The Florida Springs Interdisciplinary Science Study is 

an integrated U.S. Geological Survey science effort that 

builds on the knowledge of Federal, State, and local partners to address serious human health and ecological concerns that have arisen regarding Florida’s spring waters 

(Florida Springs Task Force, 2000). The steady increase in 

nitrate concentrations observed during the past 40 years 

threatens the aesthetic, cultural, and recreational value of 

these springs. The Upper Floridan aquifer, which supplies 

water to springs, is important not only for human consumption, but also for supporting critical ecological habitats for 

a variety of species. The USGS chose Manatee Springs as 

the location for this pilot study because of ongoing work 

being conducted by the Suwannee River Water Management District (SRWMD) and other scientific investigations 

supported by the State. The USGS work at this first magnitude spring will address the following objectives to build on 

existing work:

• Determine the major source(s) of nutrient enrichment; 

• Develop baseline surveys of organisms that may be 

suitable for examining the ecological effects of nutrient enrichment in spring waters; 

• Determine the occurrence of other contaminants of 

concern that could be associated with nutrient enrichment in spring waters (e.g. pharmaceuticals, pesticides 

and their degradates); 

• Delineate areas most vulnerable to contamination 

based on geologic conditions and current land-use 

practices; and

• Assess how changing land-use practices have affected 

concentrations of nutrients and other contaminants in 

the spring. 

Springs in the Lower Suwannee River Basin:

The first phase of the USGS Interdisciplinary Science 

Study is focused on Manatee Springs, a first-magnitude 

spring that discharges about 140 cubic feet per second 

(91 million gallons per day) of water from the Upper 

Floridan aquifer into a 1,200-foot spring run, which flows 

southward to the Suwannee River. Nitrate-N concentrations in Manatee Springs have increased substantially from 

less than 0.4 milligrams per liter (mg/L) in 1946 to more 

than 1.5 mg/L during the past few years. Elevated nitrate 

concentrations combined with high spring flows have contributed substantial loads of nitrogen to the Suwannee 

River from Manatee Springs as well as from several other 

first-magnitude springs along the river. Elevated nitrate 

concentrations in rivers can accelerate eutrophication, 

resulting in expansive algal blooms that deplete oxygen and 

may lead to fish kills or other deleterious impacts. Such 

adverse ecological effects have been indicated by an 

increase in periphyton biomass along the lower reaches of 

the Suwannee River (Hornsby and Mattson, 1998). Also of 

concern are the effects of high nitrate concentrations in the 

Suwannee River on the estuary of this river system, which 

together with the Suwannee River has been designated an 

Outstanding Florida Waterbody, a State Aquatic Preserve, 

and a National Wildlife Refuge. 

Ecological and Hydrogeologic Diversity of the 

Suwannee River System:

The Suwannee River has the greatest diversity of subterranean decapod crustaceans anywhere in the world. 

These stygobiotic organisms are obligate cave dwellers that 

complete their entire life cycle in submerged underground 

systems. Yet, the distributions, abundances, ecological 

requirements, and sensitivity to changes in water quality of 

this fauna are still largely unknown. In addition, the existence of planktonic or nektonic microcrustaceans in aquifer 

habitats of north Florida is undocumented, despite their 

Figure 1. Photograph of main spring pool at 

Manatee Springs.

U.S. Geological Survey

Fact Sheet FS-008-03

Florida Springs Interdisciplinary Science Study
occurrence and diversity in south Florida and other major 

karst systems. The roles of subterranean fauna in the surface- and ground-water trophic web and the processing of 

nutrients have not been studied. Moreover, many of the 

hypogean species (those found underground, including both 

obligate and occasional cave-dwelling forms that require or 

prefer subterranean habitats for a portion of their lives) are 

thought to have limited populations that could be especially 

susceptible to ground-water perturbation, yet their status, 

sensitivity, and vulnerability are largely undocumented 

(Walsh, 2001). Based on these considerations, subterranean 

species are being evaluated as potentially important biological indicators of water-quality changes and for their suitability for long-term monitoring. 

The hydrogeology of the Suwannee River basin is 

highly varied in terms of its underlying geologic framework, its complicated karst-dominated flow regime, water 

quality, and endemic aquatic habitats. The character of the 

Suwannee River changes dramatically as it flows downstream from southern Georgia, reflecting the hydrogeology, 

physiography, and land cover of the region it drains. Surface 

drainage characteristics dominate the upper two-thirds of 

the basin. A relatively thin layer of highly porous sands 

overlies the Floridan aquifer system in the southern third of 

the basin, where the Suwannee River reflects more groundwater characteristics. Downstream from White Springs, 

Florida, the Suwannee River receives inflow from over 

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Figure 2. Map showing location of Manatee Springs and 

other springs sampled in Suwannee River Basin to assess 

sources and chronology of nitrate contamination.

200 known springs. The influx of ground water from the 

Floridan aquifer system buffers the acidity and darker color 

of predominantly tannic surface water with the relatively 

constant flow of clear, mineral-rich aquifer water. Relatively 

constant and elevated nitrate concentrations are observed in 

the middle and lower Suwannee River where spring inflow 

dominates the river water chemistry. Nutrients originate in 

part from fertilizers added to crops to stimulate growth, and 

from animal wastes from dairy and poultry operations. Animal wastes may also carry pathogens and bacteria, including the protozoan parasite Cryptosporidium parvum. 

Besides agriculture, growing urban centers within the basin 

contribute additional sources of nutrients and contaminants.

SCOPE AND METHODS OF MANATEE 

SPRINGS STUDY

In the first phase of the study, innovative interdisciplinary techniques incorporating the fields of hydrology, 

geochemistry, microbiology, ecology, and geography are 

being used to study sources of nutrient enrichment on spring 

water discharging to the Suwannee River and associated 

ecological impacts. The state-of-the-art techniques 

described below have been used effectively in many diverse 

hydrogeologic environments; however, they are now being 

tested for their applicability in the complex karst systems 

found in the Suwannee River basin. It is hoped that scientific 

findings from this study will enhance work already being 

conducted at this spring by our partners and cooperators.

1. Determining Sources of Nitrate: 

 1.1 Geochemical Tracer Techniques:

Analyses of isotopic and other chemical tracers in 

water samples from Manatee Springs during base-flow 

conditions in 1998-2001 indicated that nitrate likely originates from both inorganic (fertilizers) and organic (animal and/or human wastes) sources of nitrogen. 

Residence times of ground water discharging from the 

spring were highly variable and ranged from 7 to 

27 years. Recent water samples collected by cave divers 

from several locations in the Manatee Springs conduit 

system indicated variable nitrate concentrations, which 

could be related to different land-use activities. 

In this study, water samples are being collected from 

the main vent at Manatee Springs during base- and highflow conditions to assess the fate of nitrate during 

extreme flow conditions. To better resolve sources of 

inorganic and organic nitrogen in spring waters and to 

assess the fate of nitrate, water samples are being analyzed for both oxygen and nitrogen isotopes of nitrate. In 

addition, measurements of other chemical tracers, such as 

dissolved gases (Ar, N2, N2O), nitrogen isotopes of N2, 
Figure 3. Photograph of the pallid cave 

crayfish (Procambarus.pallidus), a blind cavedwelling crustaceon found in ground water of 

the Floridan aquifer in the Suwannee River 

Basin.

Figure 3. Photograph of the pallid cave 

crayfish (Procambarus.pallidus), a blind cavedwelling crustaceon found in ground water of 

the Floridan aquifer in the Suwannee River 

Basin.

and stable hydrogen and oxygen isotopes of water are 

being used to assess nitrate transformation reactions in 

the aquifer due to denitrification or other processes. 

The age or average residence time of ground water 

discharging from these springs is being estimated using 

transient tracer techniques during base-flow and highflow conditions. The spring water age can be used to 

assess the relative proportions of young water from 

shallow parts of the aquifer and older water from deeper 

parts of the aquifer (Katz and others, 1999). Water 

samples are being collected and analyzed for the transient environmental tracers: chlorofluorocarbons 

(CCl3F, CCl2F2, and C2Cl3F3); tritium and its decay product, 

helium-3; and sulfur hexafluroride 

(Katz and others, 2001).

Other tracers of ground-water 

discharge that are being used 

include naturally occurring radium 

(Ra) isotopes (223,224,228,226Ra) of 

the Uranium-series decay chain. 

Briefly, these four naturally occurring Ra isotopes have a very different geochemical signature in 

freshwater compared to mineralized aquifer water. This attribute, 

in addition to well-known source 

functions, a wide range of half-lives 

(3.6 days to 1,600 years), and highly elevated groundwater concentrations make radium an ideal tracer to 

examine surface-water to ground-water exchange across 

the riverbed interface (Swarzenski, 1999). 

1.2 Microbiological Tracer Techniques:

Standard and state-of-the-art microbial water-quality 

indicators are being used to screen water samples to 

determine if spring waters are being influenced by fecal 

sources (Griffin and others, 1999, 2000). Source tracking assays are being employed to differentiate between 

animal and human fecal contamination using F+ specific 

RNA coliphage and human-specific virus assays. A 

viral tracer study is being conducted to determine if 

areas around Manatee Springs affect water quality 

through focused recharge, such as through sinkholes or 

other solution features. 

2. Inventory of organisms for monitoring 

water-quality effects:

Exploratory surveys are being conducted during baseand high-flow conditions to assess the current status of the 

hypogean community in the spring system. Understanding 

the diversity and relative abundance of the stygobiotic 

organisms in various parts of the spring system is essential 

to identifying species vulnerable to nitrate contamination 

and those that would be suitable for further water-quality 

monitoring. Organisms that exhibit both positive and negative sensitivities to water quality changes are being evaluated 

for long-term monitoring or physiological experimentation. 

By initiating studies of this unusual fauna, multiple avenues 

of research are likely to be found for evaluating trophic linkages, ecological functions, and community responses associated with anthropogenic disturbances.

Surveys of the stygobiotic fauna utilize three principal 

sampling methods: (1) pumping and filtering water from 

existing wells and solution cavities to sample microcrustaceans; (2) using of borehole videography to visually count 

macroinvertebrates; and (3) diving in 

spring vents, caverns, and large conduits to conduct transect surveys and 

to estimate population abundances of 

decapod crustaceans. Organisms are 

collected by qualitative and quantitative methods, preserved, and distributed to taxonomic specialists for 

systematic identification. In association with hydrochemical, geophysical, and geographic information, 

biological data can then be analyzed 

to determine patterns in diversity, distribution, or abundance of the stygobiotic fauna as a function of water-quality characteristics, 

flow conditions, land-use activities, and other integrators of 

physical conditions as they relate to ecological responses. 

3. Assessing the occurrence of other 

contaminants from agricultural activities: 

Information is limited concerning the occurrence of 

“exotic” contaminants, such as pharmaceuticals, bacteria, 

pesticides, herbicides, and their transformation products 

(degradates) in water from the Upper Floridan aquifer. 

However, herbicides have been detected in trace concentrations in 9 of 15 springs discharging from the Upper Floridan aquifer in southern Georgia (Hippe, 1997). Pesticide 

and herbicide use is potentially high in the Suwannee River 

basin due to large crop acreages of corn, peanuts, tobacco, 

and watermelons in the middle and lower Suwannee River 

basin. Low concentrations of these compounds, and their 

transformation products, may result in observable effects on 

aquatic organisms and pose an environmental risk (Kolpin 

and others, 2002). Water samples from Manatee Springs are 

being collected and analyzed for selected pesticides, herbicides and their metabolites, and antibiotics to assess the 

occurrence of contaminants (other than nutrients) associated with various agricultural activities in the basin. 
4. Delineating the contributing area to the 

spring and assessing land-use changes:

The SRWMD recently installed nine monitoring wells 

in the vicinity of Manatee Springs. Water-level data from 

these wells provides critical information on ground-water 

flow patterns near the spring, and are being used by 

SRWMD to construct a high resolution map of the hydrologic contributing area to the spring. These data are being 

used to calibrate an existing ground-water flow model and 

particle tracking model to assess ground-water flow to the 

spring. The contributing area of the spring mapped by 

SRWMD will be used to spatially analyze land-use data, 

soil distributions, water-use patterns, and population data to 

identify potential sources of nutrients and to estimate the 

nutrient contributions from each source based on the latest 

land-use compilations. Recent aerial photography is being 

incorporated with 1994 land-use coverages to determine 

land-use changes that have occurred in the basin during the 

past 5-10 years so that current observations can be considered in the context of future estimates of nutrient loading.

Several water-quality monitoring programs 

involving springs are already underway by State 

and local agencies, as are baseline faunal and floral 

inventories, contaminant and experimental studies, 

and investigations to examine organism and community-level responses. Integrating techniques 

from multiple disciplines within the USGS is a 

powerful approach for assessing sources of contamination to ground-water resources and potential 

effects on ecosystems. This integrated information 

from several fields of study, will reduce the uncertainty regarding the identification of anthropogenic 

sources of contamination in ground water discharging from springs. Understanding how human activities on the surface affect the aquifer system, will 

aid the development of more effective strategies to 

protect spring waters from further degradation and 

remediate springs that are already contaminated.

SUMMARY

For more information, please contact:

BRIAN G. KATZ, Project team leader, 

Research Hydrologist, e-mail:

bkatz@usgs.gov

U.S. Geological Survey

Florida Integrated Science Center

227 N. Bronough St., Ste. 3015

Tallahassee, FL 32301

Contributing Scientists:

DALE W. GRIFFIN, Microbiologist, e-mail:

dgriffin@usgs.gov

PETER W. SWARZENSKI, Geologist, e-mail:

pswarzen@usgs.gov

U. S. Geological Survey

Florida Integrated Science Center

600 4th St. South 

St. Petersburg, FL 33701

STEPHEN J. WALSH, Research Biologist, e-mail:

steve_walsh@usgs.gov

HOWARD L. JELKS, Research Biologist, e-mail:

howard_jelks@usgs.gov

U.S. Geological Survey

Florida Integrated Science Center 

7920 NW 71st St.

Gainesville, FL 32653

REFERENCES

Florida Springs Task Force, 2000, Florida’s 

springs: Strategies for protection and 

restoration: Report prepared for the 

Florida Department of Environmental 

Protection, 57 p.

Griffin, D., Gibson, C.J. III, Lipp, E.K., Riley, 

K. Paul, J.H., and Rose, J.B., 1999. 

Detection of Viral Pathogens by Reverse 

Transcriptase PCR and of Microbial 

Indicators by Standard Methods in the 

Canals of the Florida Keys: Applied and 

Environmental Microbiology, v. 65, p. 

4118-4125.

Griffin, D. W., Stokes, R., Rose, J.B., and Paul. 

J.H., 2000. Bacterial Indicator 

Occurrence and the Use of an F+ Specific 

RNA Coliphage Assay to Identify Fecal 

Sources in Homosassa Springs, Florida: 

Microbial Ecology, v. 39, p. 56-64.

Hippe, D.J., 1997, Pesticide occurrence in the 

Upper Floridan aquifer in the Dougherty 

Plain and Marianna Lowlands districts, 

southwestern Georgia and adjacent areas 

of Alabama and Florida: Proceedings of 

the 1997 Georgia Water Resources 

Conference, University of Georgia, 

Athens, Georgia, p. 65-67.

Hornsby, H.D., and Mattson, R., 1998, Surface 

water quality and biological monitoring 

network: Suwannee River Water 

Management District Annual Report 

WR-98-02.

Katz, B.G., Hornsby, H.D., Böhlke, J.K., and 

Mokray, M.F., 1999, Sources and 

chronology of nitrate contamination of 

springwaters, Suwannee River Basin, 

Florida: U.S. Geological Survey WaterResources Investigations Report 99-

4252, 54 p.

Katz, B.G., Böhlke, J.K., and Hornsby, H.D., 

2001, Timescales for nitrate 

contamination of spring waters, northern 

Florida, USA: Chemical Geology, v. 179, 

p. 167-186.

Kolpin, D.W., Furlong, E.T., Meyer, M.T., 

Thurman, E.M., Zaugg, S.D., Barber, 

L.B., and Buxton, H.T., 2002, 

Pharmaceuticals, hormones, and other 

organic wastewater contaminants in U.S. 

streams, 1999-2000: A national 

reconnaissance: Environmental Science 

and Technology, v. 36, p. 1202-1211.

Swarzenski, P.W., 1999, Re-examining 

freshwater-saltwater interface processes 

using radium isotope systematics. U.S. 

Geological Survey, FS-065-99, 2p.

Walsh, S.J., 2001, Freshwater macrofauna of 

Florida karst habitats, in Kuniansky, E.L., 

ed., U.S. Geological Survey Karst 

Interest Group Proceedings, U.S. 

Geological Survey Water-Resources 

Investigations Report 01-4011, 211 p.

Tallahassee, Florida 

2003