` 

Importance of River Flow to the Apalachicola River-Bay System

Robert J. Livingston 

Department of Biological Science, 

Florida State University, 

Tallahassee, Florida 32306 USA 

September 2008 

Report to the Florida Department of Environmental Protection 

 
Abstract

The Apalachicola River is one of the last major free flowing, unpolluted alluvial systems 

in the conterminous United States, and is a major center for endemic and endangered species. 

Seasonal river flooding provides the engine for mobilization and transfer of nutrients and detritus 

between the Apalachicola wetlands and associated river and bay areas. Food webs leading to 

high production of oysters, shrimp, blue crabs and fin fishes in Apalachicola Bay are linked to 

river flows that control salinity regimes and nutrient dynamics of the estuary. Since the mid1970’s, the State of Florida has spent over $239 million through land acquisition to protect the 

Apalachicola River and Bay system. A major planning effort has been in progress for decades. 

Scientific reviews indicate that there has been a serious change in recent Apalachicola flow rates 

with an increase of the frequency and severity of low flow periods during droughts. These 

changes are due, in part, to water use in the upper parts of the Tri-river system. There will be 

increased municipal and agricultural development in the Tri-River Basin in future years that will 

put more pressure on river flows during drought periods. Increased frequency and duration of 

recent droughts have been associated with losses of about 3 million canopy trees in the non-tidal 

Apalachicola River wetlands. Recent droughts have caused kills of federally “protected” 

mussels. Minimum flows of 8000 cfs are likely to be required for maintenance of existing 

unionid populations, and are essential for recovery of federally listed species. Flow management 

for riverine and wetland productivity, biodiversity and endangered species should be based on 

historical seasonal and interannual river flow rates. Nutrient-induced phytoplankton productivity 

is an important component of estuarine food webs in the Apalachicola Estuary. The alluvial 

river also provides organic matter that fuels detrital food webs in the bay. Autochthonous and 

allochthonous organic carbon creates the resources for consumers in the Apalachicola Estuary. 

Recent bay sediment analyses suggest a decrease in riverine organic matter supply and a change 

in sediment clay content supply and/or distribution for the bay that are related, in part, to 

anthropogenic river alterations. This loss of detrital matter could adversely affect key food webs 

in the bay. Recent salinity increases due to droughts have adversely affected the highly 

productive upper bay grass beds. The dominant, commercially important populations of the 

Apalachicola estuary (oysters, blue crabs, penaeid shrimp, sciaenid fishes) are adapted to varying 

salinities. High salinities and reduced nutrient loading adversely affect such species. 

Commercial fishing landings during the 2007 drought suffered decreases of white shrimp (down 

90%), brown shrimp (down 55%), blue crabs (down 55%) and flounder (down 40%). The most 

productive oyster bars in the bay were destroyed by predation during this drought. With reduced 

flows, as salinity goes up, population productivity is reduced due to altered habitat conditions 

and enhanced predation, competition and disease. With a more permanent reduction of 

freshwater flows below a level specific for the receiving system, the physically controlled, highly 

productive river-estuarine system will eventually become a high diversity, biologically 

controlled bay of substantially reduced fishery potential. It is likely that increased frequency and 

duration of river flow reductions in the future due to water removal by upstream human activities 

will eventually result in the loss of the Apalachicola resource. This process has already started in 

the Apalachicola system. Future, long-term changes in atmospheric conditions could lead to 

exacerbation of current reductions of river flows. There is a real need to organize a 

comprehensive scientific research program to evaluate the impacts of reduced river flow rates, 

and to use the objective findings to develop a water conservation plan for the ACF basin. The 

extrinsic and intrinsic value of the Apalachicola River and Bay system demands nothing less. 

2
Table of Contents

 Page 

I. Rationale and Conclusions 4

II. Documentation for Rationale and Conclusions 14

A. Apalachicola River Basin 14 

B. Apalachicola Bay System 18 

C. General Ecology 19 

1. River Flows, the Apalachicola Floodplain and the Bay 21

2. Estuarine Productivity 22

3. Biological Response to Apalachicola River Flows 26

4. Habitat Type and Population Distribution 28

5. Trophic Organization of the Bay 45

6. Long-term Changes of Trophic Organization 48

7. The Apalachicola Oyster Industry 56

8. Recent Droughts and River Flow Changes 62

III. Management of the Apalachicola River-Bay System 66 

IV. Current Threats to the Apalachicola River-Bay System 69 

1. Cumulative Reductions of Apalachicola River Flow Rates 69 

2. Recent Actions by the Federal Government 70 

V. Conclusions 72 

VI. Literature Cited and Bibliography 76 

List of Tables 91 

List of Figures 92 

3
I. Rationale and Conclusions

Temperate alluvial rivers and their associated estuaries are among the most productive 

and economically valuable aquatic resources in the world. Freshwater/saline wetlands and 

associated coastal areas account for high quality habitats that nurture numerous, important aquatic 

species. Transfers of nutrients and organic compounds from alluvial rivers to wetlands and 

receiving bay areas represent an important process in river-dominated systems (Howarth 1988, 

Baird and Ulanowicz, 1989; Livingston, 1984; Livingston et al., 2000). Nutrient input from river 

sources has been closely associated with autochthonous phytoplankton production in receiving 

coastal areas. River-driven particulate organic matter maintains detritivorous food webs in 

estuaries (Livingston, 1983, 1984). However, the relative importance of different sources of both 

inorganic nutrients and organic carbon (dissolved and particulate) can vary from system to system 

(Peterson and Howarth, 1987). These differences can be related to the specific tidal and 

hydrological attributes of a given coastal area (Odum et al., 1979). Loading of nutrients due to 

urban runoff, agricultural wastes and industrial discharges often have an opposite effect on 

riverine-estuarine productivity (Livingston, 2007). Anthropogenic nutrients can cause damaging 

plankton blooms, associated deterioration of the estuarine food webs, and loss of major seafood 

resources (Livingston, 2000, 2002, 2005). 

High natural productivity of alluvial rivers is closely related to continuous water input 

within the bounds of natural climatological cycles. The Apalachicola River remains in a 

relatively natural state with low human populations and low levels of industrialization and 

farming. Aquatic habitats of the Apalachicola River floodplain depend on river flows in terms of 

frequency and duration of inundation and saturation. Floodplain vegetation is closely associated 

with the extent and timing of river flows and flooding. Seasonal flow changes are important to 

the life cycles of many terrestrial and aquatic species along the river. Since 80-85% of the fishes 

use the floodplain as a food source, wetlands inundation is a critical part of the life history of 

these species. There have been recent increases of the frequency and duration of low flows 

during drought periods (Light et al., 1998). This has led to the loss of 3 million canopy trees in 

the non-tidal flood plain of the river. Reduced river flows could also affect state-listed wetlands 

plant species such as Sideroxlyon lycioides (Apalachicola buckthorn), S. thornei (Thorne’s 

buckhorn), and Leitneria floridana (corkwood). Federally protected species such as Gulf sturgeon 

4
(Acipenser oxyrinchus desotoi- threatened. 56 FR 49653) are also dependent on natural river 

flows. 

The Apalachicola River contains a number of freshwater bivalve and gastropod mollusks, 

with high endemism and threatened/endangered mussels. Recent surveys of the Apalachicola and 

Chipola Rivers indicated the presence of five federally protected mussel species: Amblema 

neislerii (Fat threeridge), Elliptoideus sloatianus (Purple bankclimber), Elliptio chipolaensis

(Chipola slabshell), Lampsilis [= Hamiota] subangulata (shineyrayed pocketbook) and 

Pleurobema pyriforme (oval pigtoe) (EnviroScience, Inc., 2005). Field surveys indicated that 

unionids in the Apalachicola River occur in shallow channel margins, sloughs and tributaries that 

undergo rapid depth fluctuations (EnviroScience, Inc., 2005). These areas are “critically 

important to the survival of threatened and endangered mussels in the Apalachicola and lower 

Chipola Rivers.” Purple bankclimbers were eliminated by recent (2000, 2002) low flows, and did 

not re-colonize affected areas (EnviroScience, Inc., 2005). Flow reductions below 8000 cubic 

feet second-1 (cfs) have been associated with mussel kills. Purple bankclimbers were eliminated 

by recent (2000, 2002) low flows, and did not re-colonize affected areas (EnviroScienc, Inc., 

2005). Zimmerman (2006) noted “numerous dead and dying mussels including fat threeridge” at 

discharges of 5400 cfs. Minimum flows of 8000 cfs are required for maintenance of existing 

slough and channel margin unionid populations, and are considered essential for recovery of 

federally listed species (EnviroScience, 2005; Zimmerman, 2006). Apalachicola River flow rates 

should follow functionally-equivalent historical patterns to maintain the highly diverse and 

productive species that are adapted to the natural periodicity of this system. 

The river dominates the Apalachicola Bay system as a source of freshwater, nutrients, and 

organic matter. Together with local rainfall and wind events, the river is closely associated with 

the estuarine salinity regime and coastal productivity (Livingston, 1983, 1984, 2000, 2005; 

Livingston et al., 1997, 1999, 2000). Fresh water discharges from the Apalachicola River, 

together with regional rainfall, create a salinity gradient in the estuary (Figure 1). Reduced and 

highly variable salinity in the bay prevents access of open Gulf predators (stenohaline; adapted to 

high salinity) to the oyster resources (Crassostrea virginica) of the bay. Important commercial 

populations such as penaeid shrimp, blue crabs (Callinectes sapidus) and sciaenid fishes move 

into the bay from offshore spawning grounds to nursery in the highly productive estuarine waters. 

5
These species also benefit from reduced/variable salinities that limit predation. Without adequate 

river water input, the Apalachicola estuary, one of the most prolific in North America, would be 

transformed into a much less productive system. 

Figure 1: Model of the Apalachicola Bay system showing key features that result in extremely 

high primary and secondary productivity. 

Nutrient loading from the river, in the form of inorganic nitrogen and phosphorus 

compounds, is distributed in form of particulate matter, colloidal conglomerates, and dissolved 

compounds (Figure 1). Inorganic nutrients (NH3, NO2, NO3, PO4) are taken up rapidly by 

phytoplankton (microscopic floating plants), thus leading to relatively low concentrations of such 

nutrients in the bay. The high level of dissolved inorganic nutrients that are loaded into the 

estuary from the river creates conditions for very high phytoplankton productivity that forms the 

basis for key food webs in the bay. This includes food for oysters and clams. Zooplankton that 

feed on the phytoplankton support high numbers of anchovies (Anchoa mitchilli) and gulf 

menhaden (Brevoortia patronus). These species, in turn, represent a primary food source for 

various fishes and invertebrates in the estuary. Particulate organic matter from the bodies of 

6
plants and animals, together with particulate and dissolved organic carbon loaded from the river, 

accumulate in the sediments where infaunal microfauna, microflora and macrofauna form 

important elements of detrital food webs for the bay. Depositional (sedimentary) areas that 

receive fresh water input are particularly important as nursery areas for the young of fishes and 

invertebrates that spawn offshore (Figure 1). 

 

Nutrients adhere to the particulate organic matter (detritus) that eventually falls into the 

sediments of the shallow Apalachicola system (Figure 1). This nutrient-rich organic matter is 

colonized by microbial components to form the basis of important detrital food webs. Infaunal, 

detritus-feeding macroinvertebrate assemblages that live in the sediments of the bay are 

dominated by various species of worms and crustaceans that include Mediomastus ambiseta, 

Hobsonia florida, Grandidierella bonnieroides and Streblospio benedicti. The infauna form the 

food base for sciaenid fishes (Atlantic croaker [Micropogonias undulatus], spot [Leiostomus 

xanthurus], and sea trout (Cynoscion spp.) that dominate the estuarine fish populations. Shallow 

depths and extremely high bottom productivity explain why the Apalachicola estuary is a primary 

nursery along the Gulf coast for blue crabs (Callinectes sapidus) and white shrimp (Litopenaeus 

setiferus). These species form the basis of highly lucrative fisheries in the region. The outer bay, 

having higher salinities than the upper parts of the Apalachicola estuary, is dominated by species 

such as silver perch (Bairdiella chrysoura), pigfish (Orthopristis chrysoptera), least squid 

(Lolliguncula brevis), pink shrimp (Farfantepenaeus duorarum), brown shrimp (Farfantepenaeus 

aztecus), and various important game fishes (Figure 1). 

Submerged aquatic vegetation (SAV) contributes to the high level of estuarine 

production. These plants provide habitat and organic matter that form the basis for important 

estuarine food webs. In the upper bay, there have been dense growths of submerged aquatic 

vegetation (SAV) dominated by Vallisneria americana, Ruppia maritima, and Potamogeton sp. 

These SAV species are adapted to low light penetration and low, varying salinities. Recent 

salinity increases due to a prolonged drought have adversely affected the East Bay grass beds that 

represent an important habitat and source of productivity for the upper bay. Shoal grass 

(Halodule wrightii) is dominant in the highly productive seagrass areas off St. George Island. 

Enhanced watercolor and turbidity due to river input restricts development of dominant sea grass 

species such as Thalassia testudinum (turtle grass) and Syringodium filiforme (manatee grass). 

7
These species are adapted to clear water and high salinities, and are thus restricted to shallower 

areas in the outer regions of the Apalachicola system such as along the St. James Island area from 

the City of Carrabelle to Alligator Harbor. Submerged aquatic vegetation thus complements the 

high phytoplankton productivity of river-dominated parts of the estuary, giving rise to an 

important sports fishing industry in the region. The intricate combination of fresh water input, 

nutrient loading, water quality factors, high biological productivity, salinity distributions and the 

diversity of natural habitats have contributed to the relatively high commercial and sports fishery 

values of the Apalachicola River-Bay system (Figure 1). 

 

Due to decades of planning and management initiatives, the Apalachicola River and Bay 

system remains one of the most protected aquatic areas in the world. A coalition of local, state 

and federal personnel instituted advanced land planning in Franklin County in the 1970's and 

early 1980’s. This effort was based on an extensive scientific database that was used as the 

anchor for management initiatives. This included the establishment of the Apalachicola River 

and Bay Estuarine Sanctuary in 1979. This sanctuary, now called a National Estuarine Research 

Reserve, included purchases of about 78,000 ha (hectares) of wetlands, and remains one of the 

largest such Reserves in the country. State officials along the river and the bay carried out a 

series of major purchases of wetlands. These purchases have been extended to the present day. 

Public land holdings accompanied regional and local planning efforts designed to mitigate the 

effects of human activities. Purchases of the barrier islands were added to acquisitions of the East 

Bay and Apalachicola River wetlands to complete a ring of publicly owned lands around the most 

environmentally sensitive areas of the system. The State of Florida has spent over $239 million 

for these land acquisitions, based almost entirely on scientific reports that prioritized the order of 

ecological value of the various river and bay resources. The major management effort for the 

Apalachicola system would be undone by increased drought frequency and enhanced low-flow 

conditions due to upriver water removal by human activities. 

Nutrient loading is defined as the product of nutrient concentration times water flow 

rates. This differs from the actual concentration of nutrients in the water, as loading is a dynamic 

process rather than a simple concentration variable. Naturally high nutrient loading from the river 

should thus not be confused with the high concentrations of nutrients that flood into the river and 

bay from urbanized areas during rain events. Urban storm water runoff occurs due to replacement 

8
of natural systems with impervious surfaces that exacerbate the extent of the flow in space and 

time during storms. The high concentrations of nutrients in the water entering the bay cause 

blooms of destructive microalgae and plankton that are associated with reduced oxygen and toxic 

impacts on estuarine biota. Reduced river flow can accentuate the bloom impacts by reducing 

turnover rates of the water and eliminating the flushing of the planktonic bloom species. 

 

Livingston (2007) outlined the adverse impacts of nutrient loading from industrial, 

agricultural and urban sources on a similar estuary (the Perdido Bay system) along the west 

Florida Gulf coast. These impacts indicate how the natural attributes of temperate river-bay 

systems are destroyed by anthropogenic loading of nutrients from various sources. In the Perdido 

system, initial diatom blooms were replaced by raphidophytes and dinoflagellates in time. Bloom 

effects on phytoplankton assemblages included initial reductions of species richness/diversity and 

direct/indirect replacement processes. Long-term occurrences of plankton blooms and related 

changes in phytoplankton composition were accompanied by altered food web processes and 

losses of key fish and invertebrate populations. Raphidophyte (Heterosigma akashiwo) and 

dinoflagellate (Prorocentrum cordatum) blooms were statistically associated with reduced 

invertebrate and fish community variables, and creating serious disruptions of bay food webs. 

Natural seasonal and interannual trends of river flows represent an important factor in the 

timing and extent of the plankton blooms due to urban development in coastal areas (Figure 2). 

The relatively high natural nutrient loading of the Apalachicola River is an important component 

of the influence of nutrients on high bay productivity. Without the naturally high river flow rates, 

anthropogenic nutrient inputs could have an enhanced adverse effect on bay water quality and 

populations by stimulating toxic blooms that would reduce bay productivity. Thus, natural river 

flows are a major component in the maintenance of phytoplankton associations that form the basis 

of the bay productivity. There is evidence that urban development and storm water runoff are 

already having an adverse effect on the productivity of the Apalachicola system (Livingston, 

2008). The complex interrelationships of river flow and cultural eutrophication have been 

outlined in various studies (Livingston, 2002, 2007). There is ample evidence that low river flow 

conditions that are enhanced by anthropogenic activities would exacerbate the impact of urban 

runoff and treated sewage on bay productivity during extended drought periods. 

9
Figure 2: Model of the Apalachicola Bay system showing potential impacts of reduced river flow 

leading to plankton blooms and reduced secondary productivity. 

The seasonal and interannual drought/flood periodicity of river flows is an important 

factor in the maintenance of riverine and estuarine productivity (Livingston, 2000, 2002, 2005). 

Freshwater and estuarine species in the Apalachicola system are adapted to natural drought/flood 

flow cycles. This has led to temporal successions of species that contribute to the high biological 

productivity of the system. Bay productivity is high due to loading of nutrients and organic 

matter from the river and autochthonous production by benthic plants. Lowered Apalachicola 

River flow would reduce detritus loading from wetlands areas. Associated reductions of 

nutrients, along with changes of water quality associated with reduced river flow during droughts, 

would lead to altered phytoplankton productivity (Figure 3). These alterations would disrupt river 

and bay food webs and reduce overall secondary production. The impacts of natural droughtrelated reductions of river flows would be exacerbated by up-river human activities in the form of 

urban and agricultural use of river water. Human-related reductions of river flow would expand 

the scope and duration of the associated reduction of river and bay productivity (Figure 3). 

10
Figure 3: Model of the Apalachicola Bay system showing potential impacts of reduced river flow 

to the bay leading to seriously reduced secondary productivity. 

There is evidence that droughts in recent years have become longer and more extreme 

leading to related reductions of Apalachicola River flows. Continuation of these trends will result 

in a decided adverse impact on river and bay productivity. The enhancement of the impacts of 

natural drought conditions due to removal of river water use by human activities is likely to 

exceed the resilience of the river and bay, thus altering the natural processes that are responsible 

for the high productivity of the system. 

11
The salinity of the Apalachicola Bay system is controlled to a considerable degree by the 

Apalachicola River (Livingston 1984). The Apalachicola Bay system has historically provided 

90% of Florida’s oysters (10% nationally). The very high oyster production in the Apalachicola 

system depends on a combination of variables that are directly and indirectly associated with 

fresh water input. Increased salinity would allow increased oyster mortality due to predation and 

disease. This same process would also adversely affect other commercially important fishes and 

invertebrates due to increased predation on the nurserying organisms. The Apalachicola estuary 

is a major nursery for white shrimp and blue crabs. Both species utilize the bay as a highly 

productive nursery, and, along with oysters, form the basis for important commercial fisheries. 

Increased salinity due to reduced river flows lowers the nursery function of the bay for such 

species due, in part, to increased predation from stenohaline offshore species. Recent prolonged 

low-flow events during droughts have adversely affected bay and Gulf fisheries for white shrimp, 

blue crab and sciaenid fish populations. In addition, reduced nutrient loading due to lower river 

flows would lead to altered phytoplankton that, in turn, would alter food webs that support the 

highly valued commercial and sports fisheries. In this way, reduced river flows due to 

anthropogenic activities, would lead to direct and indirect adverse impacts on the commercial 

fisheries along the Apalachicola River-Bay system. 

Information from various sources indicates that there has been a serious change in the 

Apalachicola flow rates with an increase of the frequency and severity of low flow periods during 

droughts. There is also evidence that these changes are due, in part, to water use in the upper 

parts of the Tri-river system. Flood plain areas of the river and commercial fisheries in the 

Apalachicola estuary have already been seriously damaged in the most recent droughts. These 

impacts have been enhanced recently by the increased frequency and virulence of low river flows. 

It is likely that increased frequency and duration of river flow reductions in the future due to 

water removal by upstream human activities will eventually lead to the loss of the Apalachicola 

resource though serial reductions of bay resilience. There would be habitat and productivity 

changes that would be accompanied by the elimination of the riverine wetlands, loss of the 

nursery function of the bay and destruction of the naturally high productivity associated with key 

aquatic species. 

12
A noted above, there has been a considerable investment by local, state and federal 

associations and agencies in terms of time and money to manage the Apalachicola drainage 

system. After a series of legal disputes among the states of Florida, Georgia and Alabama for 

water rights in the ACF system for almost 2 decades, negotiations among the governors of these 

states broke down in February 2008. In April 2008, the U. S. Army Corps of Engineers (U. S. A. 

C. E., 2008) released a modified Interim Operation Plan (IOP) that would allow Georgia to keep 

more water in reservoirs such as Lake Lanier during droughts. This would essentially result in 

even lower river flows than those associated with the original IOP during droughts with the onus 

of lower flows placed on the natural resources of the Apalachicola River and Bay system. Flows 

would thus fluctuate below 5000 cfs during droughts. The modified IOP was approved by the U. 

S. Fish and Wildlife Service. The Corps’ modified Interim Operation Plan does not include any 

requirement that Georgia implement effective conservation efforts designed to limit the impact of 

enhanced drought effects on Florida resources. These actions indicate that the application of 

minimum flow requirements has been progressively minimized by federal environmental 

agencies. 

According to the Carnegie Institution for Science (2008), there is evidence that the jet 

streams in the northern hemisphere have weakened with an increased northward movement in 

recent years. These changes fit the predictions of global warming models and have implications 

for the frequency and intensity of future storms, including hurricanes. Storm paths in North 

America are likely to shift northward as a result of the jet stream changes. This change could 

lead to less rain in the already drought-stricken SE United States. There is no way to confirm the 

long-term effects of these changes that are likely due to global climate trends. If the projections 

of reduced rainfall in the ACF region are true, however, it would place even more emphasis on 

the need for an advanced water conservation effort in the Tri-River area. The increase of the 

frequency and intensity of droughts in the Apalachicola system is a fact, and the potential for 

further reductions of rainfall and natural river flow should be included in calculations for water 

conservation efforts. It is possible that future, long-term changes in atmospheric conditions 

could lead to further reductions of river flows. 

13
II. Documentation for Rationale and Conclusions

A. Apalachicola River Basin

The Apalachicola River-Bay system is part of a major drainage area (the ChattahoocheeFlint-Apalachicola [ACF] basin) of about 48,500 km2

(square kilometers). This system is located 

in western Georgia, southeastern Alabama, and northern Florida (Figure 4). There are 13 dams 

on the Chattahoochee River and 3 dams on the Flint River. The Apalachicola River, 21st in flow 

magnitude in the conterminous United States, is one of the few alluvial systems that remains free 

flowing in the country. The river flows 171 km from the confluence of the Chattahoochee and 

Flint Rivers (the Jim Woodruff Dam) to its terminus in the Apalachicola estuary (Figure 1). 

Average flow rates have historically approximated 690 m3

s-1 (1958-1980) with annual high flows 

averaging 3,000 m3

s-1 (Leitman et al., 1982; Leitman et al., 1991). The forested floodplain, about 

450 km2, is the largest in Florida (Leitman et al., 1982). Forestry is the primary land use in the 

floodplain (Clewell, 1977). Other activities include minor agricultural and residential use, bee 

keeping, tupelo honey production, and sports/commercial fishing (Livingston, 1983, 1984). 

Figure 4: The Apalachicola-Chattahoochee-Flint (ACF or Tri-River) drainage basin. 

 

Tn. N.C.

S.C.

Al. Ga.

Fl.

Al.

Fl.

Ga.

Fl.

Al.

Ga.

Apalachicola River

Apalachicola Bay

0

km

40 80

BASIN LIMITS

BASINLIMITS

Atlanta, Georgia

Columbus, Georgia

Apalachicola, Florida

Gulf of Mexico

N

Chattahoochee

 River

Flint River

Chipola River

Jim Woodruff Dam

Lake Seminole

Lake Lanier

14
The Apalachicola system represents an unusually important example of a natural river 

basin that has remained relatively free of human impacts. The Apalachicola River and Bay 

system is located in one of the least populated areas along the Gulf coast (Figure 5). Over the 

past 35 years, the Florida State University Aquatic Research Group (Dr. Robert J. Livingston, 

Director) has carried out a continuous analysis of the Apalachicola drainage system with most of 

the primary field work carried out between 1971-1991 and 2005-2007. In recent years, it has 

become apparent that sources of fresh water flows (i.e., the Chattahoochee and Flint Rivers) to the 

Apalachicola River-Bay system will be under increasing pressure from municipal and agricultural 

development, particularly in Georgia. 

Figure 5: Human population distribution in North Florida. This figure is a composite of 

information provided by the National Oceanic and Atmospheric Administration, the Florida 

Department of Environmental Protection, and the ESRI Corporation. 

15
The Apalachicola River is one of the last major free flowing, unpolluted alluvial systems 

in the conterminous United States. The importance of freshwater flows to the Apalachicola 

floodplain has been extensively studied (Cairns, 1981; Elder and Cairns, 1982; Mattraw and 

Elder, 1982; Light et al., 1998, 2006). Based on a long history of management efforts 

(Livingston, 2002), the unique characteristics of the river-flood plain have been the subject of 

various studies. The importance of freshwater flows to the Apalachicola floodplain has been 

extensively documented (Light et al., 1998, 2006). As a consequence of this effort, various 

aspects of the Apalachicola upland drainage system have been found to be critical to the overall 

resource management approach for the basin (Livingston and Joyce, 1977): 

1) The Tri-River system extends from the Piedmont to the Gulf of Mexico. The 

Apalachicola drainage basin receives biotic exchanges from the Piedmont, the Atlantic 

Coastal Plain, the Gulf Coastal Plain, and peninsular Florida. This accounts for the high 

quality of the terrestrial animal biota of the river floodplain (Means, 1977). 

 2) Floodplain forests include many terrestrial plant species of which 9 are narrowly 

endemic, 28 endangered, 17 threatened, and 30 rare (Clewell, 1977). 

3) Of the north Florida drainages, the Apalachicola River contains the largest number of 

freshwater bivalve and gastropod mollusks, with high endemism and a number of rare and 

endangered species (Heard, 1977). 

 

4) Eighty six fish species have been noted in the Apalachicola River system, including 3 

endemics, important anadromous species, and an important sports and commercial fishery 

(Yerger, 1977). 

5) Apalachicola River wetlands represent a center of endemism for terrestrial species, 

which includes federally protected species of amphibians, reptiles, and birds (Means, 

1977). Due to the high diversity of wetland and upland habitats, the highest species 

density of amphibians and reptiles in North America (north of Mexico) occurs in the upper 

Apalachicola basin. 

Hoehn (2002) noted that aquatic habitats of the Apalachicola River and floodplain depend 

on river flows in terms of frequency and duration of inundation and saturation. Regular seasonal 

changes of flow rates are important to the life cycles of various invertebrate and fish species along 

the river system. Since 80-85% of the Apalachicola River fish species use the floodplain as a food 

source (Light et al., 1998), wetlands inundation is a critical part of the life history of these species. 

Crayfish, an important species in terms of biomass, are directly controlled by annual river 

fluctuations (Bass, 2002). Spawning of various species is also dependent on river levels with 

16
rapid flow reductions usually having a negative effect on this process (Hoehn, 2002). Critical 

habitats for anadromous species such as striped bass are dependant on flow rates. 

The Apalachicola floodplain is important to various freshwater fisheries, although most of 

the more important fisheries (e.g., striped bass, Morone saxatilis; sturgeon, Acipenser 

oxyrhynchus) have been destroyed or seriously impaired due to habitat destruction by 

channelization and damming in the Chattahoochee and Flint Rivers (Livingston and Joyce, 1977; 

Livingston, 1984). Dredging activities, mandated by the U. S. Congress have led to serious 

habitat damage along the Apalachicola River with a minimum of economic justification for such 

channelization (Leitman et al., 1991). The Apalachicola River-wetlands system has been the 

subject of land purchase efforts by Florida state officials, and is one of the few such systems that 

is largely in public hands. 

Associations of floodplain habitat and river flows explain how such effects result in lost 

habitat and aquatic populations (Light et al, 1998; Hoehn, 2002). Declining water levels caused 

by reduced spring-summer flows and erosion of the river channel have adversely affected many 

plant and animal species dependent on the historical seasonal pattern of river fluctuations (Light 

et al., 2006). Although large floods exceeding 100,000 cfs are still occurring as frequently as in 

the past (about 3 times per decade), there has been an increase in the frequency and duration of 

low flows (Helen Light, Pers. Comm., 2008). Recent surveys of the non-tidal floodplain forest 

indicate that drying of floodplain tree composition has occurred in response water-level declines 

in the river, and that swamp forests, which grow in the lowest and wettest parts of the floodplain, 

have been affected the most (Darst and Light, 2007). An estimated loss of nearly 3 million 

canopy trees in swamp forests of the floodplain has occurred as a result of declining water levels 

in the Apalachicola River (Helen Light, Pers. Comm., 2008). 

Flow reductions could have an impact on state-listed wetlands plant species such as 

Sideroxlyon lyciodes, S. thornei, S. lyciodes and Leitneria floridana. According to Ziewitz 

(2003), federally protected species include the Gulf sturgeon (Acipenser oxyrinchus desotoi). 

Recent surveys of the Apalachicola and Chipola Rivers indicate the presence of five federally 

protected mussel species: Amblema neislerii (Fat threeridge), Elliptoideus sloatianus (Purple 

bankclimber), Elliptio chipolaensis (Chipola slabshell), Lampsilis [= Hamiota] subangulata

17
(shineyrayed pocketbook) and Pleurobema pyriforme (oval pigtoe). Recent surveys 

(EnviroScience, Inc., 2005) have shown that unionids in the Apalachicola River occur in shallow 

channel margins, sloughs and tributaries that undergo rapid depth fluctuations. These areas are 

“critically important to the survival of threatened and endangered mussels in the Apalachicola and 

lower Chipola Rivers” (EnviroScience, Inc., 2005). Purple bankclimbers were eliminated by 

recent (2000, 2002) low flows, and did not re-colonize affected areas (EnviroScience, Inc., 2005). 

Zimmerman (2006) noted “numerous dead and dying mussels at various locations including fat 

threeridge” at discharges of 5400 cfs. Minimum flows of 8000 cfs are likely to be required for 

maintenance of existing slough and channel margin unionid populations, and are likely essential 

for recovery of federally listed species (EnviroScience, 2005; Zimmerman, 2006). Reduced river 

flows and physical alterations to the river are considered threats to these species. 

Various sources of information regarding the Apalachicola River system indicate that flow 

management for riverine and wetland productivity, biodiversity and endangered species should be 

based on historical intra- and interannual flow rates of the Apalachicola River. Projected flow 

rates of the Apalachicola River should follow historical patterns to maintain the highly diverse 

and productive species that are currently adapted to the natural periodicity of this system. 

 

B. Apalachicola Bay System

Results of previous studies indicated that the Apalachicola estuary has been historically in 

a relatively natural state (Livingston, 1984; Livingston et al., 1997, 2000, 2003). A sparse human 

population, together with a low level of industrial and municipal development, has been 

associated with historically high water and sediment quality (Livingston, 1984, 2000, 2002, 

2005). Published results included various subjects: hydrology (Meeter et al. 1979), the effects of 

anthropogenic activities such as agriculture (Livingston et al., 1978) and forestry (Duncan, 1979, 

Livingston and Duncan, 1979, Livingston et al., 1976), and the importance of salinity levels to the 

community structure of estuarine organisms (Livingston, 1979; Livingston et al., 2000, 2003). 

The basic distribution of the estuarine populations was analyzed (Edmiston, 1979; Estabrook, 

1972; Laughlin, 1979; Laughlin and Livingston, 1982; Livingston, 1976b, 1977, 1981b, 1983; 

Livingston et al., 1974; 1976, 1977, Mahoney, 1982, Mahoney and Livingston, 1982, McLane, 

1980, Purcell, 1977, Sheridan, 1979; Sheridan and Livingston, 1979, 1983). Various studies were 

18
also carried out concerning the trophic organization of the estuary (Laughlin, 1979; Livingston et 

al., 1997; Sheridan, 1978) that includes microbial ecology (Federle et al., 1983; White, 1983; 

White et al., 1977, 1979a, 1979b). 

Overall, the extensive studies of the Apalachicola system indicated that the relatively 

natural interaction of relatively undisturbed river-bay interactions, along with little human 

development in the vicinity of the estuary, resulted in an extremely productive bay system with 

high levels of secondary productivity relative to other river-dominated estuaries such as the 

Choctawhatchee and Escambia systems to the west. 

C. General Ecology

There is considerable natural variability of freshwater fluxes in the various sub-basins of 

the north Florida Gulf region (Livingston, 1984a, 1989, 2000). Most of the river systems are 

composed of a series of tributaries that drain sub-basins into the main stem. The sub-basins 

often follow different hydrological cycles (Livingston et al., 1989, 1990) than the main stem, 

depending on regional rainfall patterns and the highly variable physiographic conditions in the 

different regions. Some drainage basins extend into Alabama and Georgia. Temporal patterns 

and volumes of river discharge to associated estuaries depend on the cumulative climatological 

conditions and seasonally varying evapo-transpiration rates in associated watersheds. 

Flooding plays a role during winter and early spring months in the north Florida 

drainages. Winter-spring flooding in the alluvial streams is a product of reduced evapotranspiration rates during winter rainfall peaks along the heavily vegetated drainage basins 

(Livingston, 1984). Reduced summer surface flows are due to increased evapo-transpiration in 

vegetated flood plains. Evapo-transpiration in existing reservoirs is also a major component of 

the water balance in the Tri-river system (Leitman, 2003a). Up-river withdrawals of river water 

by municipal and agricultural activities represent another cause of reduced flows. Surface-flows 

are minimal during the fall low-flow period. Alluvial systems such as the Apalachicola have 

flow patterns that are thus more correlated with seasonal rainfall patterns in Georgia and 

Alabama (where high percentages of the respective drainage basins are located) than in Florida 

(Meeter et al., 1979). The smaller streams along Apalachee Bay are associated with relatively 

19
limited estuarine areas, whereas the alluvial, river-dominated estuaries (Apalachicola, 

Choctawhatchee, Escambia) to the west are proportionately larger due to the higher river flows. 

The Apalachicola estuary (Figure 6) is about 62,879 ha in area, and is a shallow lagoonand-barrier-island complex oriented along an east-west axis. Water movement is controlled by 

wind currents and tides as a function of the generally shallow depths (Livingston 1984, 

Livingston et al., 1999, 2000) that constitute a major feature of the system. Upland marshes grade 

into fringing grass beds, soft-sediment areas, and oyster reefs. A series of passes control 

interactions of the bay with the Gulf of Mexico; these passes, together with river flows and bay 

configuration, have major effects on the salinity structure of system (Livingston, 1983, 1984). 

The Apalachicola River dominates water quality in the bay system, and represents the chief 

source of freshwater input. As such, the river represents a major source of coastal productivity in 

the region (Livingston, 1983, 1984; Livingston et al., 1997, 1999, 2000, 2002, 2005). 

Figure 6: The Apalachicola Bay system showing location of long-term sampling stations (1972-

1984). 

20
1. River Flows and the Apalachicola Floodplain and Bay

The Apalachicola River system has the greatest flow rates of all the river-drainages along 

the northeast Gulf. The importance of freshwater flows to the Apalachicola floodplain has been 

extensively studied (Cairns, 1981; Elder and Cairns, 1982; Mattraw and Elder, 1982; Light et al., 

1998). Apalachicola River nutrient loading to the estuary is the highest of the major alluvial river 

systems along the Gulf coast of Florida (Livingston, 2000), and remains relatively high without 

apparent widespread hypereutrophication in the bay. River flow rates from 1950-2008 have been 

characterized by a number of major drought events (1954-1955, 1968-1969, 1980-1981, 1987-

1988, 1999-2001; 2007-present). In terms of river flow, the most recent droughts have been 

extreme, with relatively low minimum rates of flow. 

The scientific question of resilience comes into play here with respect to how long the bay 

can continue to be affected by low river flows before adverse changes of food web structure and 

productivity become permanent. The dominant, commercially important populations of the 

Apalachicola estuary are adapted to varying salinities (euryhaline). With reduced flows, salinity 

goes up, reducing physical stress to offshore stenohaline populations (adapted to high salinity). 

These species enter the bay resulting in increased species richness and predation pressure on 

existing bay species. Individual bay population productivity is reduced accordingly due to 

enhanced predation and competition. The physical stress of the natural (pulsed) river-estuarine 

system is a major factor in the prolonged high productivity of the Apalachicola estuary. Changes 

in nutrient loading, salinity and light penetrability are important elements in the determination of 

the trophic response of the system. Within limited natural bounds, these processes vary little in 

terms of qualitative and quantitative aspects of the trophic organization of the bay. Below a 

certain level of river flow, the estuary becomes a very different system with initial increases in the 

biota. However, with prolonged reductions of river flow, there are eventual decreases in 

biological production due to reduced nutrient loading and phytoplankton production. 

Under the natural range of river flow variation, the physically unstable estuary has been 

associated with a relatively stable biological system over interannual periods of time (Livingston 

et al., 1997). River flow changes within the specific limits of seasonal variation result in a 

generally stable biological progression through time. With consistent reductions of flow rates 

21
during a prolonged drought, the clarification of a turbid system leads to rapid changes in the 

pattern of primary production, which, in turn, becomes associated with major changes in the 

trophic organization of the system. With the prolongation of the restricted river flows, the 

formerly physically controlled biological system gradually changes to a more biologically 

controlled system. Trophic response time would be measured in years from the point of the 

initiation of low flow conditions. Eventually, permanent reductions of freshwater flows would 

then lead to major reductions of biological productivity. With the more or less permanent 

reduction of freshwater flow below a level specific for the receiving system, the physically 

controlled, highly productive river-estuarine system would eventually become a high diversity, 

biologically controlled bay of substantially reduced fishery potential. Although the exact pattern 

of the loss of bay resilience to these controlling factors cannot be predicted, the overall process of 

fisheries losses has been confirmed by the considerable scientific database concerning the 

Apalachicola Bay system. 

2. Estuarine productivity

A generalized review of the factors that add to the productivity of a river-dominated 

estuary is shown in Figure 7. Fresh water flows from the upland river-wetlands system carry 

nutrients and particulate organic matter into the estuary. The nutrients cause increased production 

of natural phytoplankton populations. Detrital food webs are fed by loading of organic matter 

(dissolved and particulate) that is primarily associated with bottom (benthic) trophic interactions. 

The planktonic trophic organization and the detrital food webs account for the high levels of 

estuarine secondary productivity. Reduced salinity in the estuary due to freshwater inputs from 

the river favors reduced predation by offshore (Gulf) populations that are not adapted to the low 

and highly variable salinities of the estuary. Relatively few fish and invertebrate populations 

outside of the infaunal invertebrates actually breed in the estuary. Most bay populations migrate 

into the bay as juveniles that use the high naturally high productivity of the bay to grow to sizes 

that are commercially valuable. This includes the penaeid shrimp, blue crabs and sciaenid fishes 

that form the backbone of the commercial value of the Apalachicola Bay system. Some species 

such as clams and oysters that are indigenous to the estuary add to the value of the estuary. In 

areas distant from the immediate effects of the river, sea grass beds become abundant, and, 

22
together with associated upland wetlands, form the basis of complex and highly productive parts 

of the overall bay productivity (Livingston, 2008). 

Figure 7: Model of the interaction between the Apalachicola River and Bay with respect to the 

riverine contributions to bay primary and secondary productivity. 

The combination of low levels of pollution, the lack of hypereutrophication due to 

nutrient pollution, and undisturbed estuarine habitats has made the Apalachicola system a highly 

productive body of water that is relatively rare in the United States today. The association 

between alluvial freshwater input and estuarine productivity has been indirectly established in a 

number of estuaries (Cross and Williams, 1981). In a study of 64 estuaries in the Gulf of Mexico, 

Deegan et al. (1986) found that freshwater input was highly correlated (R = 0.98) with fishery 

harvest. Funicelli (1984) found that upland carbon input was in some way associated with 

estuarine productivity. Armstrong (1982) noted that nutrient budgets in Texas Gulf estuaries 

were dominated by freshwater inflows, and that shellfish and finfish production was a function of 

nutrient loading rates and average salinity. However, few studies have evaluated more detailed 

facets of the linkage of the freshwater river-wetlands with estuarine productivity (Livingston 

1981a). The sources of high productivity are subject to complex seasonal and interannual 

fluctuations that are closely associated with climatological conditions. 

23
In response to projections of anthropogenic freshwater use by Georgia over the next 30-50 

years (Livingston, 1988), a long-term program was initiated to analyze data generated during the 

1970’s and 1980’s, and to determine how projected reduced flows of the Tri-river system would 

affect the Apalachicola River-bay system (Livingston et al., 1997, 2003). 

The linkage between upland freshwater wetlands and the rich estuarine biota of associated 

estuaries underscores the importance of ecosystem-level research in management processes 

(Livingston and Loucks, 1978). Studies concerning the distribution of wetland vegetation in the 

Apalachicola floodplain indicated that vegetation type was associated with water-level depth and 

fluctuation and duration of inundation (Leitman et al., 1982). Litter fall in the Apalachicola 

floodplain (800 gm-2) is higher than that noted in many tropical systems and almost all warm 

temperate systems (Elder and Cairns, 1982). The authors found that annual deposition of litter 

fall in the bottomland hardwood forests of the Apalachicola River floodplain approximates 

360,000 metric tons (mt). Seasonal river flooding provides for the transfer of detritus from the 

wetlands to associated aquatic areas (Cairns, 1981; Elder and Cairns, 1982). 

Livingston et al. (1974) indicated that, in addition to providing particulate organics that 

fueled the bay system, river input determined nutrient loading to the estuary. Of the 214,000 

metric tons (mt) of carbon, 21,400 mt of nitrogen, and 1,650 metric tons (mt) of phosphorous that 

is delivered to the estuary over a given year, over half is transferred during the winter-spring flood 

peaks (Mattraw and Elder, 1982). Bay studies (Livingston, 1976, 1981a, 1983, 1984, 2000, 2002) 

corroborated the timing of these flow events with the delivery of nutrients and dissolved and 

particulate organic matter as an important factor in the maintenance of the estuarine primary 

production (autochthonous and allochthonous). There were direct links between the estuarine 

food webs and freshwater discharges (Livingston, 1981a, 1983, 1984). Particulate organic carbon 

delivered to the estuary followed seasonal and interannual fluctuations that were closely 

associated with river flow (Livingston, 1991a; R2 = 0.738). During summer and fall months, there 

was no direct correlation of river flow and detritus movement into the bay. By winter, there was a 

significant relationship between micro-detrital loading and river flow peaks. 

It has been recognized that phytoplankton productivity is a major determinant of 

secondary production in many coastal systems. Boynton et al. (1982) reported that the 

24
Apalachicola system has high phytoplankton productivity relative to other river-dominated 

estuaries, embayments, lagoons, and fjords around the world. Nixon (1988) showed that the 

Apalachicola Bay system ranks high in overall primary production compared to other such 

systems. Up to 50% of the phytoplankton productivity of the Apalachicola estuary is explained 

by Apalachicola River flow (Myers 1977, Myers and Iverson 1977, 1981). In the Apalachicola 

system, orthophosphate availability limited phytoplankton during both low and high salinity 

winter periods and during the summer at stations with low salinity (Iverson et al., 1997). 

Nitrogen was limiting during summer periods of moderate to high salinity in the Apalachicola 

estuary. Flow rates affected the development of nutrient limitation in the Apalachicola estuary. 

Nutrient limitation was highest during low-flow summer periods. The physiography of the 

Apalachicola estuary is an important factor in the high primary productivity of the system. The 

bay is relatively shallow, and wind action is associated with periodic peaks of phytoplankton 

production as inorganic nutrients, regenerated in the sediments, are mixed through turbulence into 

the euphotic zone (Livingston et al., 1974; Iverson et al., 1997). In deeper estuaries, nutrients can 

be sequestered in the sediments and thus can be lost in terms of phytoplankton production. Water 

depth is thus an important factor in the natural productivity of the Apalachicola estuary. 

Recent studies have further documented the influence of the Apalachicola River on 

nutrient and organic carbon loading to the bay. Chanton and Lewis (1999) found that, although 

there were inputs of large quantities of terrestrial organic matter, net heterotrophy in the 

Apalachicola Bay system was not dominant relative to net autotrophy during a 3-year period. 

Chanton and Lewis (2002), using δ13C and δ34S isotope data, noted clear distinctions between 

benthic and water column feeding types. They found that the estuary depended on river flows to 

provide flood-plain detritus during high-flow periods, and dissolved nutrients for estuarine 

primary productivity (plants) during low flows. Floodplain detritus was significant in the 

important East Bay nursery area, thus showing that peak flows were important in washing such 

detritus into the estuary. Winter/spring periods of high river flow and macrodetritus delivery to 

the bay (Livingston, 1981a) were coincident with increased infaunal abundance (McLane, 1980). 

Four out of the 5 dominant infaunal species at river-dominated stations were detritus feeders. The 

transformation of nutrient-rich particulate organic matter from periodic river-based influxes of 

dissolved and particulate organic matter coincided with abundance peaks of the detritus-based 

25
(infaunal) food webs of the Apalachicola system (Livingston and Loucks, 1979; White et al., 

1979a, 1979b; Livingston, 1984)). A mechanism for the direct connection of increased infaunal 

abundance was described by Livingston (1983, 1984) whereby microbial activity at the surface of 

the detritus (Federle et al., 1983a) led to microbial successions (Morrison et al., 1977) that then 

provided food for a variety of detritivorous organisms (White et al., 1979a, 1979b; Livingston, 

1984). 

Mortazavi et al. (2000a) found that phytoplankton productivity in river-dominated parts of 

the Apalachicola estuary was limited by phosphorus in the winter (during periods of low salinity) 

and nitrogen during summer periods of high salinity. The Dissolved Organic Nitrogen (DON) 

input was balanced by export from the estuary. Mortazavi et al. (2000b) determined temporal 

couplings of nutrient loading with primary production in the estuary. Around 75% of such 

productivity occurs from May through November, with primary control due to grazing. Mortazavi 

et al. (2000c) gave detailed accounts of the nitrogen budgets of the bay. These studies indicated 

that phytoplankton productivity was an important component of estuarine food webs along the 

Gulf coast, and that a combination of river-derived organic matter and autochthonous organic 

carbon provided the resources for consumers in river-dominated estuaries of the Gulf coast. 

3. Biological Response to Apalachicola River Flows

An intensive field study was carried out during the period from March 1972 through July 

1984. This included monthly collections of water quality and biological data concerning infaunal 

macroinvertebrates, epibenthic macroinvertebrates and fishes (Livingston et al., 1997). The data 

were summed across all taxonomic lines and translated into the various trophic levels that 

included herbivores (feeding on phytoplankton, benthic algae), detritivores (feeding primarily on 

particulate organic matter), omnivores (feeding on plants and animals), primary carnivores 

(feeding on herbivores), secondary carnivores (feeding on primary carnivores) and tertiary 

carnivores (feeding on secondary carnivores). All data were expressed as ash-free dry weight m-1

month-1 or as percent ash-free dry weight m-2 month-1. The data were presented as monthly means 

of a series of stations (3, 4, 5, 6, 4a, 5a, 5b) in East Bay. 

26
 River flows during the last half of the 20th century and early parts of the 21st century are 

shown in Figure 8. There was a major drought during the mid-1950’s. During the intensive study 

period (1975-1984), interannual river flows followed model predictions (Meeter et al., 1979) with 

peak flows in 1975 and 1979, and a drought from 1980-1981 (Figure 8). The model noted by 

Meeter et al. (1979) indicated low fall flows, peak flows during winter-early spring periods, 

spring and fall low flow periods and low summer flows (relative to winter-spring flows) due to 

high evapotranspiration rates during warm months. This drought, characterized by the lowest 

winter-spring river flow levels during the 9.5-year study period, was a defining feature of the 

long-term habitat data with sustained high salinities during the 2-yr drought (1980-1981) 

(Livingston et al., 1997). 

Figure 8: Three-month moving averages of monthly Apalachicola River flows from October 

1950 through May 2008. Data were provided by the U. S. Geological Survey (Sumatra, Florida 

gage). Blue lines designate drought conditions. 

 

Apalachicola River Flow (Sumatra)

0

500

1000

1500

2000

2500

3000

1950/101951/101952/101953/101954/101955/101956/101957/101958/101959/101960/101961/101962/101963/101964/101965/101966/101967/101968/101969/101970/101971/101972/101973/101974/101975/101976/101977/101978/101979/101980/101981/101982/101983/101984/101985/101986/101987/101988/101989/101990/101991/101992/101993/101994/101995/101996/101997/101998/101999/102000/102001/102002/102003/102004/102005/102006/102007/10

date

There was an extreme drought from 1999-2001 (Figure 8) that was followed by the most 

recent drought period (2007-present). It is during these droughts that bay conditions are most 

susceptible to anthropogenic reductions of river flow when the combined natural and 

anthropogenic flow rate decreases have documented adverse effects on the receiving bay. 

27
4. Habitat Type and Population Distribution

The bay is characterized by a series of dominant species that are euryhaline (adapted to 

varying salinities), and able to nursery in the extreme salinity variations of the bay. An extensive 

stomach content analysis was carried out with the dominant fish and invertebrate species. The 

long-term database was re-organized according to the ontogenetic feeding stages of the 

numerically dominant species. Trophic units were averaged by month over the 14-year study. 

The actual distribution of the key estuarine species is based on microhabitat organization that, in 

turn, is based on various conditions related to river flow processes. By transforming the data 

according to ontogenetic (developmental) feeding stages, we were able to evaluate population 

distribution according to a basic, functional process (feeding) that defined the nurserying 

organism. 

 

 Infaunal macroinvertebrates 

In terms of frequency of occurrence during the sampling effort, the infaunal 

macroinvertebrate assemblages in East Bay are dominated by species such as Mediomastus 

ambiseta (below surface deposit feeder and detritivorous omnivore), Hobsonia florida (abovesurface deposit feeder and detritivorous omnivore), Grandidierella bonnieroides

(grazer/scavenger and general omnivore), Streblospio benedicti (above-surface deposit feeder 

and detritivorous omnivore), and Parandalia americana (primary carnivore). Larger types of 

infaunal macroinvertebrates include the plankton-feeding herbivores Mactra fragilis and Rangia 

cuneata. Dominant epibenthic macroinvertebrates in East Bay over the period of study include 

the palaemonetid shrimp (Palaemonetes spp.: detritivorous omnivores), xanthid crabs 

(Rhithropanopeus harrisi: primary carnivores), blue crabs (Callinectes sapidus: primary 

carnivores at < 30 mm; secondary carnivores at > 30 mm), and penaeid shrimp (L. setiferus, F. 

duorarum and F. aztecus: primary carnivores at <25 mm; secondary carnivores at > 25 mm). 

Most of these invertebrate species are browsers, grazers, or seize-and-bite predators. 

 Penaeid shrimp 

The numerically dominant invertebrates included white shrimp and blue crabs that, 

together, represent about 70% of the total numbers taken over the14-year study period. The white 

28
shrimp, Litopenaeus setiferus, is the numerically dominant penaeid species in the Apalachicola 

system. White shrimp enter the bay during spring months, and are caught in otter trawls during 

summer-fall months. Young-of-the-year white shrimp (< 25mm) are first noted in East Bay 

during early summer months. They remain in the East Bay area throughout the summer. The 

second trophic unit of this species is concentrated in East Bay during summer and fall months. 

The largest white shrimp trophic unit is located mainly just west of the river mouth and in parts of 

East Bay. White shrimp are largely absent in the bay by mid-to late November through 

December. White shrimp represent the most commercially valuable population in the 

Apalachicola estuary, and are distributed in areas most affected by river flows. This distribution 

is compatible with the importance of freshwater inflows and the resulting productivity that 

accompanies such flows. The low numbers associated with drought conditions is compatible with 

known aspects of white shrimp life history patterns. 

 

Pink shrimp (Farfantepenaeus duorarum) and brown shrimp (Farfantepenaeus aztecus) 

occur in lower numbers than the white shrimp. Pink shrimp are usually associated with higher 

salinities than white shrimp, and young-of-the-year also are most abundant during early fall in 

East Bay. This appears to be related to food availability in areas receiving freshwater flow. 

Young brown shrimp are most abundant during late spring, with the primary pattern of 

distribution just west of the river mouth and in East Bay areas. Once again, areas receiving direct 

freshwater runoff from the river are favored by both species. 

 Callinectes sapidus

The blue crab (Callinectes sapidus) is another commercially important species in the 

Apalachicola system. Young-of-the-year blue crabs appear in the bay during winter months and 

are largely concentrated in East Bay and along the main river channel of the bay. Secondary 

increases of this trophic unit occur during late summer to fall months in the upper bay. The next 

trophic stage appears in the bay during February with secondary peaks during summer months. 

This trophic stage is centered in East Bay. The largest blue crab trophic unit is found in highest 

numbers during summer months in East Bay. In all 3 blue crab trophic stages, the East Bay 

nursery area appears to be the favorite habitat. Spatial-temporal blue crab distribution appears to 

29
be associated with the relationship of the individual trophic units to freshwater inputs from the 

river. 

The long-term trends of invertebrate distribution indicate that invertebrate numbers are 

associated with river flow even though such manifestations of habitat preference vary by species 

and by trophic unit within each species. High invertebrate numbers during the drought of 1980-

1981 were due in large part to blue crab predominance. Each species has a very different set of 

habitat needs through its ontological development, with major differences in the spatial/temporal 

patterns of habitat use. The one unifying feature that affects such distributions appears to be 

increased concentrations of invertebrate populations in areas associated with the entry of 

freshwater into the upper bay. These areas are notable for relatively high organic carbon and 

nutrient loading and associated productivity. Trophic unit distribution displays a broad spectrum 

of diverse phase interactions with river input to the bay over seasonal and interannual periods. 

Feeding habit changes are related to habitat-oriented differences in available food. 

Fishes 

 

Dominant fishes in East Bay include the plankton-feeding primary carnivore Anchoa 

mitchilli (bay anchovy) and benthic feeding primary carnivores such as spot (Leiostomus 

xanthurus), hogchokers (Trinectes maculatus), young Atlantic croakers (Micropogonias 

undulatus: < 70 mm) and silver perch (Bairdiella chrysoura: 21-60 mm). Secondary carnivores 

among the dominant fishes include larger croakers (> 70 mm), Gulf flounder (Paralichthys 

albigutta), and sand seatrout (Cynoscion arenarius). Tertiary carnivores in East Bay include the 

larger spotted seatrout (C. nebulosus), southern flounder (P. lethostigma), largemouth bass 

(Micropterus salmoides) and gars (Lepisosteus spp). With the exception of the bay anchovies, all 

of the above species live near the sediment-water interface with most of the trophic organization 

of the bay dependent on interactions among bottom living infaunal (living in or on sediments) and 

epibenthic (living above sediments) macroinvertebrates and fishes. The primary fish dominants, 

representing about 80% of total fish numbers taken over the sampling period, include bay 

anchovies, seatrout, spot, and Atlantic croaker. 

30
 Anchoa mitchilli 

The youngest bay anchovies enter the bay during early summer, and are located mainly in 

East Bay. They eventually move to the river in the late fall. The second anchovy trophic unit 

moves to the river area during fall months. Overall, this species is closely tied to freshwater flows 

from the Apalachicola River, and populations move from summer distributions in East Bay to fall 

distributions in the Apalachicola River channel. Long-term changes of the anchovy trophic units 

indicated peak numbers of the first trophic unit between peak river flows (1973-75) and drought 

conditions (1980-81). Peak numbers were noted during the first year of the drought, with major 

decreases during succeeding years. This distribution was consistent with the postulated increases 

of plankton during the first year of the drought. The second trophic unit showed relatively low 

numbers during and after the 1980-81 drought. 

 Cynoscion arenarius

The sand seatrout, a piscivorous fish that feeds primarily on anchovies (Sheridan and 

Livingston 1979), reaches peak numbers during late spring and early summer. The distribution of 

the first 2 trophic units is located largely in East Bay and around the Apalachicola River mouth 

from late spring to early fall. The larger sand seatrout are located mainly near the river channel of 

the bay. This distribution generally follows that of the bay anchovies. The long-term trends of 

this species indicate relatively low numbers during the second year of the drought followed by 

subsequent increases during succeeding years. The patterns of anchovy distribution in time could 

reflect predation pressure by the sand seatrout. 

 Leiostomus xanthurus

 Young-of-the-year spot enter the bay during winter-early spring periods, and are 

concentrated in East Bay and areas near the river mouth. Older spot move to the lower parts of 

Apalachicola Bay. This distribution in consistent with known distributions of infaunal 

macroinvertebrate distribution in space and time, and is a trophic response to herbivorous and 

omnivorous species that respond directly to river inflows to the bay. Temporal changes of spot 

indicated a major increase of young spot during the second year of the drought followed. 

31
 Micropogonias undulatus

Young-of-the-year Atlantic croaker enter the bay during winter-spring months and are 

located mainly in East Bay and west of the river mouth. The larger forms move throughout the 

bay during summer months. There were no overt temporal trends of this species. 

Apalachicola Bay ecology is closely associated with freshwater input from the 

Apalachicola River (Livingston, 1984a). The distribution of epibenthic organisms in the 

Apalachicola Estuary follow a specific spatial relationship to river flows. Stations most affected 

by the river are inhabited by anchovies (Anchoa mitchilli), spot (Leiostomus xanthurus), Atlantic 

croaker (Micropogonias undulatus), gulf menhaden (Brevoortia patronus), white shrimp 

(Litopenaeus setiferus), and blue crabs (Callinectes sapidus). The outer bay stations are often 

dominated by species such as silver perch (Bairdiella chrysoura), pigfish (Orthopristis 

chrysoptera), least squid (Lolliguncula brevis), pink shrimp (Farfantepenaeus duorarum), brown 

shrimp (Farfantepenaeus aztecus), and other shrimp species (Trachypenaeus constrictus). Sikes 

Cut, an artificial opening to the Gulf that is maintained by the U. S. Army Corps of Engineers, is 

characterized by salinities that resemble the open gulf. This area is dominated by species such as 

least squid, anchovies, Cynoscion arenarius, Etropus crossotus, Portunus gibbesi, and Acetes 

americanus. 

Field analyses of long-term change of infaunal and epibenthic invertebrates and fishes are 

based on a series of studies executed continuously from 1972-1984 (Livingston, 1984). Crosscorrelation analyses of long-term changes of infaunal and epibenthic invertebrates and fishes over 

the intensive study period indicated that dominant bay populations followed a broad spectrum of 

diverse phase interactions with river flow and associated changes in salinity over interannual 

periods of drought and flood conditions. Long-term (14-year) trends of penaeid shrimp indicated 

direct associations with river flow (Livingston, 1991b). Fish populations also followed diverse, 

species-specific phase angles with river flows. Fish numbers usually peaked one month after 

river flow peaks (winter periods) whereas invertebrate numbers were inversely related to peak 

river conditions with increases during summer months (Livingston, 1991b). Top fish dominants 

such as spot were prevalent in winter-spring months of river flooding whereas peak numbers of 

32
penaeid shrimp usually occurred in summer and fall months. River flow was thus a controlling 

factor for biological organization of the Apalachicola estuary (Livingston, 1991b). 

The response of the bay to river flows is complex due to species-specific responses to the 

river-directed habitat changes and responses of the food web to nutrient loading and 

phytoplankton production. 

 Marshes and Submerged Aquatic Vegetation

The primary non-forested coastal fringe is dominated by freshwater and brackish marshes 

in the Apalachicola delta above East Bay (Figure 9a; Livingston, 1984). The fresh water 

dominants include bulrushes (Scirpus spp.), cattails (Typha domingensis), and other species such 

as saw grass (Cladium jamaicense). Brackish species include Juncus roemerianus and Spartina 

alterniflora. These marshes are highly productive and, together with the loading of river nutrients 

and organic matter, contribute to the enhanced nursery function of East Bay. 

 Figure 9a: Seagrass and wetland habitats of the Apalachicola Drainage System. 

33
The primary distribution of the submerged aquatic vegetation (SAV) in the Apalachicola 

estuary is shown in Figure 9a. The color and turbidity of river input tends to limit the distribution 

of the benthic macroflora to the shallow fringes of the estuary. Upper East Bay has historically 

been inhabited by dense beds dominated by tapeweed (Vallisneria americana), widgeon grass 

(Ruppia maritina), and pondweed (Potamogeton pusillus). These beds have been well studied 

(Livingston and Duncan, 1979; Purcell, 1977), and are dominated by the snail Neritina reclivata

and various crustaceans and polychaete worms. Dominant fishes include killifish (Lucania 

parva), silversides (Menidia beryllina) and centrarchids such as largemouth bass (Micropterus 

salmoides). These areas serve as nursery grounds for penaeid shrimp and other crustaceans and 

fishes at early stages of their ontogenetic progressions in the bay. 

The predominant macrophyte species in the mesohaline and higher salinity areas off St. 

George Island (Figure 9a) is shoalgrass (Halodule wrightii) with other species such as Gracilaria

spp. and manatee grass (Syringodium filiforme) also represented. Sheridan and Livingston 

(1983) noted that the infaunal macroinvertebrates in this part of the bay were among the most 

speciose in the northern hemisphere. This infauna included various species used as food for the 

abundant blue crabs (Callinectes sapidus), pink shrimp (Farfantepenaeus duorarum), pinfish 

(Lagodon rhomboides) and spotted seatrout (Cynoscion nebulosus) in this part of the bay. 

The seagrass beds off St. James Island (Figures 9a, 9b) are dominated by turtle grass 

(Thalassia testudinum) and manatee grass (Syringodium filiforme) (Livingston, 2008). Water 

quality data and depth distributions indicated that between depths of 1 to 2 m, depth-related light 

penetration becomes limiting to the grass beds. Light limitation is an important factor in the 

development of seagrass beds in the area. Light penetration is limited by color and turbidity. 

Based on the distribution of these factors, the data indicate that the combination of runoff from 

the Carrabelle River and the depth of the water in areas east of the river are important 

determinants of SAV distribution. Sea grasses and macroalgae provide habitat and productivity 

that supports a diverse and productive trophic organization. Dominant fishes in these beds 

included high numbers of pigfish (Orthopristis chrysoptera), pinfish (Lagodon rhomboides), and 

silver perch (Bairdiella chrysoura) (Livingston, 1984). Dominant species taken with the 

trammel nets in the seagrass beds included southern flounder (Paralichthys albigutta), spotted 

34
seatrout (Cynoscion nebulosus), and sharks of various types (Livingston, 1984). Storm water 

runoff from urban development has recently caused high loading of nitrogen and phosphorus into 

the St. George Sound at concentrations that have stimulated plankton blooms. These blooms are 

characterized by increased turbidity, alterations of the dissolved oxygen regime and reduced light 

penetration. 

Figure 9b: Distribution of submerged aquatic vegetation (density) in near-shore areas of St. 

George Sound during 2006-2007. Water quality stations (Livingston, 2006a) are shown along 

with upland wetlands systems. 

 

 East Bay

East Bay (Figure 9c) is a major nursery ground for various populations. Dominant fishes 

in East Bay include the plankton-feeding primary carnivore Anchoa mitchilli (bay anchovy) and 

benthic feeding primary carnivores such as spot (Leiostomus xanthurus), hogchokers (Trinectes 

maculatus), Atlantic croakers (Micropogonias undulates < 70 mm) and silver perch (Bairdiella 

chrysoura: 21-60 mm). Secondary carnivores among the dominant fishes include larger croakers 

35
(> 70 mm), Gulf flounder (Paralichthys albigutta), and sand seatrout (Cynoscion arenarius). 

Tertiary carnivores in East Bay include the larger spotted seatrout (C. nebulosus), southern 

flounder (P. lethostigma), largemouth bass (Micropterus salmoides) and gars (Lepisosteus spp). 

With the exception of the bay anchovies, all of the above species live near the sediment-water 

interface with most of the trophic organization of the bay dependent on interactions among 

bottom living infaunal and epibenthic macroinvertebrates and fishes. Plankton-feeding bay 

anchovies (Anchoa mitchilli) are also dominant in East Bay. Invertebrates in East Bay are 

dominated by penaeid shrimp and blue crabs. 

Figure 9c: Station distribution in East Bay for the long term trophic analyses involving infaunal 

and epifaunal macroinvertebrates and fish. 

 

A listing of the 9.5 year averages of the monthly data for East Bay are given in Table 1. 

Sediments in western parts of East Bay (station 4) were relatively silty. The same is true of the 

small embayment in eastern parts of the system (station 4a) and a tidal creek affected by runoff 

36
from upland forestry operations in Tate’s Hell Swamp (station 5b). The area in the upper bay 

(station 5a) was mainly sandy. Western parts of East Bay were denoted by considerable amounts 

of leaf matter during periods of high winter-spring river flows relative to eastern sections (Figure 

9a). Watercolor increased in eastern parts of the bay due to runoff from clear-cut areas in Tate’s 

Hell Swamp. Turbidity was highest in areas adjacent to input from the Apalachicola River 

(station 4a). Dissolved oxygen and pH were lowest in the area receiving runoff from the cleared 

areas in the contributing drainage area (5b). Total weights of fishes and invertebrates were 

highest in areas adjacent to the river where the detrital food webs were particularly strong. The 

Atlantic Croaker (Micropogonias undulatus) and blue crabs (Callinectes sapidus) were also more 

abundant in western sections of the bay whereas white shrimp (P. setiferus) were most numerous 

at stations 4a and 5a. Overall, areas affected by runoff from the clear-cut areas were denoted by 

the lowest overall secondary production. These data indicate the importance of the river as a 

source of organic matter for the detrital food webs of the bay and the impact of clear-cutting on 

eastern sections of East Bay. 

Table 1. Averages of physico-chemical and biological variables sampled during the 9.5–year 

survey of East Bay taken monthly from 2/1997-7/1984. Stations are noted in Figure 9. b=bottom, 

s=surface. n/smp=numbers per sample. FII (fish, invertebrates, infauna). C1 (primary carnivores), 

C2 (secondary carnivores), MICU (Micropogonias undulates), CALSAP (Callinectes sapidus), 

PENSET (Litopenaeus setiferus). 

Factor S-4 S-4A S-5A S-5B

%silt 32.500 41.300 2.500 49.900

bsalinity (ppt) 10.014 3.244 5.054 4.257

scolor (Pt-Co Units) 53.640 60.447 73.803 115.548

bTurbidity (NTU) 23.171 20.311 22.781 17.535

sD.O.(mgL-1) 8.285 8.956 8.675 7.900

nOxygen Anom (mgL-1) -0.593 0.167 -0.182 -0.868

bpH (pH Units) 7.264 7.401 7.363 6.982

fish totwt(gm2

) 0.099 0.057 0.047 0.036

inv totwt (gm2

) 0.026 0.022 0.012 0.014

FIIC1 (gm2

) 0.575 0.050 0.474 0.035

FIIC2 (gm2

) 0.088 0.045 0.025 0.022

MICUn/smp 26.759 17.623 21.421 13.743

CALSAPn/smp 3.741 3.392 2.868 2.993

PENSETn/smp 4.157 9.189 7.205 2.683

37
 Detritus-based Food Webs

Leaf matter, as a form of macrodetritus, enters the bay in areas dominated by river flow 

(Livingston, 1984). These inputs occur during winter-early spring periods (Figure 9d), and are 

influenced by peak river flow flooding in river wetlands areas. Microdetritus (small particulates) 

fluxes into the bay from the river also peak during winter-spring periods (Figure 9e). Livingston 

(1984) outlined the detrital food webs with respect to influxes of particulate organic matter that 

amounts to about 214,000 mt (metric tons) annually (Mattraw and Elder, 1982). Livingston 

(1984) noted that micro- and macroparticulate matter had a direct relationship with river flooding 

with the exact timing of peak river flows and productivity of river wetlands as key determinants 

of the short-term fluctuations and long-term trends of the input of allochthonous (derived from 

outside the system) organic matter into the bay (Livingston, 1981a, b). Detrital inputs were 

significantly associated with seasonal trends of river flows during winter-spring periods. Local 

marshes also contribute to the export of detrital aggregates to the bay (Ribelin and Collier, 1979). 

Figure 9d: Leaf matter taken in otter trawls in East Bay taken monthly from January 1975-

February 1981. 

East Bay leaf matter (dry weight)

0

50

100

150

200

250

300

350

400

450

Jan-75

Apr-75

Jul-75

Oct-75

Jan-76

Apr-76

Jul-76

Oct-76

Jan-77

Apr-77

Jul-77

Oct-77

Jan-78

Apr-78

Jul-78

Oct-78

Jan-79

Apr-79

Jul-79

Oct-79

Jan-80

Apr-80

Jul-80

Oct-80

Jan-81

date

DryWt-A04-g/trwl DryWt-A5a-g/trwl

38
Figure 9e: Microdetritus taken in water samples in the lower Apalachicola River monthly from 

August 1975-March 1982. 

Apalachicola River Microdetrit

0

10000

20000

30000

40000

50000

60000

75/0875/1276/0476/0876/1277/0477/0877/0977/1077/1278/0278/0378/0478/0678/0778/0878/10

78/11

78/1279/0279/0379/0479/0679/0779/0879/10

79/11

79/1280/0280/0380/0480/0680/0780/0880/10

80/11

80/1281/0281/0381/0481/0681/0781/0881/1081/1282/0182/02

date

DryWt(mg/1000L)-A08 3 per. Mov. Avg. (DryWt(mg/1000L)-A

Particulate organic matter is colonized by morphologically diverse prokaryotic and 

microeukaryotic assemblages (White, 1983) that can be defined by complex chemical signatures 

such as phospholipid alkyl fatty acids (prokaryotes, microeukaryotes) and fatty lipids (anaerobicaerobic bacteria) (White, 1983; Federle et al., 1983; Livingston, 1984). There is a succession of 

microbiota that colonize the particulate matter deposited into the bay with initial bacteria 

succeeded by diatoms and fungal mycelia (Bobbie et al., 1978). Grazing amphipods feed on the 

microbiota that live on leaf matter (Morrison and White, 1980). Amphipod distribution is 

significantly associated with bacterial fatty acids (White et al, 1979a, b). This base of the detrital 

food webs is controlled by epibenthic predators (Federle et al., 1983). Various forms of nutrients 

and dissolved organic nitrogen and phosphorus compounds contributed by the river are thus 

transformed into a nutritious mixture of particulate matter through microbial activity that forms 

the basis of the detrital food webs dominated by amphipods, gastropod mollusks, isopods and 

commercially valuable decapods (white shrimp, blue crabs). The numerical abundance of the 

litter-associated populations is strongly aligned with the availability of detritus (Livingston, 

39
1984). The distribution of these detrital associations is determined by temperature, salinity, and 

the biochemical features of the microbial communities with detritivorous macroinvertebrates as 

the link between the microbial producers and numerically important populations of fishes and 

invertebrates. 

Oyster Bars

Oyster bars represent an important habitat in the Apalachicola estuary, providing cover 

and food for diverse assemblages (Livingston, 1984). This includes bryozoans, flatworms, 

annelids, gastropod and pelecypod mollusks, arthropod crustaceans and fishes. Oyster ecology 

will be treated below. 

Sub-tidal (soft sediment) Areas

Around 70% of the Apalachicola Bay system is composed of sub-tidal, unvegetated, soft 

sediment areas. This habitat is dominated by polychaete worms (deposit and suspension feeders) 

and amphipods. Studies documented by Livingston (2002) were carried out at stations in East 

Bay and St. George Sound (Figure 9f). Water quality and biological samples were taken 

monthly at stations 3 and 5a (July 1978-June 1984) and station ML (November 1981-August 

1986). The biological organization reflected the differences between the highly productive mud 

flats in East Bay and the productive seagrass beds of St. George Sound. Fresh water quality and 

quantity in the loadings to the respective areas are quite different in terms of nutrients. These 

differences also extend to the most important food web components in these areas that are 

represented by infaunal macroinvertebrates that live in and on the sediments in the respective 

study areas. The most obvious difference between the aquatic habitats of East Bay (stations 3 

and 5a) and St. George Sound (station ML) is the lack of direct (station 3) or indirect (station 5a) 

Apalachicola River flow at station ML. East Bay station 3, which receives direct river flow, had 

lower salinity, temperature, and dissolved oxygen anomaly than the other sites. Bottom salinity 

in East Bay ranged from essentially freshwater conditions during winter-spring floods to 

salinities between 10 and 20 ppt (parts per thousand) during the fall low water periods. There 

were rapid changes in salinity at station 3. Station ML was characterized by high salinity and 

less salinity variability. During periods of high Apalachicola River flow, salinity was not 

markedly reduced in St. George Sound and there was evidence (low salinities during summer 

40
months) that local runoff was responsible for the relatively small seasonal differences in salinity 

in this area of the bay. Station 5a was outside of the direct effects of the river; however, this 

station received periodic highly colored fresh water input from adjacent upland swamps. 

 

Figure 9f: Chart showing stations used in East Bay and St. George Sound for the 

comparative analysis of the river-dominated upper bay (stations 3 and 5a) and the high salinity 

sound area (station ML). 

One hundred and sixty-six taxa were collected at station ML compared with 47 and 40 at 

stations 3 and 5a, respectively, over the long-term sampling program. The dominant organisms 

(i.e., those species comprising the top 90% of density) at each site were comprised of 9 (station 

41
3), 10 (station 5a) and 28 taxa (station ML) (Livingston, 2002). The polychaete Mediomastus 

ambiseta was the numerical dominant at all stations. The three most abundant taxa comprised 

over 50% of the total infaunal density at all three sites. Long-term means of community indices 

differed among stations over the period of record with the highest density at station 3, the 

greatest number of taxa at station ML, and the greatest biomass at station 5a. Analysis of the 

long-term field data indicated that species richness reached maximal levels in all three sampling 

areas during fall, a period of relatively low numerical abundance. 

Fine-scale community variation was examined with the replicated sets of 100 core 

samples taken at each of the three study sites in October 1981. Data from the replicate sets are 

presented graphically in Figure 9g. Infaunal abundance per core was highest at station 3 and 

lowest at station ML. Species richness per core was highest at station ML and lowest at station 

5a. Relative dominance per core was highest at station 3 and lowest at station ML. Station 3 had 

high numbers m-2 with a relatively low cumulative species richness (21 species). Numerical 

dominants were the polychaetes Mediomastus ambiseta and Streblospio benedicti. Station 5a 

was moderately productive in terms of numerical abundance with low cumulative species 

richness (10 species) and high dominance of the same species noted at Station 3. A total of 72 

species was found at station ML with low dominance of the most numerically abundant species. 

Dominants included Apoprionospio pygmaea, Paraprionospio pinnata and Mediomastus 

ambiseta. 

These data indicate that areas affected by river flow are highly productive in terms of 

secondary productivity but are low in species richness due to the highly variable environment in 

such areas. Parts of the bay distant from river input are higher in species richness but lower in 

secondary productivity. These data indicate what would happen to the bay if river flows are 

reduced due to increased incidence and intensity of low flows during droughts. The bay would 

be inhabited by more species, but the overall productivity would be reduced as euryhaline 

populations were reduced due to increased salinity and reduced primary productivity. The 

physically controlled, highly productive system would be replaced by a biologically controlled, 

speciose system with lower secondary production. 

42
Figure 9g: Three-dimensional view of numbers of individuals, species richness, and top 

dominant numbers of infaunal macroinvertebrates taken from 100 core samples at stations 3, 5a 

and ML. 

43
The influence of river flow on receiving areas was observed as a gradient of increasing 

temporal habitat stability with distance from the river. Salinity variation as well as ambient 

salinity at any given time appeared to be primary factors that defined the East Bay habitat. Areas 

directly (station 3) and indirectly (station 5a) affected by Apalachicola River flow had high 

salinity variation relative to areas distant from such flow (station ML). Although important 

habitat variables had high levels of variation within short-term periods at river-dominated sites, 

such variation was relatively consistent from year to year. Other variables such as watercolor 

and oxygen anomaly had significant annual differences at river-dominated stations relative to 

areas not directly affected by river flow. There were thus fundamental differences of habitat 

stability between a system that was physically dominated by freshwater runoff (East Bay) and an 

area that was little influenced by changes in river flow (St. George Sound). The Sound is mainly 

influenced by rainfall and storm water runoff from adjacent land areas. These differences of 

runoff result in distinctive forms of species composition and trophic organization. 

The Apalachicola River thus serves as the dominant habitat feature of the receiving 

estuary. River flow elements contribute both directly and indirectly to a series of habitats that 

maintain the overall high secondary production of the estuary. Surrratt et al. collected sediment 

cores from three sites in Apalachicola Bay and analyzed for organic carbon (C), total nitrogen 

(N), and total phosphorus (P) concentrations and delta13C and delta15N stable isotopic 

abundances. According to this recent research, 

“Carbon and nitrogen concentrations, ratios, and stable isotopes coupled with 

grain-size shifts for the bay suggest a decrease in river organic matter supply and 

a change in sediment clay content supply and/or distribution for the bay. Overall, 

the applied indicators suggest an increase in marine influence on the organic 

matter in the estuary. These shifts appear to be associated with Apalachicola 

River management practices coupled with sea-level rise in the Gulf of Mexico. “ 

Samples taken near the river mouth indicated that organic matter deposition was driven by both 

natural (i.e., hurricanes and droughts) and anthropogenic (i.e., hydrologic river alteration and 

dredging) activities. After the drought of 1981, Woodruff Dam operation procedures and the 

resultant river discharge patterns could have affected mass sedimentation rates and organic 

loading within the estuary. Coupling ACF River discharge alterations with sea-level rise appears 

to account for the modification of organic matter loading to the bay. 

44
5. Trophic Organization of the Bay

Physical, chemical and biological (infauna, epibenthic macroinvertebrates, fishes) samples 

were taken at fixed stations in East Bay (Figure 9) monthly from 1975-1984 (9.5 years; 

Livingston et al., 1997). East Bay is the primary nursery area for the Apalachicola Bay system. 

These data were used to transform the descriptive field information into a trophic organization for 

the estuary. Detailed descriptions of methods for the field collection of physical and chemical 

data have been provided by Livingston (1979, 1981a, 1982, 1984a, b, 2000, 2002) and Livingston 

et al. (1974, 1976). 

All of the biological data (as biomass.m-2.mo

-1 of the infauna, epibenthic 

macroinvertebrates and fishes) were transformed from species-specific data into a new data 

matrix based on trophic organization as a function of ontogenetic (developmental) feeding stages 

of the species found in the estuary over the multi-year sampling program. Ontogenetic feeding 

units were determined from a series of detailed stomach content analyses carried out with the 

various epibenthic invertebrates and fishes in the region (Sheridan 1978, 1979, Laughlin 1979, 

Sheridan and Livingston 1979, 1983, Livingston 1980, 1982, 1984b, unpublished data, Stoner and 

Livingston 1980, 1984, Laughlin and Livingston 1982, Stoner 1982, Clements and Livingston 

1983, 1984, Leber 1983, 1985). Based on the long-term stomach content data for each size class, 

the fishes and invertebrates were re-organized into their trophic ontogenetic units using cluster 

analyses. An example of such an analysis is given for the blue crab, Callinectes sapidus (Figure 

10). Generic codes are given in Table 2. 

45
Table 2: Generic Codes for the Trophic Ontogenetic Units. 

AMPHIP AM Amphipods OPHIUR OP Ophiuroids

ANNELI AN Annelids ORGCON OR Organic remains

APPENA AP Appendicularians OSTRAC OS Ostracods

ANIMRM AR Animal remains POLYLA PL Polychaetes (larvae)

BARNAC BA Barnacles (ad,juv) POLYCH PO Polychaetes (ad,juv)

BIVALV BI Bivalves (ad,juv) PLNTRM PR Plant remains

BARLAR BN Barnacles (larvae) PYNCNO PY Pycnogonida

BRASPE BR Branchiopods RADIOL RA Radiolarians

BRYOZO BZ Bryozoans REPTIL RP Reptilia

CAMBAR CA Cambaridae SANDGR SA Sand grains

CEPHCO CD Cephalochordates SHRIMP SH Shrimp (ad,juv)

CEPHAL CE Cephalopoda SIPUNC SI Sipunculids

CHAETO CH Chaetognaths SPONGE SP Sponge matter

CILLIO CI Ciliophora STOMAT ST Stomatopods

CLADOC CL Cladocerans TANAID TA Tanaids

CNIDAR CN Cnidaria TREMAT TM Trematodes

COPEPO CO Copepods (calanoid,cyclopoid) TUNSPE TN Tunicates

CRABBS CR Crabs (ad,juv) TURBEL TR Turbellarians

CRUSRM CS Crustacean remains UNIDEN UN Unidentified/unknown

CHITON CT Chitons HOLOTH HO Holothuroidia

CUMACE CU Cumaceans HYDRAC HY Hydracarina

DETRIT DE Detritus INVEGG IE Invertebrate eggs

DIATOM DI Diatoms INSLAR IL Insect larvae

DECALA DL Decapod larvae INSECT IN Insects

ECHINO EC Echinoderms INSPUP IP Insect pupae

EGGCAS EG Egg cases ISOPOD IS Isopods

FISHEG FE Fish eggs MICALG MA Microalgae

FISHLA FL Fish larvae MOLLAR ML Molluscan larvae

FORAMS FO Foraminiferans MYSIDS MY Mysids

FECALP FP Fecal pellets NEMATD NE Nematodes

FISHRM FR Fish remains (ad,juv) NEMERT NM Nemerteans

GASTRO GA Gastropods OLIGOC OL Oligochaeta

GENSPE GS Genus/species dummy

HARPAC HC Copepods (harpacticoid)

HEMICH HE Hemichordates

HIRSPE HI Hirudinia

46
Figure 10: Ontogenetic feeding units of blue crabs (day vs. night collections). 

47
The data show how the diet of the blue crabs taken in the Apalachicola estuary changes as 

the organisms grow. This analysis was carried out for the all the major invertebrate and fish 

species in the Apalachicola system. These data express the lifetime feeding habits in a far more 

detailed and significant way than just looking at the adult feeding behavior. This is important in 

what is essentially a nursery system where by fishes and invertebrates use the highly productive 

estuary as a nursery for the growth and maintenance of juveniles. 

Infaunal macroinvertebrates were also organized by feeding preference based on a review 

of the scientific literature (Livingston 2000, 2002). The field data for the infauna, fishes and 

invertebrates were re-ordered into trophic levels (i.e., herbivores, omnivores, three levels of 

carnivores [C1, C2, C3]) so that monthly changes in the overall trophic organization of the system 

could be determined over the study period. The data were summed across all taxonomic lines and 

translated into the various trophic levels that included herbivores (feeding on phytoplankton and 

benthic algae), omnivores (feeding on detritus and various combinations of plant and animal 

matter), primary carnivores (feeding on herbivores and detritivorous animals), secondary 

carnivores (feeding on primary carnivores and omnivores) and tertiary carnivores (feeding on 

primary and secondary carnivores and omnivores). Data were given as ash-free dry mass.

m-2.mo

-1 

or as percent ash-free dry mass.m-2.mo

-1. 

We assumed that feeding habits (at this level of detail) did not change over the period of 

observation, based on previous analyses of species-specific fish feeding habits that remained 

stable in Apalachee Bay over a 6-7-yr period (Livingston 1980). In this way, the long-term 

database of the collections of infauna, epibenthic macroinvertebrates and fishes was re-organized 

into a quantitative and detailed trophic matrix based not solely on species (Livingston 1988) but 

on the complex ontogenetic feeding stages of the various organisms in East Bay. 

6. Long-term Changes of Trophic Organization

Livingston et al. (1997) provided important evidence of how droughts affect the key 

trophic components of the Apalachicola Bay system through time. Physical/chemical and 

biological samples (infauna, epibenthic macroinvertebrates, fishes) were taken monthly at fixed 

stations in East Bay from February 1975-August 1984. The field data were then re-ordered into 

trophic levels so that monthly changes in the overall trophic organization of East Bay could be 

48
determined over the study period. . High flows occurred during the winter-spring months of most 

years and low flows occurred during summer-fall months (Figure 11). From May 1980 through 

the end of 1981, there was a major drought with substantially lower river flows during the winterspring of 1981. Flow rates during the 20-mo period prior to the winter of 1982 were consistently 

below the long-term (40-yr) monthly means and were often less than 50% of what East Bay 

usually receives in the way of freshwater runoff from the river. The following 2.5 yr were 

characterized by a general return to the prevailing patterns of Apalachicola River flow as noted 

during the period from 1978 through the winter of 1980. 

Figure 11: Apalachicola River flows, monthly, from February 1975 through June 1984. Data 

were provided by the U. S. Geological Survey (Sumatra, Florida gage). 

Apalachicola RIver Flow

0

500

1000

1500

2000

2500

75/0275/0475/0675/0875/1075/1276/0276/0476/0676/0876/1076/1277/0277/0477/0677/0877/1077/1278/0278/0478/0678/0878/1078/1279/0279/0479/0679/0879/1079/1280/0280/0480/0680/0880/1080/1281/0281/0481/0681/0881/1081/1282/0282/0482/0682/0882/1082/1283/0283/0483/0683/0883/1083/1284/0284/0484/06

date

APRIV 3 per. Mov. Avg. (APRIV)

The most outstanding aspect of the bay salinity over the period of study was the sustained 

high salinities during the 2-yr period of drought (1980-1981) (Figure 12). Watercolor was lowest 

and Secchi disk readings (light penetration) were highest during the drought period of 1980-1981 

with Secchi readings in 1980 being significantly different (p < 0.05) from preceding years. Color 

levels during the drought years were significantly (p < 0.05) different from those taken during 

49
preceding and succeeding years. The period during the 1980-1981 drought was also characterized 

by periodically high positive values of dissolved oxygen anomalies. All physical-chemical 

indices returned to previous levels during the period following this drought. 

Figure 12: Water quality indices (Secchi depths, watercolor, salinity) taken monthly from 

February through June 1984. Also shown are the 3-month moving averages of the data. 

EAST BAY

0.1

1

10

100

1000

75/0275/0675/1076/0276/0676/1077/0277/0677/1078/0278/0678/1079/0279/0679/1080/0280/0680/1081/0281/0681/1082/0282/0682/1083/0283/0683/1084/0284/06

date

SECCHI COLOR

SALINITY 3 per. Mov. Avg. (SECCHI) 3 per. Mov. Avg. (COLOR) 3 per. Mov. Avg. (SALINITY)

DROUGHT

50
Infaunal abundance was highest during the early part of the drought period. However, 

there was a sharp reduction of infaunal numbers by spring 1982 at which time the lowest numbers 

of the data series were found. Infaunal numbers taken during the peak drought years (1980 and 

1981) were significantly lower than those of all other collection years. During summer 1981 (the 

latter part of the drought period), infaunal trophic diversity dropped significantly (p < 0.05) to the 

lowest level of the survey period. Invertebrate trophic diversity followed the trends of infaunal 

trophic diversity with sustained low levels during the spring and summer of 1981. Fish numbers 

and fish trophic diversity were lowest during the majority of the drought. The drought conditions 

of 1980-1981 were thus associated with initial increases of numbers of organisms of various types 

that was followed by a general decrease of numbers and trophic diversity. 

The long-term trends of the trophic groupings in East Bay are shown in Figure 13. The 

mean monthly biomass of herbivores over the study period was 2.39 g/m2

 with averages of 0.21 

g/m2 for omnivores, 0.53 g/m2

 for primary carnivores, 0.04 g/m2 for secondary carnivores and 

0.004 g/m2 for tertiary carnivores. There was a marked increase in the herbivore biomass during 

the beginning of the drought. Herbivore biomass peaks coincided with low winter river flows, 

peak turbidity, low water color and increased Secchi depths. The more frequent periods of 

positive oxygen anomaly during the drought also coincided with the high levels of herbivore 

biomass. There was a marked decrease of herbivore biomass that started during the second half 

of the drought. Herbivore biomass virtually collapsed during the following year with the lowest 

levels occurring during spring-summer 2003. There was not a complete recovery of herbivores 

through the end of the sampling period. 

Omnivore biomass peaked during the period of increasing herbivore biomass in the 1980-

1981 drought. There was a general decrease of omnivore biomass during the succeeding 2 yr. 

Once again, there was not a complete recovery of the omnivores during the study period. Primary 

carnivore biomass increased during fall 1980 and continued at high levels through spring 1981. 

After the drought, primary carnivore biomass declined to levels way below the pre-drought 

conditions. There was no recovery of the C1 carnivores during the post-drought months of the 

study. The biomass of secondary carnivores increased incrementally from the onset of the 

drought with peaks that generally coincided with those of the primary carnivores. There was no 

overt recovery of this group during the months following the drought. The tertiary predators were 

51
virtually absent during the 1980-1981 drought period. Overall, the drought of 1980-1981 had a 

profound effect on the trophic organization of East Bay. This impact remained at various trophic 

levels during the 2.5-year period of river flow recovery. 

Figure 13: Fish, infaunal and invertebrate (FII) trophic levels (herbivores, omnivores, C1 

carnivores, C2 carnivores) taken monthly from February through June 1984. Also shown are the 

12-month moving averages of the data. 

East Bay

0.001

0.01

0.1

1

10

100

75/0275/0675/1076/0276/0676/1077/0277/0677/1078/0278/0678/1079/0279/0679/1080/0280/0680/1081/0281/0681/1082/0282/0682/1083/0283/0683/1084/0284/06

date

FIIHER FIIOMN

FIIC1 FIIC2

12 per. Mov. Avg. (FIIHER) 12 per. Mov. Avg. (FIIOMN) 12 per. Mov. Avg. (FIIC1) 12 per. Mov. Avg. (FIIC2)

DROUGHT

52
The trophic data were examined on a relative basis by expressing the mass of each trophic 

level as a percent of each monthly total (Figure 14). This enabled a view of an aspect of trophic 

structure different from absolute mass. The herbivores showed the most pronounced dominance 

during the first 17 mo of the 1980-1981 drought. After this period, there was a distinct decrease 

of the herbivores as a percentage of the monthly totals. The omnivores showed an almost 

diametrically opposite reaction with relative decreases during the drought and increases during 

the 2-yr period following the drought. The primary carnivores had the highest percentages during 

the year after the drought while the secondary and tertiary carnivores had the highest such 

percentages during the first and second years following the drought. This pattern of prolonged 

delays of the primary, secondary and tertiary carnivores was evident only as percentages of the 

monthly biomass totals during the latter stages and following the end of the drought at which 

times overall biomass was low. 

Figure 14: Fish, infauna, invertebrate (FII) trophic data taken monthly from 2/75-8/84 in East 

Bay. Data represent % of total biomass for each category (herbivores, omnivores, C1, C2, 

C3 carnivores). 

53
Livingston et al. (1997) found that, within limited natural bounds of freshwater flow from 

the Apalachicola River, there was little change in the trophic organization of the Apalachicola 

estuary over prolonged periods. The physical instability of the estuary was contrasted with the 

biologically stable estuarine system. However, when a specific threshold of freshwater reduction 

was reached during the drought (1980-1981), clarification of the normally turbid and highly 

colored river-estuarine system led to rapid changes in the pattern of primary production, which, in 

turn, were associated with major changes of the trophic structure of the system. Increased light 

penetration due to the cessation of river flow was postulated as an important factor in the 

temporal response of bay productivity and herbivore/omnivore abundance. There was a marked 

increase in the herbivore biomass during the beginning of the drought of 1980-1981. Herbivore 

biomass peaks coincided with low winter river flows, peak turbidity, low water color and 

increased Secchi depths. More frequent periods of positive oxygen anomaly (high dissolved 

oxygen) during the drought also coincided with the high levels of herbivore biomass indicating 

increased phytoplankton activity. However, reduced river flows were likely associated with 

reduced nutrient loading that then led to the reduction of plankton and the eventual collapse of the 

various trophic groups in East Bay. 

There are problems with relating bay productivity to specific reductions or threshold 

levels of freshwater as referenced above. This threshold must be discussed with caution, for there 

is likely no particular flow below which the river falls that will always cause the type of effects 

observed in this study. The level of flow reduction and its subsequent effects are no doubt 

influenced as much by the timing and duration of the event as by the absolute magnitude. The 

1980-1981 drought did not encompass the lowest flows seen on the river; however, the 

combination of two lower than average dry season flows with an unusually low wet season flow 

resulted in the dramatic trophic effects observed. Thus, permanent base flow reductions of even a 

relatively small magnitude could cause the system to be more vulnerable to droughts of less 

magnitude than examined here. The response of the river and the bay to serial increases in 

duration and intensity of low flow patterns during drought occurrences would likely be nonlinear, thus leading to exacerbation of productivity losses of with time. This leads to the question 

of at what point would the Apalachicola system be altered to a point of no return to its former 

high level of biological productivity. 

54
The concepts of biological stability and resilience have been defined in various ways (see 

Harrison [1979], and Santos and Bloom [1980], for a brief review of the semantic problems 

encountered). Stability is generally defined as the ability of a given system, once perturbed, to 

return to its previous state. Resilience refers to the degree, manner, and pace of restoration of the 

initial system function and structure following a disturbance (Westman, 1978). Cairns and 

Dickson (1977) referred to various parameters of a recovery index: proximity of re-colonization 

sources, mobility of propagules, physical and chemical suitability of habitat for re-colonization, 

toxicity of the disturbed habitat, and effectiveness of human management initiatives to facilitate 

rehabilitation. There are, however, differences in the resilience of species to natural disturbances 

relative to disruptions caused by humans. Anthropogenic disturbances that occur outside of the 

evolutionary experience of a given species may have a more adverse impact on the ability of that 

population to recover relative to natural changes that occur through time. 

Based on the observed trends in the Apalachicola estuary, postulated permanent 

reductions of freshwater flows due to anthropogenic activities could lead to major reductions of 

biological productivity (i.e. invertebrate and fish populations) in the Apalachicola Bay system 

(Livingston et al., 1997). There was no real recovery of the trophic order during the 2.5-year 

period of returned river flows following the 1980-81 drought. This indicated that recovery of the 

bay following a drought could not be predicted from these data. The response of the bay to a 

series of droughts could be dependent on serial loss of resilience. It is not possible to predict 

when the rubber band would no longer snap back. However, the long-term data indicated that, 

with increased reductions of freshwater flow due to anthropogenic use of water, a point would 

come where flow rates would fall below levels that would sustain high productivity. In this event, 

the physically controlled, highly productive river-estuarine system would become a species-rich, 

biologically controlled bay with an altered food web and substantially reduced productivity of its 

commercial and sports fisheries. 

The severe losses of the oyster, shrimp and blue crab production during the most recent 

and ongoing drought would lend credence to the hypothesis of non-linear response in the form of 

accelerated loss relative to drought frequency and intensity. 

55
 7. The Apalachicola Oyster Industry

Research on the extensive Apalachicola oyster (Crassostrea virginica) reefs goes back to 

the work of Swift (1896) and Danglade (1917). The Apalachicola estuary has accounted for 

about 90% of Florida's commercial fishery (Whitfield and Beaumariage, 1977), and about 10% of 

the oyster production in the U. S. Conditions in the Apalachicola Bay system are highly 

advantageous for oyster propagation and growth (Menzel, 1981, Menzel and Nichy, 1958; Menzel 

et al., 1966; Livingston, 1984) with reefs covering about 7% (4,350 hectares) of bay bottom 

(Livingston, 1984). Growth rates of oysters in this region are among the most rapid of those 

recorded (Ingle and Dawson, 1952, 1953) with harvestable oysters taken in 18 months. The 

distribution of oyster bars in the estuary (Figure 15) does not differ substantially from that 

described over 100 years ago. 

Figure 15: Location of oyster bars in the Apalachicola Bay system oyster study. 

56
Livingston et al. (1999, 2000) outlined life history descriptions of the Apalachicola oyster 

population. Hurricane Elena struck the Apalachicola estuary in fall 1985, and destroyed major 

portions of the most productive oyster reefs in the bay. Storms, including hurricanes, occur 

frequently along the northern gulf coast. Hurricanes occur with the highest frequency during 

summer-fall months, overlapping the usual spawning season for oysters. After Elena, there was 

an adaptive response to the storm in the form of an unprecedented increase of spawning and spat 

fall success. Oysters are relatively well adapted to disturbances such as storms, even when the 

immediate effects include substantial damage to the existing population. Under such 

circumstances, the resilience of the oysters was enhanced by specific aspects of its life history 

that include rapid and massive spawning capabilities, a relatively high rate of growth due to the 

usually optimal habitat conditions in the Apalachicola estuary, and the return of habitat 

availability and natural productivity of this system within days to weeks of the disturbance. The 

return of the Apalachicola oyster population was aided by other by-products of the storm that 

included the absence of natural predators (including human beings). The overall outcome of 

oyster population changes thus indicated an adaptive response and high resilience to storm 

effects of this species that allowed survival under even extreme conditions of natural storminduced stress. 

Long-term changes of the Apalachicola oyster population should be placed within the 

context of major habitat-controlling features such as Apalachicola River flow. Meeter et al. 

(1979) found that oyster landings from 1959 to 1977 were correlated negatively with river flow. 

The highest oyster landings coincided with drought conditions. Wilber (1992), using oyster data 

from 1960 to 1984, found that river flows were correlated negatively with oyster catch per unit 

effort within the same year and positively with catches 2 and 3 yr later. Highest oyster harvests 

occurred in 1980-1981, coinciding with a major drought. Predation on newly settled spat during 

periods of high salinity was given as a possible explanation of the 2-yr time lags between low 

flow events and subsequent poor production. Livingston et al. (1997) found that increases of the 

Apalachicola Bay non-oyster bivalve mollusk populations during droughts was based on changes 

in the trophic organization of the estuary. The relatively high oyster production during low flow 

years was probably due to increased primary productivity as a function of altered physical 

conditions (i. e., increased light penetration) in the receiving estuary. Increased productivity 

57
contributed to increased growth rates and ultimately increased oyster production. Such changes 

in river flow and oyster productivity were regular and occurred within prescribed progressions of 

river flow fluctuations. However, prolonged droughts eventually induced serious reductions of 

oysters due to the effects of increased predation and disease as noted below. 

Overall oyster production is concentrated on three eastern bars (Cat Point [CP], East Hole 

[EH], Platform [PL]) that are located just off East Point (Figures 15,16). These areas are 

subjected to a convergence of highly colored surface water from East Bay (i.e., influenced by the 

Apalachicola River/Tate’s Hell Swamp drainage) and high velocity bottom water currents moving 

westward from St. George Sound. Maximum growth occurs during periods of low water 

temperature and high salinity variation. Oyster mortality is highest at St. Vincent’s Bar (SV) and 

areas associated with Sike’s Cut (SK) (Figure 16). These are the parts of the bay distant to river 

influence (with high salinity) but also in close proximity to the entry of oyster predators from the 

Gulf through the respective passes. The most important oyster predator is the gastropod mollusk, 

Thais haemastoma. Oyster mortality is low at the highly productive reefs in the eastern part of 

the bay (Cat Point, East Hole). Statistical analyses indicated that oyster mortality was positively 

associated with maximum bottom salinity and surface residual current velocity (Livingston et al., 

2000). Mortality was inversely related to oyster density, bottom residual velocity, and bottom 

salinity. 

Oyster bar growth (actual number of oysters in a given bar) and density (numbers of 

oysters per unit area) were highest at the East Hole, Cat Point, and Platform reefs (i.e., the eastern 

reefs) (Figure 16). Oyster density was lowest in oyster reefs located in St. Vincent Sound. High 

oyster bar growth (Figure 16) was concentrated mainly in eastern oyster growing areas (Cat Point, 

East Hole, Platform). Bar growth, defined as oyster density times bar area, was directly 

associated with high surface watercolor and Secchi readings and average bottom current 

velocities. These results are consistent with the findings that most of the oyster production in the 

bay occurs in areas subjected to a convergence of highly colored surface water from East Bay 

(i.e., influenced by the Apalachicola River/Tate’s Hell Swamp drainage) and high velocity bottom 

water currents moving westward from St. George Sound. Based on the distribution of oyster 

density, the primary oyster growing areas were in eastern sections of the bay with maximum 

growth during periods of low water temperature and high salinity variation. 

58
Figure 16: Distribution of oyster larvae, spat fall, density, new growth, and % mortality in the 

Apalachicola Bay system. 

Stations 

0

1000

2000

3000

SC PK SL BB PA CT DB KL SV PC SK NH HO GB SG CP EH PL PB SP

1985

1986

4240 4590 3505

Oyster larvae

(nm-3)

0

1000

2000

3000

SC PK SL BB PA CT DB KL SV PC SK NH HO GB SG CP EH PL PB SP

Oyster larvae

(nm-3)

1985

1986

4240 4590 3505

0

5

10

15

20

Spatfall 

rate

(nshell1wk-1)

1985

1986

28 21

0

500

1000

Oyster 

density

(nm-2)

1510

0.0

5.0

10.0

New oystergrowth rate

Individual (mgAFDWd-1)

Whole bar (kgAFDWd-1, in 500s)

0

20

40

60

80

SC PK SL BB PA CT DB KL SV PC SK NH HO GB SG CP EH PL PB SP

Per cent

mortality

Western Bay Central Bay Eastern ...

Open side

Closed side

0

5

10

15

20

Spatfall 

rate

(nshell1wk-1)

1985

1986

28 21

0

20

40

60

80

SC PK SL BB PA CT DB KL SV PC SK NH HO GB SG CP EH PL PB SP

0

500

1000

Oyster 

density

(nm-2)

1510

0.0

5.0

10.0New oyster growth rate

Individual (mgAFDWd-1)

Per cent

mortality

Western Bay Central Bay Eastern 

Open side

...

Closed side

0

500

1000

Oyster 

density

(nm-2)

1510

59
We calculated a time-averaged model for summer oyster mortality by running a 

regression analysis with averaged predictors derived from a hydrodynamic model and observed 

(experimental) mortality rates throughout the estuary. Based on the model, we determined that 

high salinity, relatively low-velocity current patterns, and the proximity of a given oyster bar to 

entry points of saline Gulf water into the bay were important factors that contributed to 

increased oyster mortality (disease and predation) (Livingston et al., 2000). Mortality was a 

major determinant of oyster production in the Apalachicola estuary with predation as a 

significant aspect of such mortality. By influencing salinity levels and current patterns 

throughout the bay, the Apalachicola River was important in controlling such mortality. 

Actual mortality data were plotted in Figure 17 so that the behavior of the model relative 

to real data could be observed. The distribution of mortality during 1985 (moderately low river 

flow year) was highest in areas directly affected by high salinity; such mortality was also near the 

entry points of oyster predators (St. Vincent Bar, Scorpion, Pickalene, Porter’s Bar). Predation on 

the primary eastern oyster bars was usually relatively low. The projections of oyster mortality for 

1986 (a drought year characterized by much lower river flow than 1985) were considerably 

higher, especially on the highly productive bars in eastern sections of the bay. Experimental 

oyster mortality data taken during May 1986 (Figure 17) tended to confirm the model projections. 

During 1986 the projected predation on high producing bars such as Cat Point, East Hole, 

Platform and Sweet Goodson would have been extensive. These model projections were verified 

by losses of oysters on the eastern bars during the most recent drought periods. 

 The effect of river flow, as an indirect determinant of oyster mortality due to predation 

through primary control of salinity regimes, was a major factor in the development of oysters in 

Apalachicola Bay. Model results indicated that reductions of river flow would be accompanied 

by substantial reductions in oyster stocks. Predation is an active factor in the determination of 

oyster production in the Apalachicola system. An example of its importance is the near total 

demise of the St. Vincent oyster bar following the opening of Sike’s Cut in the mid-1950’s. 

Oyster bar associations include various organisms that prey on oysters (Menzel et al., 1958, 

1966). Our experiments indicated that oyster mortality in the Apalachicola system was related to 

salinity as a determinant of oyster predation and the geographic position of the reef relative to the 

60
natural (East Pass, West Pass, Indian Pass) and man-made (Sike’s Cut) entry points of predators 

from the Gulf. 

Figure 17: Map of projected oyster mortality in the Apalachicola Bay system based on the 

statistical model for mortality in 1985 and the hydrodynamic model results for (A) 

1985. (B) 1986. (C) 1991. Circles indicate observed mortality values from oyster 

predation experiments (1985, May-August average). 

The association of increased oyster mortality with extent and duration of reduced river 

flow is consistent with the initial increase of oyster production at the initiation of the drought that 

is followed by oyster losses during an extended period of low river flows. Increased mortality 

with prolonged drought is verified by oyster losses during recent droughts. 

61
By coupling hydrodynamic modeling with descriptive and experimental biological data, 

Livingston et al. (2000) were able to determine the effects of potential freshwater diversions on 

oyster production in Apalachicola Bay. The very high oyster production rates in the 

Apalachicola system depend on a combination of variables that are directly and indirectly 

associated with freshwater input as modified by wind, tidal factors, and the physiography of the 

bay. River flow reduction, whether through naturally occurring droughts, through increased 

upstream anthropogenic (consumptive) water use, or a combination of the two, could have 

serious long-term, adverse consequences for oyster populations. Based on the findings of 

Livingston et al. (1997, 2000), the authors concluded that an anthropogenic reduction of 

freshwater flow during relatively low-flow periods could extend and exacerbate the effects of 

natural drought periods on the bay through enhanced oyster mortality by predation and disease. 

Reductions of oyster production that are part of the natural cycle of river flow could thus be 

extended or, under extreme conditions, made permanent, thereby eliminating the naturally high 

oyster production of the Apalachicola system. 

8. Recent Droughts and River Flow Changes

A comparison of the bottom salinities at Cat Point Bar (CP) and the Dry Bay (DB) 

indicated relatively high salinities at Cat Point during various time periods (1996, 1995, 1999-

2001). During a recent drought (1999-2002), there was a series of extremely low-flow periods. 

Data, provided by the Apalachicola National Estuarine Reserve (Lee Edmiston, Pers. Comm.), 

indicated that the Cat Point area had systematically higher bottom salinities than Dry Bar. The 

prolonged drought of 1999-2002 was associated with the most consistently high salinities since 

the initial study period by the Livingston research group (1972-1990). These salinities peaked 

during 2001. The salinity maxima were consistently high from 1991-2001 whereas salinity 

minima showed pronounced increases during 2001. This trend was consistent with the relatively 

low standard deviations during 2001, an observation that has significance when oyster trends 

during this period are taken into account. 

It should be recognized that various species take advantage of natural drought-flood 

conditions on an interannual basis. This results in a temporal succession of dominant species 

based on long-term adaptive responses to a natural range of river flows. 

62
A review of river flow rates below 10000 cfs from 1950-2008 is given in Table 3. 

Based on a comparison of the low flows during the study period, the lowest flows from 1954-

1990 were generally less frequent than those from 1999-present. In general, the averages of 

the low flows for periods from 1999-2007 were lower than those from 1954-1990. These data 

indicate that in the most recent decade, low-flow periods associated with reservoir and other 

water management practices during droughts have been more severe in terms of both duration 

and extent. 

Table 3: Apalachicola River flow rates (Sumatra) below 10000 cfs over the period from 

10/1950-5/2008. 

year/mnth

Average of

flow(cfs)

Average of

flow(m3/sec) year/mnth

Average of

flow(cfs)

Average of

flow(m3/sec)

1954/09 9380 266 1999/09 8612 244

1954/10 8575 243 1999/10 8051 228

1954/11 9064 257 1999/11 7996 226

1955/10 8834 250 1999/12 9300 263

1955/11 8231 233 2000/06 6085 172

1955/12 9622 272 2000/07 5631 159

1956/01 9209 261 2000/08 5878 166

1956/06 9902 280 2000/09 7302 207

1956/11 9894 280 2000/10 6515 185

average 9190 260 2000/11 7368 209

1981/09 9963 282 2001/09 8665 245

1981/10 7598 215 2001/10 6790 192

1981/11 6574 186 2001/11 6479 183

average 8045 228 2001/12 7947 225

1986/06 9981 283 2002/05 9902 280

1986/07 8355 237 2002/06 8397 238

1986/08 7382 209 2002/07 7591 215

1986/09 8437 239 2002/08 7939 225

1986/10 7323 207 2002/09 9509 269

1987/10 9565 271 average 7630 216

1987/11 8968 254 2006/06 8214 233

1987/12 9806 278 2006/07 6930 196

1988/06 9989 283 2006/08 7072 200

1988/07 8038 228 2006/09 8899 252

1988/08 7460 211 2006/10 7854 222

average 8664 245 2007/05 8565 243

1990/09 9083 257 2007/06 6175 175

1990/10 9157 259 2007/07 6194 175

1990/11 9884 280 2007/08 6207 176

average 9375 265 2007/09 6412 182

2007/10 7727 219

2007/11 6762 191

2007/12 7282 206

average 7253 205

63
During the 1999-2002 drought, there was a collapse of oystering in the Eastern reefs from 

Cat Point to East Hole. In a 2002 field assessment by the Florida Department of Environmental 

Protection (G. S. Gunter, Pers. Comm.), lowered oyster productivity in eastern bay reefs was 

accompanied by large numbers of predators that included oyster drills, crown conchs, scallops 

and sea urchins. Hard and soft corals were noted on Porter’s Bar during these field surveys (G. 

S. Gunter, Pers. Comm.). With a return of higher river flows during 2003, there was an increase 

of observed oysters on the Cat Point and East Hole with an accompanied reduction of oyster 

predators (G. S. Gunter, Pers. Comm.), During the 2002 collapse of the eastern oyster reefs, 

commercial oystering continued in northern sections of western bars such as Dry Bar and upper 

St. Vincent Bar (G. S. Gunter, Pers. Comm.). The above observations during the 1999-2002 

drought represent field verification of model predictions made by Livingston et al. (2000). With 

permanent reductions of Apalachicola River flow in the region related, in part, to reservoir and 

other recent water management practices, the adverse effects of natural droughts would be 

accentuated. Over prolonged periods, the resilience of the bay to such events would be 

systematically reduced which could then lead to more permanent reductions of those forms of 

secondary production (such as oysters, shrimp, blue crabs and sciaenid fishes) that depend on the 

interannual cycling of natural river flows into the bay. 

 The most recent drought (2007-present) followed a similar pattern to that described for 

the 1999-2002 drought. During this drought, salinities in East Bay have reached unprecedented 

high levels (>30 ppt) (L. Edmiston, J. Wanat, Pers. Comm.). The highly productive eastern bars 

have been adversely affected by predators and disease (the exact proportions could not be 

determined; G. Lewis, Pers. Comm.). Cat Point, the leading oyster producing reef in the bay, was 

hit hard by predators during the recent drought. Oyster catches have been largely restricted to 

lower producing bars in the western parts of the bay during the period of increased salinity. 

These observations represent field verifications of the oyster model results described above 

(Livingston et al., 2000). 

Grass beds in the upper bay, dominated by Vallisneria americana, have been adversely 

affected by recent droughts (L. Edmiston, Pers. Comm.). This submerged aquatic vegetation 

(SAV) supports a productive food web in East Bay (Purcell, 1977). Based on a survey of the 

SAV in East Bay in June 2005, Hurricane Dennis took out all the SAV in both the lower river and 

64
East Bay. The grass beds started to return the following year. However, the grass beds have all 

but disappeared again since the most recent drought. The high salinities associated with the 

drought are thought to be responsible for the loss of the East Bay SAV due to the fact that such 

vegetation is adapted to low and varying salinity (L. Edmiston, J., Pers. Comm.). 

Trawl data (L. Edmiston, J. Wanat, Pers. Comm.) indicate that, after initial increases of 

population density during the beginning of the 1999-2002 drought, there were subsequent 

reductions that followed the model noted by Livingston et al.(1997) (see above). The trawl data 

taken by Edmiston and Wanat indicate severe reductions of white shrimp in East Bay and the 

Apalachicola estuary as a whole over the past 2 years. Pink shrimp increased modestly during 

2007, but the numbers of this species did not compensate for the loss of the white shrimp in the 

bay. Relatively few blue crabs were taken in East Bay during 2007. Commercial fishing landings 

data taken during 2007 reflected decreases of white shrimp (down 90%), brown shrimp (down 

55%), blue crabs (down 55%) and flounder (down 40%) relative to 2004-2006 and 2006 periods. 

The severely reduced landings of key commercial species represents a practical example of how 

low river flows, exacerbated by upstream human activities, have adverse effects on the 

Apalachicola estuary. 

Although it is too early to assess the final outcome of this latest drought, it is clear that 

the commercial resources of the bay are currently in danger of being lost for an as yet 

undetermined period. If the increased incidents of low river flow regimes during severe drought 

periods in recent decades continues as a trend into the future, the bay productivity in terms of the 

key commercial species will inevitably give way to replacement by less important species in 

terms of their fisheries value. The resilience of the bay is being serially reduced by the increased 

severity and length of the reduced river flows during droughts. There is evidence that non-linear 

responses by key bay populations to reductions of river flows have already occurred. The almost 

total lack of effective water conservation efforts in the Tri-river system has undoubtedly 

exacerbated an already serious loss of Apalachicola River and Bay productivity. 

65
III. Management of the Apalachicola River-bay System

Because of the generally pristine state of the Apalachicola drainage system, planning and 

management was carried out as preemptive activity rather than a restoration effort (Figure 18). 

Figure 18: Map showing major elements of the Apalachicola Management Plan. 

66
The extensive studies of the Apalachicola system that have been carried out since 1972 

were used to develop an ecosystem-based management program that included the purchase of 

wetlands associated with both the river and the bay (Figure 18). The scientific data provided the 

objective basis for the development of the Apalachicola management program that has been 

documented by Livingston (1976b, 1977, 1980, 1982b, 1983, 2000, 2002). 

The primary objectives of much of the early planning were related to maintaining natural 

flows to receiving areas and they included the following: 

1) Purchases of environmentally critical lands in the Apalachicola drainage system that 

now include most of the river-bay wetlands systems (Figure 18). 

2) Designation of the Apalachicola system as an Area of Critical State Concern, (Florida 

Environmental Land and Water Act of 1972; Chapter 380, Florida statutes). 

3) Creation of cooperative research efforts to determine the potential impact of activities 

such as ongoing forestry management programs, urban development, and pesticide 

treatment programs. 

4) Making provisions for aid to local governments in the development of comprehensive 

land use plans, a function that is vested primarily at the county commission level in 

Florida. 

Documentation of facts concerning the Apalachicola Basin (Livingston and Joyce, 1977) 

provided the initial details of the unique ecological status of the Apalachicola system. The 

linkage between the upland freshwater wetlands and the Apalachicola estuary via nutrient loading 

analyses together with related bay studies led to purchases of river-wetlands by the Florida 

Department of Natural Resources as part of the Environmentally Endangered Land program 

(Chapter 259, Florida statutes). The initial purchase was thirty thousand acres of hardwood 

wetlands in the lower Apalachicola in December 1976 (Pearce, 1977; Figure 18). This was to be 

the first of many wetland purchases in the Apalachicola region that have continued up to the 

present time. Upland and coastal wetlands along the Apalachicola River and the East Bay area 

(Tate’s Hell Swamp; Figure 18) have been recently purchased by state agencies. 

Since the mid-1970’s, the State of Florida has spent over $239 million through land 

acquisition to protect the wetlands system of the Apalachicola River and Bay system. Currently, 

major parts of the Apalachicola River river-wetland system is held by public agencies for 

67
preservation and management (Figure 18). This is a unique situation in terms of protective 

measures of large river-estuarine systems in the United States. The state of Florida has devoted 

considerable time and expense to assure that the wetlands along the Apalachicola River-Bay 

system remain viable relative to the importance of such wetlands to the productivity of this 

drainage basin. 

Thanks to the efforts of the same coalition of local and state personnel that instituted land 

planning in Franklin County in the early 1970's, the Apalachicola scientific database was used to 

establish the Apalachicola River and Bay Estuarine Sanctuary in 1979. This sanctuary, now 

designated a National Estuarine Research Reserve, included the purchase of about 78,000 ha in 

the bay system (Figure 18). The original designation included $3.8 million for land purchases in 

the East Bay wetlands. The reserve remains one of the largest such systems in the country. The 

Florida government purchased Little St. George Island in 1977 (Figure 18). Somewhat later, an 

area above the East Hole oyster beds (Unit 4 EEL; Figure 18) was purchased through the efforts 

of the Trust for Public Lands (Caroline Reusch, Pers. Comm.). St. Vincent Island was already a 

federal preserve administered by the U. S. Department of the Interior (Figure 18). The east end of 

St. George Island is a state park. After considerable legal proceedings, most of the western 

section of St. George Island (the Plantation, Figure 18) was planned for maximum protection of 

island freshwater drainages, associated wetlands, and upland vegetation. 

In a relatively short period, land purchases on the barrier islands were added to the 

purchases of the East Bay and Apalachicola River wetlands to complete a ring of publicly owned 

lands around the most environmentally sensitive areas of the Apalachicola River-Bay system 

(Figure 18). When combined with state regulations (Aquatic Preserve, Area of Critical State 

Concern) and a Franklin County management program designed to protect the bay from urban 

runoff, most of the land-water interfaces were thus protected from the effects of human activities. 

The management of a river-dominated estuary should be based on protection and control 

of fresh water sources, nutrients, and organic matter with a minimization of physical alterations 

that often lead to increased salinity stratification and the associated loss of the nursery function 

of the estuary. These processes underlie the very basis of riverine and estuarine productivity. It 

is clear that fisheries production, the nursery function, and the productivity of individual 

68
populations depend on species-specific responses to combinations of freshwater input, salinity 

changes, food web processes, and interspecific predation and competition. Due to the lack of 

science-based management of river-estuarine systems throughout the United States, these areas 

are quietly succumbing to the detrimental effects of a range of human activities (Livingston, 

2000, 2007). These effects can be avoided, but only if adequate research is directed to a 

scientific determination of the fresh water needs and nutrient-loading tolerances of coastal 

systems. 

Based on established relationships in a series of river-estuarine systems along the NE 

Gulf of Mexico, management of these resources should be based on the following: 

1) protection of freshwater and coastal wetlands

 

2) maintenance of adequate freshwater input to sustain natural productivity and the 

important nursery function of the river-bay system 

3) minimization of physical alterations of the river-estuary that could lead to adverse 

changes involving nutrient transfer and salinity distribution, and 

4) management of local municipal development and agricultural runoff to minimize input 

of toxic agents, nutrients, and disease vectors to receiving river-estuarine systems.

IV. Current Threats to the Apalachicola River-bay System

1. Cumulative Reductions of Apalachicola River Flow Rates

Agricultural and municipal interests along the Apalachicola-Chattahoochee-Flint system 

continue to increase pressure on the freshwater resources of the Tri-river basin. There are 

proposals to re-allocate water in the Lake Lanier storage from hydropower to water supply for 

rapidly growing Atlanta, Georgia metropolitan area. Models (Livingston, 1988) indicated that 

agricultural use of water in the Tri-river system would eventually lead to serious depletion of 

freshwater input to the Apalachicola from the Georgia area. Recent analyses (Livingston et al., 

2003) found that depletions of freshwater in the basin already represented a significant portion of 

low flow during summer months, and forecasted demands for the ACF basin suggested that such 

losses would become even greater with time especially in low-flow summer months. 

69
Leitman (2003a) and Leitman et al. (2003) reviewed cumulative monthly freshwater 

deficits during three major drought events in the Apalachicola systems (mid-1950’s, mid-1980’s, 

1999-2002). In developing the comparisons, the authors expected that the unimpaired flow 

results would correspond to fluctuations in the rainfall data over the entire period of record. A 

cumulative deficit evaluation of the drought events showed that the greatest cumulative rainfall 

deficit occurred during the mid 1950’s drought event, but the greatest flow deficit occurred during 

the 1999–2002 drought event. Leitman (2003a, b) found that during average years, the net evapoprecipitation losses from impoundments in the ACF basin were considerable; these losses in the 

Flint and Chattahoochee areas far exceeded consumptive losses in the year 2000 for municipal 

and industrial uses for the entire Chattahoochee system (including metro Atlanta and Columbus, 

Georgia) for all months between May and October except August. If the net evapo-precipitation 

losses for 1986 were considered, such losses exceeded the consumptive losses for municipal and 

industrial demands for all months between May and September. 

The net evapo-precipitation losses for 1999 exceeded the consumptive losses for 

municipal and industrial demands for April, May, August and September. The drought of 1999-

2002 had lower river flows but higher precipitation levels than those observed during the drought 

of the 1950’s. The differences were related to higher consumptive uses (via the evaporation 

losses from the impoundments and reservoir management practices) during the 1999-2002 

drought. The low oyster production during the drought was thus directly related to low river 

flows and high salinities due, in part, to anthropogenic changes in the Flint and Chattahoochee 

Rivers including (among other anthropogenic factors) the building and management of dams and 

their resulting reservoirs. 

Leitman et al. (2003) concluded that flows of the Apalachicola River at the 

Chattahoochee gage during drought events have been affected by consumptive demands, and that 

the Corps of Engineers daily unimpaired flow data at the Columbus gage for the years 1999-2001 

do not totally reflect these impacts. 

2. Recent Actions by the Federal Government

After a series of legal proceedings over the past 2 decades among the states of Florida, 

Georgia and Alabama for water rights in the ACF system, negotiations among the governors of 

70
these states broke down in February 2008. In April 2008, the U. S. Army Corps of Engineers (U. 

S. A. C. E., 2008) released a federal proposal that would allow Georgia to keep more water in 

reservoirs during droughts. This would essentially result in lower river flows during droughts into 

the Apalachicola River with the onus of lower flows placed on the natural resources of the 

Apalachicola River and Bay system. There is no mention of any form of conservation effort that 

would be designed to limit the impact of such droughts on the Florida resources. 

According to a report by the Carnegie Institution for Science (2008), the following 

evidence of long-term changes in the atmosphere was published: 

“The Earth’s jet streams, the high-altitude bands of fast winds that strongly 

influence the paths of storms and other weather systems, are shifting—possibly in 

response to global warming. Scientists at the Carnegie Institution determined that 

over a 23-year span from 1979 to 2001 the jet streams in both hemispheres have 

risen in altitude and shifted toward the poles. The jet stream in the northern 

hemisphere has also weakened. These changes fit the predictions of global 

warming models and have implications for the frequency and intensity of future 

storms, including hurricanes.... Storm paths in North America are likely to shift 

northward as a result of the jet stream changes. Hurricanes, whose development 

tends to be inhibited by jet streams, may become more powerful and more 

frequent as the jet streams move away from the sub-tropical zones where 

hurricanes are born.” 

This change could mean less rain in the already drought-stricken SE United States. There 

is no way of confirming the long-term effects of climate changes due to Global Warming. There 

is ample scientific information that there are major changes taking place in recent decades. If the 

projections of reduced rainfall in the ACF region are true, it would place even more emphasis on 

the need for an advanced water conservation effort in this area. The increase of the frequency 

and intensity of droughts in the Apalachicola system is a fact, however, and the potential for 

further reductions of rainfall and river flow should be included in an calculations for water 

conservation efforts. It is possible that future, long-term changes in atmospheric conditions 

could lead to further reductions of river flows. There is a real need to organize a comprehensive 

scientific study program to evaluate the impacts of reduced river flow rates, and to use the 

objective findings to develop a water conservation plan for the ACF basin. 

71
V. Conclusions

1. The Apalachicola River is one of the last major free flowing, unpolluted alluvial systems 

in the conterminous United States. The Apalachicola River has historically been among the most 

productive systems in the northern hemisphere, and is a major center for endemic and 

endangered species. Seasonal flooding provides the engine for mobilization and transfer of the 

nutrients and detritus between the Apalachicola wetlands and associated river and bay areas. 

Food webs leading to high production of oysters, shrimp, blue crabs and fin fishes in 

Apalachicola Bay are linked to river flows that control salinity regimes and nutrient dynamics of 

the bay. 

2. Apalachicola River wetlands represent a center of endemism for terrestrial species that 

includes amphibians, reptiles, and birds. Due to the high diversity of wetland and upland 

habitats, the highest species density of amphibians and reptiles in North America (north of 

Mexico) occurs in the upper Apalachicola basin. The Apalachicola River and floodplain depend 

on natural river flows in terms of frequency and duration of inundation and saturation. 

3. The Apalachicola River has the greatest flow rates of all the river-drainages along the 

northeast Gulf of Mexico. River input dominates salinity and water quality in the bay system. 

The river represents a major source of productivity in the adjoining coastal region. 

4. There has been a considerable investment by local, state and federal associations and 

agencies in terms of time and money to manage the Apalachicola drainage system. Since the 

mid-1970’s, the State of Florida has spent over $239 million through land acquisition to protect 

the Apalachicola River and Bay system. Currently, major parts of this system are held by public 

agencies for preservation and management. This is a unique situation in terms of protective 

measures of large river-estuarine systems in the United States. 

5. Scientific reviews indicate that there has been a serious change in the Apalachicola flow 

rates with an increase of the frequency and severity of low flow periods due to droughts. There 

is also evidence that these changes are due, in part, to water use in the upper parts of the Tri-river 

system. The drought of 1999-2002 had lower river flows but higher precipitation levels than 

those observed during the drought of the 1950’s. The differences could be related to higher 

consumptive uses during the 1999-2002 drought. There will be increased municipal and 

agricultural development in the Tri-River Basin in future years that will put more pressure on 

river flows during drought periods. 

6. Increased frequency and duration of recent droughts have been associated with losses of 

about 3 million canopy trees in the non-tidal Apalachicola River wetlands. Low-flow regimes of 

river flows during recent droughts have caused kills of federally “protected” mussels. Numerous 

dead and dying mussels at various locations have been noted during a recent drought. Minimum 

flows of 8000 cfs are likely to be required for maintenance of existing slough and channel 

margin unionid populations, and are essential for recovery of federally listed species. 

7. Different sources of information regarding the Apalachicola River system indicate that 

flow management for riverine and wetland productivity, biodiversity and endangered species 

72
should be based on historical seasonal and interannual flow rates of the Apalachicola River. 

Projected flow rates of the Apalachicola River should follow these patterns to maintain the 

highly diverse and productive species that are currently adapted to the natural periodicity of this 

system. 

8. Results of previous studies indicate that the Apalachicola estuary has been in a relatively 

natural state historically. The undisturbed progression of river-bay interactions, along with little 

human development in the Apalachicola basin, resulted in a productive bay system with high 

levels of secondary productivity relative to other river-dominated estuaries. 

9. The response of the bay to river flows is complex due to species-specific responses to the 

river-directed habitat changes and responses of the food web to nutrient loading and 

phytoplankton production. The river contributes to a broad spectrum of habitats that 

accommodate commercially important species. The distribution of oysters and epibenthic fishes 

and invertebrates in the Apalachicola Estuary follows a specific spatial relationship to river 

flows. Dominant bay populations follow a broad spectrum of diverse phase interactions with 

river flow and associated changes in salinity over interannual periods of drought and flood 

conditions 

10. Nutrient-induced phytoplankton productivity is an important component of estuarine food 

webs along the Gulf coast. The alluvial river also provides river-derived nutrients and organic 

matter that fuel the planktonic and detrital food webs. The combination of these sources of 

autochthonous and allochthonous organic carbon provides the resources for consumers in the 

Apalachicola Estuary. Reduced river flows and flooding will diminish this loading leading to a 

collapse of useful productivity in receiving coastal areas. There is evidence that recent extended 

periods of low river flow have already adversely affected organic carbon loading to the bay. 

11. Recent research was conducted on the nutrient history in Apalachicola Bay sediments. 

Samples taken near the river mouth indicated that organic matter deposition was driven by both 

natural (i.e., hurricanes and droughts) and anthropogenic (i.e., hydrologic river alteration and 

dredging) activity. After the drought of 1981, Woodruff Dam operation procedures and the 

resultant river discharge patterns could have affected mass sedimentation rates and organic 

loading within the estuary. “Carbon and nitrogen concentrations, ratios, and stable isotopes 

coupled with grain-size shifts for the bay suggest a decrease in river organic matter supply and a 

change in sediment clay content supply and/or distribution for the bay.” Coupling ACF River 

discharge alterations with sea-level rise appears to clearly account for the modification to organic 

matter sources for the entire bay.

12. The dominant, commercially important populations of the Apalachicola estuary (oysters 

[Crassostrea virginica], blue crabs [Callinectes sapidus], penaeid shrimp [Litopenaeus setiferus, 

Farfantepenaeus spp.], and sciaenid fishes [Cynoscion spp.]) are adapted to varying salinities. 

With reduced flows, salinity goes up, reducing physical stress that results in increased species 

richness as stenohaline populations (adapted to high salinity in offshore Gulf areas) enter the 

bay. Individual population productivity is reduced accordingly due to altered habitat conditions 

and enhanced predation, competition and disease. 

73
13. Within natural boundaries of river flows, food web processes in the bay vary little in 

terms of qualitative and quantitative interactions. Below a certain level of river flow, however, 

the estuary becomes a very different system. With prolonged reductions of river flow, there are 

eventual decreases in biological production due to reduced nutrient loading and altered 

phytoplankton assemblages. Together with associated habitat changes, the commercially 

important populations are replaced by less productive species as the value of the bay is 

substantially reduced. With the more or less permanent reduction of freshwater flows below a 

level specific for the receiving system, the physically controlled, highly productive riverestuarine system will eventually become a high diversity, biologically controlled bay of 

substantially reduced fishery potential. 

14. Brackish water submerged aquatic vegetation (SAV) dominated by Vallisneria 

americana in East Bay has served as nursery grounds for penaeid shrimp and other crustaceans 

and fishes at early stages of their ontogenetic (developmental) progressions in the bay. 

Shoalgrass (Halodule wrightii) with other species such as Gracilaria spp. and manatee grass 

(Syringodium filiforme) represent highly productive habitats along St. George Island with the 

infaunal macroinvertebrates in this part of the bay among the most speciose in the northern 

hemisphere. The grass bed fauna includes species used as food for the abundant blue crabs 

(Callinectes sapidus), pink shrimp (Farfantepenaeus duorarum), pinfish (Lagodon rhomboides) 

and spotted seatrout (Cynoscion nebulosus). The seagrass beds off St. James Island are 

dominated by turtle grass (Thalassia testudinum) and manatee grass (Syringodium filiforme). 

These grass beds provide habitat for southern flounder (Paralichthys albigutta), spotted seatrout 

(Cynoscion nebulosus), and various species of sharks. 

15. The drought of 1980-1981 had a profound effect on the trophic organization of East Bay. 

This impact remained at various trophic levels during the 2.5-year period of river flow recovery. 

Similar changes during more recent droughts indicate a relatively similar response of dominant 

estuarine species to prolonged droughts. There is evidence that anthropogenic reductions of river 

flow that occur outside of the evolutionary experience of a given species may have an enhanced 

adverse impact on the ability of that population to recover relative to natural changes to which 

the species has adapted through time. 

16. During the most recent decade, low flows experienced during droughts have been more 

severe in terms of both duration and extent. Recent salinity increases due to low flows during 

droughts have adversely affected oyster beds and the East Bay grass beds that represent 

important habitats and sources of productivity for the upper bay. Commercial fishing landings 

during the 2007 drought were associated with decreases of white shrimp (down 90%), brown 

shrimp (down 55%), blue crabs (down 55%) and flounder (down 40%). Major losses in key 

oyster producing areas were noted due to high salinities and associated mortality due to predation 

and/or disease. It is not clear how these changes will affect long-term production of these 

species. The severe losses of the oyster, shrimp and blue crab production during the most recent 

and ongoing low flow events during droughts lends credence to the hypothesis of a non-linear 

response in the form of accelerated loss relative to low flow frequency and intensity during 

droughts. 

74
17. Losses of commercial fisheries, together with impacts on river wetlands, represent a 

threat to unique cultural and economic resources of the Apalachicola system. It is likely that the 

current losses could be expanded indefinitely as resilience of the system is serially reduced by 

the increased frequency and duration of droughts. This condition is exacerbated by 

anthropogenic reductions of fresh water flows due to urbanization and agriculture in upstream 

areas. 

18. Scientists at the Carnegie Institution determined that over a 23-year span from 1979 to 

2001, the jet streams in both hemispheres have risen in altitude and shifted toward the poles. 

This change could mean less rain in the already drought-stricken SE United States. There is no 

way of confirming the long-term effects of climate changes due to Global Warming. There is 

ample scientific information that there are major changes taking place in recent decades. If the 

projections of reduced rainfall in the ACF region are true, it would place even more emphasis on 

the need for an advanced water conservation effort in this area. 

19. After a series of legal proceedings for almost 2 decades among the states of Florida, 

Georgia and Alabama for water rights in the ACF system, negotiations among the governors of 

these states broke down in February 2008. In April 2008, the U. S. Army Corps of Engineers (U. 

S. A. C. E., 2008) released a federal proposal that would allow Georgia to keep more water in 

reservoirs during droughts. This would essentially result in lower river flows during droughts 

into the Apalachicola River with the onus of lower flows placed on the natural resources of the 

Apalachicola River and Bay system. 

20. It is not clear if the long-term resilience of the river and bay has been lessened by recent 

drought events, but it is likely that increased frequency and duration of river flow reductions in 

the future due to water removal by upstream human activities will eventually result in the loss of 

the Apalachicola resource. There have already been habitat and productivity changes that have 

led to elimination of the riverine wetlands as noted by substantial reductions of native trees in the 

flood plain, loss of the nursery function of the bay and destruction of the naturally high 

productivity associated with key aquatic species in the river and bay. 

21. The increase of the frequency and intensity of low flows during droughts in the 

Apalachicola system is a fact, and the potential for further reductions of rainfall and river flow 

due to anthropogenic activities and climate changes should be included in calculations for water 

conservation efforts. Despite scientific evidence for a growing crisis in the Apalachicola system, 

there has been little effort in upstream areas for effective implementation of water conservation 

efforts. There is a real need to organize a comprehensive scientific study program to evaluate the 

impacts of reduced river flow rates, and to use the objective findings to develop and implement 

an appropriate water conservation plan for the ACF basin. 

75
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List of Tables

Table 1: Averages of physico-chemical and biological variables sampled during the 9.5–year 

survey of East Bay taken monthly from 2/1997-7/1984. 

Table 2: Generic codes for the trophic ontogenetic units. 

Table 3: Apalachicola River flow rates below 5000 cfs over the period from 1995-2003. 

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List of Figures

Figure 1: Model of the Apalachicola Bay system showing key features that result in extremely 

high primary and secondary productivity. 

Figure 2: Model of the Apalachicola Bay system showing potential impacts of reduced river flow 

leading to plankton blooms and reduced secondary productivity. 

Figure 3: Model of the Apalachicola Bay system showing potential impacts of reduced river 

flow to the bay leading to seriously reduced secondary productivity. 

Figure 4: The Apalachicola-Chattahoochee-Flint (ACF or Tri-River) drainage basin. 

Figure 5: Human population distribution in North Florida. This figure is a composite of 

information provided by the National Oceanic and Atmospheric Administration, the 

Florida Department of Environmental Protection, and the ESRI Corporation. 

Figure 6: The Apalachicola Bay system showing location of long-term sampling stations. 

Figure 7: Model of the interaction between the Apalachicola River and Bay with respect to the 

riverine contributions to bay primary and secondary productivity. 

Figure 8: Monthly averages of Apalachicola River flow from October 1951 through September 

2003. Data were provided by the U. S. Geological Survey (Sumatra, Florida gage). 

Figure 9a: Seagrass and wetland habitats of the Apalachicola Drainage System. 

Figure 9b: Distribution of submerged aquatic vegetation (density) in near-shore areas of St. 

George Sound during 2006-2007. Water quality stations (Livingston, 2006a) are shown 

along with upland wetlands systems. 

Figure 9c: Station distribution in East Bay for the long term trophic analyses involving infaunal 

and epifaunal macroinvertebrates and fish. 

 Figure 9d: Leaf matter taken in otter trawls in East Bay taken monthly from January 1975-

February 1981. 

Figure 9e: Microdetritus taken in water samples in the lower Apalachicola River monthly from 

August 1975-March 1982. 

Figure 9f: Chart showing stations used in East Bay and St. George Sound for the comparative 

analysis of the river-dominated upper bay (stations 3 and 5a) and the high salinity sound 

area (station ML). 

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Figure 9g: Three-dimensional view of numbers of individuals, species richness, and top 

dominant numbers of infaunal macroinvertebrates taken from 100 core samples at 

stations 3, 5a and ML. 

Figure 10: Ontogenetic feeding units of blue crabs (day vs. night collections). 

Figure 11: Apalachicola River flows, monthly, from February 1975 through June 1984. Data were 

provided by the U. S. Geological Survey (Sumatra, Florida gage). 

Figure 12: Water quality indices (Secchi depths, watercolor, salinity) taken monthly from 

February through June 1984. Also shown are the 3-month moving averages of the data. 

Figure 13: Fish, infaunal and invertebrate (FII) trophic levels (herbivores, omnivores, C1 

carnivores, C2 carnivores) taken monthly from February through June 1984. Also shown 

are the 12-month moving averages of the data. 

Figure 14: Fish, infauna, invertebrate (FII) trophic data taken monthly from 2/75-8/84 in East 

Bay. Data represent % of total biomass for each category (herbivores, omnivores, C1, C2, 

C3 carnivores). 

Figure 15: Location of oyster bars in the Apalachicola Bay system oyster study. 

Figure 16: Distribution of oyster larvae, spatfall, density, new growth, and % mortality in the 

Apalachicola Bay system. 

Figure 17: Map of projected oyster mortality in the Apalachicola Bay system based on the 

statistical model for mortality in 1985 and the hydrodynamic model results for (A) 

1985. (B) 1986. (C) 1991. Circles indicate observed mortality values from oyster 

predation experiments (1985, May-August average). 

Figure 18: Map showing major elements of the Apalachicola Management Plan.