` 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 mid-1970’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.

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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

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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

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(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.

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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

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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).

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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

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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.

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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 drought-

related 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).

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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.

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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.

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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.

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II. Documentation for Rationale and Conclusions

A. Apalachicola River Basin The Apalachicola River-Bay system is part of a major drainage area (the Chattahoochee-

Flint-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 m3s-1 (1958-1980) with annual high flows

averaging 3,000 m3s-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

BASI

NLI

MIT

S

Atlanta, Georgia

Columbus, Georgia

Apalachicola,Florida

Gulf of Mexico

N

Chattahoochee River

Flint River

Chipola River

Jim Woodruff Dam

Lake Seminole

Lake Lanier

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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 evapo-

transpiration 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 lagoon-

and-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)

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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 (above-

surface 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).

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). Cross-

correlation 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 49.900bsalinity (ppt) 10.014 3.244 5.054 4.257scolor (Pt-Co Units) 53.640 60.447 73.803 115.548bTurbidity (NTU) 23.171 20.311 22.781 17.535sD.O.(mgL-1) 8.285 8.956 8.675 7.900nOxygen Anom (mgL-1) -0.593 0.167 -0.182 -0.868bpH (pH Units) 7.264 7.401 7.363 6.982fish totwt(gm2) 0.099 0.057 0.047 0.036inv totwt (gm2) 0.026 0.022 0.012 0.014FIIC1 (gm2) 0.575 0.050 0.474 0.035FIIC2 (gm2) 0.088 0.045 0.025 0.022MICUn/smp 26.759 17.623 21.421 13.743CALSAPn/smp 3.741 3.392 2.868 2.993PENSETn/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-7

5

Oct

-75

Jan-

76

Apr

-76

Jul-7

6

Oct

-76

Jan-

77

Apr

-77

Jul-7

7

Oct

-77

Jan-

78

Apr

-78

Jul-7

8

Oct

-78

Jan-

79

Apr

-79

Jul-7

9

Oct

-79

Jan-

80

Apr

-80

Jul-8

0

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

75/0

875

/12

76/0

476

/08

76/1

277

/04

77/0

877

/09

77/1

077

/12

78/0

278

/03

78/0

478

/06

78/0

778

/08

78/1

078

/11

78/1

279

/02

79/0

379

/04

79/0

679

/07

79/0

879

/10

79/1

179

/12

80/0

280

/03

80/0

480

/06

80/0

780

/08

80/1

080

/11

80/1

281

/02

81/0

381

/04

81/0

681

/07

81/0

881

/10

81/1

282

/01

82/0

2

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 (anaerobic-

aerobic 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 (Bo