U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2004–3108

October 2004

Prepared in cooperation with

South Florida Water Management District and

Biscayne National Park

Changing Salinity Patterns in Biscayne Bay, Florida

Printed on recycled paper

Introduction

Biscayne Bay, Fla., is a 428-square-mile (1,109-square-kilometer) subtropical estuarine ecosystem that includes Biscayne 

National Park, the largest marine park in the U.S. national park 

system (fig. 1). The 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 pristine waters of the bay supported abundant and diverse fauna and flora, and the bay was a 

nursery for the adjacent coral-reef and marine ecosystems.

In the 20th century, urbanization of the Miami-Dade County 

area profoundly affected the environment of the bay. Construction 

of powerplants, water-treatment plants, and solid-waste sites and 

large-scale development along the shoreline stressed the ecosystem. 

Biscayne National Monument was established in 1968 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). The monument was enlarged in 1980 

and designated a national park.

Water Control—An Altered System

As the population of South Florida grew during the 20th 

century, demands increased for protection from seasonal flooding 

and for water for human consumption and for agriculture. These 

demands led to the construction of extensive water-control structures throughout South Florida, most notably by the Central and 

Southern Florida (C&SF) Project. The C&SF Project, authorized 

by Congress in 1948, altered the seasonal delivery of freshwater 

and thus affected the wetlands, estuaries, and coastal environments 

of South Florida, including Biscayne Bay.

During the 1980s and 1990s, momentum built for restoration of 

more natural flows to the fragile environments of South Florida, 

leading to the approval of the Comprehensive Everglades Restoration Plan (CERP) as part of the Water Resources Development Act 

of 2000. The primary goal of the CERP is to restore the timing, 

quantity, quality, and distribution of freshwater so that the ecosystem conditions approximate predevelopment conditions as closely 

as possible.

Objectives

Before restoration can occur, baseline conditions of the environment prior to significant human alteration must be established, 

and the range of variation within the natural system must be determined. Natural ecosystems evolve over time, and so it is important 

to understand what portion of present-day change is due to human 

activity and what portion is due to natural variations. For example, 

what role has climate change or sea-level rise played in shaping 

Biscayne Bay as it exists today? 

Research for the U.S. Geological Survey’s (USGS) Ecosystem 

History of Biscayne Bay Project has two objectives—to examine 

historical changes in the ecosystem at selected sites on a decadal to 

centennial scale and to correlate these changes with natural events 

and anthropogenic alterations in the South Florida region. Emphasis is placed on historical changes to amount, timing, and sources 

of freshwater influx and the resulting effects on salinity and water 

quality. By reconstructing the patterns of change prior to significant 

alteration of the environment, we can predict what the environment 

would have looked like without human alteration and can estimate 

what portion of change may be related to human activity. The 

results of this work are providing restoration planners with information on the predevelopment conditions of Biscayne Bay and will 

allow them to set realistic targets for restoration.

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Figure 1. Satellite image map of Biscayne Bay, Fla., showing sites where 

USGS cores were collected and the boundary of Biscayne National Park 

(blue dashed line). Image cropped from John W. Jones, Jean-Claude 

Thomas, and Gregory B. Desmond, 2001, South Florida Everglades satellite 

image map: USGS Miscellaneous Investigations Series Map I–2742; see 

http://sofia.usgs.gov/projects/remote_sens/sflsatmap.html. 
Uncovering the History of an Ecosystem 

The history of an ecosystem is recorded in the sedimentary 

record—the sediments themselves and the faunal and floral 

remains in those sediments. Retrieving historical information 

recorded in sediments follows basic principles of geology (primarily the law of superposition and the principle of uniformity, that is, 

the present is the key to the past) and utilizes many paleoecological and geochemical tools.

USGS cores are collected from areas within a South Florida 

ecosystem that have sufficient sediment thickness and as little 

bioturbation (digging and burrowing by animals), storm disruption, and erosion as possible. The cores are then X-rayed (fig. 2), 

described, and cut into 0.4- to 2-inch-thick (1- to 5-centimeterthick) samples. Age models are developed for the cores by using 

radiogenic isotopes of lead and carbon. Additional information on 

sample ages comes from the first occurrence of Australian pine 

pollen (Casuarina) in a core. Australian pine is an exotic species introduced to South Florida around the beginning of the 20th 

century, and it provides an excellent stratigraphic marker for the 

early 1900s.

In order to determine past changes in salinity, the core samples 

undergo analyses for plant and animal assemblages and for shell 

biochemistry. The key to both types of analyses is to study and 

understand the ecology of the living organisms in South Florida. 

Figure 3 illustrates how this process works for assemblage analyses. If we understand how and under what conditions a plant or 

animal lives today, then we can extrapolate that information to 

interpret past environments. Studies of living animals and plants in 

the estuaries of South Florida have been conducted since 1995. Part 

of this modern dataset includes information on salinity preferences 

of animals, which we assume remain consistent over time. Thus, 

when we find remains of animals in our core samples that are the 

same animals studied in the modern environment, we can estimate 

the range of salinity that existed when they were alive.

The biochemical analyses work in much the same way. Organisms having calcareous (CaCO3

) skeletons record information 

about the water in which they secrete their skeletons. The metal/

calcium ratios of shells from microscopic invertebrates (ostracodes) have been calibrated to salinity in the modern environment, 

and so these ratios can be calculated for ostracodes from core 

samples and a salinity value derived. (See box for an explanation 

of salinity values.)

The results of the assemblage analyses are plotted as the percent abundance of key indicator groups in each sample in the core 

(figs. 4 and 5). These plots give a picture of the changes throughout the time of deposition of the core. By examining a number of 

different indicators from each core, we increase our confidence in 

our interpretations, and we provide a more detailed description of 

what the past environment was like.

Changes in Biscayne Bay Salinity

Cores from nine sites in Biscayne Bay (fig. 1) have been 

analyzed. These analyses are described in the reports listed in the 

references box. The results indicate that the Biscayne Bay ecosystem has undergone many significant changes over the last 100 to 

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 due to its enclosed configuration 

(see fig. 1). Currently, this area is less influenced by the urbanization that has taken place to the north, and there are few developed 

areas along the shoreline. Despite this relative isolation, the area 

has undergone distinctive changes 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. At Card 

Bank, the salinity historically has shown rather large variations on 

multidecadal and centennial time scales relative to those seen at 

central Biscayne Bay sites, but marine influence at Card Bank has 

increased over the last century. The salinity of Middle Key basin 

has increased steadily since before 1900 (fig. 4).

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Figure 2. X-radiographs and schematic sections of the top 80 cm of 

USGS cores collected from Featherbed Bank, Biscayne Bay, Fla., in 

2002. Scale is in centimeters. X-radiographs were done compliments 

of Mariners Hospital, Tavernier, Fla. Schematic drawings show occurrence of laminations and remains of plants and shells. 

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The mudbanks of central Biscayne Bay have become increasingly marine and increasingly stable (less fluctuation in salinity) 

during the last 100 years (fig. 5). No indications of interdecadal 

salinity extremes or periods of hypersalinity have been found 

in cores from Featherbed and No Name Banks. The salinity has 

ranged from estuarine to marine (polyhaline to euhaline; see box) 

throughout the period recorded in the sediment cores.

The nearshore cores from north of Black Point and Chicken 

Key have 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. In the last 20 to 30 years, salinity at both sites has 

increased to polyhaline conditions, and there is evidence of an 

increase in salinity fluctuations during the same time period.

Implications for Restoration

One overwhelming trend emerges from the analyses of all the 

cores examined—increasing salinity in the Biscayne Bay system. 

Although the timing of the onset of increased salinity varies at the 

different core sites, there are no exceptions to this trend. In the 

nearshore sites, the increase in average salinity has been accompanied by an increase in variability of salinity. In contrast, the central 

Biscayne Bay sites have shown increasingly stable salinity over the 

last century and indications of increasing marine influence. These 

trends could be a result of rising sea level, of changes to the natural 

flow of freshwater, or both, but the timing of changes at some of 

the nearshore sites suggests that both factors are involved.

These results have significant 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 set by CERP) and targets for the nearshore 

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 set performance measures, to predict system response to 

changes invoked by restoration efforts, and to enlighten the public 

on what the natural system of the bay looked like prior to significant human alteration of the environment.

Acknowledgments

This project has been jointly funded by the South Florida Water 

Management District and the U.S. Geological Survey Priority Ecosystems Studies Program. The work has been done in cooperation 

with Biscayne National Park.

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Figure 3. Diagram showing how information on modern conditions is used to interpret the historical environmental conditions from the remains 

of plants and animals found in cores collected from the study area.
For additional information on ecosystem history research in 

South Florida, refer to:

http://sofia.usgs.gov/flaecohist/

Figure 4. Key molluscan salinity indicators in Middle Key core from 

nearshore area of Barnes Sound. Percent abundances of indicator 

species in core segments are plotted against depth (in centimeters) 

on the left and approximate calendar year on the right. Red arrows 

track increased numbers of estuarine species. Black arrow shows 

decreasing influx of freshwater species. Combined the indicators show 

a steady increase in salinity upwards in the core and decreasing influx 

from freshwater and terrestrial environments.

Figure 5. Key salinity indicators in No Name Bank core from central 

Biscayne Bay. Percent abundances of indicator species in core segments and magnesium/calcium (Mg/Ca) ratios derived from ostracode 

shells are plotted against depth (in centimeters) on the left and calendar year on the right. Red arrows track increased numbers of marine 

species, indicating increasingly marine and increasingly stable salinity. 

Black arrows highlight decreasing numbers of species that thrive in 

fluctuating salinity. Red dashed line shows a shift in the Mg/Ca ratio of 

ostracode shells (a proxy for salinity) from more fluctuating salinity to 

more stable salinity in the upper part of the core.

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Ishman, S.E., Cronin, T.M., Brewster-Wingard, G.L., Willard, 

D.A., and Verardo, D.J., 1998, A record of ecosystem change, 

Manatee Bay, Barnes Sound, Florida: Journal of Coastal 

Research, v. 26, p. 125–138.

Stone, J.R., Cronin, T.M., Brewster-Wingard, G.L., Ishman, S.E., 

Wardlaw, B.R., and Holmes, C.W., 2000, A paleoecologic 

reconstruction of the history of Featherbed Bank, Biscayne 

National Park, Biscayne Bay, Florida: U.S. Geological Survey Open-File Report 00–191, 41 p., available online at 

http://pubs.usgs.gov/openfile/of00-191/

Wingard, G.L., Cronin, T.M., Dwyer, G.S., Ishman, S.E., Willard, 

D.A., Holmes, C.W., Bernhardt, C.E., Williams, C.P., Marot, 

M.E., Murray, J.B., Stamm, R.G., Murray, J.H., and Budet, C., 

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., available online at 

http://pubs.usgs.gov/of/2003/of03-375/

Wingard, G.L., Cronin, T.M., Holmes, C.W., Willard, D.A., Dwyer, 

G.S., Ishman, S.E., Orem, W., Williams, C.P., Albietz, J., Bernhardt, C.E., Budet, C., Landacre, B., Lerch, T., Marot, M.E., and 

Ortiz, R., 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, 101 

p., available online at http://pubs.usgs.gov/of/2004/1312/

References on Biscayne Bay Ecosystem History

For further information, please contact:

G. Lynn Wingard

U.S. Geological Survey

926A National Center

Reston, VA 20192

Telephone: 703–648–5352

E-mail: lwingard@usgs.gov