USGS Open-File Report 00–164

Reefs, Corals, and Carbonate Sands:
Guides to Reef-Ecosystem Health and Environments
ENVIRONMENTAL QUALITY AND PRESERVATION—

A healthy reef ecosystem builds a
protective offshore barrier to
catastrophic wave action and storm
surges generated by tropical storms
and hurricanes.
Introduction
In recent years, the health of the
entire coral reef ecosystem that lines
the outer shelf off the Florida Keys
has declined markedly. In particular,
loss of those coral species that
are the building blocks of solid reef
framework has significant negative
implications for economic vitality of
the region. What are the reasons for
this decline? Is it due to natural
change, or are human activities (recreational
diving, ship groundings,
farmland runoff, nutrient influx,
air-borne contaminants, groundwater
pollutants) a contributing factor
and if so, to what extent? At risk
of loss are biologic resources of the
reefs, including habitats for endangered
species in shoreline mangroves,
productive marine and wetland
nurseries, and economic fisheries.
A healthy reef ecosystem builds
a protective offshore barrier to catastrophic
wave action and storm
surges generated by tropical storms
and hurricanes. In turn, a healthy
reef protects the homes, marinas,
and infrastructure on the Florida
Keys that have been designed to
capture a lucrative tourism industry.
A healthy reef ecosystem also protects
inland agricultural and livestock
areas of South Florida whose
produce and meat feed much of the
United States and other parts of the
world.
In cooperation with the National
Oceanic and Atmospheric Administration’s
(NOAA) National Marine
Sanctuary Program, the U.S. Geological
Survey (USGS) continues longterm
investigations of factors that may
affect Florida’s reefs. One of the first
steps in distinguishing between natural
change and the effects of human
activities, however, is to determine
how coral reefs have responded to
past environmental change, before the
advent of man. By so doing, accurate
scientific information becomes available
for Marine Sanctuary management
to understand natural change and
thus to assess and regulate potential
human impact better. The USGS studies
described here evaluate the distribution
(location) and historic vitality
(thickness) of Holocene reefs in South
Florida, relative to type of underlying
bedrock morphology, and their varied
natural response to rising sea level.
These studies also assess movement
and accumulation of sands, relative
to direction of prevailing energy, and
origin of the component sand grains.
Geophysical data collected with highresolution
sound-wave instruments
that provide pictures of the sediment
and bedrock are used to interpret
sediment thickness. Reef thickness is
determined by collecting limestone
rock cores by drilling. Drill cores
through reefs are used to identify the
coral species that built them and to
determine how reefs reacted to rising
sea level. These data are supplemented
by using isotope-dating techniques to
derive the carbon-14 (C14) age of the
corals and mangrove peat in the cores.
Mangrove peat forms in very shallow
water and at the shoreline but is found
today buried beneath offshore reefs.

Aerial photograph of spurs and grooves at Sand Key Reef, located southwest of Key West, Florida. Spurs and
grooves are oriented perpendicular to incoming waves. Spurs are approximately 6 m (20 ft) wide.

Background Information
Geologic time is classified into
various categories, one of which is an
epoch. The Pleistocene Epoch spanned
time from ~1.77 million (1.77 Ma)
to 10,000 years ago (10 ka) and was
a period of alternating glacial and
interglacial stages with corresponding
rapidly fluctuating high-amplitude sea
levels. The last glacial interval, or
Ice Age, occurred at the end of the
Pleistocene when sea level is believed
to have been more than 130 meters
below present (1 m = 3.281 feet).
The Holocene Epoch followed, beginning
about 10 ka, and extends to the
present. The first ~3,000 years of the
Holocene were marked by a period
of rapidly melting Ice Age glaciers
and warming oceans. The rapidity at
which these events occurred caused an
initial rapid rise in the most recent
sea-level fluctuation. Sea-level curves
derived from isotope dating of corals
and mangrove peat relative to their
locations below present sea level indicate
that the rapid rate of Holocene
sea-level rise began to slow about 7
ka.
In South Florida, the bedrock
beneath the Florida Keys and reef
tract is Pleistocene. Some Pleistocene
reefs in Florida are as much as
30 m in height, 0.5 kilometer (1
km = 0.6214 mile) in breadth, and
extend the length of the reef tract,
indicating optimal environmental conditions
for coral growth during that
time. Pleistocene reefs are cumulative
in that they alternately grew, died
from exposure during lowstands of
sea level, and were re-colonized by
corals during the next rise in sea level.
By contrast, Holocene reefs flourished
continuously during the latest rise in
sea level and attained a maximum
of 16.8 m in thickness within 5,000
years, indicating that conditions for
coral growth then were also excellent.
C14 ages show that the reefs lived
from about 7 to 2 ka. The fact
that Holocene reefs are thinner than
Pleistocene reefs may seem at first
glance to be a reflection of comparatively
less time for development.
However, Holocene growth was constrained
primarily by a slowing of the
rate of sea-level rise that limited space
for upward expansion and, in Florida,
by flooding of the inner shelf at ~2
ka that created Florida and Biscayne
Bays. Rising sea level altered water
depth, which affected wave energy
and circulation and changed water
chemistry and temperature. Sea level
at 2 ka was ~0.5 m lower than
today, and tidal influx of deleterious
murky, nutrient-rich bay water and
cold Gulf of Mexico water to the clear
warm waters surrounding the reefs
had begun.
Environmental Signatures in Reefs,
Corals, and Carbonate Sands
By examining the evolutionary
geologic record of the reef-tract ecosystem,
we can understand what controls
where and why reefs grow.
Because coral larvae generally settle
on sites where the bottom is hard
and free of sediment, reefs began
growing on elevated bedrock. Sands,
which prevent reef establishment,
filled depressions. To grow, corals
require narrow conditions: relatively
shallow depths and normal salinity,
clear nutrient-poor water, and warm
temperatures. The primary control of
these conditions, in other words, reef
growth, is sea level. The primary control
of reef distribution is the availability
of a hard, elevated, sediment-free
surface, in other words, the landscape
or topography of the bedrock under
the reefs. In Florida, the bedrock surface
was dry land until about 7 to 6 ka
when the sea began to flood what is
now the reef tract.
Much can be learned about
Holocene reefs, corals, sediments, and
environments by core drilling through
the reefs. Coral-rock cores show that,
in general, the components of
Holocene topography mimic those of
the Pleistocene, i.e., Holocene reefs
began growth on top of Pleistocene
reefs, and uncemented Holocene sediments
overlie cemented Pleistocene
sediments. Some reef cores contain
mangrove peat at the bottom that
formed when the bedrock shelf surface
was exposed in the early
Holocene. Presence of peat offshore
indicates an earlier shoreline position
and a period of lower sea level. C14
dating of the peat tells us when the
old shoreline existed, and location of
the peat ‘x’ meters below present sea
level tells us the depth of the previous
shoreline relative to present sea level.
Reef Records
The Holocene coral species recovered
in cores are framework builders.
Many single cores from individual
reefs contain species of head corals
at the bottom and branching corals at
the top, indicating a change in environmental
conditions at that location
through time. An analysis of a number
of cores from transects across a reef
shows the same coral zones through
time and space, i.e., seaward headcoral
zones shifted landward to
branching-coral zones within the same
reef. The shift occurred as the reef
migrated or grew landward (called
backstepping) over carbonate sands
with rising sea level. In both examples,
the massive head corals grew
first, indicating that quiet-water conditions
(> 5 m) prevailed first.
Branching forms that prefer the surf
zone (< 5 m) then replaced the head
corals. C14 ages on both types of
corals give us the times in the area
where the cored reefs are located
when sea conditions were quiet and
then became high energy. The coral
zones developed in response to flooding
of Pleistocene-reef islands that
once lined the edge of the margin
during the early period of lower
Holocene sea level. The reef islands
had protected the head corals from
high-energy waves. Their submergence
removed that protection and
allowed the surf zone to move landward,
creating the high-energy environment
required by the branching
corals. Not all Holocene reefs were
able to keep pace with sea-level rise,
however. Those that did not survive
died because sea level rose too quickly
for them to maintain their ideal depth
and they slipped below their threshold.
Holocene corals also built magnificent
spurs and grooves on windward
sides of reefs. The spurs thrived
until the corals became overcrowded.
Constrained by position of overhead
sea level and presence of sand-filled
grooves at either side, the corals eventually
succumbed for lack of space.
Few coral spurs are actively accreting
today.
C14 age dates from corals at
the outer-shelf margin show that
Holocene reefs began growing sooner
off the lower Keys than off the upper
Keys, a result of earlier shelf flooding
because of lower bedrock elevation
to the southwest. However, Holocene
reefs lived longer off the upper Keys
than off the lower Keys, a result
of later flooding and protection from
adverse oceanic elements by the
Pleistocene-reef islands at the margin.

Healthy ecosystem components—head and branching
reef-building corals in clear Florida water in
1971. Tiny coral polyps, soft-bodied animals living
in colonies like bees, build coral reefs. Each polyp
constructs an outer skeleton of hard limestone that
adds a new layer to the reef. Diameter of head coral
is approximately 0.7 m.

Today, outer-shelf reefs off the upper
Keys are protected by the linear island
of Key Largo not from high wave
energies but from the turbid nutrientladen
water of Florida Bay (Plate 1).
Reefs less than 2 ka are very thin,
indicating that conditions for coral
growth in more recent times were
not as good as those in the earlier
Holocene. In modern times as recently
as in the 1960s, Holocene reefs supported
actively accreting corals to
some degree. Very few such reefs are
alive today and those that are, are in
very poor condition.
One of the best places to see
inside a fossil reef is at the old quarry
at Windley Key Fossil Reef State Park
on Windley Key in the middle Keys
(Plate 1). The coral species comprising
the emergent Pleistocene reef are
the massive framework-building head
corals that live in low-energy conditions.
The corals in this reef indicate
that sea level was too high for a surf
zone to have existed where they grew.
It is commonly believed that sea level
at that time, 125 ka, was 7.6 m higher
than at present, and it is known that
sea level has not been as high since
then.

Coral Records
Individual corals also contain
environmental signatures—within
annual growth bands. Coral growth
bands are like tree rings and are visible,
just like bone structures in dental
or medical x-rays, when the coral core
is cut into slabs and x-rayed. In a core
from a live coral, growth bands can be
counted back from the surface beginning
with the year of coring to obtain
the age at the bottom. Some growth
bands are wider than others and are
called stress bands. They indicate a
period during deposition of the annual
band when water temperatures were
unusually warm or cold. Some bands
fluoresce under ultraviolet light in
response to an infusion of humic acids
that became bonded to the skeleton.
Fluorescent humic acids are a component
of fresh water. Thus, presence of
a fluorescent coral band indicates a
period of high freshwater influx onto
the reef during deposition of the band.
The study of annual coral growth
bands is called sclerochronology.
Records in Carbonate Sands
Finally, even the coarse- and finegrained
carbonate sands that line the
reef tract contain environmental signatures.
Sands record geologic pro-
cesses. For example, seismic profiles
across a submerged terrace off the
northeastern part of the shelf margin
show linear low-elevation features
believed to be incipient reefs that have
been buried by sediment. Their burial
indicates that prevailing energy there
during the Pleistocene was onshore
as it is today and that during a lowstand
in sea level, winds and waves
along that part of the terrace washed
sands landward. Along the southwestern
part of the terrace, however, essentially
sediment-free backreef troughs
behind immense linear reefs indicate
longshore energy and sand transport.
It is just this longshore sand-transport
direction, parallel to the reefs and
arc-shaped margin, that kept young
incipient reefs there sediment free and
allowed corals to re-colonize the hard
reef surfaces and to build extensive
reef ridges during the repeated rises
in Pleistocene sea level. Other types
of sedimentary processes are observed
on the roughly rectangular sand-covered
Marquesas-Quicksands ridge farther
west in the Gulf of Mexico. The
ridge is ~10 m higher in elevation
than the surrounding shelf and is
thus isolated from sand importation.
Five processes occur on the ridge. (1)
Sands are produced in place (geological
source) by the dominant organisms,
several species of a calcareous
green alga (biological origin). (2) The
sands are molded into prominent tidal
bars and sand waves that lie directly
on bedrock, which are evidence of the
strength and direction of current flow
across the ridge. (3) The sands fill
shallow (~3 m) bedrock lows on the
ridge and (4) accrete behind bedrock
highs such as at Halfmoon Shoal, a
response to underlying bedrock topography.
In time, (5) they are swept
westward and off the ridge by the
currents, as shown in seismic profiles
of westward-dipping bedforms at the
west edge of the ridge. The Quicksands
are so named, even on navigational
charts, because the sands are
always in motion.
Sands also record the types of
organisms in the reef tract, and in the
case of corals, sand analysis reveals
whether they are healthy. Carbonate
sediments in reef ecosystems consist
of skeletal remains of the biota that
inhabit the reef. Thus, they contain
a record of change in biota through
space (laterally) and time (vertically,
through sediment cores), and through
these biotic changes the sands reflect
corresponding changes in the environment.
Hence, sands in a reef ecosys-
tem are bioindicators of the health of
the reef community and the quality
of environmental conditions. Plastic impregnated
thin sections of sediment
samples are used to identify and count
grains under a microscope.
Sand-grain analyses conducted in
1963 and in 1989 showed that a
significant increase in coral grains
occurred in surface sands in areas off
the middle and lower Keys over those
26 years. The increase correlates with
an observed increase in nutrient influx
and decline in coral reef health in the
same areas and time. In other words,
much higher percentages of coral fragments
occur in areas where there are
diseased and dead corals than in areas
where corals are healthy. The reason
is twofold: algae grow on dead coral
surfaces, attracting grazers, and bioerosion
of dead skeletal material—
yet two more processes indicated by
the sands, these biologic—is associated
with organisms that break down
dead coral. Fish bite off attached
algae along with bits of skeletal coral,
herbivorous sea urchins graze, and
sponges, algae, fungi, barnacles, and
bivalves bore into the coralline rock.
Parrotfish and boring sponges are the
major bioeroders. The same studies
showed an increase in grains of a
calcareous green alga in areas off
the upper Keys. Proliferation of calcareous
algae (preservable as sand
grains) and fleshy red, blue, green,
and brown algae (non-preservable)
is also commensurate with increased
nutrient supply and a declining ecosystem.
Increases in both coral and
algal sand grains and in observed
growth of fleshy algae correlate with
a conceptual model that shows the
effects of increasing nutrients on
organisms that comprise the bottom-dwelling
population in a reef ecosystem
and how that population will
change. Is the nutrient influx natural,
or is it the result of human activities?
The USGS studies described here provide
part of the scientific background
needed before these questions can be
answered—an understanding of natural
changes within past ecosystems.

Left (photo): X-radiograph of slabbed core from a species
of head coral (Montastrea annularis) at Hen and
Chickens Reef showing white annual growth bands.
Note wide abnormal stress band deposited in the
coral skeleton as a response to unusually cold water
temperatures during the winter of 1941-42. The live
head coral was sampled in the spring after deposition
of the 1955-56 annual band. See Plate 1 for location
of Hen and Chickens Reef. Approximate vertical
distance between annual bands is 1 cm.

Above (photo): X-radiographs showing correlation of banding
in seven different Montastrea annularis coral
heads at Hen and Chickens Reef. Four at left are
from heads killed by cold in the winter of 1969-70.
Three at right are from corals that were alive and
healthy when sampled in September 1974. Topmost
right-hand stress bands joined by bold line correlate
with time of demise of corals in left x-radiographs.
Stress band for 1941-42 in five left x-radiographs
indicates that conditions were equally severe for
those five corals. Other minor stress bands occur
that are very faint or that do not correlate from coral
to coral. Normal annual bands are correlative among
all corals.

Plate 1. Index map showing tip of South Florida and Cape Sable, the Florida Keys, the
Marquesas Keys in the Gulf of Mexico, and a map of the thickness of Holocene reefs
and sediments that overlie Pleistocene bedrock along the shelf and margin. Colors
on the map represent different thicknesses ranging from bare rock (white) to thinnest
(pale pinks) to thicker (dark reds) to thickest (rust). Linear white area in seaward
part of map denotes bare rock on seaward side of a Pleistocene reef that forms the
shelf margin. A submerged terrace lies at the toe of this reef. In general, the map
shows that most of the sediments on the shelf and on the submerged terrace are ~3
m thick. Areas of thinnest coverage occur along the inner shelf, on the landward side
of Hawk Channel (major bedrock depression between the Keys and shelf margin), and
on the Marquesas-Quicksands ridge. Deep water on three sides of the ridge and a
current-swept, sediment-free channel on the east side indicate that ridge sediments
are formed in place. Note the Marquesas Keys formed in a shallow, nearly circular
bedrock depression that also contains ~3 m of sediment, determined by probing
to bedrock with a rod. The thickest shelf accumulations occur in backreef troughs
behind the Pleistocene margin reef. Sediment is virtually nonexistent along a
submerged rock ledge bordering the south-southeast sides of the Keys and at the
seaward edge of the Pleistocene margin reef. The terrace outlier reefs are also
sediment free. The thickest (40+ m) sediment accumulation in the study area occurs
on the upper slope south of the Marquesas Keys in 80 to 190 m of water.
The Florida Keys are divided naturally by shape and composition. The upper and
middle Keys are composed of a long arc- shaped coral reef. Known as the Key Largo
Limestone, the reef parallels the shelf margin. The lower Keys consist of cemented
sandbars. Called the Miami Limestone, the bars formed more or less perpendicular to
the reef and margin. Both rock formations accumulated approximately 125 ka when
sea level was about 7.6 m higher than present.

Any loss of the economically viable
and physically essential coral reef
ecosystem would have significant,
potentially very dangerous economic,
health, and safety impacts on the
densely populated Florida Keys and
South Florida mainland.

References Cited in Text:
Lidz, B.H., 1997, Fragile Coral Reefs of the Florida
Keys: Preserving the Largest Reef Ecosystem in the
Continental U.S. U.S. Geological Survey Open-File
Report 97-453, 4 p., 1 Plate.
Lidz, B.H., 2000, Bedrock Beneath Reefs: the
Importance of Geology in Understanding Biological
Decline in a Modern Reef Ecosystem. U.S.
Geological Survey Open-File Report 00-046, 4 p., 1
Plate.
Lidz, B.H., (in prep.), Surface Features of the Florida
Keys and Reef Tract:
(1) North Key Largo to Vaca Key and The Elbow
Reef to Sombrero Reef,
(2) Vaca Key to Key West and Sombrero Reef
to Eastern Dry Docks,
(3) Key West to the Marquesas-Quicksands Ridge
and Eastern Dry Docks to Rebecca Shoal.

The USGS serves the nation by providing basic,
objective, and informative scientific knowledge
on Earth history and processes, and on human
impact on resources. Two of the most effective
ways are through descriptive and interpretive
maps and through the USGS marine homepage on
the world wide web at:
http://marine.usgs.gov.

This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey editorial standards or with the North American Stratigraphic Code. Reference therein to
any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or
favoring by the United States Government or any agency thereof.

Aerial photograph showing tidal bars and sand
waves near the west side of the Marquesas Keys.
Tidal bars are 1 m high and are oriented north/south
in response to strong north/south currents. Sand
waves on top of tidal bars are oriented perpendicular
to the bars and many sand waves are awash at
spring low tide. Dark areas are grass and various
species of a calcareous green alga. Distance across
photo is approximately 2.5 km.

Summary
The geologic record of the Florida
Keys reef tract is a rich archive
of evidence for numerous significant
past environmental changes. (1) Thick
cumulative Pleistocene and continuous
Holocene coral-growth records verify
previous existences of healthy reef
ecosystems and thus the optimal conditions
under which they grew. (2)
Dated mangrove peat found beneath
offshore reefs documents the times
and locations of earlier, seaward,
shorelines. (3) Landward reef migration
is evidence of rising sea level.
(4) Shifts from head-coral zones to
branching-coral zones within a reef
are signs of changing conditions from
quiet water to presence of surf and
are thus evidence for flooding of once
protective offshore reef islands. (5)
Annual stress bands in corals indicate
periods of severe water-temperature
changes, and fluorescent bands verify
weather variations that produced high
freshwater influx to the reef. (6)
Sands record geologic processes of
transport direction, scouring of backreef
troughs, in-place formation,
strength and direction of currents,
infilling of bedrock depressions, and
accretion behind bedrock highs, as
well as biologic processes of grazing
for algae and resultant bioerosion of
coral skeletons. (7) Sands are bioindicators
of the types of reef organisms
and the general health of corals
through space and time.
These geologic signatures are
guides to reef-ecosystem health and
environment and prove that conditions
have been both good and bad for
reef ecosystems in the past. Is the
fragile modern ecosystem undergoing
yet another natural decline, or are
human activities responsible or, at
the very least, an added component?
We cannot know without first understanding
the evolutionary history and
characteristics of ancient reefs, the
processes that produced or destroyed
them, and the responses they had
to environmental change. The reefs,
corals, and carbonate sands are far
more important than simply being
major components in a reef ecosystem.
Their history and what they can
tell us about past environmental conditions
comprise one of the baselines
from which understanding the decline
of the modern reef system must be
derived.

WAYS IN WHICH MAPPED BEDROCK, SEDIMENT, AND
SEAFLOOR INFORMATION BENEFIT THE ECOSYSTEM

Management Issues
1. Understanding the direct relation between geologic framework and biologic
resources, such as localization of biotic communities.
2. Understanding the direct relation between geologic framework and physical
processes, such as direction and rate of groundwater flow.
3. Understanding the direct relation between protective islands, open tidal
passes, and sources and effects of deleterious waters on reef vitality.
4. Understanding the direct relation between, and variety in, localized physical
environments and biological communities.
5. Understanding the relation between dominant organisms and dominant
sediment components and how changes in dominant sediment components
indicate changes in the biotic community.
6. Integrating scientific knowledge with resource-stewardship practices to
attain sustainable archeological, ecologic, and socioeconomic (tourism,
commercial fisheries) systems
7. Improving capabilities for restoration and preservation of each
ecosystem component
8. Predicting variability and evaluating effects of coastal processes and
ecosystem response to natural (rise/fall of sea level) and anthropogenic
(pollutants) influences
9. Educating the visiting public with accurate scientific knowledge of:
• how and why the many varieties of reef-tract resources exist
• how and why each type is an integral part of the ecosystem and
must be preserved
• how and why each can be damaged or destroyed and if destroyed,
how an out-of-balance ecosystem will respond
10. Assessing impacts on the ecosystem before issuing treasure-hunting permits
11. Informing politicians, the media and public visually and descriptively of
locations and types of various habitats and environments prior to
on-site visits

Ecosystem Issues
1. Mitigation of physical damages due to boat anchors, divers, or ship
groundings and choice of the best and most effective type of restoration—
by transplanting live corals directly onto elevated bare rock or onto
prefabricated cement substrates placed in sandy areas.
2. Mitigation of sewage-disposal practices—by changing cesspools and
shallow injection wells that empty into porous rock to wastewater-treatment
plants and requiring holding tanks on boats
3. Mitigation of abnormal Everglades drainage—by removing levees and
canals to restore natural water flow
4. Mitigation of runoff pollution—by reducing use of fertilizers and chemicals
in inland farmlands
5. Siting and choice of equipment for installing fixed navigational structures
and lighthouses (i.e., in barren sand holes or on bare bedrock)
6. Siting of mooring-buoy anchorages (i.e., in barren sand holes surrounded
by live-rock habitats)
7. Siting and choice of equipment for maintaining dredged channels and
digging trenches for stormwater drainage pipes (i.e., sand removal with
minimal siltation and turbidity)
8. Siting of areas least susceptible to pollution and turbidity for transplanting
corals and sea grasses, such as areas where sediment is thick or thin,
sand or mud, or where the porous limestone is coated with caprock (i.e.,
thin sand or bare rock allow potentially contaminated ground waters to
reach surface waters and reefs; areas of thick sand or mud or caprock
form impervious aquicludes)

Systematic shelf-wide USGS mapping of sediment-constituent
grains (Lidz, 1997), bedrock topography (Lidz, 2000), reef and
sediment thickness (this report), and seabed features
and bottom environments (three reports, in prep.) aids both
Sanctuary management-policy and ecosystem issues.

For more information,
please contact:
Barbara H. Lidz
U. S. Geological Survey
600 4th Street South
St. Petersburg, FL 33701
phone: 727-803-8747 x3031
fax: 727-803-2030
blidz@usgs.gov

This report is preliminary and has not been reviewed for
conformity with U.S. Geological Survey editorial standards
or with the North American Stratigraphic Code. Reference
therein to any specific commercial product, process, or
service by trade name, trademark, manufacturer, or otherwise
does not necessarily constitute or imply its endorsement, recommendation,
or favoring by the United States Government
or any agency thereof.