Suwannee River Basin and Estuary: An

Integrated Watershed Science Program

White Paper 

By Brian G. Katz1 and Ellen A. Raabe2

1

U.S. Geological Survey

2010 Levy Avenue

Tallahassee, FL 32310

2

U.S. Geological Survey

600 4th Street South

St. Petersburg, FL 33701

Open-File Report 2005-1210

U.S. Department of the Interior

U.S. Geological Survey
DISCLAIMER

This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey (USGS) editorial 

standards nor with the North American Stratigraphic Code. Any use of trade, product, or firm names is for descriptive 

purposes only and does not imply endorsement by the USGS. Neither the United States Government, nor any agency 

thereof, nor any of their employees, makes any warranty, expressed or implied, or assumes any legal liability or 

responsibility for the accuracy, completeness, or usefulness of any information, product, or process disclosed in this 

report, or represents that its use would not infringe on privately owned rights. Any views and opinions of the authors 

expressed herein do not necessarily state or reflect those of the Government or any agency thereof. 
i

Table of Contents

1.0 Executive Summary ...................................................................................................................1

2.0 Background ..................................................................................................................................2

2.1 USGS Workshop and Initiative ...........................................................................................2

2.2 Partnerships ..........................................................................................................................3

2.3 Reason for effort 2.3 Reason for effort ................................................................................................................... ...................................................................................................................3

2.4 Acknowledgments ...............................................................................................................4

3. The Suwannee River Basin and Estuary The Suwannee River Basin and Estuary ............................................................................................. ............................................................................................. 4

3.1 Suwannee Region ................................................................................................................4

3.2 Hydrogeology ........................................................................................................................4

3.3. Water Resources .................................................................................................................6

3.4 Ecosystem Function .............................................................................................................7

3.5 Socio-economic Conditions ..............................................................................................9

4. Suwannee River Basin Issues and Research Needs ..........................................................10

4.1 Threats to Water Resources ............................................................................................10

4.1.1 Water Supply ....................................................................................................................10

4.1.2 Water quality ....................................................................................................................11

4.2 Human Health ....................................................................................................................12

4.3 Ecosystem Threats .............................................................................................................14

4.3.1 Habitat Threats ................................................................................................................14

4.3.2 Threats to Species ..........................................................................................................15

4.4 Economic Base ...................................................................................................................16

5. Strategy .........................................................................................................................................17

5.1 Partnering for an Integrated Watershed Database .....................................................17

5.2 Science Plan, Workshops, and the Future ...................................................................18

SELECTED REFERENCES ................................................................................................................18
ii
1

1.0 Executive Summary

 The Suwannee River Basin (SRB) of southern Georgia 

and north-central Florida is one of the largest (28,600 

km2) and most ecologically unique blackwater river 

systems of the southeastern United States. The SRB 

is the only major drainage basin entirely within the 

Coastal Plain and contains an unrivaled mixture of 

subtropical forests, wetlands, springs, blackwater 

rivers, and estuarine habitats. The variety of habitats in 

the basin supports a range of species from temperate 

to subtropical, including several Federally or State 

endangered and protected species. The SRB and Estuary 

also support a burgeoning economy based on agriculture, 

commercial and recreational fisheries, clam farming, and 

ecotourism. 

Originating in the Okefenokee Swamp and the 

headwaters of the Alapaha, Withlacoochee and Little 

Rivers, the Suwannee River meanders for over 400 

km through southern Georgia and northern Florida 

before emptying into the Gulf of Mexico. Its chemical 

character changes dramatically as it progresses 

downstream, reflecting differences in hydrogeology, 

physiography, and land cover. In drainage area and total 

discharge, it is the second largest river in Florida and is 

designated an Outstanding Florida Water by the Florida 

Department of Environmental Protection (FDEP). The 

Suwannee River is unimpounded and undiverted and 

has been referred to as one of the most pristine and 

undeveloped river systems in the United States. 

However, the natural resources of the SRB ecosystem 

are vulnerable to a growing number of environmental 

threats. Increased use of pesticides and fertilizers, 

runoff from dairy and poultry farms, and additional 

point and non-point sources of contamination threaten 

the quality of groundwater and surface water in the 

basin. Increases in nitrate concentrations from human 

activities are causing human health concerns and adverse 

ecological effects. Issues related to water supply are 

also a major concern in the basin. Consumptive use of 

water resources is increasing in the SRB due to farm 

irrigation requirements and to increasing demands 

of a rapidly growing human population. Proposals 

for diverting water from the Suwannee River to help 

satisfy the domestic water needs of the greater Tampa 

metropolitan area have been considered over the last 

decade. However, the effects of such withdrawals on 

riverine or estuarine habitats and fauna are inadequately 

known and cannot be predicted without further study 

of the ecosystem. The establishment of minimum flows 

and levels (MFL) for surface and groundwater has been 

mandated by the State of Florida in an effort to provide 

protection to aquatic habitats, wetlands, and water 

supply (FL STAT 373, 1995). Currently existing data are 

inadequate to establish informed decisions on MFLs. 

More effective management of water resources in the 

SRB would greatly benefit from increased knowledge 

about the interactions among hydrologic processes, 

climate variability, ecosystem and human health, 

and economic development. As a model of relatively 

undisturbed large rivers in the southeastern United 

States, the Suwannee River provides an unparalleled 

opportunity for assessing its natural resources and for 

demonstrating how to manage them proactively. The 

vital interplay among agriculture, socio-economic 

pressures, underlying geology, changing river hydrology, 

and unique biological resources from the headwaters 

to the estuary is now recognized. This inclusive 

perspective presents an opportunity for the U.S. 

Geological Survey (USGS) to work closely with other 

agencies, both local and federal, in addressing issues of 

the SRB. As part of an action plan to address important 

resource-management issues in the basin and estuary, 

the USGS Florida Integrated Science Center (FISC) has 

initiated talks, workshops, and an interagency science 

plan.

The USGS is tasked with providing reliable scientific 

information to describe and understand the Earth, to 

manage its natural resources, and to enhance the quality 

of life. The USGS is well situated to address the larger 

concerns of the SRB by facilitating an integrated 

interagency research effort that links water availability 

and quality to ecosystem function and health across 

county and state boundaries. The USGS, along with 

Florida’s Suwannee River Water Management District 

(SRWMD), and other Federal and State agencies have 

been conducting monitoring and research studies in 

the basin and estuary for several decades. However, a 

more holistic approach is needed to address the myriad 

of information needs and to provide supportive data for 
2

meeting management objectives for the entire ecosystem. 

It is to this end that the combined forces of the USGS 

FISC have embarked on the Suwannee River Basin and 

Estuary Initiative to provide timely and appropriate 

scientific information prior to additional impairment 

of the basin and its various components. Efforts will 

include sustained interagency cooperation, development 

of an integrated watershed-resource information tool, 

annual workshops, an interagency science plan, and the 

development of watershed-level models for economic, 

hydrologic, and ecosystem resources.

2.0 Background

The States of Florida and Georgia, the Federal 

government, and other local organizations identified 

the Suwannee River Basin (SRB) and the Suwannee 

River Estuary System (SRES) as an ecosystem in 

need of protection because of its unique biota and 

important water resources. A growing number of 

environmental threats to the basin and estuary include 

nitrate contamination of spring waters, elevated mercury 

levels in fish, habitat loss for ecologically important 

and threatened species, microbiological contamination 

of shellfish, excessive withdrawal of groundwater for 

agricultural activities, and loss of floodplain habitat. 

Organizations with vested interests in the region formed 

a coalition, the Suwannee Basin Interagency Alliance 

(SBIA), to promote interagency management of water 

and natural resources throughout the basin.

The hydrogeology and ecological diversity of the 

watershed and estuary along with the wealth of 

background information provide a unique opportunity 

for the USGS to integrate process studies of surface 

water, groundwater, spring flow, estuarine hydrology, 

and ecosystem health into a holistic science program that 

is relevant to stakeholder concerns and consistent with 

integrated science priorities. An integrated approach is 

needed to address a myriad of scientific questions and 

to provide a supportive data framework for meeting 

management objectives for the entire ecosystem. 

2.1 USGS Workshop and Initiative

The USGS has taken the lead in addressing basin 

priorities by holding a successful workshop on integrated 

science issues at Cedar Key, Florida, September 22-24, 

2004 (Katz and Raabe, 2004). Four main goals of the 

workshop were to (1) bring together research scientists 

within and outside the USGS who are conducting studies 

in the basin and estuary, (2) provide an update on current 

scientific studies in the basin and estuary, (3) develop 

research priorities and needs, and (4) develop an action 

plan for future coordinated research activities. 

The Cedar Key workshop built upon the first basin-wide 

conference in April 2001 sponsored by the SBIA (SBIA, 

2001). A clear message that emerged from both the 2004 

Cedar Key Workshop and the 2001 SBIA Conference 

is the importance of partnerships between public 

and private agencies and other stakeholders. These 

partnerships have been instrumental in identifying and 

solving problems that affect water quality and ecosystem 

integrity.

Current research activities were presented in 2004 by 

more than 40 Federal, State, industry, and university 

scientists on four topics: hydrogeology, water quality, 

ecosystem dynamics, and information management. 

There were more than 120 attendees from over 30 

different agencies. Workshop participants identified 

science and management priorities and data gaps during 

breakout-session discussions in each topical area. 

Attendees also discussed developing an interagency 

science plan as the next step in coordinating science 

activities in the basin. The workshop closed with a 

discussion of an interagency science plan and the 

identification of three priorities for an interagency 

effort: (1) an integrated-data clearing house, (2) an 

interstate watershed study, and (3) integrated basin-wide 

models. 

The USGS was identified at the Cedar Key workshop as 

the agency best suited to develop a program that links 

water availability and quality to ecosystem function 

and health across jurisdictional boundaries and to 

provide a framework for an integrated knowledge base. 

Future USGS activities will include the coordination 

of SRB science activities through the development and 

implementation of an interagency science plan, annual 

workshops, integrated information management and 

modeling, and other integrated science products. Efforts 

to date on the Suwannee Initiative, including workshop 

results, are available at the USGS Gulf of Mexico 

website (http://gulfsci.usgs.gov/index.html).
3

2.2 Partnerships

The importance of interstate cooperation in managing 

the water and related land resources of the SRB has been 

recognized for more than a decade. In 1995, after a year 

of informal discussions among interested agencies, the 

SBIA was organized to promote ecosystem management 

throughout the basin. The SBIA is co-chaired by Florida 

and Georgia and has an executive committee made up 

of the Suwannee River Water Management District 

(SRWMD), the Georgia Environmental Protection 

Division (EPD), Florida Department of Environmental 

Protection (FDEP), and the U.S. Fish and Wildlife 

Service (USFWS). Several other Federal, State, and local 

agencies, as well as private organizations participate in 

SBIA activities. Unfortunately, the SBIA does not have 

an operating budget and the agencies are participating 

on a voluntary basis. However, resources provided by 

participating agencies have resulted in several notable 

accomplishments: the production of a LANDSAT 

satellite composite image of the entire Suwannee Basin 

in poster format, a 1998 SRWMD report on surfacewater quality, the 2001 SBIA Conference (Four Rivers, 

Two States, One Basin), and a cost-share agreement 

between the Georgia Soil and Water Conservation 

Commission (GASWCC) and the SRWMD for a person 

to promote and coordinate interstate management issues. 

Two other partnerships in the basin include the 

Suwannee River Partnership and the Upper Suwannee 

River Watershed Initiative (USRWI). The Suwannee 

River Partnership is a 53-member farm-based group 

that uses a non-regulatory approach to address nutrient 

impacts to water quality in the Lower Suwannee and 

Santa Fe River basins in north-central Florida. The 

emphasis is on voluntary incentive-based programs 

to reduce nutrient loading that will help protect the 

environment and public health. As of 2004, plans for 

reducing loading using best-management practices have 

been adopted by 92 percent of the 40 dairies, 97 percent 

of the 140 poultry farms, and 28 percent of row-crop 

farms. The proportion of nutrient loading from each 

source is unknown at this time. This issue needs to 

be addressed and is a worthy topic for future research 

studies. Over $20 million in cost-share funds have 

been provided by the U.S. Department of Agriculture 

Natural Resources Conservation Service (USDANRCS), SRWMD, Florida Department of Agriculture 

and Consumer Services (FDACS), FDEP, and from 

individual farmers. Studies are being conducted by 

several agencies to evaluate the effectiveness of bestmanagement operations and maintenance in several parts 

of the basin.

Similar efforts are being developed in the State of 

Georgia. The USRWI is a multi-agency effort designed 

to protect water quality in the Upper SRB. They 

have been holding summits for the past five years to 

educate citizens to be more aware of the problems and 

ways to protect and clean up the waters of the basin. 

Agencies and groups involved in the USRWI include 

the Pollution Prevention Assistance Division of the 

Georgia Department of Natural Resources (GDNR), 

University of Georgia Biological and Agricultural 

Engineering, South Georgia Regional Development 

Council, Alapaha Soil and Water Conservation District, 

Middle South Georgia Soil and Water Conservation 

District, Seven Rivers Resource Conservation and 

Development, University Georgia College Agricultural 

and Environmental Sciences, USDA Agricultural 

Research Service (USDA-ARS), Southeast Watershed 

Lab, Georgia Chapter Soil and Water Conservation 

Society, USDA-NRCS, Georgia EPD, and Mid-South 

Resource Conservation and Development.

2.3 Reason for effort

The USGS has been conducting research in the basin and 

estuary for nearly 100 years. Research and monitoring 

have addressed water quality, surface-water discharge, 

groundwater/surface-water exchange, floodplain forests, 

the Gulf sturgeon, benthic macrofauna, and estuarine 

habitat. Additional research is being conducted in the 

basin by agencies and university researchers. The 

missing element in the past has been integration, both 

basin-wide and inter-disciplinary. A more holistic 

approach is needed to address myriad scientific 

questions and to provide a supportive data framework 

for meeting resource-management objectives for the 

entire ecosystem in the basin and estuary.

The USGS has a vested interest in the basin and estuary 

and is committed to continue working with State and 

local agencies and other interested groups to provide 
4

unbiased scientific information about key resourcemanagement issues. The framework established by SBIA 

for interagency cooperation serves as a starting point for 

a new USGS research initiative in the Suwannee River 

Basin and Estuary to actively address an integrated 

assessment of the basin’s physical, biological, and water 

resources, and to serve as a model for future integrated 

watershed programs.

This white paper provides relevant background material 

to science and resource managers about key issues in 

the Suwannee River Basin and Estuary that will help 

in developing a comprehensive and integrated science 

program. This paper addresses basin and estuary 

threats, science priorities, interagency coordination, 

and integrated science goals. Long-term goals of 

the Suwannee Initiative are to establish a basin-wide 

knowledge base, strong interagency collaboration for 

monitoring and research, and integrated basin-wide 

models that can be applied to more impacted river basins 

in other parts of the United States. The white paper also 

serves as a foundation for strengthening partnerships 

in a basin-wide, interstate effort. A clear message that 

emerged from both the 2004 Cedar Key Workshop 

and the 2001 SBIA Conference is the importance of 

partnerships between public and private agencies and 

other stakeholders. These partnerships have been 

instrumental in identifying and solving problems that 

affect water quality and ecosystem integrity. Several 

notable examples of these fruitful partnerships are the 

Suwannee River Partnership, the USRWI, and the SBIA. 

2.4 Acknowledgments

Thanks are extended to FISC scientists and managers 

who have contributed to this effort. Also, contributions 

from personnel from Federal, State, and local partnering 

agencies are gratefully acknowledged and have 

significantly improved this document.

3. The Suwannee River Basin and Estuary

3.1 Suwannee Region

The SRB is located entirely within the Coastal Plain 

physiographic region of the southeastern U.S., extending 

from Cordele, Georgia, to Cedar Key, Florida, at the 

Gulf of Mexico (Figure 1). From the eastern headwaters 

in the Okefenokee Swamp to the Gulf of Mexico, the 

SRB has been referred to as one of the most pristine 

and undeveloped river systems in the United States. 

It contains a unique combination of subtropical and 

temperate forests, swamps, fresh and tidal wetlands, 

and habitat for aquatic and terrestrial wildlife. The 

expansive and grassy estuary provides one of 

the most significant nearshore habitats in the 

northeastern Gulf of Mexico. The Suwannee River is 

one of only a few rivers within the U.S. that has suffered 

negligible damage from human activities, including 

damming, channeling, redirection, or the introduction of 

large quantities of contaminants. 

The entire watershed connecting DOI trust lands from 

the Okefenokee National Wildlife Refuge (NWR) to 

the Lower Suwannee NWR (LSNWR) harbors a rich 

assemblage of exceptional biological, geological, and 

hydrological resources, and supports an assortment 

of ecologically important species. Significant tracts 

of land within the SRB are protected and managed by 

local, State, and Federal natural resource agencies, 

non-government organizations, and private landowners. 

There are over 50 recreation sites along the river 

and its tributaries, including many state and county 

parks. Organizations with important land-management 

activities within the watershed include: USFWS 

(Okefenokee and LSNWR), U.S. Forest Service (USFS), 

Florida SRWMD, Florida Department of Parks and 

Recreation, Florida Fish and Wildlife Conservation 

Commission (FFWCC), FDEP, GDNR, The Nature 

Conservancy, and several silviculture and mining 

corporations. Selected sites along the Suwannee 

River and tributaries are currently monitored for water 

quality and limited benthic sampling by the USGS 

Water Resources Discipline and National Water Quality 

Assessment Program (NAWQA), Florida SRWMD, and 

the FFWCC.

3.2 Hydrogeology

Geology, climate, and hydrology are intimately linked in 

the Suwannee River Basin. Variations in the underlying 

geology, precipitation, hydrologic cycle, and general 

climate provide the backdrop for a diverse and complex 

watershed. The hydrogeology in the SRB is highly 

varied in terms of its underlying geologic framework 

and consists of three distinct, but dynamically linked 
5

hydrologic regimes. The basin covers nearly 28,600 km2

drained by the Suwannee, Alapaha, Withlacoochee, 

and Santa Fe Rivers. The SRB includes the 1,500 km2

Okefenokee Swamp, the Nation’s second largest wetland 

complex, small streams, blackwater rivers, tidal salt 

marshes, and hundreds of springs. Headwaters for the 

Suwannee River originate in two distinct areas of the 

Atlantic Coastal Plain of Georgia. The eastern headwaters 

are predominantly in the Okeefenokee Swamp, and the 

western headwaters include the Alapaha, Little, and 

Withlacoochee Rivers (Figure 1). 

The hydrologic and chemical characteristics of the 

Suwannee River change dramatically as the river flows 

toward the Gulf of Mexico, reflecting differences in the 

underlying geology and physiography of each region 

it drains. Surface-drainage characteristics, including 

streams, lakes and wetlands, are more abundant in the 

upper two-thirds of the SRB and the Upper Santa Fe 

River basin. Surface drainage exists where soils contain 

more clays and fine sediments that are resistant to 

infiltration. These up-gradient waters are acidic and teacolored as a result of residence-time and flow through 

G E O R G I A

F L O R I D A

30 Kilometers

30 Miles

0 20

0 20

84°

32°

31°

30°

29°

83° 82°

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

EXPLANATION

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

Albers Equal-Area Conic Projection,

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

Suwannee River Drainage Basin

Okefenokee Swamp and NWR

Lower Suwannee River NWR

Suwannee River Estuary System (SRES)

Gulf of Mexico

Cody Scarp

GA

FL Location

map

Big Bend

Figure 1. Location map showing the Suwannee River Basin and Estuary system.
6

forested swamps with decaying vegetation. Down 

gradient, in the southern third of the SRB, a relatively 

thin layer of highly porous sands overlies limestone karst 

and the Floridan Aquifer system. The water quality of 

the Lower Suwannee River exhibits strong groundwater 

characteristics. Downstream of White Springs, FL, the 

Suwannee River receives inflow from over 200 known 

springs. The influx of clear, mineral-rich groundwater 

from the Floridan Aquifer buffers the acidity and darker 

color of predominantly surface water from upstream. 

The relative absence of surface-water features such as 

streams, lakes, and wetlands indicates areas of direct 

recharge of rainfall to the aquifer in the karst-dominated 

region. 

The transition between the karst region and up-gradient 

region includes many stream-to-sink subbasins, where 

stream flow is abruptly captured by sinkholes and routed 

to the aquifer. This transition zone lies along a feature in 

Florida known as the Cody Escarpment. The Suwannee 

River is the only stream in the SRB flowing across the 

escarpment that is not fully captured by sinkholes. This 

area and the numerous springs along the reaches of 

the Lower Suwannee River act as points of interaction 

between surface water and groundwater. 

The SRES consists of the tidal portion of the Suwannee 

River, nearshore intertidal and subtidal zones, a small 

delta, and the Gulf of Mexico from Horseshoe Beach 

to Cedar Key. A series of oyster reefs and a shallow 

offshore shelf provide a measure of protection for this 

otherwise everted and open-estuarine system. The 

coastal area is characterized by low topographic and 

bathymetric gradients, sedimentary deposits over karst 

limestone, and the Floridan Aquifer is at or near the land 

surface throughout this coastal region (Montague and 

Odum, 1997). The tidal river is bordered by wetland 

and upland forests, freshwater marsh, and brackish 

marsh habitat. The lower and nearshore estuary is 

characterized by a mixture of fresh and saltwater marsh, 

tidal creeks, mudflats, submerged aquatic vegetation 

(SAV), and submerged sand and shell features. The 

estuary, its creeks, rivers, and emergent zones provide 

wildlife habitat for many ecologically important and 

valued species. The SRES is a productive estuary. An 

area of elevated phytoplankton seaward of the Suwannee 

River outflow was attributed to light and nutrient 

availability (Bledsoe and Phlips, 2000). The coastal 

waters are influenced not only by surface freshwater 

inputs and tidal exchange, but also by submarine 

groundwater discharge. Evidence for submarine springs 

and seeps is apparent from the relatively high radium 

concentrations in estuary and offshore waters (Burnett 

and others, 1990). Submarine groundwater discharge 

may also contain elevated concentrations of nutrients 

and carbon. The estuary system is thought to be mostly 

pristine, but the shellfish industry has been negatively 

impacted in the past by contamination. 

3.3. Water Resources

Effective management of water resources in the basin 

and estuary is essential for water sustainability, human 

health and the viability of the ecosystem, agricultural 

needs, and economic development. To address these 

issues, it is critical that historical and current information 

are available regarding amounts and fluctuations in 

rainfall, discharge, recharge, and the interaction between 

surface water and groundwater. In 1995, the State of 

Florida mandated that all water management districts 

establish minimum flows and levels (MFLs) for basins 

and subbasins. MFLs are defined as the flow or level 

of surface water or groundwater at which further 

withdrawals of water would be significantly harmful to 

the water resources or ecology of the area (Florida Water 

Resources Act, 1995, Statute, Ch. 373.042). Also, 

detailed hydrologic information is needed for accurate 

calculations of total maximum daily loads (TMDLs), 

the maximum amount of a pollutant that a waterbody 

can receive and still meet water quality standards, 

which have been established by the U.S. Environmental 

Protection Agency (EPA) Clean Water Act (Section 303). 

Historical and current hydrologic information are 

available for many sites throughout the basin and 

provide a useful framework to build on. Stream flow 

has been continuously monitored in the SRB since 

the establishment of one of the first gauges in Florida, 

Suwannee River at White Springs, in 1906. This gage is 

still in operation and currently the USGS and SRWMD 

monitor river levels or flow at over 60 gauges in the 

basin through cooperative programs with the States 

of Florida and Georgia. Ten of these gauges are in 

Georgia in the upper reaches of the Suwannee and two 

tributaries, the Alapaha and Withlacoochee Rivers. The 

remaining gauges are in Florida and include sites on the 
7

Withlacoochee, Alapaha, and Santa Fe Rivers as well as 

the main stem of the Suwannee. Stream flow also has 

been measured for several decades in small watersheds 

within the Upper Suwannee River Basin. The Little 

River watershed near Tifton, Georgia, was instrumented 

in 1967 for rainfall and stream flow measurements by 

the Southeast Watershed Research Laboratory (SEWRL) 

of the USDA-ARS. The 334 km2 Little River watershed 

includes seven gaged sub-watersheds ranging in size 

from 2.6 to 115 km2. The original hydrologic network 

consisted of 55 rainfall gauges, eight flow-measurement 

sites, and three floodplain alluvial groundwater-stage 

recorders. In 1981 this network was reduced to the 

current design of 29 rainfall gauges and five flowmeasurement sites (http://sacs.cpes.peachnet.edu/sewrl/). 

A regional surface-water network was begun in 1989 

by the Suwannee River Water Management District to 

assess water quality in priority water bodies as identified 

in the Surface Water Improvement and Management 

(SWIM) Program. Currently, SRWMD maintains 

the Water Assessment Regional Network (WARN) 

to monitor river, lake, and groundwater levels, river 

discharge, rainfall, and surface- and groundwater quality 

conditions (Hornsby and others, 2003). Water levels 

in 21 lakes are monitored daily, weekly, or monthly, 

depending on the specific water body. Streams and river 

levels are measured at varying frequencies at 51 sites, 19 

of which are maintained by USGS. A flood-monitoring 

network consists of 23 river gauges, of which 19 are 

automated. In addition, rainfall data are collected from 

55 monthly stations, of which 31 contain tipping-bucket 

rain gauges that provide near real-time data. 

Spring flow in the Lower SRB is being measured at 14 

gauges installed in 2001-2002, including the Ichetucknee 

springs system, Troy, Fanning, and Manatee Springs, 

which provide a substantial amount of the base flow 

to the Suwannee River. The SRWMD maintains 

groundwater-monitoring networks that include records 

of groundwater level for 1,028 wells. Most of these 

wells are only measured during record high or low flow 

conditions, and 362 wells are inactive. Monthly water 

levels are being measured at 181 wells, of which 73 

have continuous recorders. SRWMD maintains two 

groundwater quality networks, which began in October 

2000: (1) a trends network consisting of 97 wells 

tapping the Floridan Aquifer system that are sampled 

quarterly, and (2) a status network consisting of 146 

randomly selected wells that are sampled once per year. 

Groundwater quality data exist for over 1,700 wells that 

have been sampled from 1975 to present.

Effective management of water resources in the basin 

would benefit from linked hydrologic and water-quality 

models and integrated monitoring that crosses all 

jurisdictional boundaries. A well-developed hydrologic 

model of the watershed and estuary system that 

addresses surface and groundwater interactions, seasonal 

and inter-annual variability in rainfall and recharge, and 

long-term climate forecasts would facilitate assessment 

of water supply and demand and greatly assist resource 

managers.

3.4 Ecosystem Function

A series of multi-disciplinary studies of physical, 

chemical, and biological processes in the basin is needed 

to understand complex interactions among system 

components. The Suwannee River is one of only a 

few rivers within the U.S. with relatively intact historic 

hydrologic form and function. The SRB and Estuary 

are known for high-quality wildlife habitats, including 

pine flatwoods, freshwater swamps, salt marshes, and 

seagrass beds. The SRB habitats support terrestrial 

and aquatic communities and several Federally or State 

protected species including the threatened Gulf sturgeon 

(Acipenser oxyrinchus desotoi), the endangered West 

Indian manatee (Trichechus manatus latirostris), and 

rare freshwater mussel species. Tree species richness 

in wetland forests of the Lower Suwannee River 

floodplain is among the highest of North American 

river floodplains. The spring systems in the Lower SRB 

contain the greatest diversity of obligate, subterranean 

decapod crustaceans in the world. Yet, little is 

known about this fauna regarding their distribution, 

abundance, ecological requirements, and sensitivity to 

changes in water quality and other abiotic stressors. 

The basin ecosystem, in addition to intrinsic natural 

values, supports commercial and recreational fisheries, 

ecotourism, and recreational opportunities for basin 

residents and visitors. Existing management of the basin 

is focused on individual tracts of land or individual 

resources within the watershed. A comprehensive 

research plan is needed to identify how watershed 

habitats are linked not only to each other, but to wildlife, 
8

water quality, surface water and groundwater supply, 

underlying geology, and human activities.

The SRB includes two USFWS NWR. The Okefenokee 

NWR encompasses approximately 396,000 acres 

in Georgia and contains most of the 438,000 acre 

Okefenokee Swamp. This refuge provides sanctuary and 

breeding grounds for migratory birds, endangered and 

threatened species, and other wildlife. The LSNWR was 

established to protect 20 miles of the Suwannee River 

upstream from its mouth in Florida with approximately 

52,000 acres including river floodplain, wetlands, and 

uplands. 

Research on individual species includes life history and 

habitat use by manatees (Langtimm and Beck, 2003), 

and Gulf sturgeon (Sulak and others, 2002). Historical 

data are being used to build a comprehensive model 

of Gulf sturgeon life history, ecology, habitat use, 

population biology, and behavior (Sulak and Randall, 

2002). Other studies are assessing habitats for freshwater 

species such as rare freshwater mussel species endemic 

to the SRB and a faunal inventory to provide baseline 

information on freshwater fishes and mussels at 

springs within the Florida State Park system (Lydeard 

and others, 1999). The USGS Southeast Amphibian 

Research and Monitoring Initiative (SEARMI) is 

responsible for monitoring the status of 144 species 

of amphibians from the southeast, Puerto Rico, and 

the Virgin Islands (Dodd and Smith, 2003). Research 

has been conducted in the Okeefenokee NWR and 

LSNWR, where little or no historical amphibian data 

currently exist. SEARMI has documented 19 species of 

frogs and four species of salamanders from LSNWR. 

A comprehensive quantitative assessment is being 

made of the diversity, biomass, abundance, and species 

dominance of the benthic invertebrate macrofaunal 

populations inhabiting the Suwannee River and adjacent 

river-mouth estuary (Brooks and Sulak, 2004).

The SRES is a productive and relatively unaltered 

natural system where the Suwannee River enters the 

Gulf of Mexico. The SRES harbors shallow habitat, 

seagrass, saltmarsh, and low-salinity conditions along 

the coast from Horseshoe Beach to Cedar Key. The 

estuary is a State Aquatic Preserve, a part of the 

LSNWR, and has been designated an Outstanding 

Florida Water. This grassy stretch of coast, with few 

natural sandy beaches, is best known for its fishing and 

shellfish industry. The SRES contains expansive oyster 

reefs, sand bars, tidal creeks, salt marsh, submerged 

aquatic vegetation, and productive clam leases. These 

estuarine habitats support ecologically important and 

valued fish species, many during breeding, nursery, and 

juvenile phases. SRES contains large areas of estuarine 

habitat for many ecologically important and valued 

fish and mammal species, such as the Gulf sturgeon 

and the West Indian manatee. The Florida Fish and 

Wildlife Research Institute (FFWRI) at the Kirkpatrick 

Marine Lab in Cedar Key, Florida, maintains an active 

monitoring program of fish communities and aquatic 

habitats in the estuary.

Previous USGS coastal research utilized a time series 

of remotely sensed imagery, historic charts, and aerial 

photography to identify short-term fluctuation and longterm changes along the Big Bend marsh coast (Raabe 

and Stumpf, 1997; Raabe and others, 2004). This earlier 

effort included the SRES in an evaluation of regional 

coastal-vegetation change, marine transgression, and 

adaptation of the ecosystem to fluctuations in sea 

level, drought, and catastrophic events such as storm 

surge. A similar approach to biomass change in the 

basin, landcover alteration, flooding regimes, detailed 

topography, water quality, and habitat can be mapped 

and modeled using various remotely sensing and 

mapping tools and lined to ground-based data such as 

discharge, drought index, precipitation, fire, logging, and 

biological resources. 

Interrelated ecological and hydrodynamic issues are 

being investigated in the SRES by USGS in cooperation 

with the USFWS and the FDEP. Hyperspectral remotely 

sensed imagery is being used to link structural habitat 

with hydrologic conditions, and relate fish usage to 

habitats in the estuary (Raabe and others, in press; 

Dennis and others, 2001). This study linked expertise 

from several disciplines to understand this ecologically 

complex and dynamic system better. The mapping effort 

highlights the links in the estuary between underlying 

geology, surface water and groundwater hydrology and 

marine conditions. The estuary is coupled to floodplain 

and watershed dynamics, as well as to sea level and 

marine conditions in the Gulf of Mexico. The SRES 

and portions of the Gulf of Mexico are now being 

evaluated through remote sensing, empirical data, and 
9

the development of a three-dimensional hydrodynamic 

and transport model to understand the relation between 

salinity characteristics, groundwater, and freshwater flow 

in the estuary. 

Similar efforts to map habitat, link species to habitat, 

and model hydrology are needed throughout the SRB. 

Effective research and informed management of 

the basin’s ecological resources would benefit from 

integrated efforts and a basin-wide resource information 

tool. By incorporating state-of-the-art imagery and 

mapping techniques with biologic and hydrologic 

investigations, this integrated effort would provide the 

needed links between hydrology and ecology of the SRB 

from Georgia’s swamplands and wetlands to the Florida 

estuary at the Gulf of Mexico.

3.5 Socio-economic Conditions

Historically, the SRB has been largely rural, sparsely 

populated, and undeveloped. Agriculture accounts for 

most of the developed land uses within the SRB in 

both Georgia and Florida, including silviculture, row 

crops, and pasture. The forest industry, primarily pine 

plantations, is active in large areas of the SRB and 

provides timber and fiber for mills. Trends over the last 

decade indicate a general shift toward more intensive 

production of food and forage crops as well as animals. 

In recent years, ecotourism has boomed, attracting 

visitors to the clear springs, scenic waterways, abundant 

wildlife, and rural landscapes.

 Population growth and development within the SRB 

have been steady since the 1960s. The population in the 

basin increased from 384,000 in 1990 to about 430,000 

in 2000. Growth projections in and around the SRB 

indicate a similar increase in population over the coming 

decade. Irrigated acreage has increased considerably in 

the SRB over the last several decades as technologies 

have improved and market conditions have changed. 

Crops and products from the SRB include dairy and 

poultry, fruits and vegetables, grains, pasture, and 

forestry products. Basin-wide precipitation and runoff 

is the primary water source for agriculture, industry, 

and urban development. Small surface-water reservoirs 

supplement water supply in Georgia, and groundwater 

from the Floridan Aquifer supplements the water supply 

in the Florida karst region. 

Finding the balance between economic growth, human 

health, and protection of natural resources is a challenge 

across the United States. Partnerships in the SRB and 

Estuary system continue to demonstrate the importance 

of collaboration among State, local, and Federal agencies 

in addressing watershed issues at the local scale with a 

national perspective. Over the past 20 years, the USDAARS and the University of Georgia have established 

fundamental knowledge on the functions of riparian 

ecosystems for stream-corridor restoration in the Upper 

SRB. Best management practices (BMP) in stream 

corridor and riparian management efforts incorporate 

an integrated approach that accounts for different types 

of pollutant sources, including livestock enterprise. 

Several agricultural management efforts in the western 

headwaters of the SRB are voluntary, incentive-based 

projects. In Florida, the SRWMD has taken a proactive 

approach for resource management by land acquisition, 

cooperative studies with other agencies, and extensive 

monitoring networks. The Suwannee River Partnership, 

a farm-based cooperative effort, has obtained over 

$20 million in cost-share funding from USDA-NRCS, 

SRWMD, FDACS, FDEP, and from individual farmers 

to create voluntary incentive-based programs that reduce 

nutrient loading to groundwater. Recent cooperative 

studies between the USGS and SRWMD have addressed 

issues such as timescales and sources of nitrate 

contamination of groundwater, hydrodynamics of flow 

to the estuary system, and potential impacts of flow 

reductions on tidal floodplain forests.

Apart from intrinsic natural values, the riverine, 

estuarine, and spring systems support commercial and 

recreational fisheries, ecotourism, and recreational 

opportunities for basin residents and visitors. Issues 

related to water quantity are a major concern for these 

activities in the basin. The SRB contains an abundance 

of water that is sought by more developed parts of the 

State in addition to water supply demands within the 

basin itself. Effective management of water resources 

in the SRB would benefit from improved knowledge 

about the interactions among human activities, economic 

development, climate variability, hydrologic processes, 

and ecological function.
10

4. Suwannee River Basin Issues and 

Research Needs

4.1 Threats to Water Resources

Competing demands on the natural resources of the 

SRB require a better understanding of the sources and 

effects of contamination, water withdrawals, and climate 

change and the interactions among these stressors. 

Climate variation alone can result in significant changes 

in rainfall, with subsequent impacts on surface-water and 

groundwater supply. Natural fluctuation in water supply, 

coupled with water consumption, can place added 

stress on biological communities. Intermittent droughts 

in Florida over the last two decades have heightened 

concerns about management of water resources within 

the watershed. In the future, it will be desirable to 

improve interagency communication and coordination 

of groundwater and surface water monitoring, as well as 

developing predictive capabilities.

Improvements to Basin-Wide Water 

Resources Information and Management

• Develop and apply consistent and comparable datacollection methods

• Establish improved technique and coordination 

among agencies and across jurisdictions

• Ensure spatial distribution and environmental 

coverage

• Develop integrated land-use and land-cover database: 

past, present, and planned

• Develop improved groundwater/surface water 

interaction models

• Improve predictive capabilities

4.1.1 Water Supply

Consumptive use of water resources is increasing 

in the SRB due to farm irrigation requirements and 

to increasing demands of a rapidly growing human 

population. Although the Suwannee is undiverted, 

groundwater is already being mined for bottling at 

several spring sources (about one million gallons/

day near Ginnie Springs and Madison Blue Spring). 

Changes in the groundwater-flow regime can have 

impacts on stream ecosystems by changing in-stream 

flow characteristics, and water temperature and quality. 

Feedback loops can start from a single event or source, 

resulting in degradation or loss of resource quality or 

capacity. For instance, a change in flow regime through 

hydrologic alterations can have important impacts 

on stream ecosystems by changing in-stream flow 

characteristics and water temperature. Higher water 

temperatures reduce oxygen solubility and thus tend 

to reduce dissolved-oxygen concentrations. Further, 

increased water temperatures increase the rate of 

metabolic activity in natural waters, which in turn can 

increase oxygen consumption by aquatic organisms. 

Adequate groundwater is especially important in the 

Lower Suwannee River where spring systems are 

abundant. Demands for groundwater from intensifying 

urban development and extensive agricultural activities 

in this part of the basin have resulted in increased 

withdrawals of water from the Upper Floridan Aquifer. 

As an example of water-quantity-related problems, some 

springs in the SRB have essentially stopped flowing at 

certain times of the year due to lowering of the water 

table that results from pumping and lower recharge to 

the aquifer. A growing population, changing land use, 

and increased demands on natural resources are altering 

the rural nature of the SRB. 

Proposals for diverting water from the Suwannee River 

to help satisfy the domestic water needs of the greater 

Tampa metropolitan area have been considered over the 

last decade. The effects of such withdrawals on riverine 

or estuarine habitats and fauna are inadequately known 

and cannot be predicted without an integrated study and 

model of the ecosystem.

Water Supply/Water Budget Research 

Needs and Opportunities

• Extend hydrologic models to include climate-change 

scenarios:

• Evaluate past and potential interannual and 

seasonal variations
11

• Tie MFLs to regional changes in climate, 

precipitation, and sea level

• Basin-wide hydrologic model

• Extend and integrate surface and groundwater 

models across Florida and Georgia

• Identify and map existing land use and projected 

changes in water consumption

• Model impact of changes in water use on springs, 

biological resources, and water quality 

• Extend water budget models to estuary

• Improve and standardize data-collection 

techniques in Lower Suwannee and Estuary

• Evaluate seasonal and interannual variations in 

estuarine mixing zones

• Assess coastal groundwater discharge and role of 

submarine springs

• Model tidal and freshwater interactions

4.1.2 Water Quality

Although studies in the basin indicate generally good 

overall water quality, large nitrogen inputs to the land 

surface from fertilizers, animal wastes, sewage effluent 

(septic tanks and land application of treated sewage 

effluent), and atmospheric deposition, are raising 

concerns regarding human and ecosystem health. This 

problem occurs along most of the entire course of 

the Suwannee River, as evidenced by massive mats 

of benthic filamentous algal turf from Big Shoals to 

the lower parts of the basin. Nitrate concentrations 

in groundwater and spring waters have increased 

substantially from near background concentrations of 

less than 0.1 mg/L in the 1960s and 1970s (Rosenau 

and others, 1977) to more than 5 mg/L in the late 1990s 

at some first-magnitude springs (Hornsby and Ceryak, 

1999; Katz and others, 1999). In some areas of the basin, 

nitrate-N concentrations in the Upper Floridan Aquifer 

(the source of water supply) exceed the maximum 

contaminant level of 10 mg/L for drinking water. Also 

of concern are the effects of high nitrate concentrations 

in the SRES, such as contamination of the local shellfish 

industry and impacts to coastal fisheries.

Elevated nitrate concentrations in rivers can cause 

eutrophication, which can result in algal blooms and 

depletion of oxygen that can lead to fish kills (Bledsoe 

and Phlips, 2000). Increases in nitrate concentrations 

from human activities may cause adverse ecological 

effects, indicated by an increase in periphyton biomass 

along the middle and lower reaches of the Suwannee 

Results of water quality degradation:

Potential human health effects

Loss of economic base (fishery, shellfish industry, 

recreation, ecotourism)

Loss of important species or habitats

Sources of water quality degradation:

Atmospheric deposition (Hg)

Concentrated animal-feeding operations

Cropland farming

Waste-disposal systems (human)

Industrial wastes

Land-surface/land-cover alterations

Drought or other hydrologic change

Types of contamination:

Nitrogen and other nutrients

Pesticides, chemical compounds and their 

metabolites

Sediment load and reduced water clarity

Toxins: mercury and organic chemicals

Endocrine disruptor compounds

Pathogens, Bacteria, and Parasites

Infectious disease: Cryptosporidium parvum
12

River (Hornsby and Mattson, 1998). High nitrate 

concentrations are also a major concern in the SRES.

Bioaccumulation of mercury in certain fish species 

is an important water-quality issue in the Suwannee 

River Basin. Mercury levels in crayfish, sunfish, 

and largemouth bass increased significantly in the 

Suwannee River with increasing distance upstream of 

its mouth (Chasar and others, 2004). Fish-consumption 

advisories for mercury in largemouth bass have been 

issued for the Santa Fe River, a major tributary to the 

Suwannee River. Also, fish-consumption advisories 

for mercury have been issued for stream segments in 

the Alapaha, Withlacoochee, and Upper Suwannee 

subbasins in Georgia. Additional work needs to be done 

to evaluate how mercury sources and transport and local 

biogeochemical processes affect mercury concentrations 

in water and biota. 

Water quality within the basin, the river floodplain, river 

channels, springs, wetlands, and estuary is essential to 

both human and ecosystem health. Animal production 

(swine and poultry) with confined feeding operations is 

expected to increase in the Coastal Plain. Management 

of water quality in the SRB will require consistent 

basin-wide monitoring networks, a linked basin-wide 

database, hydrologic models, and the monitoring of areas 

where BMPs have been implemented to evaluate their 

effectiveness in reducing nutrient loading and economic 

viability.

Water Quality Research Gaps and 

Opportunities 

• Evaluate natural reduction of elevated nitrate via 

surface water/groundwater interactions:

• Role of wetlands in denitrification process

• Effects of mixing of organic-carbon-rich river 

water with groundwater and reduction of nitrate 

due to denitrification in the aquifer during high 

flow conditions

• Evaluate occurrence of agricultural chemicals in 

groundwater, springs, river, and estuary

• Assess impact of endocrine-disruptor compounds, 

pesticides, and their degradates to aquatic system 

health

• Assess impact of atmospheric transport of mercury 

and other airborne contaminants on human health and 

ecology

• Apply sediment-transport algorithm to evaluate 

sediment-transport process

• Investigate use of acoustic-velocity meters as 

surrogate sediment indicator

• Link water quality to biogeochemical processes:

• Biological interactions from micro to macro 

scales

• Physical and chemical interactions in water, soil, 

and rock

• Link water quality from headwaters to estuary:

• What are the minimum flows and levels needed to 

preserve water quality and protect ecosystem and 

human health?

• Investigate relations among nutrient-enriched 

freshwater and the health, productivity, and 

sustainability of the downstream and estuarine 

ecosystems

• Address effect of nutrient loads in Upper 

Suwannee on biota in the estuary

4.2 Human Health 

The occurrence of natural and anthropogenic 

contaminants in water and their effect on human health 

has become an increasing environmental concern. 

Naturally occurring contaminants in the SRB and 

Estuary include airborne dusts that can be transported 

from western Africa in trade winds across the Atlantic 

Ocean to the Caribbean and to the southeastern U.S. 

These dusts contain a variety of plant, animal, and 

opportunistic human pathogens from 20 different 

bacterial genera and fungi that contain both pathogenic 

and nonpathogenic members (Kellogg and others, 

2004). Radionuclides that are present in Hawthorn 

Group sediments overlying the Upper Floridan Aquifer 

represent another source of natural contaminants. 

Gamma rays, alpha particles, and beta particles that 

are given off during radioactive decay or uranium or 
13

thorium-decay series nuclides (e.g. 222Rn, 226Ra, 224Ra, 228Ra, 234U, and 238U) are all ionizing radiation. Each 

type of radiation has the potential to damage or destroy 

living cells. For example, radium in drinking water is 

known to increase cancer risk, primarily for bone and 

sinus cancer (Mays and others, 1985). Exposure to radon 

gas has been recognized by the Surgeon General of the 

United States as being second only to cigarette smoking 

as a cause of lung cancer (U.S. Environmental Protection 

Agency, 1992).

Atmospheric transport and deposition of mercury 

is an important health issue. Total maximum daily 

loads (TMDLs) for total mercury were established 

for the protection of public health associated with the 

consumption of fish in Georgia. Impaired waters that 

were listed on the State of Georgia’s 2000 Section 

303(d) list were located in streams in the Alapaha, 

Withlacoochee, and the Upper Suwannee subwatersheds 

in Georgia. 

Several human health concerns are associated with 

elevated nitrate concentrations in groundwater used 

for drinking. Infants under six months of age who 

ingest nitrate in drinking water are susceptible to 

methemoglobinemia, which can lead to reduced 

blood-oxygen levels and can result in death. For these 

health concerns, the U.S. EPA established a maximum 

contaminant level (MCL) for nitrate of 10 mg/L as 

nitrogen (N) for drinking water. Another study found an 

increased risk of non-Hodgkins lymphoma associated 

with nitrate concentrations of 4 mg/L or more in rural 

drinking-water supplies. 

Little is known about the presence of bioactive 

chemicals in surface and groundwaters in the basin. 

The presence of these compounds in aquatic systems 

originates from the waste disposal of human and 

veterinary pharmaceuticals and from active ingredients 

in personal care products. Recent studies have shown 

that pharmaceuticals, endocrine-disrupting chemicals 

(hormones), and other organic wastewater contaminants 

are present in streams throughout the U.S. (Kolpin 

et al., 2002). Although present in generally very low 

concentrations, little is known about the potential 

interactive effects on human health and the health 

of aquatic organisms that may occur from complex 

mixtures of organic wastewater contaminants and their 

metabolites in surface waters. 

During prolonged wet periods, when river floodwaters 

flow into the karstic Aquifer system along the Lower 

Suwannee River corridor, there is an opportunity for 

waterborne pathogens (e.g. Cryptosporidium and 

Giardia oocysts) to enter the aquifer system. Also, 

these waters contain very high concentrations of 

naturally occurring organic matter, which could react 

with disinfectants such as chlorine and produce harmful 

trihalomethanes and haloacetic acids.

In the late 1980s, contaminants from human and dairy 

wastes were transported in river water and closed the 

oyster industry at the mouth of the Suwannee. Better 

waste-management systems that replaced failing septic 

tanks, and management of the upstream dairy farms 

served to improve water quality in the estuary. A 

prospering clam industry, designed to bolster failing 

economy of coastal counties, is now established between 

the Suwannee River mouth and Cedar Key. Cedar 

Key clams are highly sought after and are now the 

largest source of farm-raised clams in the U.S. Water 

quality monitoring continues in the clam leases as well 

as renewed interest in upstream land-use and land use 

change. Future failures to maintain water quality at 

the mouth of the Suwannee and Estuary is a constant 

threat to the newly established local economic base. In 

addition, natural disasters such as the 2004 hurricane 

season can wreak havoc on the clam leases, effectively 

destroying the 2004 crop. 

Research Opportunities in Human Health

• Endocrine disruptor chemicals and organic 

wastewater compounds 

• Mercury methylation and accumulation in fish tissue

• Fate of nitrate in drinking water and aquatic systems

• Radionuclide occurrence in drinking water and 

associated health issues

• Pathogens and bacteria influx to karstic groundwater 

during flood periods

• Elevated natural organic material and the formation of 

disinfection by-products
14

4.3 Ecosystem Threats

Changing land use and a growing human population 

threaten ecological resources in the basin through 

pollution, geographic limitation, food web disruption, 

water supply, and the introduction of invasive species. 

Alteration in the timing, duration, and frequency of 

flooding and the concomitant degradation of water 

quality directly threaten aquatic habitat and species. 

Natural environmental variability, such as drought or 

severe storms, may further impair ecosystem resilience. 

The SRB lies entirely within the Coastal Plain province, 

yet it straddles the climatic boundary between temperate 

and subtropical species distributions, where tropical 

species reach their northern limits, and temperate species 

reach their southern limits. Adaptations forced by 

climate change, such as the migration of ‘borderline’ 

species, places additional stress on biological resources. 

Threats to ecological resources may be further subdivided into habitat threats and threats to species, each 

with distinct research needs.

In general, methods that link geographic distribution of 

hydrologic and physical features with human activities 

and biological resources will more effectively serve 

ecosystem management efforts to address basin-wide 

ecosystem threats.

General Ecosystem Threats

• Natural environmental variation such as precipitation 

and temperature

• Alteration to water supply

• Pollution and disease

• Geographic constraints through land use or climate 

change

• Alteration of trophic dynamics (nutrient/energy 

transfer)

• Invasive species

4.3.1 Habitat Threats

Habitats in the basin are closely linked to topography, 

hydrology, climate, soils and geology. Each habitat is 

limited geographically by the co-occurrence of specific 

environmental characteristics. As pressures increase 

from human activities, the total area available for each 

habitat is decreased and connectivity between habitats 

may be eliminated. Today there are insufficient data in 

the basin on the location and condition of habitats or of 

imminent threats to habitats. A primary research need 

is a thorough mapping of basin features and the habitats 

associated with each suite of features. An analysis of 

land use and projected land use is needed to evaluate 

existing and potential threats to habitat area, habitat 

links, and habitat quality. Also needed is an evaluation 

of the role of water supply to habitat quality and a 

hydrologic model for evaluating future scenarios. Water 

quality and water supply play important roles in the 

value of habitat to particular species. Small alterations 

to the flooding regime, nutrient loads, and water clarity 

can have profound impacts on the species present. 

The role of water supply in the viability of habitats 

varies between the Upper and Lower Suwannee Basin, 

and the estuary system. Surface water storage and 

flow plays a critical role in the Upper Suwannee, but 

groundwater plays an equally vital role in habitat 

quality of the Lower Suwannee. The role of water 

in the estuary is even more complex and will require 

monitoring and modeling of surface water, groundwater, 

and tidal waters. Research needs in the estuary include 

determination of submarine groundwater discharge 

to coastal areas, source identification of wastewater 

contaminants, and models of salinity and nutrienttransport processes. 

Threats to habitat are linked to threats to species because 

individual species requirements for territory, feeding 

area, migration, and gene pool are directly linked to 

habitat availability, links between habitats, and access to 

nutrients, shelter, and suitable reproductive conditions. 

An emphasis on integrated science efforts between 

habitat research and species research is necessary. A 

recently completed USGS study addressed the issue of 

potential reductions of flow for wetlands protection by 

relating hydrologic conditions, soils, and vegetation of 

floodplain forests to river flow in the Lower Suwannee 

River (Light and others, 2002). Research opportunities 

include the characterization of wetland habitats in the 

Upper SRB and relating these to amphibian and mussel 

research studies. 
15

Habitat Conservation Research Gaps and 

Opportunities

• Identify and map terrestrial and aquatic habitats

• Utilize existing data and state-of-the-art remote 

sensing capabilities for complete spatial 

coverage of basin habitats

• Map and model topographic, hydrologic, and 

structural features such as spring watersheds and 

submarine groundwater discharge

• Identify patch size, connectivity and landscape 

mosaic

• Identify community composition

• Evaluate natural variability within habitat 

• Identify and model changing water supply on habitats

• Identify and model changing water quality

• Identify changes to habitat structure or function

• Identify impact of changing land use on habitats

• Identify and model alterations to habitat size and 

connectivity

• Evaluate potential habitat degradation from 

pollution

• Link habitat threats to species threats

• Link manatee foraging needs to sea grass 

mapping and monitoring

• Evaluate invasive species and loss of habitat

4.3.2 Threats to Species

Individual biological species are susceptible to changes 

in climate, land use, habitat alteration, water quality 

and supply, and changing food resources. Species 

conservation requires not only conservation of habitat, 

but also an understanding of population dynamics, 

genetics, predator/prey relations, nutrient cycling, 

and interplay with the human landscape. Competing 

land-use activities, recreation, economics, and cultural 

history can impede the process to conserve and protect 

the biological resources of the basin. Specifically, the 

balance between human economics, natural resources, 

and biological communities requires dedicated 

management to provide information and incentives to 

basin population and visitors. Additionally, introduced 

species can displace native species. One widespread 

but barely studied invasive, the Asian clam, Corbicula 

fluminea, has probably driven several native mussel 

species to near extinction in the river. However, the 

filter-feeding Asian clam may be an important player 

now in consuming excess phytoplankton production 

resulting from excess nutrients. Two other nonindigenous species found in the SRB are the Cuban tree 

frog (Osteopilus septentrionalis) and the red-eared slider 

(Trachemys scripta elegans).

Decreased flow and degraded water quality at springs 

threaten the many faunal species that depend on spring 

habitat. The Florida manatee is of special concern 

because of its endangered status and dependence on 

natural springs as warm water refugia during cold 

winters. The Gulf sturgeon, a subspecies of Atlantic 

sturgeon, was listed as threatened under the Engangered 

Species Act in 1991, when populations declined 

after a century of fishing for meat and caviar. Gulf 

sturgeon eat by siphoning tiny invertebrates from the 

mud deposited on the estuary floor. They migrate up 

the Suwannee River from the Gulf of Mexico in the 

springtime to spawn, but do not feed while in the river. 

Interdisciplinary approaches are critically needed to 

relate population ecology of the Gulf sturgeon and 

manatee to habitat and hydrology, and together to assist 

State and Federal managers in identifying management 

actions and assessing their efficacy. Adaptive 

management models would greatly benefit from the 

integration of hydrodynamic and water-quality models 

with ecological research focused on species, biological 

communities, and their habitats.

Threats to Species: Research Gaps and 

Opportunities

• Identify keystone species and functions (example is 

blue crab in estuary)

• Productivity and role in ecosystem balance

• Versus flagship species (charismatic) 

• Versus indicator species (indicative of a specific 

parameter)
16

• Map species distribution, biodiversity, and link to 

habitat

• Identify populations, isolation, and genetic 

viability

• Identify susceptibility to changes in water supply 

and water quality

• Identify species mobility in response to climate 

and other changes

• Identify vulnerable populations and interrelated 

populations

• Develop BMP to conserve existing viable 

populations

• Assess role of benthic macrofauna and algal flora

• Role in mitigating sediment surface oxygen levels

• Impacts from changing water supply, load and 

quality

• Role in productivity, food web and trophic levels

• Evaluate abundance, biomass, diversity, and 

turnover rates

• Changes to habitat structure or function

• Evaluate role of subterranean fauna (planktonic 

microcrustaceans)

• Evaluate populations and locations

• Assess sensitivity to groundwater perturbations

• In trophic cycle and processing of nutrients; role 

as water quality indicators

• Evaluate sources and cycling of nutrients in 

terrestrial, fresh and tidal waters

• Conduct trophodynamic forensic studies with 

stable isotopes

• Define nutrient sources and sinks

• Evaluate recovery and survival of endangered or 

threatened species

• Relate to health and function of ecosystem

• Assess efficacy of management efforts

4.4 Economic Base

The economic base in the SRB currently consists of 

agriculture, silviculture, mining and other industries, 

and ecotourism. Alteration of the water supply directly 

threatens agricultural activities, existing populations, 

and development plans. Unregulated development 

and degradation of water quality threaten all resourcebased industries including fishing, aquaculture, and 

ecotourism. Water withdrawal or obstruction of recharge 

zones may pose long-term risks for economic viability. 

Management in the basin needs an effective plan for 

water supply and land use that will support sustainable 

economic growth without risk to water supply and 

natural resources of the region. Development, evaluation, 

and application of BMPs, outreach, and education will 

continue to play an important role in establishing a 

balance between land use, sustainable economic growth, 

human health, and a productive ecosystem. 

Continued degradation of water quality could have a 

major impact on the economy of local communities 

in the basin. A recent study found that about 190,000 

people visited Ichetucknee Springs State Park in 2002 

and spent about $22.7 million in the communities 

surrounding the park (Bonn and Bell, 2004). This area 

has higher poverty and unemployment rates than State 

averages and benefits from the growth of the ecotourism 

industry. It is estimated that nature-based tourism could 

double in the next 10 years, and this increase could 

create more than 2,200 new jobs throughout the region.

Research Opportunities in Basin Economics

• Evaluate impact of best management practices on 

economy and natural resources

• Evaluate cost/benefit of agricultural practices (timing/

amount of fertilizer and water)

• Develop models and evaluate scenarios for land use 

and economic growth

• Evaluate potential for ecotourism, impact, and value 

of coordinated education

• Evaluate incentives for environmentally sensitive 

development
17

• Develop and evaluate educational programs 

(Master Farmers Curriculum, Florida 

Yards and Neighborhoods, Natural/Organic Farming 

Techniques)

5. Strategy

Management of the nation’s freshwater resources 

must address water supply and water quality for urban 

growth, food production, and industry. Competing 

needs for adequate water supply have resulted in threats 

to human and ecosystem health in many watersheds 

throughout the U.S. The Suwannee River watershed 

offers a unique opportunity to study effects of excessive 

nutrient loading, increasing freshwater withdrawals, 

and habitat degradation in a relatively pristine area that 

is undergoing extensive changes in land use and water 

consumption. Attention has been drawn recently to 

the SRB, following proposals to divert water to fulfill 

demands in populous counties in the Tampa metropolitan 

area. The vital interplay among agriculture, socioeconomic pressures, underlying geology, changing 

river hydrology, and unique biologic resources from 

the headwaters to the estuary is now recognized. The 

Suwannee River drains 21 counties in Georgia and 

13 counties in Florida and plays an important role in 

estuarine productivity at the Gulf of Mexico. As a model 

of relatively undisturbed large rivers in the southeastern 

United States, the SRB provides an unparalleled 

opportunity for assessing its natural resources and 

for demonstrating how to coordinate the interstate 

management of watershed and estuarine resources 

successfully. 

5.1 Partnering for an Integrated Watershed 

Database

The key to coordinating multi-agency research studies 

in the Suwannee Basin and Estuary is to leverage 

partnerships to develop integrated research and resource 

management tools. The SBIA, which operates in a 

planning and advisory capacity, promotes the sharing 

of information and resources by Georgia and Florida. 

This information sharing allows for leveraging of the 

limited funds that each State has available for water, 

natural resources, and economic activities. Constraints 

on State agencies limit their jurisdictional authority. 

Federal agencies (USDA, FWS, EPA) currently involved 

in the SRB have specific mandates that limit issues or 

geographic extent of their activities. The USGS mandate 

and skill set is appropriate to meet this challenge. 

The Consortium of Universities for the Advancement of 

Hydrologic Studies, Inc. (CUAHSI) in conjunction with 

the National Science Foundation (NSF), is developing 

a network of hydrologic observatories (HO) across the 

U.S. that focuses on issues related to the science and 

management of hydrologic systems. If the proposed HO 

for the SRB is funded, this effort will coincide with the 

USGS initiative in a complementary fashion. Valdosta 

State University (VSU) is also seeking NSF funding for 

an undergraduate research program in the SRB. This 

effort is supported by various agencies including the 

USGS. Combined efforts by universities, and local, 

State and Federal agencies promise a solid foundation 

for research and cooperation in the SRB. 

The existing partnership framework will serve as the 

basis for a collaborative effort to develop an Integrated 

Watershed Resource Information Tool. Primary efforts 

are being focused on the creation of a data portal to 

provide links among data bases containing hydrologic, 

biologic, water quality, and geographic information. 

This effort can facilitate cooperation among agencies by 

identifying data gaps and information needs. The USGS 

is committed to developing a prototype information tool, 

supported through a web-based environment, which 

links land use, biology, water, and geology information 

from various agencies working in the basin and estuary. 

Links to existing data sets will eliminate the need to 

have all data in a single location. This arrangement will 

permit individual agencies to continue to collect and 

develop mission-specific information while making the 

final products and datasets available to a wider science 

and management community. The web-link concept is 

conducive to a dynamic research environment, in which 

updates are initiated by the participating agency or 

research scientists, rather than a third party. An example 

of an interactive information resource tool is the 

Invasive Species Information Node, where information 

regarding invasive species is updated by experts (http://

invasivespecies.nbii.gov/). The geospatially-linked 

resource-information tool will serve as a model for 

developing similar data systems for other watersheds. 
18

Another example of a flexible data server is the USGS 

Hydrologic Data Web Portal developed by the USGS 

for the Southwest Florida Water Management District 

(SWFMD). 

 A preliminary effort targeted at data integration will be 

developed this year (FY2005) for presentation at the next 

workshop. The initial effort will focus on land use and 

existing hydrologic datasets. Over time it is expected to 

include links to imagery of the basin, dynamic mapping 

products, hydrologic models, and biological resources. 

All parties concerned have also expressed a strong 

interest in the development of watershed models to 

address various economic, hydrologic, and biologicalresource scenarios. This resource information tool will 

set the stage for future modeling activities. 

 5.2 Science Plan, Workshops, and the Future

The next workshop for the Suwannee Initiative is 

planned for June 2005 in Folkston, Georgia, near 

the eastern headwaters of the Suwannee River. The 

workshop will be held at the Okefenokee Educational 

Research Center (OERC), a new facility dedicated to 

promote education and research in the Okefenokee 

Swamp. Topics to be discussed include coordination 

of research activities described in the Science Plan for 

the Suwannee River Basin and Estuary system, and 

the continued development of a web-based resource 

information tool.

The specific goals of the 2005 workshop are to:

1. initiate interstate dialogue

2. develop a science plan framework

3. identify key issues and agencies/researchers to 

address issues

4. continue developing the web-based resource 

information tool.

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