U.S. Geological Survey Science Support 

Strategy for Biscayne National Park and 

Surrounding Areas in Southeastern Florida

By Melinda A. Wolfert-Lohmann, Christian D. Langevin, Sonya A. Jones, 

Chris D. Reich, Georgiana L. Wingard, Ilsa B. Kuffner, and Kevin J. Cunningham

Open-File Report 2007-1288 

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

For product and ordering information:

World Wide Web: http://www.usgs.gov/pubprod

Telephone: 1-888-ASK-USGS

For more information on the USGS--the Federal source for science about the Earth, its natural and living resources, 

natural hazards, and the environment:

World Wide Web: http://www.usgs.gov

Telephone: 1-888-ASK-USGS

Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the 

U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation: 

Wolfert-Lohmann, M.A., Langevin, C.D., Jones, S.A., and others, 2008, U.S. Geological Survey 

Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern 

Florida: U.S. Geological Survey Open-File Report 2007-1288, 48 p.
iii

Contents

1.0 Abstract..................................................................................................................................................1

2.0 Introduction............................................................................................................................................1

2.1 Partnerships..................................................................................................................................2

2.2 Acknowledgments .......................................................................................................................3

3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida ...........3

3.1 Ecosystem.....................................................................................................................................3

3.1.1 History................................................................................................................................5

3.1.2 Function.............................................................................................................................5

3.2 Hydrology ....................................................................................................................................11

3.2.1 Surface Water................................................................................................................11

3.2.2 Ground Water.................................................................................................................11

3.2.3 Water Quality..................................................................................................................14

3.3 Socioeconomic Conditions .........................................................................................................18

4.0 U.S. Geological Survey Research Issues and Needs...................................................................19

4.1 Ecosystem Stresses...................................................................................................................19

4.2 Water Deliveries.........................................................................................................................20

4.3 Contaminants..............................................................................................................................21

4.4 Database and Geographic Information System Issues.......................................................22

5.0 Current or Recently Completed Studies in and around Biscayne 

National Park.................................................................................................................................22

6.0 Potential U.S. Geological Survey Research Projects in and around Biscayne

National Park.................................................................................................................................35

6.1 Ecosystem Stresses ..................................................................................................................36

6.2 Water Deliveries ........................................................................................................................41

6.3 Contaminants..............................................................................................................................43

6.4 Database and Geographic Information System Issues.......................................................45

7.0 References Cited.................................................................................................................................46

Figures

 1. Map showing location of Biscayne National Park in southeastern Florida ...................................4

 2. Map showing location of core sites in Biscayne Bay, Florida ..........................................................6

 3. Graphs showing percent abundance of key molluscan salinity indicators in Middle Key 

core segments from the nearshore area of Card Sound...................................................................7

 4. Graphs showing percent abundance of key salinity indicator species in No Name 

Bank core segment from central Biscayne Bay and magnesium-calcium 

ratios derived from ostracod shells.......................................................................................................8

 5. Schematic showing infrared changes in Biscayne Bay salinity in recent centuries 

based on indicators from cores between Card Bank and central Biscayne Bay .........................9

 6. Cross section showing relations of geologic formations, aquifers, and semipermeable 

units of the surficial aquifer system across central Miami-Dade County ....................................13

 7. Diagram showing relation between pore classes I and III and touching-vug and 

conduit-pore types, respectively, for the Fort Thompson Formation and Miami 

Limestone in the Lake Belt area of Miami-Dade County .................................................................15

 8. Diagram showing relation between pore class II and matrix porosity..........................................16

 9. Diagram showing three-dimensional conceptual hydrogeologic model of 

the Biscayne aquifer for the Lake Belt area in north-central Miami-Dade County ....................17
iv

Photographs

 1. Red mangrove in Biscayne Bay............................................................................................................2

 2. H-alicia shipwreck..................................................................................................................................3

 3. Biscayne Bay mangroves near Black Point.......................................................................................7

 4. Seagrass in Biscayne Bay.....................................................................................................................9

 5. Biscayne National Park patch reef....................................................................................................10

 6. Montstrea cavernosa infected with black band disease ..............................................................10

 7. Sea fan (Gorgonia sp.) in Biscayne Bay ...........................................................................................12

 8. Sponge (unidentified) in Biscayne Bay.............................................................................................12

 9. Alina’s Reef drilling in Biscayne National Park................................................................................16

 10. Scientist/diver collecting pore-water samples at Alina’s Reef, Biscayne National Park.........18

 11. Alina’s Reef in Biscayne Bay ..............................................................................................................20

 12. Water sampling syringe and mini-piezometer used for collection of reef sediment

 pore waters ...........................................................................................................................................21

 13. Monitoring wells located on Alina’s Reef.........................................................................................21
v

Conversion Factors and Vertical Datum

Multiply By To obtain

centimeter 0.3937 inch (in.)

meter (m) 3.281 foot (ft) 

meter per day (m/d) 3.281 foot per day (ft/d)

kilometer (km) 0.6214 mile (mi)

hectare (ha) 2.471 acre

square meter (m2) 10.76 square foot (ft2) 

cubic meter (m3) 264.2 gallon (gal) 

cubic decimeter (dm3

) 0.2642 gallon (gal) 

cubic meter (m3

) 0.0002642 million gallons (Mgal) 

liter per minute (L/min) 0.2642 gallon per minute (gal/min)

Temperature in degrees Celsius (°C) may be converted to degrees 

Fahrenheit (°F) as follows: °F = (1.8 × °C) + 32.

Vertical coordinate information is referenced to National Geodetic Vertical 

Datum of 1929 (NGVD 29).

Acronyms and Abbreviations

AVHRR Advanced Very High Resolution Radiometer

CERP Comprehensive Everglades Restoration Plan

CUES Comprehensive Urban Ecosystems Studies

DERM Department of Environmental Resources Management

EAARL Experimental Advanced Airborne Research Lidar

EPOC emerging pollutants of concern

GIS Geographic Information System

LSI landscape stress indicator

MAP Monitoring and Assessment Plan

MPA marine-protected area

MS222 Tricaine Methanesulfonate

NASA National Aeronautics and Space Administration

NOAA National Oceanic and Atmospheric Administration

ppb parts per billion

ppm parts per million

ppt parts per thousand

SAV submerged aquatic vegetation

SHARQ Submersible Habitat for Analyzing Reef Quality

USGS U.S. Geological Survey
vi
1.0 Abstract

The U.S. Geological Survey conducts a wide range of 

research in and around the Biscayne National Park region of 

southern Florida. This research encompasses the biologic, 

ecologic, meteorologic, geologic, and hydrologic components 

of the system, including water-quality analyses, ground-water 

modeling, hydrogeologic-data collection, ecologic-habitat 

evaluations, wetlands characterizations, biogeochemistry of 

ecosystems, and paleo-ecologic analyses. Relevant information is provided herein for researchers and managers interested 

in the Biscayne Bay area and about current U.S. Geological 

Survey efforts that address important resource protection and 

management issues. Specifically, managers and scientists are 

provided with information on current and recently completed 

U.S. Geological Survey projects and a sample listing of 

potential U.S. Geological Survey research projects addressing 

relevant issues that face the study area.

2.0 Introduction

The primary goal of the Comprehensive Everglades 

Restoration Plan (CERP) is to restore the timing, quantity, 

quality, and distribution of freshwater within the greater 

Everglades ecosystem so that the ecosystem conditions 

approximate predevelopment conditions as closely as possible. 

The changes proposed within CERP will alter the current 

hydrologic conditions that exist within the region, which 

includes Everglades National Park, Biscayne National Park, 

and Big Cypress National Preserve. The magnitude of the 

changes proposed for this highly complex, diverse, and unique 

ecosystem has raised concern about the long-term effects of 

the restoration on different components of the system. For 

example, restoration efforts that benefit the terrestrial parts of 

the Everglades may have a negative effect on the estuaries of 

Florida Bay and Biscayne Bay. Land-management agencies 

have raised questions, such as:

•	 How will restoration projects affect groundwater flows?

•	 Will restoration of wetlands result in increases 

in coastal aquifer heads which, in turn, may 

cause the return of ground-water upwelling in 

Biscayne Bay?

•	 How would the return of freshwater to Biscayne 

Bay affect the submerged aquatic vegetation, 

benthic habitats, and fauna of Biscayne Bay?

•	 Would increases in coastal runoff lead to the 

addition of nutrients and other constituents 

to Biscayne Bay waters and potential 

phytoplankton blooms?

The potential for further habitat deterioration exists in 

Biscayne National Park and the surrounding area in southern 

Florida. This threat, coupled with the numerous species of 

threatened and endangered animals and plants that reside 

U.S. Geological Survey Science Support Strategy for 

Biscayne National Park and Surrounding Areas in 

Southeastern Florida

By Melinda A. Wolfert-Lohmann, Christian D. Langevin, Sonya A. Jones, Chris D. Reich, 

Georgiana L. Wingard, Ilsa B. Kuffner, and Kevin J. Cunningham
2 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

in the area, resulted in a Federal mandate to prevent further 

habitat degradation. Additionally, the health of Biscayne Bay 

is an integral measure of the health of the coral reefs that lie 

within Biscayne National Park. These reefs constitute the 

northern part of an approximate 241-ha chain of reefs that 

extend south along the Florida Keys. This reef-tract represents 

the only living coral bank barrier reef in North America, 

and the third longest coral barrier reef in the world. Many 

scientists, managers, and private citizens believe that the key 

to preserving this unique and endangered coastal ecosystem, 

as well as the terrestrial Everglades wetlands, is the timing, 

quantity, quality, and distribution of freshwater flows into 

the system.

Since the passage of the Water Resources Development 

Act of 2000 and the approval of CERP, a substantial amount 

of time and effort has been spent developing management 

paradigms and conducting research on the location, storage, 

and movement of water through the greater Everglades 

ecosystem into Everglades National Park and Florida Bay. 

Comparatively little research, however, has been conducted 

regarding how the restoration effort affects the coastal and 

estuarine resources to the east and west of the axis of the 

restoration.

The U.S. Geological Survey (USGS) conducts a wide 

range of research in and around the Biscayne National Park 

region of southern Florida. This research encompasses the 

biologic, ecologic, meteorological, geologic, and hydrologic 

components of the system, including water-quality analyses, 

ground-water modeling, hydrogeologic-data collection, ecologic 

habitat evaluations, wetlands characterizations, biogeochemistry 

of ecosystems, and paleo-ecologic analyses. Summaries of the 

recently completed projects or projects engaged by the USGS 

are presented in this report. Even with the breadth of research 

that is performed by the USGS and other agencies and universities, more research is necessary to more fully understand the 

ecosystem. A primary goal of this report is to document the 

scope of USGS research in and near Biscayne Bay to provide 

others with information on current efforts and promote future 

collaborative research efforts with the USGS. 

This report provides relevant information for researchers 

and managers interested in the Biscayne Bay area and about 

current USGS efforts that address important resource protection and management issues. Therefore, this report serves 

primarily as a forum to provide managers and scientists with 

information on USGS projects and a sample listing of potential USGS research projects addressing relevant issues that 

face the study area. 

2.1 Partnerships

Partnerships between the USGS and Federal, State, 

local, and private agencies are necessary for the successful 

completion of research in Biscayne National Park, and all 

agencies involved share a concern and desire to assist in the 

restoration efforts. The scope of work involved requires that 

all agencies work together to establish common goals, most 

of which would not be attainable without the joint effort of all 

involved. These partnerships also ensure that research efforts 

are relevant to current issues, ensure that critical research is 

done in a timely fashion, and allow for further collaborative 

efforts among many different agencies and groups of interested parties.

One large partnership that has been formed is the 

Recover CERP Group (2004; 2006), consisting of Federal and 

State agencies, such as the South Florida Water Management 

District, U.S. Army Corps of Engineers, U.S. Fish and Wildlife 

Service, and National Oceanic and Atmospheric Administration. 

These agencies also have partnered with the USGS individually 

and together for a variety of research projects. Other USGS 

partnerships include those with Biscayne National Park, the 

University of Miami, Florida International University, Duke 

University, and Southern Illinois University at Carbondale.

Photo 1. Red mangrove in Biscayne Bay. 

Photograph courtesy of R. Alleman, South Florida Water 

Management District (used with permission).
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 3

2.2 Acknowledgments

We would like to extend our appreciation to the many 

USGS scientists, who provided assistance and information 

for the creation of this document. Additionally, we would like 

to extend special thanks to Gary Brewer of the USGS, who 

assisted in coordinating contact with individual researchers; 

Biscayne National Park scientists Richard Curry, Sarah 

Bellmund, and others; and South Florida Water Management 

District researchers Rick Alleman and Teresa Coley for their 

insight on the major issues facing Biscayne National Park.

3.0 Description of Biscayne National 

Park and Surrounding Areas in 

Southeastern Florida

Biscayne National Park (fig. 1) in southeastern Florida 

is the largest marine park in the National Park system, 

and encompasses about 172,924 ha, of which 95 percent is 

covered by water. The park consists of four distinct environments: (1) Biscayne Bay, (2) northern islands of the Florida 

Keys, (3) mangrove forest along the shoreline of Biscayne 

Bay, and (4) coral reef tract. The park originally was established as a national monument in 1968 and later designated 

as a national park by Congress in 1980, “in order to preserve 

and protect for the education, inspiration, recreation, and 

enjoyment of present and future generations a rare combination of terrestrial, marine, and amphibious life in a tropical 

setting of great natural beauty” (Public Law 90-606).

Biscayne National Park is bordered by a major 

metropolitan area with more than 2.3 million people, yearround agricultural and plant nursery communities, and the 

Everglades. These entities provide the park with a unique 

setting as well as a source of diverse issues.

3.1 Ecosystem

The four environments within Biscayne National Park 

provide diverse terrestrial and marine habitats for the large 

variety of resident animal and plant species, many of which 

are endangered or threatened. Hardwood hammocks are a 

terrestrial habitat for such animal species as the Key Largo 

wood rat, zebra butterflies, and rare Schaus swallowtails. 

Plants found in these areas include gumbo limbo, Jamaican 

dogwood, Strangler fig, and the rare semaphore prickly-pear 

cactus. Mangrove forests form the transition zone between 

the terrestrial and marine environments and provide habitat 

for a variety of bird species, such as the roseate spoonbill, 

snowy egret, tricolored heron, and the wood stork. Rare and 

endangered species, such as the American crocodile and 

eastern indigo snake, also inhabit these areas. Biscayne Bay 

is a natural habitat for more than 1,000 species of animals, 

including the following:

•	 More than 500 species of fish, such as the 

silver perch, hogfish, red grouper, and 

yellow-fin mojarra;

•	 More than 800 invertebrate species, 

including 150 species of crabs, shrimp, 

lobsters, and sponges;

•	 Sea turtles, such as the Atlantic green 

turtle, leatherback, and loggerhead;

•	 Mammals, such as the endangered West 

Indian manatee; and

•	 At least 50 different species of coral.

Photo 2. H-alicia shipwreck. 

Photograph courtesy of R. Alleman, 

South Florida Water Management 

District (used with permission).
4 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

27

95

836

1

874

1

997

1

41

826

1

Study

area

Lake

Okeechobee

Biscayne

Bay

ATLANTIC OCEAN

Biscayne Bay

25°45 ́

25°30 ́

25°15 ́

26°00 ́

80°45 ́ 80°30 ́ 80°15 ́

Florida Bay

Coconut

Grove

Deering

Estate

Mowry Canal

EVERGLADES

NATIONAL

PARK

COLLIER COUNTY

MIAMI-DADE COUNTY

0 5 10 15 MILES

0 5 10 15 KILOMETERS

EXPLANATION

BROWARD COUNTY

MIAMI-DADE COUNTY

MONROE COUNTY

Homestead

Tamiami Canal

Snapper Creek Canal

Mowry Canal

Canal 111

Canal

Canal Canal

Creek

Black

Model Land

Cutler

Ridge

Princeton

DrainCanal

Cutler

FLORIDA’S TURNPIKE

Levee 67A

Levee 67C

Levee 67

WATER

CONSERVATION

AREA 3A

WATER

CONSERVATION

Levee 29 AREA 3B

Levee 30

Levee 31N

North

Miami

Snake Creek

Biscayne Canal

Little River Canal

Hialeah Miami Canal

Miami

Silver

Bluff

Virginia

Key

Barnes

Sound

Card

Sound

FLORIDA’S TURNPIKE

Cor l al Gable

n

s Ca a

MIAMI-DADE COUNTY

Canal

CANAL OR STREAM

BISCAYNE NATIONAL ROAD

PARK BOUNDARY

LAKE

Base from U.S. Geological Survey digital data

Universal Transverse Mercator projection, Zone 17

Pacific

Reef

Caesar

Creek

Hawk

Channel

Hawk

Channel

Elliott

Key

Florida Reef Tract

LAKE BELT AREA

Old South

Dade

Landfill

Miami-Dade

County

Landfill

Figure 1. Location of Biscayne National Park in southeastern Florida.
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 5

3.1.1 History

Biscayne Bay began forming between 5,000 and 3,000 

years ago as sea level rose and southern Florida was flooded. 

Throughout most of its history, the waters of Biscayne Bay 

supported a rich and diverse ecosystem of marine fauna 

and flora, and the bay served as a nursery for the adjacent 

coral-reef and marine ecosystems. As Biscayne Bay evolved 

and formed, natural cyclical change occurred as a result of 

large-scale physical variation, such as sea-level and climate 

change, and from changes in biota living in and around the 

bay. Because natural ecosystems evolve over time, one needs 

to understand what portion of present-day change in Biscayne 

Bay is due to human activity and what portion is due to 

natural variations. To be sustainable and cost effective, restoration targets and performance measures need to be based on 

the natural system prior to substantial human alteration of the 

environment, and restoration efforts need to focus on changes 

associated solely with anthropogenic activity.

The USGS, in cooperation with South Florida Water 

Management District and Biscayne National Park, has 

conducted research on the history of Biscayne Bay by 

examining the sediments and faunal and floral remains in 

nine radiometric dated cores (fig. 2) from selected sites 

within Biscayne Bay (Ishman and others, 1998; Wingard and 

others, 2003; 2004). Results indicate that the Biscayne Bay 

ecosystem underwent many substantial changes between the 

last 100 and 500 years. Southern Biscayne Bay, including 

Card Sound and Barnes Sound, has been relatively isolated 

from direct marine influence for at least the last two centuries 

because of its enclosed configuration by barrier islands. 

Currently, this area is less affected by the urbanization that 

has occurred to the north, and few developed areas exist along 

the shoreline. Despite its relative isolation, however, the area 

has changed substantially during the last century. The three 

sites examined (Card Bank, Middle Key basin, and Manatee 

Bay) all show increasing salinity during the last 100 years. 

The salinity of Middle Key basin has increased steadily since 

the late 1800s (fig. 3). At Card Bank, salinity has varied 

substantially on multidecadal and centennial time scales 

relative to the variation observed at central Biscayne Bay 

sites, but marine influence at Card Bank has increased over 

the last century. The mud-banks of central Biscayne Bay have 

become increasingly marine and increasingly stable (showing 

less fluctuation in salinity) during the last 100 years. No 

indications of interdecadal salinity extremes or periods of 

hypersalinity have been found in cores from Featherbed and 

No Name Banks (figs. 4 and 5). Salinity has ranged from 

estuarine to marine (polyhaline to euhaline) throughout the 

period recorded in the sediment cores. The near-shore cores 

from north of Black Point and Chicken Key indicate a history 

of fluctuating salinity. At both sites, the oldest sediments with 

faunal remains show deposition under conditions of slightly 

elevated (mesohaline to polyhaline) salinity relative to the 

overlying layers, succeeded by a period of lower (mesohaline) 

salinity. During the last 20 to 30 years, salinity at both sites 

has increased to polyhaline conditions, and there is evidence 

of an increase in the magnitude of salinity fluctuations during 

the same time period.

An increasing salinity trend is evident in the Biscayne 

Bay system (fig. 5) over the past decades (Wingard and 

others, 2004), although the timing and onset of the salinity 

increase varies. At the near-shore sites, average salinity has 

increased and been accompanied by increased variability. 

In contrast, salinity has increased and become increasingly 

stable over the last century at the central Biscayne Bay sites. 

These trends could be a result of rising sea level, of changes 

to the natural flow of freshwater, or both; however, the timing 

of changes at some of the near-shore sites may indicate that 

both factors are involved. These results have several implications for restoration planning. First, sea-level rise and the 

recognition that Biscayne Bay appears to be evolving toward 

a more marine environment must be factored into the planning process. Second, generalized performance measures 

(goals established by CERP) and targets for the near-shore 

and wetland areas may not reflect the natural variability 

seen at these sites. Examining decadal to centennial trends 

in a variety of habitats within the Biscayne Bay ecosystem 

provides a realistic means to: (1) set performance measures, 

(2) predict system response to changes invoked by restoration 

efforts, and (3) better inform the public about predevelopment 

conditions of the system.

3.1.2 Function

Substantial portions of Biscayne National Park include 

three major habitats characteristic of subtropical continental 

shelves: mangrove forests, seagrass beds, and coral reefs. 

Of these, coral reefs have been studied most extensively by 

the USGS. The connectivity between these habitats is widely 

recognized (Ogden and Gladfelter, 1983), and a number of 

ecologically and economically important species spend part 

of their life histories in more than one habitat. Seagrass beds 

and mangrove forests are nursery grounds for a variety of 

popular edible fish (snappers, grunts, and groupers), as well 

as Panulirus argus, the spiny lobster. Many coral reef fish 

(yellowtail snapper, French grunt, striped parrotfish, and 

the rainbow parrotfish) along reefs with mangrove habitat 

nearby show greater biomass than those found along reefs 

where mangroves have been removed (Mumby and others, 

2004). Additionally, mangroves benefit associated marine 

ecosystems by buffering sedimentation and other land 

effects, filtering contaminants from runoff, and preventing 

shoreline scour (Ogden and Gladfelter, 1983). Seagrass beds 

stabilize sediments and provide foraging habitat for many 

commercially important reef species. Additionally, seagrass 

beds and mangroves serve detrital food webs by processing 

dissolved and particulate organic matter.
6 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Manatee Bay

Middle

Key

basin

Card

Sound

Card Bank

Biscayne Bay

Featherbed

Bank

No Name Bank

North of Black Point

Chicken Key

Miami

80°30 ́ 80°15 ́

25°45 ́

25°30 ́

25°15 ́

0 5 10 MILES

0 5 10 KILOMETERS

EXPLANATION Base from U.S. Geological Survey digital data

Universal Transverse Mercator projection, Zone 17

1996-97 CORE LOCATION AND NAME

2002 MUDBANK CORE LOCATION AND NAME

2003 NEARSHORE CORE LOCATION AND NAME

BISCAYNE NATIONAL

PARK BOUNDARY

27

95

836

874

1

997

1

41

826

1

ATLANTIC OCEAN

Homestead

Tamiami Canal

Canal 111

Canal

Model Land

Cutler

Ridge

Levee 67A

Levee 67C

Levee 31N

Miami Canal

Barnes

Sound

Figure 2. Location of core sites in Biscayne Bay, Florida.
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 7

Mangroves are also affected by chemicals and contaminants 

(such as herbicides) in the water. Because mangroves are a 

coastal tropical species, they are susceptible to hurricanes, as 

well as changes in salinity, tides, water temperature, and soil 

characteristics.

The mangrove forests in Biscayne National Park consist 

of three mangrove species: the red mangrove (Rhizophora 

mangle), black mangrove (Avicennia germinans), and white 

mangrove (Laguncularia racemosa) (Smith, and others, 

1994; Odum and others, 1982). The band of tall mangroves 

present along the shoreline of Biscayne Bay occasionally 

exceeds 15 m in height, and in certain areas, extends up to 

200 m inland. Mangrove height decreases further inland, 

averaging about 1.5 m (Smith, and others, 1994). Within these 

forests, the majority of the trees are red mangroves. Bands 

of mixed mangrove forests are also present on the keys that 

surround Biscayne Bay. The mangrove forests benefit the local 

ecosystem and nearby population by providing (1) habitat for 

various types of wildlife, (2) protection from storm-related 

winds and flooding, (3) protection from soil erosion, (4) 

natural water filtration that helps improve water quality and 

clarity, and (5) a source of food for marine organisms that, in 

turn, are a food source for larger organisms (Odum and others, 

1982).

Mangroves are susceptible to a variety of anthropogenic and environmental threats. In recent decades, the high 

demand for bayside housing has resulted in the destruction 

of extensive tracts of mangrove forest, although State and 

local ordinances now help protect mangroves from removal. 

Photo 3. Biscayne Bay mangroves near Black Point (from 

Wingard, 2004).

EXPLANATION

DECREASING NUMBER OF

FRESHWATER SPECIES

INCREASING NUMBER OF

ESTUARINE SPECIES

0 5 10 15 0 100 50 0 1 5 5 0 0 10

Terrestrial

Gastropods

Hydrobiids

(mollusks)

Cyrenoida and

Polymesoda

(mollusks)

Anomalocardia

(mollusks)

DEPTH, IN CENTIMETERS BELOW

SEDIMENT WATER INTERFACE

Freshwater

indicators

Low

salinity

indicators

Fluctuating

salinity

indicators

APPROXIMATE YEAR

0

10

20

30

40

50

60

70

80

~1900

2003

PERCENT ABUNDANCE

Figure 3. Percent abundance of key molluscan 

salinity indicators in Middle Key core segments from 

the nearshore area of Card Sound. Combined, the 

indicators show a steady increase in salinity upward 

in the core and decreasing influx from freshwater 

and terrestrial environments. (Modified from fig. 18, 

Wingard, 2004.)
8 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Figure 4. Percent abundance of key salinity indicator species in No Name Bank core segment from 

central Biscayne Bay and magnesium-calcium (Mg/Ca) ratios derived from ostracod shells.

EXPLANATION

DECREASING NUMBER OF

MARINE SPECIES

INCREASING NUMBER OF

MARINE SPECIES

SHIFT IN THE Mg/Ca CONTENT

OF OSTRACOD SHELLS--From

fluctuating to more stable

salinity in the lower and upper

parts of the core, respectively

0 0 5 10 15 2 4 6 2 8 0 0 5 10 0 40 60 80

ABUNDANCE, IN PERCENT

30 40 50

Mg/Ca

(millimoles per

mole)

2000

1950

1900

1850

1800

1750

1700

1650

Fluctuating

salinity indicators

Marine salinity

indicators

Malzella

[ostracode]

Brachidontes

[mollusk]

Archaias/

Articulina

[foraminifer]

Bairdiids

[ostracode] Salinity

150

100

50

0

DEPTH, IN CENTIMETERS BELOW SEDIMENT 

WATER INTERFACE

YEAR
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 9

Figure 5. Infrared changes in Biscayne Bay salinity in recent 

centuries based on indicators from cores between Card Bank 

and central Biscayne Bay.

Seagrasses are marine plants that are considered to be 

essential components of coastal ecosystems. The Smithsonian 

Marine Station at Fort Pierce (2003) noted that seagrasses 

support high biodiversity, and “because of their sensitivity 

to changes in water quality, they have become recognized 

as important indicator species that reflect the overall health 

of coastal ecosystems.” Seagrasses provide habitat for many 

different species of marine life, including several endangered 

species, such as the West Indian Manatee. Additionally, they 

help provide sediment stabilization, and contribute to the 

carbon budget (Lirman and Cropper, 2003).

In Biscayne Bay, seagrass beds cover up to 64 percent 

of the seafloor (Department of Environmental Resources 

Management, 1985) and consist of seven species: turtle grass 

(Thalassia testudinum), shoal grass (Halodule wrightii), 

manatee grass (Syringodium filiforme), three types of 

Halophilia, and Ruppia maritime (Browder and others, 2005). 

Of these species, Thalassia testudinum, Halodule wrightii, 

and Syringodium filiforme make up over 70 percent of the 

coverage (Lirman and Cropper, 2003). 

Photo 4. Seagrass in Biscayne Bay (from 

Wingard, 2004).

0

DEPTH, IN CENTIMETERS BELOW

SEDIMENT WATER INTERFACE50

100

150

200

~1900 AD

Card

Bank

Core

Featherbed

Bank

Core

No Name

Bank

SOUTH Core NORTH

EXPLANATION

EURYHALINE AND

POLYHALINE

EURYHALINE

DOMINANT

POLYHALINE

AND EUHALINE

EURYHALINE,

POLYHALINE,

AND EUHALINE

INFERRED SALINITY

APPROXIMATE

POSITION OF

1900 TIMELINE
10 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

It has been estimated that Biscayne Bay has lost about 

43 percent of its seagrass coverage since the 1940s (Florida 

Department of Fish and Wildlife, 2003). Seagrass communities are sensitive to several anthropogenic and natural 

environmental threats, especially changes in water quality, 

as noted earlier. Canal outflows are a major source of waterquality degradation, because they can contain high nutrient 

and chemical loads, such as sulfides and modified dissolved 

oxygen levels. In addition, large freshwater outflows occur 

that substantially change salinities in Biscayne Bay. Natural 

environmental threats include temperature increases, disease, 

and hurricanes (Lirman and Cropper, 2003). 

The coral reef habitat in Biscayne National Park varies 

widely in form and function. Within Biscayne Bay, temperature, sedimentation, and salinity seem to limit coral abundance 

and diversity, particularly to the west (Lirman and others, 

2003). A comprehensive survey of hard-bottom habitat within 

the bay revealed 12 species of hard corals, with the density 

of coral colonies inversely related to mean sediment depth 

(Lirman and others, 2003). Expansive and shallow seagrass 

beds are present between the outer shoreline of the Biscayne 

National Park keys and about 4 km seaward where the water 

deepens. At about 3 to 7 km from the shoreline, seagrass 

beds surround patch reefs with depths between about 1 and 

6 m. Deeper fore reef habitat is present about 7 km from the 

shoreline of the keys. 

Coral reefs around the world have experienced marked 

degradation over the past three decades due to a number of 

global and local scale stressors (Hoegh-Guldberg, 1999; 

Hallock, 2001; Hughes and others, 2003; Pandolfi and others, 

2005). Within Biscayne National Park, research shows a 

gradual decline in the average annual growth of an important 

reef-building coral Montastrea annularis (Hudson, and others, 

1994). Fisheries stocks in Biscayne National Park show 

signs of heavy exploitation: 77 percent of 35 species of fish 

that could be analyzed are over fished, and stock biomass 

is critically low (Ault and others, 2001). Fishing pressure 

(mainly skilled recreational) is particularly high in readily 

accessible areas directly seaward of Caesar’s Creek (Harper 

and others, 2000).

Photo 5. Biscayne National 

Park patch reef.

Photograph by Mark Bonito.

Photo 6. Montstrea cavernosa

infected with black band disease.

Photograph by Ilsa Kuffner, U.S. Geological 

Survey.
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 11

In general, the lagoon patch reefs inside Biscayne 

National Park show greater coral cover, biodiversity (Miller 

and others, 2000), and topographic complexity (Brock and 

others, 2004) than the adjacent outer fore reefs. Densities 

of coral recruits were consistent across the shelf (Miller and 

others, 2000) and seem to be comparable with other areas 

in the Caribbean (Edmunds, 2000). One study found higher 

recruit densities on patch reefs in the lower keys than in the 

upper keys (Moulding, 2005), whereas another study found 

no latitudinal gradient (Tougas and Porter, 2002). In another 

study, two inshore patch reefs showed lower rates of herbivory 

compared to two offshore reefs, but algal biomass (which is 

seasonally dynamic) did not correlate with the pattern (Lirman 

and Biber, 2000). The patch reefs in Biscayne National Park 

showed better resistance to Hurricane Andrew compared to 

the outer fore reefs (Blair and others, 1994), although the 

damage spatially was inconsistent (Tilmant and others, 1994). 

Evidence is lacking to determine whether inshore patch reefs 

are subject to greater anthropogenic stress than outer reefs 

due to their closer proximity to land-based sources. The few 

studies that address this topic, however, do not support the 

hypothesis because patch reefs studied seem to be in better 

condition than the offshore reefs (Glynn and others, 1989; 

Szmant and Forrester, 1996; Miller and others, 2000). 

Although global stressors (for example, increases in 

water-surface temperature and sea level rise) are largely beyond 

the control of local resource managers, local-scale stressors 

can be understood and mitigated. For example, the occurrence 

of coral diseases in the Florida Keys is increasing (Porter and 

others, 2002), but evidence is unclear whether the increase is 

related directly to anthropogenic factors. Disease outbreaks have 

caused major changes in the coral community structure in many 

areas of the Caribbean and Florida in the recent past (Aronson 

and Precht, 2001), and evidence suggests that elevated nutrient 

levels potentially could increase the severity of coral diseases 

(Bruno and others, 2003). Because of the potential changes 

to Biscayne National Park water quality that may result from 

CERP, it is prudent to make research in this area a priority. 

At this juncture in CERP, it is important to understand the 

relation between nutrient (both dissolved and particulate) input 

and community structure in all of the major marine habitats 

represented within Biscayne National Park boundaries.

3.2 Hydrology

The hydrology of southeastern Florida is complex because 

of the dynamic interaction between ground water and surface 

water. The surface-water component consists of a managed 

system of canals, control structures, levees, and a small portion 

of overland flow. The underlying ground-water network in this 

area is characterized by a shallow surficial aquifer system and 

the deeper Floridan aquifer system. Parker and others (1955) 

and Kohout (1960) have suggested that the ground water 

discharging into Biscayne Bay originates from the Biscayne 

aquifer, which is part of the surficial aquifer system.

Prior to dredging and construction of the surface-water 

canal and levee system throughout the Everglades and 

southeastern Florida, the water level was about 1.8 m higher 

(Thorhaug and others, 1976) than it is today. This loss of 

upland water pressure has decreased fresh ground-water 

discharge to Biscayne Bay. The replumbing of the predevelopment system reduced the seaward hydraulic gradient that 

supplied freshwater to offshore submarine springs throughout 

Biscayne Bay, and lowered ground-water levels throughout 

the area (Buchanan and Klein, 1976). The lowering of inland 

water levels has caused substantial reductions in submarine 

spring flows.

3.2.1 Surface Water

The dynamics of the surface-water system are governed 

by both natural and anthropogenic features. The Atlantic 

Coastal Ridge, a physiographic feature, separates the 

Everglades from the Atlantic Ocean and Biscayne Bay. This 

ridge is between 5 and 15 km wide and roughly parallels the 

coast in the northern half of Miami-Dade County. In southern 

Miami-Dade County, the ridge is located farther inland, and 

low-lying coastal marshes and mangrove swamps adjoin 

Biscayne Bay. Historically, the transverse glades (low-lying 

areas that cut through the ridge) allowed high-standing 

surface water in the Everglades to drain into Biscayne Bay. 

Throughout much of the area, a complex network of levees, 

canals, and water-control structures is now used to manage 

the water resources. The major canals, operated and maintained by the South Florida Water Management District, were 

constructed to prevent low-lying areas from flooding and 

prevent saltwater intrusion into the Biscayne aquifer. These 

canals are mostly within the low-lying transverse glades to 

more effectively route surface water toward Biscayne Bay.

3.2.2 Ground Water

In Miami-Dade County, the surficial aquifer system 

includes all rocks and sediments from land surface downward 

to the top of the intermediate confining unit, defined by a 

substantial decrease in permeability (fig. 6). The rocks and 

sediments are composed mostly of limestone, sandstone, sand, 

shell, and clayey sand and range in age from Holocene to 

Pliocene (Causaras, 1987). The permeability of rock and sediment within the surficial aquifer system is variable, allowing 

the system to be divided into one or more aquifers separated by 

less-permeable or semiconfining units. The uppermost part of 

these water-bearing units is the Biscayne aquifer (Parker, 1951; 

Parker and others, 1955), and the lowermost water-bearing 

unit is the gray limestone aquifer (Fish and Stewart, 1991; 

Reese and Cunningham, 2000). The geology and hydrology 

of the Biscayne aquifer in Miami-Dade County have been the 

subject of numerous studies (Parker and Cooke, 1944; Parker 

and others, 1955; Kohout, 1964; Perkins, 1977; Causaras, 

1987; Labowski, 1988; Shinn and Corcoran, 1988; Fish and 
12 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Photo 7. Sea fan (Gorgonia sp.) in Biscayne Bay. 

Photograph courtesy of R. Alleman, South Florida 

Water Management District (used with permission).

Photo 8. Sponge (unidentified) in Biscayne Bay. 

Photograph courtesy of R. Alleman, South Florida 

Water Management District (used with permission).
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 13

Stewart, 1991; Galli, 1991; Solo-Gabriele and Sternberg, 1998; 

Nemeth and others, 2000; Langevin, 2001; Sonenshein, 2001; 

Cunningham and others, 2004a,b; 2006a,b).

The Biscayne aquifer is the primary aquifer in southeastern Florida and has been declared a sole-source aquifer 

(Federal Register Notice, 1979). Parker (1951) named 

and defined the Biscayne aquifer as a hydrologic unit of 

water-bearing rocks that carries unconfined ground water in 

southeastern Florida. Later, Fish (1988), defined the Biscayne 

aquifer more completely as:

That part of the surficial aquifer system in southeastern Florida composed of (from land surface 

downward) the Pamlico Sand, Miami Oolite [Limestone], Anastasia Formation, Key Largo Limestone, 

and Fort Thompson Formation (all of Pleistocene 

age) and contiguous, highly permeable beds of the 

Tamiami Formation of Pliocene and late Miocene 

age where at least 10 ft (about 3 m) of section is 

highly permeable, with a horizontal hydraulic conductivity of at least 1,000 ft/d (about 305 m/d).

Fish (1988) provided further definition of the base of the 

Biscayne aquifer:

If there are contiguous, highly permeable (having 

hydraulic conductivities of about 100 ft/d [about 

30.5 m/d] or more) limestone or calcareous sandstone beds of the Tamiami Formation, the lower 

boundary is the transition from these beds to subjacent sands or clayey sands. Where the contiguous 

beds of the Tamiami Formation do not have sufficiently high permeability, the base of highly permeable limestone or sandstones in the Fort Thompson 

Formation, Anastasia Formation, or Key Largo 

Limestone is the base of the Biscayne aquifer.

Figure 6. Relations of geologic formations, aquifers, and semipermeable units of the surficial aquifer 

system across central Miami-Dade County (from Reese and Cunningham, 2000).

Pamlico Sand

Pinecrest Sand

Unnamed

formation

Fort Thompson

Formation

Anastasia

Fm

Anastasia

Fm

Miami Limestone

Tamiami

Formation

Semiconfining

unit

CSU

Water-table aquifer

Peace River Formation

EAST

NGVD 29 NGVD 29

100 100

50 50

200 200

150 150

ALTITUDE, IN FEET

BELOW NGVD 1929

ALTITUDE, IN FEET

BELOW NGVD 1929

Miami Limestone

WEST

Ochopee Limestone

SA

Biscayne

aquifer

Gray Limestone

aquifer

ICU

EXPLANATION

VERTICAL SCALE GREATLY EXAGGERATED

5 MILES

5 KILOMETERS

0

0

HYDROSTRATIGRAPHIC BOUNDARY (RED TEXT

IDENTIFIES HYDROSTRATIGRAPHIC UNITS)

CONFINING TO SEMICONFINING UNIT

LIMESTONE

QUARTZ SAND

OR SANDSTONE

SILT OR MUDSTONE

CSU

ICU

SA

Fm

INTERMEDIATE CONFINING UNIT

SAND AQUIFER

FORMATION
14 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

The Biscayne aquifer recently has been described as 

a karst aquifer (Cunningham and Aviantara, 2001; Vacher 

and Mylroie, 2002; Cunningham and others, 2004a,b and 

2006a,b; Renken and others, 2005). This revised view has 

implications that may fundamentally alter the definition of 

the hydrogeologic framework needed for reliable simulation 

of ground-water movement and solute transport. Karst aquifers traditionally are characterized by three types of porosity: 

interparticle matrix porosity, fracture porosity, and large 

cavernous porosity (Martin and Screaton, 2001). This has led 

many researchers to view karst aquifers as two component 

systems, where much of the ground-water storage occurs 

in the matrix porosity, fractures, or both, and much of the 

ground-water flow and transport takes place in large dissolutional conduits (Martin and Screaton, 2001). However, in the 

young eogenetic karst that defines the Pleistocene limestone 

of the Biscayne aquifer, a fourth porosity type―touchingvug porosity―is especially important for ground-water 

transport (Vacher and Mylroie, 2002; Cunningham and 

others, 2006a,b). The triple porosity of the Biscayne aquifer 

is typically: (1) a matrix of interparticle and separate vug 

porosity, providing much of the storage; (2) touching-vug 

porosity, creating stratiform ground-water flow passageways; 

and (3) less common conduit porosity composed mainly 

of bedding plane vugs, thin solution pipes, and cavernous 

vugs―these three conduit porosity types are all pathways 

for conduit ground-water flow (figs. 7- 9). Stratiform refers 

to the three-dimensional aspects of porosity; that is, it is 

constrained to a layer, bed, or stratum with lateral continuity 

(Jackson, 1997).

In the 246-km2 (95-mi2 ) Lake Belt area west of 

Biscayne Bay, Cunningham and others (2004a,b; 2006a,b) 

have shown that porosity and permeability of the Biscayne 

aquifer are related to past depositional environments 

and how sediments were deposited during repeated past 

sea-level changes. In the Lake Belt area, six depositional 

environments containing major lithologic components of 

the Biscayne aquifer―the Tamiami Formation, the Fort 

Thompson Formation, and the Miami Limestone―include: 

(1) middle ramp, (2) platform margin-to-outer platform, 

(3) open-marine platform interior, (4) restricted platform 

interior, (5) brackish platform interior, and (6) freshwater 

terrestrial environments. High-frequency cycles form the 

fundamental building blocks of the rocks of the Biscayne 

aquifer. Vertical lithofacies assemblages, which have 

stacking patterns that reoccur, fit within the high-frequency 

cycles. Upward-shallowing subtidal cycles, upwardshallowing paralic cycles, and aggradational subtidal cycles 

define three types of ideal high-frequency cycles that occur 

within the Fort Thompson Formation and Miami Limestone. 

Based on vertical cycle patterns, high-frequency cycles 

group into two cycle sets: an older progradational cycle set, 

and an overlying, younger aggradational cycle.

The geologic framework of Biscayne National Park 

has been investigated by core drilling along a northwest to 

southeast transect from Black Point to Pacific Reef. Seven 

sites were core drilled and monitoring wells installed as part 

of a ground-water characterization project (Reich and others, 

2006). The cores were described and used to extend the 

onshore geologic framework of the aquifer (Fish and Stewart, 

1991; Cunningham and others, 2004a,b) seaward into 

Biscayne Bay. The Miami Limestone and Fort Thompson 

Formation extend into the bay, and a facies change occurs 

at Elliott Key to a more reefal limestone as the Miami 

Limestone grades laterally into the Key Largo Limestone. 

The Key Largo Limestone is buried to the east under modern 

sediments within Hawk Channel and a Holocene reef cap out 

on the Florida Reef Tract. Age-dated coral within the cores 

indicates the Pleistocene-Holocene boundary is about 10 m 

below NGVD 29 along the shelf edge at Pacific Reef. 

3.2.3 Water Quality

There are numerous sources of potential ground-water 

and surface-water contaminants in the terrestrial areas 

adjacent to Biscayne National Park. The shoreline and 

nearby upland areas have been extensively developed. The 

upland areas contain numerous deeply dredged pits (rock 

mines), lakes, and water storage sites that collect and hold 

urban surface-water runoff. The highly permeable limestone 

substrate of the region makes the ground-water system highly 

susceptible to the infiltration and spread of nonpoint-source 

pollutants from surface-water runoff and the dredged sites. 

In addition, a large Class I landfill (the South Dade Landfill 

at Black Point) was established in 1978 in an area directly 

adjacent to Biscayne Bay and Biscayne National Park. It 

replaced an earlier, privately owned Class I landfill, that 

was unlined and sited about 1-3 ft (0.3-0.9 m) into the 

local water table in southern Miami-Dade County, and was 

operated between 1950 and 1978 (McKenzie, 1983; Shinn 

and Corcoran, 1988). The newer facility has resulted in the 

creation of a large mound of municipal waste (the older 

landfill material has largely decomposed and now forms a 

low-profile hill), with a strong potential for ground-water 

contamination, which could be transported into Biscayne 

National Park through ground-water flow paths. Some 

ground-water infiltration of nutrients and contaminants from 

the urban developments and the municipal waste facility have 

been documented; the concentration of ammonia nitrogen in 

local ground water, including that of Biscayne National Park, 

has increased by more than 40 ppm above normal background levels of 10 ppb.

The question of whether nutrients from human sources 

reach the outer reef tract in southern Florida remains 

unresolved. Some researchers contend that anthropogenic 

nutrients are the key factor responsible for the increase in 

fleshy macroalgae observed on Florida (and many other) 
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 15 Figure 7. Relation between pore classes I and III and touching-vug and conduit-pore types, respectively, for the Fort Thompson Formation and Miami Limestone in the Lake Belt area of Miami-Dade County. (A) Four common types of touching-vug porosity: fossil moldic, intra-burrow, irregular vugs, and inter-root-cast porosity for pore class I. (B) Two types of conduit porosity (cavernous and bedding-plane vugs) that are rather untypical for pore class I. (C) Thin, vertical conduits that are a typical pore type of pore class III. From Cunningham and others, 2006a.

Photo of Quarry Sample

5 inches

Thin Solution Pipes inVery Low Porosity Matrix

Leaky,low-permeabilityzone

Pore Class I Pore Class III

Touching-Vug Porosity Conduit Porosity

Cavernous Vugs

Bedding-Plane Vugs

Inter-Root-Cast Porosity

Fossil-Moldic Porosity

Irregular Vugs

Thin Solution Pipes

B

C G-3792

G-3794

G-3792

22

23

Thin Solution Pipes

Very Low Porosity Matrix Miami

Limestone

Fort

Thompson

Formation

50

55

60

15

20

Example of conduit flow

through bedding plane vugs

Example of conduit flow through touching-vugs

Matrix Fossil Mold

Tortuous Ground-Water Flow

Exampleof conduitflow throughverticalsolutionpipes

Leaky,low-permeabilityzone

5 inches

Diagram of Quarry Sample

Intra-Burrow Porosity

48

51

G-3770

A

DEPTH BELOW LAND

SURFACE, IN FEET

Vug-to-vug Flow

G-3795

45

4647

21.8

21.9

22.0

Vug

G-3717

DEPTH BELOW LAND

SURFACE, IN FEET

DEPTH BELOW LAND

SURFACE, IN FEET

DEPTH BELOW LAND

SURFACE, IN FEET

DEPTH BELOW LAND SURFACE, IN FEET DEPTH BELOW LAND

SURFACE, IN FEET
16 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Figure 8. Relation between pore class II and matrix porosity. Ground-water flow through the matrix is generally 

matrix-to-vug-to matrix flow. Core sample of pelecypod floatstone and rudstone lithofacies shown in photograph is 

from the Fort Thompson Formation. From Cunningham and others, 2006a.

Pore Class II

Matrix Porosity

Matrix-to-Vug-to-Matrix Flow

Particles

Interparticle

Porosity

Fossil-Moldic

Porosity

Ground-Water

Flow

1 inch0

Photo 9. Alina’s Reef drilling in Biscayne 

National Park. 

Photograph by Chris Reich, 

U.S. Geological Survey.
3.0 Description of Biscayne National Park and Surrounding Areas in Southeastern Florida 17

Figure 9. Three-dimensional conceptual hydrogeologic model of the Biscayne 

aquifer for the Lake Belt area in north-central Miami-Dade County (modified from 

Cunningham and others, 2006b).

North

L-29 Canal

C-9 Canal

C-1W Canal L-31N Canal

L-30 Canal

EXPLANATION

PEAT, MUCK, MARL, AND/OR FILL

PORE CLASS I

PORE CLASS III

PORE CLASS II

0

0

5 10 MILES

5 10 KILOMETERS
18 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

reefs (Lapointe, 1997; Lapointe and others, 2002), whereas 

others believe that a combination of hurricanes and declines 

in herbivory caused by overfishing and disease (Diadema 

antillarum die-off) are the main causes, and nutrients play 

a much smaller role (Hughes, 1994; Szmant and Forrester, 

1996; Lirman, 2001; Szmant, 2002). Although preliminary 

research shows that ground water beneath reefs does contain 

nutrients, a USGS study (Reich and others, 2006) indicates 

that “ground water beneath the reefs do contain nutrients, 

principally ammonium (Shinn, 1993) and soluble silicates, 

at levels many times higher (10 to 300) than that of normal 

seawater, and evidence for a direct linkage to coral reef 

degradation is lacking.” Discharge of treated wastewater 

into the Lower Floridan aquifer (about 800 m [2,600 ft] 

below land surface) is another possible source of contamination for Biscayne National Park. Additional surface-water 

pollutants enter Biscayne National Park from the Miami 

River, Turkey Point Nuclear Power Plant, and from heavy 

metals and petroleum from several coastal marinas (Lidz, 

2002). With the projected changes outlined in CERP, 

additional research is needed to adequately determine the 

connection among nutrients, contaminants, and coral reef 

health, particularly in areas such as Biscayne National Park 

where a number of potential eutrophication sources exist. 

Resource managers in Florida have expressed a considerable need for scientific research to address the issue (Keller 

and Causey, 2005). 

3.3 Socioeconomic Conditions

Population growth and development in southeastern 

Florida place considerable anthropogenic stress upon the 

natural resources of the area. In 2000, the population of 

Miami-Dade County (which includes Biscayne National 

Park) was about 2,250,000 (U.S. Census Bureau, 2000) and 

has since increased to more than 2,350,000. The population is expected to grow even further in the coming years, 

increasing the demand for agriculture, water supply, and 

sewage treatment, as well as increasing air pollution, land 

pollution, and developed areas. Water inflow to Biscayne 

National Park occurs primarily through a series of canals 

and levees operated by the South Florida Water Management 

District. The possibility of additional pollution through 

these waterways caused by future population growth is of 

concern; however, a larger issue is CERP, signed into law 

in 2000. One goal of CERP is to remove canal and levee 

infrastructures in the watershed to restore the predevelopment southward flow of water into Everglades National 

Park. If research on the effects of changing the quantity, 

quality, timing, and distribution of water is not performed 

before CERP is fully implemented, the planned modifications may create additional problems for Biscayne National 

Park in the future.

The increasing population in the region also may 

increase park visitation and consequent stress to the 

Biscayne National Park ecosystem. Increased recreational 

activities within the park may result in overfishing, additional boat damage to threatened seagrass beds and coral 

reefs, and increased trash and pollutants. Additionally, 

invasive nonnative species have been introduced into the 

park ecosystem. These species compete for resources, and in 

some instances (for example the snail Melanoides tuberculatus), introduce diseases that can threaten the health of park 

visitors and native animal populations.

Photo 10. Scientist/diver collecting pore-water 

samples at Alina’s Reef, Biscayne National Park.

Photograph by Chris Reich, U.S. Geological Survey.
4.0 U.S. Geological Survey Research Issues and Needs 19

4.0 U.S. Geological Survey Research 

Issues and Needs

USGS scientists working in Biscayne National Park 

and surrounding areas have identified several environmental 

resource issues where substantial gaps in information exist 

and further research is needed. The research needs have been 

grouped into four major categories: (1) ecosystem stresses; 

(2) water deliveries; (3) contaminants; and (4) database 

and Geographic Information System (GIS) issues. Selected 

potential USGS projects that address many of these issues are 

described later.

4.1 Ecosystem Stresses

Rapid population growth and associated development 

during the 20th century have resulted in aquatic habitat loss 

at an unprecedented rate. This is especially true in coastal 

wetland areas of the Nation where at least one-third of 

threatened and endangered species reside (Murdock, 1994). 

Brackish coastal wetlands are being developed or otherwise 

degraded and destroyed at an accelerating rate as a direct 

and indirect effect of urbanization. These problems make it 

essential to identify and study the different indicator species 

in the region to determine how urbanization affects them and 

their associated habitats.

As described earlier, Biscayne National Park is bordered 

by developed areas within Miami-Dade County and includes 

a substantial amount of sensitive estuarine areas and fragile 

ecosystems within its boundaries, such as the coral reef 

and reef-associated habitat. As with most other reefs in the 

region, those within Biscayne National Park have experienced 

substantial declines in coral cover and fish biomass/abundance, 

as well as increased algal cover and incidence of coral disease. 

Despite the semiprotected status of these resources within 

Biscayne National Park, reef habitats have not shown any 

signs of recovery since the protection laws were established. 

Water-quality issues, including increased levels of nutrients 

and water-borne pathogens, are hypothesized to be a primary 

cause of these observed changes. Although the previously 

described modifications under CERP are pending, baseline 

community structure data are unavailable for many areas 

throughout the park. These data are needed to: (1) accurately 

assess and document the positive or negative effects associated 

with changes in freshwater delivery patterns, and (2) determine 

the effects of terrestrially derived contaminants upon the 

Biscayne National Park estuary and ecosystem. 

In the future, it is also important to know, not only what 

is currently in Biscayne Bay, but to develop models that can 

describe the potential habitat suitability for these different 

flora and fauna. This will provide managers and others with 

a method to assess how potential changes to the system may 

alter the habitat and affect the populations of different species 

that reside in these habitats. 

In addition to habitat stress, there are major stresses to 

the many different species of flora and fauna in Biscayne 

National Park and Biscayne Bay. The shoreline of Biscayne 

Bay is highly developed and is considered one of the 10 most 

endangered parks in the national park system (National Parks 

Conservation Association, 2001). Pollutants can potentially 

enter Biscayne Bay from multiple point and nonpoint sources 

including boats, canals, quarrying operations, the Class 1 

landfill described earlier, several C and D landfills, military 

operations, a sewage-treatment plant, urban and agricultural 

runoff, and submarine ground-water springs. Additional 

studies are needed to determine which of these, if any or 

all, directly affect Biscayne Bay. Because the effects of 

these sources on the fauna and flora (including the microbial component) of Biscayne National Park have not been 

characterized fully, additional study is needed to address the 

following questions:

•	 Are anthropogenic chemicals changing bay 

microbial community compositions, resulting 

in modulation of nutrient cycling or increases in 

opportunistic pathogens?

•	 Do pollutants entering Biscayne Bay ultimately 

reach the reef tract, or are they remediated by 

other natural or anthropogenic factors within the 

bay?

•	 How severe are the effects of these pollutant 

stressors on the fauna and flora of Biscayne Bay?

To fully determine the threats to the Biscayne National Park 

ecosystem, studies in addition to those listed above would 

be necessary. These studies may involve the use of models, 

field-data collection, or both to determine or extrapolate the 

following:

•	 Past and/or future ecological conditions in 

Biscayne Bay,

•	 Relation between the distribution of bay 

organisms and freshwater flows and 

contaminants,

•	 Relation between salinity and the Biscayne 

National Park ecosystem or its components,

•	 Critical ranges for ecological species targets, and

•	 Present floral and faunal species distributions.
20 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

4.2 Water Deliveries

During the last century, Biscayne Bay has been affected 

greatly by anthropogenic alteration of the environment 

through urbanization of the Miami-Dade County area and 

alteration of predevelopment surface-water flow. The alterations of historical quantity, quality, timing, and distribution 

of freshwater flow into the bay have changed the shoreline 

and associated submerged aquatic vegetation (SAV). Current 

CERP goals are to restore predevelopment flows of freshwater 

into Biscayne Bay that would ultimately begin the restoration of the natural fauna and flora. Predevelopment baseline 

conditions first need to be determined to establish targets and 

performance measures for restoration. To accomplish this 

task, it is necessary to examine patterns of temporal change 

in salinity, water quality, vegetation, and benthic fauna in 

Biscayne Bay between the last 100 and 300 years and examine 

the causes of change. These historical data also can be applied 

to help predict system characteristics in the future with and 

without CERP. Additionally, it is necessary to understand the 

geologic framework of the aquifer and the general patterns of 

surface-water flow that existed prior to the construction of the 

canal systems to create a better approximation of the predevelopment flow system.

Currently, CERP plans to reestablish flows in the 

Everglades system and surrounding areas, including Biscayne 

Bay. The changes proposed within this plan may substantially 

alter current hydrologic conditions in the park, and may even 

cause offshore springs in Biscayne Bay to once again become 

sites of freshwater discharge. Additionally, these activities 

that reestablish ground-water flow may create the potential for 

“flushing” stagnant and possibly contaminated ground water 

into the offshore marine ecosystem. If this scenario were to 

occur, there is a large potential for the deterioration of habitat 

for the many different threatened or endangered species of 

plants and animals that reside along the coastline of Biscayne 

Bay, in the bay, and on the coral reef tract. Therefore, it is 

essential that these hydrologic conditions are determined prior 

to any water-delivery changes made by CERP in order to 

protect these sensitive ecosystems.

Collective knowledge of the subsurface hydrogeology 

beneath Biscayne Bay and offshore reef areas is limited, but 

necessary for connecting the better known onshore hydrogeology to the offshore. The current hydrogeology of the bay 

is based mainly on lithologic data from shallow coreholes 

that have not been linked to the context of the new karst 

hydrostratigraphic conceptual model that has been developed 

onshore by Cunningham and others (2006a,b). A cost effective 

means of linking the onshore hydrogeologic model is through 

acquisition and interpretation of high-resolution marine-reflection seismic data throughout the bay. The seismic data could 

be combined with new offshore coreholes that fully penetrate 

the Biscayne aquifer, thus providing critical data for mapping 

a much improved hydrologic framework that is needed for 

development of more accurate ground-water flow simulations. 

The new modeling could be used to quantify rates and flows of 

freshwater to Biscayne Bay for managing the bay ecosystems 

and improve delineation of coastal saltwater intrusion.

Photo 11. Alina’s Reef in Biscayne Bay. 

Photograph by G.L. Wingard, U.S. Geological Survey.
4.0 U.S. Geological Survey Research Issues and Needs 21

In addition to the subsurface characteristics of Biscayne 

Bay, it is necessary to determine sediment thickness and the 

hydraulic characteristics within Biscayne Bay. This information serves as model input and is necessary to accurately 

determine how closely surface water and ground water 

interact within the bay.

Biscayne National Park has a vested interest in better 

understanding how submarine ground-water discharge has 

affected Biscayne Bay during the past and present, and 

how CERP modifications will affect future ground-water 

and surface-water flows. New technologies recently have 

been used to successfully identify and quantify submarine 

ground-water discharge in Biscayne Bay (Swarzenski and 

others, 2004a,b). Geophysical tools, such as direct-current 

continuous resistivity profiling, have been used in several 

marine and estuarine areas to discern the subsurface 

freshwater-saltwater interface and freshened ground-water 

masses. Monitoring wells within the bay were used as 

controls in matching in-situ ground-water salinity and values 

obtained using continuous resistivity profiling. Other means 

used to delineate ground-water discharge are electromagnetic 

seepage meters and in-situ radon-222. Radon-222 is particularly well suited as a submarine ground-water discharge 

tracer in southern Florida because: (1) radon-222 concentrations in ground water are several orders of magnitude 

greater than those measured in surface waters (Swarzenski 

and others, 2006), and (2) radon-222 is a chemically inert 

noble gas, and also has a short half-life (t1/2 = 3.8 days). 

Surface waters where radon-222 is elevated typically 

coincide with areas of enhanced submarine ground-water 

discharge. These technologies could be used in Biscayne 

Bay and surrounding waters to increase current knowledge 

of subsurface ground-water flow patterns; the results could 

then be placed in the context of potential ecological effects 

(Kim and Swarzenski, 2005). 

As mentioned above, monitoring wells have been 

installed within Biscayne National Park and along the coastline in northern Biscayne Bay. During the installation of 

these monitoring wells, rock cores were collected to obtain 

lithologic and hydrostratigraphic information about the rocks 

beneath Biscayne Bay and the reef tract. Additional coring 

sites may be necessary if modeling efforts require additional 

information about permeability, porosity, or chemistry that 

can be obtained from monitoring wells. The installation of 

pressure sensors in wells may be useful for understanding 

hydraulic gradients across Biscayne National Park. Dye and 

isotope tracers, as well as monitoring of springs and their 

associated benthic communities along coastal Biscayne Bay, 

would allow better management of minimum flows and levels. 

4.3 Contaminants

A better understanding of ground-water chemistry (for 

example, nutrients, pathogens, and emerging contaminants) is 

needed throughout Biscayne Bay for several reasons. In combination with much needed seepage estimates, knowing certain 

constituents may help explain spatial and temporal variations 

in SAV. Greater knowledge of fluxes at different locations, for 

example, along the western shoreline of Biscayne Bay, shoreline of upper Keys (for example, Elliott Key), or along the coral 

reef tract, will enhance current knowledge about how ground 

water may affect various benthic and pelagic biota.

Photo 12. Water sampling syringe and mini-piezometer 

used for collection of reef sediment pore waters. 

Photograph by Chris Reich, U.S. Geological Survey.

Photo 13. Monitoring wells located on Alina’s Reef. 

Wells are installed with screens at different depths 

below reef cap.

Photograph by Chris Reich, U.S. Geological Survey.
22 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Various potential sources of contaminants to Biscayne 

Bay and Biscayne National Park exist, but quantifying their 

threat to the bay is difficult. For example, a current study of 

the effects of the Old South-Dade Landfill and the MiamiDade County landfill and water-treatment plant on nearshore 

and offshore ground water has been undertaken. High ammonium concentrations have been found in nearshore surfaceand ground-water samples; however, the levels are not high 

enough to indicate that either landfill is a source. Additional 

monitoring wells would be needed between the nearshore 

Biscayne Bay wells and the landfill to understand nitrogen 

processes as well as other chemical variations along onshore 

to offshore flowpaths.

One potential source of pollution is the Florida Power and 

Light nuclear powerplant. The 270-km-long array of canals 

used in the process of discharging high temperature water 

from the powerplant and reusing the cooler canal water may 

affect nearshore communities. The effects of elevated water 

temperature on nearshore communities are not fully quantified. One question that may need to be addressed is whether 

natural microbial communities in the subsurface or surface 

waters will be affected in a way that alters the quality of water 

delivered to Biscayne Bay.

The growth, persistence, and spatial distribution of 

bacteria in aquatic and sediment systems are directly influenced by the quantity and quality of nutrients and organic 

matter. The rates at which native (autochthonous) and foreign 

(allochthonous) microbes assimilate these nutrients are 

affected by temperature and salinity. The potential sources 

of pollution in the coastal waters of Biscayne National Park 

contribute nutrients as well as thermal energy that increases 

the temperature of the receiving ground waters. The occurrence and persistence of microbial indicators, such as fecal 

coliform bacteria, enterococci, coliphage, and Clostridium 

perfringens, and pathogens, such as Escherichia coli and 

Serratia marcescens, and human enteroviruses, in the water 

column and sediments of marine systems may be enhanced 

by increased nutrient concentrations and in-situ temperatures. 

The increased occurrence and persistence of the indicators thereby increase the risk of disease in humans, marine 

mammals, invertebrates, and possibly coral reefs that come in 

contact with these contaminated waters.

4.4 Database and Geographic Information 

System Issues

Over the past 50 years, a large amount of data collection and research has taken place in Biscayne National Park. 

Large portions of the data have been transferred into a digital 

database, which includes raster and vector coverages of the 

park and the surrounding areas. To serve the data to all interested parties, there is a need to create a geodatabase of all the 

available data. Some examples of the information available are 

topology, land use, vegetation, and bathymetry. The database 

would include an inventory of current data-collection activities 

in and around the park from all involved agencies, such as the 

USGS, Biscayne National Park, Miami-Dade Department of 

Environmental Resource Management, U.S. Army Corps of 

Engineers, South Florida Water Management District, U.S. 

Fish and Wildlife Service, and local universities. It would 

include long-term network activities as well as projectoriented activities, such as multidisciplinary data from 

biology, hydrology, geology, hydrogeology, ecology, and so 

forth. This database can function as a tool for researchers 

who are (1) interested in contributing their data for other 

researchers to use, (2) trying to locate and fill gaps in research 

needs, and (3) working closely with park managers in identifying concerns that affect their park.

The ability to compile and use the data collected from 

a variety of sources is essential to all current and future 

researchers as well as to local and regional managers. Once 

the data are compiled into a centralized database, the database 

can be utilized to create a large host of evaluation tools, such 

as models and GIS coverages. One important issue that can 

be addressed using these GIS maps is land use and preservation/restoration. Land use and preservation/restoration decisions have substantial but highly uncertain effects on water 

quality and quantity, flow patterns, and ecosystem health 

in the Greater Everglades Ecosystem. These environmental 

and ecological factors, however, have economic value that 

currently is being ignored (or only partially considered) 

in these decisions. To address these issues successfully, a 

research program is needed that involves: (1) estimating the 

economic value of environmental and ecological resources 

affected by development and preservation/restoration 

decisions, (2) aggregating and quantifying the substantial 

uncertainties associated with these decisions, and (3) creating 

a decision support system that will provide land managers 

and local officials with a clearer idea of the economic 

consequences of various courses of action.

5.0 Current or Recently Completed 

Studies in and around Biscayne 

National Park

To show how the USGS is assisting and/or supplementing 

needed research in Biscayne National Park and Biscayne Bay, 

several USGS scientists have composed descriptions of their 

current or recently completed research projects. These projects 

are examples of studies that are supplying managers with 

the information they need to address the problems that face 

Biscayne Bay.
5.0 Current or Recently Completed Studies in and around Biscayne National Park 23

Project Description Index

Biscayne Bay Coastal Wetlands..................................................................................................................................24

Historical Changes in Salinity, Water Quality, and Vegetation in Biscayne Bay........................................................24

Ground-Water Discharge to Biscayne Bay .................................................................................................................25

Development of an Integrated Surface Water and Ground-Water Model of Biscayne Bay and Analysis 

of the Hypersalinity Events in Southwestern Biscayne Bay ..........................................................................25

Ground- and Surface-Water Impacts on Water Quality and Ecology: Science to Assist Resource 

Management at Biscayne National Park.......................................................................................................26

Remote Sensing of Water Turbidity and Sedimentation in Florida Bay and Biscayne Bay........................................27

Contaminant Effects on Biological Resources: Sediment Quality in Canals that Discharge into 

Biscayne Bay, Miami-Dade County, Florida ................................................................................................27

Temporal and Spatial Variation in Seagrass-Associated Fish and Invertebrates in South Florida: Nearshore 

Seagrass Community of Biscayne Bay, Florida ............................................................................................28

Inventory of the Amphibians and Reptiles of Big Cypress National Preserve, Biscayne National Park, 

and Buck Island Reef National Monument....................................................................................................28

Application of Landscape Ecology to the Design of Marine Protected Areas............................................................29

Environmental Assessment of Effects of Rotenone on Seagrass Beds.........................................................................30

Assessment of Emerging Pollutants of Concern (EPOCs) in Wastewater Influent and Effluent at the 

South Miami-Dade Wastewater Treatment Plant and Biscayne Bay Coastal Environment..........................30

Biogeochemistry of Ecosystems in Biscayne Bay .......................................................................................................31

Biogeochemical Measurements of Reef Health...........................................................................................................31

Ground Water Characterization in Marine Areas of Biscayne National Park............................................................32

Analysis of Historical Water-Quality Data in Southern Florida ................................................................................33

Remotely Sensed Rugosity Measurements and Patch Reef Community Structure in Biscayne National Park ...........34

Comprehensive Urban Ecosystems Studies (CUES): Activities Planned for the Miami Urban Area 

and Adjacent Portions of the Greater Everglades Ecosystem...................................................................... 34
24 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Biscayne Bay Coastal Wetlands

K. Cunningham and M. Wacker, USGS Florida Integrated Science Center—Ft. Lauderdale, Fla.

The objective of the CERP Biscayne Bay Coastal Wetlands Project is to rehydrate wetlands and reduce point-source 

discharge to Biscayne Bay. The project will replace lost overland flow and partially compensate for the reduction in groundwater seepage by redistributing, through a spreader system, available surface water entering the area from regional canals. The 

proposed redistribution of freshwater flow across a broad front is expected to restore or enhance freshwater wetlands, tidal 

wetlands, and nearshore bay habitat. A primary goal of the project is to develop a realistic representation of ground-water flow 

within the karst Biscayne aquifer.

Recently, Cunningham and others (2004a) demonstrated that a dual-porosity conceptual model is appropriate for this karst 

aquifer system consisting of a series of interlayered diffuse-carbonate and conduit flow zones that are arranged vertically within 

the context of a high frequency sequence stratigraphy. Mapping these ground-water flow units is key to the development of 

models that simulate ground-water flow from the Everglades and urban areas through the coastal wetlands to Biscayne Bay.

As participants in this pilot project, the South Florida Water Management District, the U.S. Army Corps of Engineers, and 

the USGS are working together to better understand the hydrogeologic framework of the surficial aquifer system in the Biscayne 

Bay coastal wetlands in Miami-Dade County.

Because little detailed hydrogeologic data exist for the surficial aquifer system (to depth) in this area, the Biscayne 

Bay Coastal Wetlands Project Delivery Team proposes to install two monitoring well sites and collect the necessary detailed 

hydrogeologic data.

Historical Changes in Salinity, Water Quality, and Vegetation in Biscayne Bay

G.L. Wingard, T. M. Cronin, D. Willard, W. Orem, P. Swart, G. Dwyer, S. Ishman and E. Gaiser, USGS Reston, VA; and C. W. Holmes, 

USGS Florida Integrated Science Center—St. Petersburg, Fla.

During the last century, Biscayne Bay has been greatly affected by anthropogenic alteration of the environment through 

urbanization of the Miami-Dade County area, and alteration of natural flow. The sources, timing, delivery, and quality of 

freshwater flow into the bay, and the shoreline and subaquatic vegetation have changed. Current restoration efforts are directed 

toward restoring “natural” flow of freshwater into Biscayne and Florida Bays and to restore the natural vegetation, but first the 

predevelopment conditions prior to substantial human alteration must be determined to establish targets for restoration. This 

project examines the predevelopment patterns of temporal change in salinity, water quality, vegetation, and benthic fauna in 

Biscayne Bay during the last 100 to 300 years and examines the causes of change.

The objectives of this project are to: (1) examine, in broad context, historical changes that have occurred within the 

Biscayne Bay ecosystem at selected sites on a decadal-centennial scale, and (2) correlate these changes with natural events and 

anthropogenic alterations in southern Florida. Specific emphasis will be placed on historical changes to the (1) amount, timing, 

and sources of freshwater influx and the resulting effects on salinity and water quality; (2) shoreline and subaquatic vegetation; 

and (3) relation between sea-level change, onshore vegetation, and salinity. In addition, a detailed examination of historical 

seasonal salinity patterns will be derived from biochemical analyses of mollusks, ostracods, foraminifera, and corals. The 

coral data will allow comparison of marine and estuarine trends, examination of the linkage between the two systems, and will 

provide precise chronological control. Land-management agencies (principally, the South Florida Water Management District, 

U.S. Army Corps of Engineers, and Biscayne National Park) can use the data obtained from this project to establish performance 

criteria for restoring predevelopment flow, and to understand the consequences of altered flow. These data also can be used to 

forecast potential problems as upstream changes in water delivery are made during restoration.
5.0 Current or Recently Completed Studies in and around Biscayne National Park 25

Ground-Water Discharge to Biscayne Bay

C.D. Langevin, USGS Florida Integrated Science Center—Ft. Lauderdale, Fla.

The goal of Everglades restoration is to restore the ecosystem of southern Florida to conditions that closely resemble 

predevelopment conditions. Much of the restoration will occur by making substantial changes to the structures and operational 

procedures of the existing water-management system. These changes, however, must not harm the ecosystem of Biscayne Bay, 

which is already threatened by reductions in fresh ground-water flow caused by development.

Prior to the construction of the extensive canal network in southern Florida, offshore springs discharged large quantities of 

fresh ground water into Biscayne Bay. During this time, most of the freshwater flow to Biscayne Bay occurred either as spring 

flow or continuous seepage of fresh ground water along the coast of the bay. When drainage canals were constructed to reduce 

flooding in the area, the mechanism for transporting water to the bay was altered substantially. Rather than receiving a continuous supply of fresh ground water, Biscayne Bay received wet-season pulses of canal discharge. Biologists have confirmed that 

the change in timing and location of freshwater flow to the bay has harmed the Biscayne Bay ecosystem. Seagrass beds, and the 

juvenile fish that use them as refuge, no longer receive a continuous supply of freshwater―a requirement for their survival.

The purpose of this project, better known as the “Ground-Water Flows to Biscayne Bay,” is to determine how planned 

restoration alternatives will affect the bay by providing answers to the following questions: 

•	 How much fresh ground water is currently discharging to Biscayne Bay?

•	 How will south Florida restoration efforts affect the quantity of fresh ground-water flow to Biscayne Bay?

To answer these questions, ground-water flow to Biscayne Bay is being simulated with a computer model. The model will 

help identify which of the restoration alternatives will result in fresh ground-water flows to the bay that are most beneficial to its 

ecosystem.

Development of an Integrated Surface Water and Ground-Water Model of Biscayne Bay and 

Analysis of the Hypersalinity Events in Southwestern Biscayne Bay

M.A. Wolfert and C.D. Langevin, USGS Florida Integrated Science Center—Ft. Lauderdale, Fla., and J.D. Wang, University of 

Miami, Miami, Fla.

Throughout the last century, Biscayne Bay has been impacted by human alteration of the natural environment through 

urbanization of the Miami-Dade County area and modifications of natural freshwater flows to the bay. The altered hydrology 

of the natural system has reduced the seaward ground-water gradient that historically supplied freshwater by way of submarine 

springs throughout Biscayne Bay to offshore areas of the bay. The absence of this gradient has reduced or eliminated flow from 

these springs. Data collected in recent years in Biscayne National Park indicate that hypersalinity (for example, salinity greater 

than 35 ppt) events are occurring every few years in nearshore regions of the bay.

The primary objective of this project is to investigate the cause or causes of the hypersalinity events observed in recent 

years in south-central Biscayne Bay. This objective will be addressed using the following approach:

•	 Existing empirical data and output from other numerical models will be evaluated to identify the methods needed to 

determine causes of hypersalinity in Biscayne Bay;

•	 A computer model will be developed to describe the effect of surface-water flows on salinity in the bay;

•	 The completed surface-water flow model will be coupled with a completed ground-water model, which is currently in 

the calibration stage of development; and

•	 The integrated surface-water and ground-water model for Biscayne Bay and the surrounding areas will be used to 

perform hydrogeologic investigations to determine if and how changes in shallow ground-water flow are affecting 

Biscayne Bay salinities.
26 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Ground- and Surface-Water Impacts on Water Quality and Ecology: Science to Assist Resource 

Management at Biscayne National Park

M.A. Wolfert and C.D. Langevin, USGS Florida Integrated Science Center—Ft. Lauderdale, Fla.

CERP aims to reestablish predevelopment natural flows in the Everglades system and surrounding areas including Biscayne 

Bay. The changes proposed within this plan may substantially alter the hydrologic conditions that exist in Everglades National 

Park and Biscayne National Park. There are system-wide management issues and environmental and water-supply concerns 

about how restoration efforts will affect ground-water flows, including those between Everglades National Park and Biscayne 

National Park, and along the L-31N and C-111 canals. For example, restoration of wetlands may lead to increases in coastal 

aquifer heads and cause offshore springs in Biscayne Bay to once again become sites of substantial freshwater discharge in 

Biscayne National Park. Accordingly, CERP restoration activities may more rapidly flush ground water and any associated 

contaminants into the offshore marine ecosystem. If this scenario were to occur, there is considerable potential for the deterioration of habitat for many different threatened or endangered species of plants and animals that reside along the coastline 

of Biscayne Bay, within the bay, or along the coral reef tract. Unlike the surface-water system, which has been extensively 

compartmentalized and channelized, ground-water flow in the aquifers beneath Everglades National Park and Biscayne National 

Park is interconnected and not as amenable to partial domain simulation. A comprehensive model is needed to reliably and credibly assess simultaneous ground-water effects to both parks.

The goal of this project is to determine how freshwater deliveries, which are believed to be critical to the perpetuation 

of ecologically sensitive coastal habitats, have changed, and will change, as the various State and Federal land-management 

agencies implement different portions of the restoration plan for the southern Florida/Everglades ecosystem. During the past 5 

years, a substantial amount of time and effort was spent developing different management paradigms to locate, store, and move 

water through the Everglades ecosystem into Everglades National Park and Florida Bay. Although there was some effort to 

project how the altered hydrology may affect the resources of the Florida Keys and the coral reef areas closely associated with 

Florida Bay, there was much less effort to determine how the alterations may affect the coastal and estuarine resources to the 

east and west of the axis of the restoration. This project will supply the scientific information and understanding needed to make 

informed ecosystem restoration decisions in these other areas.

The primary objective of this project is to develop a numerical model to characterize detailed ground-water flow patterns 

and discharge rates to the Biscayne Bay estuary, and to examine the migration paths of contaminants to the estuaries, bay, and 

coral reef. This will require the development of numerical surface water and ground-water models of Biscayne National Park. 

A substantial amount of uncertainty remains, however, in simulating and predicting patterns and rates of submarine groundwater discharge.

A primary science objective of this project is to improve the accuracy of modeling submarine ground-water discharge to 

a coastal marine estuary. This objective will be achieved by applying the latest numerical modeling techniques and developing 

new techniques for the simulation of density dependent ground-water flow. Results from the carbonate hydrostratigraphy 

component and other field studies in the bay will provide information about preferential flow paths within the aquifer and 

possible submarine discharge locations.

With an improved scientific understanding and a reliable numerical tool, this project will address many of the scientific 

questions posed by Biscayne National Park restoration issues. For example, the surface- and ground-water models will be used 

to estimate predevelopment rates of overland flow and submarine ground-water discharge, and predict the effects of Everglades 

restoration on future freshwater inflows to the bay. It is expected that simulated flow patterns will correlate with ecological 

indicators of stressed communities, providing insight into the causes of ecosystem degradation.
5.0 Current or Recently Completed Studies in and around Biscayne National Park 27

Remote Sensing of Water Turbidity and Sedimentation in Florida Bay and Biscayne Bay

B. Wertz, USGS Florida Integrated Science Center—St. Petersburg, Fla.

A decline in water clarity in Florida Bay has been observed following the seagrass dieoffs that have occurred since the late 

1980’s. Algal blooms and discolored water have been reported in Florida Bay over the last several years and factors such as the 

resuspension of material and nutrients from the bottom have been suggested as a potential cause. Monthly monitoring programs 

by Florida International University and the Florida Department of Environmental Protection have documented blooms through 

chlorophyll measurements.

The current project uses remote sensing to examine resuspension events, the distribution of turbid water, and changes in 

the patterns of water clarity in the bay. The project also is conducting comparisons between chlorophyll values collected from 

the shipboard monitoring programs and pre-cruise reflectances to assess whether there is a link between resuspension events 

and algal blooms. The next step is to extend the Advanced Very High Resolution Radiometer (AVHRR) dataset further back by 

compiling data collected prior to the seagrass dieoffs and to incorporate Landsat data for limited high resolution analysis.

Contaminant Effects on Biological Resources: Sediment Quality in Canals that Discharge into 

Biscayne Bay, Miami-Dade County, Florida

P.V. Winger and P.J. Lasier, USGS Patuxent Wildlife Research Center, University of Georgia, Athens, GA

A study of sediment quality was conducted in the freshwater canals of Miami-Dade County to aid in understanding 

the effects of stormwater runoff to Biscayne Bay. This study coincided with an assessment by the National Oceanic and 

Atmospheric Administration (NOAA) of sediment quality within the Biscayne Bay estuary. Using a weight-of-evidence 

approach, surficial sediment samples were collected at 178 sites along 23 canals. The samples were analyzed for a comprehensive suite of chemical contaminant concentrations, and a battery of toxicity tests was performed that included: (1) chronic 

toxicity testing of solid-phase sediments using Hyalella azteca, (2) acute toxicity testing of pore water using H. azteca, and (3) 

Microtox bioassay using Vibrio fischeri of dichloromethane extracts of solid-phase sediments. Samples were collected during 

two time periods: 1995-96 and 2001-02. The data from both time periods were merged for evaluation, because they showed no 

large systematic changes in chemical concentrations or toxicity between periods. 

A total of 178 samples were collected from 178 sites. Only 30 of these samples (collected from 11 sites scattered across the 

study area) did not contain toxins. A total of 71 sites were classified as slightly degraded, because samples taken from these sites 

had slightly elevated concentrations of contaminants or toxicity, but not both. The slightly degraded conditions were distributed 

among most of the canals (19 of 23), and therefore, represented the most widespread classification. Moderately degraded 

sediments were identified at 63 sites and were the predominant condition in 8 canals. The moderately degraded conditions were 

characterized by elevated chemical contamination and/or severe toxicity. Fourteen sites located along eight canals were classified as being the most degraded, because samples contained excessive concentrations of contaminants and had high toxicity. 

The incidence of chemical contamination in Miami-Dade County canals was approximately equivalent to that in nationwide 

databases and in several large estuaries, considerably less than in industrialized bays and harbors of other regions of the United 

States, but slightly higher than in the adjoining saltwater of Biscayne Bay. Overall, the incidence and level of toxicity observed 

in the Miami-Dade County freshwater canals was comparable to levels observed in other southeastern study areas, but lower 

than in several national databases which included results of surveys conducted in the more industrialized regions.
28 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Temporal and Spatial Variation in Seagrass-Associated Fish and Invertebrates in South Florida: 

Nearshore Seagrass Community of Biscayne Bay, Florida

M.B. Robblee, USGS Florida Integrated Science Center—Ft. Lauderdale, Fla.; and J.A Browder, NOAA National Marine Fisheries 

Service, Miami, Fla.

Loss and/or degradation of coastal wetlands and nearshore estuarine habitat is a long-term threat to the ecosystem of 

Biscayne Bay and its associated productivity. These habitats are dependent upon restoring a more natural quantity, quality, 

timing, and distribution of freshwater flow to Biscayne Bay. CERP and the Lower East Coast Regional Water Supply Plan could 

substantially affect freshwater flow to Biscayne Bay. Special projects in CERP will be designed to restore estuarine habitat in 

Biscayne Bay that has been diminished by past and current water-management practices. Both CERP and Lower East Coast 

Regional Water Supply Plan require periodic assessments to evaluate the effect of new CERP projects as they are implemented. 

Science-based performance measures are needed to quantify change, and targets are needed to indicate whether restoration is 

succeeding. Scientific workshops have revealed a lack of essential information about coastal wetlands and nearshore biological 

communities with which to develop performance measures and guide the design of the Biscayne Coastal Wetland Restoration 

Project. It is important to start acquiring this information.

Because of its clear, shallow waters, Biscayne Bay’s benthic community is a primary source of its productivity and diversity. The benthic animal community, consisting of small forage fish, juvenile game fish, and invertebrates such as pink shrimp, 

is particularly well developed in the shallow nearshore zone adjacent to the mainland and may be dependent upon freshwater 

inflow. The pink shrimp is an important commercial and recreational species in Biscayne Bay, as is the blue crab. Gray snapper 

is highly sought recreationally, both in the bay and on the nearshore reef. These species are linked to nearshore environments, 

but their relationships in these areas with freshwater inflow have received minimal investigative attention. Scientific information 

on this topic is needed to develop performance measures based on these species and their community.

The proposed study has four elements: (1) characterization of the spatial and temporal patterns of density and diversity of 

fish and macro-invertebrates (emphasis on caridean and penaeid shrimps including the pink shrimp, Farfantepenaeus duorarum) 

in seagrass habitats of the mainland nearshore zone, as well as in the deeper water commercial fishing zone; (2) evaluation of 

the relationship of variability in shrimp catch rates of commercial vessels operating in the commercial fishing zone with shrimp 

densities in fished versus unfished seagrass habitats; (3) examination of trends in commercial pink shrimp fisheries in relation 

to freshwater inflow and salinity; and (4) evaluation of relationships between fishes utilizing mangrove fringe habitats and the 

abundance and diversity of fish and macro-invertebrates in adjacent seagrass habitats.

This study focuses largely on characterizing the animal communities present in seagrass habitats in Biscayne Bay. Existing 

commercial catch data (Pamela Eyo, National Marine Fisheries Service, written commun. 2006) and supplemented USGS data 

will be analyzed in relation to the new data on shrimp densities in seagrass beds to address the second and third elements of this 

study. Close collaboration with a related study (J. Serafy, University of Miami, oral commun., 2006) documenting fish usage of 

mangrove fringe habitats in our study area will address the fourth element.

Inventory of the Amphibians and Reptiles of Big Cypress National Preserve, Biscayne National Park, 

and Buck Island Reef National Monument

K.G. Rice, USGS Florida Integrated Science Center—Ft. Lauderdale, Fla.

In response to concerns about the lack of basic knowledge of the amphibians and reptiles inhabiting U.S. Department of 

the Interior lands, inventory programs are being instituted nationwide. This study describes the goals and objectives, sampling 

methods, complicating factors, and the expected outcomes of proposed amphibian and reptile surveys in Big Cypress National 

Preserve, Biscayne National Park, and Buck Island National Monument.

The primary goal of this project is to inventory the amphibians and reptiles of Big Cypress National Preserve, Biscayne 

National Park, and Buck Island National Monument. The inventories will provide information about the status and distribution of the species of amphibians and reptiles on these Department of the Interior lands. Sampling at these parks will involve a 

multitiered approach that involves data collection for three specific models:

•	 Species Richness—To use this model, many plots will be used that may be visited only once during the study.

•	 Proportion of Area Occupied—For this model, some of the plots used for species richness will be visited several times 

within a given season.

•	 Detection Probability—On a subsample of the plots that are visited repeatedly, we will also gather data that will allow 

us to estimate the detection probability of some species using models like dual observer and mark and recapture.
5.0 Current or Recently Completed Studies in and around Biscayne National Park 29

Application of Landscape Ecology to the Design of Marine Protected Areas

L.E. Dunsmore, USGS, Florida Integrated Science Center—Gainesville, Fla.

Coral reef ecosystems and associated fisheries are experiencing declines throughout the Caribbean. Marine-protected areas 

(MPAs), one of the most highly advocated forms of ecosystem-based management, are intended in most cases to provide a spatial 

refuge for intensely exploited species and also may help alleviate threats to marine biodiversity. To design new ecosystem-based MPAs 

and set realistic expectations about the performance of existing MPAs, it is necessary to determine whether large-scale measures of 

habitat are correlated with reef fish assemblage parameters of interest to resource managers; for example, abundance of targeted fishes 

and species diversity.

To date, most MPAs focus on single habitats, potentially neglecting functional linkages among habitats (that is, juvenile settlement 

and adult foraging areas) that benefit reef fishes at critical times during their life history (St. Mary and others, 2000). The opportunity 

still exists, however, to design and manage MPAs as entire ecosystems, based on habitat requirements of important reef-associated 

fishes. Recent advances in marine mapping technologies provide the opportunity to ascertain whether MPAs can be cited today based 

on available scientific knowledge.

The purpose of the current project is to determine whether landscape indices, such as habitat diversity and total area of specific 

habitats that have proven valuable in terrestrial systems, can be used to predict reef fish assemblage parameters of interest to resource 

managers, including species diversity and abundance of exploited species. Empirical datasets from three protected areas with 

differing levels of reef fish protection―Virgin Islands National Park, Florida Keys National Marine Sanctuary, and Biscayne National 

Park―will help determine how applicable this new technology is for addressing conservation science questions.

Research for the current study is conducted within the three MPAs described above, with the following four objectives:

Objective 1: Develop landscape metrics using benthic maps and geospatial analysis (Virgin Islands National Park)―Metrics 

commonly used in terrestrial systems will be calculated for 16 reef sections using benthic habitat maps. Principal components analysis 

will be used to determine whether a large set of the original correlated landscape habitat metrics can be reduced to a small number of 

transformed uncorrelated variables.

Objective 2: Determine the relations between landscape metrics and fish assemblage parameters―The relation of landscape metrics 

and reef fish assemblage structure will be explored in Virgin Islands National Park as preexisting reef fish census data are available. 

Census data collected in 1994 and 2001 using a point-count method at a total of 16 reef sections will be coupled with the calculated 

landscape metrics and analyzed using linear regression and multivariate statistical procedures. A total of at least 16 reef fish censuses 

per 25,000-m2 reef provide sufficient sampling effort to determine mean values for each assemblage parameter. Landscape-level 

metrics will be correlated with reef fish assemblage parameters using linear regression, with landscape metrics as independent variables 

and entire assemblage parameters as dependent variables. Step-wise multiple regression analysis will be used with metrics at each 

distance (100, 250, 500, and 1,000 m) as independent variables and entire assemblage parameters (for example, species richness, total 

abundance, and abundance of particular trophic guilds) as dependent variables. Principal components analysis, an unconstrained ordination technique, will be used to summarize data redundancy to describe the relation between various landscape metrics and individual 

reef fish assemblage parameters, such as species richness. If principal components can be identified, these will be used as variables in 

a step-wise multiple regression model.

Objective 3: Test hypothesis that proximity to, and/or total area of, seagrass predicts abundance of specific fishes within Virgin Islands 

National Park and Biscayne National Park―Using existing habitat maps from the Virgin Islands National Park, 20 reefs will be 

selected based on specific criteria. Landscape metrics of proximity and area of seagrass will be calculated at various spatial extents. 

Randomly generated sampling stations will be identified in ArcView using a random point script. Linear regression will be used to 

test the prediction that species diversity, total abundance, and abundance of adult and juvenile grouper, snapper and grunts will be 

greatest at sites with the greatest seagrass coverage. ANOVA will be used to determine if there is a significant difference in total species 

richness and abundance of adult and juvenile snappers, grunts, and groupers between seagrass and non-seagrass reefs. Benthic habitat 

maps will be generated using recent (2002) aerial photos of Biscayne National Park using IMAGINE and ArcView 8.1. A total of 20 

small (less than 3,000 m2

) discrete reef patches (of similar size and shape) on a gradient of low to high seagrass area will be selected. 

Linear regressions will be performed using total seagrass area as the independent variable and fish assemblage parameters as dependent 

variables. Standard ANOVA procedures will be used to examine differences between reefs with and without seagrass.

Objective 4: Compare results between fished and unfished areas in the Florida Keys National Marine Sanctuary―Eighteen special 

protected areas within the Florida Keys National Marine Sanctuary and their reference (fished) sites will serve as study locations. 

Landscape metrics (seagrass areal coverage and habitat diversity) will be calculated using existing benthic habitat maps developed by 

functional magnetic resonance imaging. Reef fish censuses will be used to determine average values for reef fish assemblage parameters 

such as total species richness, abundance, mean abundance of adult and juvenile grouper, snapper and grunts. Linear regression will be 

used to determine the relations between the reef fish assemblage parameters and the seagrass metrics for MPAs and control sites.
30 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Environmental Assessment of Effects of Rotenone on Seagrass Beds

P. Schofield, USGS Florida Integrated Science Center—Gainesville, Fla.

The National Park Service, though the Natural Resource Challenge action plan, has initiated a program of biological inventories for vertebrates and vascular plants within 270 National Park units that have significant natural resources. These inventories 

are 1 of 12 data layers that the National Park Service is in the process of compiling to assist park management based on sound 

scientific information about the natural resources managed by the park.

The majority of these inventories use non-destructive techniques for species identification, such as visual counts, acoustic 

signature matching, field observations, and tracking. For most of these techniques, the National Environmental Protection Act 

provides a categorical exclusion that allows for this type of field work.

By nature, cryptic fish are difficult, if not impossible, to see with the naked eye because they have a well-developed 

mimicry of their surrounding habitats. These fish in complex environments, such as coral reefs, mangrove roots, or dense aquatic 

vegetation, and because of their visual mimicry, remain largely unstudied. The role of these cryptic fish, therefore, is uncertain in 

the ecosystems they inhabit, and some may remain unknown to the scientific world.

The primary objective of the National Park Service Vertebrate and Vascular Plant Inventories program is to document the 

presence of more than 90 percent of the species living within National Park lands. The southern Florida/Caribbean network 

developed a study plan in December 2000 that identifies these cryptic fish as a priority dataset that should be funded for comprehensive inventories in many of the network parks. The Network Science and Technical Committee have identified the need for 

an environmental assessment of rotenone effects on the ecosystem when used for cryptic reef fish sampling.

The National Park Service units involved would include Big Cypress National Preserve, Biscayne National Park, Buck 

Island Reef National Monument, Everglades National Park, Dry Tortugas National Park, Salt River National Historic Site and 

Ecological Preserve, and Virgin Islands National Park. The ecosystems to be sampled with this technique include seagrass 

meadows and sand bottoms. Because inventories will be conducted infrequently, this is not to be considered a monitoring 

technique. Rotenone will be used within contained areas to ensure that only a targeted habitat is sampled and to minimize bykill. 

Alternatives to be explored include no-action, use of Tricaine Methanesulfonate (MS222), use of clove oil, and mechanical 

methods if applicable.

Assessment of Emerging Pollutants of Concern (EPOCs) in Wastewater Influent and Effluent at the 

South Miami-Dade Wastewater Treatment Plant and Biscayne Bay Coastal Environment

A. C. Lietz (retired), USGS Florida Integrated Science Center—Ft. Lauderdale, Fla.

A primary goal of CERP is the restoration of natural water flows and historical hydroperiods in the southern Florida 

ecosystem, including the Biscayne Bay Coastal Wetlands adjacent to Biscayne National Park. In the original Central and 

Southern Florida Project Comprehensive Review Study Final Integrated Feasibility Report and Programmatic Environmental 

Impact Statement (Restudy) it was determined that Biscayne Bay and Biscayne National Park were not receiving an adequate 

supply of freshwater to ensure adequate restoration. The Restudy team evaluated the use of reclaimed water as a viable source 

of additional water to accomplish these goals. Highly treated wastewater then was identified as a potential source of additional 

water supply. A critical question, however, that must be addressed in the application of reused water to the Biscayne Bay Coastal 

Wetlands is the degree to which certain constituents in reclaimed water may adversely affect the aquatic biota of the ecosystem 

in question. This is especially true for constituents identified as emerging pollutants of concern (EPOCs) that could adversely 

affect the sensitive biota of Biscayne National Park.

CERP proposes to develop one of two advanced wastewater treatment pilot facilities at the current South District 

Wastewater Treatment Plant in southern Miami-Dade County. Superior, advanced treated reuse wastewater from this facility will 

be used to replace and augment freshwater flows to the sensitive Biscayne Bay and Biscayne National Park ecosystems as well 

as restore more natural hydroperiods to the Biscayne Bay Coastal Wetlands. As part of a current CERP project, the USGS is 

examining the presence and concentration of EPOCs in wastewater influent and effluent at the wastewater treatment plant.

Marine activities in Biscayne National Park, as well as urban and agricultural activities in the adjacent coastal areas, may 

also contribute contaminants (including EPOCs) to the park environment. This situation underscores the need to assess the 

possible occurrence, distribution, and probable sources of EPOCs in Biscayne National Park and the adjacent coastal environment prior to using advanced treated wastewater to restore natural flow and hydroperiods to the Biscayne Bay Coastal Wetlands.
5.0 Current or Recently Completed Studies in and around Biscayne National Park 31

Biogeochemistry of Ecosystems in Biscayne Bay

B.H. Lidz, E.A. Shinn, and C.D. Reich, USGS Florida Integrated Science Center—St. Petersburg, Fla.

Baseline ecosystem status and pollution data for Biscayne Bay are lacking. Biscayne National Park contains the southern 

part of the bay, as well as (1) the longest stretch of mangrove forest remaining on Florida’s east coast, (2) 14 threatened or 

endangered wildlife species, and (3) the northernmost coral reefs in the continental United States. The bay acts as a buffer zone 

for these reefs. Human activity affects the coastal marine environment of southern Florida through urban development; air, land, 

and water pollution; intense recreational and commercial use; introduction of pathogens and nutrients from sewage-disposal 

injection wells and shoreline landfills; and physical damage to coral reefs and other bottom communities caused by derelict 

fishing gear, boat anchors and ship groundings. Nutrient enrichment increases oxygen depletion in coastal waters, which can 

stress or kill biota. Coastal land-use practices (marina, agricultural and industrial development) cause contamination by chemical 

pollutants, pesticides, petroleum products, fertilizers, and heavy metals. Each effect alters the coastal ecosystems and has 

important implications for human issues, including the health of swimmers, fishery nurseries and resources, and management of 

coastal land development.

The USGS and University of Southern Florida, in cooperation with the National Park Service and Biscayne National Park, 

are assessing environmental quality in Biscayne Bay to provide pre-Everglades restoration baseline data and decision products 

that will facilitate restoration and/or preservation of ecosystems within the bay. Surface-sediment data will be used to construct 

contour maps of grain size, heavy-metal distribution and concentration, foraminiferal assemblages diagnostic of pristine to 

heavily polluted waters, and dominant types of skeletal sand grains. These products will characterize present conditions in the 

bay and can be applied to monitor future changes in biota (due to environment, water quality, and pollution) as well as document 

past changes by comparison of the sediment data with historical records determined from analogous studies of sediment cores.

In general, overall results of the Phase I pilot study along the western bay margin indicate that: (1) the highest concentrations of heavy metals are near densely urbanized areas, (2) most abnormalities in foraminiferal shells are near the Black Point 

landfill, and nearshore ecosystems within the bay are under stress. The stress is probably due both to natural causes (such as 

rising sea level) and anthropogenic causes (such as increased pollution). Phase II bay-wide geochemical, sedimentary, and 

microfaunal analyses are designed to delineate more precise trends in pollution, and will include the origin of biogenic sand 

grains that will identify the biotic structure of benthic communities.

Biogeochemical Measurements of Reef Health

R.B. Halley, USGS Florida Integrated Science Center—St. Petersburg, Fla.

Community scale measurements of reef metabolic processes will be taken during 24-hour time periods over different 

benthic bottom types using the Submersible Habitat for Analyzing Reef Quality (SHARQ). This incubation chamber, 

constructed of an anodized aluminum frame and clear vinyl sheeting, isolates water over the substrate and accentuates changes 

in water chemistry that reflect key biogeochemical parameters. The large size of SHARQ (11 m2) allows areas of study to 

be identified on aerial photographs. Analytical results, therefore, can be used to help characterize the benthic community of 

Biscayne National Park. We propose that measurements of rates of calcification, photosynthesis, and respiration will provide 

important baseline information and serve as a basis for evaluating long-term change years to decades in the future. Identical 

measurements are being made in Hawaii and Florida Bay, with further study planned in the U.S. Virgin Islands to make interregional comparisons and evaluate contrasting benthic settings.

The short-term objectives of this project are to: (1) collect continuous biogeochemical data for 24-hour periods from four 

well-characterized bottom types; (2) use the data to calculate rates of calcification, dissolution, photosynthesis, and respiration; 

and (3) place the metabolism rates for Biscayne National Park in context with other reef study sites. The long-term objectives are 

to characterize metabolism rates at four sites in Biscayne National Park and re-occupy sites to identify trends.

For this project, SHARQ is used to examine the response of reef biogeochemical processes to elevated partial pressure 

of carbon dioxide (pCO2) in the water column. An internal circulation system (260 L/min) generates turbulent water flow and 

is aided by the flexibility of the chamber, which enables oscillatory water motion to be translated through the structure. The 

chamber isolates about 7.0 m3 of water over 12 m2 of seafloor so that gas exchange, seawater circulation, and changes in water 

chemistry can be controlled and quantified. A closed-loop, flow-through system is employed to continuously measure dissolved 

oxygen, pH (on the free scale), salinity, and temperature. Filtered water samples for total alkalinity and nutrient measurements 

were removed from a sampling port in the flow-through system at 4-hour intervals. 
32 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

During July 2002, we began to examine the effects of elevated atmospheric carbon dioxide on the health of coral reefs. 

An early observation was that reef sand partially dissolves as carbon dioxide increases and partially buffers corals from adverse 

effects. To examine the dissolution process, we conducted two experiments on sand.

A SHARQ was deployed at a 5-m depth over reef sand and allowed to stabilize for 24 hours. During the first experiment, 

two additions of carbon dioxide were made at noon on July 13 and 14, 2002, and monitored until July 15. The SHARQ was 

opened and surface sediments were mixed and allowed to equilibrate with ambient water for 24 hours. On July 16, the second 

experiment began with three injections of carbon dioxide during the afternoon. The second experiment was monitored until noon 

July 18. A second SHARQ, identical to the first but with a vinyl floor, was deployed near the first as a control.

We are currently evaluating the data and planning follow-up experiments in the near future. Preliminary evaluation of the 

data indicates that more sediment dissolution occurs than had been expected, and results indicate that sediment dissolution may 

provide a mechanism for buffering Biscayne coral reefs from pH changes associated with elevated atmospheric carbon dioxide.

Ground Water Characterization in Marine Areas of Biscayne National Park

R.B. Halley, P.W. Swarzenski , Christopher Reich, and Don Hickey, USGS Florida Integrated Science Center—St. Petersburg, Fla., 

and R. Curry, Biscayne National Park

Biscayne National Park is a marine park that is bordered by a metropolitan area consisting of more than one million people. 

Extensive development has occurred along the shoreline and nearby upland areas, and natural upland water flow has been altered 

substantially through a complex network of drainage canals and dredged waterways. In addition, numerous deeply dredged 

ponds, lakes and water-storage sites that collect and hold urban surface run-off also are present in these upland areas.

The infiltration and dispersion of nonpoint source pollutants into the ground-water system from the surface runoff and 

dredged sites is likely to be substantial for a number of reasons. The highly porous limestone substrate of the region, known as 

the Biscayne aquifer, flows directly into Biscayne Bay. In addition, Class 1 municipal landfill was established during the 1970s 

adjacent to southern Biscayne Bay and Biscayne National Park. This landfill consists of municipal waste that has considerable 

potential to affect local ground-water and the subsurface flow of contaminants into the park. Previous studies have documented 

some infiltration of nutrients and contaminants from urban developments and the municipal waste facility. The extent, however, 

to which these contaminants flow beneath and resurface within Biscayne Bay and offshore reef-area waters has not been 

determined. According to McNeill (2000), 10 of the 17 injection wells at the Miami-Dade Water and Sewer South District plant 

were constructed improperly, creating a relatively open pathway for upward migration of injected effluent. As a result, ammonia 

was detected in shallow monitoring wells within 11 years of first injection. This differs substantially from the initial 343-year 

estimate for upward migration of effluents.

Recent declines in offshore coral reef health may be linked to declines in ground-water or surface-water quality, or possibly 

other ecosystem stress factors. For park managers to make informed management decisions concerning the loss of park marine 

resources, the park needs additional information about the current extent of ground-water pollution and its possible effects on 

park resources. The current project uses geochemical and hydrogeologic information to determine whether ground water enters 

Biscayne Bay and the nearby coral reef tract through coastal aquifers; the approach has two objectives.

The first objective is to use water quality (geochemistry) to identify water mass signatures. Geochemical tracers, including 

isotopes of radon and radium or cations and anions (for example, calcium, and magnesium), will be used to help identify specific 

water masses. Other water-quality parameters will be used to identify potential sources of contamination to the ecosystem. Air 

and surface-water sources are relatively easy to investigate but ground water beneath a marine system is much more difficult 

to access. This project will quantify four field constituents (pH, dissolved oxygen, salinity, and temperature) and water-quality 

parameters that include nutrients (primarily nitrogen and phosphorus species), trace elements (zinc, copper, and arsenic), wastewater compounds (17-beta-estradiols, coprostanol, caffeine, and surfactants), pesticides (Lindane, Endosulfan, and DDT). These 

constituents will help characterize the ground water beneath Biscayne Bay and provide some index of their potential threat to 

surface-water quality within Biscayne National Park.

The second objective of this project is to characterize the flow regime beneath Biscayne Bay and within Biscayne National 

Park. Ground-water flow is driven by changes in water level (the potentiometric surface gradient) in the adjacent Biscayne 

aquifer. In southern Florida, potentiometric ground-water surfaces have been investigated extensively in inland areas, and along 

the coastline to some extent, but no information exists for offshore areas. Offshore natural flow gradients are complicated 

by tidal pumping, which creates flow patterns in marine ground waters. Although tidal pumping has been investigated using 

seepage meters, it is quantified most accurately by observation wells. Determining the pressure gradients produced between 

ground water and surface water through tidal pumping potentially can provide data about vertical and horizontal ground-water 

movement.
5.0 Current or Recently Completed Studies in and around Biscayne National Park 33

Analysis of Historical Water-Quality Data in Southern Florida

B.F. McPherson (retired), USGS Florida Integrated Science Center—Tampa, Fla.

This project provides a review and analysis of historical water-quality data in Everglades National Park, Big Cypress 

National Preserve, Loxahatchee National Wildlife Refuge, and nearby coastal waters of southern Florida. This information 

will help establish water-quality standards and baseline conditions in the parks, and will help agencies evaluate how CERP 

hydrologic modifications will affect regional water quality. The objectives of this study are to: (1) compile, review, and edit 

water-quality data and construct a working database; and (2) analyze and evaluate the compiled data to describe historical 

water-quality conditions and trends in Big Cypress National Preserve, Everglades National Park, Loxahatchee National Wildlife 

Refuge, and Department of the Interior coastal waters. These analyses will provide a baseline for evaluating how CERP-related 

modifications may affect water quality in the parks and refuge.

This study supports several projects listed in the U.S. Department of the Interior science plan, including the following: 

•	 Loxahatchee National Wildlife Refuge Internal Canal Structure—This study provides data and analysis of historical 

hydrologic and water-quality conditions in the refuge needed to develop the specific hydrologic and ecological targets 

for the project. 

•	 Water Conservation Area 3 Decompartmentalization and Sheetflow Enhancement, 

•	 Additional Water for Everglades National Park and Biscayne Bay Feasibility Study―This study provides data and 

analyses of historical hydrologic, land use, and water-management changes, and water-quality conditions in Big 

Cypress National Preserve, Everglades National Park and Loxahatchee National Wildlife Refuge. These data and 

analyses complement ongoing hydrologic, paleoecological, and modeling investigations in these Department of the 

Interior lands; clarify linkages between geologic, hydrologic, chemical and biological processes in the Everglades; and 

support the development of hydrologic targets for the restoration projects.

Principal findings of the current project are as follows:

•	 Major physical alterations of the landscape and associated water-management practices in the greater Everglades have 

altered water quality over the last 40 years.

•	 Water quality in canals that drain agricultural lands is characterized by relatively high concentrations of dissolved 

solids, nutrients, and pesticides compared with background levels.

•	 Canal-water inflow has altered the water quality of Everglades National Park and Loxahatchee National Wildlife 

Refuge marshes.

•	 Water quality in marshes away from canals is affected by seasonal changes in rainfall and water levels, as well as 

variation in geology, hydrology, and vegetation.

During phase 2 of the study, water quality and flow data for Shark River and Trout Creek were compiled. Currently, the 

data are being organized and arranged for computing nutrient fluxes.
34 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Remotely Sensed Rugosity Measurements and Patch Reef Community Structure in Biscayne 

National Park

I.B. Kuffner, J.C. Brock, Rikki Grober-Dunsmore, V.E. Bonito, T.D. Hickey, and M.S. Harris, USGS Florida Integrated Science 

Center—St. Petersburg, Fla.

With the realization of the need for coral reef ecosystem management across large spatial scales, scientists and resource 

managers currently are seeking variables that are easily measured over large areas and correlate well with the status of reef 

resources. In this study, we investigate the ability of new technology in airborne laser surveying (National Aeronautics and Space 

Administration [NASA] Experimental Advanced Airborne Research Lidar [EAARL]) to predict the status of shallow (less than 

15 m) coral reef ecosystems. After large portions of Biscayne National Park were surveyed remotely using EAARL, reef fish 

and benthic community structure variables were measured using traditional methods in situ on 12 patch reefs. At independent, 

randomly selected stations (n = 16 per reef), we measured rugosity (topographic complexity of the benthos) and the abundance 

and species richness of macroalgae, reef fish, gorgonians, and other sessile invertebrates. EAARL submarine topography data 

were used to quantify rugosity at spatial scales unobtainable using traditional in situ methods.

Rugosity, important in providing information about surface area and shelter availability for reef organisms, has been shown 

to correlate positively with reef-fish species richness, abundance, and biomass. Previously, the inability to measure rugosity on 

spatial scales appropriate to the organisms of interest had constrained research efforts. We conducted correlation, ANOVA, and 

linear regression analyses to elucidate the predictive power of EAARL rugosity measurements in describing the variance in reef 

community structure. EAARL rugosity indices were significantly correlated with in situ rugosity measurements and with species 

richness of fishes. Additionally, relations were found between benthic cover variables and herbivorous fish abundance. The 

EAARL shows promise as a technique to predict coral reef community structure over large areas, and may be a useful tool for 

managers that inventory and protect coral reef resources.

Comprehensive Urban Ecosystems Studies (CUES): Activities Planned for the Miami Urban Area and 

Adjacent Portions of the Greater Everglades Ecosystem

Paul Hearn, USGS, Reston, Va.

Working within the geospatial framework of the USGS National Map, the Comprehensive Urban Ecosystems Studies 

(CUES) initiative is intended to develop web-based science applications to address key issues in the urban areas of the Nation. 

CUES will integrate data from The National Map with thematic data and web-based tools to apply USGS science expertise 

to critical issues including security, vulnerability of water resources, natural hazards, urban sprawl, and the conservation and 

protection of parklands and other natural resources.

Work began in fiscal year 2005 to design and develop a CUES website for the greater Miami area (Miami-Dade County) 

and adjacent portions of the greater Everglades ecosystem (Loxahatchee National Wildlife Refuge, Biscayne National Park, and 

Everglades National Park). The initial stages of this effort, which is expected to continue for the next 3 to 5 years, involve:

•	 Gathering and integrating the best-available foundation-layer datasets for The National Map, including imagery, landcover, transportation, hydrology, elevation, geographic names, boundaries, and structures;

•	 Developing a web interface and map viewer to support the display and download of both base mapping and thematic 

data, and the web deployment of selected science applications for decision support; and

•	 Communicating with other U.S. Department of the Interior agencies, such as the National Park Service and U.S. Fish 

and Wildlife Service, as well as local government agencies and local universities to identify key issues and potential 

science applications for deployment on the CUES/Miami website.
Research Project Description Index 35

Research Project Description Index

Ecosystem History of Biscayne Bay............................................................................................................................36

Determining Relationships between Remotely Sensed Measures of Reef Habitat Complexity, Reef Fish 

Assemblages, and Benthic Community Structure..........................................................................................37

Characterization of the Histopathology of White Diseases of Corals at Biscayne National Park .............................37

Distribution of Non-Native Gastropod Melanoides tuberculatus (Red-Rimmed Melania) and Potential 

Associated Parasites in Biscayne National Park...........................................................................................38

Resolving Boundaries of Management Units for a Broadly Distributed Indicator Species, the Diamondback 

Terrapin (Malaclemys terrapin), in Biscayne National Park, Florida..........................................................39

Effects of Altered Fresh Water Delivery to Biscayne National Park: Consequences to Reefs and 

Reef-Associated Macro and Microbial Communities....................................................................................40

Conceptual Hydrogeologic Model of the Karst Biscayne Aquifer in Support of Ground-Water Flow 

Simulations from Everglades National Park to Biscayne National Park ......................................................41

Ground-Water Inputs to Biscayne National Park: Impacts on the Estuary and Coral Reef.......................................42

Quality of Surface-Water Discharge into Biscayne Bay .............................................................................................42

Reconnaissance for Emerging Pollutants of Concern (EPOCs) in Biscayne National Park and the 

Adjacent Biscayne Bay Coastal Environment...............................................................................................43

Anthropogenic Influences on Biota and Biogeochemistry of Biscayne Bay: Integration of Chemical, 

Geological, and Molecular Genetic Data.....................................................................................................43

Occurrence, Survival, and Risk Assessment of Microbial Indicators and Pathogens in Ground Waters 

and Marine Waters and Sediments within Biscayne National Park..............................................................44

A GIS-Based Decision Support System for the Greater Everglades Ecosystem Restoration .....................................45

6.0 Potential U.S. Geological Survey 

Research Projects in and around 

Biscayne National Park

To better describe how the USGS can assist and/

or supplement needed research in Biscayne National Park 

and Biscayne Bay, several USGS scientists have composed 

descriptions of potential research projects. These projects are 

examples of studies that could supply managers with needed 

information to address the problems that face Biscayne Bay 

in the near future. Each of the projects address important 

independent issues, but additionally most of them also address 

specific CERP Monitoring and Assessment Plan issues, which 

can be found in the Monitoring and Assessment Plan (MAP) 

Part 1 chapter 3 and MAP Part 2 section 9 Southern Estuaries 

Module documentation (RECOVER, 2004; RECOVER, 2006) 

and topics from the National Park Service’s “Vital Signs” 

network. The topics of research include ecosystem stresses, 

water deliveries, contaminants, and database and GIS issues. 
36 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

6.1 Ecosystem Stresses

Ecosystem History of Biscayne Bay

G. Lynn Wingard, Thomas M. Cronin, Debra A. Willard, Charles W. Holmes, William Orem, and W. Bane Schill

During the last century, Biscayne Bay has been greatly affected by anthropogenic alteration of the environment through 

urbanization of the Miami-Dade County area and alteration of natural flow. The sources, timing, delivery, and quality of freshwater flow into the bay, as well as the shoreline and subaquatic vegetation have changed. The goal of current restoration efforts 

is to restore natural flow of freshwater into Biscayne Bay and restore the natural fauna and flora. To accomplish this, however, 

pre-alteration baseline conditions need to be determined to establish targets and performance measures for restoration.

This project examines the natural patterns of temporal change in salinity, water quality, vegetation, and benthic fauna in 

Biscayne Bay over the last 100 to 300 years and examines the causes of change. The work will answer the following questions:

•	 What were the natural patterns of change and the range of variation within the system, particularly the supply of 

freshwater and salinity, prior to substantial anthropogenic alteration?

•	 What component of the changes seen in Biscayne Bay during the 20th century is due to anthropogenic alteration and 

what is due to natural change?

•	 How have past changes in climate and sea level altered the system in terms of changes to the water mass, and corresponding changes to the biota?

Once the natural cycles of change and the patterns of the system response to those changes are determined, the next step is 

to predict what the system will look like in the future. In addition, the ecosystem history data can be used to test the hydrologic 

and biologic models.

Shallow sediment cores will be collected from areas within the ecosystem that have been targeted as areas of interest, for 

example, areas located near historical ground-water upwelling. This work will build on and fill in gaps from previous project 

work (Wingard and others, 2003; 2004). Cores are collected, x-rayed, and described, and then cut into 1- to 2-cm-thick samples. 

Age models are developed for the cores using Pb-210 and C-14 radioisotopes, and the first-occurrence horizon of Casuarina

pollen. Core samples will be evaluated for any biotic remains, sediment geochemistry, and shell geochemistry. Biotic assemblages are compared to modern assemblages to interpret environmental characteristics at the time of deposition of each sample.
Research Project Description Index 37

Determining Relationships between Remotely Sensed Measures of Reef Habitat Complexity, Reef 

Fish Assemblages, and Benthic Community Structure

John C. Brock, G. Todd Kellison, and Ilsa B. Kuffner

As anthropogenic activities degrade coral reef ecosystems worldwide, resource managers are in an increasing need of 

methods to identify target areas for conservation and management actions. Studies in coral reef ecosystems have documented 

relationships between levels of habitat complexity (for example, rugosity) and reef fish and benthic community structure. 

Methods that would enable (1) accurate determination of habitat complexity measures over large spatial scales and with minor 

in-water effort, and (2) subsequent prediction of spatially explicit reef fish and benthic community structure would be of great 

benefit to resource managers. Such methods are currently lacking.

Building on recent research (Brock and others, 2003; I.B. Kuffner, U.S. Geological Survey, written commun., 2007), 

we will assess relationships between remotely sensed measures of reef habitat complexity (for example, rugosity and elevational change; measured with National Aeronautics and Space Administration [NASA] Experimental Advanced Airborne 

Research Lidar [EAARL]) and reef fish and invertebrate community structure (for example, species richness and intra-species 

abundance). This project will address four main research questions:

•	 Are there predictive relationships between lidar-measured values of habitat complexity and measures of reef fish and 

benthic community structure? If so,

•	 At what spatial scales do these predictive relationships exist?

•	 What species groupings (for example, taxonomic or trophic) are most responsive to changes in habitat complexity?

•	 Do these relationships differ between patch and continuous-reef environments?

Initial studies will focus on a portion of the northern Florida Keys reef tract (Biscayne National Park), using both patch 

reefs and continuous reef habitat. We will calculate scale-specific habitat complexity measures from LIDAR data, and collect 

reef fish and benthic community structure data from scuba visual censuses. We will utilize statistical approaches such as linear 

regression, MANOVA, and principal component analysis to assess relationships between habitat measures and fish and invertebrate community structure. Subsequent work will expand to other areas (for example, Dry Tortugas National Park) to determine 

if habitat-species relationships are consistent across larger spatial scales. 

Results will demonstrate a novel technique to assess measures of habitat complexity over large spatial scales, and provide: 

(1) insight about the ecological processes governing species distribution in coral reef ecosystems, (2) predictive tools for 

managers to determine areas that should be targeted for management and conservation, and (3) information to resource managers 

in Biscayne National Park for the purpose of developing a General Management Plan and a Fisheries Management Plan.

Characterization of the Histopathology of White Diseases of Corals at Biscayne National Park

Lou Sileo and Valerie Bochsler

An issue that is currently important at Biscayne National Park is characterizing the microbial communities that are associated with diseased and healthy corals and sea grasses, as well as providing a rapid diagnosis of disease and identification of 

pathogenic microbes in tissues, coral mucus, sediments, the benthic boundary layer, and the water column.

Diseases with unknown or equivocal contributing factors are an important cause of mortality in corals. The National 

Wildlife Health Center has a long institutional history of determining the cause of coral diseases. Few studies of diseased corals 

have been multidisciplinary; the National Wildlife Health Center, in cooperation with other institutions, can collect matching 

companion samples of diseased corals and do multidisciplinary diagnostic procedures in histopathology, microbiology, virology, 

parasitology, ultrastructure and molecular biology. Various “white” diseases of coral have been attributed to infections by 

Serratia marcescens, Aurantimonas coralicida, and unidentified vibrios; these reports need repetitive confirmation. Published 

descriptions of the histopathology of the various white diseases are inadequate, and management of these diseases is not feasible 

until their cause or causes are identified.

This project will determine (1) whether the histopathology of white diseases of corals at Biscayne National Park is the same 

as at the U.S. Virgin Islands, and (2) whether Serratia marcescens, Aurantimonas coralicida, and vibrios are the causes. Field 

work in Biscayne National Park will include collection of samples from diseased and reference corals for laboratory tests at the 

National Wildlife Health Center and other collaborating institutions.
38 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Distribution of Non-Native Gastropod Melanoides tuberculatus (Red-Rimmed Melania) and Potential 

Associated Parasites in Biscayne National Park

G. Lynn Wingard, W. Bane Schill, and James B. Murray

A non-native gastropod, Melanoides tuberculatus (Family Thiaridae; common name Red-Rimmed Melania), has been 

found in relatively large numbers in samples collected from Biscayne National Park in 2003. The presence of this species raises 

several issues of concern to local resource managers: (1) the role of the species as an intermediate host to human parasites, 

Clonorchis sinensis (liver fluke) and Paragonimus westermani (lung fluke); (2) the potential displacement of native species; and 

(3) the potential effect on the health of animals within the park. The Thiaridae reproduce by means of parthenogenesis; therefore, a single individual can start a new colony and their reproductive rates are extremely high. A previous study documented as 

many as 23,000 per square meter near Coral Gables, Florida (Roessler and others, 1977). M. tuberculatus is an intermediate host 

for several parasitic organisms that potentially affect animals: (1) Philophthalmus megalurus—an avian parasite that affects the 

eyelids of waterfowl; (2) Centrocestus formosanus—a trematode that burrows into the gills of fish, and then enters mammals 

or birds that consume the fish; and (3) Haplorchis—a parasite that infects the muscle tissue of fish. In addition, there is some 

documentation of Paragonimus affecting mammals that eat raw crustaceans.

The primary objective of this project is to provide information about Melanoides tuberculatus that will enable Biscayne 

National Park managers to determine whether the species poses a substantial threat to human or animal health within the 

park. To address this issue, the following questions need to be answered:

•	 How widespread is M. tuberculatus and what is its distribution within southern Florida?

•	 What factors control its distribution? (Potential controlling factors include salinity, pH, water temperature, and 

nutrient levels.)

•	 Have there been multiple and/or continual introductions of the species, or are the individuals present the result of a 

single introduction that established a colony?

•	 Do the populations currently present in the parks contain any harmful parasites that might be a threat to humans or to 

native animal populations?

Live individuals will be collected from selected sites to be tested for the presence of parasites. Samples will be sent to 

Leetown, West Virginia, following established protocols for microbiology/parasitology analyses. A minimum of 60 individual 

M. tuberculatus collected at each site will provide a 95-percent probability of detection of the parasites if the incidence of 

infection is greater than 5 percent of the population. Field surveys will be conducted at various sites in Biscayne National Park 

to determine distribution and densities of M. tuberculatus. Collections will be made along salinity transects, moving from 

freshwater out into polyhaline to euhaline conditions. Water chemistry and other environmental parameter data will be collected 

as well as native mollusk population data. Individuals from the M. tuberculatus populations identified in the distribution study 

will be sampled to determine genetic diversity. If limited introductions of the species are occurring into the estuaries, low 

genetic diversity is expected at each site because of parthenogenesis; however, higher genetic diversity is expected if multiple or 

continual introductions are occurring.
Research Project Description Index 39

Resolving Boundaries of Management Units for a Broadly Distributed Indicator Species, the 

Diamondback Terrapin (Malaclemys terrapin), in Biscayne National Park, Florida

Kristen Hart, Tim L. King, and Carole C. McIvor

Human population expansion during the 20th century has resulted in aquatic habitat disappearance at an unprecedented 

rate. Perhaps no habitat (and its associated species) illustrates this trend more conclusively than coastal wetlands in the United 

States, where at least one-third of the threatened and endangered species of the Nation reside (Murdock 1994). Brackish coastal 

wetlands are being developed, and otherwise degraded, and destroyed at an accelerating rate as a direct and indirect effect of 

human development through urbanization.

Diamondback terrapins (Malaclemys terrapin) exist as geographic populations that occupy brackish waters along the 

Atlantic and Gulf coasts of North America (Ernst and others, 1994). Diamondback terrapins once supported a multimillion 

dollar restaurant trade, before overharvesting and habitat degradation severely affected populations. Currently, the terrapin is 

listed as a Threatened Species in Massachusetts and a Species of Special Concern in several other states that have conducted 

inventory and monitoring efforts. The status of this species is unknown for other areas.

Effective conservation and restoration plans require clearly definable units of management. Diamondback terrapins are 

restricted to the brackish coastal waters of North America along the Atlantic Ocean and Gulf of Mexico. This presumably 

continuous distribution would seem to provide a mechanism to facilitate gene, exchange, and thus prevent the development of 

distinct evolutionary lineages. Terrapin populations, however, have been shown to exhibit extensive morphological differentiation with seven subspecies recognized (Ernst and others, 1994). This distribution and the observed morphological differentiation 

seem contradictory, suggesting that the distribution may not be continuous but instead consist of discrete populations. Until now, 

no genetic information was available concerning the fine-scale population structure, levels of gene flow, or relatedness of any 

geographic collection of M. terrapin.

To develop management strategies for maintaining evolutionarily important terrapin lineages that will ensure long-term 

population stability and reduce the need for protection through regulatory processes, we undertook a study to develop a thorough 

understanding of the evolutionary relationships (for example, gene exchange) among geographically proximate and distal collections of M. terrapin. During 2001-05, we conducted both range-wide and fine-scale studies of M. terrapin microsatellite DNA 

variation to quantify population structure and define population boundaries for the species. In southern Florida, we analyzed 

samples from Key Largo, the Everglades (Gulf Coast), and Tampa. Samples from the east coast of Florida or Biscayne Bay, 

however, were lacking.

By examining the genetic makeup of individuals from Biscayne National Park, we will determine whether terrapins living 

in this bay in southern Florida are unique or instead part of a single large population. We will also determine whether Biscayne 

Bay terrapins are exchanging genes with turtles from the Florida Keys and the Everglades, thus effectively moving across greater 

distances than individuals would be expected to travel (based on ecological studies).

The specific objectives of the current study are to:

•	 Define the genetic population structure among multiple geographic collections of diamondback terrapins from 

southern Florida;

•	 Delineate management units and evolutionarily important lineages among geographic collections of diamondback 

terrapins from southern Florida;

•	 Compare results from genetic analysis of southern Florida terrapin samples with those obtained from analysis of 

samples collected throughout the entire range of the species; and

•	 Promptly report the findings of this research to all the State and Federal stakeholders.

This project will involve sampling geographically separate collections of diamondback terrapins (M. terrapin) in southern 

Florida and examining levels of gene flow among populations to clearly define populations and management units. The Biscayne 

Bay M. terrapin samples will be used in the current project to determine effective population size, relatedness of individuals, and 

fine-scale population structure for terrapins residing within park boundaries.

This project will provide State and Federal resources managers with information on the boundaries of the southern Florida 

metapopulations of the M. terrapin. Summarized information about genetic variability at each polymorphic marker and the 

portioning of genetic variability among diamondback terrapin populations sampled also will be made available to interested 

Federal, State, or local agencies as well as universities and interested user groups.
40 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Effects of Altered Fresh Water Delivery to Biscayne National Park: Consequences to Reefs and 

Reef-Associated Macro and Microbial Communities

Ilsa Kuffner, John Lisle, Chris Reich, and Peter Swarzenski

Coral-reef community structure is affected continually by anthropogenic factors, particularly in reef areas adjoining 

populous, highly developed coastlines. Biscayne National Park is bordered by an urban metropolis of 2.3 million people within 

Miami-Dade County, and includes a substantial amount of coral reef and reef-associated habitat within its boundaries. As 

with other reefs in the region, these areas within Biscayne National Park have experienced substantial declines in coral cover 

and fish biomass/abundance, and increases in algal cover and incidence of coral disease. Despite the semiprotected status of 

these resources within Biscayne National Park, reef habitats are not showing signs of recovery. Water-quality issues, including 

increased levels of nutrients and water-borne pathogens, are hypothesized to have played a key role in these observed changes. 

With the impending alteration of the water-management system as part of CERP, it is important to collect baseline data on 

community structure throughout Biscayne National Park so that positive or negative effects associated with changing patterns of 

freshwater delivery to the area can be assessed and documented.

The objectives of the project are as follows: 

•	 Collect baseline algal community structure data in areas where nutrient-laden submarine ground-water discharge is 

suspected to be measurably increased due to CERP.

•	 Collect baseline microbial community structure, diversity, and physiological function data in areas where nutrientladen submarine ground-water discharge is suspected to be measurably increased due to CERP.

•	 Evaluate areas to determine if cascading effects of algal community change, including reduced coral cover, coral 

recruitment, and recruit survival, are not apparent.

•	 Evaluate areas to determine if cascading effects of microbial community change are not affecting key processes such 

as sediment dissolution, nitrogen fixation, nutrient remineralization, sulfide production, and nutrient fluxes from 

sediments to the reefs.

•	 Evaluate to determine if microbial indicators of coral pathogens found in human fecal wastes are not being transported 

by way of submarine ground-water discharge or surface waters affected by submarine ground-water discharges to the 

reefs.

Based upon existing knowledge of freshwater delivery derived from observational and modeling studies (Szwarzenski, 

2004a, Langevin, 2001), sites will be selected for quarterly monitoring of benthic and microbial communities and processes 

therein. The goal will be to select sites within Biscayne National Park along a gradient of existing and predicted freshwater 

delivery levels.
Research Project Description Index 41

6.2 Water Deliveries

Conceptual Hydrogeologic Model of the Karst Biscayne Aquifer in Support of Ground-Water Flow 

Simulations from Everglades National Park to Biscayne National Park

Kevin J. Cunningham

Water diversions and excessive nutrients and contaminants within the Everglades wetlands have decimated populations of 

wading birds and other animals to near extinction levels. In Biscayne Bay, the degradation of estuarine and marine waters has 

caused declines in the marine community. Because of the inextricable link between surface-water levels in the wetlands and 

underlying fresh ground-water flows to the coast, “getting the water levels right” in the Everglades wetlands is an important 

aspect of ecologic restoration in both the terrestrial wetlands and coastal marine environments. The best water-management 

strategy includes managing the relation between hydrology and biological community components, including wading birds, 

coral reefs, and vegetation, by managing optimal timing and distribution of freshwater flows. Critical to the management of the 

hydrologic component is accurate simulation of ground-water flow from the Everglades wetlands to the coast of Biscayne Bay. It 

has been realized recently, however, that current conceptual representations of the Biscayne aquifer in ground-water flow simulations are not realistic, especially as they relate to nutrient and contaminant transport, thus decisions based on them are suspect.

Current ground-water models for the Biscayne aquifer assume that the aquifer is a porous medium with essentially homogeneous hydraulic properties (for example, Wilsnack and others, 2000). The Biscayne aquifer, however, is actually a heterogeneous, dual-porosity, karst system characterized by intergranular matrix porosity and well-connected, larger scale secondary 

cavities (Cunningham and others, 2004a). These different types of porosity create a heterogeneous distribution of permeability, 

and consequently, flow rates in a given area depend on whether ground-water flow is through matrix, cavities, or a combination of both. Diffuse and non-laminar flow occurs predominately within the intergranular porosity, whereas turbulent flow may 

occur within the conduit-pore system of connected cavities. Rates of flow within the conduit-pore system clearly are more rapid 

than within the matrix, as demonstrated by a USGS tracer test at the Northwest Well Field in Miami-Dade County (Renken and 

others, 2005). During the test, the apparent mean advective flow velocity of the tracer was one order of magnitude or greater 

than the rate predicted by simulations that assume diffuse flow. A critical consideration to modeling contaminant and nutrient 

distribution and flow rates within the karst Biscayne aquifer is that the contaminants are influenced by the relative proportion 

and spatial arrangement of matrix and conduit porosity. The conceptual karst hydrogeologic model to be developed in this study 

is intended to provide a framework that accurately represents the distribution of matrix and conduit porosity for numerical 

simulations of ground-water flow and nutrient and contaminant transport on a regional scale.

The objectives of the project are to:

•	 Provide information about changes in ground-water flow to Biscayne National Park resulting from Everglades restoration;

•	 Develop a karst hydrogeologic conceptual model based on cyclostratigraphic concepts for use in simulation of groundwater flows from Everglades National Park to offshore Biscayne National Park;

•	 Provide information about freshwater flow from Everglades National Park to offshore Biscayne National Park; and

•	 Develop modeling procedures for simulation of flow in dual-porosity karst aquifers.

This project will involve the following tasks:

•	 Drill and install onshore and offshore well clusters in Biscayne National Park, each including a shallow, intermediate, 

and deep ground-water monitoring well;

•	 Collect cores and advanced geophysical logs;

•	 Instrument wells and collect water level, salinity, and temperature data;

•	 Produce a karst hydrogeologic conceptual model by integrating analyses of cores, borehole geophysical logs, 

cyclostratigraphy, and hydrologic data; and

•	 Provide data to the Flows to Coral Reefs U.S. Department of the Interior Landscape Project for development of 

modeling procedures to integrate the karst hydrogeologic conceptual model in simulations of ground-water flow and 

solution transport.
42 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Ground-Water Inputs to Biscayne National Park: Impacts on the Estuary and Coral Reef

Robert Halley, Christian Langevin, and Chris Reich

Biscayne National Park and Biscayne Bay receive ground- and surface-water flow from the Everglades. Surface water flows 

through numerous canals that transect highly developed lands (urban and agricultural) and can potentially transport high loads 

of nutrients and other contaminants to the bay. In addition, ground water that is recharged in these onshore areas is transported 

through the highly transmissive Biscayne aquifer and discharged along the coastline. Additional research to quantify groundwater flux to the bay is needed to further characterize chemical transport from ground to surface waters as well as validate 

current (and future) ground-water flow models.

The purpose of this project is to determine whether freshwater presently is seeping into the bay. If so,

•	 Determine where, and what known or identifiable pollutants are being delivered with it, and

•	 Predict how Everglades restoration (CERP) and installation of 300 aquifer storage wells farther inland may affect 

offshore reefs.

The activities for this project will involve collecting pressure measurements in existing monitoring wells to determine 

onshore to offshore hydraulic gradients. Hydraulic gradients will be utilized to refine the ground-water flow model for Biscayne 

Bay. Water samples also will be collected from existing wells to complement existing water-quality data. Selected sites where 

identified springs may occur will be monitored using seepage meters to obtain flux measurements during varying dry and wet 

periods throughout the year.

Quality of Surface-Water Discharge into Biscayne Bay

P.V. Winger and P.J. Lasier

Surface-water discharge to Biscayne Bay occurs primarily through canal inflows; these have the potential to be affected 

adversely by stormwater runoff and point and nonpoint-source discharges associated with extensive municipal and industrial 

development within the Biscayne Bay watershed. Potential impairment of the estuarine resources of Biscayne Bay from these 

freshwater inflows is high, and an evaluation of them is needed to provide information of sufficient accuracy to develop management plans that can protect and preserve this unique and valuable estuarine system over the long term. Previous studies have 

indicated that a number of the canal inflows to Biscayne Bay have degraded water quality, as demonstrated by elevated concentrations of contaminants and toxicity to test organisms.

Because the quality of sediment reflects the quality of the surface water, the weight of evidence approach will be used to 

determine the quality of freshwater in canals discharging into Biscayne Bay. Specifically, inflow water quality will be determined by measuring contaminants in the sediments and toxicity of solid-phase sediment and sediment porewater.

The objective of this study is to determine the quality of water that discharges into Biscayne Bay and identify sources 

that are degraded. Areas that are identified as having degraded conditions can then be targeted by the appropriate management 

agency, such as the Department of Environmental Resources Management (DERM), for cleanup and/or remediation.

Completion of this study will involve the following tasks:

•	 Select study sites in the canals that discharge into Biscayne Bay,

•	 Collect sediments to analyze in the laboratory,

•	 Measure contaminant residues in the sediments,

•	 Determine chronic toxicity of solid-phase sediments,

•	 Determine acute toxicity of pore water,

•	 Determine physical characteristics of the sediments, and

•	 Determine sediment quality using the weight-of-evidence approach.
Research Project Description Index 43

6.3 Contaminants

Reconnaissance for Emerging Pollutants of Concern (EPOCs) in Biscayne National Park and the 

Adjacent Biscayne Bay Coastal Environment

A.C. Lietz (Retired)

A primary purpose of the CERP is the restoration of natural water flows and historical hydroperiods in the ecosystem 

of southern Florida, including the Biscayne Bay Coastal Wetlands adjacent to Biscayne National Park. As part of the plan, 

reclaimed wastewater will be used from the South District Wastewater Treatment Plant, and of particular concern is the presence of emerging pollutants of concern (EPOCs) in reused wastewater. In a recent study, the presence of EPOCs in wastewater 

influent and effluent was detected at the wastewater treatment plant (Lietz and Meyer, 2006). An additional and necessary step 

is to document the possible occurrence and concentration of EPOCs in Biscayne National Park and the adjacent coastal environment prior to using reclaimed wastewater so that a baseline of EPOC concentration levels will be available for future studies.

The objective of this project is to develop a reconnaissance of EPOCs by documenting their occurrence, concentrations, 

and possible sources in Biscayne National Park and the adjacent coastal environment. This reconnaissance will develop an 

EPOC database to be used as a baseline for comparison of contamination levels after the implementation of the use of reclaimed 

wastewater to establish historical hydroperiods and more natural flow to the Biscayne Bay Coastal Wetlands. The scope of this 

project will involve (1) selection of critical Biscayne National Park and adjacent coastal canal sites for reconnaissance sampling, 

and (2) sampling and analysis at the above-mentioned sites for the EPOCs identified by Koplin and others (2002).

Anthropogenic Influences on Biota and Biogeochemistry of Biscayne Bay: Integration of Chemical, 

Geological, and Molecular Genetic Data

G. Lynn Wingard, W. Bane Schill, and James B. Murray 

The Biscayne Bay shoreline is highly developed and has been listed as one of the 10 most endangered coastal parks of the 

389 park units in the National park system. Pollutants enter Biscayne Bay from multiple point and non-point sources, including 

boats, canals, quarrying operations, a Class I landfill, several C and D landfills, military operations, a sewage treatment plant, 

urban and agricultural runoff, and submarine ground-water springs. Large tracts of seagrass, primarily Thalassia testudinum, 

colonize the shallow areas of western Biscayne Bay and provide habitat (including nurseries) for many aquatic organisms as 

well as biofiltration for the marine ecosystem. The extensive surface area of Thalassia plants as well as the sediments underlying 

Thalassia beds harbor microbes capable of performing a number of important ecosystem functions including nitrogen cycling, 

sulfur and metal reduction, and metabolism of organic pollutants. Increased research is required to better characterize the types 

of pollutants entering the bay waters, their fate in the environment, and how life in the bay is affected by the interactions of 

multiple stressors. Because water circulation patterns (as seen in satellite images) indicate that many inputs to Biscayne Bay are 

swept southward and out to the coral reef tracts (with an estimated residence time of 7-10 days), additional research is required 

to determine the spatial extent of pollutant effects.

The primary objective of this project is to determine the effects of anthropogenic activities on the fauna and flora (including 

the microbial component) of Biscayne National Park. Specific questions to be addressed include:

•	 What are the sources of pollution (for example, metals, agrochemicals, and endocrine disrupters) entering Biscayne 

Bay and are there synergistic effects with other forms of pollutants such as thermal input? How severe are the effects 

of these pollutant stressors on the fauna and flora of Biscayne Bay?

•	 Do pollutants entering Biscayne Bay ultimately reach the reef tract, or are they remediated by other natural or anthropogenic factors within the bay?

•	 Are anthropogenic chemicals changing bay microbial community compositions resulting in modulation of nutrient 

cycling or increases in opportunistic pathogens?

Samples will be collected at sites that extend from Coral Gables in northern Biscayne Bay to the C-111 Canal in southern 

Barnes Sound. Multiple sites are located in the vicinity of Black Point near a landfill, sewage treatment plant, quarrying operations, and three power plants (one nuclear and two oil burning). Four types of analyses will be performed on the samples:

•	 Metal Analysis: Organisms that secrete biogenic carbonate (for example, Porites sp.) and are representative of multiple 

trophic levels will be analyzed to determine the type and amount of anthropogenic chemicals sequestered within 

the carbonate matrix. Porites make an ideal study organism because they are found from within the bay out to the 

reef tract.
44 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

•	 Organic Analysis: Water samples will be quantified for a suite of organic compounds (for example, atrazine, metalochlor, glyphosate, bisphenol A, alkylphenols, and total steroids).

•	 Microbial Analysis: Several key groups of microbes will be monitored using advanced molecular methods, including quantitative (real-time) polymerase chain reaction, laser scanning cytometry, terminal restriction fragment length 

polymorphism, and fluidized microarray to detect their presence, species composition, and reaction to environmental 

conditions.

•	 Genetic Analysis: Microbial samples from specimens of Porites collected across the system from bay to reef tract will 

be genetically identified to determine a typical microbial community.

Occurrence, Survival, and Risk Assessment of Microbial Indicators and Pathogens in Ground Waters 

and Marine Waters and Sediments within Biscayne National Park

John Lisle, Chris Reich, and Robert Halley

Biscayne National Park is the largest marine park in the national park system. Four distinct ecosystems have been identified 

within the park and include Biscayne Bay, the northern islands of the Florida Keys, mangrove forest along the shoreline of the 

park, and a coral reef tract. All of these ecosystems have experienced some degree of decline in their respective productivity 

during the recent past. Two contributing factors are: (1) increased volumes of terrestrial runoff (non-point discharge) into 

Biscayne National Park that contain elevated concentrations of nutrients, organics and microbials; and (2) substantial reductions 

in the volume of fresh submarine ground water discharge from the coastline within Biscayne National Park due to flood control 

projects within the Everglades. The karst geology of this area increases the complexity of these problems because it allows 

relatively rapid infiltration of surface waters, point and non-point septic discharges, and subsurface septic waste injection into 

the surficial aquifer system, a major contributor to submarine ground-water discharge.

Ongoing efforts to monitor the effect of submarine ground-water discharge and point and non-point discharges on the 

water quality of Biscayne National Park have focused on nutrients, physical constituents, and trophic levels at or above that 

of phytoplankton. To date, there has been no organized effort to determine the concentrations of microbial indicators (that is, 

fecal coliforms, enterococci, Clostridium perfringens, and coliphage) and known pathogens of environmental interest (that is, 

Escherichia coli, Serratia marcescens, and human enterovirus) in surface runoff, shoreline submarine ground-water discharge, 

and ground water from an inland-to-reef tract vector within Biscayne National Park.

We are proposing a project that will use existing USGS monitoring wells within Biscayne National Park, along with 

identified sites of point and non-point discharges and zones of confirmed submarine ground-water discharge, to determine the 

abundances of selected microbial indicators and pathogens in the respective sample types. Environmental diffusion chambers, 

designed by the USGS, also will be used to determine the survival rates of selected microbial indicators and pathogens in sediments, surface waters (marine and fresh), and ground waters within Biscayne National Park.

The proposed project is designed to address the following questions: 

•	 What are the abundances of microbial indicators and pathogens in surface-water runoff, submarine ground-water discharge, ground water, and waters at the reef tract within Biscayne National Park?

•	 Which factors in each of the sample types inhibit/enhance the survival rates of microbial indicators and pathogens?

•	 Is there an increased risk to humans and other mammals that come in contact with these waters based on microbial risk 

assessment modeling?

The proposed project will involve the following four activities:

•	 Collection of water samples from (1) fresh surface-water discharges into Biscayne National Park, (2) sites identified 

as having substantial submarine ground-water discharge, (3) USGS monitoring wells that are located within Biscayne 

National Park; and collection of sediment cores from selected sites including the reef tract;

•	 Analysis of these samples for fecal coliforms, enterococci, E. coli, Clostridium perfringens, coliphage, Serratia marcescens, and enterovirus;

•	 Use of the data obtained from the analyses, to calculate the human health risk, if any, associated with contact with 

these waters; and

•	 Determination of survival rates for selected microbial indicators and pathogens using in situ environmental diffusion 

chambers.
Research Project Description Index 45

6.4 Database and Geographic Information System Issues

A GIS-Based Decision Support System for the Greater Everglades Ecosystem Restoration

Richard L. Bernknopf and Paul Hearn, Jr.

Land use and preservation/restoration decisions have substantial, but highly uncertain, effects on water quality and quantity, 

flow patterns, and ecosystem health in the greater Everglades ecosystem. These environmental and ecological factors, however, 

have economic values that currently are not being (or only partially) considered in these decisions. A program of research is 

needed to: (1) estimate the economic value of environmental and ecological resources affected by development and preservation/restoration decisions, (2) aggregate and quantify the large uncertainties associated with these decisions, and (3) develop a 

decision support system that will provide land managers and local officials with a clearer idea of the economic consequences of 

various courses of action.

The objectives of this project are to:

•	 Develop and test a method to estimate the benefits and costs of ecosystem restoration projects in the greater Everglades 

ecosystem;

•	 Develop, estimate, and test integrated ecological and economic indicators that measure the effect of restoration efforts 

on natural and anthropogenically altered environments—test areas will include Loxahatchee National Wildlife Refuge, 

Biscayne National Park, and Everglades National Park;

•	 Provide U.S. Department of the Interior land managers with a GIS-based decision support system that is capable of 

estimating the socioeconomic implications of land-use decisions, and provide a method to assess land allocations and 

their economic values that includes the consideration of uncertainty. (Test areas include the Miami-Dade County urban 

development boundary and Everglades Agricultural Area.)

The proposed project includes two primary components, a cost-benefit analysis and decision support system development.

Cost-Benefit Analysis

Conduct a cost-benefit analysis of an investment project intended to increase ecosystem sustainability. The application 

would be designed to estimate the benefits and costs of the construction of a multi-mile bridge along the Tamiami Trail to 

improve water flow. Benefit estimation will include the willingness to pay for environmental services.

Decision Support System Development

•	 Task 1―Gather and integrate required base and thematic data and build GIS with integrated decision support system 

software, using cost share with the Comprehensive Urban Ecosystem Systems (CUES) project for the greater Everglades ecosystem.

•	 Task 2―Develop, estimate, and test a landscape stress indicator (LSI) for Loxahatchee National Wildlife Refuge, 

Biscayne National Park, and Everglades National Park. Stressors are severe storms, agrochemicals, mining, and human 

encroachment. The landscape stress indicator will be a spatial vulnerability metric in the decision support system that 

is used to assess the relative ecological and economic sustainability of a given land area.

•	 Task 3―Develop and implement a land allocation and land valuation model that includes explicit consideration of 

associated uncertainties in the Miami-Dade County urban development boundary or the Everglades Agricultural Area.

•	 Task 4―Develop and test a Bayesian (probabilistic) network as a decision framework for tasks 2 and 3.
46 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

7.0 References Cited

Aronson, R.B., and Precht, W.F., 2001, White-band disease and the 

changing face of Caribbean coral reefs: Hydrobiologia, v. 460, 

p. 25-38.

Ault, J.S., Smith, S.G., Meester, G.A., Juo, J., and Bohnsack, 

J.A., 2001, Site characterization for Biscayne National Park: 

Assessment of fisheries resources and habitats: NOAA Technical 

Memorandum NMFS-SEFSC-468, p. 156.

Blair, S.M., McIntosh, T.L., and Mostkoff, B.J., 1994, Impacts of 

Hurricane Andrew on the offshore reef systems of central and 

northern Dade County, Florida: Bulletin of Marine Science, v. 54, 

no. 3, p. 961-973.

Brock, J.C., Wright, C.W., Clayton, T.D., and Nayegandhi, A., 2004, 

LIDAR optical rugosity of coral reefs in Biscayne National Park, 

Florida: Coral Reefs, v. 23, no. 1, p. 48-59.

Browder, J.A., Alleman, Richard, Markley, Susan, Ortner, Peter, 

and Pitts, P.A., 2005, Biscayne Bay conceptual ecological model: 

Wetlands, v. 25, no. 4, p. 854-869.

Bruno, J.F., Petes, L.E., Harvell, C.D., and Hettinger, A., 2003, 

Nutrient enrichment can increase the severity of coral diseases: 

Ecology Letters, v. 6, p. 1056-1061.

Buchanan, T.J., and Klein, Howard, 1976, Effects of water 

management of fresh-water discharge to Biscayne Bay: University 

of Miami Symposium Biscayne Bay: Past/Present/Future, 

April 2-3.

Causaras, C.R., 1987, Geology of the surficial aquifer system, 

Dade County, Florida: U.S. Geological Survey Water-Resources 

Investigations Report 86-4126, 240 p., 3 sheets.

Cunningham, K.J., and Aviantara, A., 2001, Characterization 

of the karstic Biscayne aquifer in southeastern Florida using 

ground-penetrating radar, digital optical borehole images and 

core (abstract), in Kuniansky, E.L., ed., U.S. Geological Survey 

Karst Interest Group Proceedings, St. Petersburg, Florida, 

February 13-16, 2001: U.S. Geological Survey Water-Resources 

Investigations Report 01-4011, p. 134.

Cunningham, K.J., Carlson, J.L., Wingard, G.L., and others, 2004a, 

Characterization of aquifer heterogeneity using cyclostratigraphy 

and geophysical methods in the upper part of the karstic Biscayne 

aquifer, southeastern Florida: U.S. Geological Survey WaterResources Investigations Report 03-4208, 46 p., 5 pls.

Cunningham, K.J., Renken, R.A., Wacker, M.A., and others, 2006a, 

Application of carbonate cyclostratigraphy and borehole geophysics 

to delineate porosity and preferential flow in the karst limestone 

of the Biscayne aquifer, SE Florida, in Harmon, R.S., and 

Wicks, C., eds., Perspectives on Karst Geomorphology, Hydrology, 

and Geochemistry—A tribute volume to Derek C. Ford and 

William B. White: Geological Society of America Special Paper 

404, p. 191-208.

Cunningham, K.J., Wacker, M.A., Robinson, Edward, and others, 

2004b, Hydrogeology and ground-water flow within the L31N 

Seepage Management Pilot Project area, Miami-Dade County, 

Florida: U.S. Geological Survey Scientific Investigations Map 

I-2846, 1 pl.

Cunningham, K.J., Wacker, M.A., Robinson, Edward, and others, 

2006b, A cyclostratigraphic and borehole-geophysical approach 

to development of a three-dimensional conceptual hydrogeologic 

model of the karstic Biscayne aquifer, southeastern Florida: U.S. 

Geological Survey Scientific Investigations Report 2005-5235, 

69 p.

Department of Environmental Resources Management, 1985, 

Biscayne Bay today, a summary report on its physical and 

biological characteristics: Miami-Dade County Department of 

Environmental Resources Management Report.

Edmunds, P.J., 2000, Patterns in the distribution of juvenile corals and 

coral reef community structure in St. John, U.S. Virgin Islands: 

Marine Ecology Progress Series, v. 202, p. 113-124.

Federal Register Notice, October 11, 1979, v. 44, no. 198.

Fish, J.E., 1988, Hydrogeology, aquifer characteristics, and groundwater flow of the surficial aquifer system, Broward County, 

Florida: U.S. Geological Survey Water-Resources Investigations 

Report 87-4034, 92 p.

Fish, J.E., and Stewart, M.T., 1991, Hydrogeology of the surficial 

aquifer system, Dade County, Florida: U.S. Geological Survey 

Water-Resources Investigations Report 90-4108, 50 p.

Florida Fish and Wildlife Conservation Commission, 2003, 

Conserving Florida’s seagrass resources: Developing a coordinated statewide management program: St. Petersburg, Report by 

prepared by Marine Research Institute.

Galli, Gianni, 1991, Mangrove-generated structures and depositional 

model of the Pleistocene Fort Thompson Formation (Florida 

Plateau): Facies, v. 25, p. 297-314.

Glynn, P.W., Szmant, A.M., Corcoran, E.F., and Cofer-Shabica, S.V., 

1989, Condition of coral reef cnidarians from the northern Florida 

reef tract: Pesticides, heavy metals, and histopathological examination: Marine Pollution Bulletin, v. 20, no. 11, p. 58-576.

Hallock, P., 2001, Coral reefs, carbonate sedimentation, nutrients, 

and global change, in Stanley, G.D., ed., The History and 

Sedimentology of Ancient Reef Ecosystems: Amsterdam, Kluwer, 

387–427.

Harper, D.E., Bohnsack, J.A., and Lockwood, B.R., 2000, 

Recreational fisheries in Biscayne National Park, Florida, 

1976-1991: Marine Fisheries Review, v. 62, no. 1, p. 8-26.

Hoegh-Guldberg, O., 1999, Climate change, coral bleaching and the 

future of the world’s coral reefs: Australian Journal of Marine and 

Freshwater Research, v. 50, p. 839-866.

Hudson, J.H., Hanson, K.J., Halley, R.B., and Kindinger, J.L., 1994, 

Environmental implications of growth rate changes in Montastrea 

annularis: Biscayne National Park, Florida: Bulletin of Marine 

Science, v. 54, no. 3, p. 647-669.

Hughes, T.P., 1994, Catastrophes, phase shifts, and large-scale degradation of a Caribbean coral reef: Science, v. 265, p. 1547-1551.

Hughes, T.P., Baird, A.H., Bellwood, D.R., and others, 2003, Climate 

change, human impacts, and the resilience of coral reefs: Science, 

v. 301, p. 929-933.

Ishman, S.E., Cronin, T.M., Brewster-Wingard, G.L., and others, 

1998, A record of ecosystem change, Manatee Bay, Barnes Sound, 

Florida: Proceedings of the International Coastal Symposium 

(ICS98): Journal of Coastal Research, Special Issue, no. 26, 

p. 125-138.
7.0 References Cited 47

Jackson, J.A. (ed.), 1997, Glossary of geology (4th ed.): Alexandria, 

Va., American Geological Institute, 769 p.

Keller, B.D., and Causey, B.D., 2005, Linkages between the Florida 

Keys National Marine Sanctuary and the South Florida Ecosystem 

Restoration Initiative: Ocean and Coastal Management, v. 48, 

p. 869-900.

Kim, G., and Swarzenski, P.W., 2005, Submarine ground-water 

discharge (SGD) and associated nutrient fluxes to the coastal 

ocean, in Liu, K.-K., Atkinson, L., Quinones, R., and TalaueMcManus, L., eds., Carbon and Nutrient Fluxes in Continental 

Margins—A Global Synthesis: New York, Springer-Verlag.

Kohout, F.A., 1960, Cyclic flow of saltwater in the Biscayne aquifer 

of southeastern Florida: Journal of Geophysical Research, v. 65, 

no. 7, p. 2133-2141.

Kohout, F.A., 1964, Flow of fresh water and salt water of the 

Biscayne aquifer of the Miami area, Florida: U.S. Geological 

Survey Water-Supply Paper 1613-C, p. C12-35.

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

others, 2002, Pharmaceuticals, hormones, and other wastewater 

contaminants in U.S. streams, 1999-2000: Environmental Science 

and Technology, v. 36, no. 6, p. 1202-1211.

Labowski, J.L., 1988, Geology, hydrology, and water monitoring 

program, Northwest Wellfield Protection Area: Metropolitan 

Dade County, Fla., Department of Environmental Resources 

Management Technical Report 88-3, 60 p.

Langevin, C.D., 2001, Simulation of ground-water discharge to 

Biscayne Bay, southeastern Florida: U.S. Geological Survey 

Water-Resources Investigations Report 00-4251, 127 p.

Lapointe, B.E., 1997, Nutrient thresholds for bottom-up control of 

macroalgal blooms on coral reefs in Jamaica and southeast Florida: 

Limnology and Oceanography, v. 42, no. 5, p. 1119-1131.

Lapointe, B.E., Matzie, W.R., and Barile, P.J., 2002, Biotic phaseshifts in Florida Bay and fore reef communities of the Florida 

Keys: Linkages with historical freshwater flows and nitrogen 

loading from Everglades runoff, in Porter, J.W., and Porter, K.G., 

eds., The Everglades, Florida Bay, and Coral Reefs of the Florida 

Keys—An Ecosystem Sourcebook: Boca Raton, Fla., CRC Press, 

p. 629-648.

Lidz, B.H., 2002, Chemical pollutants and toxic effects on benthic 

organisms, Biscayne Bay: A pilot study preceding Florida 

Everglades Restoration: U.S. Geological Survey Open-File Report 

02-308, 4 p.

Lietz, A.C., and Meyer, M.T., 2006, Evaluation of emerging contaminants of concern at the South District Wastewater Treatment Plant 

based on seasonal events, Miami-Dade County, Florida, 2004: U.S. 

Geological Survey Scientific Investigations Report 2006-5240, 

38 p.

Lirman, D., 2001, Competition between macroalgae and corals: 

Effects of herbivore exclusion and increased algal biomass on coral 

survivorship and growth: Coral Reefs, v. 19, no. 4, p. 392-399.

Lirman, D., and Biber, P., 2000, Seasonal dynamics of macroalgal 

communities of the northern Florida reef tract: Botanica Marina, 

v. 43, p. 305-314.

Lirman, D., and Cropper, W.P., Jr., 2003, The influence of salinity on 

seagrass growth, survivorship, and distribution within Biscayne 

Bay, Florida: Field, experimental, and modeling studies: Estuaries, 

v. 26, no. 1, p. 131-141.

Lirman, D., Orlando, B., Macia, S., Manzello, D., and others, 2003, 

Coral communities of Biscayne Bay, Florida and adjacent offshore 

areas: Diversity, abundance, distribution, and environmental correlates: Aquatic Conservation: Marine and Freshwater Ecosystems, 

v. 13, p. 121-135.

Martin, J.B., and Screaton, E.J., 2001, Exchange of matrix and 

conduit water with examples from the Floridan aquifer, in

E.L. Kuniansky, ed., U.S. Geological Survey Karst Interest 

Group Proceedings: U.S. Geological Survey Water-Resources 

Investigations Report 01-4011, p. 38-44.

McKenzie, D.J., 1983, Water quality at and adjacent to the South 

Dade County Solid Waste Disposal Facility: U.S. Geological 

Survey Water Resources Investigations Report 83-4003, 37 p.

McNeill, D.F., 2000, A review of upward migration of effluent 

related to subsurface injection at Miami-Dade Water and Sewer 

South District Plant: Report prepared for the Sierra Club-Miami 

group, 30 p.

Miller, M.W., Weil, E., and Szmant, A.M., 2000, Coral recruitment 

and juvenile mortality as structuring factors for reef benthic 

communities in Biscayne National Park, USA: Coral Reefs, v. 19, 

no. 2, p. 115-123.

Moulding, A.L., 2005, Coral recruitment patterns in the Florida Keys: 

Revisita de Biologia Tropical, v. 53, p. 75-82.

Mumby, P.J., Edwards, A.J., Arlas-Gonzalez, J.E., and others, 2004, 

Mangroves enhance the biomass of coral reef fish communities in 

the Caribbean: Nature, v. 427, p. 533-536.

Murdock, N.A., 1994., Rare and endangered plants and animals of 

southern Appalachian wetlands, in Trettin, C.C., Aust, W.M., and 

Wisniewski, J., eds., Wetlands of the interior southeastern United 

States: Dordrecht, v. 77, p. 385-405.

National Parks Conservation Association, 2001, Group names 

annual list of America’s ten most endangered national parks: 

[accessed November 27, 2006] http://www.npca.org/media_center/

press_releases/2001/page.jsp?itemID=27598999

Nemeth, M.S., Wilcox, W.M., and Solo-Gabriele, H.M., 2000, 

Evaluation of the use of reach transmissivity to quantify leakage 

beneath Levee 31N, Miami-Dade County, Florida: U.S. Geological 

Survey Water-Resources Investigations Report 00-4066, 80 p.

Odum, W.E., McIvor, C.C., and Smith, T.J., III, 1982, The ecology of the mangroves of south Florida: A community profile: 

Washington, D.C., U.S. Fish and Wildlife Service, Office of 

Biological Services Report FWS/OBS-81/24, 144 p.

Ogden, J.C., and Gladfelter, E.H., 1983, Interactions between 

mangroves, seagrass beds, and coral reefs in the coastal zones of 

the Caribbean: UNESCO Reports in Marine Science v. 23.

Pandolfi, J.M., Jackson, J.B.C., Baron, N., and others, 2005, Are 

U.S. coral reefs on the slippery slope to slime?: Science, v. 307, 

p. 1725-1726.
48 USGS Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

Parker, G.G., 1951, Geologic and hydrologic factors in the perennial 

yield of the Biscayne aquifer: American Water Works Association 

Journal, v. 43, no. 10, p. 817-835.

Parker, G.G., and Cooke, C.W., 1944, Late Cenozoic geology 

of southern Florida with a discussion of the ground water: 

Tallahassee, Florida Geological Survey Bulletin 27, 119 p.

Parker, G.G., Ferguson, G.E., Love, S.K., and others, 1955, Water 

resources of southeastern Florida: U.S. Geological Survey 

Water-Supply Paper 1255, 965 p.

Perkins, R.D., 1977, Depositional framework of Pleistocene rocks in 

south Florida, in Enos, Paul, and Perkins, R.D., eds., Quaternary 

Sedimentation in South Florida: Geological Society of America 

Memoir 147, p. 131-198.

Porter, J.W., Kosmynin, V., Patterson, K.L., and others, 2002, 

Detection of coral reef change by the Florida Keys Coral Reef 

Monitoring Project, in Porter, J.W., and Porter, K.G., eds., The 

Everglades, Florida Bay, and Coral Reefs of the Florida Keys: An 

Ecosystem Sourcebook: Boca Raton, Fla., CRC Press, p. 749-769.

RECOVER Team, 2004, CERP Monitoring and Assessment Plan: Part 

1—Monitoring and Supporting Research: [accessed May 7, 2007] 

http://www.evergladesplan.org/pm/recover/recover_map.aspx:

RECOVER Team, 2006, CERP Monitoring and Assessment Plan, 

Part 2—Assessment Strategy for the MAP: [accessed May 7, 

2007] http://www.evergladesplan.org/pm/recover/recover_map_

part2.aspx:

Reese, R.S., and Cunningham, K.J., 2000, Hydrogeology of the gray 

limestone aquifer in southern Florida: U.S. Geological Survey 

Water-Resources Investigations Report 99-4213, 244 p.

Reich, C.D., Halley, R.B., Hickey, T.D., and Swarzenski, P.W., 2006, 

Groundwater characterization and assessment of contaminants 

in marine areas of Biscayne National Park: U.S. National Park 

Service Water Resources Division Technical Report Series, 182 p. 

http://sofia.usgs.gov/publications/reports/bisc_gw_char/index.html

Renken, R.A., Shapiro, A.M., Cunningham, K.J., and others, 2005, 

Assessing the vulnerability of a municipal well field to contamination in a karst aquifer: Environmental and Engineering Geoscience, 

v. 11, no. 4, p. 341-354.

Roessler M.A., Beardsley, G.L., and Tabb, D.C., 1977, New records 

of the introduced snail, Melanoides tuberculata (Mollusca: 

Thiaridae) in South Florida: Florida Scientist, v. 40. p. 87-94.

St. Mary, C.M., Osenberg, C.W., Frazer, T.K., and Lindberg, W.J., 

2000, Stage structure, density dependence and the efficacy 

of marine reserves: Bulletin of Marine Science, v. 66, no. 3, 

p. 675-690.

Shinn, E.A, 1993, Geology and human activity in the Florida Keys: 

U.S. Geological Survey Fact Sheet (unnumbered), [accessed 

December 14, 2004] http://pubs.usgs.gov/fs/florida-keys/

Shinn, E.A., and Corcoran, Eugene, 1988, Contamination by landfill 

leachate, south Biscayne Bay, Florida: Final report to Sea Grant, 

University of Florida, Gainesville, 11 p.

Smith, T.J., III, Robblee, M.B., Wanless, H.R., and Doyle, T.W., 

1994, Mangroves, hurricanes, and lightning strikes: Assessment 

of Hurricane Andrew suggests an interaction across two differing 

scales of disturbance: BioScience, v. 44, no. 4, p. 256-262.

Smithsonian Marine Station at Fort Pierce, 2003, Seagrass habitats: 

[accessed December 1, 2007] http://www.sms.si.edu/irlspec/

Seagrass_Habitat.htm

Solo-Gabriele, Helena, and Sternberg, Leonel, 1998, Tracers of 

Everglades waters: Water Environment Federation Technical 

Exhibition and Conference 1998, in Proceedings of the Water 

Environment Federation 71st Annual Conference and Exposition, 

Orlando, Fla., v. 4, p. 323-333.

Sonenshein, R.S., 2001, Methods to quantify seepage beneath Levee 

30, Miami-Dade County, Florida: U.S. Geological Survey WaterResources Investigations Report 01-4074, 36 p.

Swarzenski, P.W., Bratton, J., and Crusius, J., 2004a, Submarine 

groundwater discharge and its role in coastal processes and ecosystems: U.S. Geological Survey Open-File Report 2004-1226, 4 p. 

http://sofia.er.usgs.gov/publications/ofr/2004-1226/

Swarzenski, P.W., Burnett, B., Reich, C., Dulaiova, H., Martin, R., 

and Meunier, J., 2004b, Novel geophysical and geochemical 

techniques to study submarine groundwater discharge in Biscayne 

Bay, Fla.: U.S. Geological Survey Fact Sheet 2004-3117, 4 p.

Swarzenski, P.W., Orem, W.G., McPherson, B.F., Baskaran, M. and 

Wan, Y., 2006, Biogeochemical transport in the Loxahatchee River 

Estuary: The role of submarine groundwater discharge: Marine 

Chemistry, v. 101, no. 3-4, p. 248-265.

Szmant, A.M., 2002, Nutrient enrichment on coral reefs: Is it a major 

cause of coral reef decline?: Estuaries, v. 25, no. 4b, p. 743-766.

Szmant, A.M., and Forrester, A., 1996, Water column and sediment 

nitrogen and phosphorus distribution patterns in the Florida Keys, 

USA: Coral Reefs, v. 15, p. 21-41.

Thorhaug, A., Roessler, M.A., Tabb, D.C., 1976, Man’s impact on 

the biology of Biscayne Bay: University of Miami Symposium 

“Biscayne Bay: Past/Present/Future,” April 2-3.

Tilmant, J.T., Curry, R.W., Jones, J., Szmant, A., Zieman, J.C., Flora, 

M., Robblee, M.B., Smith, D., Snow, R.W., and Wanless, H., 1994, 

Hurricane Andrew’s effects on marine resources: BioScience, 

v. 44, no. 4, p. 230-237.

Tougas, J.I., and Porter, J.W., 2002, Differential coral recruitment 

patterns in the Florida Keys, in Porter, J.W., and Porter, K.G., 

eds., The Florida Everglades, Florida Bay, and Coral Reefs of the 

Florida Keys—An Ecosystem Sourcebook: Boca Raton, Fla., CRC 

Press, p. 789-811.

U.S. Census Bureau, 2000, Time series of Florida intercensal population estimates by county: April 1, 1990 to April 1, 2000: [accessed 

July 1, 2007] http://www.census.gov/popest/archives/2000s/

vintage_2001/CO-EST2001-12/CO-EST2001-12-12.html

Vacher, H.L., and Mylroie, J.E., 2002, Eogenetic karst from the 

perspective of an equivalent porous medium: Carbonates and 

Evaporites, v. 17, no. 2, p. 182-196.

Wilsnack, M.M., Welter, D.E., Nair, S.K., Montoya, A.M., and others, 2000, North Miami-Dade County ground-water flow model: 

West Palm Beach, Florida, South Florida Water Management 

District, Hydrologic Systems Modeling Division, 40 p.

Wingard, G.L., 2004, Changing salinity patterns in Biscayne Bay, 

Florida: U.S. Geological Survey Fact Sheet 2004-3108, 4 p.

Wingard, G.L., Cronin, T.M., Dwyer, G.S., and others, 2003, 

Ecosystem history of southern and central Biscayne Bay: 

Summary report on sediment core analyses: U.S. Geological 

Survey Open-File Report 03-375, 110 p. 

Wingard, G.L., Cronin, T.M., Holmes, C.W., and others, 2004, 

Ecosystem history of southern and central Biscayne Bay: 

Summary report on sediment core analyses—Year two: U.S. 

Geological Survey Open-File Report 2004-1312, 117 p.