U.S. Department of the Interior

U.S. Geological Survey

Open File Report 2004-1198

April, 2004

Suwannee River Basin and Estuary Initiative:

Executive Summary

Management of the nationʼs freshwater resources must 

address water supply and water quality for urban growth, 

food production, and industry. It is also widely recognized 

that the timing, duration, and distribution of water flow 

is essential to natural ecosystem function, as has been 

powerfully illustrated in the Florida Everglades. Attention 

has been drawn to the basin of the Suwannee River, 

following proposals to divert water to fulfill demands in 

the populous counties of Pinellas and Hillsborough. In 

1994, a mandate was issued to the Suwannee River Water 

Management District (SRWMD) to set minimum flow 

requirements for the river. 

In response to the growing number of environmental 

threats in the Suwannee River Basin (SRB), the States of 

Florida and Georgia, the federal government, and other 

local organizations have identified the Suwannee River as 

an ecosystem in need of protection because of its unique 

biota and important water resources. Organizations with 

vested interests in the region formed a coalition, the 

Suwannee Basin Interagency Alliance (SBIA), to promote 

interagency management of water and related natural 

resources throughout the basin. 

The goals of the SBIA include improved coordination in 

the identification, management, and scientific knowledge 

of the natural resources in the basin. To date, however, 

an integrated assessment of the physical, biological, 

and water resources has not been completed. The U.S. 

Geological Survey (USGS) is well situated to address the 

larger concerns of the basin by addressing specific research 

questions linking water supply and quality to ecosystem 

function and health across county and state boundaries. 

The USGS is tasked with providing reliable scientific 

information to describe and understand the Earth, to 

Minimum flow is defined as “...the limit at 

which further withdrawals would be 

significantly harmful to the water resources 

or ecology of the area.” (Florida Water 

Resources Act; Chapter 373.042, F.S.)

Photo courtesy of US Geological Survey
2

manage natural resources, and to enhance the quality of 

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

Florida Integrated Science Center (FISC) have embarked 

on the Suwannee River Basin and Estuary Initiative to 

provide timely and appropriate scientific information 

prior to serious impairment of the SRB and its various 

components.

SUWANNEE RIVER BASIN

The Suwannee River drainage basin of southeastern 

Georgia and north central Florida is one of the largest 

(28,600 km2) and most ecologically unique blackwater 

river systems of the Southeast. Originating in the 

Okeefenokee Swamp, the Suwannee River meanders 

over 400 km through southern Georgia and the Florida 

peninsula before emptying into the eastern Gulf of Mexico 

just north of Cedar Key. It is the only major drainage 

basin entirely within the Coastal Plain and its expansive 

estuary provides among the most significant near-shore 

habitats in the northeastern Gulf of Mexico. 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. 

The Suwannee River is unimpounded, undiverted, and 

relatively unpolluted, and has been referred to as one 

of the most pristine and undeveloped river systems in 

the United States. The entire watershed harbors a rich 

assemblage of exceptional biological, geological, and 

hydrological resources. The Suwannee River provides an 

unparalleled opportunity for studying its natural resources 

and for demonstrating how to proactively manage them 

successfully. The knowledge gained can serve as a model 

for other, more disturbed, river systems.

HYDROLOGY AND GEOLOGY

The hydrogeology in the SRB is highly varied in terms 

of underlying geology, complicated karst-dominated 

flow regime, water quality, and endemic aquatic habitats. 

The SRB includes the Okeefenokee Swamp, many small 

streams, large rivers, a multitude of springs, extensive tidal 

salt marshes, and a productive estuary. The character of 

the Suwannee River changes dramatically as it progresses 

downstream, reflecting the hydrogeology, physiography, 

and land cover of the region it drains. Surface drainage 

characteristics dominate the upper two-thirds of the SRB, 

where soils contain clays and fine sediments that are 

resistant to surface water infiltration to the subsurface. 

Streams, lakes, and wetlands are abundant in the upper 

SRB and its tributary basins.

In the southern third of the SRB, a relatively thin layer of 

highly porous sands overlies the Floridan aquifer system, 

and the water of the Suwannee River exhibits strong 

ground-water characteristics. Here, the Floridan aquifer 

system is the principal source of water supply, and the 

relative absence of surface-water features such as streams, 

lakes, and wetlands is indicative of direct recharge of 

rainfall to the aquifer. The physiographic transition 

between the highlands and lowlands includes stream-tosink sub-basins, where stream flow is abruptly captured by 

sinkholes and routed to the aquifer. The Suwannee River 

is the only stream in the SRB flowing across the transition 

that is not fully captured by sinkholes. The transition area 

GEORGIA

FLORIDA

SUWANNEE

RIVER BASIN

Okeefenokee

Swamp White

Springs

Tallahassee Jacksonville

Horseshoe Beach

Cedar Key

Ichetucknee

Springs

State Park

Cordele

KILOMETERS

0 50 MILES

0 50

Suwannee River Santa Fe

River

GULF OF MEXICO

ATLANTIC

OCEAN

Photo courtesy of P. Carmichael
3

and the numerous springs along the lower river are points 

of interaction between surface water and ground water.

Streamflow in the SRB has been continuously monitored 

for nearly 100 years at one of the first gages that was 

established at White Springs, Florida, in 1906. The USGS 

and the Suwannee River Water Management District 

monitor river levels at more than 60 additional gages 

through Federal-State cooperative programs. Flow in the 

SRB varies annually with rainfall, but typically is highest 

in March-April due to runoff from spring storms, and 

lowest in November-December due to drier fall weather. 

The largest widespread floods in the SRB occurred during 

the month of April (1948, 1973, and 1998). Tropical 

storms also can cause flooding in the summer and fall, as 

occurred in September 1964 from Hurricane Dora. Record 

droughts in the SRB occurred in 1954-56 and 1999-2001, 

when record low flows were recorded throughout the 

basin.

WATER QUALITY

The natural resources of the Suwannee River ecosystem 

are vulnerable to a growing number of water quality 

issues. Research on threats to water quality is critically 

needed by local, state, and federal agencies responsible for 

protection of basin resources. Increased use of pesticides 

and fertilizers, run-off from dairy and poultry farms, and 

contaminants from pulp mills and phosphate mines are of 

growing concern due to effects on air and water quality 

and fragile aquatic species. 

Water-quality conditions in the Suwannee River and its 

tributaries reflect the physical setting of the SRB. The 

highland areas, which are dominated by surface drainage, 

typically have more acidic water, higher levels of sediment 

and particulate matter, and higher variability in flow. 

Downstream of White Springs, Florida, the Suwannee 

River receives ground-water inflow from over 200 known 

springs. The relatively constant influx of clear mineral-rich 

water from the Floridan aquifer buffers the acidity and 

darker color of the predominantly surface water from the 

upper two-thirds of the basin. 

Select sites along the Suwannee River and tributaries are 

currently monitored for water quality and limited benthic 

sampling by the USGS and National Water Quality 

Assessment Program (NAWQA), the SRWMD (State of 

Florida), and the Florida Fish and Wildlife Conservation 

Commission (FFWCC). 

Although research studies in the basin indicate generally 

good overall water quality, human health and ecological 

concerns have arisen recently because of the large 

nitrogen inputs to the land surface from fertilizers, animal 

wastes, and atmospheric deposition. This problem occurs 

primarily in the middle and lower Suwannee and lower 

Santa Fe Rivers in Florida, where spring-water and diffuse 

upward leakage of ground water contribute substantial 

loads of nitrate-N. Nitrate concentrations in ground water 

and spring waters have increased substantially from near 

background concentrations of less than 0.1 mg/L in the 

1960s and 1970s to more than 5 mg/L in the late 1990s. In 

some areas of the basin, nitrate-N concentrations in ground 

water from the Upper Floridan aquifer exceed the Federal 

and State maximum contaminant level of 10 mg/L for 

drinking water.

Elevated nitrate concentrations in rivers can cause 

eutrophication, resulting in algal blooms and depletion 

of oxygen that can lead to fish kills. An increase in 

periphyton biomass along the middle and lower reaches 

of the Suwannee River may be another indication of 

increased nitrate concentrations. Also of concern are the 

effects of high nitrate concentrations downstream in the 

Suwannee River estuary. 

Why special concern about Suwannee River 

Basin?

• Water supply and quality

• Recreational and commercial fishing

• Ecotourism

• Silviculture and agriculture

• Critical aquatic and terrestrial habitat

Photo courtesy of US Geological Survey
4

Other contaminants, such as pharmaceuticals and 

antibiotics, originate from concentrated animal feeding 

operations and waste disposal systems. Animal wastes 

can be a source of bacteria and infectious waterborne 

pathogens. The introduction of chemical compounds and 

their metabolites, associated with pesticides, fertilizers, 

and industrial activities, can also pose ecological and 

human health risks. In addition, atmospheric deposition 

is a significant source of nitrogen and potentially toxic 

contaminants, including mercury and organic chemicals. 

Water-quality conditions dictate the health of aquatic 

ecosystems, and in turn, affect human health. 

WATER SUPPLY

Competing demands on the natural resources of the 

Suwannee River ecosystem require a better understanding 

of the effects of contamination, water withdrawals, and 

climate change, and the interactions of these stressors. 

Climate variation alone can result in significant changes 

in rainfall, with subsequent impacts on surface 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. 

Adequate ground water is especially important in the 

Lower Suwannee spring system. Demands for ground 

water from urban development and extensive agricultural 

activities in the basin have resulted in increased 

withdrawals from the Upper Floridan aquifer. As an 

example of water-supply related problems, some springs 

in the SRB have essentially stopped flowing during certain 

times of the year.

Consumptive use of water resources is increasing in the 

Suwannee River basin due to farm irrigation requirements 

and to increasing demands of a rapidly growing human 

population. Although the Suwannee is undiverted, water is 

already being mined for bottling at several spring sources, 

with more than a million gallons/day being withdrawn. 

Changes in flow regime can have 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. 

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. 

ECOSYSTEM FUNCTION

A suite of well-integrated multi-disciplinary studies on the 

physical, chemical, and biological processes in the basin is 

needed to understand complex interactions of the systemʼs 

components. The Suwannee basin contains a unique 

mixture of subtropical forests, wetlands and swamps, 

springs, tidal and blackwater rivers, and a productive 

estuary. A comprehensive research plan to identify how 

these habitats are linked to each other, to water quality, 

to surface and ground water supply, to underlying 

geology, and to human activities will aid management and 

conservation of basin resources.

The Suwannee River is one of only a few rivers within 

the U.S. that has suffered negligible damage from human 

activities such as damming, channeling, redirection, 

and the introduction of large quantities of contaminants. 

The variety of habitats in the basin supports important 

biological communities and several federally or state 

protected species including the threatened Gulf Sturgeon, 

the endangered West Indian Manatee, 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 Suwannee 

River spring system also contains 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 

Photo courtesy of US Geological Survey
5

sensitivity to changes in water quality and other abiotic 

stressors. 

The Suwannee River Estuary System (SRES) is a 

productive and relatively unaltered natural estuary where 

the Suwannee meets the Gulf of Mexico. The SRES 

harbors shallow habitat, sea grass, and low-salinity 

conditions along the coast from Horseshoe Beach to Cedar 

Key. The estuary has been designated an Outstanding 

Florida Water, and is also a State Aquatic Preserve and 

a National Wildlife Refuge. SRES contains large areas 

of oyster reefs, sand bars, tidal creeks, salt marsh, and 

submerged aquatic vegetation. These estuarine habitats 

support ecologically important and valued fish species, 

many during breeding, nursery, and juvenile phases. At 

present a USGS multi-disciplinary study is underway to 

better understand fish habitat suitability and utilization, 

and the influence of tidal marine and freshwater flow 

on habitats in the estuary. Data are being evaluated on 

hydrologic processes, multispectral habitat mapping, and 

fish utilization of the SRES.

SOCIO-ECONOMIC FORCES

Effective management of water resources in the SRB 

would benefit from increased knowledge about the 

interactions between climate variability, hydrologic 

processes, ecological function, and human activities. 

Population growth and development within the SRB 

has been steady since the 1960s. Basin population 

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. 

Agriculture accounts for most of the developed land uses 

within the SRB in both Georgia and Florida, including 

silviculture, row crops, and pasture. Irrigated acreage has 

increased considerably in the SRB over the last several 

decades as technologies have improved and market 

conditions have changed. Water sources are primarily 

from basin-wide precipitation and runoff, small surfacewater reservoirs in Georgia, and as ground water from the 

Floridan aquifer in Florida. Trends over the last decade 

indicate a general shift towards more intensive production 

of food, forage crops and livestock. Agricultural crops 

and products from the SRB include dairy, poultry, fruits 

and vegetables, grains, pasture, and forestry products. 

Silviculture, primarily pine plantations, covers large areas 

of the SRB and provides timber and fiber for mills. 

Issues related to water supply are a major concern in 

the basin. The SRB contains an abundance of water 

that is sought by more developed parts of the state. 

The SRB also supports fisheries, both commercial and 

recreational, a productive shellfish industry at Cedar 

Key, hunting, boating, diving and other recreational 

activities. Ichetucknee Springs State Park alone accounts 

for a quarter of a million visitors who spend $17 million 

annually in that community. Ecotourism is a thriving 

business in Florida, attracting national and international 

visitors to springs and other scenic locations in the SRB.

ACTION PLAN

A holistic, multi-disciplinary approach is needed 

to address the SRBʼs research needs and to provide 

supportive data for meeting management objectives of the 

entire ecosystem. The USGS has completed statistical 

summaries on stream flow history and groundwater levels, 

water quality monitoring, spring monitoring, biological 

assessments, reduced flow impact on lowland forests, 

habitat mapping, and estuarine links between habitat, 

Photo courtesy of US Geological Survey

Photo courtesy of R. Sparkman
6

biological communities and water supply. Long-term 

biological assessments by the USGS have been limited 

to individual species. While important, protection of 

individual species cannot guarantee broad conservation of 

the Suwannee Riverʼs biological resources. 

The white paper to follow will include a list of proposed 

action plans and research priorities that USGS scientists 

are considering for the future. The success of any or all of 

these plans depends on continued broadly based interest 

and fiscal support. 

The USGS is interested in developing a strategic plan 

in cooperation with federal, state and local agencies 

to identify and implement studies addressing the most 

compelling research issues and management questions, 

and to conduct fundamental monitoring studies. The USGS 

plans to convene a meeting with concerned agencies to 

discuss cooperative science efforts in the basin.

Potential Cooperators and Partners

Florida Dept. of Agriculture and Consumer Services

Florida Department of Environmental Protection

Florida Department of Health

Florida Fish and Wildlife Conservation Commission

Florida Geological Survey

Georgia Department of Natural Resources

Mote Marine Laboratory

Suwannee River Water Management District

U.S. Department of Agriculture 

U.S. Fish and Wildlife Service

U.S. Forest Service

University of Florida

University of Georgia

University of South Florida

Environmental consortia:

Ichetucknee Springs Water Quality Working Group

National Wildlife Federation

The Nature Conservancy

Santa Fe Springs Water Quality Working Group

Save our Suwannee

Brian Katz Ellen Raabe

U.S. Geological Survey U.S. Geological Survey

2010 Levy Ave, Tallahassee, FL 32310 600 4th Street South, St. Petersburg, FL 33701

(850) 942-9500 X3018 727-803-8747 x3039

bkatz@usgs.gov eraabe@usgs.gov

For more information please contact:

Why should the USGS be involved?

• USGS possesses unique technical 

and scientific capability

• USGS scientists have expertise in 

hydrology, geology, biology, and 

geography

• USGS specializes in integrated science and unbiased products

• A comprehensive, integrated 

approach is required in the 

Suwannee Basin

• USGS can partner with federal 

and state agencies to provide the 

holistic effort that is needed

Florida Integrated Science Center

Photo courtesy of US Geological Survey