Geophysical Mapping of Oyster Habitats in a Shallow 

Estuary; Apalachicola Bay, Florida 

By David C. Twichell1, Brian D. Andrews1, H. Lee Edmiston2, and William R. Stevenson3 

1 U.S. Geological Survey, Woods Hole, Coastal and Marine Geology Program, Massachusetts 02543 

2 Apalachicola NERR/FDEP, 261 7th Street, Apalachicola, Florida 32320 

3 NOAA Coastal Services Center, 2234 South Hobson Avenue, Charleston, South Carolina 29405

U.S. Geological Survey Open-File Report 2006-1381 

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 2007 

For product and ordering information: 

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its natural and living resources, natural hazards, and the environment: 

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Suggested citation: 

Twichell, D.C., Andrews, B.D., Edmiston, H.L. and Stevenson, W.R., 2007, Geophysical mapping 

of oyster habitats in a shallow estuary, Apalachicola Bay, Florida: U.S. Geological Survey 

Open-File Report 2006-1381, DVD-ROM. Also available online at 

http://pubs.usgs.gov/of/2006/1381/. 

For information, contact dtwichell@usgs.gov. 

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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 material contained within this report. 

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iii

Contents 

Contents ..............................................................................................................................................................................iii

Section 1: Introduction ......................................................................................................................................................1

Section 2: Data Collection and Processing....................................................................................................................1

Survey Platforms.............................................................................................................................................................1

Bathymetric Data............................................................................................................................................................2

Sidescan-Sonar Imagery...............................................................................................................................................3

Seismic-Reflection Data................................................................................................................................................3

Section 3: Preliminary Geologic Interpretation.............................................................................................................4

Setting...............................................................................................................................................................................4

Estuary-Floor Morphology ............................................................................................................................................4

Subsurface Geology.......................................................................................................................................................6

Geologic Controls on Oyster Bed Distribution...........................................................................................................7

Summary...........................................................................................................................................................................7

Section 4: References........................................................................................................................................................8

Section 5: Maps ..................................................................................................................................................................9

Spatial Data .......................................................................................................................................................................10

Data Catalog ..................................................................................................................................................................11

Raster Data-...................................................................................................................................................................12

Acknowledgments............................................................................................................................................................15

Figures 1-19........................................................................................................................................................................16
Geophysical Mapping of Oyster Habitats in a Shallow 

Estuary; Apalachicola Bay, Florida 

by David C. Twichell, Brian D. Andrews, H. Lee Edmiston, and William R. Stevenson 

Section 1: Introduction

This report presents high-resolution geophysical data, interpretive maps, and a preliminary 

discussion about the oyster habitat and estuary-floor geology within Apalachicola Bay, Florida (fig. 

1). During two research cruises, conducted in 2005 and 2006, approximately 230 km2 of the bay 

floor were surveyed using interferometric-bathymetry, sidescan-sonar, and chirp seismic-reflection 

techniques. The research was conducted as part of a cooperative program between the U.S. 

Geological Survey (USGS), the National Oceanic and Atmospheric Administration Coastal 

Services Center (CSC), and the Apalachicola Bay National Estuarine Research Reserve. The 

Apalachicola Bay National Estuarine Research Reserve was established in 1979 to provide 

opportunities for long-term monitoring and research to provide a basis for more informed coastal 

management decisions for this estuary. 

Apalachicola Bay is the largest oyster fishery in Florida (Whitfield and Beaumariage, 

1977), and the primary objective of this program is to develop a suite of maps that define oyster 

habitat distribution and estuary-floor geology within the bay. The resulting maps will assist in 

effective management of oyster resources and provide a reference geologic framework for future 

scientific and applied research. 

Section 2: Data Collection and Processing 

Survey Platforms 

Two survey platforms were used to collect geophysical data in Apalachicola Bay (fig. 2). 

The RV Rafael, a 6.3 m outboard motor propelled vessel with an ~ 1.5 m draft, was used to survey 

sections of the bay where water depths exceeded 2 m. An Autonomous Surface Vehicle (ASV), 

IRIS, was used to survey sections of the bay where water depths were between 0.75 and 2 m. ASV 

IRIS is a 2-m long, battery powered remote vehicle that surveys pre-programmed tracklines. 

Bathymetric, sidescan-sonar, seismic-reflection, and navigation data were all collected from both 

platforms. 

1
Bathymetric Data 

Aboard the RV Rafael, an SEA Submetrix 2000 Series interferometric sonar, operating at a 

frequency of 234 kHz, was used to collect bathymetric data along survey track lines spaced ~ 100 

m apart (fig. 3). The instrument was mounted on a rigid pole at the bow of the vessel, and was 

deployed 1 m below the water surface. A GPS antenna was mounted on top of the pole over the 

sonar head to record ship position during the surveys. The interferometric-sonar system has two 

channels that collect depth data in a continuous swath on both sides of the vessel. The width of the 

swath was generally 7-10 times the water depth. For example, in water depths of 3 m, the 

interferometric sonar can achieve a 15 m range to each side of the ship's track, or 30 m total swath 

width. Within Apalachicola Bay, swath widths were generally between 20 and 40 m. 

Single-beam bathymetry was derived from chirp, seismic-reflection profiles collected by 

ASV IRIS along track lines that were spaced ~ 75 m apart (fig. 3). The bay floor along each chirp 

profile was digitized and sampled at 50 shot intervals, or approximately every 3-5 m along the 

survey track, depending on vessel speed. Depths were digitized in two-way travel times and 

converted to depths in meters using a velocity of sound in water of 1500 m/s, and exported as XYZ 

soundings. 

On both vessels, motion (heave, pitch, roll, and yaw) was recorded with a TSS DMS 2-05 

Attitude Sensor. Aboard the RV Rafael, the sensor was mounted immediately above the SEA 

Submetrix 2000 Series transducers, and on ASV IRIS it was mounted on the mast at the center of 

the vessel. Navigation was recorded using Real Time Kinematic Differential Global Positioning 

System (RTK-DGPS). The interferometric sonar is an angle-measuring system; depth accuracy 

decreases with increasing horizontal range. The combined angular accuracy of the SEA Submetrix 

2000 Series and the TSS DMS 2-05 attitude sensor is documented as 0.1 degrees. Assuming 

constant angular accuracy, and using the International Hydrographic Organization (IHO, 

http://www.iho.shom.fr/) standard requirement of 0.3 m accuracy in < 30 m water depth, all data 

collected during the two surveys fall within the IHO accuracy standards. However, vertical 

accuracy is also directly affected by the accuracy of navigation data and tidal measurements. RTKDGPS vertical accuracy is assumed to be 0.05 to 0.1 m. 

The real-time RTK setup included a reference base station on St. George Island and a radio 

repeater on the highest section of the Bryan Patton Bridge to ensure complete area coverage. The 

GPS reference station was established on St. George Island using a 3 day average of positions from 

six 12 hour datasets. The positions were calculated for these datasets using the Online Position 

Service (OPUS) provided by the National Geodetic Service 

(http://www.ngs.noaa.gov/OPUS/What_is_OPUS.html). The GPS-RTK vertical was calibrated to 

the tidal benchmark MLLW at the Apalachicola River Station ID 8728690. 

Seamless bathymetric coverage for the entire survey area was not feasible, due to the bay's 

relatively shallow nature and time constraints. Instead, survey lines were designed to provide 100% 

coverage with sidescan-sonar data, but using the wider swath of the sidescan-sonar coverage 

resulted in gaps between adjacent interferometric bathymetry swaths. Data gap widths varied as a 

function of water depth. In the deepest portion of the survey area, near West Pass, data gaps were 

10-20 m, and in the shallowest section, south of the town of Apalachicola, data gaps were ~ 80 m 

(fig. 3). Swath data were processed and gridded using Linux-based SwathEd software (UNB, 

2005). The bathymetric data have a vertical resolution of approximately 1% of water depth. The 

final swath bathymetric grid was produced using a 2 m/pixel resolution, and delivered as a 

GeoTIFF raster image. 

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Swath and single-beam bathymetric data were used as inputs for a regional bathymetric 

model that provided 100% coverage of the area through interpolation (fig. 4 and Mapsheet 1). 

Production of the model required three processing steps. First, a Triangulated Irregular Network 

(TIN) model was generated using the track-line swath (5 m cell size, including interline gaps), and 

single-beam (derived from ASV IRIS seismic-reflection profiles) bathymetric data. Second, the TIN 

model was converted to a 25 m cell-size raster grid using the Natural Neighbors method. Finally, a 

low-pass, 3 x 3 filter was applied to smooth irregular features within the 25 m grid. Complete 

details of these methods are described in the raster metadata in Section 5. 

Sidescan-Sonar Imagery 

Acoustic backscatter data were collected using two sidescan-sonar systems. A Klein 3000 

dual-frequency (100/400 kHz) sidescan sonar was deployed from RV Rafael, and towed alongside 

the vessel ~ 1 m below the surface. Track lines were spaced 100-125 m apart, and the sidescan 

swath was 75-100 m to each side of the track. ASV IRIS collected backscatter data with an Edgetech 

4200FS sidescan sonar. The sidescan transducers were mounted on a metal frame between the two 

pontoons ~ 0.5 m below the sea surface. The sidescan was set to image 50 m to each side of the 

track lines. 

Backscatter intensity, as recorded with sidescan sonar, is an acoustic measure of variations 

in the physical properties of the sea floor (fig. 5 and Mapsheet 2). Sidescan-sonar imagery was 

processed such that high backscatter (relatively strong acoustic returns) is represented by white, and 

low backscatter (relatively weak acoustic returns) is represented by black. In Apalachicola Bay, 

backscatter variability is generally caused by sea-floor roughness. Due to the low incidence angles 

associated with towed systems, topographic highs and lows can be interpreted based on acoustic 

shadows. 

All sidescan-sonar data were acquired using Triton-Elics ISIS acquisition software, and 

were processed using LINUX-based Xsonar/Showimage (Danforth 1997) to sub-sample the data to 

8-bit imagery, correct slant-range and beam-angle distortions, and remove striped noise. Sonar data 

from each survey line were mapped in geographic space with Xsonar, using a 1-m pixel resolution, 

then imported as raw image files to PCI Geomatics GCPworks (PCI Geomatica version 8.2), where 

they were combined to create composite mosaics (Paskevich, 1996). The mosaic was exported as a 

GeoTIFF raster image for further analysis in ArcGIS (ESRI, Inc). 

Both 100 and 400 kHz data were collected with each sidescan-sonar system, but 100 kHz 

data were used for the final 1-m mosaic covering the main portion of the bay, surveyed by RV 

Rafael, because the lower frequency data contained less acoustic noise. The data collected from R/V 

Rafael is distributed in 3 images, separated by field season and variations in acquisition parameters. 

ASV IRIS acquired 15 survey days of backscatter data over the shallowest sections of the Bay, 

including known oyster bars (fig. 3). Mosaics of these data are distributed in 13 images, due to 

substantial geographic separation. The backscatter data collected with the ASV IRIS were processed 

using the same methods as the data collected from the RV Rafael, except the high frequency data 

(400 kHz) data were used and were mosaiced to a range of 20-30 meters to remove the noise in the 

far range of the data. 

Seismic-Reflection Data 

High-resolution, seismic-reflection profiles were collected from both the R/V Rafael and 

ASV IRIS along 2,372 km of track line, which were spaced ~ 75 - 100 m apart (fig. 3). During the 

first seven survey days of the 2005 cruise aboard the R/V Rafael (Julian Days 76-83), seismic data 

were acquired using a Knudsen 320b chirp system (3.5-12 kHz). The remaining seismic data, 

3
collected from both survey vessels during 2005 and 2006, were acquired using Edgetech FSSB 424 

(4-24 kHz) systems. The Knudsen was used initially because of easier side-mount deployment from 

R/V Rafael in shallow water environments. However, profile comparisons showed that the 

Edgetech FSSB-424 provided higher-quality data, so it was used throughout the subsequent survey 

periods. The seismic data from the R/V Rafael were acquired as SEG-Y files using Delph Seismic+ 

in 2005 and SBLogger in 2006. On ASV IRIS they were acquired as .jsf using jstar, and then 

converted to SEG-Y. All seismic data were processed using SIOSEIS (http://sioseis.ucsd.edu/) and 

Seismic Un*x (http://www.cwp.mines.edu/cwpcodes/) to produce jpg images of each of the seismic 

profiles. 

Section 3: Preliminary Geologic Interpretation 

Setting

Apalachicola Bay is a large estuary located along the coast of the Florida panhandle 

between Tallahassee and Pensacola (fig. 1). It is approximately 65 km long and 5.5 to 12 km wide, 

except at its western end, where it narrows to less than 2 km. The estuary is shallow, having a mean 

depth of 2 to 2.4 m. It is divided into four provinces: St. George Sound, Apalachicola Bay, East 

Bay, and St. Vincent Sound (fig. 1). The western end and southern side of the estuary are shielded 

from the open Gulf of Mexico by a string of barrier islands: Dog Island, St. George Island, Little St. 

George Island, and St. Vincent Island. The eastern end of the estuary is open to the Gulf of Mexico. 

Salt water exchange occurs at its eastern end and through four inlets: East Pass, between Dog and 

St. George Islands, Government Cut, between St. George and Little St. George Islands, West Pass, 

between Little St. George and St. Vincent Islands, and Indian Pass, at the western end of St. 

Vincent Island. 

The Apalachicola River delivers freshwater to this estuary where it enters through East Bay. 

It is the largest river in the state of Florida (Leitman and others, 1983), and its drainage basin 

includes large parts of eastern Alabama and western Georgia. Its headwaters are in northern 

Georgia (fig. 1). 

The Quaternary geology of the Apalachicola Bay region records several dramatic changes 

in sea level that were caused by periodic glacial retreat and advance (Riggs, 1980). During glacial 

periods, when sea level was low, the Apalachicola River incised channels across the present coastal 

and inner-shelf region (Donoghue, 1993), building deltas on the middle and outer shelf (McKeown 

and others, 2004; Gardner and others, 2005). During interglacial periods, sea level rose and the 

paleo-river channels were filled with deltaic and estuarine deposits (Schnable and Goodell, 1968). 

The present Apalachicola Bay estuary appears to have formed starting 3,000 to 4,000 years ago 

with the formation of the barrier islands that rim the bay (Stapor, 1975; Donoghue and White, 

1995). After the initial formation of the barrier islands, sea level continued to rise, and the delta 

continued to retreat (Donoghue and White, 1995). Fine-grained prodelta sediment accumulated 

beyond the delta front, but largely within the bay, with little escaping to offshore regions (Bedosky, 

1987). It is in this estuarine setting that oysters thrive. 

Estuary-Floor Morphology 

Apalachicola Bay is a broad shallow estuary that contains four subareas: East Bay, St. 

Vincent Sound, Apalachicola Bay, and St. George Sound (fig. 4). Navigation charts (NOAA, 1996; 

2000) show that East Bay, the area adjacent to the Apalachicola River delta, is the shallowest part 

of the estuary, having no depths greater than 2 m. Much of St. Vincent Sound is also less than 2 m 

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deep, but a narrow 5-7 m deep trough extends approximately 6 km eastward from Indian Pass. The 

data collected during this survey cover the Apalachicola Bay and St. George Sound sections of the 

estuary, which are its deepest parts. No data were collected in East Bay or St. Vincent Sound. 

Within these areas, the estuary has a generally smooth floor that increases in depth southward from 

2 m in the north to 4 m in the south (fig. 4 and Mapsheet1). Depths locally exceed 15 m on the 

shoreward side of West Pass. St. George Sound is the deepest part of the estuary, and much of its 

floor is smooth, with depths of 3 to 4m. Depths increase to 4 - 6 m in the eastern part of this sound, 

where the sea floor is more irregular and shaped into a series of broad, low-relief depressions and 

mounds. 

Deviations from the smooth, regional, bathymetric pattern are caused by three forms of 

shoals: shore-attached lobate shoals, linear shoals, and small shoals. Shoal locations and names, 

identified by the Apalachicola Bay National Estuarine Research Reserve, or from NOAA 

navigation charts (NOAA, 1996; 2000), are shown on figure 6. Lobe-shaped shoals extend 

northward from St. George and Little St. George Islands into the southern side of the bay. The 

largest are Pelican Bar, in St. George Sound, and Cedar Point and Higgins Shoals, in Apalachicola 

Bay. Higgins Shoal is located shoreward of a former inlet on Little St. George Island that was open 

in 1860 (fig. 7). It appears to be the remnant of a flood-tidal delta that formed while the inlet was 

active. The other lobate shoals, located along the north side of the islands, may have also originated 

in flood-tidal delta settings. 

Linear shoals exceeding 4 km in length are found in St. George Sound and Apalachicola 

Bay (fig. 6). All of these shoals trend roughly perpendicular to the long axis of the bay, and four of 

the six have one end attached to the shore. The largest, St. Vincent Bar, is located at the western 

end of Apalachicola Bay. It extends southeastward from the northeastern tip of St. Vincent Island 

to within 1.5 km of Little St. George Island. A deep channel extends eastward from West Pass, 

separating the southern tip of St. Vincent Bar from Little St. George Island (fig. 4). The bar is 7 km 

long, 0.7 - 1.3 km wide, and rises to within 0.5 - 1 m of the bay surface. 

Other large linear shoals include Norman's Bar, which is separated from Hotel Bar by the 

Intracoastal Waterway, Cat Point Bar, East Hole Bar, Platform Bar, and Porter's Bar. Cat Point Bar 

extends southeastward from the eastern side of Cat Point and connects with Platform Bar. East 

Hole Bar extends northwest from St. George Island and merges with Cat Point Bar (fig. 6). This 

complex of bars forms a nearly continuous string of shoals across the bay that is only broken by 

two narrow, deeper gaps. The channel between Pelican and Platform Bars exceeds 6 m depth. The 

channel that separates Cat Point Bar from East Hole Bar was not completely surveyed by this 

study, but, where surveyed, the channel reaches 4.9 m immediately west of the Bryan Patton Bridge 

at its northwestern end and 3.2 m at its southeastern end near Platform Bar. The navigation chart 

shows that the section not surveyed by this study reaches depths between 1.5 and 2 m (NOAA, 

1996). The Intracoastal Waterway is dredged through East Hole Bar to depths exceeding 4 m (fig. 

8). The easternmost of the large linear shoals is Porter's Bar, which extends from the northern shore 

of St. George Sound southeastward for 4 km. The crests of the linear shoals rise to within 1 m of 

the bay surface, with the exception of Norman's Bar, whose crest is 2 - 2.5 m deep. The linear 

shoals are unique because they are asymmetrical, with steeper, west-facing sides (fig. 9). 

The small shoals are less than 1.5 km in length, are isolated from the shoreline, and have a 

variety of orientations (fig. 6). One cluster of these shoals, located east of St. Vincent Bar, includes 

Cable Lumps, North Spur, Sugar Lumps, and West Lumps. A second cluster lies south of the John 

Gorrie Bridge. It includes a discontinuous string of linear to circular mounds that lie immediately 

north of Norman's Bar, and the East Lumps. Two small shoals, Green Point Bar and an unnamed 

shoal, are found east of Porter's Bar. 

5
The small shoals have varied orientations. In the eastern part of St. George Sound, Green 

Point Bar and the unnamed shoal trend northwest-southeast, while shoals north of Norman's Bar 

trend north-south, and shoals in the western part of Apalachicola Bay, West, Cable, Sugar Lumps, 

and North Spur, display no dominant orientation. These smaller shoals have less relief than the 

large linear shoals, and their crests are generally deeper than 2 m. Most of the small shoals are 

asymmetrical, with steeper, west-facing sides (fig. 9), but several symmetrical shoals lie in the 

central part of Apalachicola Bay, between Norman's Bar and the John Gorrie Bridge. 

A pronounced, anthropogenic feature of the bay floor is the Intracoastal Waterway. This 

dredged channel starts near the eastern edge of the survey area, weaves around the shoals in St. 

George Sound, cuts across East Hole Bar, and extends westward to the central part of Apalachicola 

Bay, where it turns north and leads to the mouth of the Apalachicola River (fig. 4). The channel is 3 

- 5 m deep along much of its length, and dredge spoils have been deposited along its southern side, 

and is clearly visible on figure 6. Along some sections of the channel, the spoils form a continuous 

ridge with a crest as shallow as 1.7 m, while in other areas, they form discrete, circular mounds that 

are less than 200 m in diameter with crests 1.9 - 3.5 m deep (fig. 8). 

Subsurface Geology 

The late Pleistocene and Holocene history of the northern Florida shelf region has been 

generally described by Schnable and Goodell (1968); Schmidt (1984); Otvos (1985); Donoghue 

(1992; 1993); Donoghue and White (1995); McKeown and others (2004); Gardner and others 

(2005). The dense grid of chirp profiles collected during this survey provides a refined view of 

Apalachicola Bay's Holocene history specifically. Facies interpreted from the seismic-reflection 

profiles are shown in figure 11, their regional distribution is shown in figure 12, and the profile 

locations are shown in figure 13. A conceptual model showing the evolution of the bay since the 

last lowstand of sea level is shown in figure 14. During several Pleistocene lowstands of sea level, 

the ancestral Apalachicola River incised a large valley southward across the region, depositing a 

series of well-developed deltas on the middle and outer shelf, south of the present location of the 

estuary (fig. 14A). This valley was cut to depths of approximately 15 m (20 ms) into Pleistocene 

and earlier sediments beneath the bay (Donoghue, 1992; fig. 12). As sea level rose during the 

Holocene, the section of the valley underlying the outer shelf was filled during the Early Holocene, 

and the section underlying Apalachicola Bay was filled by the Middle-to-Late Holocene (fig. 14B). 

The acoustic facies filling the valley are as much as 8m (13 ms) thick and consist of parallel 

continuous reflections (fig. 11). These deposits are interpreted to be fine-grained, estuarine 

deposits. A well-defined horizon, interpreted to be the flooding surface associated with 

submergence of the bay during the late Holocene (fig. 14B), marks the top of this acoustically 

laminated facies (fig. 11). Under much of the bay, this horizon can be traced away from the paleoriver valley onto adjacent, subsurface, topographic highs (fig. 12). 

In the western part of St. George Sound and most of Apalachicola Bay, east of St. Vincent 

Bar, the flooding surface is buried by younger sediment delivered by the Apalachicola River. Chirp 

profiles show that the youngest deposits in the bay compose a delta system that is overlain by 

modern prodelta mud that continues to be supplied by the Apalachicola River (fig. 12). The delta 

system developed in the central part of the bay (fig. 14C) comprises sandy delta lobe facies with 

muddy prodelta deposits between and beyond the sandy lobes. The sandy parts of this delta system 

produce a highly-reflective, irregular surface in the chirp profiles, which stands in relief, relative to 

the surrounding muddy deposits, displaying a weakly-reflective, smooth surface (fig. 11). The 

shallow, sandy parts of the delta are organized into several fingers that protrude into the bay (fig. 

14C). The tops of most of these fingers are less than 4 m below present sea level, while the adjacent 

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lows are 4 - 5 m deep. The distribution of the shallow ridges in the seismic dataset suggests they 

represent two sets of delta lobes that advanced into the estuary. One set underlies the western part 

of Apalachicola Bay covering the area under and immediately east of St. Vincent Bar, and the 

second underlies the eastern part of the Bay under and east of Norman's Bar (fig. 12A, B). The two 

sets of delta lobes suggest two separate deltas. Donoghue and White (1995) report that the 

Apalachicola River shifted its course approximately 6,000 years ago. Initially, the river drained into 

the estuary west of the present town of Apalachicola, and then shifted eastward to its present 

course. Perhaps the two delta complexes were deposited before, and after the eastward shift 

documented by Donoghue and White (1995). 

The youngest unit is the modern, prodelta mud that overlies the mid-to-late Holocene delta 

and prodelta deposits. Its surface is the present estuary floor (fig. 11). This unit is as much as to 2.5 

m thick adjacent to the mouth of the Apalachicola River, but thins to the east and west where it 

onlaps and locally buries the older delta deposits (fig. 12). Along the southern edge of the bay it 

onlaps the back of the barrier island system (fig. 12C). The areal extent of this unit is the same as 

the mud unit identified in the sidescan-sonar imagery, and it is interpreted to be prodelta mud 

deposits associated with the modern Apalachicola River system (fig. 14D). 

Geologic Controls on Oyster Bed Distribution 

The stratigraphic evolution of Apalachicola Bay has heavily influenced the present 

distribution of oyster bars in the estuary. Oyster beds in the Apalachicola Bay part of the estuary 

rest mainly on late Holocene delta deposits (fig. 14D and fig. 15). Small beds also occur on late 

Holocene flood-tidal delta deposits and anthropogenic deposits of dredged material along the 

Intracoastal Waterway (fig. 10). The seismic profiles show that the oyster beds consistently sit on 

high-amplitude reflections and are absent in areas where only low amplitude reflections are present. 

This relationship suggests that the surfaces colonized by the oysters were sandier than the 

surrounding sea floor. The bathymetry and present distribution of oyster beds, as defined by the 

sidescan-sonar imagery, suggest that some sections of the delta surfaces were colonized and grew 

vertically, while other sections were either never colonized, or were abandoned at a later time 

because of burial by prodelta muds (fig. 15B). Sediment cores will be required to determine if 

oyster beds in the Apalachicola Bay part of the estuary initially had a broader aerial extent that has 

receded with time. 

In the St. George Sound part of the estuary, oysters have colonized abandoned flood tidal 

deltas that extend into the bay along the northern edge of St. George Island, linear ridges of 

uncertain origin that rest on Pleistocene sands, and mounds of dredged material (fig. 10). Sand 

waves cover some of the broad shoals in the eastern part of the Sound, which is well removed from 

the muddy, prodelta deposits, suggesting that tidal and storm generated currents are strong enough 

to sculpt the sandy estuary floor (fig. 10, and fig. 15C). Through sand wave migration, larger shoals 

are generated, and where salinity is appropriate, these shoals can be colonized by oysters. Green 

and Porter's Bars may be shoals that were formed by sand wave migration then stabilized when 

oysters colonized the tops. 

Summary 

Apalachicola Bay is the largest oyster fishery in Florida, and an updated map of oyster bed 

distribution was needed for the continued management of this resource. Because of the large size of 

the study area (35 km long by 8 km wide), and high turbidity of the bay waters, acoustic mapping 

tools were employed. Sidescan sonar, interferometric bathymetry, single-beam bathymetry, and 

chirp seismic-reflection systems allowed for detailed mapping of oyster bed locations and extents 

7
as well as defining their relationship to the morphology of the bay floor and underlying geologic 

features. Analysis of the resulting datasets has revealed strong relations between the stratigraphic 

and morphologic evolution of the estuary and the locations and extents of the oyster beds. 

Integration of the sidescan-sonar imagery and the bathymetric data shows that all oyster beds occur 

on shoals that stand in relief relative to the surrounding bay floor, but not all shoals are colonized 

by oyster beds. Seismic-reflection data show that many oyster beds developed on older deltaic 

deposits underlying the bay. While a variety of conditions influence oyster distribution in the bay, 

this study demonstrates that the underlying geology, particularly what appear to be late Holocene 

delta systems, has significant control over oyster distribution by providing appropriate habitat for 

their growth. 

Section 4: References 

Bedosky, S., 1987, Recent sediment history of Apalachicola Bay: Florida, M.Sc. Thesis, Florida 

State University, 235 p. 

Danforth, W.W., 1997, Xsonar/ShowImage; a complete system for rapid sidescan-sonar processing 

and display: U.S. Geological Survey Open-File Report 97-686, 77 p. 

Donoghue, J.F., 1992, Late Quaternary coastal and inner shelf stratigraphy, Apalachicola delta 

region, Florida: Sedimentary Geology, v. 80, p. 293-304. 

Donoghue, J.F., 1993, Late Wisconsinan and Holocene depositional history, northeastern Gulf of 

Mexico: Marine Geology, v. 112, p. 185-205. 

Donoghue, J.F. and White, N.M., 1995, Late Holocene sea-level change and delta migration, 

Apalachicola River region, northwest Florida, USA: Journal of Coastal Research, v. 11, p. 651-

663. 

Gardner, J.V., Dartnell, P., Mayer, L.A., Hughes Clarke, J.E., Calder, B.R., and Duffy, G., 2005, 

Shelf-edge deltas and drowned barrier-island complexes on the northwest Florida outer 

continental shelf: Geomorphology, v. 64, p. 133-166. 

Isphording, W.C., 1986, Apalachicola Bay; dynamic sedimentation in a Gulf Coast estuary: Gulf 

Coast Association of Geological Societies Transactions, v. 36, p. 471-488. 

Kofoed, J.W., and Gorsline, D.S., 1963, Sedimentary environments in Apalachicola Bay and 

vicinity, Florida: Journal of Sedimentary Petrology, v. 33, p. 205-223. 

Leitman, H.M., Sohm, J.E., and Franklin, M.A., 1983, Wetland hydrology and tree distribution of 

the Apalachicola River flood plain, Florida: U. S. Geological Survey Water-Supply Paper 2196-

A, 52 p. 

McKeown, H.A., Bart, P.J., and Anderson, J.B., 2004, High-resolution stratigraphy of a sandy, 

ramp-type margin - Apalachicola, Florida, USA, in Anderson, J.B., and Fillon, R.H., eds., Late 

Quaternary Stratigraphic Evolution of the Northern Gulf of Mexico Margin: SEPM Special 

Publication, no. 79, p. 25-41. 

NOAA, Coastal Services Center, 1999, Gulf and Caribbean Region: Apalachicola Bay, Florida - 

SPI, Grab, and Single-Beam Acoustic Data Sets, 1999: 

http://www.csc.noaa.gov/benthic/data/gulf/apa.htm. 

NOAA, National Ocean Services, 1860, Western Part of St. George's Sound, Florida, Nautical chart 

# 485, Scale 1:40,000, Online source - http://historicals.ncd.noaa.gov/historicals/histmap.asp. 

NOAA, National Ocean Services, 1996, Intracoastal Waterway Carrabelle to Apalachicola Bay; 

Carrabelle River, Nautical chart # 11404, Scale 1:40,000. 

NOAA, National Ocean Services, 2000, Intracoastal Waterway Apalachicola Bay to Lake Wimico, 

Nautical chart # 11402, Scale 1:40,000. 

8
Otvos, E.G., 1985, Barrier island genesis - Questions of alternatives for the Apalachicola coast, 

northeastern Gulf of Mexico: Journal of Coastal Research, v.1, p. 267-278. 

Paskevich, V., 1996, MAPIT; An improved method for mapping digital sidescan-sonar data using 

the Woods Hole Image Processing System (WHIPS) software: US Geological Survey Open-File 

Report 96-281, 73 p. 

Riggs, S., 1980, Intraclast and pellet phosphorite sedimentation in the Miocene of Florida: Journal 

of the Geological Society of London, v. 37, p. 285-314. 

Schmidt, W., 1984, Neogene stratigraphy and geologic history of the Apalachicola Embayment, 

Florida: Florida Bureau of Geology, Bulletin no. 58, 146 p. 

Schnable, J.E., and Goodell, H.G., 1968, Pleistocene-Recent stratigraphy, evolution, and 

development of the Apalachicola coast, Florida: Geological Society of America Special Paper 

112, 72 p. 

Stapor, F., 1975, Holocene beach ridge plain development, Northwest Florida: Zeitschrift für 

Geomorphologie, v. 22, p. 116-144. 

University of New Brunswick, 2005, SwathEd, software developed by John Hughes Clarke and the 

Ocean Mapping Group, University of New Brunswick. Online at 

http://www.omg.unb.ca/~jhc/SwathEd.html 

Whitfield, W.K., and Beaumariage, D.S., 1977, Shellfish management in Apalachicola Bay: past, 

present and future, in Livingston, R.J., and Joyce, E.A., eds., Proceedings of the Conference on 

the Apalachicola drainage system: Florida Department of Natural Resources Marine Research 

Publications, no. 26, p. 130-140. 

Section 5: Maps 

Three large-format mapsheets (1:30,000) illustrate the bathymetry, sidescan-sonar 

backscatter, and surficial geology of the Apalachicola Bay and St. George Sound survey areas. 

These mapsheets are distributed as Adobe portable document format (PDF) files that can be printed 

out on a large format plotter at 45 x 32 inches (http://pubs.usgs.gov/of/2006/1381/html/maps.htm). 

Mapsheet 1. Bathymetry, presents a regional bathymetric model for the 

area using a 25-m grid cell resolution. 

Mapsheet 2. Sidescan-sonar backscatter, shows distribution of backscatter 

values over the survey area. 

Mapsheet 3. Surficial Geology, shows the interpreted surficial geology with 

the locations of oyster bars draped over sun-illuminated bathymetry. 

9
Spatial Data 

This appendix describes the data collected for this project, where they are located, and how 

to access them depending on the software you have. The primary data format for vector data are 

personal geodatabase feature classes in the Universal Transverse Mercator (UTM) coordinate 

system, Zone 16. As a secondary format for users without access to ArcGIS 9.0, all feature classes 

in the geodatabase are also delivered as individual shapefiles in Geographic projection. The 

primary format for distribution of raster data are ESRI raster and GeoTIFF. All spatial data are 

distributed with FGDC compliant metadata. 

The organization and schema of data in the geodatabase is based on the ArcMarine data 

model developed by the ArcMarine Working Group (http://dusk2.geo.orst.edu/djl/arcgis/). Some of 

the feature classes in the geodatabase are linked to tables through relationship classes that maintain 

data integrity and establish joins between spatial data and a table objects. These relationships are 

established as a basis for joins so the user can easily see which features are related to which tables 

(see fig. 16). The relationships tab in the feature class properties also displays which table objects 

are related to the feature. The figure below (fig. 17) illustrates that the SurveyLines feature class 

participates in three different relationships that can be used as joins. 

These relationship classes can also be used as a basis for a select query. For example the 

SurveyLines feature class has tracklines from two different surveys (05001 and 06001), and two 

different MeasuringDevices (swath bathymetry and sidescan-sonar). If a user wants to see what 

survey an individual surveyline is from using the inquire tool, the identify popup box automatically 

shows that line l202f1 was collected during 05001 (fig. 18). This is the information stored in the 

SurveyInfo table that is linked by a relationship class to the Surveylines feature class. 

You can also use these attributes in a definition query to display only features with certain 

attributes. For example, a user might want to display only the bathymetric surveylines from the 

survey rafa05001 (SurveyID = 1). Using the Definition Query tab in the feature class properties, 

you can build a query based on SurveyID attribute (fig. 19). 

The general organization of spatial data on this DVD is listed below. 

GIS- parent folder for all spatial data 

OFR_1381.mxd- ArcGIS 9.2 map document with all data loaded in the table of 

contents. 

OFR_1381.pmf- ArcReader map document for use with free ArcReader Software. 

You can download Arcreader free of charge on the WWW at 

http://www.esri.com/software/arcgis/arcreader/index.html

Apalachicola.apr- Arcview 3.3 project file. 

USGS_ApalachicolaFL.mdb- ArcGIS 9.2 personal geodatabase with all vector data stored in 

feature class format. See data catalog below for more information. 

10
RASTER- folder containing all raster data in ESRI grid or GeoTIFF Formats. 

ASV- Sidescan backscatter data collected by ASV IRIS in GEOTiff Format 

ASV_SEISIMAG- Seismic profile images in jpg format collected by ASV IRIS. 

These are not hyperlinked to ASV tracklines in the ArcMap document OFR1381.mxd. 

A user can move these jpgs into the /GIS/Seisimag directory to use the relative path 

feature for hyperlinks in ArcMap. 

BATH- Raster bathymetry ESRI grid and GeoTIFF Formats. 

SEISIMAG- Seismic profile images in jpg format collected from R/V Rafael

They are hyperlinked to the seismic tracklines in the ArcMap document 

OFR_1381.mxd distributed with this OFR. 

SIDESCAN- Sidescan-sonar backscatter mosaics of collected by R/V Rafael in 

GeoTIFF format. 

SHAPEFILES- Individual shapefiles of feature classes stored in the geodatabase for users 

without ArcGIS. Shapefiles are in geographic projection. 

THUMBNAILS- Small "thumbnail" graphic of each data layer linked to the metadata. 

Data Catalog 

Vector Data- The vector data are stored and delivered together in single personal 

geodatabase. A user with ArcGIS 9.1 or higher can download the single zip file below and access 

all the vector data and associated metadata. A user without ArcGIS 9.1 or higher can access the 

layers stored in the personal geodatabase as individual shapefiles in geographic coordinate system. 

Layer (metadata) Description View Download 

USGS_ApalachicolaFL.mdb 

ARCGIS 9.2 personal geodatabase including 

all layers below and FGDC metadata in xml 

format. 

 Geodatabase

SurveyLines

Vessel navigation from R/V Rafael

representing actual tracklines along which 

bathymetry and sidescan were collected 

Geodatabase

Shapefile

11
SurficialGeology Interpreted bottom type Geodatabase

Shapefile

Basemap 

ApalachicolaBaseMap Basemap data of land features Geodatabase

Shapefile

Seismics 

ASV_SeismicLines ASV IRIS survey lines hyperlinked to seismic 

profile image 

Geodatabase

Shapefile

ASV_SeismicShot500 ASV IRIS seismic shot navigation at 500 shot 

intervals 

Geodatabase

Shapefile

SeismicLines R/V Rafael survey lines hyperlinked to 

seismic profile image 

Geodatabase

Shapefile

SeismicShot500 R/V Rafael seismic shot navigation at 500 

shot intervals 

Geodatabase

Shapefile

Raster DataThe raster data are stored and delivered outside and separate from the personal geodatabase 

in either GeoTIFF or ESRI Grid format. All raster data are in the UTM Coordinate system. Four 

raster data layers are available in geographic coordinates system denoted by the “_geog.zip” in the 

download column. 

Layer (metadata) Description View Download 

Bathymetry 

St. George Sound -Swath 

Bathymetry

2 meter resolution bathymetry in ESRI Grid 

format stg2mbath.zip

12
Apalachicola Bay- Swath 

Bathymetry

2 meter resolution bathymetry in ESRI Grid 

format apbay2mbath.zip

 

St. George Sound-Swath 

Bathymetry

2 meter resolution hillshaded color 

bathymetry in GeoTIFF format StGSnd2m_Bath.zip

Apalachicola Bay- Swath 

Bathymetry

2 meter resolution hillshaded color 

bathymetry in GeoTIFF format ApBay2m_Bath.zip

 

Bathymetric Model

25 meter resolution bathymetric model of 

Apalachicola Bay and St. George Sound in 

Geo TIFF format 

apbaybath25m.zip

Bathymetric Model Hillshade

Gray-scale hillshade of 25 meter resolution 

bathymetric model of Apalachicola Bay and 

St. George Sound in GeoTIFF format 

UTM Z16 

apbay25hs.zip

Geographic 

apbayhs_geog.zip

Backscatter 

Apalachicola Bay SidescanSonar Mosaic1 meter sidescan-sonar mosaic of 

Apalachicola Bay in GeoTIFF format 

URM Z16 

ApBayMos1m.zip

Geographic 

ABMos_geog.zip

St. George Sound SidescanSonar Mosaic1 meter sidescan-sonar mosaic of St. George 

Sound in GeoTIFF format 

UTM 16 

StGSndMos1m.zip

Geographic 

SGSMos1m_geog.zip

St. George Sound SidescanSonar Mosaic (Julian Day 098)1 meter sidescan-sonar mosaic of St. George 

Sound (Julian Day 098) in GeoTIFF format 

UTM Z16 

StGSndJD0981m.zip

Geographic 

SGSjd98_geog.zip

ASV Backscatter 

ASV Backscatter Julian Day 

154

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD154 in GeoTIFF format asv154.zip

13
ASV Backscatter Julian Day 

157

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD157 in GeoTIFF format asv157.zip

ASV Backscatter Julian Day 

158

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD158 in GeoTIFF format asv158.zip

ASV Backscatter Julian Day 

160

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD160 in GeoTIFF format asv160.zip

ASV Backscatter Julian Day 

162

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD162 in GeoTIFF format asv162.zip

ASV Backscatter Julian Day 

165

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD165 in GeoTIFF format asv165.zip

ASV Backscatter Julian Day 

172

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD172 in GeoTIFF format asv172.zip

ASV Backscatter Julian Day 

173

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD173 in GeoTIFF format asv173.zip

ASV Backscatter Julian Day 

174

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD174 in GeoTIFF format asv174.zip

ASV Backscatter Julian Day 

175

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD175 in GeoTIFF format asv175.zip

ASV Backscatter Julian Day 

176

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD176 in GeoTIFF format asv176.zip

14
ASV Backscatter Julian Day 

177

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD177 in GeoTIFF format asv177.zip

ASV Backscatter Julian Day 

178

1 meter sidescan-sonar mosaic from ASV 

IRIS collected in JD178 in GeoTIFF format asv178.zip

To hyperlink these seismic image profiles with the seismic tracklines use the "Image Title" attribute 

in the feature class to use as the hyperlink field. 

Layer (metadata) View Download 

Seismic JPEGS 

Seismic Reflection Profiles seisimag.zip

ASV Seismic Reflection Profiles asv_seisimag.zip

Acknowledgments 

Funding for this project was provided by the NOAA Coastal Services Center (CSC). We 

wish to thank Linda Rowe and Pace Wilbur of NOAA CSC for their assistance in the early stages 

of the project. In addition, we also acknowledge the interest, support, and assistance of Mark 

Finkbeiner, also of NOAA CSC, during the later stages of the project. Survey work was conducted 

by the following personnel from the USGS Sea-Floor Mapping Group in Woods Hole; Barry Irwin, 

Chuck Worley, Bill Danforth, Jane Denny, Tom O'Brien, and Emile Bergeron. Additional vessel 

support was provided by the crew at Florida DEP in Apalachicola, Florida, including Lauren Levi, 

Jenna Wanat, Megan Lamb, and Stephanie Fahrny. This report benefited from reviews by Kathy 

Scanlon, Wayne Baldwin, and Valerie Paskevich. 

15
Figures 1-19 

Figure 1. Map of Apalachicola Bay identifying regional geographic locations, physiographic features, 

and water bodies. Inset illustrates the location of the bay within the southeastern United States. 

16
Figure 2. Photographs of the survey platforms used in this study: R/V 

Rafael and Autonomous Surface Vehicle IRIS. 

17
Figure 3. Map showing geophysical track lines occupied by R/V Rafael and Autonomous Surface 

Vehicle IRIS during survey cruises in 2005 and 2006. 

18
Figure 4. Bathymetric map of the Apalachicola Bay estuary. See also Mapsheet 1

19
Figure 5. Sidescan-sonar image of the Apalachicola Bay estuary. See also Mapsheet 2. 

20
Figure 6. Map showing the names of bay-floor and geographic features within the Apalachicola Bay 

study area. Locations of sediment samples collected by NOAA Coastal Services Center (NOAA, 1999) 

that were used to verify the sidescan-sonar interpretation are shown. 

21
Figure 7. 2000 NOAA Chart (top panel) and 1860 NOAA chart (bottom panel) showing the location of 

New Inlet, a former tidal inlet near Higgins Shoal that presently is sealed (NOAA, 1860; 2000). 

22
Figure 8. Bathymetric map of the Intracoastal Waterway near the Brian Patton Bridge) showing 

dredged material south of its channel. 

23
Figure 9. Map showing the slope of the bay floor. The steepest slopes are found along the flanks of 

the Intracoastal Waterway, along the margins of the bay, and on the western sides of linear bars (eg. 

St. Vincent's Bar and Porter's Bar). 

24
Figure 10. Map showing the distribution of eleven sedimentary facies identified on the floor of 

Apalachicola Bay superimposed on a shaded-relief image of the bathymetry. 

25
Figure 11. Interpreted seismic profile showing the stratigraphic intervals underlying Apalachicola 

Bay. The deepest horizon imaged is the floor of a Pleistocene river valley. This valley was filled during 

the Early and Middle Holocene by estuarine deposits. During the Late Holocene, a delta system 

advanced into the bay. Presently mud derived form the Apalachicola River blankets large parts of 

these older stratigraphic intervals. Vertical scales for the seismic profile are provided in milliseconds 

(Two-Way Travel Time) and approximate depth in meters (assuming a seismic velocity of 1500 m/s). 

The location of profile 11 is identified on seismic profile A of figure 12 and also in figure 13. 

26
Figure 12. Line-drawing interpretations of three seismic profiles that show the estuary's shallow 

stratigraphy. Vertical scales for the profile interpretations are provided in milliseconds (Two-Way 

Travel Time) and approximate depth in meters (assuming a seismic velocity of 1500 m/s). Profile 

locations are shown in figure 13. Ages associated with the units are inferred. 

27
Figure 13. Map showing the location of the seismic profiles shown in this report. The location of 

Figure 11, which is part of profile A in figure 12 is marked by the gray line. 

28
Figure 14. Schematic block diagram showing important steps in the 

evolution of the Apalachicola Bay region since the last lowstand of 

sea level. 

29
Figure 15. Seismic profiles showing (A) oyster mounds that accumulated on an older, sandy-delta 

surface, and were subsequently buried by younger mud, (B) an oyster bar that accumulated on an 

sandy-delta surface, and remains exposed at the sea floor, and (C) sand waves in the eastern part of 

St. George Sound. The full extent of the sand waves is shown on figure 10. Vertical scales for the 

seismic profile are provided in milliseconds (Two-Way Travel Time) and approximate depth in meters 

(assuming a seismic velocity of 1500 m/s). Profile locations are shown on figure 13. 

30
Figure 16. Diagram of personal geodatabase showing origin and destination tables of relationship classes. 

31
Figure 17. ArcGIS identify results dialog box showing attributes and 

relationships for selected feature. 

32
Figure 18. The general organization of spatial data 

on this DVD is listed below. 

33
Figure 19. Example of ArcGIS Query Builder dialog box with 

query syntax. 

34