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### 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 ma jor center for endemic and endangered species. Seasonal river flooding provides the engine for mobilization and tran sfer 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 pla nning 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 severi ty of low flow periods during droughts. These changes are due, in part, to water use in the uppe r parts of the Tri-river system. There will be increased municipal and agricultura l 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 producti vity, biodiversity and endanger ed species should be based on historical seasonal and interannu al river flow rates. Nutrie nt-induced phytoplankton productivity is an important component of estuarine food we bs in the Apalachicola Estuary. The alluvial river also provides organic matter that fuels detrital food webs in the bay. Autochthonous and allochthonous organic carbon creat es 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 distribu tion for the bay that are related, in part, to anthropogenic river alterations. Th is 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 dominan t, 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 dur ing the 2007 drought suffered decr eases 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 destro yed 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 diseas e. With a more permanent reduction of freshwater flows below a level specific for the r eceiving system, the physica lly controlled, highly productive river-estuarine system will eventu ally become a high diversity, biologically controlled bay of substantially reduced fishery pote ntial. It is likely th at 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 cha nges in atmospheric conditions could lead to exacerbation of current reductions of river flow s. There is a real need to organize a comprehensive scientific research program to eval uate the impacts of reduc ed river flow rates, and to use the objective findings to develop a wa ter conservation plan for the ACF basin. The extrinsic and intrinsic value of the Apalachicola River and Ba y system demands nothing less.

2

### Table of Contents

Page

I. Rationale and Conclusions 4

II. Documentation for Ra tionale and Conclusions 14

A. Apalachicola River Basin 

### 14

B. Apalachicola Bay System 

### 18

C. General Ecology 

### 19

1. River Flows, the Apalachico la Floodplain and the Bay 

### 21

2. Estuarine Productivity 

### 22

3. Biological Response to Ap alachicola 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 Apal achicola River-Bay System 66

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

1. Cumulative Reductions of Ap alachicola River Flow Rates 

### 69

2. Recent Actions by the Federal Government 

### 70

V. Conclusions 72

VI. Literature Cite d and Bibliography 76

List of Tables 

### 91 List of Figures 

### 92

3

### I. Rationale and Conclusions

Temperate alluvial rivers and their associ ated estuaries are am ong the most productive and economically valuable aquatic resources in the world. Fr eshwater/saline wetlands and

associated coastal areas account fo r high quality habitats that nur ture 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-d ominated systems (Howarth 1988, Baird and Ulanowicz, 1989; Livingston, 1984; Livings ton et al., 2000). Nutrient input from river sources has been closely associated with autochthonous phytoplankton production in receiving coastal areas. River-driven part iculate organic matter maintain s detritivorous food webs in estuaries (Livingston, 1983, 1984). However, the re lative importance of different sources of both inorganic nutrients and or ganic carbon (dissolved a nd particulate) can vary from system to system (Peterson and Howarth, 1987). These differences can be related to th e 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 ofte n 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 all uvial rivers is closely rela ted to continuous water input

within the bounds of natural climatological cycles. The Apalachicola River remains in a relatively natural state with low human populatio ns and low levels of industrialization and farming. Aquatic habitats of th e Apalachicola River floodplain de pend on river flows in terms of frequency and duration of inundatio n and saturation. Floodplain vege tation 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 rive r. 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 increas es of the frequency a nd duration of low flows during drought periods (Light et al., 1998). This has led to the lo ss of 3 million canopy trees in the non-tidal flood plain of the rive r. Reduced river flows could al so affect state-listed wetlands plant species such as Sideroxlyon lycioides (Apalachicola buckthorn), S. thornei (Thorne’s buckhorn), and Leitneria floridana (corkwood). Federally protected sp ecies such as Gulf sturgeon

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

flows. The Apalachicola River contai ns 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., 20 05). Field surveys indicated that unionids in the Apalachicola River occur in shallo w channel margins, sloughs and tributaries that undergo rapid depth fluctuations (EnviroScience, Inc., 2005). These areas are “critically important to the survival of th reatened and endangered mussels in the Apalachicola and lower Chipola Rivers.” Purple bankclimbers were elim inated 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-c olonize 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 requ ired for maintenance of existing slough and channel margin unionid populations, and are considered essential for recovery of federally listed species (EnviroScience, 2005; Zimme rman, 2006). Apalachicola River flow rates should follow functionally-equivale nt historical patterns to maintain the highly diverse and productive species that are adapted to the natural peri odicity 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 coas tal 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 acces s 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 nurs ery in the highly produc tive estuarine waters.

5These species also benefit from reduced/variable sa linities that limit preda tion. Without adequate river water input, the Apal achicola 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 s howing key features that result in extremely high primary and secondary productivity.

Nutrient loading from the river, in th e form of inorganic nitrogen and phosphorus compounds, is distributed in form of particulate matter, colloidal conglomerates, and dissolved compounds (Figure 1). Inorganic nutrients (NH 3 , NO 2 , NO 3 , PO 4 ) are taken up rapidly by phytoplankton (microscopic floating plants), thus l eading to relatively low c oncentrations 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 produ ctivity that forms the basis for key food webs in the bay. This include s 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, re present a primary food source for

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

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

accumulate in the sediments where infaunal mi crofauna, microflora and macrofauna form important elements of detrital food webs for the bay. Depositional (s edimentary) areas that receive fresh water input are part icularly 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 (Fi gure 1). This nutrient-rich organic matter is colonized by microbial components to form the basis of importan t 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 estu arine fish populations. Shallow depths and extremely high bottom productivity expl ain 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 lucr ative fisheries in the region. The outer bay, having higher salinities than the upper parts of the Apalachicola es tuary, 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 ga me fishes (Figure 1).

Submerged aquatic vegetation (SAV) contri butes 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 prolonge d drought have adversely affected the East Bay grass beds that represent an important habita t and source of productivity fo r 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 i nput restricts development of dominant sea grass species such as Thalassia testudinum (turtle grass) and Syringodium filiforme (manatee grass).

7These species are adapted to clear water and high sa linities, and are thus restricted to shallower areas in the outer regions of th e Apalachicola system such as along the St. James Island area from the City of Carrabelle to Alligator Harbor. Su bmerged 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 comb ination of fresh water input, nutrient loading, water quality factors, high biological productivity, salinity distributions and the diversity of natural habitats ha ve 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 pl anning in Franklin County in the 1970's and early 1980’s. This effort was based on an extens ive scientific database that was used as the anchor for management initiatives. This incl uded the establishment of the Apalachicola River and Bay Estuarine Sanctuary in 1979. This sanc tuary, now called a National Estuarine Research Reserve, included purchases of about 78,000 ha (h ectares) of wetlands, and remains one of the largest such Reserves in the country. State o fficials along the river a nd the bay carried out a series of major purchases of we tlands. These purchases have been extended to the present day. Public land holdings accompanied regional and local planning effo rts 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 re sources. The major management effort for the Apalachicola system would be undone by increa sed drought frequency a nd enhanced low-flow conditions due to upriver water removal by human activities.

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

rates. This differs from the actua l concentration of nutrients in th e water, as loading is a dynamic process rather than a simple concentration variab le. Naturally high nutrient loading from the river

should thus not be confused with the high concentrations of nutrients that fl ood into the river and bay from urbanized areas during rain events. Ur ban storm water runoff occurs due to replacement

8of 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 fl ow can accentuate the bloom impacts by reducing

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

Livingston (2007) outlined the adverse impacts of nutrient loading from industrial, agricultural and urban so urces 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 dinoflagell ates in time. Bloom effects on phytoplankton assemblages included initial reductions of species richness/diversity and direct/indirect replacement processes. Long-te rm occurrences of pla nkton blooms and related changes in phytoplankton composition were acc ompanied by altered food web processes and losses of key fish and invert ebrate populations. Raphidophyte ( Heterosigma akashiwo ) and dinoflagellate ( Prorocentrum cordatum ) blooms were statistically associated with reduced invertebrate and fish community variables, and creating serious disrupti ons of bay food webs.

Natural seasonal and interannual tr ends 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 nutrien t loading of the Apalachicola Ri ver is an important component of the influence of nutrients on high bay productivit y. Without the naturally high river flow rates, anthropogenic nutrient inputs could have an enha nced adverse effect on bay water quality and populations by stimulating toxic bl ooms that would reduce bay produc tivity. 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 producti vity of the Apalachicol a system (Livingston, 2008). The complex interrelationships of river flow and cultural eutr ophication have been outlined in various studies (Livingston, 2002, 2007). There is ample evidence that low river flow conditions that are enhanced by anthropogenic ac tivities would exacerbate the impact of urban runoff and treated sewage on bay produc tivity during extende d drought periods.

9Figure 2: Model of the Apalachicola Bay system showing potential impacts of reduced river flow leading to plankton blooms and re duced secondary productivity.

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

factor in the maintenance of riverine a nd 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 contribu te 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 producti on by benthic plants. Lowered Apalachicola River flow would reduce detritus loading from wetlands areas. Associated reductions of nutrients, along with changes of wa ter quality associated with re duced river flow during droughts, would lead to altered phytoplankt on 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 flow s would be exacerbated by up-river human activities in the form of urban and agricultural use of river water. Huma n-related reductions of river flow would expand the scope and duration of the a ssociated reduction of river an d bay productivity (Figure 3).

10Figure 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 ye ars 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 al tering the natural processes that are responsible for the high productivity of the system.

11The salinity of the Apalachicola Bay system is controlled to a considerable degree by the Apalachicola River (Livingston 1984). The Apal achicola Bay system has historically provided 90% of Florida’s oysters (10% na tionally). The very high oyster production in the Apalachicola system depends on a combination of variables that are directly and indir ectly associated with fresh water input. Increased sali nity would allow increased oyster mortality due to predation and disease. This same process would also adversel y affect other commercially important fishes and invertebrates due to increased pr edation on the nurserying organisms. The Apalachicola estuary is a major nursery for white shrimp and blue cr abs. Both species utilize the bay as a highly productive nursery, and, along with oysters, form th e basis for important commercial fisheries. Increased salinity due to reduced river flows lo wers the nursery function of the bay for such species due, in part, to incr eased predation from stenohaline offshore species. Recent prolonged low-flow events during droughts have adversely affected bay and Gu lf fisheries for white shrimp, blue crab and sciaenid fish popul ations. In addition, reduced nutri ent loading due to lower river flows would lead to altered phyt oplankton that, in turn, would a lter food webs that support the highly valued commercial and sports fisheries. In this way, reduced river flows due to anthropogenic activities, would l ead to direct and indirect ad verse impacts on the commercial fisheries along the Apalachicola River-Bay system.

Information from various sources indicates th at there has been a serious change in the Apalachicola flow rates with an increase of the fr equency and severity of low flow periods during droughts. There is also evidence that these chan ges 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 increas ed frequency and virulence of low river flows. It is likely that increased fre quency and duration of river flow reductions in the future due to water removal by upstream human activities will even tually lead to the loss of the Apalachicola resource though serial reductions of bay resilience. There wo uld be habitat and productivity changes that would be accompan ied by the elimination of the riverine wetlands, loss of the nursery function of the bay and destruction of th e naturally high productivity associated with key aquatic species.

12A noted above, there has been a considerab le investment by local, state and federal associations and agencies in terms of time a nd 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 d ecades, negotiations among the governors of these states broke down in February 2008. In April 2008, th e U. S. Army Corps of Engineers (U. S. A. C. E., 2008) released a modified Interim Operatio n Plan (IOP) that would allow Georgia to keep

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

even lower river flows than those associated w ith 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 drought s. The modified IOP was approved by the U. S. Fish and Wildlife Service. The Corps’ modi fied Interim Operation Plan does not include any requirement that Georgia implement effective conser vation efforts designed to limit the impact of enhanced drought effects on Florida resources. These actions indi cate that the application of minimum flow requirements has been progres sively minimized by federal environmental agencies.

According to the Carnegie Institution for Sc ience (2008), there is evidence that the jet streams in the northern hemisphere have weaken ed 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 Apalac hicola system is a f act, and the potential for

further reductions of rainfall and natural river fl ow should be included in calculations for water conservation efforts. It is possible that futu re, long-term changes in atmospheric conditions

could lead to further reductions of river flows.

13

### II. Documentation for Ra tionale 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 km 2 (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 te rminus in the Apalachicola estuary (Figure 1). Average flow rates have hi storically approximated 690 m 3 s -1 (1958-1980) with annual high flows averaging 3,000 m 3 s -1 (Leitman et al., 1982; Leitman et al ., 1991). The forested floodplain, about

450 km 2 , is the largest in Florida (L eitman et al., 1982). Forestry is the primary land use in the floodplain (Clewell, 1977). Other activities includ e minor agricultural an d residential use, bee keeping, tupelo honey production, and sports/c ommercial fishing (Livingston, 1983, 1984).

Figure 4: The Apalachicola-Chattahoochee-Fl int (ACF or Tri-Rive r) drainage basin.

Tn. N.C.

S.C.

Al. Ga.

Fl.

Al. Fl.

Ga.

Fl. A

l

. G a

.

Apalachicola River

Apalachicola Bay 0

km

40 80 B A S I N L I M I T S

B A S I N L I M I T S Atlanta, Georgia

Columbus, Georgia

Apalachicola,

Florida

Gulf of Mexico N Chattahoochee River

Flint River

Chipola River

Jim Woodruff Dam

Lake Seminole Lake Lanier

14The Apalachicola system represents an unus ually 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 th e least populated areas along the Gulf coast (F igure 5). Over the past 35 years, the Florida State University A quatic 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 Chatta hoochee and Flint Rivers) to the Apalachicola River-Bay system will be under increas ing pressure from municipal and agricultural development, particularly in Georgia.

Figure 5: Human population distribution in Nort h Florida. This figure is a composite of information provided by the National Oceanic and Atmospheric Administration, the Florida Department of Environmental Prot ection, and the ESRI Corporation.

15The Apalachicola River is one of the last major free flowing, unpolluted alluvial systems in the conterminous United States. The importa nce of freshwater flows to the Apalachicola floodplain has been extensively studied (Cairn s, 1981; Elder and Cair ns, 1982; Mattraw and Elder, 1982; Light et al., 1998, 2006). Based on a long histor y of management efforts (Livingston, 2002), the unique characteristics of the river-flood pl ain have been the subject of various studies. The importance of freshwate r 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 th e 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 biot a of the river floodplain (Means, 1977).

2) Floodplain forests include many terrestr ial plant species of which 9 are narrowly endemic, 28 endangered, 17 threatened, and 30 rare (Clewell, 1977).

3) Of the north Florida drainages, the Apal achicola 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 a nd commercial fishery (Yerger, 1977).

5) Apalachicola River wetlands represent a cen ter of endemism for terrestrial species, which includes federally protected species of amphibians, reptil es, and birds (Means, 1977). Due to the high diversity of wetland and upland habitats, the highest species density of amphibians and reptiles in North Am erica (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 duratio n of inundation and saturation. Regular seasonal changes of flow rates are important to the life cycl es 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 hist ory of these species. Crayfish, an important species in terms of bi omass, are directly c ontrolled by annual river fluctuations (Bass, 2002). Spawning of various sp ecies is also dependent on river levels with

16rapid flow reductions usually having a negati ve effect on this pro cess (Hoehn, 2002). Critical habitats for anadromous species such as striped bass are dependa nt on flow rates.

The Apalachicola floodplain is important to va rious freshwater fisheries, although most of the more important fisheries (e.g., striped bass, Morone saxatilis ; sturgeon, Acipenser oxyrhynchus ) have been destroyed or seriously imp aired due to habitat destruction by channelization and damming in the Chattahoochee and Flint Rivers (Livingston and Joyce, 1977; Livingston, 1984). Dredging activit ies, mandated by the U. S. Congress have led to serious habitat damage along the Apalachic ola River with a minimum of ec onomic justification for such channelization (Leitman et al., 1991). The Apal achicola River-wetlands system has been the subject of land purchase efforts by Fl orida state officials, and is one of the few such systems that is largely in public hands.

Associations of floodplain habita t 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 th e river channel have ad versely affected many plant and animal species dependent on the histori cal seasonal pattern of ri ver fluctuations (Light et al., 2006). Although large floods exceeding 100,000 cf s 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). Recen t 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 fore sts, 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 o ccurred as a result of declining water levels in the Apalachicola River (Helen Light, Pers. Comm., 2008).

Flow reductions could have an impact on st ate-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 Ri vers 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 union ids in the Apalachicola River occur in shallow channel margins, sloughs and tributaries that und ergo rapid depth fluctuat ions. These areas are “critically important to the surviv al of threatened and endangered mussels in the Apalachicola and lower Chipola Rivers” (EnviroScience, Inc., 200 5). Purple bankclimbers were eliminated by recent (2000, 2002) low flows, and did not re-coloni ze affected areas (EnviroScience, Inc., 2005). Zimmerman (2006) noted “numerous dead and dyi ng 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 we tland productivity, biodiversity and endangered species should be

based on historical intra- and in terannual flow rates of the Apalachicola River. Projected flow rates of the Apalachicola River should follow hist orical patterns to maintain the highly diverse and productive species that are cu rrently adapted to the natural periodicity of this system.

B. Apalachicola Bay System

Results of previous studies indi cated that the Apalachicola estu ary has been historically in a relatively natural st ate (Livingston, 1984; Livingston et al., 1997, 2000, 2003). A sparse human population, together with a low level of industrial and munici pal development, has been associated with historically high water a nd 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 (Liv ingston et al., 1978) a nd forestry (Duncan, 1979, Livingston and Duncan, 1979, Livingst on et al., 1976), and the importan ce of salinity levels to the community structure of estuarine organisms (L ivingston, 1979; Livingston et al., 2000, 2003).

The basic distribution of the estuarine populations was anal yzed (Edmiston, 1979; Estabrook, 1972; Laughlin, 1979; Laughlin and Livi ngston, 1982; Livingston, 1976b, 1977, 1981b, 1983; Livingston et al., 1974; 1976, 1977, Mahoney, 1 982, Mahoney and Livingston, 1982, McLane, 1980, Purcell, 1977, Sheridan, 1979; Sheridan and Livingston, 1979, 1983). Various studies were

18also carried out concerning the trophic organization of the estuar y (Laughlin, 1979; Livingston et al., 1997; Sheridan, 1978) that includes microbi al ecology (Federle et al., 1983; White, 1983; White et al., 1977, 1979a, 1979b).

Overall, the extensive studies of the Apalach icola system indicated that the relatively

natural interaction of relativel y undisturbed river-bay interact ions, along with little human development in the vicinity of the estuary, resulted in an extremely productive bay system with high levels of secondary producti vity relative to other river-dom inated estuaries such as the Choctawhatchee and Escambia systems to the west.

C. General Ecology

There is considerable natural variability of fr eshwater 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 tributar ies that drain sub-basins into the main stem. The sub-basins often follow different hydrological cycles (Liv ingston et al., 1989, 1990) than the main stem, depending on regional rainfall patterns and the hi ghly variable physiographic conditions in the different regions. Some drainage basins extend into Alabama and Georgia. Temporal patterns and volumes of river discharge to associated es tuaries depend on the cumu lative climatological conditions and seasonally varying evapo-transp iration rates in associated watersheds.

Flooding plays a role during winter and early spring months in the north Florida drainages. Winter-spring flooding in the all uvial streams is a pr oduct of reduced evapotranspiration rates during winter rainfall peak s along the heavily vege tated drainage basins (Livingston, 1984). Reduced summer surface flows are due to increased evapo-transpiration in vegetated flood plains. Evapo-tran spiration in existing reservoirs is also a major component of

the water balance in the Tri-rive r system (Leitman, 2003a). Up-ri ver 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. Allu vial systems such as the Apalachicola have flow patterns that are thus mo re correlated with seasonal rain fall patterns in Georgia and Alabama (where high percentages of the respective drainage basins are loca ted) than in Florida (Meeter et al., 1979). The smaller streams along Apalachee Bay are associated with relatively

19limited estuarine areas, whereas the alluvial , river-dominated estuaries (Apalachicola, Choctawhatchee, Escambia) to the west are propor tionately larger due to the higher river flows.

The Apalachicola estuary (Fi gure 6) is about 62,879 ha in area, and is a shallow lagoonand-barrier-island complex orient ed along an east-west axis. Wa ter 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 majo r 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, t ogether with river flows and bay configuration, have major effect s 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; Li vingston et al., 1997, 1999, 2000, 2002, 2005).

Figure 6: The Apalachicola Bay system showing location of long-term sampling stations (1972- 1984).

201. River Flows and the Apalachicola Floodplain and Bay

The Apalachicola River system has the greatest flow rates of all th e 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 dominan t, commercially important populations of the Apalachicola estuary are adapted to varying salinities (euryhaline) . With reduced flows, salinity goes up, reducing physical stress to offshore stenoha line populations (adapted to high salinity). These species enter the bay resulting in increas ed species richness and predation pressure on existing bay species. Individua l bay population productivity is reduced accordingly due to enhanced predation and competition. The physical stress of the natural (p ulsed) river-estuarine system is a major factor in the prolonged high productivity of the Apalachi cola estuary. Changes in nutrient loading, salinity and li ght penetrability are im portant elements in the determination of the trophic response of the system. Within limited natural bounds, these processes vary little in terms of qualitative and quantitat ive aspects of the trophic orga nization of the bay. Below a certain level of river flow, the estuary becomes a ve ry 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 a nd phytoplankton production.

Under the natural range of river flow variation, the physic ally unstable estuary has been associated with a relatively stab le biological system over intera nnual periods of time (Livingston et al., 1997). River flow changes within the specific limits of seasona l variation result in a generally stable biological progression through time . With consistent reductions of flow rates

21during a prolonged drought, the clarification of a turbid system leads to rapid changes in the pattern of primary production, which, in turn, be comes associated with major changes in the trophic organization of the system. With the pr olongation of the restricted river flows, the formerly physically controlled biological syst em 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 sp ecific for the receiving system, the physically controlled, highly productiv e river-estuarine system would eventually become a high diversity, biologically controlled bay of subs tantially reduced fishery potent ial. Although the exact pattern of the loss of bay resilience to these controlling factors cannot be predicted, th e overall process of fisheries losses has been confirmed by the c onsiderable scientific database concerning the Apalachicola Bay system.

2. Estuarine productivity

A generalized review of the factors that add to the produc tivity of a river-dominated estuary is shown in Figure 7. Fresh water flow s from the upland river-w etlands system carry nutrients and particulate organic matter into the estuary. The nutri ents cause increased production of natural phytoplankton populations . Detrital food webs are fe d by loading of organic matter (dissolved and particulate) that is primarily a ssociated with bottom (ben thic) trophic interactions. The planktonic trophic organization and the detr ital 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 (G ulf) populations that are not adapted to the low and highly variable salinities of the estuary. Relatively few fi sh and invertebrate populations

outside of the infaunal invertebra tes actually breed in the estuary. Most bay populations migrate into the bay as juveniles that us e 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 es tuary add to the value of the estuary. In

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

22together with associated upland wetlands, form the basis of complex and highly productive parts of the overall bay produc tivity (Livingston, 2008). Figure 7: Model of the interaction between the Apalachicola River and Bay with respect to the riverine contributions to bay pr imary and secondary productivity.

The combination of low levels of polluti on, the lack of hypere utrophication due to nutrient pollution, and undisturbed estuarine habita ts 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 inpu t 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 budge ts in Texas Gulf estuaries were dominated by freshwater inflows, and that shellfish and finfish pr oduction was a function of nutrient loading rates and average salinity. Howe ver, few studies have evaluated more detailed facets of the linkage of the freshwater river-w etlands with estuarine productivity (Livingston 1981a). The sources of high productivity are subject to complex s easonal and interannual

fluctuations that are cl osely associated with cl imatological conditions.

23In response to projections of anthropogenic fr eshwater use by Georgia over the next 30-50 years (Livingston, 1988), a long-term program was initiated to anal yze 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 sy stem (Livingston et al., 1997, 2003).

The linkage between upland freshw ater wetlands and the rich es tuarine biota of associated estuaries underscores the importance of ecosyst em-level research in management processes (Livingston and Loucks, 1978). St udies concerning the distributi on of wetland vegetation in the Apalachicola floodplain indicated that vegetation type was associat ed 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 th e Apalachicola River floodplain approximates 360,000 metric tons (mt). Seasonal river flooding pr ovides for the transfer of detritus from the wetlands to associated aquatic areas (C airns, 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 duri ng 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 wi th the delivery of nutri ents and dissolved and particulate organic matter as an important factor in the maintenance of the estuarine primary production (autochthonous and allo chthonous). There were direct links between the estuarine food webs and freshwater discharges (Livi ngston, 1981a, 1983, 1984). Particulate organic carbon delivered to the estuary followed seasonal and interannual fluctuations that were closely associated with river flow (Livingston, 1991a; R 2 = 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-detr ital 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

24Apalachicola system has high phytoplankton produc tivity relative to other river-dominated estuaries, embayments, lagoons, and fjords ar ound the world. Nixon (1988) showed that the Apalachicola Bay system ranks high in overa ll primary production compared to other such systems. Up to 50% of the phytoplankton produc tivity of the Apalachicola estuary is explained by Apalachicola River flow (Myers 1977, Myer s 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 stati ons with low salinity (Iverson et al., 1997). Nitrogen was limiting during summer periods of m oderate 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-fl ow 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, a nd wind action is associated with periodic peaks of phytoplankton production as inorganic nutrients, re generated in the sediments, ar e mixed through turbulence into the euphotic zone (Livings ton 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 fact or 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 ba y. Chanton and Lewis (1999) found that, although there were inputs of large quant ities of terrestrial organic matter, net heterotrophy in the Apalachicola Bay system was not dominant re lative to net autotrophy during a 3-year period. Chanton and Lewis (2002), using δ 13 C and δ 34 S isotope data, noted clear distinctions between benthic and water column feeding types. They found that the es tuary depended on river flows to provide flood-plain detritus during high-flow periods, and dissolved nutrients for estuarine primary productivity (plants) du ring low flows. Floodplain de tritus was significant in the important East Bay nursery area, thus showing th at 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 orga nic matter from periodic river-based influxes of dissolved and particulate organi c matter coincided with abundan ce peaks of the detritus-based

25(infaunal) food webs of the Apalachicola syst em (Livingston and Loucks, 1979; White et al., 1979a, 1979b; Livingston, 1984)). A mechanism for th e direct connection of increased infaunal abundance was described by Living ston (1983, 1984) whereby microbial activity at the surface of the detritus (Federle et al., 1983a) led to microbi al 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 th at 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 sa linity. 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 account s 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 combin ation of river-derived organic matter and autochthonous organic carbon provided the resources for consumers in ri ver-dominated estuaries of the Gulf coast.

3. Biological Response to Ap alachicola River Flows

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

1984. This included monthly collections of water qua lity and biological data concerning infaunal macroinvertebrates, epibenthic macroinvertebrates and fishes (Livingston et al., 1997). The data

were summed across all taxonomic lines and tran slated into the various trophic levels that included herbivores (feeding on phytoplankton, benthic algae), detr itivores (feeding primarily on particulate organic matter), omnivores (feeding on plants and animals), primary carnivores (feeding on herbivores), secondary carnivores (feeding on primary car nivores) and tertiary carnivores (feeding on secondary carn ivores). All data were expr essed 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.

26River flows during the last half of the 20 th century and early parts of the 21 st century are shown in Figure 8. There was a major drought du ring the mid-1950’s. During the intensive study period (1975-1984), interannual river flows followed model predictions (Meet er 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) in dicated low fall flows, peak flows during winter-early spring periods, spring and fall low flow periods and low summer fl ows (relative to winter-spring flows) due to high evapotranspiration rates duri ng 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 sa linities during the 2- yr drought (1980-1981) (Livingston et al., 1997). Figure 8: Three-month moving averages of m onthly Apalachicola Rive r flows from October 1950 through May 2008. Data were provided by the U. S. Geological Survey (Sumatra, Florida gage). Blue lines desi gnate drought conditions.

Apalachicola River Flow (Sumatra)

0 500 1000 1500 2000 2500 30001950/101951/101952/101953/101954/101955/101956/101957/101958/101959/101960/101961/101962/101963/101964/101965/101966/101967/101968/101969/101970/101971/101972/101973/101974/101975/101976/101977/101978/101979/101980/101981/101982/101983/101984/101985/101986/101987/101988/101989/101990/101991/101992/101993/101994/101995/101996/101997/101998/101999/102000/102001/102002/102003/102004/102005/102006/102007/10

date

There was an extreme drought from 1999-2001 (F igure 8) that was followed by the most recent drought period (2007-present). It is duri ng these droughts that bay conditions are most susceptible to anthropogenic reductions of river flow when the combined natural and anthropogenic flow rate decreases have docum ented adverse effects on the receiving bay.

274. Habitat Type and Population Distribution

The bay is characterized by a series of domina nt species that are euryhaline (adapted to varying salinities), and able to nursery in the extreme salinity vari ations 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 accordi ng 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 ri ver flow processes. By transforming the data according to ontogenetic (developmental) feeding st ages, we were able to evaluate population distribution according to a basic, functional pr ocess (feeding) that defined the nurserying organism.

Infaunal macroinvertebrates

In terms of frequency of occurrence dur ing 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 pe riod 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; se condary carnivores at > 25 mm). Most of these invertebrate species are browse rs, grazers, or seize-an d-bite predators.

Penaeid shrimp

The numerically dominant invertebrates incl uded white shrimp and blue crabs that, together, represent about 70% of the total numbe rs taken over the14-year study period. The white

28shrimp, Litopenaeus setiferus , is the numerically dominant pen aeid 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 shri mp (< 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 specie s 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 mo st affected by river flow s. This distribution is compatible with the importance of freshwat er inflows and the resulting productivity that accompanies such flows. The low numbers associat ed 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, a nd young-of-the-year also are most abundant during early fall in East Bay. This appears to be related to food av ailability in areas rece iving 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 rive r 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 crab s appear in the bay du ring winter months and are largely concentrated in Ea st Bay and along the main river channel of the bay. Secondary increases of this trophic unit occu r during late summer to fall months in the upper bay. The next trophic stage appears in the bay during February with secondar y 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 fa vorite habitat. Spatial-temporal blue crab distribution appears to

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

river.

The long-term trends of invert ebrate distribution indicate th at invertebrate numbers are associated with river flow even though such mani festations 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 predomin ance. 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 su ch distributions appears to be

increased concentrations of i nvertebrate populations in areas associated with the entry of freshwater into the upper bay. These areas are notable for rela tively high organic carbon and nutrient loading and associated pr oductivity. Trophic unit distribution displays a broad spectrum of diverse phase interactions with river inpu t to the bay over seasonal and interannual periods. Feeding habit changes are related to habita t-oriented differences in available food.

Fishes

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

mitchilli (bay anchovy) and benthic feeding pr imary 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 sediment s) macroinvertebrates and fishes. The primary fish dominants, representing about 80% of to tal fish numbers taken over th e sampling period, include bay anchovies, seatrout, spot, and Atlantic croaker.

30Anchoa 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 dur ing the first year of the drought, with major decreases during succeeding years. This distribu tion was consistent with the postulated increases of plankton during the first year of the drought. The second trophi c unit showed relatively low numbers during and after the 1980-81 drought.

Cynoscion arenarius

The sand seatrout, a piscivorous fish that feeds primarily on an chovies (Sheridan and Livingston 1979), reaches peak numbers during late spring and early summer. The distribution of the first 2 trophic units is loca ted largely in East Bay and ar ound the Apalachicola River mouth from late spring to early fall. The larger sand seat rout are located mainly ne ar 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. Th e patterns of anchovy di stribution in time could reflect predation pressure by the sand seatrout.

Leiostomus xanthurus

Young-of-the-year spot enter the bay duri ng winter-early spring periods, and are concentrated in East Bay and areas near the rive r mouth. Older spot move to the lower parts of Apalachicola Bay. This distri bution in consistent with know n distributions of infaunal macroinvertebrate distribution in space and time, a nd is a trophic response to herbivorous and omnivorous species that respond directly to river in flows to the bay. Temporal changes of spot indicated a major increase of young spot duri ng the second year of the drought followed.

31Micropogonias undulatus

Young-of-the-year Atlantic cr oaker enter the bay during wi nter-spring months and are located mainly in East Bay and west of the ri ver mouth. The larger forms move throughout the bay during summer months. There were no ove rt temporal trends of this species.

Apalachicola Bay ecology is closely associ ated with freshwat er input from the Apalachicola River (Livingston, 1984a). The di stribution of epibenth ic organisms in the Apalachicola Estuary follow a specific spatial relati onship to river flows. St ations most affected by the river are inha bited 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 re semble 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 invert ebrates and fishes arebased on a series of studies executed continuously from 1972-1984 (Livingston, 1984). Crosscorrelation analyses of long-term changes of infa unal and epibenthic invert ebrates and fishes over the intensive study period indicated that dominan t bay populations followed a broad spectrum of diverse phase interactio ns 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 we re 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

32penaeid shrimp usually occurred in summer and fa ll 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 comp lex 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 a bove East Bay (Figure 9a; Livi ngston, 1984). The fresh water dominants include bulrushes ( Scirpu s 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, toge ther with the loadi ng of river nutrients and organic matter, contri bute to the enhanced nurser y function of East Bay.

Figure 9a: Seagrass and we tland habitats of the Apalach icola Drainage System.

33The primary distribution of the submerged a quatic vegetation (SAV) in the Apalachicola estuary is shown in Figure 9a. The color and turb idity 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 fo r penaeid shrimp and other crustaceans and fishes at early stages of their on togenetic progressions in the bay.

The predominant macrophyte species in the me sohaline 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 infaun a 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 (Figur es 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. Li ght limitation is an important factor in the development of seagrass beds in the area. Li ght penetration is limite d by color and turbidity.

Based on the distribution of these factors, the data indicate th at the combination of runoff from the Carrabelle River and the depth of the wa ter 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 or ganization. Dominant fi shes 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 be ds included southern flounder ( Paralichthys albigutta ), spotted

34seatrout ( Cynoscion nebulosus ), and sharks of various type s (Livingston, 1984). Storm water runoff from urban development has recently cause d 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 subm erged aquatic vegetation (density) in near-shore areas of St. George Sound during 2006-2007. Water quality st ations (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 pla nkton-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 incl ude 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 th e 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 macroinve rtebrates 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 trophi c analyses involving infaunal and epifaunal macroinvertebrates and fish.

A listing of the 9.5 year averages of the mont hly data for East Bay are given in Table 1. Sediments in western parts of East Bay (station 4) were relatively silty. Th e same is true of the small embayment in eastern parts of the system (station 4a) and a tidal creek affected by runoff

36from upland forestry operations in Tate’s Hell Swamp (station 5b). The area in the upper bay (station 5a) was mainly sandy. We stern parts of East Bay were denoted by considerable amounts of leaf matter during peri ods of high winter-spring river flows relative to eastern sections (Figure 9a). Watercolor increased in eas tern parts of the bay due to runo ff 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 a nd 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-c ut areas were denoted by the lowest overall secondary production. These da ta 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 sa mpled during the 9.5–year survey of East Bay taken mont hly from 2/1997-7/1984. Stations ar e noted in Figure 9. b=bottom, s=surface. n/smp=numbers per sample. FII (fish, inve rtebrates, 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(gm 2 

### ) 0.099 0.057 0.047 0.036 inv totwt (gm 2 

### ) 0.026 0.022 0.012 0.014 FIIC1 (gm 2 

### ) 0.575 0.050 0.474 0.035 FIIC2 (gm 2 

### ) 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

37Detritus-based Food Webs

Leaf matter, as a form of m acrodetritus, enters the bay in areas dominated by river flow (Livingston, 1984). These inputs occur during wint er-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 durin g winter-spring periods (F igure 9e). Livingston (1984) outlined the detrital food webs with respec t 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 matte r had a direct relations hip with river flooding with the exact timing of peak ri ver flows and productivity of rive r wetlands as key determinants of the short-term fluctuations and long-term tren ds of the input of allochthonous (derived from outside the system) organic matter into the bay (Livingston, 1981a, b). De trital inputs were significantly associated with seasonal trends of river flows during winter-spring periods. Local marshes also contribute to the expo rt of detrital aggreg ates to the bay (Ribe lin 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 450Jan-75Apr-75Jul-75Oct-75Jan-76Apr-76Jul-76Oct-76Jan-77Apr-77Jul-77Oct-77Jan-78Apr-78Jul-78Oct-78Jan-79Apr-79Jul-79Oct-79Jan-80Apr-80Jul-80Oct-80Jan-81



### date DryWt-A04-g/trwl DryWt-A5a-g/trwl

38Figure 9e: Microdetritus taken in water samples in the lower Apalachicola River monthly from August 1975-March 1982.



### Apalachicola River Microdetri t

0 10000 20000 30000 40000 50000 6000075/0875/1276/0476/0876/1277/0477/0877/0977/1077/1278/0278/0378/0478/0678/0778/0878/1078/1178/1279/0279/0379/0479/0679/0779/0879/1079/1179/1280/0280/0380/0480/0680/0780/0880/1080/1180/1281/0281/0381/0481/0681/0781/0881/1081/1282/0182/02



### dat e 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, microeukaryot es) 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 w ith initial bacteria succeeded by diatoms and fungal mycelia (Bobbie et al., 1978). Grazing amphipods feed on the microbiota that live on leaf matter (Morri son and White, 1980). Amphipod distribution is significantly associated with bacter ial fatty acids (White et al, 1979a, b). This base of the detrital food webs is controlled by epibenthic predators (F ederle 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 partic ulate matter through microbi al 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 st rongly aligned with the availa bility of detritus (Livingston,

391984). The distribution of these detrital associati ons is determined by temperature, salinity, and

the biochemical features of the microbial comm unities 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 habita t in the Apalachicola estuary, providing cover and food for diverse assemblages (Livingston, 19 84). This includes bryozoans, flatworms, annelids, gastropod and pelecypod mollusks, arth ropod 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). Wate r quality and biological samples were taken monthly at stations 3 and 5a (July 1978-J une 1984) and station ML (November 1981-August 1986). The biological organizati on reflected the differences be tween the highly productive mud flats in East Bay and the produc tive seagrass beds of St. Geor ge Sound. Fresh water quality and quantity in the loadings to the respective areas ar e quite different in term s of nutrients. These differences also extend to the most important food web components in these areas that are represented by infaunal macroinvertebrates that li ve in and on the sediments in the respective study areas. The most obvious di fference between the aquatic habitats of East Bay (stations 3 and 5a) and St. George Sound (station ML) is the lack of direct (sta tion 3) or indirect (station 5a) Apalachicola River flow at stati on ML. East Bay station 3, which receives direct river flow, had lower salinity, temperature, and dissolved oxygen a nomaly than the other sites. Bottom salinity in East Bay ranged from essentially freshwat er conditions during wi nter-spring floods to salinities between 10 and 20 ppt (p arts per thousand) during the fa ll low water periods. There were rapid changes in salinity at station 3. Station ML was characterized by high salinity and less salinity variability. Duri ng periods of high Apalachicola River flow, salinity was not markedly reduced in St. George Sound and th ere was evidence (low salinities during summer

40months) 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 eff ects 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 compar ed 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

413), 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 dens ity at all three sites. Long-t erm 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 sta tion ML, and the greatest biomass at station 5a. Analysis of the long-term field data indicated th at species richness reached maxima l levels in all three sampling areas during fall, a period of re latively 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 ri chness per core was highest at st ation ML and lowest at station 5a. Relative dominance per core was highest at st ation 3 and lowest at station ML. Station 3 had high numbers m -2 with a relatively low cumulative spec ies richness (21 species). Numerical dominants were the polychaetes Mediomastus ambiseta and Streblospio benedicti . Station 5a was moderately productive in terms of nume rical abundance with low cumulative species richness (10 species) and high dominance of the sa me species noted at Station 3. A total of 72 species was found at station ML with low domina nce of the most numerically abundant species.

Dominants included Apoprionospio pygmaea

, Paraprionospio pinnata and Mediomastus

ambiseta.

These data indicate that areas affected by ri ver flow are highly productive in terms of secondary productivity but are low in species ric hness due to the highly variable environment in such areas. Parts of the bay distan t 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 dr oughts. The bay would be inhabited by more species, but the overall produc tivity would be reduced as euryhaline populations were reduced due to increased sa linity and reduced primary productivity. The physically controlled, highly productive system w ould be replaced by a biologically controlled, speciose system with lower secondary production.

42Figure 9g: Three-dimensional view of numbers of individua ls, species richness, and top dominant numbers of infaunal macroinvertebrates taken from 100 core samples at stations 3, 5a and ML.

43The influence of river flow on receiving areas was observed as a gradient of increasing temporal habitat stability with distance from th e river. Salinity varia tion as well as ambient salinity at any given time appeared to be primary factors that defi ned the East Bay habitat. Areas directly (station 3) and indire ctly (station 5a) affected by Ap alachicola River flow had high salinity variation re lative to areas distant from such fl ow (station ML). Although important habitat variables had high levels of variation with in 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 ri ver 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 fr om adjacent land areas. These differences of runoff result in distinctive forms of sp ecies composition and trophic organization.

The Apalachicola River thus serves as th e dominant habitat feature of the receiving estuary. River flow elements contribute both directly and indirectly to a se ries of habitats that maintain the overall high secondary pr oduction of the estuary. Surrratt et al. collected sediment cores from three sites in Apalachicola Bay and an alyzed for organic carb on (C), total nitrogen (N), and total phosphorus (P ) concentrations and delta 13 C and delta 15 N stable isotopic abundances. According to this recent research,

“Carbon and nitrogen concentrations, ratio s, and stable isotopes coupled with grain-size shifts for the bay suggest a d ecrease in river organic matter supply and a change in sediment clay content supply and/or distribution fo r the bay. Overall, the applied indicators suggest an incr ease in marine influence on the organic matter in the estuary. These shifts app ear to be associated with Apalachicola River management practices coupled with s ea-level rise in the Gulf of Mexico. “

Samples taken near the river mouth indicated th at 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 di scharge alterations with sea-level rise appears

to account for the modification of organic matter loading to the bay.

445. Trophic Organization of the Bay

Physical, chemical and biological (infauna, epibenthic macroi nvertebrates, fishes) samples

were taken at fixed stations in East Ba y (Figure 9) monthly from 1975-1984 (9.5 years; Livingston et al., 1997). East Bay is the primary nursery ar ea for the Apalachicola Bay system. These data were used to transform the descriptiv e field information into a trophic organization for the estuary. Detailed descripti ons of methods for the field coll ection 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 organizatio n as a function of ontogenetic (d evelopmental) feeding stages of the species found in the estuary over the mu lti-year sampling program. Ontogenetic feeding

units were determined from a series of detaile d stomach content analyses carried out with the various epibenthic invertebrates and fish es 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 stom ach 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 an alysis is given for the blue crab, Callinectes sapidus (Figure 10). Generic codes are given in Table 2.

45Table 2: Generic Codes for th e 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

46Figure 10: Ontogenetic feed ing units of blue crabs (day vs. night collections).

47The data show how the diet of the blue crab s taken in the Apalachicola estuary changes as the organisms grow. This analys is was carried out for the all the major invertebrate and fish species in the Apalachicola system . These data express the lifetim e feeding habits in a far more detailed and significant way than ju st looking at the adult feeding be havior. This is important in what is essentially a nursery system where by fi shes and invertebrates use the highly productive estuary as a nursery for the growth and maintenance of juveniles.

Infaunal macroinvertebrates were also organi zed 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 in to trophic levels (i.e., herbivor es, omnivores, three levels of carnivores [C1, C2, C3]) so that monthly changes in the overall trophic orga nization of the system could be determined over the study period. The data were summed across all taxonomic lines and

translated into the various tr ophic levels that included herb ivores (feeding on phytoplankton and benthic algae), omnivores (feeding on detritus an d various combinations of plant and animal matter), primary carnivores (feeding on herbivor es and detritivorous animals), secondary carnivores (feeding on primary carnivores and om nivores) 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 leve l 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 (L ivingston 1980). In this way, the long-term

database of the collections of infauna, epibenthic macroinvertebra tes and fishes was re-organized into a quantitative and detailed trophic matrix ba sed 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) prov ided important evidence of how droughts affect the key trophic components of the Apalachicola Bay sy stem through time. Physical/chemical and biological samples (infauna, epibenthic macroinver tebrates, 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 ch anges in the overall trophic orga nization of East Bay could be

48determined over the study period. . High flows occurred during the winter-spring months of most years and low flows occurred during summer-fa ll months (Figure 11). From May 1980 through the end of 1981, there was a major drought with s ubstantially 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 we re often less than 50% of what East Bay usually receives in the way of freshwater runoff from the ri ver. The following 2.5 yr were characterized by a general return to the prevailing patt erns of Apalachicola River flow as noted during the period from 1978 through the winter of 1980.

Figure 11: Apalachicola River flows, monthl y, 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 250075/0275/0475/0675/0875/1075/1276/0276/0476/0676/0876/1076/1277/0277/0477/0677/0877/1077/1278/0278/0478/0678/0878/1078/1279/0279/0479/0679/0879/1079/1280/0280/0480/0680/0880/1080/1281/0281/0481/0681/0881/1081/1282/0282/0482/0682/0882/1082/1283/0283/0483/0683/0883/1083/1284/0284/0484/06



### date APRIV 3 per. Mov. Avg. (APRIV)

The most outstanding aspect of the bay salin ity over the period of study was the sustained high salinities during the 2-yr period of drought (1980-1981) (Figur e 12). Watercolor was lowest and Secchi disk readings (light penetration) were highest during the drought period of 1980-1981 with Secchi readings in 1980 be ing significantly different (p < 0.05) from preceding years. Color levels during the drought y ears were significantly (p < 0.05) different from those taken during

49preceding and succeeding years. The period during the 1980-1981 drought was also characterized by periodically high positive values of dissolved oxygen a nomalies. All physical-chemical indices returned to previous levels du ring the period following this drought.

Figure 12: Water quality indices (Secchi dept hs, watercolor, salinity) taken monthly from February through June 1984. Also shown are th e 3-month moving averages of the data.



### EAST BAY

0.1

1 10 100 100075/0275/0675/1076/0276/0676/1077/0277/0677/1078/0278/0678/1079/0279/0679/1080/0280/0680/1081/0281/0681/1082/0282/0682/1083/0283/0683/1084/0284/06



### date SECCHI COLO R SALINITY 3 per. Mov. Avg. (SECCHI) 3 per. Mov. Avg. (COLOR) 3 per. Mov. Avg. (SALINITY)

DROUGHT

50Infaunal 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 numbe rs 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 divers ity 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 dur ing the spring and summer of 1981. Fish numbers and fish trophic diversity were lowest during th e majority of the drought. The drought conditions

of 1980-1981 were thus associated with initial incr eases 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 herbivor es over the study period was 2.39 g/m 2 with averages of 0.21 g/m 2 for omnivores, 0.53 g/m 2 for primary carnivores, 0.04 g/m 2 for secondary carnivores and 0.004 g/m 2 for tertiary carnivores. There was a mark ed 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 Se cchi depths. The more frequent periods of positive oxygen anomaly during the drought also co incided with the high levels of herbivore

biomass. There was a marked decrease of herbi vore biomass that started during the second half of the drought. Herbivore biomass virtually collapsed during the fo llowing 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 comple te recovery of the omnivores during the study period. Primary carnivore biomass increased during fall 1980 an d continued at high levels through spring 1981. After the drought, primary carnivore biomass dec lined 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 incr eased 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 fo llowing the drought. The tertiary predators were

51virtually absent during the 1980-1981 drought period. Overall, the drought of 1980-1981 had a profound effect on the trophic organi zation of East Bay. This impact remained at various trophic levels during the 2.5-year peri od of river flow recovery.

Figure 13: Fish, infaunal and invertebrate (F II) 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 10075/0275/0675/1076/0276/0676/1077/0277/0677/1078/0278/0678/1079/0279/0679/1080/0280/0680/1081/0281/0681/1082/0282/0682/1083/0283/0683/1084/0284/06



### 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

52The 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, th ere was a distinct decrease of the herbivores as a percentage of the monthly totals. The omnivores showed an almost diametrically opposite reaction w ith relative decreases during the drought and increases during the 2-yr period following the drought. The primar y carnivores had the highest percentages during the year after the drought while the secondary and tertiary car nivores 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 car nivores was evident only as percentages of the monthly biomass totals during th e latter stages and following th e end of the drought at which

times overall biomass was low. Figure 14: Fish, infauna, inverteb rate (FII) trophic data taken monthly from 2/75-8/84 in East Bay. Data represent % of total biomass fo r each category (herbivores, omnivores, C1, C2, C3 carnivores).

53Livingston et al. (1997) found th at, within limited natural bounds of freshwater flow from the Apalachicola River, there was little change in the trophic organizati on of the Apalachicola estuary over prolonged periods. The physical instab ility of the estuary was contrasted with the biologically stable estuarine system. However, wh en a specific threshold of freshwater reduction was reached during the drought (1980-1981), clarif ication of the normally turbid and highly colored river-estuarine system led to rapid change s 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 herb ivore/omnivore abundance. There was a marked increase in the herbivore biomass during th e beginning of the drought of 1980-1981. Herbivore biomass peaks coincided with low winter rive r flows, peak turbidity, low water color and increased Secchi depths. More frequent peri ods of positive oxygen anomaly (high dissolved oxygen) during the drought also co incided 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 reduc tion of plankton and the eventual collapse of the various trophic groups in East Bay.

There are problems with relating bay productivi ty 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 leve l of flow reduction and its su bsequent 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 seas on 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 syst em 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 exacerbati on of productivity losses of with tim e. This leads to the question of at what point would the Apalach icola system be altered to a point of no return to its former high level of biological productivity.

54The concepts of biological stability and resilie nce have been defined in various ways (see Harrison [1979], and Santos and Bloom [1980], for a brief revi ew of the semantic problems encountered). Stability is generally defined as the ability of a given system, once perturbed, to return to its previous state. Re silience refers to the degree, manne r, and pace of restoration of the initial system function and structure following a disturbance (Westma n, 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 habita t for re-colonization, toxicity of the disturbed habitat, and effectivenes s 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 disturban ces that occur outside of the evolutionary experience of a give n species may have a more advers e impact on the ability of that population to recover relativ e to natural changes that occur through time.

Based on the observed trends in the Apal achicola estuary, postulated permanent reductions of freshwater flows due to anthropogeni c activities could lead to major reductions of biological productivity (i.e. invertebrate and fi sh populations) in the Apalachicola Bay system (Livingston et al., 1997). Ther e 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 depende nt on serial loss of resilience. It is not possible to predict when the rubber band would no long er 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 produc tivity. In this event, the physically controlled, highly productive river-estuar ine system would b ecome 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 hypot hesis of non-linear response in the form of

accelerated loss relative to dr ought frequency and intensity.

557. 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 commerci al fishery (Whitfield and Beau mariage, 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 rate s of oysters in this region ar e among the most rapid of those recorded (Ingle and Dawson, 1952, 1953) with harv estable 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 oyste r bars in the Apalachicol a Bay system oyster study.

56Livingston et al. (1999, 2000) outlined life history descrip tions of the Apalachicola oyster population. Hurricane Elena struck the Apalachic ola 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. Hurric anes 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 subs tantial damage to the exis ting population. Under such circumstances, the resilience of the oysters was enhanced by specific aspects of its life history that include rapid and massive sp awning capabilities, a re latively high rate of growth due to the usually optimal habitat conditions in the Apal achicola 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 wa s aided by other by-product s of the storm that

included the absence of natural predators (including human beings ). The overall outcome of oyster population changes thus indicated an ad aptive response and hi gh resilience to storm effects of this species that allowed survival under even extreme conditions of natural storminduced stress.

Long-term changes of the Apalachicola oyste r population should be placed within the context of major habitat-controlli ng features such as Apalachicol a River flow. Meeter et al. (1979) found that oyster landings from 1959 to 1977 were correlated negatively with river flow. The highest oyster landings coinci ded with drought conditions. W ilber (1992), using oyster data from 1960 to 1984, found that river flows were co rrelated negatively with oyster catch per unit effort within the same year and positively with cat ches 2 and 3 yr later. Highest oyster harvests occurred in 1980-1981, coinciding with a major dr ought. Predation on newly settled spat during periods of high salinity was give n as a possible explanation of the 2-yr time lags between low flow events and subsequent poor production. Livi ngston et al. (1997) found that increases of the Apalachicola Bay non-oyster bivalve mollusk popul ations during droughts was based on changes in the trophic organization of the estuary. The re latively high oyster production during low flow years was probably due to increased primary productivity as a functi on of altered physical conditions (i. e., increased light penetration) in the receiving estuary. Increased productivity

57contributed to increased growth rates and ultimately increased oyster production. Such changes in river flow and oyster productiv ity were regular and o ccurred within prescr ibed progressions of

river flow fluctuations. Howeve r, prolonged droughts eventually induced serious reductions of oysters due to the effects of increased predation and disease as noted below.

Overall oyster production is concen trated 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 surf ace 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 gr owth occurs during periods of low water temperature and high salinity variation. Oyster mo rtality 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 proxi mity to the entry of oyster predators from the Gulf through the respective passes. The most important oyster pred ator is the gastropod mollusk,

Thais haemastoma . Oyster mortality is low at the highl y productive reefs in the eastern part of the bay (Cat Point, East Hole). Statistical anal yses indicated that oyste r mortality was positively associated with maximum bottom salinity and surface residual current velocity (Livingston et al., 2000). Mortality was inversely related to oyste r 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 cons istent 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 Apalachic ola River/Tate’s Hell Swamp drai nage) and high velocity bottom water currents moving westward from St. Geor ge Sound. Based on the distribution of oyster density, the primary oyster growi ng areas were in eastern secti ons of the bay with maximum growth during periods of low water temp erature and high sali nity variation.

58Figure 16: Distribution of oyster larvae, spat fa ll, 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 3505Oyster 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 SPOyster larvae(nm-3) 1985 1986 4240 4590 3505

0 5 10 15 20Spatfallrate(nshell1wk-1) 1985 1986 28 21

0 500 1000Oysterdensity(nm-2) 1510

0.0 5.0 10.0New 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 SPPer centmortality

Western Bay Centra l Bay Eastern

... Open side

Closed side

0 5 10 15 20Spatfallrate(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 1000Oysterdensity(nm-2) 1510

0.0 5.0 10.0New oystergrowth rate Individual (mgAFDWd -1 )Per centmortality

Western Bay Centra l Bay Eastern Open side

... Closed side

0 500 1000Oysterdensity(nm-2) 1510

59We 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 estu ary. Based on the model, we determined that high salinity, relatively low-veloci ty current patterns, and the proxi mity of a given oyster bar to entry points of saline Gulf water into the ba y were important factor s that contributed to increased oyster mortality (disea se and predation) (Livingston et al., 2000). Mortality was a major determinant of oyster production in th e Apalachicola estuary with predation as a significant aspect of such mortality. By infl uencing salinity levels and current patterns throughout the bay, the Apalachicola River was important in controlling such mortality.

Actual mortality data were plo tted in Figure 17 so that the be havior of the model relative

to real data could be observe d. 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 (S t. Vincent Bar, Scorpion, Pickalen e, Porter’s Bar). Predation on the primary eastern oyster bars was usually relative ly low. The projections of oyster mortality for 1986 (a drought year characterized by much lo wer river flow than 1985) were considerably higher, especially on the highly pr oductive bars in eastern secti ons 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 produc ing bars such as Cat Point, East Hole,

Platform and Sweet Goodson would have been extens ive. 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. Predati on 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 in clude various organisms that prey on oysters (Menzel et al. , 1958, 1966). Our experiments indicated that oyster morta lity in the Apalachicola system was related to salinity as a determinant of oyste r predation and the geographic posi tion of the reef relative to the

60natural (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 mort ality in 1985 and the hydrodynamic model results for (A) 1985. (B) 1986. (C) 1991. Circles indicate observed mortality values from oyster predation experiments (1 985, May-August average).

The association of increased oyster mortality with extent and duration of reduced river

flow is consistent with the ini tial increase of oyster production at the initiation of the drought that is followed by oyster losses during an extended pe riod of low river flows. Increased mortality with prolonged drought is verified by oyster losses during recent droughts.

61By coupling hydrodynamic modeling with descri ptive and experimental biological data, Livingston et al. (2000) we re able to determine the effects of potential freshwater diversions on oyster production in Apalachicola Bay. Th e 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 na turally occurring droughts, through increased upstream anthropogenic (consumptive) water use, or a combination of the two, could have serious long-term, adverse c onsequences 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 pr edation 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 salin ities at Cat Point during va rious time periods (1996, 1995, 1999- 2001). During a recent drought (1999-2002), there wa s a series of extremely low-flow periods. Data, provided by the Apalachicola National Es tuarine 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 Li vingston research group (1972-1990) . These salinities peaked during 2001. The salinity maxi ma were consistently high from 1991-2001 whereas salinity minima showed pronounced increases during 2001. Th is trend was consistent with the relatively low standard deviations during 2001, an observation that has si gnificance when oyster trends during this period are taken into account.

It should be recognized that various species take adva ntage 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.

62A 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 lo wer than those from 1954-1990. These data indicate that in the most recent decade, low-fl ow 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

63During the 1999-2002 drought, there was a collapse of oystering in the Eastern reefs from

Cat Point to East Hole. In a 2002 field assessm ent by the Florida Department of Environmental Protection (G. S. Gunter, Pers. Comm.), lowere d oyster productivity in eastern bay reefs was accompanied by large numbers of predators that in cluded oyster drills, crown conchs, scallops

and sea urchins. Hard and soft corals were not ed on Porter’s Bar during these field surveys (G. S. Gunter, Pers. Comm.). With a return of hi gher 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 ob servations during the 1999-2002 drought represent field verification of model predictions made by Li vingston 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 resi lience of the bay to such events would be systematically reduced which coul d then lead to more permanent reductions of those forms of secondary production (such as oysters, shrimp, blue crabs and sciaenid fi shes) that depend on the interannual cycling of natura l river flows into the bay.

The most recent drought (2007-present) followe d a similar pattern to that described for the 1999-2002 drought. During this drought, saliniti es 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 produci ng 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 west ern parts of the bay during the period of increased salinity. These observations represent fiel d 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 Ba y (Purcell, 1977). Based on a survey of the SAV in East Bay in June 2005, Hurricane Dennis t ook out all the SAV in both the lower river and

64East 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 S AV 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 Livings ton et al.(1997) (see above ). The trawl data taken by Edmiston and Wanat indica te 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 specie s did not compensate for the lo ss 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 wh ite shrimp (down 90%), brown shrimp (down 55%), blue crabs (down 55%) and flounder (dow n 40%) relative to 2004-2006 and 2006 periods. The severely reduced landings of key commercial species represents a pr actical 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 curren tly in danger of being lost for an as yet undetermined period. If the increased incidents of low river flow regi mes 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. Th ere is evidence that non-linear responses by key bay populations to reductions of river flows have already occurred. The almost

total lack of effective wate r conservation efforts in the Tri-river system has undoubtedly exacerbated an already serious loss of Ap alachicola 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 restoratio n effort (Figure 18).

Figure 18: Map showing major elements of the Apalachicola Management Plan.

66The extensive studies of the Apalachicola syst em that have been carried out since 1972 were used to develop an ecosystem-based mana gement 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 progr ams, 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 pr imarily at the county commission level in Florida.

Documentation of facts concerning the Apalach icola Basin (Livingston and Joyce, 1977) provided the initial details of the unique ecologi cal status of the Apal achicola system. The linkage between the upland freshwat er wetlands and the Apalachicol a estuary via nutrient loading analyses together with related bay studies le d 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 Apal achicola region that have continued up to the present time. Upland and coastal wetlands along th e 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 Flor ida has spent over $239 million through land acquisition to protect the wetlands system of the Apalachicola Ri ver and Bay system. Currently, major parts of the Apalachicola River river-w etland system is held by public agencies for

67preservation 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 wetla nds to the productivity of this drainage basin.

Thanks to the efforts of the same coalition of local and state pers onnel that instituted land planning in Franklin County in the early 1970's, th e Apalachicola scientific database was used to establish the Apalachicola River and Bay Estu arine Sanctuary in 1979. This sanctuary, now designated a National Estuarine Research Reserv e, included the purchase of about 78,000 ha in the bay system (Figure 18). The original desi gnation 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 (Figur e 18). Somewhat later, an area above the East Hole oyster beds (Unit 4 EEL; Figure 18) was purchas ed 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. Departme nt of the Interior (Fig ure 18). The east end of St. George Island is a state park. After consid erable legal proceedings, most of the western section of St. George Island (the Plantation, Fi gure 18) was planned for maximum protection of island freshwater drainages, associ ated 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 Rive r wetlands to complete a ring of publicly owned lands around the most environmentally sensitiv e areas of the Apalachicola River-Bay system (Figure 18). When combined with state regula tions (Aquatic Preserve, Area of Critical State Concern) and a Franklin County management pr ogram 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 estuar y should be based on pr otection and control of fresh water sources, nutrients , and organic matter with a mini mization of physical alterations that often lead to increased salinity stratificatio n and the associated loss of the nursery function of the estuary. These processes underlie the very basis of riverine and es tuarine productivity. It is clear that fisheries production, the nursery function, and the productivity of individual

68populations depend on species-specific responses to combinations of freshwater input, salinity changes, food web processes, and interspecific predation and comp etition. Due to the lack of science-based management of ri ver-estuarine systems throughout the United States, these areas are quietly succumbing to the detrimental effect s 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 relationshi ps in a series of river-es tuarine systems along the NE Gulf of Mexico, management of these re sources should be based on the following:

1) protection of freshw ater and coastal wetlands

2) maintenance of adequate freshwater i nput to sustain natural productivity and the important nursery function of the river-bay system

3) minimization of physical alte rations of the river-estuary that could lead to adverse changes involving nutrient transfer and salinity distribution, and

4) management of local municipal developmen t and agricultural runoff to minimize input of toxic agents, nutrients, and disease vect ors to receiving river-estuarine systems.



### IV. Current Threats to the Apalachicola River-bay System

1. Cumulative Reductions of Ap alachicola River Flow Rates

Agricultural and municipal interests along the Apalachicola-Chatta hoochee-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 Lani er storage from hydropower to water supply for rapidly growing Atlanta, Georgia metropolitan ar ea. 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 Ge orgia 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.

69Leitman (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 au thors expected that the unimpaired flow results would correspond to fluctuat ions 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 greates t flow deficit occurred during the 1999–2002 drought event. Leitman (2003a, b) found that during average years, the net evapoprecipitation losses from impoundment s in the ACF basin were cons iderable; 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 Octobe r except August. If th e net evapo-precipitation losses for 1986 were considered, such losses exc eeded 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, Ma y, August and September. The drought of 1999- 2002 had lower river flows but higher precipitati on 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 dire ctly related to low river flows and high salinities due, in part, to anthropogenic changes in the Flint and Chattahoochee Rivers including (among other an thropogenic factors) the building and management of dams and their resulting reservoirs.

Leitman et al. (2003) concluded that fl ows of the Apalachicola River at the Chattahoochee gage during drought events have b een 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

70these states broke down in February 2008. In Ap ril 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 lowe r flows placed on the natural resources of the Apalachicola River and Bay system. There is no me ntion 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-altit ude 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 th e 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 fo r 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 al ready 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 majo r changes taking place in recent decades. If the projections of reduced rainfall in the ACF regi on 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 sy stem is a fact, however , and the potential for

further reductions of rainfall and river flow s hould be included in an calculations for water conservation efforts. It is possible that futu re, 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 impact s 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 oyste rs, shrimp, blue crabs and fin fishes in Apalachicola Bay are linked to river flows that c ontrol 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. Du e to the high diversity of wetland and upland habitats, the highest sp ecies density of amphibians and rept iles in North America (north of Mexico) occurs in the upper Apalachicola basi n. The Apalachicola Ri ver and floodplain depend on natural river flows in terms of freque ncy and duration of i nundation and saturation.

3. The Apalachicola River has the greatest flow rates of all the ri ver-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 pr oductivity in the adjoining coastal region.

4. There has been a considerable investment by local, state and fede ral 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 ove r $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 b een a serious change in the Apalachicola flow rates with an increase of the frequency and seve rity 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 precip itation 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 droug hts have been associated with losses of about 3 million canopy trees in the non-tidal Apalach icola 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 r ecent 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 pr oductivity, biodiversity and endangered species

72should be based on historical s easonal and interannual flow rate s of the Apalachicola River. Projected flow rates of the Apalachicola Rive r 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 i ndicate that the Apalachicola estuary has been in a relatively natural state historicall y. The undisturbed progression of river- bay interactions, along with little human development in the Apalachicola basin, re sulted in a productive bay system with high levels of secondary produc tivity relative to other ri ver-dominated estuaries.

9. The response of the bay to river flows is comp lex 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 fo llows a specific spatial relationship to river flows. Dominant bay populations follow a broad spectrum of di verse phase interactions with river flow and associated changes in salin ity 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 fl ooding 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 adversel y 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 th at organic matter deposition was driven by both natural ( i.e., hurricanes and droughts) and anthropogenic ( i.e., hydrologic river alteration and dredging) activity. After th e drought of 1981, Woodruff Dam ope ration procedures and the resultant river discharge patterns could have affected mass sedimentation rates and organic loading within the estuary. “Carbon and nitroge n 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-leve l rise appears to clearly account for the modification to organic matter sources for the entire bay.

12. The dominant, commercially important populati ons of the Apalachicol a 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 phys ical stress that results in increased species richness as stenohaline populati ons (adapted to high salinity in offshore Gulf areas) enter the bay. Individual population producti vity is reduced accordingly due to altered habitat conditions and enhanced predation, competition and disease.

7313. Within natural boundaries of river flows, food web processes in the bay vary little in terms of qualitative and quantitativ e interactions. Below a certai n level of river flow, however, the estuary becomes a very different system. W ith prolonged reductions of river flow, there are eventual decreases in biologi cal production due to reduced nutrient loading and altered phytoplankton assemblages. Together with asso ciated habitat change s, the commercially important populations are replaced by less produc tive 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 phys ically controlled, hi ghly productive riverestuarine system will eventually become a high diversity, biologically controlled bay of substantially reduced fishery potential.

14. Brackish water submerged aquati c 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 ontogeneti c (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 spec ies 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 indicat e a relatively similar response of dominant estuarine species to prolonged droug hts. There is evidence that anthropogenic reductions of river flow that occur outside of the evolutionary experience of a give n species may have an enhanced adverse impact on the abili ty of that population to recover re lative to natural changes to which the species has adapted through time.

16. During the most recent decade, low flows e xperienced during droughts have been more severe in terms of both duration and extent. Re cent salinity increases due to low flows during droughts have adversely affected oyster beds and the East Ba y grass beds that represent important habitats and sources of productivity for the upper bay. Commercial fishing landings during the 2007 drought were associated with d ecreases of white shrimp (down 90%), brown shrimp (down 55%), blue crabs (down 55%) a nd flounder (down 40%). Major losses in key oyster producing areas were noted due to high salini ties 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 dur ing droughts lends credence to th e hypothesis of a non-linear response in the form of accelerated loss relati ve to low flow frequency and intensity during droughts.

7417. Losses of commercial fisheries, together with impacts on river wetlands, represent a threat to unique cultural and econom ic 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 du e 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 rise n in altitude and shifted toward the poles. This change could mean less rain in the alrea dy drought-stricken SE United States. There is no way of confirming the long-term effects of clim ate changes due to Global Warming. There is ample scientific information that there are majo r changes taking place in recent decades. If the projections of reduced rainfall in the ACF regi on are true, it would place even more emphasis on the need for an advanced water c onservation 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 Ap ril 2008, the U. S. Army Corps of Engineers (U. S. A. C. E., 2008) released a federal proposal th at would allow Georgia to keep more water in reservoirs during droughts. This would essent ially 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 th at increased frequency and durati on 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 b een habitat and productivity changes that have led to elimination of the riverine wetlands as not ed 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 aqua tic species in th e river and bay.

21. The increase of the frequency and inte nsity 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 a nd climate changes should be incl uded 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 fo r effective implementatio n of water conservation efforts. There is a real need to organize a comp rehensive scientific study program to evaluate the impacts of reduced river flow rates, and to us e the objective findings to develop and implement an appropriate water conservation plan for the ACF basin.

75

### VI. Literature Cite d and Bibliography

Armstrong, N. E. 1982. Responses of Texas estu aries to freshwater inflows. Pages 103-120 in V. S. Kennedy, editor. Estuarine Comparisons. Acad emic Press, New York, New York, U. S. A.

Baird, D. and R. E. Ulanowicz. 1989. The seasonal dynamics of the Chesapeake Bay ecosystem. Ecological Monographs 59: 329-364.

Blanchet, R. H. 1979. The distribution and abunda nce of ichthyoplankton in the Apalachicola Bay, Florida area. M. S, Thesis. Florida State University, Tallahassee, Florida. U. S. A.

Blumberg, A. F. and Mellor, G. L. 1980 A coas tal ocean numerical model. In Mathematical modeling of Estuarine Physics, Proceedings of the International Symposium, Hamburg, 24-26 August 1978 (Sundermann, J. and Holz, K. P., eds). Springer-Verlag, Berlin, pp. 203-214.

Blumberg, A. F. and Mellor, G. L. 1987 A description of a three-dimensional coastal ocean circulation model. In Three-dimensional Coastal Ocean Models (Heaps, N.S., ed). American Geophysical Uni on, Washington, D.C., pp. 1-16.

Bobbie, R. J., S. J. Morrison, and D. C. White . 1978. Effects of substrat e biodegradability on the mass and activity of the associated estuarine microbiota. Applied Environmental Microbiology 35: 179-184.

Boynton, W. R., W. M. Kemp, and C. W. Keefe. 1982. Comparative analysis of nutrients and other factors influencing estuarin e phytoplankton produc tion. Pages 69-90 in V. S. Kennedy, editor. Estuarine Comparisons. Academic Press, New York, New York, U. S. A.

Cairns, D. J. 1981. Detrital production and nutrient re lease in a southeastern flood-plain forest. M. S. Thesis. Florida State Universit y. Tallahassee, Florida, U. S. A.

Cairns, J. Jr., and K. L. Dickson. 1977. Recovery of streams and spills of hazardous materials. In, pp. 24-42, J. Cairns, Jr., K. L. Dickson, and E. E. Herricks, Editors, Recovery and Restoration of Damaged Ecosystems, Universi ty of Virginia Press, Charlottesville, Virginia, USA.

Carnegie Institution for Science, Department of Global Ecology, Geophysical Research Letters, 2008. Changing Jet Streams May Alter Path s of Storms and Hurricanes.

Chanton, J. and F. G. Lewis. 1999. Plankton and dissolved inorganic carbon isotopic composition in a river-dominated estuary: Apalachico la Bay, Florida. Estuaries 22: 575-583.

Chanton, J. and F. G. Lewis. 2002. Examinati on of coupling between primary and secondary production in a river-dominated estuary: Apal achicola Bay, Florida, U. S. A. Limnol. Oceanogr. 47: 683-697.

76Christensen, J. D., Monaco, M. E., Livingston, R. J., Woodsum, G., Battista, T. A., Klein, C. J., Galperin, B. and Huang, W. 1998 Potential imp acts of freshwater inflow on Apalachicola Bay, Florida oyster ( Crassostrea virginica ) populations: coupling hydrologic and biological models. NOAA/NOS Strategic Environmental Assessments Division Report

, Silver Spring, Maryland. 58 pp.

Clements, W. H. and R. J. Livingston. 1983. Ov erlap and pollution-induced variability in the feeding habits of filefish (Pisces: Monacanthidae) from Apalachee Bay, Florida. Copeia (1983): 331-338.

Clements, W. H. and R. J. Livingston. 1984. Pr ey selectivity of the fringed filefish Monacanthus ciliatus (Pisces: Monacanthidae): ro le of prey accessibility. Mar. Ecol. Prog. Ser 16: 291- 295.

Clewell, A. F. 1977. Geobotany of the Apalachicola River region. Pages 6-15 in R. J. Livingston, editor. Proceedings of the conference on the Apalachicola drainage system. Florida Department of Natural Resources, Marine Resources Publication 26. St. Petersburg, Florida, U. S. A.

Cloern, J. E., A. E. Alpine, B. E. Cole, R. L. J. Wong, J. F. Arthur and M. D. Ball. 1983. River discharge controls phytoplankton dynamics in the northern San Francisco Bay estuary. Estuarine, Coastal and Shelf Science 16: 415-429.

Cross, R. D. and D. L. Williams. 1981. Procee dings of the national symposium on freshwater flow to estuaries. Fish and Wildlife Service, Washington, D. C., U. S. A.

Danglade, E. 1917. Conditions and extent of the wate r level oyster beds and barren bottoms in the vicinity of Apalachicola, Florida. Appendi x V, Reports of the U.S. Commissioner of Fishes for 1916, Bureau of fishes Document No. 841. 75 pp.

Darst, M.R., and Light, H.M., 2007 Drying of Fl oodplain Forests Associated with Water-Level Decline in the Apalachicola River, Flor ida—Interim Results, 2006: U.S. Geological Survey Open-File Report 2007-1019, 32 p.

Dayton, P. K., M. J. Tegner, P. E. Parnell, and P. B. Edwards. 1992. Temporal and spatial patterns of disturbance and recovery in a kelp fo rest community. Ecological Monographs 62: 421- 445.

Deegan, L. A., J. W. Day, Jr., J. G. Gosselink, A. Yanez-Arancibia, G. Soberon Chavez, and P. Sanchez-Gil. 1986. Relationships among physical characteristics, vegetation distribution, and fisheries yield in Gulf of Mexico estuaries. Pages 83-100 in D. A. Wolfe, editor. Estuarine Variability. Academic Press, Inc., New York, New York, U. S. A.

Denman, K. and T. Platt. 1977. Time series an alysis in marine ecosystems. Pages 227-242 in H. H. Shugart, Jr. editor. Time Series and Ecological Processes. Siam Institute for Mathematics and Society, Philadelphia, Pennsylvania, U. S. A.

77Duncan, J. L. 1977. Short-term effects of stor m water runoff on the epibenthic community of a north Florida estuary (Apalachicola, Florida) . M. S. Thesis. Florida State University, Tallahassee, Florida, U. S. A.

Edmiston, H. L. 1979. The zooplankton of the Apal achicola Bay system. M. S. Thesis. Florida State University, Tallahassee, Florida, U. S. A Elder, J. F. and D. J. Cairns. 1982. Production and decomposition of forest litter fall on the Apalachicola River floodplain, Florida. U. S. Geological Survey Water-Supply Paper 2196.

EnviroScience, Inc. 2005. Freshwater mussel and habitat surveys of the Apalachicola River, Chipola River, and selected sloughs /tributaries. Final Report.

Estabrook, R. H. 1973. Phytoplankton ecology and hydr ology of Apalachicola Bay. M. S. Thesis. Florida State University. Tallaha ssee, Florida, U. S. A.

Ezer, T. and Mellor, G. L. 1997 Simulations of the Atlantic Ocean with a free surface sigma coordinate ocean model. Journal of Geophysical Research 102 647-657.

Federle, T. W. , R. J. Livingston, D. A. Meet er, and D. C. White. 1983. M odification of estuarine sedimentary microbiota by exclusion of epiben thic predators. Journal of Experimental Marine Biological Ecology 73: 81-94.

Funicelli, N. A. 1984. Assessing and managing effects of reduced freshwater inflow to two Texas estuaries. Pages 435-446 in V. S. Kennedy, Editor. The Estuary as a Filter. Academic Press. New York, Ne w York, U. S. A.

Gorsline, D. S. 1963. Oceanography of Apalachicola Bay. Pages 145-176 in Essays in marine geology in honor of K. O. Emery. University of Southern California Press, Los Angeles, California, USA.

Harrison, G. W. 1979. Stability under environmental stress: resistance, resi lience, persistence, and variability. Am. Nat. 113:659-669.

Hayes, P. F., and R. W. Menzel. 1981. The re productive cycle of ear ly setting Crassostrea virginica (Gmelin) in the northern Gulf of Mexi co, and its implications for population recruitment. Biol. Bull. 160:80-88.

Heard, W. H. 1977. Freshwater mollusca of the Apalachicola drainage. Pages 20-21 in R. J. Livingston, editor. Proceedings of the conference on the Ap alachicola drainage system. Florida Department of Natural Resources , Marine Resources Publication 26. St. Petersburg, Florida, U. S. A.

Hoehn. T. 2002. Apalachicola-Chattahoochee-Flint Ri ver water control plan technical assistance document. Florida Department of Envir onmental Protection, Ta llahassee, Florida.

78Howarth, R. W. 1988. Nutrient limitation of net primary production in marine ecosystems. Annual Reviews of Ecology and Systematics 19: 89-110.

Ingle, R. M., and C. E. Dawson. 1952. Growth of the American Oyster Crassostrea virginica (Gmelin) in Florida Waters. Bull. Mar. Sci. Gulf and Caribbean 2:393-404.

Ingle, R. M., and C. E. Dawson. 1953. A survey of Apalachicola Bay, Technical Series No. 10. State of Florida Board of Conservation 38 pp.

Iverson, R. L., W. Landing, B. Mortazawi, and J. Fulmer. 1997. Nutrient transport and primary productivity in the Apalachicola River and Bay. F. G. Lewis, Ed. Apalachicola River and Bay Freshwater Needs Assessment. Repor t to the ACF/ACT Comprehensive Study. Northwest Florida Water Management Distri ct, Havana, Florida. Unpublished Report.

Kemp, W. M. and W. R. Boynton. 1984. Spatial and temporal coupling of nutrient inputs to estuarine primary production: the role of part iculate transport and decomposition. Bulletin of Marine Science 35: 522-535.

Laughlin, R. A. 1979. Trophic ecology and population di stribution of the blue crab, Callinectes sapidus , Rathbun, in the Apalachicola estuary (North Florida, U.S.A.) Ph. D. Dissertation. Florida State University. Tallaha ssee, Florida, U. S. A.

Laughlin, R. A. and R. J. Livingston. 1982. Envi ronmental and trophic determinants of the spatial/temporal distribution of the brief squid ( Lolliguncula brevis ) in the Apalachicola Estuary (North Florida, USA). Bulle tin of Marine Science 32: 489-497.

Leber, K. M. 1983. Feeding ecology of decapod cr ustaceans and the influence of vegetation on foraging success in a subtr opical seagrass meadow. Ph. D. Dissertation, Florida State University, Tallahassee, Florida.

Leber, K.M. 1985. The influence of predatory decapods, refuge, and mi crohabitat selection on seagrass communities. Ecology 66: 1951-1964.

Lehman, P. W. 1992. Environmental factors asso ciated with long-term changes in chlorophyll concentration in the Sacramento-San Joaquin delta and Suisun Bay, California. Estuaries 15: 335-348.

Leitman, S.F. 2003a. An evaluation of evapo-pr ecipitation loses from impoundments in the ACF basin. Unpublished report.

Leitman, S.F. 2003b. Review of cumulative monthl y deficits during three major drought events. Unpublished report.

Leitman, H. M., J. E. Sohm, and M. A. Frank lin. 1982. Wetland hydrology and tree distribution of the Apalachicola River floodplain, Florida. U. S. Geological Survey Report 82. U. S. Government Printing Office, Washington, D. C. U. S. A. 92 pp.

79Leitman, S., L. Ager, and C. Mesing. 1991. The Ap alachicola experience: Environmental effects of physical modifications to a river. In R. J. Livingston, Editor. The Rivers of Florida. Springer-Verlag, New York, New York, U. S. A.

Leitman, S., J. Dowd, and Skelly Hombeck-Pelham. 2003. An evaluation of observed and unimpaired flow and precipitation duri ng drought events in the ACF basin. Proceedings of the 2003 Georgia Water Resources Conference , held April 23-24, 2003, at the University of Georgia, Kathryn J. Hatche r, editor, Institute of Ecology, The University of Georgia, Athens, Georgia.

Light, H.M., Darst, M.R., and Grubbs, J.W., 1998, Aqua tic habitats in relation to river flow in the Apalachicola River floodplain, Florida: U.S. Geological Survey Professional Paper 1594, 77 p.

Light, H.M., Vincent, K.R., Darst, M.R., and Price, F.D., 2006, Water-Level Decline in the Apalachicola River, Florida, from 1954 to 2004, and Effects on Floodplain Habitats: U.S. Geological Survey Scientific Investig ations Report 2006-5173, 83 p., plus CD.

Livingston, R. J. 1975. Resource management and estuarine function with application to the Apalachicola drainage system. Estuarine Po llution Control and Assessment 1: 3-17.

Livingston, R.J. 1975. Resource management and es tuarine function with application to the Apalachicola drainage system (North Florid a, U.S.A.).Office of Water and Hazardous Materials, U.S. Environmental Protection Agen cy: included in final collection of papers (reviewed and published for subm ission to the Congress of th e United States), Estuarine Pollution Control and Assessment, Vol. 1, 3-17.

Livingston, R. J. 1976. Dynamics of organochlorin e pesticides in estuarine systems and their effects on estuarine biota. Invited paper, Proc eedings of the Third In ternational Estuarine Research Federation Conference, Galveston Te xas. October, 1975. Estuarine Processes I., 507- 522.

Livingston, R. J. 1976a. Diurnal and seasonal fluctuations of organisms in a north Florida estuary. Estuarine and Coastal Ma rine Science 4: 373-400.

Livingston, R. J. 1976b. Environmenta l considerations and the management of barrier islands: St. George Island and the Apalach icola Bay system. Pages 86-102 in Barrier Islands and Beaches. Technical Proceedings of the 1976 Barrier Islands Workshop. Annapolis, Maryland, U. S. A.

Livingston, R. J. 1977. The Apalachicola dile mma: Wetlands development and management initiatives. Pages 163-177 in National Wetlands Protection Symposium; Environmental Law Institute and the Fish and Wildlife Service. Washington, D. C. U. S. A.

Livingston, R. J., 1978. Short- and Long-term Effect s of Forestry Operations on Water Quality and the Biota of the Apalachicola Estuary (North Florida, U. S. A.). Technical Paper No.

805, Florida Sea Grant, National Oceanic and Atmospheric Administration, Gainesville, Florida.

Livingston, R. J. 1979. Multiple factor interactions and stress in coastal systems: A review of experimental approaches and field implications. Pages in F. J. Vernberg, Editor. Marine Pollution: Functional Responses. Academic Press, Inc. New York, U. S. A.

Livingston, R.J. 1980. Ontogenetic tr ophic relationships and stress in a coastal seagrass system in Florida. Pages 423-435 in V.S. Peterson, editor. Estuarine perspectives. Academic Press, New York, New York, USA.

Livingston, R. J., 1980. Critical Hab itat Assessment of th e Apalachicola Estuary and Associated Coastal Areas. Final Report, Coastal Plains Regional Commission, Tallahassee, Florida.

Livingston, R. J. 1980. The Apalachi cola experiment: research and management. Oceanus 23: 14- 21.

Livingston, R.J. 1981. Between the Idea and Reality. V.P.I. Publ. Prog. Ser. (Invited paper), 31- 59.

Livingston, R. J. 1981a. River-deriv ed input of detritus into th e Apalachicola estuary. Pages 320- 332 in R. D. Cross and D. L Williams editors. Proceedings of the national symposium on freshwater inflow to estuarie s. Fish and Wildlife Service, Washington, D. C., U. S. A.

Livingston, R. J. 1981b. Man's impact on the distri bution and abundance of Sciaenid fishes. Pages 189-196 in Sixth Annual Marine Recreational Fisheries Symposium; Sciaenids: Territorial Demersal Resources. National Marine Fisher ies Service. Houston, Texas, U. S. A.

Livingston, R. J. 1982a. Trophic or ganization in a coastal sea grass system. Marine Ecology Progress Series 7: 1-12.

Livingston, R. J. 1982b. Between the idea and the reality: An essay on the problems involved in applying scientific data to resear ch management problems. Pages 31-59 in A. Donovan and A. L. Berge, Editors. Working papers in science and technol ogy studies. Virginia Polytechnic Institution, Black sburg, Virginia, U. S. A.

Livingston, R.J. 1982. Review of the Distribution of Trace Metals in the Apalachicola/Chipola Drainage System. Final Report. Apalachee Regional Planning C ouncil, Blountstown, Florida.

Livingston, R. J. 1983. Resource atlas of the Ap alachicola estuary. Florida Sea Grant College Publication. Gainesville, Florida, U. S. A.

Livingston, R. J. 1983. Compendium of Knowledge Concerning the Fl int River System (Georgia). Final Report, Science Advi sory Committee for the Flint River Ecosystem Study, Montezeuma, Georgia.

81Livingston, R. J. 1983. The Biota of St. George Island. Final Report. Franklin County Board of County Commissioners, Apalachicola, Florida.

Livingston, R. J. 1983. Field an d Semi-Field Validation of La boratory-derived Aquatic Test Systems. U. S. Environmental Prot ection Agency, Gulf Breeze, Florida.

Livingston, R. J. 1983. Identification and Analysis of Sources of Pollution in the Apalachicola River and Bay System. Final Report, Flor ida Department of Natural Resources, Tallahassee, Florida.

Livingston, R. J. 1983. Review an d Analysis of the Environmenta l Implications of the Proposed Development of the East Point Breakwater a nd Associated Dredging Operations Within the East Point Channel (Apalachicola Bay Sy stem). Final Report. Franklin County Board of County Commissioners, Ap alachicola, Florida.

Livingston, R. J. 1984. Long-te rm Effects of Dredging and Open-water Disposal on the Apalachicola Bay System. Final Report, National Oceanic and Atmospheric Administration, Washington, D. C.

Livingston, R.J. 1984. The ecology of the Apalachicola Bay system: an estuarine profile. US Fish and Wildlife Service FWS/PBS 82/05. 148 pp.

Livingston, R. J. 1984. Field characterizatio n study of a Gulf coastal seagrass system. Unpublished report for the U. S E nvironmental Protection Agency.

Livingston, R. J. 1985. Application of scientific research to resource management: case history, the Apalachicola Bay system. Pages 103-125 in N. L. Chao and W. Kirby-Smith, editors. Proceedings of the International Sympos ium on Utilization of Coastal Ecosystems: Planning, Pollution, and Productivity. Fundacao Universidad do Rio Grande. Rio Grande, Brazil.

Livingston, R. J. 1986. Ecological processes of r ecruitment in coastal epibenthic macrobiota. Proc., IOC/FAO Workshop on recruitment in tropical coastal demersal communities. Report # 44, 151-166.

Livingston, R. J. 1987. Field sampli ng in estuaries: the relations hip of scale to variability. Estuaries 10: 194-207.

Livingston, R. J. 1988. Inadequacy of species-level designations fo r ecological studies of coastal migratory fishes. Environmental Biology of Fishes 22: 225-234.

Livingston, R. J. 1988. Projected ch anges in estuarine c onditions based on models of long-term atmospheric alteration. Repor t CR-814608-01-0, U. S. Environmental Protection Agency, Washington, D. C.

82Livingston, R. J. 1990. Application of Scientific Data to the Ma nagement of the Apalachicola Oyster Resource. Final Report, National Oceanic and Atmospheric Administration through the Florida Department of Envir onmental Regulation, Wa shington, D. C. and Tallahassee, Florida.

Livingston, R. J. 1990. Inshore marine habitats. Pages 549-573 in R. L Myers and J. J. Ewel, editors. Ecosystems of Florida. University of Central Florida Pr ess, Orlando, Florida, USA.

Livingston, R.J. 1991. Medium sized rivers: gulf coastal plain. In: Bi odiversity of the Southeastern U. S. eds: C. T. Hackney et al., 434 pp., Ecological Society of America.

Livingston, R. J. 1991. Historical relationships between research and resource management in the Apalachicola River-estuary. Ecological Applications 1: 361-382.

Livingston, R. J. 1991a. The Rivers of Florida. Springer-Verlag, Ne w York, New York, U. S. A.

Livingston, R.J. 1991b. Historical Relationships Between Research and Resource Management in the Apalachicola River-estuary. Ec ological Applications 4: 361-382.

Livingston, R. J. 1997. Eutrophication in estuaries a nd coastal systems: relationships of physical alterations, salinity stratification, and hypoxia. Pages 285-318 in F. J. Vernberg, W. B. Vernberg and T. Siewicki, eds. Sustainabl e Development in the Southeastern Coastal Zone. University of South Carolina Press, Columbus, South Carolina, U. S. A.

Livingston, R. J. 2000. Eutrophication Processes in Coastal Systems: Origin and Succession of Plankton Blooms and Effects on Secondary Production. CRC Press, Inc. Boca Raton, Florida. 327 pp.

Livingston, R. J. 2002. Trophic Orga nization in Coastal Systems. CRC Press, Inc. Boca Raton, Florida. 388 pp.

Livingston, R. J. 2005. Restoration of Aquatic Systems. CRC Press, Inc. Boca Raton, Florida, 424 pp.

Livingston, R. J. 2007. Phytoplankt on Bloom Effects on a Gulf Es tuary: Water Quality Changes and Biological Response. Ecologi cal Applications 17: 110-128.

Livingston, R. J. 2008. Water quality and seagrass su rvey in the Carrabelle River and St. George Sound. Unpublished report for the Apalachicol a Riverkeepers and City of Carrabelle.

Livingston, R. J., G. Kobylinski, F. G. Lewis, and P. Sheridan. 1976. Analysis of long-term fluctuations of estuarine fish and invertebrate populations in Apalachicola Bay. Fish. Bull. 74(2): 311-321.

83Livingston, R. J., R. S. Lloyd, and M. S. Zimmerman. 1976. Dete rmination of adequate sample size for collections of benthic macrophytes in polluted and unpollute d coastal areas. Bulletin of Marine Science 26: 569-575.

Livingston, R. J. and E. A. Joyce, Jr. 1977. Proc eedings of the conference on the Apalachicola drainage system, 23-24 April , 1976, Gainesville , Florida. Florida Department of Natural Resources. Florida Marine Research Publicati ons 26. St. Petersburg, Florida, U. S. A.

Livingston, R. J. and O. L Loucks. 1978. Produc tivity, trophic interactions, and food-web relationships in wetlands and a ssociated systems. Pages 101-119 in P. E. Greeson, J. R. Clark, and J. E. Clark, editors. Wetland f unctions and values: the state of our understanding. American Water Re sources Association. Lake Buen a Vista, Florida, U. S. A.

Livingston, R. J., and J. Duncan. 1979. Short- an d long-term effects of forestry operations on water quality and epibenthic a ssemblages of a north Florida estuary. Ecological Processes in Coastal and Marine Systems, Ed. R. J. Livingston.

Livingston, R. J. and J. L. Duncan. 1979. Climatologi cal control of a north Florida coastal system and impact due to upland forestry management. Pages 339-382 in R. J. Livingston editor. Ecological Processes in Coastal and Marine Systems. Plenum Press, New York, New York, U. S. A.

Livingston, R. J., R. L. Iverson, R. H. Estabr ook, V. E. Keys, and J. Taylor, Jr. 1974. Major features of the Apalachicola Bay system: Physiography, biota, and resource management. Florida Scientist 4: 245-271.

Livingston, R. J., G. J. Kobylinski, F. G. Le wis, III, and P. F. Sheridan. 1976. Long-term fluctuations of epibenthic fish and invertebrate populations in Apalachicola Bay, Florida. Fishery Bulletin 74: 311-321.

Livingston, R. J., P. S. Sheridan, B. G. McLa ne, F. G. Lewis, III, and G. G. Kobylinski. 1977. The biota of the Apalachicola bay system : functional relationships. Pages 75-100 in R. J. Livingston, editor. Proceedings of the conference on the Apalachicola drainage system. Florida Department of Natural Resources , Marine Resources Publication 26. St. Petersburg, Florida, U. S. A.

Livingston, R. J., N. P. Thompson, and D. A. Meeter. 1978. Long-term variation of organochlorine residues and assemblages of epibenthic organisms in a shallow north Florida (USA) estuary. Marine Biology 46: 355-372.

Livingston, R.J., John Cairns, Jr ., and K. Dickson, 1978. Eds. Biol ogical Data in Water Pollution Assessment: Quantitative and Statistical Analyses: American Society for Testing and Materials.

84Livingston, R. J., K. R. Smith, and W. H. Clemen ts. 1984. Distribution of Macroinvertebrates in the Flint River-Lake Blackshear System. Fina l Report, Science Advisory Committee for the Flint River Ecosystem Study, Montezeuma, Georgia.

Livingston, R. J., and S. H. Wolfe (1988). Rest oration and preservation ranks of water bodies within the Northwest Florida Water Management District. Report for the Northwest Florida Water Management District.

Livingston, R. J., X. Niu, F. G. Lewis, and G. C. Woodsum. 1997. Freshw ater input to a Gulf estuary: Long-term control of trophi c organization. Ecol. Appl. 7: 277-299.

Livingston, R. J., Howell, R. L., Niu, X., Lewis, F. G. and Woodsum, G. C. 1999. Recovery of oyster reefs ( Crassostrea virginica ) in a gulf estuary following disturbance by two hurricanes. Bulletin of Marine Science, Gulf and Caribbean 64, 75-94.

Livingston, R. J., F. Graham Lewis, III, Glenn C. Woodsum, Xufeng Niu, R. L. Howell, IV, G. L. Ray, J. D. Christensen, M. E. Monaco, T. A. Battista, C. J Klein, B. Galperin, and W. Huang. 2000. Coupling of physical and biologica l models: response of oyster population dynamics to freshwater input in a shallow Gu lf estuary. Est. Coast. Shelf Sci.50: 655-672.

Livingston, R. J., S. Leitman, Gl enn C. Woodsum, B. Galperin, P Homann, J. D. Christensen, and M. E. Monaco. 2003. Relationships of river flow and productivity of the Apalachicola River-bay system. Final Report, NOS/CCM A Biogeography Program, National Oceanic and Atmospheric Administration.

Mahoney, B. M. S. 1982. Seasonal fluctuations of benthic macrofauna in the Apalachicola estuary, Florida. The role of predation and larval availability. Ph. D. Dissertation. Florida State University. Tallahassee, Florida, U. S. A.

Mahoney, B. M. S. and R. J. Livingston. 1982. Seasonal fluctuations of benthic macrofauna in the Apalachicola estuary, Florida, USA. Marine Biology 69: 207-213.

McLane, B. G. 1980. An investigation of the infauna of East Bay-Apalachicola Bay. M. S. Thesis. Florida State University, Tallaha ssee, Florida, U. S. A.

Mattraw, H. C. and J. F. Elder. 1982. Nutrient and detritus transport in the Apalachicola River, Florida. 1984. U. S. Geological Su rvey Water-Supply Paper 2196-C.

Means, D. B. 1977. Aspects of the significance to terrestrial vertebrates of the Apalachicola River drainage basin, Flor ida. Pages 37-67 in R. J. Livingston, editor. Proceedings of the conference on the Apalachicola drainage system. Florida Department of Natural Resources, Marine Resources Publication 26. St. Petersburg, Florida, U. S. A.

Meeter, D. A., and R. J. Livi ngston. 1978. Statistical methods app lied to a four-year multivariate study of a Florida estuarine system. Invited paper, Biological Data in Water Pollution Assessment: Quantitative and Statistical Anal yses. American Society for Testing and

85Materials. Special technical publication 652. Ed s., John Cairns, Jr., K. Dickson, and R. J. Livingston.

Meeter, D.A., R.J. Livingston, and G. Woodsum . 1979. Short and long-term hydrologic cycles of the Apalachicola drainage system with app lication to Gulf coas tal populations. Pages 315- 338 in R. J. Livingston, Editor. Ecological Proc esses in Coastal and Marine Systems. Plenum Press, New York, New York, U. S. A.

Menge, B. A. 1992. Community regulation: unde r what conditions are bottom-up factors important on rocky shores. Ecology 73: 755-765.

Menzel, R. W., N. C. Hulings, and R. R. Hath away. 1966. Oyster abundance in Apalachicola Bay, Florida in relation to biotic associations in fluenced by salinity and other factors. Gulf Research Reports 2: 73-96.

Menzel, R. W. and F. E. Nic hy. 1958. Studies of the distribution and feeding habits of some oyster predators in Alligator Harbor, Florid a. Bulletin of Marine Science Gulf and Caribbean 8: 125-145.

Mittlebach, G. G. 1988. Competition among refuging surf-fishes and effects of fish density on littoral zone invertebra tes. Ecology 69: 614-623.

Mittlebach, G. G., C. W. Osenberg, and M. A. Leibold. 1988. Trophic rela tions and ontogenetic niche shifts in aquatic ecosystems. Pages 219-235 in B. Ebenman and L. Persson, editors. Size-structured populations. Springer-Verlag, Berlin, Germany.

Morrison, S. J., J. D. King, R. J. Bobbie, R. E. Bechtold, and D. C. White. 1977. Evidence of microfloral succession of allochthonous plant litt er in Apalachicola Bay, Florida, U. S. A. Marine Biology 41:229-240.

Mortazavi, B., R. L. Iverson, W. M. Landi ng, and W. Huang, 2000a. Phosphorus budget of Apalachicola Bay: a river-dominated estuary in the northeastern Gulf of Mexico. Mar. Ecol. Prog. Ser. 198: 33-42.

Mortazavi, B., R. L. Iverson, W. M. Landing, F. G. Lewis, and W. Huang, 2000b. Control of phytoplankton production and biomass in a ri ver-dominated estuary: Apalachicola Bay, Florida USA. Mar. Ecol. Prog. Ser. 198: 19-31.

Mortazavi, B., R. L. Iverson, and W. Huang, 2000c..Dissolved organic nitrogen and nitrate in Apalachicola Bay, Florida: spatial distribu tions and monthly budgets. Mar. Ecol. Prog. Ser. 214: 79-91.

Myers, V. B. 1977. Nutrient limitation of phytopl ankton productivity in north Florida coastal systems: technical considerations; spatial patterns; and wind mixing effects. Ph. D. Dissertation. Florida State University . Tallahassee, Florida, U. S. A.

86Myers, V. B. and R. J. Iverson. 1977. Aspects of nutrient limitation of phytoplankton productivity in the Apalachicola Bay system. Pages 68-74 in R. J. Livingston, editor. Proceedings of the conference on the Apalachicola drainage system. Florida Department of Natural Resources, Marine Resources Publication 26. St. Petersburg, Florida, U. S. A.

Myers, V. B., and R. J. Iverson. 1981. Phosphorus and nitrogen limited phytoplankton productivity in Northeastern Gulf of Mexico coastal estuaries. Pages 569-582 in B J. Nielson and L. E. Cronin, editors. Estuaries and Nutrients. Humana Press, Clifton, New Jersey, U.S.A.

Nichols, F. H. 1985. Increased benthic grazing: an alternative explan ation for low phytoplankton biomass in northern San Francisco Bay duri ng the 1976-1977 drought. Estuarine, Coastal and Shelf Science 21: 379-388.

Nixon, S. W. 1980. Between coastal marshes and co astal waters-a review of twenty years of speculation and research on the role of salt marshes in estuarine productivity and water chemistry. Pages 438-525 in P. Hamilton and K. B. MacDonald, editors. Estuarine and wetland processes, Plenum Press, New York, USA.

Nixon, S. W. 1981. Freshwater inputs and estuarine productivity. Pages 31-57 in Cross, R. D. and D. L. Williams, editors. Proceedings of the National Symposium on Freshwater Inflow to Estuaries. U. S. Fish and Wildlife Servi ce, Office of Biological Services. FWS/OBS81/04.

Nixon, S. W. 1988. Physical energy inputs and th e comparative ecology of lake and marine ecosystems. Limnology and Oceanography 33: 1005-1025.

Odum, W. E., J. S. White, and J. C. Pickral. 1979. Factors controlling the flux of particulate organic carbon from estuar ine wetlands. Pages 69-82 in R. J. Livingston editor. Ecological Processes in Coastal and Marine Systems. Pl enum Press, New York, New York, U. S. A.

Pearce, J. W. 1977. Florida's environmentally endangered land acquisition program and the Apalachicola River system. Pages 141-145 in R. J. Livingston, editor. Proceedings of the conference on the Apalachicola drainage system. Florida Department of Natural Resources, Marine Resources Publication 26. St. Petersburg, Florida, U. S. A.

Peterson, Bruce J. and Robert W. Howarth. 1987. Su lfur, carbon, and nitrogen isotopes used to trace organic matter flow in the salt-marsh estuaries of Sapelo Island, Georgia. Limnology and Oceanography 32: 1195-1213.

Peterson, C. H. 1982. The importance of predation a nd intra- and interspecific competition in the population biology of two infaunal suspension feeding bivalves, Protothaca staminea and Chione undatella . Ecological Monographs 52: 437-475.

Peterson, C. H. 1992. Competition for food and it s community-level implications. Benthos Research 42: 1-11.

87Peterson, B. J. and R. W. Howarth. 1987. Sulfur , carbon, and nitrogen is otopes used to trace organic matter flow in the salt-marsh estuar ies of Sapelo Island, Georgia. Limnology and Oceanography 32: 1195-1213.

Power, M. P. 1992. Top-down and bottom-up forces in food webs: do plants have primacy? Ecology 73: 733-746.

Purcell, B. H. 1977. The ecology of the epibenthic fauna associated with Vallisneria americana beds in a north Florida estuary. M. S. Th esis. Florida State University. Tallahassee, Florida, U. S. A.

Reise, K. 1978. Experiments on epibenthic pred ation in the Wadden Sea. Helgolander wiss. Meeresunters 31: 51-101.

Santos, S. H., and S. A. Bloom. 1980. Stability in an annually defaunated estuarine soft-bottom community. Oecologia 46:290-294.

Sheridan, P F. 1978. Trophic relationships of domin ant fishes in the Apalachicola Bay system (Florida). Ph. D. Dissertation. Florida State Un iversity. Tallahassee, Florida, U. S. A.

Sheridan, P. F. 1979. Trophic resource utilizati on by three species of sciaenid fishes in a northwest Florida estuary. Northeast Gulf Science 3: 1-15.

Sheridan, P. F. and R. J. Livingston. 1979. Cyclic trophic relationships of fishes in an unpolluted, river-dominated estuary in North Florida. Pages 143-161 in R. J. Livingston editor. Ecological Processes in Coastal and Marine Systems. Plenum Press, New York, New York, U. S. A.

Schroeder, W. W. 1978. Rive rine influence on estuaries: a case study. Pages 347-364 in V. S. Kennedy, editor. Estuarine inte ractions. Academic Press, New York, New York, USA.

Sheridan, P. F. 1978. Trophic relationships of dom inant fishes in the Apalachicola Bay system (Florida). Dissertation. Florida State Un iversity. Tallahassee, Florida, USA.

Sheridan, P. F. 1979. Trophic resource utilizati on by three species of sciaenid fishes in a northwest Florida estuary. Northeast Gulf Science 3: 1-15.

Sheridan, P. F. and R. J. Livingston. 1983. Abunda nce and seasonality of infauna and epifauna inhabiting a Halodule wrightii meadow in Apalachicola Ba y, Florida. Estuaries 6: 407- 419.

Smith D. E., M. Laffler, and G. Mackiernan. 1992. Oxygen dynamics in the Chesapeake Bay. Maryland Sea Grant College, College Park, Maryland, USA.

88Snedaker, S., D. de Sylva, and D. Cottrell. 1977. A review of the role of freshwater in estuarine ecosystems. Final Report, Southwest Florid a Water Management Di strict, Brooksville, Florida, USA.

Stoner, A. W. 1976. Growth and food conversion efficiency of pin-fish (Lagodon rhomboides) exposed to sublethal concentrations of bleached kraft mill effluents). M.S. Thesis, Florida State University. Tallahassee, Florida.

Stoner, A. W. 1982. The influence of benthic macr ophytes on the foraging behavior of pinfish Lagodon rhomboides (Linnaeus). J. Exper. Ma r. Biol. Ecol. 58: 271-284.

Stoner, A. W. and R. J. Livi ngston. 1980. Distributional ecology and food habits of the banded blenny Paraclinus fasciatus (Clinidae): a resident in a mob ile habitat. Mar. Biol. 56: 239- 246.

Stoner, A. W. and R. J. Livi ngston. 1984. Ontogenetic patterns in diet and feeding morphology in sympatric sparid fishes from seagra ss meadows. Copeia (1984): 174-187.

Surratt, D., J. Cherrier, L. Robinson and J. Cable. 2008. Chronology of sediment nutrient geochemistry in Apalachicola Bay, Florida (U. S. A). J. Coastal Res. 24 (3): 660-671.

Swift, F. 1896. Report of a survey of the oyste r region of St. Vincent Sound, Apalachicola Bay, and St. George Sound, Florida. U.S. Commission of Fish and Fisheries. Report of the U.S. Commission for 1896. Appendix 4, pp. 187-221.

Toner, William. 1975. Oysters and the good 'ol boys. Planning 41: 10-15.

Trush, W. J., S. M. McBain, and L. B. Leopol d. 2000. Attributes of an alluvial river and their relation to water policy and management. PNAS 97: 11858-11863.

Westman, W. E. 1978. Measuring the inertia and resilience of ecosystem s. Bioscience 28:705-710.

U. S. Army Corps of Engineers, 2008. Modificati on the current Interim Oper ations Plan (IOP) at Jim Woodruff Dam.

Welch, B. L., R. B. Whitlatch, and W. F. Bohlen. 1982. Relationship between physical characteristics and organic carbon sources as a basis for comparing estuaries in southern New England. Pages 53-67 in V. S. Kennedy, editor. Estuarine comparisons. Academic Press, New York, New York, USA.

White, D. C. 1983. Analysis of microorganisms in terms of quantity a nd activity in natural environments. Microbes in th eir natural environments. Society for General Microbiology Symposium 34: 37-66.

89White, D. C., R. J. Bobbie, S. J. Morrison, D.K. Oesterhof, C. W. Taylor, and D. A. Meeter. 1977. Determination of microbial activity of lip id biosynthesis. Limnology and Oceanography 22: 1089-1099.

White, D. C., R. J. Livingston, R. J. Bobbie, and J. S. Nickels. 1979a. Effects of surface composition, water column chemistry, and time of exposure on the composition of the detrital microflora and associ ated macrofauna in Apalachicola Bay, Florida. Pages 83-116 in R. J. Livingston, Editor. Ecological Processe s in Coastal and Marine Systems. Plenum Press, New York, Ne w York, U. S. A.

White, D. C., W. M. Davis, J. S. Nickels, J. D. King, and R. J. Bobbie. 1979b. Determination of the sedimentary microbial biomass by extracta ble lipid phosphate. O ecologia 40: 51-62.

Whitfield, W. K., Jr., and D. S. Beaumariage. 1977. Shellfish management in Apalachicola Bay: Past, present, and future. Proceedings of the Conference on the Apalachicola Drainage System. Eds. R. J. Livingston and E. A. Joyce, Jr. Florida Department of Natural Resources Mar. Res. Publ. 26: 130-140.

Wilber, D. H. 1992. Associations between fres hwater inflows and oyster productivity in Apalachicola Bay, Florida. Est. Coastal Shelf Sci. 35: 179-190.

Yerger, R. W. 1977. Fishes of the Apalachicola River. Pages 22-33 in R. J. Livingston, editor. Proceedings of the conference on the Apalachic ola drainage system. Florida Department of Natural Resources, Marine Resources Publica tion 26. St. Petersburg, Florida, U. S. A.

Ziewitz, J. 2003. Summary of rela tionships between flow regime and species protected under the Endangered Species Act on the Apalachicola River. U. S Fish and Wildlife Service, unpublished report.

Zimmerman, G. F. 2006. Declaration, U. S. District Court, Northe rn District of Alabama.

90

### List of Tables

Table 1: Averages of physico-chemical and biological variables sa mpled during the 9.5–year survey of East Bay take n 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.

91

### List of Figures

Figure 1: Model of the Apalachicola Bay system s howing key features that result in extremely high primary and secondary productivity.

Figure 2: Model of the Apalachicola Bay system s howing potential impacts of reduced river flow leading to plankton blooms and re duced 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-Fl int (ACF or Tri-River) drainage basin.

Figure 5: Human population distribution in Nort h 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 showi ng 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 pr imary and secondary productivity.

Figure 8: Monthly averages of Apalachicola Ri ver flow from Octobe r 1951 through September 2003. Data were provided by the U. S. Geologi cal Survey (Sumatra, Florida gage).

Figure 9a: Seagrass and wetla nd habitats of the Apalach icola Drainage System.

Figure 9b: Distribution of submerged aquatic ve getation (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 th e long term trophic analyses involving infaunal and epifaunal macroinvertebrates and fish.

Figure 9d: Leaf matter taken in otter trawls in East Bay take n 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 (s tations 3 and 5a) and the high salinity sound area (station ML).

9293 Figure 9g: Three-dimensional vi ew of numbers of individuals , species richness, and top dominant numbers of infaunal macroinvert ebrates taken from 100 core samples at stations 3, 5a and ML.

Figure 10: Ontogenetic feeding units of bl ue crabs (day vs. night collections).

Figure 11: Apalachicola River fl ows, monthly, from February 1975 through June 1984. Data were provided by the U. S. Geological Su rvey (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 i nvertebrate (FII) trophic levels (herbivores, omnivores, C1 carnivores, C2 carnivores) taken monthly fr om 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 fr om 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 oys ter 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 obser ved mortality values from oyster predation experiments (1 985, May-August average).

Figure 18: Map showing major elements of the Apalachicola Management Plan.