subregional study area 

(fig. 2) contribute to the flow of the Lower Suwannee and 

Lower Santa Fe Rivers (Rosenau and others, 1977; Hornsby 

and Ceryak, 1998; Scott and others, 2004; fig. 2). Five springs 

can be considered first-order springs (average discharge 

greater than 100 ft3/s), and most of the remaining are secondorder springs (average discharge greater than 10 ft3/s). Nine of 

these springs and numerous unnamed springs contribute about 

350 ft3/s to the upper reaches of the Ichetucknee River, which 

drains the Santa Fe River at a point 7.1 mi upstream from the 

mouth of the Santa Fe River.

Spring-flow totals were computed for two river reaches 

and compared to the total average pickup estimated for these 

reaches. This calculation gives an estimate of how much 

of the total ground- and surface-water exchange is derived 

from known springs and how much is derived from unnamed 

springs or more diffuse exchanges. Two reaches were evaluated for this analysis (fig. 11): (1) reach 1 (as previously 

described) along the Santa Fe River downstream from the 

Fort White gaging station and along the Suwannee River from 

Branford to the Wilcox gaging station (this reach also includes 

the Ichetucknee River); and (2) reach 2 along the Santa Fe 

River from U.S. Highway 441 to the Fort White gaging 

station. For reach 1, the springs identified by Rosenau and 

others (1977) accounted for about 800 ft3/s or about 55 percent 

of the estimated 1,500 ft3/s net ground-water outflow during 

water years 1942-99. If the additional springs identified by 

Hornsby and Ceryak (1998) are included, then springs account 

for about 1,300 ft3/s or about 85 percent of the long-term 

average net ground-water outflow in this reach. For reach 2, 

the springs identified by Rosenau and others (1977) accounted 

for about 600 ft3/s or about 75 percent of the estimated 

800 ft3/s net ground-water outflow during water years 1942-71 

(the period of concurrent data for the two gaging stations that 

define the limits of this reach). If the additional springs identified by Hornsby and Ceryak (1998) are included, then springs 

account for about 700 ft3/s or about 90 percent of the longterm average net ground-water outflow in this reach. Data 

from reaches 1 and 2 indicate that springs are the dominant 

source of ground water to the Lower Suwannee and Lower 

Santa Fe Rivers.

140

150

160

170

180

FLOW, IN CUBIC

FEET PER SECOND

1.8

2.2

2.6

3.0

2.0

2.4

2.8

WATER LEVEL, IN FEET

ABOVE NGVD 1929

24-HOUR TIME, MAY 20-22, 1997

0000

20 21 22

0600 1200 1800 2400 0600 1200 1800 2400 0600 1200 1800 2400

WATER LEVEL

FLOW

Figure 38. Tidally induced changes in spring pool elevation and spring flow in Manatee Springs during May 1997.
Closer inspection of the spring-flow data reveals that 

spring flow is clustered along some reaches and more evenly 

distributed along other reaches. A substantial fraction of the 

ground-water outflow measured in reaches 1 and 2 is derived 

from clusters of springs. For example, the springs clustered 

around Ginnie Springs on the Santa Fe River just upstream 

from the gaging station near Fort White (fig. 2) account for 

about 40 percent of the long-term average net ground-water 

outflow to reach 2. Similarly, the Ichetucknee Springs group 

(fig. 2) accounts for about 25 percent of the long-term average 

net ground-water outflow to reach 1.

Another location of concentrated flow occurs in the reach 

of the Suwannee River between the gaging stations near Old 

Town and Wilcox (station indexes 8 and 7 at river miles 23.5 

and 33.5, respectively, fig. 11). The average spring discharge 

along this reach was 330 ft3/s (about 24 ft3/s per mile of river), 

and is derived from three springs (fig. 2): Fanning Springs 

(median discharge equal to 110 ft3/s), Little Fanning Springs 

(median discharge equal to 20 ft3/s), and Manatee Springs 

(median discharge equal to 210 ft3/s). The concentration of 

spring flow along this reach, although high, is smaller than 

that occurring in the previously described reaches of the Upper 

Ichetucknee where the median spring-flow contribution was 

about 100 ft3/s per mile of river, and in reach 1 of the Santa Fe 

River where the median spring-flow contribution was about 

95 ft3/s per mile of river.

Spring discharge along other reaches of the Lower 

Suwannee and Lower Santa Fe Rivers was lower than the 

above river reaches. The spring-flow contributions to these 

remaining reaches ranged from a minimum of 3.6 ft3/s 

per mile of river in the reach of the Suwannee River between 

Branford and the mouth of the Santa Fe River, to a maximum 

of 16 ft3/s per mile of river in the reach of the Suwannee River 

between Hart Springs (near river mile 43) and the gaging 

station near Wilcox (fig. 2).

Data collected during several periods of relatively 

steady streamflow also indicated that the reach of the Lower 

Suwannee River between the Branford gaging station and the 

point just upstream from Rock Bluff Springs (near the Bell 

gaging station, fig. 2) received little net ground-water outflow 

(excluding the contributions from the mouth of the Santa Fe 

River). The streamflow pickup (excluding the Santa Fe River) 

along this 20-mi reach ranged from -166 to 90 ft3/s during 

several periods (August 1996, August 1998, August 1999, and 

September 1999) of relatively steady streamflow. Streamflow 

pickup in the segments of this reach upstream and downstream 

from the Santa Fe River was also negligible or small during 

these periods. The measured change in streamflow in the reach 

of the Suwannee River between the Branford gaging station 

and the point just upstream from the mouth of the Santa Fe 

River generally ranged from -50 to 50 ft3/s, and the pickup in 

the reach downstream from the mouth from the Santa Fe River 

to just upstream from Rock Bluff Springs ranged from 0 to 

135 ft3/s.

Evaluation of Ground-Water and 

Surface-Water Exchanges Using a 

Hydrologic Model

Interactions between ground and surface water were 

evaluated using a hydrologic model that simulates groundwater flows and levels in the Upper Floridan aquifer, streamflows and levels in the Lower Suwannee and Lower Santa Fe 

Rivers, and the exchange of water between the aquifer and 

two river reaches. The hydrologic model consists of separate 

aquifer and river submodels that have been linked through the 

river leakage terms (in the conservation of mass equations of 

the submodels) to form a coupled ground- and surface-water 

flow model. The hydrologic model gives additional insight 

into how the Upper Floridan aquifer and Lower Suwannee and 

Lower Santa Fe Rivers interact and how this interaction might 

be affected by changes within the system and at the system 

boundaries. The subsequent sections describe the: (1) model 

construction and calibration of the coupled model; (2) model 

evaluation of ground- and surface-water exchanges during water 

years 1998-99; (3) model evaluations of the effects of various 

hypothetical water-withdrawal scenarios on streamflow in the 

Lower Suwannee River; and (4) limitations of the model.

Model Construction

The hydrologic models of ground- and surface-water 

flow were developed in two phases. Each model was first 

constructed by translating a conceptual model of a particular 

aspect of the flow system into a mathematical model. Following construction, the models were calibrated by adjusting 

model parameters within the range of uncertainty until the 

best possible agreement was obtained between measured and 

simulated water levels and flows.

The subsequent sections describe the construction of the 

models of ground-water flow, surface-water flow, and groundand surface-water interactions in the subregional study 

area. Construction of the models occurred in three phases: 

(1) construction of a ground-water flow model of the Upper 

Floridan aquifer; (2) construction of a surface-water flow 

model of the Lower Suwannee and Lower Santa Fe Rivers; 

and (3) linking the two models to construct a coupled groundwater and surface-water flow model.

Ground-Water Flow Model

An uncoupled, transient (unsteady-state), ground-water 

flow model was developed during this study. The model 

area is coincident with the subregional study area (fig. 1) 

and includes: (1) areas where the Upper Floridan aquifer 

contributes ground water to the Lower Suwannee and Lower 

Santa Fe Rivers; and (2) areas to the north and south of the 

Suwannee River where the aquifer contributes ground water 

to the Gulf of Mexico and to streams draining into the Gulf 

of Mexico (fig. 39). The model was used to simulate transient 

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  47
48  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Figure 39. Model grid and lateral boundary conditions for the subregional ground-water flow model.

ALACHUA

LEON

GRADY

MARION

G E O R G I A

F L O R I D A

SUWANNEE

LAFAYETTE

DIXIE

LEVY

GILCHRIST

COLUMBIA

TAYLOR

MADISON

HAMILTON

JEFFERSON

THOMAS

BROOKS

LOWNDES ECHOLS

CLINCH

WARE

CHARLTON

BAKER

UNION

BRADFORD

CITRUS SUMTER

WAKULLA

NASSAU DUVAL CLAY PUTNAM

30°

84° 83° 82°

29°

1 10 20 30 40 50 60 70 90 100 120 140

1-

10-

30-

40-

50-

60-

70-

80-

90-

100-

110-

120-

130-

140-

150-

160-

20-

80 110

C O L U M N S

R O W S

EXPLANATION

SPECIFIED HEAD

MODEL-CALCULATED HEAD

DRAIN PACKAGE CELL

RIVER PACKAGE CELL

STREAMFLOW ROUTING PACKAGE

CELL (uncoupled model) OR

BRANCH CELL (coupled model)

GENERAL-HEAD BOUNDARY

SUWANNEE RIVER WATER MANAGEMENT

DISTRICT BOUNDARY

G u l f o f M e x i c o

0 20 40 MILES

0 20 40 KILOMETERS

130

Suwannee River

S

R

anta Fe iver
ground-water flows and levels for each day during water years 

1998-99 and was developed to serve as the ground-water flow 

component (submodel) of the coupled model. The uncoupled 

model is identical to the ground-water flow submodel present 

in the coupled model, with the exception of the method used 

to represent the exchange of water between the rivers and 

the Upper Floridan aquifer. In the uncoupled version, water 

levels in the rivers were specified as input to the model. In the 

coupled version, water levels in the rivers were computed and 

output by the model.

Mathematical Basis and Approach

The MODFLOW computer program (McDonald and 

Harbaugh, 1988; Harbaugh and McDonald, 1996) was used 

to simulate ground-water flow within the Upper Floridan 

aquifer in the subregional study area. The program uses a 

finite-difference scheme to integrate the partial differential 

equation for three-dimensional, saturated ground-water flow 

under equilibrium (steady-state) or nonequilibrium (transient) 

conditions (McDonald and Harbaugh, 1988):

 ∂x

∂ Kxx∂x

∂h

⎝ ⎠ ⎛ ⎞

∂y

∂ Kyy∂y

∂h

⎝ ⎠ ⎛ ⎞

∂z

∂ Kzz∂z

∂h

⎝ ⎠ + + ⎛ ⎞ – W Ss∂t

∂h = , (6)

where

Kxx, Kyy and Kzz are hydraulic conductivity values along 

the x-, y-, and z-coordinate axes, in feet 

per day (which are assumed parallel to the 

major axes of hydraulic conductivity);

h is the hydraulic head at some point in the 

system, in feet;

W is a volumetric flux per unit volume of 

aquifer and represents sources or sinks of 

water (for example, wells, recharge, and 

leakage with rivers), in feet3/(feet3*day);

Ss is the specific storage of the aquifer at 

some point in the system, in feet-1; and

t is time, in days.

In this study, vertical flow within the Upper Floridan 

aquifer is assumed to be negligible in comparison to horizontal 

flow. Accordingly, ground-water flow was simulated using 

a two-dimensional (vertically averaged) representation of 

ground-water flow in which the term ∂z

∂ Kzz∂z

∂h

⎝ ⎠ ⎛ ⎞ is dropped 

from equation 6. The resulting system is also assumed to be 

isotropic (Kxx = Kyy) at a given point in the system) for lack of 

more detailed data indicating otherwise.

The exchange of water between rivers and the Upper 

Floridan aquifer is calculated as follows:

Q = Criv (Z – h), (7)

where

Q is the flow between the river and aquifer, in cubic feet 

per day;

Criv is the conductance of the connection between the river 

and aquifer, in feet squared per day;

Z is the water-surface elevation (stage) of the river, in 

feet; and

h is the hydraulic head (ground-water level) in the aquifer 

beneath the river, in feet.

Note that if Z > h then Q > 0 and the simulated flow direction 

will be from the river to the aquifer; if Z < h, then Q < 0

and the simulated flow direction will be from the aquifer to 

the river. For a given aquifer cell that is adjacent to a river, 

the value of Q calculated in equation 7 is added to all other 

sources and sinks (for example, well pumping or recharge) 

active in the cell, and this summation is used as the value of 

W in equation 6.

The ground-water flow model is constructed by: (1) using 

a grid to discretize the aquifer into many small units or cells; 

(2) formulating a ground-water flow equation for each cell 

with appropriate values of K, W, and S; and (3) specifying the 

appropriate values of flow, head, or head-dependent flows in 

cells along the model boundaries. These three steps result in 

a system of equations that is solved using the “preconditioned 

conjugate-gradient” method (Hill, 1990), which yields an 

estimate of hydraulic head and flow at every cell in the model.

Discretization and Model Boundaries

The ground-water flow model developed in this study 

employs a rectangular grid defined by 163 rows and 148 

columns (fig. 39), with a uniform spacing of 5,000 ft for the 

width of each row and column. One model layer (McDonald 

and Harbaugh, 1988, p. 2-3) is used in the model, so the model 

simulates two-dimensional, areal (but not vertical) movement 

of ground water in the Upper Floridan aquifer.

The boundary of the ground-water model along the Gulf of 

Mexico is defined by model cells (referred to herein as “coastal 

boundary” cells) that are in the Gulf and contiguous with the 

Florida coastline in the subregional study area (fig. 39). The 

ground-water level of each coastal boundary cell is fixed at a 

value 0 ft (which was approximately equal to NGVD 1929 in 

this area during the study period) for each model time step. 

Discharge from the Upper Floridan aquifer to the Gulf of 

Mexico is represented by the simulated flow between the coastal 

boundary cells (in which the ground-water level is fixed) and 

adjacent cells on the landward side of the coastline (in which 

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  49
50 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

ground-water levels are calculated by the model). This type of 

boundary was chosen so that discharge from the Upper Floridan 

aquifer could occur only in the near-shore areas. This is consistent with the previous discussion, indicating that the westward 

limit of the freshwater-saltwater interface (which represents a 

no-flow boundary for the ground-water flow system) is probably 

within 1 mi of the Gulf shoreline.

The northern and western boundaries of the model 

represent no-flow boundary conditions. The northern no-flow 

boundaries of the ground-water flow model are formed by 

ground-water flow lines that terminate in the Suwannee River 

at Branford (figs. 2 and 23) and originate in upgradient areas 

to the west and east. The western part of this northern boundary originates along the axis of the potentiometric high west 

of the Suwannee River in Lafayette County. At this point, 

the western, no-flow model boundary is formed by a groundwater flow line that follows the gradient of the potentiometric 

surface of the Upper Floridan aquifer southwest through Dixie 

County to the coastline of the Gulf of Mexico.

The eastern part of the northern no-flow boundary of the 

model is drawn by beginning on the Suwannee River in Branford (figs. 2 and 23) and following the reverse (upgradient) 

path of the flow line to a point that approximately coincides 

with the limits of the unconfined part of the Upper Floridan 

aquifer. At this point, a head-dependent flux or general-head 

boundary (McDonald and Harbaugh, 1988, p. 11-1) is established that is approximately coincident with, or just west of, 

the boundary between parts of the Upper Floridan aquifer that 

are unconfined and parts that are overlain by the intermediate 

confining unit (fig. 14). General-head boundaries function by 

calculating flow across the model boundary that is proportional to the difference between the model-calculated groundwater level in the model cell adjacent to the boundary and a 

user-specified ground-water level at another point outside of 

the model boundary. These user-specified ground-water levels 

were calculated by interpolating (in space and time) from 

a series of seven potentiometric surface maps of the Upper 

Floridan aquifer that represent points in time that defined 

the general shape of the ground-water level time series along 

this boundary during water years 1998-99. The actual flux of 

water is calculated by MODFLOW, which: (1) simulates the 

ground-water level at a boundary cell; (2) calculates the waterlevel difference between the active boundary cell and the 

user-specified water level at the upgradient cell outside of the 

model boundary; and (3) multiplies the water-level difference 

by the conductance of the Upper Floridan aquifer along the 

flow path between the two points. These conductance values 

were set equal to the transmissivity along the flow path multiplied by 5,000 ft (the width of one face of a model cell) and 

divided by the length of the flow path (in this case, the width 

of one face of a model cell, also 5,000 ft).

The general-head boundary transitions to a no-flow 

boundary near the intersection of the boundaries between Alachua, 

Levy, and Marion Counties (fig. 39). The no-flow boundary 

extends south to the highest point on the potentiometric “high” 

west of Rainbow Springs. At this point, the no-flow boundary 

is located along the flow path directed downgradient from the 

potentiometric high, terminating at the boundary along the 

coastline of the Gulf of Mexico.

Representing Sources and Sinks of Water

The sources and sinks used in the ground-water flow 

model are identical to those previously described in the 

“Ground-Water Hydrology” section. Various MODFLOW 

packages (McDonald and Harbaugh, 1988, p. 1-1) were used 

to represent recharge, well pumpage, and exchanges between 

the Upper Floridan aquifer and rivers, springs, and wetlands.

Recharge was represented in the ground-water flow 

model using the MODFLOW Recharge Package (McDonald 

and Harbaugh, 1988, p. 7-1). Recharge values were estimated 

for each cell using rainfall and pan evaporation data and the 

daily SMA algorithm (E.P. Weeks, U.S. Geological Survey, 

written commun., 1993) as previously described.

Ground-water withdrawals from wells were represented using the Well Package (McDonald and Harbaugh, 

1988, p. 8-1). Monthly ground-water withdrawals from 

October 1997 to September 1999 were estimated as previously 

described. Daily values for each well were then determined 

by dividing the monthly ground-water withdrawal for a given 

month by the number of days in that month.

The River Package (McDonald and Harbaugh, 1988, 

p. 6-1) and Streamflow-Routing Packages (Prudic, 1989) were 

used to represent exchanges between the Upper Floridan aquifer and the major rivers in the uncoupled ground-water flow 

model. Estimates of the water level of the river and riverbed 

conductance are required for each cell in the model grid as 

input for these packages. The water level at each grid cell was 

estimated by interpolating between the water levels at gaging 

stations for each day from October 1997 to September 1999. 

The Drain Package (McDonald and Harbaugh, 1988, p. 6-1) 

was also used to estimate discharge from selected streams and 

springs in the Waccasassa River network of streams, as well 

as the wetlands connected to streams draining coastal areas 

adjacent to the Gulf of Mexico.

 Representation of Hydraulic Properties

The Block-Centered Flow Package (McDonald and 

Harbaugh, 1988, p. 5-1) was used to represent hydraulic 

properties in the ground-water flow model. A confined layer 

type was specified and was considered appropriate for the 

subregional study area because the magnitude of ground-water 

level changes is generally small relative to the thickness of the 

aquifer (transmissivity changes little as water levels fluctuate). An alternative model was tested in which transmissivity 

was set equal to hydraulic conductivity, and then multiplied by 

the saturated thickness of the freshwater section of the Upper 

Floridan aquifer and surficial sediments; however, this model 

failed to improve the quality of the ground-water flow models. 

Geographic variations in transmissivity were represented by 

assigning different values of transmissivity to groups of cells 
(transmissivity zones) in different areas. For example, the 

cells under the potentiometric surface high in Gilchrist County 

were treated as a single transmissivity zone with a smaller 

value of transmissivity than in the surrounding areas, which 

were treated as separate transmissivity zones. Specific yield 

estimates were required for the transient subregional model 

and were assigned a value of 0.2.

Surface-Water Flow Model

An uncoupled model of open-channel flow in the Lower 

Suwannee and Lower Santa Fe Rivers was constructed as a 

preliminary step to speed the development of the final coupled 

model of the subregional study area. The coupled model 

requires more extensive computer time than the uncoupled 

model, and therefore, much more testing was possible during 

calibration than would have otherwise been possible. This 

open-channel flow model was not coupled with a groundwater flow model, and thus, is not capable of calculating 

exchanges between the rivers and the Upper Floridan aquifer. 

Accordingly, exchanges with the ground-water system were 

estimated for selected periods and provided as input to the 

model. The subsequent sections describe the mathematical 

basis of the model, how the two rivers were represented in 

the mathematical model (schematic and discretization), and 

how channel and floodplain hydraulic characteristics were 

represented in the model.

Mathematical Basis and Approach

The BRANCH mathematical model (Schaffranek and 

others, 1981; Schaffranek, 1987) was used to simulate openchannel flow in selected reaches of the Lower Suwannee and 

Lower Santa Fe Rivers. The program uses a finite-difference 

scheme to integrate the de Saint Venant equations (Cunge and 

others, 1980), which are equations of conservation of mass 

(continuity) and conservation of momentum that describe 

unsteady, one-dimensional flow in open channels. The 

continuity equation is:

+ = 0

∂

∂

+

∂

∂

q x

Q

t

z B ; (8)

where

B is the channel top width, in feet;

z is the water-surface elevation in the channel, in feet;

t is the elapsed time since the beginning of the 

simulation, in seconds;

Q is the discharge in the channel, in cubic feet per second;

x is the distance measured along the channel centerline, 

in feet; and

q is the lateral outflow from, or inflow to, the channel, in 

cubic feet per second per foot of river channel.

The conservation of momentum equation is:

( ) 0cos 21 2

3 3/42

2

2 + − = ∂

∂ + ∂∂ + ∂∂ + ∂∂ α ξ Ua gAB QQ

RA

k

x

Z

x

A

gA

BQ

x

Q

gA

BQ

t

Q

gA

 (9)

where

g is the acceleration of gravity, in feet per second squared;

A is the submerged cross-sectional area of the channel, in 

feet squared;

β is the momentum or Boussinesq coefficient (dimensionless), which compensates for the nonuniform velocity 

distribution in the channel;

k is the flow-resistance coefficient of the channel, in 

seconds2/feet2/3;

R is the hydraulic radius of the channel, in feet;

ξ is a dimensionless wind-resistance coefficient; and 

Ua is the wind velocity, in feet per second, making an angle, 

α, with the positive x-axis.

The open-channel flow model is developed by: (1) defining the 

channel centerline and discretizing it into smaller segments; 

(2) discretizing the time to be simulated by the model into 

smaller increments of time (time steps); (3) specifying the 

values of flow or water levels at upstream and downstream 

boundaries at the beginning and end of each of these time 

steps; and (4) formulating the continuity and momentum 

equations by specifying appropriate values for the coefficients 

and independent variables in the continuity and flow 

equations.

 Step four may also include specifying the flow at one 

or more internal locations of the model for each time step to 

simulate streamflow gains or losses resulting from groundand surface-water exchanges or contributions from tributaries. 

These four steps result in a system of equations that are solved 

using a weighted, four-point, implicit-solution technique 

(Schaffranek and others, 1981; Schaffranek, 1987), which 

yields an estimate of water level and discharge for each time 

step at the ends of each segment in the model.

Schematic and Discretization

 The streamflow model developed for this study simulates 

53 mi of the Suwannee River between the gaging stations 

at Branford at river mile 76.1 (map index no. 5, fig. 11) and 

near Old Town at river mile 23.5 (map index no. 8, fig. 11), 

and simulates about 18 mi of the Santa Fe River between the 

gaging station near Fort White at river mile 18.3 (map index 

no. 14, fig. 11) and the mouth of the Santa Fe River. The 

model could not be extended to include the Suwannee River 

downstream from the gaging station near Old Town because a 

continuous set of stage data for water years 1998-99 was not 

available at any of the downstream gaging stations.

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  51
52  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Discretization of the simulated reaches of the Suwannee 

and Santa Fe Rivers was accomplished by first overlaying a map 

of the grid from the previously described ground-water flow 

model on a map of the centerline of the Suwannee and Santa 

Fe Rivers. The rivers are divided into segments at the points of 

intersection between the river centerlines and the ground-water 

model grid. This step was necessary because the software that 

links the ground-water flow and streamflow models requires 

that each river segment be assigned to only one aquifer model 

grid cell (Swain and Wexler, 1996). More segments were added 

in some instances to minimize the differences in length between 

the longest and shortest segments in the overall network of 

segments. Other segments were added so that points of interest 

(such as the confluence between the Suwannee and Santa Fe 

Rivers, gaging stations, and other flow measurement locations) 

within the network would coincide with the end of a segment. 

This approach ensures that simulated values of streamflow and 

water levels would be available for comparison with points 

where these values have been observed or estimated from 

measurements in the field (the ends of segments are locations 

where the model simulates river levels, flow, average velocity, 

channel top width, and submerged cross-sectional areas). This 

process of spatial discretization resulted in a network of 278 

river segments that range from 480 to 1,900 ft in length. Implementing the BRANCH model also requires grouping contiguous 

segments into “branches” to improve the efficiency of calculations (Schaffranek and others, 1981). Accordingly, the 278 river 

segments were grouped into 71 branches, with each containing 

2 to 4 segments.

Several time periods were simulated during development of the model. These time periods were generally about 

1 month in duration for the uncoupled simulations that were 

used to refine the initial estimates of the channel roughness 

values and cross-sectional geometry of the segments in the 

model. After the calibration phase of the uncoupled model 

was completed, the BRANCH (river) model was coupled with 

the MODFLOW (aquifer) model and simulations were made 

from October 1, 1997, to September 30, 1999. For both the 

uncoupled and coupled models, the simulation periods were 

discretized into 15-minute time intervals. Boundary-value data 

were obtained from hourly streamflow estimates at the gaging 

stations on the Suwannee River at Branford and the Santa 

Fe River near Fort White, and from 15-minute interval stage 

measurements taken at the gaging station on the Suwannee 

River near Old Town. The necessary 15-minute interval data 

for the upstream flow boundaries were obtained by interpolating between the hourly flow data obtained from the Branford 

and Fort White gaging stations.

Hydraulic Characteristics of the River Channel and 

Floodplain

The final step in developing the uncoupled, open-channel 

flow model was defining the geometry and roughness of the 

river channel and floodplain. As previously mentioned, most 

of the river channel and floodplain geometry and roughness 

data for the present study were obtained from digital 

(computer) input files that were used to develop a watersurface profile model for an earlier flood study conducted 

by the U.S. Army Corps of Engineers (U.S. Army Corps of 

Engineers, 1989; John Good, Suwannee River Water Management District, written commun., 1996). Some differences 

probably exist between the digital input files obtained from the 

U.S. Army Corps of Engineers (USACE) for use in the present 

study and the input files that were used in the final version of 

the water-surface profile model from the earlier flood study 

by the USACE. For example, numerous fields in the input 

files obtained from the USACE have erroneous values of 

Manning’s roughness coefficient (equal to 99), which indicates 

that these files were probably working “templates” for input 

files used to calibrate the water-surface profile model. For 

this reason, the digital files obtained from the USACE were 

used only as a starting point for calibrating the uncoupled, 

open-channel flow model in the present study. Other channel 

geometry data, including field measurements (taken during the 

present study) and discharge measurements notes (containing 

depth and water-level data), were also obtained for a few sites.

Both sources of data were reformatted for input to the 

FEQUTL computer program (Franz and Melching, 1997). This 

program uses the geometry and roughness data to generate 

hydraulic tables that specify values of the hydraulic properties 

(such as depth, area, top width, and conveyance) at different 

water-surface elevations at individual cross sections along the 

river system. A hydraulic table was generated for each cross 

section where channel and floodplain geometry data were 

available. Hydraulic tables for the cross sections at the ends 

of the river segments used in the BRANCH model were then 

generated by interpolating between the sections with geometry 

and roughness data using the FEQUTL XSINTERP command.

Coupled Ground-Water and Surface-Water 

Flow Model

The final phase of the model construction process was 

to construct the coupled model to simulate ground-water flow 

in the Upper Floridan aquifer, open-channel flow in selected 

reaches of the Lower Suwannee and Lower Santa Fe Rivers, 

and the exchange of ground water and surface water between 

the Upper Floridan aquifer and both rivers. Development of 

the coupled model makes it possible to simultaneously simulate changes in river stage and flow and ground-water levels 

and flow in response to changing stresses on the river-aquifer 

system.

The MODBRANCH computer program (Swain and 

Wexler, 1996) was used to simulate water levels and flows 

in the Lower Suwannee River, Lower Santa Fe River, and 

contiguous Upper Floridan aquifer. This program also simulates the dynamic exchange of water between these two rivers 

and the aquifer, using Darcy’s law to compute the leakage 

(eq. 8) between the river channel and aquifer (Swain and 

Wexler, 1996, p. 4):
B(Z h) b

K

q − ′

′ = , (10)

where

b

K

′

′ is the leakage coefficient of the river-aquifer connection, 

in days-1 (the hydraulic conductivity, K′, in feet per day, 

divided by the flow path length, b′ , in feet);

B is the river topwidth, in feet;

Z is the river stage, in feet; and

h is the hydraulic head (ground-water level) in the aquifer 

adjacent to the river, in feet.

MODBRANCH consists of modified versions of MODFLOW 

(McDonald and Harbaugh, 1988; Harbaugh and McDonald, 

1996) and BRANCH (Schaffranek and others, 1981). These 

modifications: (1) contain mechanisms for using MODFLOWcalculated ground-water heads in equation 10; (2) incorporate 

results of equation 10 into the continuity equation (eq. 8) 

in BRANCH and the ground-water flow equation (eq. 6) 

in MODFLOW; and (3) account for the different time-step 

lengths that typically are used when applying MODFLOW 

and BRANCH, especially with regard to maintaining 

consistency in the mass balances calculated by each of the two 

submodels (Swain and Wexler, 1996, p. 2). Accommodating 

different time-step lengths was necessary because changes in 

streamflow typically occur over minutes and hours, whereas 

changes in aquifer flow typically occur over minutes, days, or 

months (Swain and Wexler, 1996). Therefore, MODBRANCH 

allows multiple BRANCH time steps to occur during a given 

MODFLOW time step or stress period (Swain and Wexler, 

1996). This is accomplished by: (1) running MODFLOW for 

one stress period; (2) interpolating the ground-water heads 

for the starting and ending times of each BRANCH time step; 

(3) formulating and solving the BRANCH model equations 

for each time step; (4) averaging the leakage rates calculated 

for all river segments in each MODFLOW aquifer cell over 

the MODFLOW stress period; and (5) passing these average 

leakage rates back to MODFLOW. Consistent mass-balance 

results are obtained by iterating between MODFLOW and 

BRANCH (repeating steps 1 to 5) until the simulated water 

levels in the river and aquifer have converged to stable values.

Note that equation 10 is analogous to equation 7 used 

in the uncoupled model. The primary difference is that river 

stage, Z, is simulated (calculated) by the model in equation 

10, unlike equation 7, which assumes that the stage is known. 

Therefore, the coupled model makes it possible to evaluate 

changes in river stage that result from changes in recharge 

rates, ground-water pumping, or rates of upstream runoff into 

the simulated river system.

Model Calibration

Calibration of the simulation models was performed in 

two steps. In the first step, the uncoupled subregional groundwater flow model and the uncoupled surface-water flow 

model were calibrated independently. In the second step, the 

uncoupled ground- and surface-water flow models that were 

calibrated in step one were linked to form a coupled model of 

ground water and surface water.

Uncoupled Ground-Water Flow Model

Calibration of the uncoupled ground-water flow model 

was accomplished primarily by adjusting the conductive 

properties used in the model in an effort to optimize the correspondence of measured and simulated ground-water levels and 

streamflows at locations where measured data were available 

(figs. 4 and 27). All of these conductive properties depend 

on the hydraulic conductivity and thickness of different parts 

of the aquifer. In the uncoupled ground-water flow model 

constructed for the present study, the conductive properties include aquifer transmissivity, riverbed conductance, 

and general-head boundary conductance (McDonald and 

Harbaugh, 1988; Harbaugh and McDonald, 1996).

Most of the ground-water model calibration effort was 

devoted to determining the values of aquifer transmissivity 

parameters, which are areas (zones) with unique values of 

transmissivity. Early versions of the uncoupled ground-water 

flow model attempted to simulate the ground-water flow 

system using only two parameter values: (1) a low transmissivity value used in two zones corresponding to the potentiometric high areas under the Waccasassa Flats (in Gilchrist 

County) and in southern Levy County; and (2) a higher transmissivity value in the rest of the subregional study area. These 

versions yielded promising model fits in the low transmissivity 

zones but poor fits in the remaining area. Subsequent efforts 

attempted to improve the model fit by subdividing this latter 

area into a few additional zones, using the conceptual model 

and discrepancies between simulated and measured groundwater levels as a guide for delineating the boundaries of the 

new zones. For example, zones were added in areas along the 

Gulf Coast, in areas paralleling the rivers, and areas east of the 

Waccasassa Flats, where data indicated that the transmissivity 

values were probably higher than in adjacent areas.

A map of the transmissivity zones and the values used 

in the final version of the uncoupled ground-water flow 

model is shown in figure 40. Values for transmissivity and 

other parameters are given in tables 4 and 5. The values were 

obtained using a least-squares regression approach (Hill, 1998; 

Doherty, 2000) which was implemented using the parameter 

estimation (PEST) optimization software (Doherty, 2000). No 

attempt was made to constrain the value that could be obtained 

from the optimization software. Observation weights were 

calculated using the methods described by Hill (1992; 1998). 

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  53
54  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

For transmissivity parameters 1 to 10, 95-percent confidence 

intervals are given in table 4 and composite and composite-scaled sensitivities are given in table 6. Transmissivity 

parameters 12 to 16 do not have confidence intervals or sensitivities because their values were fixed during the latter stages 

of model calibration when the model became insensitive to 

these parameters and the regression began to have problems 

converging. The values used for these “fixed parameters” are 

consistent with the values obtained in previous calibrations 

when the parameters were estimated using regression analysis. 

The parameter value and confidence interval for parameter 11 

(the multiplier used to estimate riverbed conductance values as 

part of the river and streamflow routing packages ) are given in 

table 4, and composite sensitivities for this parameter are given 

in table 6.

Confidence intervals for each of the model parameters 

were relatively tight, indicating that the estimated values 

were well resolved (table 4). This inference, however, should 

be taken with some caution because confidence intervals 

were estimated using a linearity assumption that may not be 

valid for the full width of the confidence limits (Doherty, 

2000, p. 5-21). Moreover, the parameter values depend on 

the delineation of the parameter zone boundaries, which are 

also subject to uncertainty. Because the parameter confidence 

intervals were relatively narrow, correlations between parameters did not seem to be a problem. The absolute values of 

the correlation coefficients were less than 0.95 for all of the 

possible combinations of parameters. The highest correlations 

were -0.85 between transmissivity parameters 2 and 10, -0.90 

between parameters 4 and 8, -0.84 between parameters 5 ad 6, 

and -0.82 between parameters 3 and 10.

Santa Fe River

Suwannee River

COLUMBIA

SUWANNEE

DIXIE

MARION

UNION

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

30°

83° 82°

29°

0 20 MILES

0 20 KILOMETERS

G u l f o f M e x i c o

EXPLANATION

SUBREGIONAL MODEL

BOUNDARY

PARAMETER NUMBER

TRANSMISSIVITY–In square

feet per day

4

142,000

1

15,200

10

1,540,000

7

596,000

13

325,000

2

12,900

8

1,770,000

14

9 6,000,000

1,690,000 3

88,700

6

437,000

4

142,000

4

142,000

12

3,000

16

18,000,000

5

113,000

2

12,900

15

6,000,000

Figure 40. Calibrated transmissivity distribution from the uncoupled ground-water flow model.
Table 4. Estimated parameter values and 95-percent confidence limits from the uncoupled ground-water 

flow model.

[Parameter numbers for transmissivity parameters correspond to the map index numbers for the transmissivity zones 

shown in fig. 41. Parameter label refers to the parameter names that are used in the computer input and output files for the 

Parameter Estimation (PEST) program (Doherty, 2000). Transmissivity parameter values and confidence limits are reported 

in units of feet squared per day, and the riverbed conductance multiplier parameter value and confidence limits are reported 

in units of feet per day]

Parameter type Parameter 

number

Parameter

label Estimated value

95-percent confidence limits

Lower limit Upper limit

Transmissivity 1 t2e4w 15,206.9 14,866.9 15,554.6

Transmissivity 2 t2e4t 12,885 12,763.8 13,007.4

Transmissivity 3 t6e4w 88,709.6 87,082.8 90,366.8

Transmissivity 4 t6e4i 142,058 139,122 145,055 

Transmissivity 5 t1e5w 112,513 109,412 115,700

Transmissivity 6 t5e5 436,512 366,522 519,867

Transmissivity 7 t5e5c 596,010 575,485 617,268

Transmissivity 8 t5e5wc 1.767649 × 106 1.657172 × 106 1.885491 × 106

Transmissivity 9 t1e6r 1.692817 × 106 1.645372 × 106 1.741630 × 106

Transmissivity 10 t2e6w 1.544231 × 106 1.487747 × 106 1.602860 × 106

Riverbed conductance

 multiplier

11 srpc1 807.971 644.570 1,012.79

Table 5. Specified parameter values from the uncoupled ground-water flow model.

[Parameter numbers for transmissivity parameters correspond to the map index numbers for the 

transmissivity zones shown in fig. 41. Parameter label refers to the parameter names that are used in 

the computer input and output files for the Parameter Estimation (PEST) program (Doherty, 2000). 

Transmissivity parameter values are reported in units of feet squared per day. General-head boundary 

and riverbed conductance values are reported in units of feet squared per day. Specific yield values are 

dimensionless]

Parameter type Parameter 

number

Parameter 

label Fixed value

Transmissivity 12 t5e3 3,000

Transmissivity 13 t1e5c 325,000

Transmissivity 14 t2e6 6.0 × 106

Transmissivity 15 t5e6 6.0 × 106

Transmissivity (of Ichetucknee Trace, upgradient

 from Ichetucknee River Headsprings)

16 tiche 1.8 × 106

Conductance of general-head boundary 17 ghb2 6.0 × 106

Conductance of general-head boundary 18 ghb3 6.0 × 106

Riverbed conductance 19 riv1 2.0 × 106

Riverbed conductance (upper reach of the

 Ichetucknee River that contains the Ichetucknee

 Springs Group)

20 rivich 8.5 × 106

Specific yield 21 sy1 0.2

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  55
56  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

The model was most sensitive to transmissivity 

parameters 2 (composite sensitivity of 24) and 4 (composite 

sensitivity of 15), and least sensitive to the riverbed conductance parameter 11 (composite sensitivity of 0.9) and transmissivity parameter 6 (composite sensitivity of 1.6) as noted 

in table 6. Generally, the sensitivity of the model to a given 

parameter was a function of the number of observations in that 

zone and the proximity of a head-dependent flux or constanthead boundaries. For example, the most sensitive transmissivity parameters contained either numerous observation wells 

or a few wells with a high frequency of data collection. The 

least sensitive transmissivity parameters, such as parameter 6, 

contained only a few wells with limited data and were close 

to the rivers or the eastern general-head boundary. Higher 

sensitivities result in more accurate parameter estimates, and 

lower sensitivities result in less accurate parameter estimates; 

however, even the least sensitive parameters were sensitive 

enough to have well-resolved values.

Analysis of the model residuals indicates relatively good 

correspondence between the simulated and measured groundwater levels and streamflows. The average ground-water level 

residual was 0.2 ft, and the 10th, 25th, 50th, 75th, and 90th 

percentiles of the residuals were -3.0, -1.5, 0.1, 1.8, and 3.6, 

respectively. The minimum ground-water level residual was 

-24 ft and the maximum residual was 11 ft. The estimation of 

this minimum residual could be improved by increasing the 

transmissivity of part of the northern Waccasassa Flats potentiometric high surrounding well s291 (figs. 18 and 27). This 

was not done, however, because only one head observation 

was available at well s291.

Time series of measured and simulated ground-water 

levels are shown for selected wells near the Lower Suwannee 

River (fig. 41). The time series of measured and simulated 

ground-water levels in other wells are essentially the same as 

those in the coupled model, which is discussed later.

The spatial distribution of ground-water level residuals 

during high and low water-level periods are shown in figures 42 

and 43, respectively. Spatial trends are largely absent from the 

data, with the possible exception of an area in central Levy 

County during a high water-level period ( fig. 42). During this 

period, the simulated ground-water levels in a cluster of wells 

in central Levy County are 2 to 9 ft higher than measured 

ground-water levels. The higher levels in this area seem to 

be an artifact of the initial conditions used in the uncoupled 

model, and are not present in the final coupled model.

Time series of measured and simulated daily mean streamflows in the Suwannee River near Wilcox are shown in figure 44. 

Streamflow was simulated relatively well, reproducing the pattern 

Table 6. Values of composite and composite-scaled parameter sensitivities for the uncoupled 

ground-water flow model. 

[Sensitivities measure the amount of change in the model input for a given change in the value of a parameter 

(see fig. 27 for well locations). Parameter numbers for transmissivity parameters correspond to the map index 

numbers for the transmissivity zones shown in fig. 40. Parameter label refers to the parameter names that are 

used in the computer input and output files for the Parameter Estimation (PEST) program (Doherty, 2000). 

Composite-scaled sensitivities indicate the total amount of information provided by the observations for a 

given parameter (Hill, 1998). Composite sensitivities are equal to the composite-scaled sensitivity divided by 

the log10-transformed parameter value. Transmissivity parameter values are reported in units of feet squared 

per day. The riverbed conductance multiplier value is reported in units of feet per day. Composite sensitivity 

values are reported in units of log10 (feet squared per day) for transmissivity parameters, and in units of log10

(feet squared per day) for the riverbed conductance parameter. All composite-scaled sensitivity values are 

dimensionless]

Parameter 

type

Parameter 

number

Parameter 

label Value Composite sensitivity

Compositescaled 

sensitivity

Transmissivity 1 t2e4w 15,206.9 6.4 27

Transmissivity 2 t2e4t 12,885 24 99

Transmissivity 3 t6e4w 88,709.6 12. 59

Transmissivity 4 t6e4i 142,058 15 79

Transmissivity 5 t1e5w 112,513 8.2 41

Transmissivity 6 t5e5 436,512 1.6 9.1

Transmissivity 7 t5e5c 596,010 4.8 28

Transmissivity 8 t5e5wc 1.767649 × 106 4.4 27

Transmissivity 9 t1e6r 1.692817 × 106 5.9 37

Transmissivity 10 t2e6w 1.544231 × 106 8.8 55

Riverbed conductance

 multiplier

11 srpc1 807.971 0.9 2.5
5

10

15

20

25

ELEVATION, IN FEET ABOVE NGVD 1929

0

5

10

15

20

0

5

10

15

20

5

10

15

20

25

1998

O N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

ELEVATION, IN FEET ABOVE NGVD 1929

Well t059

Well s331

Well s330

Simulated Well s315

Measured

Figure 41. Time series of measured ground-water levels and ground-water levels that were simulated with the ground-water flow 

model, October 1997 to September 1999 (location of wells s315, s330, s331, and t059 are shown in fig. 27).

of fluctuations in measured streamflow in this reach. The mean 

residual flow in this reach was about 300 ft3/s, which represents 

about 3 percent of the average annual flow and about 20 percent of 

the average annual ground-water discharge to this reach. The mean 

residual of the simulated flows in the Santa Fe River upstream 

from the gaging station near Fort White (map index no. 14, fig. 11) 

was 150 ft3/s, which represents about 20 percent of the mean 

ground-water discharge to this reach.

Uncoupled Surface-Water Flow Model

Calibration of the uncoupled model of surface-water flow 

in the Lower Suwannee and Lower Santa Fe Rivers primarily 

consisted of adjusting the channel and floodplain roughness 

parameter. This parameter was adjusted until the simulated 

river water levels and flows matched those that were measured 

in May and August 1997, August 1998, and September 1999. 

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  57
58  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Flow measurements during these periods were obtained using 

acoustic Doppler current profilers (ADCPs) that were operated 

nearly continuously for 10 to more than 48 hours at many of 

the measured sites. Data from these measurements were used 

to estimate ground-water inflow along the Lower Suwannee 

and Lower Santa Fe Rivers. These data were then used to 

represent ground-water inflow to both rivers in the uncoupled 

surface-water flow model, by specifying them as inflows to 

selected cross sections in the model.

Calibrated roughness values for the Suwannee River 

were similar to those in the model input files obtained from 

an earlier study by the U.S. Army Corps of Engineers (1989). 

The within-channel values of the roughness parameter, represented as Manning’s n coefficient (Chow and others, 1988), 

varied from 0.027 to 0.0385 in the uncoupled model developed for the present study, compared with values of 0.030 to 

0.035 in the USACE model input files. Overbank (floodplain) 

roughness values were identical for the two models, except 

for the reach of the Suwannee River upstream from river mile 

60.31 (fig. 11), where the uncoupled model in this study had a 

value of 0.15, compared with the value of 0.20 in the USACE 

input files.

Differences between the models were slightly greater for 

the Lower Santa Fe River. Downstream from river mile 19 

(fig. 11), the within-channel roughness value was 0.025 for 

the uncoupled model in this study compared with the value 

of 0.045 in the USACE model input files. Upstream from 

this reach, the within-channel roughness value was identical 

(0.035) in both models. The overbank roughness value was 

0.15 (downstream and upstream) for the model used in this 

study, compared with values of 0.28 (downstream) and 0.20 

(upstream) in the USACE model input files.

Some changes in the channel geometry data in the 

USAC model input files were needed during calibration of 

the uncoupled surface-water flow model to more accurately 

reflect field conditions and improve simulated river water 

levels and flows. For the Santa Fe River, most of the channel 

geometry changes were made in the reach between the gaging 

stations near Hildreth (map index no. 16, fig. 4) and at the 

mouth of the Ichetucknee River. These changes were made to 

reflect observations near the Hildreth gaging station, where the 

channel elevation was about 7 ft deeper than that indicated in 

the USACE model input files, and to improve the simulation 

of stage in this reach. Changes were also made: (1) upstream 

near river mile 13 (fig. 11) to reduce the influence of one 

Figure 42. Spatial distribution of ground-water level residuals from the 

ground-water flow model during a high water-level period.

Figure 43. Spatial distribution of ground-water level residuals from the 

ground-water flow model during a low water-level period.

30°00’

29°00’

30’

0 20 MILES

0 20 KILOMETERS

10

SIMULATED MINUS MEASURED 0 (Unleveled well)

SIMULATED MINUS MEASURED 0 (Leveled well)

SIMULATED MINUS MEASURED 0 (Unleveled well)

SIMULATED MINUS MEASURED 0 (Leveled well)

GROUND-WATER LEVEL–In the Upper Floridan aquifer.

Values in feet above NGVD 1929. Contour interval is 10 feet.

Interpolated from measurements taken in September 1999

<

<

≥

≥

EXPLANATION

LAFAYETTE

DIXIE

LEVY

GILCHRIST

ALACHUA

MARION

COLUMBIA

TAYLOR

UNION

83°30’ 83°00’ 82°30’

CITRUS

SUWANNEE

G u l f o f M e x i c o

80

70

60

50

40

30

20

10

20 10

70

60

40

30

20 10

50

40

30

50

10

20

3040

50

50

70

60

50

40

30

80

6.2

1.3

4.1

0.4 1.9

1.6 0.1

0.0

6.1 5.8

3.9

-5.0

-0.5

-4.8

-4.0

-5.2

-0.5 -0.5

-7.5

-0.3

-2.8

-1.8

-7.1

-11.8

-5.4

-5.0 -8.2

-1.0

-4.0

30°00’

29°00’

30’

0 20 MILES

0 20 KILOMETERS

LAFAYETTE

DIXIE

LEVY

GILCHRIST

ALACHUA

MARION

COLUMBIA

TAYLOR

UNION

83°30’ 83°00’ 82°30’

CITRUS

SUWANNEE

G u l f o f M e x i c o

40

10

20

30

40

50

60

70

80

20

30

40

50

60

80

60

60

50

70

-4.1

0.2

0.2

7.0

9.1

-2.5

-1.1

-3.5

-11.0

2.3

1.6

-6.9

-1.7

3.4

9.1 3.2

3.2

2.1

2.5

5.2

3.0

1.3

1.8 0.5 0.3

7.3

1.1

-0.6

-0.7

-1.1

-1.4

-1.1

-0.9

1.7

4.4

10

SIMULATED MINUS MEASURED 0 (Unleveled well)

SIMULATED MINUS MEASURED 0 (Leveled well)

SIMULATED MINUS MEASURED 0 (Unleveled well)

SIMULATED MINUS MEASURED 0 (Leveled well)

GROUND-WATER LEVEL–In the Upper Floridan aquifer.

Values in feet above NGVD 1929. Contour interval is 10 feet.

Interpolated from measurements taken in March 1998

<

<

≥

≥

EXPLANATION
section that may not have represented the cross sections in 

this reach; and (2) near the low-water shoals just downstream 

from the Fort White gaging station (map index no. 14, fig. 11) 

based on depth measurements taken on the shoals during this 

study. For the Suwannee River, the channel geometry used 

in the uncoupled surface-water flow model was identical to 

that of the USACE model input files, except for a short reach 

near river mile 62 (fig. 11) where the deepest parts of the 

cross sections were lowered to reflect the deeper elevations of 

sections just upstream and downstream from this reach.

To simplify calibration of the uncoupled surface-water 

flow model, the Suwannee and Santa Fe Rivers were calibrated separately. In both instances, streamflow was specified 

as the upstream boundary condition and stage was specified 

as the downstream boundary condition. Additionally, the 

Suwannee River was calibrated in a “downstream” fashion 

by sequentially calibrating reaches between the Branford and 

Bell gaging stations, Branford and Wilcox gaging stations, and 

Branford and Old Town gaging stations (fig. 11 and table 1). 

Use of the Gopher River gaging station (map index no. 10, 

fig. 11) as a downstream boundary condition was not possible 

because the water-level dataset for this station contained long 

periods of missing data during the study.

Results from the calibration of the Santa Fe River segment 

of the model are presented in table 7. Simulated water-surface 

elevations (stages) were about 1.1 and 0.8 ft lower than 

measured stages at the Fort White gaging station (map index 

no. 14, fig. 11) at 08:00 local time on August 14, 1999, and 

September 27, 1999, respectively. Farther downstream at the 

gaging station near the mouth of the Ichetucknee River (map 

index no. 15, fig. 4), simulated stages were 0.2 ft lower and 

0.6 ft higher than measured stages for the same time periods, 

respectively, mentioned above. The simulated stage was 0.2 ft 

higher than the measured stage at the gaging station near 

Hildreth (map index no. 16, fig. 4) during the September time 

period (measured data were unavailable at this location for the 

August time period). Flow measurements were not used to calibrate the model of the Santa Fe River because flow conditions 

were steady during the calibration periods, and gains and losses 

along the river were supplied as inputs to the model.

0

10,000

20,000

30,000

40,000

50,000

60,000

1998

O

FLOW, IN CUBIC FEET PER SECOND

N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

Simulated

Measured

Figure 44. Time series of measured and simulated streamflows in the Suwannee River near Wilcox, Florida (map index no. 7, fig. 11). 

Simulated flow values are from the uncoupled ground-water flow model.

Table 7. Simulated and measured water-surface elevations in the Lower Santa Fe River for selected time 

periods.

[Locations are shown in fig. 4. Simulated values are from the uncoupled surface-water flow model; elevations in feet 

above NGVD 1929]

Location

Water-surface elevation

August 14, 1998 September 27, 1999

Simulated Measured Simulated Measured

Santa Fe River near Fort White (station 02322500) 21.54 22.67 21.22 21.99

Santa Fe River at the mouth of the Ichetucknee River 10.11 10.30 8.51 7.92

Santa Fe River near Hildreth (station 02322570) 9.72 Missing 7.54 7.34

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  59
60 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

For the final uncoupled model of the Suwannee River 

between the Branford and Old Town gaging stations, the 

difference between simulated and measured stages ranged 

from less than 0.1 to 3.8 ft for the range of conditions used in 

the calibration effort. Under low-water conditions on September 27, 1999, simulated stages were generally within 0.1 ft 

of measured stages at the Branford gaging station, about 1 ft 

lower than measured stages at the gaging station near Bell, and 

within 0.1 ft at the gaging station near Wilcox; some of the 

lowest measured stages were erroneous (too low) because of 

clogged intakes at the gaging station (fig. 45). Under average 

streamflow conditions during August 18-19, 1997, simulated 

stages were generally within 0.1 ft of measured stages at the 

Branford gaging station, about 1.7 ft lower than measured 

stages at the gaging station near Bell, and about 0.2 to 0.3 ft 

higher at the gaging station near Wilcox (fig. 46). Under high 

0

2

4

6

8

10

SEPTEMBER 1999

1

STAGE, IN FEET ABOVE NGVD 1929

2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

SIMULATED STAGE AT BRANFORD

SIMULATED STAGE NEAR BELL

SIMULATED STAGE NEAR WILCOX

MEASURED STAGE AT BRANFORD

MEASURED STAGE NEAR WILCOX

MEASURED STAGE NEAR BELL

EXPLANATION

Figure 45. Comparison of simulated and measured water-surface elevations in the Lower Suwannee River during September 1999. 

Locations are shown in fig. 11.

SIMULATED INSTANTANEOUS STAGE AT BRANFORD

SIMULATED INSTANTANEOUS STAGE NEAR BELL

SIMULATED INSTANTANEOUS STAGE NEAR WILCOX

MEASURED INSTANTANEOUS STAGE NEAR WILCOX

MEASURED DAILY MEAN STAGE AT BRANFORD

MEASURED DAILY MEAN STAGE NEAR WILCOX

MEASURED INSTANTANEOUS STAGE NEAR BELL

18

0000 1200 2400

19

EXPLANATION

24-HOUR TIME, AUGUST 16-20, 1997

0

5

10

15

20

1200 2400 1200 2400

20

1200 2400 1200 2400

16 17

STAGE, IN FEET

ABOVE NGVD 1929

Figure 46. Comparison of simulated and measured water-surface elevations in the Lower Suwannee River during August 19997. 

Locations are shown in fig. 11.
streamflow conditions in March 1998, simulated stages were 

3 to 3.5 ft lower than measured values at the Branford gaging 

station, 3.1 to 3.8 ft lower at the Bell gaging station, and 1 to 

1.5 ft lower at the Wilcox gaging station.

Patterns of simulated and measured streamflows were 

similar for the Lower Suwannee River gaging stations near 

Bell and near Wilcox, and at the cross section upstream from 

Manatee Springs (fig. 4) during September 28-30, 1999 

(fig. 47). The simulated tidal minimum and maximum flows, 

however, were more extreme than the measured flows at the 

gaging station near Wilcox. Similar results were obtained in 

the simulation of the average streamflow condition during 

August 18-20, 1997 (fig. 48), although simulations of some 

of the flows were affected by problems with the downstream 

gaging station near Old Town (fig. 6) during low tide. More 

importantly in terms of the study objectives, comparisons 

indicated that simulated daily streamflows are probably within 

5 to 10 percent of measured streamflows (based on interpolating and extrapolating from the instantaneous measurements 

with the ADCPs).

Coupled Ground-Water and Surface-Water 

Flow Model

Calibration of the coupled ground- and surface-water 

flow model consisted of verifying that the parameter values 

obtained in the calibrations of the uncoupled ground- and 

surface-water flow models yielded acceptable results when 

used in the coupled model. The parameter values used in the 

coupled model were identical to those used in the uncoupled 

models, with the exception of riverbed leakance used by 

the river submodel, BRANCH’, in the coupled model. The 

BRANCH’ submodel calculates the conductance between 

the river and aquifer in each river segment by multiplying the 

simulated river topwidth by user-specified values of segment 

length and riverbed leakance (hydraulic conductivity divided 

by flow path length). In the uncoupled ground-water flow 

model, the riverbed conductance is specified by the user 

directly. An attempt was made to use riverbed leakance values 

in the coupled model that were equivalent to those used in the 

uncoupled ground-water flow model (by dividing the riverbed 

FLOW, IN CUBIC FEET PER SECOND

28

0000 0600 1200 1800 2400

29

24-HOUR TIME, SEPTEMBER 28-30, 1999

-1,000

0

1,000

2,000

3,000

4,000

5,000

0600 1200 1800 2400 0600 1200 1800 2400

30

6,000

7,000

8,000

EXPLANATION

MEASURED FLOW NEAR WILCOX

MEASURED FLOW ABOVE MANATEE SPRINGS

MEASURED FLOW NEAR BELL

SIMULATED FLOW ABOVE MANATEE SPRINGS

SIMULATED FLOW NEAR WILCOX

SIMULATED FLOW NEAR BELL

Figure 47. Comparison of simulated and measured flows in the Lower Suwannee River during September 1999. 

Locations are shown in fig. 4.

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  61
62  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

conductance values used in the uncoupled model by average 

river topwidth values). However, these equivalent values 

proved to be too high for stable convergence of the coupled 

model, even after adjusting some of the parameters that were 

used to solve the coupled model equations. Accordingly, 

the leakance values were decreased incrementally until, at a 

riverbed leakance value of 0.09 sec-1 (1.0 × 10-6 days-1), the 

coupled model would converge to a stable solution.

Generally, simulated ground-water levels in the coupled 

model were similar to those in the uncoupled ground-water 

flow model. The ground-water level residuals were reasonably 

unbiased, with the mean and median values of all residuals 

equal to -0.5 and -0.7 ft, respectively, and with 50 percent of 

the residuals ranging from -3.0 to 2.2 ft, and 90 percent ranging from -6.7 to 5.1 ft. The minimum and maximum residuals 

were similar in magnitude to those obtained from the uncoupled ground-water flow model.

Comparisons of measured and simulated ground-water 

levels in selected wells during water years 1998-99 are shown 

in figures 49 to 51. The similarity between measured and 

simulated ground-water levels generally did not depend on 

geographic location (figs. 52 and 53), but there were some 

exceptions. For example, some of the better matches were 

evident in three of the four wells north of the Santa Fe River 

(for example, well s245 in fig. 49). Additionally, simulated 

ground-water levels in wells s315, s330, s331, s346, and t059 

(fig. 50) along the Suwannee River upstream from river mile 

25 generally compared fairly well with measured water levels, 

although the matches were not as good as those achieved in 

the uncoupled ground-water flow model because of the low 

riverbed leakance values that were necessary for model stability. Good matches were also generally obtained in wells in the 

Chiefland Limestone Plain east of the Suwannee River and in 

western Alachua County (for example, wells s364 and s337, 

fig. 49).

Conversely, the matches for three of the four wells along 

the Suwannee River downstream from river mile 25 were not 

as good as in upstream locations (for example, well s360, 

fig. 51). The poor match in this area may be due to difficulty 

in accurately simulating recharge rates in this area during the 

summer periods of 1998 and 1999 and the fall of 1997. Poor 

matches also occurred at some of the wells located near karst 

features. At well s385 near Wekiva Springs, for example, 

simulated water levels were much more variable than the 

relatively constant measured water levels (fig. 51). The poor 

simulation at this site probably is because of the lack of data 

available to determine changes in transmissivity that are present in this area, as evidenced by the difficulty in improving the 

match at this site while maintaining the quality of the matches 

of wells to the east. As a result, simulated water levels in well 

s385 were somewhat low (by an average of about 4 ft) and fell 

below the elevation of the spring (by an average of about 3 ft), 

causing the spring discharge from this site not to be simulated 

by the MODFLOW Drain package. Simulated water levels in 

wells were also poor near some sinkholes that may occasionally receive storm runoff (for example, well s319, fig. 51); 

however, some simulations near other such features were 

much better (for example, well s333, fig. 49).

EXPLANATION

FLOW, IN CUBIC FEET PER SECOND

MEASURED FLOW NEAR WILCOX

MEASURED FLOW ABOVE MANATEE SPRINGS

MEASURED FLOW NEAR BELL

SIMULATED FLOW ABOVE MANATEE SPRINGS

SIMULATED FLOW NEAR WILCOX

SIMULATED FLOW NEAR BELL

18

0000 0600 1200 1800 2400

19

24-HOUR TIME, AUGUST 18-20, 1997

6,000

7,000

8,000

9,000

10,000

11,000

12,000

0600 1200 1800 2400 0600 1200 1800 2400

20

Figure 48. Comparison of simulated and measured flows in the Lower Suwannee River during August 1997. Locations are shown in fig. 4.
35

40

45

50

55

15

20

25

30

35

10

15

20

25

30

GROUND-WATER LEVEL, IN FEET ABOVE NGVD 1929

25

30

35

40

45

1998

O N D J F M A M J J A S O N D F J M A M J J A S

1997 1999

Well s333

Well s245

Well s364

Well s337

Simulated

Measured

Figure 49. Comparisons of measured and simulated (coupled model) ground-water levels from October 1997 to September 1999 for 

wells s364, s337, s245, and s333. Well locations are shown in fig. 27.

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  63
64  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

5

10

15

20

25

30

1998

O N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

0

5

10

15

0

5

10

15

20

0

5

10

15

20

5

10

15

20

25

Well s346

Well t059

Well s331

Well s330

Well s315

Simulated

Measured

GROUND-WATER LEVEL, IN FEET ABOVE NGVD 1929

Figure 50. Comparisons of measured and simulated (coupled model) ground-water levels from October 1997 to September 1999 for 

wells s315, s330, s331, s346, and t059 . Well locations are shown in fig. 27.
The simulated and measured streamflows and stages 

were generally in good agreement during water years 1998-99 

(figs. 54-59). Streamflow residuals (differences between 

simulated and measured mean daily streamflows) were 

comparable to the accuracy of “measured” flows (estimated 

from gaging-station data). For example, in the Suwannee River 

near Wilcox, 95 percent of the simulated daily mean flows 

were within 17 to 18 percent of the “rated” daily mean flows 

during water years 1998-99. These “rated” daily mean flows 

were estimates based on a relation (rating) between flow, 

stage, and water-surface slope. This rating is created, checked, 

and periodically updated using concurrent measurements of 

flow, stage, and water-surface slope that are taken, on average, 

about once every 8 weeks. Once this relation is created, hourly 

estimates of flow are made from hourly measurements of stage 

and water-surface slope. The hourly estimates for a given day 

are then averaged to compute a “rated” daily mean flow for 

that day. For the gaging station on the Suwannee River near 

Wilcox, the accuracy of this rating was described as “fair” 

for water year 1998 (95 percent of the daily mean streamflow 

values were estimated to be within 15 percent of the unknown 

true daily mean streamflow values) and “poor” for water 

year 1999 (less than 95 percent of the daily mean streamflow 

values were estimated to be within 15 percent of the unknown 

true values). Thus, the simulated daily mean flows at the 

Wilcox gaging station generally fell within (or close to) the 

confidence limits of the estimates generated from the rating at 

this location.

45

50

55

60

65

15

20

25

30

35

0

5

10

15

20

1998

O N D J F M A M J J A S O N D F J M A M J J A S

1997 1999

70

75

Well s319

Well s385

Well s360

Simulated

Measured

GROUND-WATER LEVEL, IN FEET ABOVE NGVD 1929

Figure 51. Comparisons of measured and simulated (coupled model) ground-water levels from October 1997 to September 1999 for 

wells s360, s385, and s319. Wells locations are shown in fig. 27.

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  65
66  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

The actual accuracy of the simulated flows may be better 

than indicated in the previous comparison because adjustments 

(rating shifts) that are applied to the rating are often imprecise 

because they are based on a limited set of data. This became 

apparent after analysis of the data collected during this study 

indicated that individual measurements could be randomly 

scattered around the rated or simulated flows by several 

hundred cubic feet per second. For example, the rating shift 

that was in effect during the summer of 1998 was calculated 

based on the best fit of data from eight measurements taken at 

the Wilcox gaging station from October 1997 to January 1999 

(only one of which was made during the summer of 1998). 

Subsequent analysis of the 76 flow measurements taken on 

August 12, 1998, however, indicated that the flow estimates, 

computed using this shifted rating, were about 1,000 ft3/s 

lower than the measured values during this period. Conversely, 

simulated flows were generally within 300 ft3/s of the ADCPmeasured flows during this period. If the rating shifts were 

changed during the summer period to reflect the 76 measurements, then there probably would be an even better agreement 

between the rated and simulated flows.

The coupled model also simulated streamflow reasonably well at other sites during different periods. Comparisons 

were made between simulated and ADCP-measured flows 

during field trips in the summers of 1998 and 1999, when 

flows were measured nearly continuously for 10 to 13 hours 

at most sites (figs. 57-59). The simulated instantaneous flows 

were generally within 10 percent of the measured flows at 

most of the sites. The simulated mean daily flows during these 

intensive measurements were probably even more accurate 

based on comparisons of flows averaged over the 10- to 

13-­hour measurement periods. More limited ADCP data 

also were available from routine field trips for the Suwannee 

River near Wilcox site. These data indicated that flows were 

simulated by the coupled model during these periods with an 

accuracy that was comparable to the slope-discharge rating. 

The poorest simulations probably occurred on June 9, 1998, 

when 10 ADCP streamflow measurements were taken during 

a “trough” in the tidal flow hydrograph. The ADCP and slope 

rating data indicated that the simulated daily mean flow on 

that day was probably within 10 to 20 percent of the true daily 

mean flow.

Figure 52. Potentiometric surface of the Upper Floridan aquifer and 

differences between measured and simulated ground-water levels in 

March 1998.

Figure 53. Potentiometric surface of the Upper Floridan aquifer and 

differences between measured and simulated ground-water levels in 

September 1999.

0 20 MILES

0 20 KILOMETERS

10

SIMULATED MINUS MEASURED 0 (Unleveled well).

SIMULATED MINUS MEASURED 0 (Leveled well).

SIMULATED MINUS MEASURED 0 (Unleveled well).

SIMULATED MINUS MEASURED 0 (Leveled well).

GROUND-WATER LEVEL–In feet above NGVD 1929.

Contour interval is 10 feet. Interpolated from

measurements taken in September 1999

<

<

≥

≥

EXPLANATION

LAFAYETTE

DIXIE

LEVY

GILCHRIST ALACHUA

MARION

COLUMBIA

TAYLOR

UNION

83°30’ 83°00’ 82°30’

30°00’

29°00’

30’

CITRUS

SUWANNEE

G u l f o f M e x i c o

80

70

60

50

40

30

20

10

20 3040

50

70

60

40

30

20 10

50

10

50

80

70

60

40

30

20 10

40

30

50

50

4.8

3.0

0.7

6.5 3.7 9.1

2.7 7.3

0.4

-2.2

-5.0

-4.9

1.5

1.2

2.0

-1.5

2.5

-11.1

-4.1

-9.0

3.5

2.6

1.4

-11.4

-5.3

-6.8

-4.9

-7.9

-4.4

30°00’

29°00’

30’

0 20 MILES

0 20 KILOMETERS

10

SIMULATED MINUS MEASURED 0 (Unleveled well)

SIMULATED MINUS MEASURED 0 (Leveled well)

SIMULATED MINUS MEASURED 0 (Unleveled well)

SIMULATED MINUS MEASURED 0 (Leveled well)

GROUND-WATER LEVEL–In feet above NGVD 1929.

Contour interval is 10 feet. Interpolated from

measurements taken in March, 1998

<

<

≥

≥

EXPLANATION

LAFAYETTE

DIXIE

LEVY

GILCHRIST

ALACHUA

MARION

COLUMBIA

TAYLOR

UNION

83°30’ 83°00’ 82°30’

CITRUS

SUWANNEE

G u l f o f M e x i c o

40

10

20

30

40

50

60

70

80

20

30

40

50

70

60

80

60

60

50

70

0.0

-0.6

-0.6

-0.4 -2.1

-0.8

-1.0

-2.2 -0.1 -6.4

-0.2

-0.2

-1.5

-10.4

-1.2

-2.7

-2.1

0.7

0.5

1.4

3.1

2.4

1.4

3.7 1.0 2.4

2.3

1.6

0.9

10.3 9.7

12.3

0.9

-2.1

-7.8
Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  67

Figure 54. Comparison of 

measured and simulated (coupled 

model) flows in the Suwannee 

River near Wilcox, Florida, October 

1997 to September 1999. Site 

location (map index no. 7) is 

shown in fig. 4.

FLOW, IN CUBIC FEET PER SECOND

1,000

2,000

5,000

10,000

20,000

50,000

80,000

O N D

1998

J F M A M J J A S O N D

1999

J F M A M J J A S

1997

Measured Simulated

Figure 55. Comparison of 

measured and simulated (coupled 

model) stage in the Suwannee 

River near Bell, Florida, October 

1997 to September 1999. Site 

location (map index no. 6) is 

shown in fig. 4.

0

5

10

15

20

25

30

1998

O

STAGE, IN FEET ABOVE NGVD 1929

N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

Measured

Simulated

Figure 56. Comparison of 

measured and simulated (coupled 

model) stage in the Suwannee 

River near Wilcox, Florida, October 

1997 to September 1999. Site 

location (map index no. 7) is 

shown in fig. 4. 0

5

10

15

20

1998

O

STAGE, IN FEET

ABOVE NGVD 1929

N D J F M A M J J A S O N D J F M A M J J A S

1997 1999

Measured

Simulated
68  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

3,000

3,500

4,000

4,500

FLOW, IN CUBIC

FEET PER SECOND

28

0 0600 1200 1800 2400 0600 1200

29

24-HOUR TIME, SEPTEMBER 28-29, 1999

EXPLANATION

SIMULATED DAILY MEAN FLOW

MEASURED INSTANTANEOUS FLOW–From

acoustic doppler current profiler

SIMULATED INSTANTANEOUS FLOW

Figure 57. Comparison of measured and simulated (coupled 

model) flows in the Suwannee River near Bell, Florida, 

September 28-29, 1999. Site location (map index no. 6) is 

shown in fig. 4.

EXPLANATION

SIMULATED DAILY MEAN FLOW

MEASURED DAILY MEAN FLOW–From slope

rating

MEASURED INSTANTANEOUS FLOW–From

acoustic doppler current profiler

SIMULATED INSTANTANEOUS FLOW

MEASURED INSTANTANEOUS FLOW–From

slope rating

FLOW, IN CUBIC FEET PER SECOND

28

0 0600 1200 1800 2400 0600 1200

29

24-HOUR TIME, SEPTEMBER 28-29, 1999

2,500

3,000

3,500

4,000

4,500

5,000

5,500

Figure 58. Comparison of measured and simulated (coupled 

model) flows in the Suwannee River near Wilcox, Florida, 

September 28, 1999. Site location (map index no 7) is shown 

in fig. 4.

FLOW, IN CUBIC FEET PER SECOND

29

1200 1800 2400 0600 1200

30

24-HOUR TIME, SEPTEMBER 29-30, 1999

1,500

2,000

2,500

3,000

3,500

4,000

4,500

5,000

5,500

6,000

6,500

7,000

7,500

MEASURED

SIMULATED

Figure 59. Comparison of measured and simulated (coupled 

model) flows in the Suwannee River above Manatee Springs 

near Chiefland, Florida, September 29-30, 1999. Site location 

(map index no. 19) is shown in fig. 4.

The simulated water budget for the subregional study 

area compared favorably with the water budget that was 

estimated independently from the model. The following 

budget terms were used in this comparison: (1) change in the 

amount of water stored in the ground-water system from the 

beginning to the end of the simulation period (water years 

1998-99); (2) exchange between the ground-water system 

and the Lower Suwannee, Lower Santa Fe, and Ichetucknee 

Rivers; and (3) discharge from the ground-water system to the 

Gulf of Mexico and to streams and wetlands draining coastal 

areas along the Gulf of Mexico. A comparison was not made 

between the simulated value of the flux of ground water across 

the general-head boundaries of the model (396 ft3/s) and the 

model-independent estimate of the flux because of the large 

uncertainty in computing an estimate of this flux. Additionally, comparisons were not made for the budget terms of 

recharge and well withdrawals because the model-independent 

estimates of these terms (4,331 and 40 ft3/s, respectively) were 

specified as inputs to the model.
The model-independent estimate of the change in the 

amount of water stored in the ground-water system within 

the subregional study area during water years 1998-99 was 

computed by multiplying the average change in groundwater levels (-0.84 ft) by the range in probable values of 

specific yield (0.1 to 0.3). This calculation resulted in an 

estimated reduction in ground-water storage ranging between 

5.1 × 109 ft3 and 1.5 × 1010 ft3 from the beginning to the end 

of the study period (or a reduction of 81 to 243 ft3/s when 

expressed as a rate of change in storage). The actual range 

of uncertainty associated with this estimate is larger because 

of uncertainties associated with the estimated value of the 

average change in ground-water levels. The corresponding 

simulated reduction in ground-water storage was 1.2 × 1010 ft3

(or 195 ft3/s when expressed as a rate of change), which fell 

within the range of the model-independent estimate. 

The model-independent, average river-aquifer exchange 

along the Lower Suwannee, Lower Santa Fe, and Ichetucknee 

Rivers was estimated to range from 2,175 to 3,200 ft3/s 

during water years 1998-99. The lower limit of this range 

was computed by adding the estimated combined average 

discharge (225 ft3/s) from Manatee Springs and Fanning 

Springs (fig. 4) to the measured average streamflow pickup 

(1,950 ft3/s) between the: (1) upstream gaging stations on the 

Suwannee River at Branford and the Santa Fe River at U.S. 

Highway 441 near High Springs; and (2) downstream gaging 

station near Wilcox. The upper limit was computed by adding 

the expected recharge to the estimated ground-water contributing area (to the Lower Suwannee River downstream from the 

gaging station near Wilcox) to the above-measured streamflow 

pickup of 1,950 ft3/s. The corresponding simulated value of 

the average river-aquifer exchange along the Lower Suwannee, Lower Santa Fe, and Ichetucknee Rivers was 2,760 ft3/s 

(within the range of the model-independent estimate).

The model-independent estimate of ground-water 

discharge to the Gulf of Mexico and to streams and wetlands 

draining coastal areas along the Gulf of Mexico was 

2,125 ft3/s. This estimate was computed by multiplying the 

estimated size of the contributing areas to the Gulf of Mexico 

by the average recharge rates to these areas during water 

years 1998-99. This model-independent estimate was nearly 

identical to the simulated value of 2,129 ft3/s.

Model Evaluation

This section describes two applications of the coupled 

model of ground- and surface-water flow. The first application is an evaluation of the temporal and spatial characteristics 

of simulated water exchanges between the Lower Suwannee 

and Lower Santa Fe Rivers and the Upper Floridan aquifer. The second application is an evaluation of the potential 

effects of future ground- and surface-water withdrawals using 

several hypothetical water withdrawal scenarios. The section 

concludes with a discussion of some of the limitations of the 

coupled model.

Temporal and Spatial Characteristics of 

Ground- and Surface-Water Exchanges

The coupled model was used to evaluate the temporal 

and spatial characteristics of exchanges of water between the 

Lower Suwannee and Lower Santa Fe Rivers and the Upper 

Floridan aquifer during water years 1998-99. This evaluation 

focused primarily on the Suwannee River downstream from 

the mouth of the Santa Fe River and upstream from river mile 

7.5, referred to as reach 3 (fig. 11), because of concerns 

about possible consequences of increased water use on flow 

in this reach. Another major group of river reaches, referred 

to collectively as reach 1 (fig. 11), is bounded by long-term 

gaging stations. As previously discussed, reach 1 consists of 

the Suwannee River between the gaging stations at Branford 

and near Wilcox (river miles 76.1 and 33.5, respectively), the 

Santa Fe River downstream from the gaging station near Fort 

White (18.3 miles upstream from the mouth of the Santa Fe 

River), and the Ichetucknee River. Simulation results from 

reach 1 were compared with estimates obtained from the 

previously described analysis of changes in streamflow and 

channel storage along this reach (referred to as the corrected 

pickup analysis).

Over the 2-year study period, simulated (coupled model) 

net ground-water inflow to reach 1 averaged about 1,400 ft3/s. 

Although this simulated value was higher than the estimate 

(1,050 ft3/s) obtained from the corrected pickup analysis 

for this reach over the same time period, the latter value has 

limited significance (with a 95-percent confidence interval 

of -1,500 to 3,600 ft3/s). As previously described, many of 

the estimates from the corrected pickup analysis have limited 

significance because of the uncertainties in the flow estimates 

from gaging stations at the upstream and downstream ends 

of the reach, and because of uncertainties in the estimates of 

channel storage changes during periods of rapidly rising or 

falling river levels. Therefore, the discrepancy between the 

simulated and corrected pickup estimates of the average net 

ground-water inflow to reach 1 during water years 1998-99 is 

not significant.

The simulated (coupled model) average ground-water 

inflows to reach 3 were about 1,600 and 1,300 ft3/s, during 

water years 1998 and 1999, respectively. The difference in 

these two values is probably attributable to: (1) high rates 

of ground-water inflow to reach 3 that occurred just before 

the onset, and just after the peak, of the El Niño-associated 

flooding during the winter-early spring of water year 1998; 

and (2) lower ground-water inflow rates to reach 3 caused by 

the extended La Niña-associated drought that occurred during 

most of water year 1999.

Shorter than annual time-scale averages support this 

inference. The simulated monthly ground-water inflows 

to reach 3 ranged from 1,000 to 2,400 ft3/s, with the maximum value occurring in April 1998, following the winter 

flood peak of late March 1998. minimum values occurred 

in September 1999 and the preceding spring and summer 

months of 1999 when extended drought conditions occurred 

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  69
70 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

in association with La Niña, and during the winter months of 

late 1997 and early 1998 when river levels were rising faster 

than ground-water levels. The simulated daily ground-water 

inflow data show a similar pattern (fig. 60). The minimum 

daily ground-water inflow (about 500 ft3/s) occurred on March 

24, 1998, which is coincident with the peak of the winter-early 

spring flood period during water year 1998. The maximum 

values (2,800 to 2,900 ft3/s) occurred on and around: 

(1) February 23, 1998, during a period of rapidly rising 

ground-water levels; and (2) April 13, 1998, about 3 weeks 

after the winter flood peak when river levels were falling faster 

than ground-water levels.

0

500

1,000

1,500

2,000

2,500

3,000

MEAN DAILY GROUND-WATER INFLOW,

IN CUBIC FEET PER SECOND

MEAN DAILY STREAMFLOW, IN CUBIC FEET PER SECOND

J F M A M J J A S O N D

100

200

5,000

500

1,000

2,000

10,000

O N D J F M A M J J A S

1997 1998 1999

20,000

50,000

100,000

A

B

Santa Fe River

near Fort White, Florida

Suwannee River

near Branford, Florida

Suwannee River

near Wilcox, Florida

Figure 60. (A) Simulated daily ground-water inflow to reach 3, and (B) measured daily streamflows in the Suwannee River at 

Bradford, Suwannee River near Wilcox, and Santa Fe River near Fort White, Florida.
Collectively, the annual, monthly, and daily data show a 

consistent pattern in which low rates of ground-water inflow 

occur during periods of peak flood levels, when the hydraulic 

gradient (aquifer level minus river level) toward the river is 

typically at its lowest point because of the high river levels. 

Low rates of ground-water inflow also occur after extended 

droughts, when ground-water storage has been depleted from 

reduced recharge. Conversely, the highest rates of groundwater inflow typically occur during periods of receding water 

levels that closely follow peak river levels. During these 

conditions, the hydraulic gradient from the aquifer to the 

river is typically greatest because river levels have fallen and 

ground-water levels are higher. The ground-water levels are 

higher because of: (1) high recharge rates associated with 

the wet conditions that lead up to the flood peak, and (2) the 

accumulation of ground water during the period of peak flooding when the high river levels impeded ground-water outflow. 

These patterns in the simulated data are also consistent with 

the patterns inferred from the corrected pickup analysis.

The simulation results from the coupled model reproduced 

the essential spatial patterns that were evident from the historic 

and study period streamflow measurements. The reaches with 

the highest average ground-water inflow rates during water 

years 1998-99 were the Ichetucknee River above U.S. Highway 27 (about 130 ft3

/s per mile of river) and the Santa Fe 

River upstream from the gaging station near Fort White to the 

upstream model boundary near U.S. Highway 27 (about 80 ft3/s 

per mile of river). As previously discussed, these reaches have 

the highest concentration of spring discharge in the subregional study area and also the greatest change in measured 

pickup under average and low-flow conditions. Additionally, 

the simulated ground-water inflows to the Suwannee River 

between the gaging station at Branford and the mouth of the 

Suwannee River (about 9 ft3/s per mile of river) and the Santa 

Fe River downstream from the Fort White gaging station (about 

7 ft3/s per mile of river) had the lowest average ground-water 

inflow rates. The reach of the Ichetucknee River upstream 

from the gaging station near Hildreth at U.S. Highway 27 

had the greatest variability in the amount of ground-water-toriver inflow; the standard deviation of the daily ground-water 

inflows was about 30 ft3/s per river mile (fig. 61). In contrast, 

the reach of the Santa Fe River downstream from the Fort 

White gaging station and the reach of the Suwannee River 

between Branford and the mouth of the Santa Fe River had the 

least variability in the amount of ground-water-to-river inflow; 

the standard deviation of the daily ground-water inflows was 3 

and 4 ft3/s per mile in these reaches, respectively.

Simulated Effects of Water Withdrawals on 

Streamflow

The effect of increased water withdrawals on the flow of 

the Lower Suwannee River is a major concern to water managers and others. Because of the closely linked ground- and 

surface-water systems in the Lower Suwannee Basin, groundwater withdrawals will, in many instances, result in decreased 

ground-water discharge to, and subsequently reduced flow in, 

the Lower Suwannee River. The coupled model of ground- and 

surface-water flow was developed, in part, as a tool to estimate 

these effects.

To explore this important potential use of the coupled 

model, 11 hypothetical water-withdrawal scenarios were 

simulated (table 8), and their effects on a set of statistical 

descriptions of streamflow (streamflow characteristics) were 

evaluated at the gaging stations on the Suwannee River near 

Bell, near Wilcox, and above the Gopher River (fig. 4 and 

table 1). Several of these scenarios (scenario group 4) correspond to those used by Light and others (2002), who evaluated 

potential changes in floodplain forest composition and the 

degree of inundation and saturation of floodplain soils along 

the Lower Suwannee River. Eight streamflow characteristics 

were evaluated for each scenario-gaging station combination. 

Three of these characteristics were the lowest daily flow that 

is not exceeded in a given year, on average, once every 2, 5, or 

10 years (1Q2, 1Q5, and 1Q10, respectively). The other five 

characteristics were the daily flows that are not exceeded 10, 

20, 50, 80, and 90 percent of the time (p10, p20, p50, p80, and 

p90, respectively).

The approach used to estimate values of each of the 

eight statistics under the various scenarios consists of three 

steps as illustrated for scenario 4 (withdrawal = 500 ft3/s) 

in the Suwannee River near Wilcox (figs. 62 and 63). In the 

first step, a given hypothetical scenario is simulated with the 

coupled model for water years 1998-99 by modifying the 

boundary conditions of the calibrated model (referred to as 

scenario 1 or the baseline scenario) to accommodate the hypothetical scenario. For example, a hypothetical scenario might 

be created by increasing the 1998-99 monthly ground-water 

withdrawal rates that were used in the calibrated model (which 

averaged, 35 ft3/s), or by reducing the flow at the upstream 

river boundaries of the calibrated model.

In the second step, the daily mean flows at each of the 

three gaging station locations are extracted from the model 

output for each day of the simulation period (water years 

1998-99). These simulated daily mean flows are then matched 

with concurrent daily mean flows that were simulated for 

the baseline conditions during water years 1998-99 using the 

results of the calibration of the coupled model.

In the third step, a linear relation is fit to the dataset 

generated in the second step, using the line-of-organic correlation method of regression analysis (Helsel and Hirsch, 1992, 

p. 276). Three linear relations (one for each gaging station) 

are produced in this step, with each relation then used to 

estimate the values of individual streamflow characteristics 

for a given scenario gaging station/combination. For example, 

the 1Q10 streamflow characteristic for the Suwannee River 

near Wilcox under scenario 4 is estimated by substituting the values of 1Q10 under baseline conditions into the 

best-fit relation between flows in the Suwannee River near 

Wilcox under scenario 4 and baseline conditions. This step 

produces a set of eight streamflow characteristics for each 

gaging station/scenario combination. Using this approach for 

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  71
72  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

estimating changes in streamflow characteristics is analogous 

to the approach used for estimating streamflow characteristics 

at sites with limited data using relations with long-term sites 

(Riggs, 1972; Helsel and Hirsch, 1992, p. 265).

Results of the scenario simulations for the three gaging 

stations are given in tables 9 to 13. The streamflow characteristics estimated for each scenario at the gaging stations 

near Bell and Wilcox, respectively, are presented in tables 9 

and 10. These streamflow characteristics could not be estimated for the gaging station on the Suwannee River above the 

Gopher River because this site did not have enough data to 

estimate baseline streamflow characteristics. The values of the 

slope and intercept parameters that define the linear relation 

between the hypothetical and baseline scenario conditions 

are presented for the gaging station on the Suwannee River 

above the Gopher River in table 11. The values can be used 

to estimate the streamflow characteristics when sufficient 

data become available at the gaging station above the Gopher 

River to estimate the baseline streamflow characteristics for 

this site. These values also can be used to estimate various 

other streamflow characteristics that were not considered in 

the examples used in this report. For this reason, slope and 

intercept parameters are presented for the gaging stations near 

Bell and Wilcox in tables 12 and 13, respectively.

Santa Fe River

Suwannee River

East Pass

Ichetucknee River

COLUMBIA

SUWANNEE

DIXIE

MARION

UNION

ALACHUA

BRADFORD

LAFAYETTE

LEVY

GILCHRIST

TAYLOR

27

441

27

441

Fanning

Springs

Bell

Branford

Fort White

Wilcox

OldTown

High

Springs

Trenton

Cross

City

Bronson

Suwannee

30°

83° 82°

29°

0 20 MILES

0 20 KILOMETERS

G u l f o f M e x i c o

EXPLANATION

02323592

AVERAGE AQUIFER TO RIVER LEAKAGE

RATE–In cubic feet per second per

mile of river

STANDARD DEVIATION OF AQUIFER TO

RIVER LEAKAGE–In cubic feet per

second per mile of river

LOCATION OF SELECTED RIVER

REACH–Alternates between gray

and light blue only for identification

SUBREGIONAL MODEL BOUNDARY

GAGING STATION–Location and number

19

10

19

10

17

7

02323500

02323000

02322500

02320500

02323590

02323570

02321975

02322000

02323592

02322700

32

9

38

14

9

4

22

6

7

3

21

17

129

28

82

13

Figure 61. Simulated average and standard deviation of ground-water leakage to selected river reaches.
Table 8. Description of baseline and hypothetical withdrawal scenarios that were simulated with the 

coupled model of ground-water and surface-water flow.

[ft3/s, cubic feet per second]

Scenario number Scenario description

1 (baseline conditions) Model boundary conditions from calibrated model of water years 1998 and 1999

 (total ground-water withdrawals were approximately 35 ft3/s).

2 Same as baseline conditions scenario except for the addition of a 540 ft3/s withdrawal

 from the Suwannee River just upstream from the gage near Wilcox.

3 Same as baseline conditions scenario except ground-water withdrawals are increased 

 by 67 percent (to approximately 58 ft3/s).

4 (100 ft3/s) Same as baseline conditions scenario except the river inflow at the upstream boundaries

 (Suwannee River near Branford and Santa Fe River near Fort White) is reduced by 

 100 ft3/s. Eighty percent of the reduction is assigned to the Suwannee boundary and 

 20 percent to the Santa Fe boundary.

4 (300 ft3/s) Same as scenario 4 (100 ft3/s) except a 300 ft3/s reduction is imposed.

4 (500 ft3/s) Same as scenario 4 (100 ft3/s) except a 500 ft3/s reduction is imposed.

4 (1,000 ft3/s) Same as scenario 4 (100 ft3/s) except a 1,000 ft3/s reduction is imposed.

4 (2,000 ft3/s) Same as scenario 4 (100 ft3/s) except a 2,000 ft3/s reduction is imposed.

5 (300 ft3/s) Combination of scenario 3 and scenario 4 (300 ft3/s).

5 (500 ft3/s) Combination of scenario 3 and scenario 4 (500 ft3/s).

5 (1,000 ft3/s) Combination of scenario 3 and scenario 4 (1,000 ft3/s).

6 (no pumping) Same as baseline conditions scenario except ground-water withdrawals are not simulated 

 (to approximate predevelopment conditions).

FLOW, IN CUBIC FEET PER SECOND

1,000

2,000

5,000

10,000

20,000

50,000

80,000

O N D

1998

J F M A M J J A S O N D

1999

J F M A M J J A S

1997

Scenario 4

(500 cubic feet per second)

Scenario 1

(baseline conditions)

Figure 62. Mean daily flows during water years 1998-99, simulated for scenarios 1 and 4 in the Suwannee River near Wilcox, Florida.

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  73
74  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Results of the scenario simulations for the three gaging 

stations indicated that instream withdrawals produced relatively straightforward changes in streamflow characteristics. 

For example in scenario 2, the hypothetical point withdrawal 

of 540 ft3/s just upstream from the Wilcox gaging station 

resulted in negligible changes in streamflow at the gaging 

station near Bell (which was upstream from the point withdrawal), and changes that were nearly equal to the instream 

withdrawal rate at the gaging stations near Wilcox and above 

Gopher River (which were both downstream from the point 

withdrawal). Similarly, for scenario group 4 (flow reductions 

of 100, 300, 500, 1,000, and 1,000 ft3/s), reductions in flows 

at the gaging stations near Bell, near Wilcox, and above the 

Gopher River were similar to the hypothetical combined flow 

reductions at the upstream gaging stations on the Suwannee 

River at Branford and the Santa Fe River near Fort White. 

For example, the version of scenario 4 with the hypothetical upstream flow reduction of 1,000 ft3/s resulted in downstream flow reductions of 988, 989, and 989 ft3/s at the gaging 

stations near Bell, near Wilcox, and above the Gopher River, 

respectively (tables 9-13). These reductions were slightly 

smaller than the upstream withdrawal rate because the flow 

reductions decreased the river stages, which increased the 

hydraulic-head gradient and ultimately increased the flux of 

ground water to the river.

Scenarios 3 and 6 represented changes in ground-water 

withdrawals from the system. Changes in streamflows (relative 

to baseline conditions) were a function of the size and location 

of the ground-water contributing area to a given gaging station 

and the geographic distribution of wells. For example, changes 

in streamflows were smallest for the gaging station near Bell 

because its contributing ground-water area was the smallest of 

the three gaging stations. Under scenario 3, streamflows were 

reduced by about 2, 7, and 14 ft3/s on average at the gaging 

stations near Bell, near Wilcox, and above the Gopher River, 

respectively (tables 9-13). Reductions in flows were less than 

they might have otherwise been because the increased groundwater withdrawals were offset, in part, by increased movement 

of ground water into the model area across the general-head 

boundaries. Under scenario 6, streamflows increased by about 

3, 11, and 20 ft3/s, on average, at the gaging stations near Bell, 

near Wilcox, and above the Gopher River, respectively (tables 

9-13). Increases in flows were less than they might have 

otherwise been because the decreased ground-water withdrawals resulted in decreasing rates of ground-water movement into 

the model area across the general-head boundaries.

Scenario group 5 (flows of 300, 500, and 1,000 ft3/s) 

represents a combination of instream and ground-water 

withdrawals. The simulation results resembled the addition or “superposition” of the results from scenarios 3 and 4 

(flows of 300, 500, and 1,000 ft3/s). For example, in scenario 

5 (300 ft3/s), streamflows decreased by 299 ft3/s at the Bell 

gaging station, which was equal to the sum of the river-flow 

reductions under scenarios 3 (2 ft3/s) and 4 (300 ft3/s) at 

297 ft3/s. Similar results were obtained at the other gaging 

stations (tables 9-13).

0

10,000

20,000

30,000

40,000

50,000

60,000

SCENARIO 1 FLOW,

IN CUBIC FEET PER SECOND

0 10,000 20,000 30,000 40,000 50,000 60,000

SCENARIO 4 FLOW,

IN CUBIC FEET PER SECOND

SCENARIO 4 (500 cubic feet per second) SIMULATION

BEST-FIT LINE

1-day, 2-year low flow

under scenario 1

conditions is 4,870

cubic feet per second.

1-day, 2-year low flow

under scenario 4

conditions is 4,377

cubic feet per second

Figure 63. Relation between daily flows during water years 1998-99, simulated for scenarios 1 and 4. The procedure for estimating the 

1-day, 2-year low-flow frequency characteristic of the Suwannee River near Wilcox with this relation is illustrated.
Table 9. Estimates of streamflow characteristics of the Suwannee River near Bell, Florida, under baseline and 

hypothetical conditions.

[The annual low flow statistics reported in columns two through four represent the magnitude of the lowest 1-day average flow 

occurring during a given year at the specified recurrence interval. For example, for scenario 1, the lowest daily average flow is not 

expected to exceed 2,890 ft3/s (cubic feet per second) in 1 year out of 10 (10-year recurrence interval), on average]

Scenario number

 for indicated 

recurrence interval,

in years

Annual lowest 1-day flow, 

in ft3/s, for indicated 

recurrence interval, in years

Daily mean flow that would be exceeded for indicated 

percent of time, in ft3/s

2-year 5-year 10-year 10 percent 20 percent 50 percent 80 percent 90 percent

1 (baseline conditions) 4,050 3,220 2,890 15,439 11,352 6,664 4,411 3,711

2 4,050 3,220 2,890 15,439 11,352 6,664 4,411 3,711

3 4,048 3,218 2,888 15,437 11,350 6,662 4,409 3,709

4 (100 ft3/s) 3,951 3,121 2,791 15,339 11,253 6,565 4,312 3,612

4 (300 ft3/s) 3,753 2,923 2,593 15,140 11,054 6,367 4,114 3,414

4 (500 ft3/s) 3,555 2,726 2,396 14,941 10,855 6,169 3,916 3,217

4 (1,000 ft3/s) 3,061 2,231 1,902 14,442 10,358 5,673 3,422 2,722

4 (2,000 ft3/s) 2,071 1,242 913 13,445 9,363 4,682 2,432 1,732

5 (300 ft3/s) 3,751 2,921 2,591 15,138 11,052 6,365 4,112 3,412

5 (500 ft3/s) 3,553 2,724 2,394 14,939 10,853 6,166 3,914 3,214

5 (1,000 ft3/s) 3,059 2,229 1,899 14,440 10,356 5,671 3,419 2,720

6 (no pumping) 4,053 3,223 2,893 15,442 11,355 6,667 4,414 3,714

Table 10. Estimates of streamflow characteristics of the Suwannee River near Wilcox, Florida, under baseline and 

hypothetical conditions.

[The annual low flow statistics reported in columns two through four represent the magnitude of the lowest 1-day average flow 

occurring during a given year at the specified recurrence interval. For example, for scenario 1, the lowest daily average flow is not 

expected to exceed 3,680 ft3/s (cubic feet per second) in 1 year out of 10 (10-year recurrence interval), on average]

Scenario number

 for indicated 

recurrence interval,

in years

Annual lowest 1-day flow, 

in ft3/s, for indicated 

recurrence interval, in years

Daily mean flow that would be exceeded for indicated 

percent of time, in ft3/s

2-year 5-year 10-year 10 percent 20 percent 50 percent 80 percent 90 percent

1 (baseline conditions) 4,870 4,050 3,680 18,835 14,631 8,426 5,666 4,817

2 4,329 3,509 3,139 18,293 14,089 7,885 5,125 4,276

3 4,862 4,043 3,673 18,829 14,624 8,419 5,659 4,810

4 (100 ft3/s) 4,771 3,951 3,582 18,735 14,532 8,327 5,567 4,718

4 (300 ft3/s) 4,574 3,754 3,384 18,535 14,333 8,129 5,370 4,521

4 (500 ft3/s) 4,377 3,557 3,187 18,336 14,134 7,931 5,173 4,324

4 (1,000 ft3/s) 3,884 3,064 2,695 17,836 13,636 7,437 4,679 3,831

4 (2,000 ft3/s) 2,896 2,078 1,709 16,837 12,640 6,446 3,691 2,844

5 (300 ft3/s) 4,567 3,747 3,377 18,529 14,326 8,122 5,363 4,514

5 (500 ft3/s) 4,370 3,550 3,180 18,329 14,127 7,924 5,165 4,317

5 (1,000 ft3/s) 3,877 3,057 2,688 17,830 13,629 7,430 4,672 3,824

6 (no pumping) 4,881 4,061 3,691 18,845 14,641 8,436 5,677 4,828

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  75
76  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Table 11. Estimates of the parameters necessary for 

estimating changes in streamflow characteristics of the 

Suwannee River above the Gopher River under baseline 

and hypothetical conditions.

[Estimates of streamflow characteristics are calculated using 

a linear relation defined by the slope and intercept parameters 

shown below. For example, if the baseline 1-day, 2-year low flow 

(1Q2) were estimated to be 5,000 ft3/s (cubic feet per second), 

then the estimate of the 1Q2 under scenario 2 conditions would 

be equal to -541 + 0.99997*5,000 = 4,459 ft3/s]

Scenario number

Parameters defining the linear relation 

between the flow occurring under the 

indicated scenario and the flow under 

baseline conditions

Intercept Slope

2 -541 0.99997

3 -15 1.00016

 4 (100 ft3/s) -98 0.99991

 4 (300 ft3/s) -295 0.99972

 4 (500 ft3/s) -491 0.99953

 4 (1,000 ft3/s) -982 0.99908

 4 (2,000 ft3/s) -1,965 0.99816

 5 (300 ft3/s) -309 0.99988

 5 (500 ft3/s) -506 0.99969

 5 (1,000 ft3/s) -997 0.99923

6 (no pumping) 22 0.99976

Table 12. Estimates of the parameters necessary for 

estimating changes in streamflow characteristics of the 

Suwannee River near Bell, Florida, under baseline and 

hypothetical conditions.

[Estimates of streamflow characteristics are calculated using 

a linear relation defined by the slope and intercept parameters 

shown below. For example, if the baseline 1-day, 2-year low flow 

(1Q2) were estimated to be 5,000 ft3/s (cubic feet per second), 

then the estimate of the 1Q2 under scenario 3 conditions would 

be equal to -2 + 1.00001*5,000 = 4,998 ft3/s]

Scenario number

Parameters defining the linear relation 

between the flow occurring under the 

indicated scenario and the flow under 

baseline conditions

Intercept Slope

2 0 0.99999

3 -2 1.00001

 4 (100 ft3/s) -99 0.99994

 4 (300 ft3/s) -296 0.99981

 4 (500 ft3/s) -493 0.99968

 4 (1,000 ft3/s) -987 0.99935

 4 (2,000 ft3/s) -1,974 0.99869

 5 (300 ft3/s) -296 0.99981

 5 (500 ft3/s) -496 0.99969

 5 (1,000 ft3/s) -989 0.99937

6 (no pumping) 3 0.99998

Table 13. Estimates of the parameters necessary for 

estimating changes in streamflow characteristics of the 

Suwannee River near Wilcox, Florida, under baseline and 

hypothetical conditions.

[Estimates of streamflow characteristics are calculated using 

a linear relation defined by the slope and intercept parameters 

shown below. For example, if the baseline 1-day, 2-year low flow 

(1Q2) were estimated to be 5,000 ft3/s (cubic feet per second), 

then the estimate of the 1Q2 under scenario 2 conditions would 

be equal to -541 + 0.99998*5,000 = 4,459 ft3/s]

Scenario number

Parameters defining the linear relation 

between the flow occurring under the 

indicated scenario and the flow under 

baseline conditions

Intercept Slope

2 -541 0.99998

3 -7 1.000057

 4 (100 ft3/s) -98 0.999912

 4 (300 ft3/s) -295 0.999734

 4 (500 ft3/s) -491 0.999555

 4 (1,000 ft3/s) -982 0.999109

 4 (2,000 ft3/s) -1,964 0.998204

 5 (300 ft3/s) -302 0.999789

 5 (500 ft3/s) -498 0.999609

 5 (1,000 ft3/s) -989 0.999160

6 (no pumping) 11 0.999915

The accuracy of these scenario predictions was estimated 

by calculating the standard deviation of a predicted flow for 

a given day during water years 1998-99 that was of the same 

magnitude as the baseline streamflow characteristic for a given 

combination of scenario, site, and streamflow characteristic. 

This standard deviation was calculated as follows (Hill, 

1992, p. 28):

syˆ

m bi ∂

∂yˆ

m V b( )ij bj ∂

∂yˆ

m

j =1

NP

∑

i =1

NP

∑

1

2

--

= (11)

where

sŷm is the standard deviation of the estimated 

value of prediction ŷm,

 

bi ∂

∂yˆ

m

 

and 

bj ∂

∂yˆ

m are the partial derivatives (sensitivities) of 

ŷm, with respect to model parameters, bi

and bj, evaluated at the set of optimal model 

parameter values, b; 

V(b)ij is the element in row, i, column, j, of the 

variance covariance matrix on the parameters (Hill, 1994, p. 57); and

i and j are indexes denoting a particular model 

parameter.
For example, the streamflow characteristic, 1Q2, under 

baseline conditions in the Suwannee River near Wilcox is 

equal to 4,870 ft3/s, and flow close to this magnitude was 

simulated at the Wilcox gaging station on April 14, 1999. The 

standard deviation of the predicted value of 1Q2 under a given 

scenario was calculated by substituting the sensitivities of 

the predicted value on this day into equation 11, yielding an 

approximation of the standard deviation for the predicted value 

of 1Q2 at the Wilcox gaging station under the given scenario. 

This process is repeated to obtain estimates of the standard 

deviation of other combinations of streamflow characteristics, 

scenarios, and gaging station locations.

Results of these calculations were consistent for all 

of the scenarios. In each of the possible combinations of 

scenarios and gaging station location, the standard deviation 

of the predicted value of a streamflow characteristic ranged 

from about 8 to 54 ft3/s. Smaller standard deviation values 

in this range corresponded to the statistics with the lower 

flows (1Q2, 1Q5, 1Q10, p10, and p20), and larger values 

corresponded to the statistics with the larger flows. As a 

result, values of the coefficient of variation of the predictions 

(standard deviation of the prediction divided by the simulated value of the prediction) were relatively consistent and 

generally less than 0.5 percent of the predicted value of each 

streamflow characteristic under the various scenarios. Results 

of these calculations for scenario 4 (500 ft3/s) are given in 

table 14. As previously stated, results of the other scenarios 

were similar, so additional tables for the other scenarios are 

not presented.

Table 14. Standard deviation and coefficient of variation of predicted values of 

selected streamflow statistics for scenario 4 (500 cubic feet per second) for 

locations on the Suwannee River corresponding to the gaging stations near Bell 

and Wilcox, Florida, and above the Gopher River.

[Site locations are shown in fig. 4]

Station name Streamflow 

statistic

Standard 

deviation, 

in cubic feet per 

second

Coefficient of 

variation, 

in percent

Suwannee River near Bell

1Q2 8.5 0.2

1Q5 7.8 0.2

1Q10 7.8 0.3

p10 15.5 0.1

p20 33.9 0.3

p50 15.7 0.2

p80 9.1 0.2

p90 8.4 0.2

Suwannee River near Wilcox

1Q2 9.4 0.2

1Q5 12.0 0.3

1Q10 13.6 0.4

p10 24.3 0.1

p20 53.5 0.4

p50 18.6 0.2

p80 9.9 0.2

p90 8.9 0.2

Suwannee River above the Gopher River

1Q2 8.7 0.2

1Q5 22.7 0.6

1Q10 27.6 0.8

p10 28.7 0.2

p20 72.5 0.5

p50 23.9 0.3

p80 7.8 0.1

p90 9.3 0.2

Evaluation of Ground-Water and Surface-Water Exchanges Using a Hydrologic Model  77
78  Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

Model Limitations

Use of the model for predictive purposes should be 

limited to estimating how flows in the Lower Suwannee 

River might change as a result of changes in patterns of 

ground-water or surface-water withdrawals. The model also 

should not be used to simulate a stress (for example, a large 

ground-water withdrawal) that would cause large groundwater level declines along the model boundaries, unless the 

simulation results are qualified. Possible exceptions include 

drawdowns that occur near the specified-head boundary condition along the Gulf of Mexico coastline (as long as the simulated ground-water levels along the coast do not fall below 

NGVD 1929), or drawdowns that occur near the head-dependent flux boundaries at the northeastern limits of the model 

area. Simulation of this latter case might require the iterative 

adjustment of the specified heads along the head-dependent 

flux boundaries until simulated drawdowns reach an equilibrium solution. Another approach would be to: (1) simulate the 

stress using a larger model (encompassing the area modeled 

in this report); and (2) use the simulated heads from the larger 

model to estimate ground-water levels along the head-dependent 

flux boundaries of the model described in this report. Alternatively, simulation results could be qualified by stating that 

the results are based on the assumption that locations of flow 

boundaries and heads at head-dependent flux boundaries are 

not changed appreciably.

Several other important limitations exist regarding use 

of the model. One limitation is that the model should not be 

used (or used with extreme caution) to estimate drawdowns 

in specific locations in response to hypothetical uses. This 

limitation arises in large part because sufficient data are not 

currently available to accurately map the conductive properties 

of the Upper Floridan aquifer at a detailed level in the subregional study area. Indeed, the work done in this and earlier 

studies, including the work by Bush and Johnston (1988) and 

other investigators conducting aquifer tests in the study area, 

represent the first steps in this mapping process. Because of 

these limitations, the transmissivity zones in the models are, 

by necessity, generalized and the locations of the boundaries 

are subject to considerable uncertainty. For this reason, sitespecific drawdown estimates are best made using site-specific 

aquifer tests at this time.

Another important limitation is that the model has not 

been tested for use in estimating the time of travel of water 

or solutes in the Upper Floridan aquifer. Estimates of time 

of travel and solute transport would require a more detailed 

understanding of spatial variations in conductive properties 

and effective porosity of the aquifer. This problem is especially severe in the vicinity of large springs where hydraulic 

conductivity and porosity are highly variable. Even when 

the large conduits to springs have been mapped, transport 

can be strongly influenced by the presence of moderate scale 

conduits (about 10-2 to 10-1 ft in diameter), which are almost 

impossible to map at present. Site-specific testing (using tracer 

techniques) again provides an interim solution, as well as 

data necessary for ultimately developing subsurface transport 

models for the subregional study area. Finally, users of the 

model should make note of parameter confidence intervals, 

model sensitivities, and geographic areas where model performance is strongest or weakest to assess the accuracy of any 

predictions made with the model.

Summary

The Lower Suwannee River and the Upper Floridan 

aquifer are closely linked hydrologic systems, and predicting 

the effects of increased water use on ground- and surfacewater flows and levels requires a quantitative understanding of the hydraulic behavior of these two systems and their 

linkages. Historic and newly collected data were evaluated to better understand the variability of water flows and 

levels in the rivers and aquifers, timing and magnitude of 

ground- and surface-water exchanges, and physical properties and processes that influence these water flows, levels, 

and exchanges. A key element of this evaluation was the 

development of a computer model capable of simulating the 

ground- and surface-water flows, levels, and exchanges as well 

as estimating the effects of hypothetical ground- and surfacewater withdrawal scenarios on streamflows.

Flow in the Lower Suwannee River is governed by 

inflows from the Upper Suwannee River, Santa Fe River (its 

major tributary), and Upper Floridan aquifer. The long-term 

average flow, as measured at the gaging station near Wilcox, 

is about 10,000 ft3/s. Substantial departures from this average 

flow rate occur over time scales that range from decadal (and 

longer) to hourly. During the study, El Niño-La Niña climatic 

conditions produced a wide range of hydrologic conditions in 

the Lower Suwannee River Basin. High rainfall totals associated with strong El Niño conditions during the winter and 

early spring of 1998 resulted in a peak daily flow in late March 

that approached 50,000 ft3/s (a flow that typically occurs only 

once every 20 to 25 years). Conversely, a La Niña-associated 

drought during the rest of water year 1998 and much of water 

year 1999 resulted in daily flows as low as 3,400 ft3/s during 

the late summer-early fall of this year (conditions that also 

typically occur once every 20 to 25 years). Over the past 60 

years, the highest flows and stages in the Lower Suwannee 

River typically occurred during March and April, and the 

lowest flows and stages typically occurred from November 

to January and in June and July. These seasonal flow patterns 

are strongly influenced by the seasonal climate patterns in the 

Upper Suwannee River basin and, to a lesser extent, on the 

climate patterns in the Santa Fe River Basin. Substantial fluctuations in water flows and levels also occur along much of 

the Lower Suwannee River because of tidal fluctuations near 

the mouth of the river and the low gradient of the river bottom, 

which falls (on average) about 0.10 to 0.15 ft/mi of river. The 

magnitude of these tidally induced fluctuations diminishes 

with increasing (mean) flow in the river and with increasing 

upstream distance from the Gulf of Mexico.
With the exception of the Lower Suwannee and Santa 

Fe Rivers and some of the coastal areas, channelized surface 

drainage is largely absent in the subregional study area. 

Drainage generally occurs through the Upper Floridan aquifer, 

which is a thick sequence of carbonate rocks subject to a 

considerable amount of dissolution. This dissolution accounts 

for the presence of karst features, such as numerous springs 

and closed depressions, and a generally high transmissivity 

in the subregional study area. Long-term average recharge 

to the aquifer is probably between 14 and 24 in/yr, although 

estimated recharge rates were two to three times this amount 

during water year 1998 because of wetter-than-normal conditions. Total ground-water withdrawals over the subregional 

study area were estimated to average about 35 ft3/s during 

water years 1998 and 1999. Estimates of minimum and maximum monthly withdrawal rates during this period were 5 and 

155 ft3/s, respectively, with the minimum rates occurring in 

January and the maximum rates (associated with peak levels of 

agricultural irrigation) occurring in May.

Data collected before and during the study were evaluated 

to estimate the magnitude and timing of exchanges of water 

between the Lower Suwannee and Lower Santa Fe Rivers 

and the Upper Floridan aquifer. Long-term net-ground-water 

discharge to much of these two rivers was estimated by calculating the change in discharge between three gaging stations 

(Suwannee River at Branford, Suwannee River near Wilcox, 

and Lower Santa Fe River near Fort White), using historic 

streamflow data collected during climate years 1942-2000. 

These data indicate that net ground-water discharge to this reach 

of the Lower Suwannee and Santa Fe Rivers (designated as 

reach 1 in this study) averages about 1,500 ft3/s, with about 

half the years during this period having estimated ground-water 

discharge rates between 1,200 and 1,900 ft3/s. The annual 

ground-water discharge estimates for reach 1 exhibited 

a substantial amount of interannual correlation, which is 

expected given the longer response time (relative to the river) 

of the adjacent ground-water system.

An attempt to estimate ground- and surface-water 

exchanges in reach 1 over short time scales was made by 

correcting the change in discharge calculations for channel 

and floodplain storage. The method yielded estimates of 

annual ground-water discharge of 1,000 and 1,100 ft3/s for 

water years 1998 and 1999, respectively. Estimates were 

also computed at seasonal, monthly, and daily time scales. 

In all instances (estimates from annual to daily time scales), 

however, the estimated values had wide confidence intervals, 

because the uncertainty of the basic daily discharge data from 

the three gaging stations were typically similar in magnitude 

to the estimated ground-water discharge. Stated differently, 

in most instances, it was not possible to determine if the 

day-to-day (or to a lesser extent, year to year) variations in 

ground-water discharge were real or due to uncertainty associated with estimating the daily discharge values at the gaging 

stations. For these reasons, estimating ground- and surfacewater exchanges by analyzing changes in discharge between 

gaging stations was considered suitable only for estimating the 

long-term characteristics of these exchanges (for example, the 

long-term, annual mean ground-water discharge to reach 1).

Analyses of historic spring-flow data and streamflow 

measurements taken during the study indicated that some river 

reaches received more ground-water inflow than others. The 

most concentrated areas of ground-water discharge coincided with large magnitude springs, which were commonly 

clustered. These concentrated areas of spring flow are located 

in the upper reaches of the Ichetucknee River (a tributary to 

the Santa Fe River), the Santa Fe River just upstream from 

the gaging station near Fort White, and the Suwannee River 

near Fanning Springs and Manatee Springs. Springs account 

for a large percentage of ground-water discharge to the Lower 

Suwannee and Lower Santa Fe Rivers (for example, about 55 

to 85 percent of the discharge in reach 1). Discharge measurements taken during the study indicated that the ground-water 

discharge to the Suwannee River between Branford and Rock 

Bluff Springs (between river miles 76 and 56) was small 

or negligible. Tidally induced variations in spring flow in 

Manatee Springs and Fanning Springs (as much as ±6 and ±12 

percent of the mean spring flow, respectively) during the tidal 

cycle were also observed.

A coupled model of river and aquifer flows and levels 

was developed to help evaluate ground- and surface-water 

exchanges and to determine how streamflows might change 

in response to changes in surface-water or ground-water use. 

The model consisted of two separate submodels: (1) groundwater flow in the Upper Floridan was simulated using the 

MODFLOW model, and (2) water flows and levels in the 

Lower Suwannee and Lower Santa Fe Rivers were simulated 

using the BRANCH model. Coupling of the two models was 

implemented using the MODBRANCH code. The model was 

calibrated to the wide range of hydrologic conditions that 

occurred from October 1997 to September 1999.

The simulated values of net ground-water inflow to 

reach 1 averaged about 1,350 ft3/s during water years 1998 and 

1999. In the Suwannee River downstream from the mouth of 

the Santa Fe River (reach 3), simulated average ground-water 

inflows were about 2,000 ft3/s during the same time period. 

Simulated monthly ground-water inflows to this reach of the 

Suwannee River ranged from 1,500 to 3,200 ft3/s, with the 

lower value occurring in November 1997 (during the early part 

of the winter-early spring flood period) and the higher value 

occurring during April 1998 (following the winter flood peak). 

Lower rates of simulated ground-water inflows also occurred 

during September 1999 after an extended period of drought. 

Abrupt changes in ground-water discharge were simulated in 

the vicinity of hydrograph peaks. For example, the simulated 

daily ground-water inflow to the Suwannee River downstream 

from the Santa Fe River changed from about 750 ft3/s near the 

time of peak flooding on the Lower Suwannee River during 

March 1998 to 3,800 ft3/s at about 20 days after the peak.

Summary  79
80 Exchanges of Water between the Upper Floridan Aquifer and the Lower Suwannee and Lower Santa Fe Rivers, Florida

These patterns in the timing of ground-water inflow 

variations also were evident in the simulated daily values of 

ground-water discharge to the Lower Suwannee River. Low 

rates of simulated ground-water discharge occurred during 

periods when the hydraulic gradient between the aquifer and 

river was low, either because river levels had risen faster than 

ground-water levels or because of extended droughts, which 

reduced aquifer storage. Conversely, high rates of groundwater discharge generally occurred shortly after flood peaks 

when river levels fell and ground-water levels (aquifer storage) 

increased as a result of higher recharge rates and the restriction 

of ground-water discharge (because of high river levels) in the 

preceding wet period.

Several hypothetical water-withdrawal scenarios were 

simulated with the model to evaluate the effects of water-use 

changes on long-term streamflow statistics. The characteristics 

for the scenarios that were evaluated include: (1) increased 

ground-water withdrawals, (2) reduced upstream river inflows 

to the Lower Suwannee and Lower Santa Fe Rivers, (3) a 

point withdrawal from the Suwannee River, and (4) combinations of these types of withdrawals. Changes in the streamflow 

statistics were calculated by developing linear relations between 

the daily flows that were simulated for a given scenario and the 

daily flows simulated during water years 1998-99. Sensitivity 

analyses indicated that the uncertainties of the predictions 

resulting from uncertainties in the transmissivity and riverbed 

conductance parameters used in the model were relatively small.

Use of the model for predictive purposes should generally 

be limited to estimating how flows in the Lower Suwannee 

River might change in response to changing patterns of water 

withdrawals. Simulations that produce large drawdowns near 

lateral no-flow boundaries should be avoided (or conducted 

with caution) and presented with appropriate qualifiers. The 

locations of the boundaries of the transmissivity zones used in 

the model are subject to considerable uncertainty and should 

be interpreted as representing only generalized patterns of 

transmissivity variations. For this reason, the model should not 

be used to make site-specific estimates of pumping-induced 

ground-water declines. Instead, these questions are best 

addressed using site-specific aquifer pumping tests. Despite 

these limitations, the model should provide useful information for evaluating future water withdrawals in the subregional 

study area, as well as providing a framework for: (1) evaluating changes in data-collection programs that integrate new 

water-level, flow, and aquifer property data; and (2) building 

enhanced models capable of answering new questions.

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